Huong Dan Hyperchem

Hng dn s dng HyperChem 7.
04
Bi 1 Bt u s dng phn mm
Nhp chut vo biu tng HyperChem, mn hnh lm vic hin ln nh sau:
Thanh tiu (title bar)

Biu din tn file ang biu din trn ca s. Nu cha lu file th tn s l
untitled
Thanh cng c la chn (menu bar)

Cha cc cng c tnh ton khc: File, Edit (hiu chnh), Build (xy dng),
Databases (d liu), Setup (t phng php tnh), Compute (tnh ton),
Annotations (ghi ch, din gii), cancel (thot), Script, v Help (tr gip).
Thanh biu tng cng c (tool bar)

Cha cc cng c cho php ta v, chn, biu din, v di chuyn cc nguyn
t, phn t. Phn bn phi thanh cng c c cha cc cng c gip ta ghi ch
thm, lu nhanh, ct, dn, in, tr gip.
Mn lm vic (workspace)
L ni biu din h phn t hin ti.
1
Hng dn s dng HyperChem 7.04
Dng hin trng tnh ton (status line)

Cho ta bit thng tin nh l s nguyn t trong mt phn t, hin trng tnh
ton, gi tr tnh ton
Tr gip (help)
Cha cc hng dn thm cho ngi s dng.
Cch s dng chut:

Mun thao tc trn cng c no ta ch vic nhp tri chut (L-Click) vo biu
tng cng c .
V d mun s dng cng c v, ta di chuyn biu tng chut n biu
tng v nhp chut:
S dng bn phm
Thay v phi dng chut ta c th dng bn phm di chuyn n nhng la
chn cn thit. V d m select menu ta nhn ng thi hai phm [Alt] +
[S] ([Alt] v [S]). chn cc la chn khc trong hp thoi ta nhp tip vo
k t tt c gch di trong mi la chn. V d chn tip select all ta
nhp ch e trn bn phm.
Cc phm tt khc:
Ctrl + N
Ctrl + O
Ctrl + S
Ctrl + X
Ctrl + C
Ctrl + V
Alt + F4
Ctrl + D
Ctrl + K
Ctrl + L
Ctrl + F
Ctrl + B
Spacebar
F2
F9
Esc
To trang lm vic mi
M file
Lu file (save) trong File menu
Ct (cut) trong File menu
Copy (copy) trong Edit menu
Dn (paste) trong Edit menu
Thot khi HyperChem
Xo (delete) trong Annotations menu
La chn tip (select next) trong Annotations menu
La chn phn trc (select previous) trong Annotations
menu
Di chuyn tip (move forward) trong Annotations menu
Di chuyn tr li (move backward) trong Annotations
menu
Di chuyn h phn t vo trung tm v biu din theo t
l mn lm vic.
Tr li kiu biu din lc trc (last rendering) trong
Display menu
Copy hnh nh (copy image) trong Edit menu
Nh mc thot (cancel) trn thanh cng c
Cc cng c quan trng trn thanh cng c
Cc thao tc trn HyperChem

M mt file v d: V d m file c ui HIN.
1. Di chuyn con tr chut n File trn thanh cng c.
2. Nhp tri chut (L-click) vo File mn hnh s hin ra nh sau:
3. Nhp tri chut vo Open. Mn hnh s hin ra nh sau:
4. Nu mn hnh list vn cn cc cht khc, c th ko thanh trt tm

kim.
ko thanh trt ta nhp tri biu tng chut vo thanh trt, gi nguyn
nh th v r chut theo chiu mun ko.
5. Mun m file no ta ch cn nhp tri (L-click) chut vo file ri nhn
tip vo nt Open trn list
Trn mn hnh s hin ra phn t cha trong file
Cch s dng Display Settings

Display settings cha cc la chn biu din h phn t trn trang lm
vic
m Display menu ta thc hin nh sau
1. Nhp tri chut vo biu tng Display trn thanh cng c. Mn hnh khi
hin ra nh sau:
S dng nhn (Labels)

Nhp tri chut vo Labels trong Display. Hp thoi Labels hin ra vi cc
la chn khc nhau, ta c th la chn hnh thc nhn biu hin ca cc
nguyn t trong h.
Atoms
None B tt c cc nhn.
Symbol Biu tng nguyn t, v d C, O, N..
Name Tn ca nguyn t theo ngn hng d liu, v d
CA, CB i vi cacbon alpha v beta.
S
th t to nguyn t.
Number
Type Kiu nguyn t, theo tc ng ca trng lc, v
d CT i vi cacbon t din trong trng lc
AMBER.
Charge in tch thc ca nguyn t.
Spin Tng spin thc (alpha-beta) ca mt nguyn t
Poputation
Mass Khi lng nguyn t
Basis set Tp hp hm c bn p dng cho nguyn t
Chirality R hoc S
RMS Gradient Ga tr v hng ca vect bin thin m t trng
lc trn mt nguyn t.
Custom t tu chn.
Residues
None B tt c cc nhn.
Name Tn hp phn, v d: TRP, ILE.
Sequence Th t hp phn t hp phn ui N (Nteminus).1,2,3
Name+Seq C tn ln th t.
Bonds

None B tt c cc nhn
Bond Length di lin kt gia cc nguyn t
Bond Order Th t lin kt tnh ton theo c hc lng t.
Hnh thc biu din phn t:

Ta hon ton c th biu din cc phn t khc nhau trong h.
Thay i hnh thc biu din:

1. Nhp tri chut vo Rendering trong Display menu
Hp thoi la chn hin ra nh sau:
Nhp tri chut vo mt trong nhng hnh thc biu din, v d chn Balls
and Cylinders (kiu hnh cu v hnh tr) th trn m hnh cc nguyn t ca
h c biu din di dng hnh cu, lin kt dng hnh tr nh sau:
Ch : HyperChem cn c cc kiu biu din khc:

- Sticks: Kiu que.
- Balls : Kiu hnh cu.
- Overlapping Spheres: Kiu hnh cu chng ln nhau.
- Dots: Kiu chm.
- Sticks & Dots: Kiu chm - gch.
t mu nn trang lm vic
t mu nn trang lm vic ta lm nh sau:
1. Nhp tri chut tch chn Preferences trong File menu.
2. Tch chn mc Window Color trong hp thoi Preferences. Mu ngm
nh cho trang lm vic ca HyperChem l mu en:

3. Tch chn White ri nhp OK xem biu din mu nn ca mn lm
vic. Mu nn lc ny l mu trng:
Ch : Nu ta t mu khc th nn s c mu khc:
- Black: Mu en.
- Blue: Mu xanh nc bin.
- Green: Mu xanh da tri.
- Cyan: Mu lc lam.
- Red: Mu .
- Violet: Mu ta.
- Yellow: Mu vng.
- White: Mu trng.
t mu sc lin kt trong phn t

1. Tch chn Preferences trong File menu.
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2. Chn mc Bond Color trong hp thoi Preferences. Tch chn mu m ta

mun t cho lin kt. V d ta chn mu en (Black). Hnh nh biu din
trn mn lm vic s nh sau:
Ch : Tu theo ta chn mu no, lin kt s c biu din theo

mu y. HyperChem ngm nh mu cho lin kt theo cc nguyn t,
nh ta c th quan st d dng cc lin kt khc nhau, tuy nhin
iu khng c li trong khi ta phi in en trng.
Mu sc ca nguyn t
HyperChem ngm nh mu sc ca cc nguyn t c trng nh sau:
Nguyn t
Mu ngm nh
11

Cacbon
Nit
Oxy
Flo
Lu hunh
Natri
Kali
St
Coban
ng
Brom
Iot
Vng
Tt c cc nguyn
t cn li
Lc lam
Xanh
Vng
Vng
Ta
Ta
Xanh
Xanh l cy
Vng
Vng
Mu trng
Ta c th t li mu sc biu din cc nguyn t theo su mu chun, cng

vi mu trng v mu en. HyperChem s dng mt tp hp mu ngm nh.
Nu ta thay i mu sc ca mt nguyn t, ta vn c th tr li vi mu
ngm nh bng cch nhp vo Revert trong hp thoi sau:
t mu mi cho nguyn t ta lm nh sau:

1. Nhp tri chut chn Element color trong Display menu.
2. Nhp tri chut vo tn nguyn t mun i mu.
3. Nhp tri chut vo mu mun i.
4. Nhp OK chn.
5. tr li mu ngm nh nhp Revert.
t ch Copy hnh nh
12

y l phn kh th v nu ta mun ly hnh nh ca HyperChem chuyn
qua trnh ng dng khc, v d nh trnh Word ca Microsoft.
1. Nhp tri chut chn Preferences trong File menu. Chn mc Setup
Image. Hnh nh hp thoi lc ny nh sau:
2. t cc la chn nh trn hnh v. Nhp OK chn.

3. Nhp F9 hoc nhp tri chut chn Copy Image trong Edit menu.
4. Nhp OK nu HyperChem t ra cu cnh bo no.
C ca s mn lm vic ca HyperChem s c Copy. Nu ta dn qua
Word th s thy nh sau:
13
Ch : HyperChem cho ta nhiu la chn copy hnh nh.

Top leve
Copy c cc hp thoi v menu ko
Window
xung nu ta nhp vo Copy image
(Ca s)
thay v nhp F9.
Workspace
Ch Copy phn mn lm vic.
HyperChem Copy c ca s lm vic HyperChem
Full screen
Copy c mn hnh, k c cc ca s
khc.
Bitmap
Lu kiu file c ui .bmp. Dng
File format
mu chun. Thch hp lu cho biu
(Kiu file)
din phn t kiu hnh cu, cc biu
ca tnh ton im n, tnh ton
bn kinh nghim.
RGB Bitmap Ging nh .bmp, dng 24 mu.
Kh hn ch trong cc ng dng
khc khng c ch 24 mu.
Metafile
File ui m rng l .wmf. Thch
hp lu vi cc kiu biu din
phn t nh Sticks, Ball and
Cylinder, Dots v Stick & Dots.
Detination(Ni File
HyperChem lu nh c phn ui l
t file)
.bmp hay .wmf vo trong file.
Clipboard
Lu nh vo b nh tm thi, mi
ln c mt nh.
Color
Tch chn lu hnh nh vi mu
sc y , nu khng n ch c
14
Cursor
Filename
dng en trng.
Tch chn im tr chut c
trong nh.
Dng t tn v v tr file t nh.
Thot khi HyperChem

C nhiu cch thot khi chng trnh lm vic
1. Nhp tri chut vo Exit trong Menu file
2. Nhp Alt + F4
c thm: Chng 1 trong HyperChem for Windows Reference Manual.
15
Bi 2. V v hiu chnh
V nguyn t v lin kt
v nguyn t ta cn c bng la chn cc nguyn t.
C hai cch thc hin iu ny

1. Nhp tri chut vo Default Element trong Menu Build.
1. Nhp lin tc hai ln chut tri (Double-click) vo cng c V
Bng la chn cc nguyn t hin ra nh sau:

la chn nguyn t no ta ch vic nhp tri chut vo nguyn t .
2. Mun bit thuc tnh ca tng nguyn t ta ch vic nhp vo biu tng
thuc tnh (Properties) trong thoi, bng cc thuc tnh ca nguyn t s
xut hin.
Sau khi la chn nguyn t mun v, nhp tri chut ln mn lm vic ta

s c nguyn t mun v.
Mn hnh hin ra c dng nh sau:
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3. Mun v lin kt ta ch vic nhn nt tri chut v r t v tr ny n v

tr khc mun v. Nu u kia l mt nguyn t khc th ta phi la chn
nguyn t li sau cng nhn nt tri chut v r t v tr nguyn t ban
u n v tr m nguyn t th hai mun biu din.
4. v phn t dng vng ta nhn v r chut ni cc nguyn t vi nhau.
17
5. To lin kt i, ba bng cch nhp tri chut vo chnh lin kt .

6. To vng lin hp bng cch nhp lin tip hai ln chut tri vo lin kt
vng c v.
7. Thm nhanh nhng nguyn t Hydro cn thiu trong phn t, nu c
bng cch nhp lin tip hai ln chut tri vo biu tng cng c la
chn trn thanh cng c.
Chn nguyn t (Selecting Atoms)

Trong phn ny ta hc nhng k thut c bn la chn mt nguyn t,
nhm nguyn t hay mt tp hp no ang biu din trn trang lm vic.
t cc hnh thc chn c mt s bc sau:

1. Nhp tri chut vo Select menu. Trn mn hnh hin ra nh sau:
18
2. Nu cc nguyn t cha c chn th hy nhp chut tri vo Atoms

chn.
Tip theo tt chn nhiu (Multiple Selections) bng cch nhp chut tri b
du tch ().
Khi ta tch chn Atoms, n v la chn nh nht chn nguyn t, vi
cng c la chn, khi ta c th la chn cc nguyn t, lin kt v gc
ring. Gii hn ny vn hot ng cho n khi ta chn Residures hoc
Molecules.
Ch : S dng la chn Atoms nu ta khng mun chn cc hp phn
hay cc phn t.
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Chn nguyn t
1. Nhp tri chut vo cng c la chn (select) trn thanh cng c, sau
di chuyn con tr xung mn lm vic.
2. t con tr chut vo nguyn t mun chn v nhp tri chut.
Nguyn t c chn s c khoanh vng sng hn cc nguyn t khc.
3. Mun chn lin kt no ta nhp tri chut vo lin kt .
4. Mun chn tt c cc nguyn t trong mn lm vic, ta thc hin bng
cch di chuyn chut n khong trng ca trang lm vic v nhp phi
chut (R-click)
Ch : nguyn t c la chn c m t trn dng hin trng:

S ch th t to ra nguyn t trong phn t
Atom
number
Tn nguyn t.
Element
name
Tn nguyn t, xut hin khi chn nguyn t trong
Atom name
protein hoc amino axit.
Trng lc p dng cho kiu nguyn t (amber,
Force Field
mm+, bio+ hoc opls).
Kiu nguyn t
Atom type
in tch nguyn t
Charge
To ca nguyn t theo h to ca phn t.
Atomic
coordinates
20
Chn nhm nguyn t

chn mt nhm nguyn t ta dng kiu chn hnh ch nht
1. Nhp tri chut vo cng c la chn trn thanh cng c.
2. Nhp ng thi tri v phi chut, gia nh vy v r to hnh ch nht
cha cc nguyn t mun chn.
3. Nh chut th tt c cc nguyn t trong hnh ch nht c chn
Chn thm mt nhm nguyn t

1. Nhp tri chut tch chn Multiple select trong Select menu
2. R chut chn nhm nguyn t mi theo hnh ch nht nh trn.
Chn cc hp phn (Residures)

Khi ta tch chn Residures, n v la chn nh nht chn cc hp phn.
Hp phn phi c ngun gc t Databases menu hoc t ngn hng d liu
Protein. HyperChem khng nhn ra nhng hp phn do ta v t cc nguyn
t.
Ch : Nu khng c hp phn no trong phn t th Residures hot
ng nh Atoms.
21
chn hp phn ta c cc cch sau:

1. Nhp tri chut vo hp phn ta mun chn. Nu cng c la chn chn
ln mt phn t, n s chn hp phn gn nht vi n.
2. Nhp phi chut vo hp phn b la chn n.
3. Chn Muiltiple trong Select menu chn nhiu m khng phi loi b
bt k la chn no trc .
4. Nhp tri chut vo vng trng trn mn lm vic chn tt c cc
nguyn t trong h phn t. Nhp phi chut vo vng trng mn lm
vic loi b tt c cc la chn.
Hp phn la chn c m t trn dng hin trng:
Number of
residures
selected
Residure
name and
number
S th t to hp phn c th s l 0 cho tt c cc
hp phn.
y l tn v th t ni tip ca hp phn ta chn.
Chn c phn t (Molecules)

Khi ta tch chn Molecules, n v la chn nh nht chn phn t ring.
Hnh thc la chn ny hot ng cho n khi ta tch chn kiu chn khc.
Cc kiu la chn phn t ging nh i vi la chn hp phn v la chn
nguyn t:
1. Nhp tri chut ln mt phn t chn n. Nu cng c la chn gn
hai phn t th n s chn phn t gn nht.
22
Loi b la chn
1. Nhp phi chut vo nguyn t chn, nu khng mun chn nguyn t
na.
2. Nhp phi chut vo gia lin kt nu mun khng chn lin kt .
3. Nhp phi chut vo khong trng trong trang lm vic loi b tt c
cc nguyn t chn.
Mu sc biu din khi la chn
Tch chn mc Select Color trong hp thoi Preferences. Tch chn Thick
line (ng m) th khi la chn cc ng biu din s la chn s m
hn:
Ch : Khi ta chn cc mu khc th khi la chn phn la chn s c

23

kiu mu tng ng.
Chn phn b (Complement Selection)

Ta thc hin chn phn b chn tt c nhng phn cha c chn v b
la chn i vi phn chn. Cch thc hin l nhp vo Complement
Selection trong Select menu.
Hp thoi la chn (Select Dialog Box)

Ta thng quan tm n hp thoi la chn khi c s la chn c bit, v d
nh ch chn nguyn t no hoc ch chn mt hp phn no .
Chn nguyn t vi gi tr xc nh theo mt

chui gi tr khc nhau. Nhp tri chut vo mt
nt xem chui gi tr thch hp trong bn
phi. Chui gi tr khc nhau m t tp hp cc
nguyn t c th chn c nh sau:
Atom Symbol Biu tng nguyn t quy c cho mi nguyn t,
By string
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Atom Name
Atom Type
Residue Name
Basis Set
Chirality
Named Selection
Remove
nh l C, N, O, F
Tn quy c cho mt nguyn t trong amino axit
hoc nucleic axit. Ch p dng cho cho tn nh
ngha trong cc mu i vi cc thnh phn ca
phn t ln. V d l CA, 1HA, 2HA i vi
cacbon alpha ni vi hydro.
Kiu nguyn t trong c hc phn t nh l CT,
HC
Tn ca mt hp phn amino axit hoc nucleic
axit, nh l GLY, ALA,
Tp hp hm c bn tnh theo Ab initio hoc DFT
quy cho nguyn t. V d: 6-31G*.
S bt i xng, R hoc S, quy cho nguyn t bt
i.
Dy cc phn la chn c t tn trc . Dy
ny gm c cc la chn nh trc nh l LINE,
POINT v PLANE, c c cc tn theo biu tng
nguyn t quy c nh l C, N, O, F
Loi b phn la chn c t tn no khi
list.
By Number
Atome Number
Residue Number
Molecule Number
Atomic Mass
Atomic Number
Electric Charge
RMS gradient
Spin Population
Chn mt nguyn t theo mt gi tr xc nh

t mt dy cc gi tr s khc nhau. Nhp tri
chut vo mt nt chn kiu s mun chn
sau nh gi tr s vo cc thch hp bn
phi.
Chn nguyn t theo s th t to ra n trong
phn t.
Chn hp phn theo s th t ni tip trong
phn t.
Theo th t to phn t.
Theo khi lng nguyn t
Theo s th t nguyn t trong bng h thng
tun hon.
Theo in tch nguyn t tnh trong c hc
lng t.
Chn theo cn bc hai bnh phng trung bnh
ca gradient.
Chn theo mt spin, da theo lng electron
alpha (hng ln) v electrong beta(hng
xung)
25

Value Gi tr s dng t cho kiu la chn thch
hp.
For Molecule(s) Chn tt c cc phn t, nu khng tch th s
gii hn theo list.
Chn theo chui (String)

1.
2.
3.
4.
5.
Chn Select trong Select menu.

Nhp tri chut chn By String trong hp thoi.
Nhp tri chut vo mt trong cc nt thch hp.
Nhp tri chut vo mt trong cc gi tr biu din bn phi.
Nhp OK chn.
Chn theo s
1.
2.
3.
4.
5.
Chn Select trong Select menu.

Chn By Number trong hp thoi.
Tch chn vo nt thch hp chn.
nh gi tr ph hp theo khong hoc xc nh.
Nu tch chn For Molecule (s) xc nh mt tp hp hoc gii hn
cc phn t. Nu khng tch chn tt c cc phn t l ngm nh.
6. Nhp OK chn.
Tn phn la chn (Name Selection)

t tn phn la chn gip ta d dng chn li chng vo ln sau. Tn phn
la chn c th l: POINT, LINE, PLANE, REACTANT, PRODUCT,
PLOT1, PLOT2, GHOST ATOMS, NMR ATOMS, QUANTUM ATOMS
hoc tn do ta t (ti a 19 k t)
POINT
LINE
Tm khi ca cc nguyn t chn.

ng thng gia hai hay nhiu nguyn t, hoc l
26
PLANE
REACTANT
PRODUCT
PLOT1
PLOT2
GHOST
ATOMS
NMR ATOMS
QUANTUM
ATOMS
Other
trc qun tnh th nht.

Mt phng to bi trc th nht v trc qun tnh th
hai ca cc nguyn t chn
Tn phn cc nguyn t cht phn ng. Dng tm
trng thi chuyn tip trong phn ng. Ch hot ng
khi ta chn mt na s nguyn t trn mn lm vic.
Tn cc nguyn t ca sn phm. Dng tm trng
thi chuyn tip. Hot ng ng thi vi Reactant.
Tn cha mt tp hp ca 2, 3 hay 4 nguyn t cng
xc nh mt di lin kt, mt gc lin kt hay
mt xon lin kt xc nh s bin thin th nng
trong khng gian mt chiu hoc hai chiu.
Dng xc nh s bit thin th nng trong khng
gian hai chiu.
Cha tp hp cc nguyn t c coi l cc nguyn t
m (ma) khi tnh ton Ab initio hoc DFT.
Cha cc nguyn t c quy cho spin nhn v s
dng trong tnh ton HyperNMR.
Cha tp hp cc nguyn t c xc nh l cc
nguyn t lng t trong s pha trng gia tnh ton
c hc lng t v c hc phn t (MM/QM).
Tn do ta t
Xo nguyn t
Xo mt nguyn t n hoc mt lin kt n
1. Nhp tri chut vo cng c v trn thanh cng c.
2. Nhp phi chut vo nguyn t hoc vo gia lin kt mun xo. Khi
nguyn t hoc lin kt s bin mt.
Xo nhiu nguyn t
1. Nhp tri chut vo cng c chn trn thanh cng c.
2. R chut chn nhng nguyn t mun xo.
3. Nhp tri chut vo Clear (xo sch) trong Edit menu.
Hp thoi xut hin hi c thc s mun xo phn la chn khng.
4. Chn Yes nu mun xo.
5. Chn No nu khng mun xo.
27
Copy nguyn t vo b nh tm thi (Clipboard)

1.
2.
3.
4.
Nhp tri chut vo cng c chn trn thanh cng c.

Nhp tri chut vo lin kt hoc nguyn t mun chn.
Chn Copy trong Edit menu.
Chn Paste trong Edit menu.
Mt bn copy ca cc nguyn t chn s c dn vo trong mn lm
vic.
t in tch hnh thc cho nguyn t trong h

Ta hon ton c th t in tch hnh thc cho mt nguyn t no trong
phn t. in tch hnh thc trong HyperChem nh sn l cc gi tr nguyn.
N ta mun t in tch hnh thc cho nguyn t no th cch lm nh
sau:
1. Chn nguyn t mun t in tch hnh thc.
2. Nhp tri chut chn Set Formal Charge trong Build menu.
Hp thoi la chn xut hin nh sau:
Ta c th t in tch hnh thc thch hp cho nguyn t chn.

0-Neutral
+1-Singly Positive
-1-Singly Negative
+2-Doubly Positive
-2-Doubly Negative
+3-Triply Positive
-3-Triply Negative
Trung tnh
Dng mt
m mt
Dng hai
m hai
Dng ba
m ba
28

Nu nh nhiu nguyn t c chn th Set Formal Charge khng hot ng,
khi ta c kiu t in tch khc.
Ch : in tch hnh thc ch c ngha biu din, khng c gi tr tnh
ton.
t in tch thc
HyperChem c th tnh ton in tch ca tng nguyn t ring bit trong
phn t, nhng ta cng c th t in tch theo mun.
Cch lm nh sau:
1. Chn nguyn t hay nhm nguyn t mun t in tch.
Hp thoi t in tch xut hin:
nh gi tr in tch thch hp m ta mun. Nhp OK chn.

Khi cc nguyn t chn s c cng in tch m ta nh vo.
t khi lng nguyn t

Cch lm tng t nh t in tch nguyn t trn, bng cch nhp tri
chut vo Set mass trong Build menu.
t di lin kt
t di lin kt cho php ta t di lin kt chn theo mun.
1. Nhp chn lin kt mun t li di.
2. Nhp chn Set Bond Length trong Edit menu. nh gi tr mun t vo
hp thoi la chn.
Nhp OK thc hin thay i di lin kt chn.
29
Ch : Lin kt chn thay i khng c l lin kt trong vng.

t gc lin kt
Cch lm tng t nh t di lin kt trn, nhng ta phi chn gc lin
kt v tch chn Set Bond Angle trong Edit menu m hp thoi la chn.
t xon lin kt
Ta cng thc hin nh cch t di lin kt trn, nhng ta phi chn bn
nguyn t lin tip to gc xon mun thay i, tch chn Set Bond Torsion
trong Edit menu.
t nhn ring
Ta c th ghi ch nhn tu cho nguyn t la chn, cch lm tng t nh
t in tch nguyn t trn. Ta tch chn Set Custom Label trong Build
menu m hp thoi v nh nhn m mnh mun vo .
t kiu nguyn t (Atom Type)

Kiu nguyn t ch c ngha khi ta thc hin tnh ton theo c hc phn t,
khng c gi tr g khi ta tnh ton bn kinh nghim. Kiu nguyn t cng
c ngm nh theo cc thit lp nh sn nu ta khng thay i g. Ta
khng nn t li kiu nguyn t nu khng r v n.
Cch t kiu nguyn t nh cch t in tch trn, ta chn nguyn t
mun t li kiu, tch chn Compile Type Rules trong Build menu. Hp
thoi la chn xut hin v ta chn kiu nguyn t m mnh mong mun.
c thm: Atom types trang 177- chng 11-quyn Computational
Chemistry.
Thay i cc thuc tnh hnh hc

Cng bc hnh hc
Vi cc kiu cng bc trong HyperChem gip ta un, thay i gc, di
lin kt theo mong mun. Vic cng bc nh vy lun nh hng n tnh
ton v kt qu cui cng. Tuy nhin HyperChem khng phi lc no cng
30

cho ta c ngay hnh hc mong mun, v vy y l mt trong nhng cng
c hu ch.
Ch : Cng bc hnh hc ch hot ng khi mt nguyn t c chn.
cng bc hnh hc ta lm nh sau:
1. Chn mt nguyn t trong h.
2. Tch chn Constrain Geometry trong Build menu.
Hp thoi la chn xut hin:
3. Tch chn hnh thc cng bc m ta mun, nhp OK chn.

4. Loi b la chn nguyn t.
5. Nhp vo Model Build thc hin cng bc chn.
Tt c cc gc lin kt ni vi nguyn t c chn s chu cng bc.
Ch : Ta cng c th b nhng cng bc va thc hin bng cch tch
chn Computed trong hp thoi cng bc v nhp vo Model Build
trong Build Menu xy dng li cu trc theo trnh xy dng.
Computed
Linear
Trigonal
Tetrahedral
Square Planar
Bipyramidal
Octahedral
Khng cng bc. Trnh xy dng quyt nh

hnh hc.
Cng bc hai lin kt to gc 1800..
Cng bc to mt phng tam gic, mi cp
lin kt to gc 1200.
Cng bc to t din, mi cp lin kt to
gc 109.470.
Cng bc to mt phng, mi cp lin kt
lin nhau to to gc 900.
To hai chp tam gic chng ln nhau.
To bt din.
31
Cng bc di lin kt
Ta c th gii hn di lin kt theo mun.
Cch lm nh sau:
1. Chn lin kt mun thay i di.
2. Nhp chn Constrain Bond Length trong Build menu.
3. Tch chn Other v nh gi tr di mong mun vo. Nhp OK

chn.
4. B chn lin kt.
5. Nhp chn Model Build trong Build menu thc hin cng bc lin
kt.
Ch : Vic cng bc lin kt lun nh hng n tnh ton, ta ch nn t
khi thy cn thit.
loi b cng bc ta chn li lin kt, tch chn Computed trong hp
thoi cng bc v thc hin nh vi cch cng bc trn.
Cng bc gc lin kt
cng bc gc lin kt no ta lm nh sau:
1. Chn gc lin kt mun thay i.
2. Chn Constrain Bond Angle trong Build menu.
32

3. Tch chn kiu gc mun thay i. Nhp OK chn.

4. B chn gc lin kt.
5. Nhp chn Model Build thc hin cng bc.
Ch : Vic cng bc gc lin kt c nh hng n gi tr tnh ton.
loi b cng bc ta lm tng t nh khi cng bc nhng tch chn
Computed trong hp thoi la chn.
Cc kiu la chn gc nh sau:
Computed
Linear
Trigonal
Tetrahedral
Orthogonal
Other
Khng cng bc
1800
1200
109.470
900
Tu t gi tr t 3600 n +3600
Cng bc lin kt xon

Cch lm tng t nh kiu cng bc gc lin kt trn. Tuy nhin y ta
phi chn lin kt xon gm t nht bn nguyn t.
Hp thoi la chn cng bc nh sau:
33
Cc kiu la chn:
Computed
Trans
Cis
Gauche+
GaucheOther
Khng cng bc
Cng bc 1800
00
600
-600
Tu gi tr t vo t 1800 n
+1800
34
Bi 3. To nhng phn t nh trong khng gian hai chiu

(2D) v ba chiu (3D).
Cch v phn t trong khng gian hai chiu.

Hiu chnh lin kt v cc nguyn t.
Biu din phn t trn khng gian ba chiu.
Lu cu trc phn t.
V phn t trn khng gian hai chiu

1. Nhp hai ln lin tip tri chut (Double-click) vo cng c v.
Hp thoi la chn nguyn t s hin ra.
2. Tch (4) trong phn Allow Arbitrary Valence, v b tch trong phn
Explicit Hydrogens.
Nu ta khng b tch Explicit Hydrogens, th hydro lun t ng thm
vo.
3. Chn nguyn t mun v, y ly v d chn Carbon.
4. Nhp tri chut, gi v r n cc im theo cng thc phn t mun v.
35
Lu bc v vo trong mt File
Trc khi thc hin sa i bc v, ta hy lu bc v li. iu ny gip ta
khng phi v li bc v ban u nu trong qu trnh chnh sa b hng.
Cch lu nh sau
1. Nhp tri chut vo Save (lu) trong File menu.
HyperChem s hin ln hp thoi c dng nh sau:
2. nh tn file m bn mun t vo mc File name.

3. t kiu ui HIN lu dng nh trong phn Save as type.
4. Nhp tri chut vo nt Save lu file.
Lc ny hp thoi lu t ng thot v ta c c hnh nh phn t
hin ti lu.
5. Nhng thao tc lc sau trn phn t v, mun lu ta ch vic nhp vo
Save. Nu mun lu vo tn file khc th ta nhp vo Save as trong File
menu.
Thay i hnh thc lin kt

Vic sa i gip ta c th biu din phn t c cha cc lin kt i, ba hay
l to vng benzen.
1. Nhp tri chut vo cng c v.
2. to lin kt i ta ch vic nhp tri chut vo gia lin kt n to ra
trc .
36
3. To lin kt ba bng cch nhp tip tri chut vo lin kt i to ra.
4. Ch : Mun sa tr li thnh lin kt n ta ch vic ln lt nhp phi

chut vo gia lin kt i, ba to ra.To vng benzen bng cch nhp
lin tip hai ln tri chut vo mch vng.
37
Biu din nguyn t di cc dng nhn khc nhau

Ta hon ton c th biu din cc nguyn t trn trang lm vic di dng
biu tng, tn, in tch, khi lng ca n.
Cch biu din nhn nguyn t

1.Nhp tri chut vo Labels trong Display menu.
Hp thoi nhn (label) hin ra nh sau:

38
2. Tch vo kiu nhn m ta mun biu din.

3. Nhp tri chut vo OK chn.
Nu ta chn kiu biu tng (symbol) th trn mn lm vic cc nguyn
t s c biu din di dng biu tng.
Chnh sa cc nguyn t
Nu trong phn t v, ta mun thay i nguyn t ny thnh nguyn t
khc th cch lm nh sau.
1. Nhp hai ln tri chut vo cng c v trn thanh cng c.
Bng cc nguyn t s hin ra.
2. Chn nguyn t mun thay th. V d chn oxi.
3. Nhp tri chut vo nguyn t mun thay th trong phn t v. V d
nh cacbon.
39
Nguyn t cacbon s c thay th bng nguyn t oxi.
Thm nhanh hydro cn thiu

nhanh chng thm nhng hydro cn thiu trong phn t ta c th thc
hin d dng, cu trc sau khi thm hydro nhanh s dng khng gian ba
chiu. Cch lm nh sau.
1. Nhp tri chut chn Add H & Model Build trong Build menu.
HyperChem s thc hin biu din phn t ta v trn khng gian ba chiu v
t ng thm nhng hydro cn thiu.
40
Nu vn khng thy hydro xut hin th hy tch (4) chn Show Hydrogens
trong Display menu.
41
Bi 4. Dch chuyn, quay v biu din h phn t theo t

l mn lm vic.
Dch chuyn phn t theo cc trc.

Quay phn t theo cc trc.
Phng to, thu nh.
Chuyn phn t thnh nhng lt nh theo trc z.
H to trong HyperChem
HyperChem c hai h to biu din phn t: H to ca ngi quan
st v h to phn t. Mi h to u c cc trc to Decac x, y v
z.
H to phn t tu thuc vo phn t , do khi dch chuyn phn t th

h to cng thay i theo. Cn h to ca ngi quan st l khng i
trong HyperChem, n c biu din nh hnh trn. Trong HyperChem khi
ta s dng cc cng c ta dng nhp tri chut dch chuyn, quay l
thc hin theo h to ngi quan st, vic dch chuyn ny xy ra cho
ton b h phn t. Ta dng phi chut dch chuyn, quay theo h to
phn t. Vic dch chuyn ny ch xy ra i vi cc nguyn t, hp phn,
phn t c chn.
42
H to ca ngi quan st
H to ca ngi quan st (Viewers Coordinate System) nh r v tr ca
cc nguyn t lin h vi ta, ngi quan st. H to ca ngi quan st
gn vi dng hnh hc mn hnh. Trc y thng ng, trc x nm ngang, trc
z thng gc vi mt phng mn hnh.
Trong h to ca ngi quan st, ta c th di chuyn phn t m khng
lm thay i cc to nguyn t. Vi cc cng c trong HyperChem, ta
dng tri chut dch chuyn cc phn t theo h to ca ngi quan
st. Cc phn t dch chuyn nh ta nag thay i v tr quan st ca mnh.
S dch chuyn nh hng ln ton b h phn t.
Vi mt s hp thoi lc chn ca HyperChem, nh l Align Viewer (t
thng ngi quan st), s dch chuyn l t ng theo to ca ngi quan
st nu khng c nguyn t no c chn.
Khi ta to mt phn t u tin, HyperChem t thng h to ca ngi
quan st v h to ca phn t do cc trc x, y v z l tng ng
nhau. Khi ta dch chuyn phn t, cc h to khng cn tng ng
nhau na. Dng Align Viewer trong Edit menu dch chuyn h to ca
ngi quan st n tng ng vi h to ca phn t.
Khi ta lu h phn t vo file HIN, HyperChem cng lu c h to ca
ngi quan st. Khi m li file ny ta s c ng h to lu.
H to ca phn t
H to ca phn t gn lin vi h phn t v nh r to ca cc
nguyn t, cc ta ny c s dng trong tt c cc tnh ton ho hc
ca HyperChem.
Ta c th xc nh to phn t ca bt k nguyn t no bng cch la
chn nguyn t . To ca nguyn t c chn xut hin trn dng
hin trng (status line).
Vi cc cng c ca HyperChem, ta dch chuyn cc nguyn t theo h to
phn t bng cch s dng nt phi chut. Vic dch chuyn ny ch tc
ng ln cc nguyn t, hp phn, v cc phn t c chn.
Cng c (Tool)
Chc nng ca nt phi chut

43

Quay theo XY
Ch quay khi c phn t c chn.
Quay theo Z
Ch quay c phn t hay nhnh c th quay c.
Dch chuyn theo XY Dch chuyn cc nguyn t hay phn t
chn.(a)
Dch chuyn theo Z
Dch chuyn cc nguyn t hay phn t
chn.(a)
a. Chc nng ca nt phi c gii hn cho ton b phn t nu Whole
molecule translation trong mc Tool ca hp thoi Preferences (trong File
menu) c tch chn.
Vi cc hp thoi ca HyperChem, nh l Align Molecules, s dch chuyn
t ng theo h to ca phn t.
Trc qun tnh

i vi cc nguyn t hay c h phn t c chn, HyperChem c th tnh
ton s chuyn ng theo qun tnh v c cc trc qun tnh. HyperChem
bo s chuyn ng theo qun tnh trn dng hin trng v biu din cc trc
qun tnh l cc ng nt t, c nh trong h to ca phn t. C ba s
chuyn ng v ba trc (trc th nht, th hai v th ba) thc hin chc
nng theo v tr v khi lng ca cc nguyn t. Cc trc qun tnh ph
thuc vo h phn t v khng ph thuc vo h to ca ngi quan st
ln h to ca phn t.
Tch chn Show inertial Axes trong Display menu biu din cc trc qun
tnh. C s trc dao (vung gc) v c nh s th t 1, 2 v 3 cho cc
trc th nht, th hai v th ba ring. Cc trc vn hin trn mn lm vic
cho n khi ta b tch Show inertial Axes trong Display menu.
Trc qun tnh th nht thng biu th khong cch di nht qua h phn t,
v trc qun tnh th ba biu th khong cch ngn nht.
44
HyperChem dng cc trc qun tnh b tr cc phn t (Xem t phn t

thng trc: Align Molecules) trn mn lm vic v khi nh r POINT,
LINE v PLANE (xem phn chn: Select). Nhng s nh r ny l trong cc
s hng ca cc trc qun tnh.
POINT
in giao nhau ca cc trc qun tnh ti tm khi ca cc

nguyn t chn.
LINE
Trc th hai ca cc nguyn t chn. (1)
PLANE
Mt phng hnh thnh t trc th nht v trc th hai,
vung gc (trc giao) vi trc th ba ca cc nguyn t
chn.
(1) Trc th nht ng vi gi tr c trng nh nht trong s chuyn ng
ca ma trn qun tnh.
45
t ch lm vic cho cc cng c

Tch chn Preferences trong File menu. Tch chn mc Tool trong hp thoi
Preferences. Hnh nh hp thoi lc ny c dng nh sau:
Cc la chn gip ta trong qu trnh s dng cc cng c quay, phng to,

dch chuyn trn mn lm vic. Gi tr t cho vic di chuyn chut t mp
ny n mp i din trong mn lm vic.
XY rotation
Nu ta t l 360 th khi dch chuyn t mp ny n

mp i din phn t s quay c 3600. Mc ny t
c gi tr t > 0 n 36000.
Z rotation
Z translation
Zoom
Clip
t c gi tr t > 0 n 36000.
t c gi tr t > 0 n 1000A0.
t c t l t > 0 n 1000 ln.
t c di dch chuyn mt ct t > 0 n
1000A0.
Khi tch chn, gip ta chuyn dch nhanh hnh nh h
phn t.
Nu ta tch chn mc ny th khi dng cng c hay hp
thoi u dch chuyn c c phn t. Nu khng tch
chn thi khi dch chuyn theo to ca phn t s ch
dch chuyn c phn la chn trong phn t. (Dch
chuyn quan st l nh nhau khi ta tch hay khng
tch, ch c s khc nhau khi dch chuyn theo to
phn t)
Fast
translation
Whole
molecule
translation
46

Ch : Tng t ta cng t c ch cho cc cng c khi s dng bn
phm bng cch t cc la chn trong mc Key ca hp thoi Preferences.
Nghch chuyn (Invert: chuyn (ho) thnh)

Nghch chuyn tin hnh chuyn ho hnh hc phn t (nghch chuyn) qua
mt im (POINT). POINT l tm khi ca mt hay nhiu nguyn t
chn. S dng hp thoi Name Selection trong Select menu xc nh
POINT. Nu to ca mt nguyn t l x, y v z (lin h vi POINT),
Invert chuyn chng thnh x, -y v -z.
Khi ta thit lp mt POINT, ta c th nghch chuyn bt k nguyn t no
chn, hoc nu khng c la chn th s nghch chuyn c h phn t.
Ch : Invert chuyn qua mu xm hot ng c khi h chn
POINT trong Name Selection.
nghch chuyn cc nguyn t v phn t ta lm nh sau:

1. Chn mt hoc nhiu nguyn t nh nghch chuyn POINT.
2. Chn Name Selection trong Select menu. Sau tch chn POINT trong
hp thoi ny v nhp OK chn.
3. B chn tt c cc nguyn t.
4. Chn Invert trong Edit menu.
Ch : Nu ta nghch chuyn cc nguyn t chn trong mt phn t
HyperChem ch nghch chuyn cc nguyn t ny v c th bp mo cc
lin kt ni vi cc nguyn t t phn ng yn ca phn t.
Ta nn t Chirality trong hp thoi Labels d dng quan st s
nghch chuyn.
V d: nghch chuyn amino axit alanine. Khi carbon alpha l mt tm
bt i, s nghch chuyn thay i s bt i ca nguyn t ny.
47
Ta cng c th dng s nghch chuyn nghch chuyn cu hnh dng gh

v dng thuyn.
Phn chiu (Reflect)

Phn chiu tin hnh chuyn ho hnh hc phn t (s phn chiu) qua mt
mt phng (PLANE). S chuyn ho phn t ny c th to ra mt hnh nh
qua gng cc nguyn t hoc ton b phn t chn. Nu PLANE l mt
phng XY, khi Reflect chuyn to ca nguyn t t x, y v z (lin h
vi PLANE) thnh x, y v -z.
S dng hp thoi Name Selection nh r PLANE. PLANE l mt phng
c xc nh theo trc qun tnh th nht v th hai ca cc nguyn t.
Phn chiu tc ng ln cc phn t c chn, hoc nu khng chn th n
tc ng ln ton b h phn t. Nu cc nguyn t c phn chiu c mt
hay nhiu tm bt i, HyperChem lm thay i s bt i ca chng.
Ch : Phn chiu chuyn qua mu xm hot ng c khi h phn t
c phn la chn vi tn l PLANE.
Ta nn t Chirality trong hp thoi Labels d quan st s thay i.
phn chiu cc nguyn t v phn t ta lm nh sau:

1. Chn t nht ba nguyn t phn chiu PLANE.
2. Chn Name Selection trong Select menu. Tch chn PLANE trong hp
thoi v nhp OK chn.
3. B la chn cc nguyn t.
4. Chn Reflect trong Edit menu.
48

V d: Phn chiu mt nhm bn ca cyclohexane:
Dch chuyn phn t theo trc xy

Ta c th dng cng c dch chuyn dch chuyn phn t n cc v tr
trn mn hnh theo cc trc X v Y.
Cch tin hnh nh sau
1. Nhp tri chut vo cng c dch chuyn.
2. Di chuyn con tr ln mn lm vic.
3. Nhp tri chut, gi v r phn t n v tr mi.
4. Nu mun dch chuyn n to c th ta c th dng hp thoi la

chn. C hai cch lm xut hin hp thoi ny:
49

- Nhp tri chut chn Translation trong Edit menu.
- Nhp lin tip hai ln tri chut vo cng c dch chuyn.
Hp thoi xut hin nh sau:
5. Nhp tri chut vo tng la chn dx, dy, dz v nh s thch hp vo .

C th dch chuyn gia cc phn la chn khc nhau nh s bng
cc nhp phm Tab trn bn phm.
6. Nhp OK chn sau khi nh cc s theo mun.
Cc mc trong hp thoi dch chuyn:
Dch chuyn ton b phn t trong mn lm vic,

nhng cho php to cc nguyn t khng thay
i. y ging nh dng nt tri chut vi cng
c dch chuyn trn mn lm vic.
Lng chuyn sang phi, A0.
Lng chuyn ln trn, A0.
Lng chuyn ra pha ngi quan st, A0.
Chuyn tm khi ca cc nguyn t c chn
n mt im mi, lm thay i to nguyn t.
y ging nh dng phi chut vi cng c dch
chuyn trn mn lm vic. Nu ch mt phn phn
t c chn, v khng c tch chn Whole
Molecule translation (trong mc Tool ca hp
thoi Preferences) th HyperChem s ch dch
chuyn phn la chn.
POINT Dch chuyn phn t hoc cc nguyn t chn
n POINT (im) xc nh trong hp thoi Name
Selection.
Origin Dch chuyn phn t hoc cc nguyn t chn
n h to ban u.
Translate
Viewer
(chuyn dch
quan st)
dx
dy
dz
Translate
Selection
(Chuyn phn
la chn)
50

Other Dch chuyn phn t hoc cc nguyn t chn
n to mi do ta t.
Dch chuyn theo trc Z

Trong HyperChem thit k cng c ta dch chuyn nhanh phn t theo
trc XY ring v trc Z ring. Tuy nhin cch lm u ging nhau. Nhng
hp thoi la chn c th to mun dch chuyn l nh nhau.
Cng c dch chuyn nhanh theo trc Z c dng sau:
Ch : a phn t dch chuyn tr li trung tm mn lm vic ta ch
cn nhp vo phm
trn bn phm.
S dch chuyn ch c tc dng khi ta dch chuyn cng c sao cho phng
dc theo cng c lun song song vi trc z ngm nh ca HyperChem, iu
c ngha l ta phi dch chuyn cng c ln xung theo trc thng ng
(trc Y).
S dng cng c phng to

i khi phi xem chi tit v tr no trn phn t ta cn phng to v tr ,
cng c khi ta mun xem ton b h th li phi thu nh va phi. Do vic
s dng cng c phng to, thu nh l cn thit.
Cch s dng cng c phng to (zoom tool)

51

1. Nhn phm Shift ng thi nhp tri chut vo gn nh phi ca biu
tng phng to, gi nh vy cho n khi phn t trn mn hnh nh nh
mong mun.
2. phng to ta cng lm tng t nhng lc ny nhp tri chut vo gc
di bn tri ca biu tng phng to.
Phn t c phng to c dng nh:
Ch : ch s dng c vi phm Shift khi HyperChem trn my l ci t.

i vi phn mm ch c copy gia cc my th khng thc hin c nh
vy m ta phi dng cc phng php khc.
Ta cng c th phng to hay thu nh bng cch iu khin trc tip chut
hoc s dng hp thoi chn kch c c th.
1. Thao tc bng chut
- Nhp tri chut vo biu tng phng to.
- Di chuyn con tr xung mn lm vic.
- Nhp tri chut v r theo phng to-nh ca biu tng phng
to hay thu nh phn t.
2. S dng hp thoi
- Ta nhp lin tip hai ln tri chut vo biu tng phng to trn thanh cng
c hoc nhp vo Zoom trong Edit menu.
Hp thoi la chn hin ra.
- nh vo kch c m ta mun phng to hay thu nh.
- Nhp OK chn.
52
+Zoom Factor: h s phng to.
t phn t tr li tm v biu din theo t l

Khi mt h phn t c m t File, n c biu din tm mn lm vic
theo kch c chun nh sn. Nhng do qu trnh thao tc lm lch v tr ban
u ca n i. Nhng ta hon ton c th a n tr li tm mn lm vic vi
t l chun nh sn.
Cch lm nh sau
1. Nhp tri chut chn Scale to Fit trong Display menu, hoc nhp nt
Spacebar trn bn phm.
Phn t s c a tr li kch c ban u v n c t vo tm mn
lm vic.
Ch : Ta c th a phn t tr li tm vi kch c chun ban u bng
cch chn gi tr 1 trong hp thoi ca cng c phng to.
Quay phn t theo phng XY

quay phn t theo cc trc x, y ta dng cng c quay.
Cch lm nh sau
1. Nhp tri chut vo cng c quay theo trc XY.
2. Di chuyn con tr xung mn lm vic.
3. Nhp tri chut, gi v r theo phng x, y m ta mun xoay phn t.
Hnh nh trn mn hnh c dng nh sau:
53
Quay phn t theo trc Z

quay phn t theo trc z ta s dng cng c quay theo trc z.
Cch lm nh sau
1. Nhp tri chut vo cng c quay theo trc z.
2. a con tr xung mn hnh.

3. Nhp tri chut v r qua tri hay phi xoay phn t theo mun.
54

Ch : R chut theo chiu ln xung khng c tc dng g trong
cch quay ny.
Ta cng c th s dng hp thoi la chn quay. Vic ny thc hin
bng cch nhp chn Rotate trong Edit menu hoc nhp lin tip hai ln
tri chut vo cng c quay trn thanh cng c hp thoi la chn xut
hin.
Hp thoi la chn quay:
Rotate About
X Axis
Y A xis
Z Axis
LINE
Angle
Apply to
Molecules
Viewer
Ta c th quay cc nguyn t la chn, hoc khng

la chn, hoc c h phn t quanh mt trc theo h
to ca ngi quan st hay h to phn t, hoc
quanh mt LINE (ng). LINE l phn la chn
c t tn ph thuc vo h phn t. Nu ta khng
th quay cc nguyn t chn, HyperChem biu
din mt dng thng tin trn thanh hin trng.
L trc trong mt phng nm ngang ca mn hnh
Trc trong mt phng thng ng ca mn hnh
Trc vung gc vi mt phng mn hnh
L tn ca phn la chn. Ta dng Name Selection
t LINE chon h phn t.
t gc quay. Gi tr thay i t 360 n +3600
Quay cc nguyn t chn hay ton b h phn t
theo cc cch:
Quay theo h to ca phn t, lm thay i to
ca cc nguyn t.
Quay theo h to ca ngi quan st, to ca
cc nguyn t khng i.
Ct phn t thnh tng lt nh theo trc Z
55

Vi cng c ct phn t theo trc z s gip cho ta quan st k hn bn trong
phn t t nhng lt ct nh
Cch lm nh sau
1. Xoay phn t bng cng c xoay sao cho khi ct ta d quan st.
2. Nhp hai ln tri chut vo cng c ct theo trc Z, hoc nhp tri chut
vo Z Clip trong Edit menu.
3. Ta c th ko thanh cun hoc chn ch s thch hp ct phn t theo

mun. Sau khi chn ct xong ta nhp OK thc hin.
Hnh nh phn t b ct v d nh sau:
56
4. Mun ct tip ta thc hin nhp li vo cng c ct v thc hin nh trn.

Ch : Ta cng c th thc hin ct phn t bng chut trn mn lm vic.
Cch lm nh sau:
1. Nhp tri chut chn cng c ct theo trc Z trn thanh cng c v di
chuyn cng c ct ln mn lm vic.
2. Nhp tri chut gi v r thng ng iu chnh v tr ct mt phng
pha trc ca phn t.
3. Nhp Phi chut, gi v r thng ng iu chnh v tr ct mt sau ca
phn t.
57

4. Di chuyn chut t mp trn xung mp di mn lm vic ta s dch
chuyn mt phng ct c khong 10A0 (Ngm nh). Ta c th xem
dch chuyn trn dng hin trng bn di ca s HyperChem.
Ch : a phn t tr li trng thi ban u ta ch vic nhp vo nt
Spacebar trn bn phm.
Ch thch hp thoi Z Clip
System
Slab
V tr xa nht ng trc v ng sau ca ton b

phn t trn mn lm vic.
V tr mt phng ct trc v sau gn vi ngi quan
st.
Dng cc dng nm (Wedge) biu din lin kt trong khng gian

HyperChem cho php ta biu din cc lin kt trong khng gian bng cch
biu din lin kt di dng cc hnh nm.
Cc hnh nm c s dng vi quy c nh sau:
58
Cch thc hin nh sau:

1. Nhp chn Rendering trong Display menu, sau chn mc Sticks v
tch chn Wedges, nhp OK ng hp thoi.
2. Nhp tri chut chn cng c v trn thanh cng c.
3. Nhn phm Shift trn bn phm ng thi nhp tri chut vo lin kt
mun biu din cho n khi c dng mong mun.
4. Nhp lin tip hai ln tri chut vo cng c la chn trn thanh cng
c dng trnh xy dng biu din li cu trc trong khng gian, nu
mun.
59
Bi 5. Xem thuc tnh cu trc phn t

Trong bi ny ta hc cch o cc thuc tnh cu trc ca phn t nh l
gc lin kt, di lin kt, gc vn
Xem thuc tnh ca nguyn t

Cch lm nh sau:
1. Nhp tri chut tch vo Atoms v b tch Multiple Selections trong
Select menu.
3. Nhp tri chut vo nguyn t mun bit c tnh.
Nguyn t c la chn s sng hn v c tnh ca phn t hin ra
thanh hin trng bn di.
Dng hin trng cho ta bit s nguyn t, tn nguyn t, in tch nguyn t

theo trng c hc phn t hin ti, to theo cc phng x, y v z.
o di lin kt
Ta hon ton c th xc nh c di cc lin kt trong phn t. Gi tr
di ny trnh by trong dng hin trng bn di.
Cch o nh sau
60

2. Nhp tri chut vo nguyn t th nht mun o ko n nguyn t th
hai ri nh chut ra.
Lin kt gia hai nguyn t s sng hn, di o c biu din dng
hin trng.
Ch : Sau khi thc hin tnh ton ti u h phn t ta c th bit c
gi tr thuc tnh khc ca h bng cch nhp chn phn mun xem hoc
xem thuc tnh c h (khng cn chn phn no) tip theo chn Propeties
trong Computer menu. Mt hp thoi thuc tnh hnh hc xut hin trn
mn lm vic, vi c h c th c c cc gi tr v nng lng ton phn,
nhit hnh thnh, momen lng cc...
o gc lin kt
o gc lin kt ta nhp tri chut vo nguyn t th nht v r n
nguyn t th ba (theo th t lp thnh gc).
Cch o gc lin kt
2. Nhp tri chut vo nguyn t th nht r n nguyn t th ba (theo th
t to nn gc) ri nh chut.
61
o gc vn
Ta c th o gc vn bng cch r chut chn hai phn t u v cui
trong bn phn t to nn gc vn.
Cch lm nh sau
2. Nhp tri chut vo phn t u r n phn t th t trong bn phn t
to nn gc vn ri gii phng chut.
Hnh nh v d nh sau:
3. Gi tr gc vn hin th trong dng tnh trng di.

62
o khong cch khng lin kt

o khong cch khng lin kt ta lm nh sau
1. Nhp tri chut tch vo Multiple Selections trong Select menu.
Vic bt Multiple Selections cho php ta chn nhiu nhm, ngoi ra khi
ta la chn nhm th hai th nhm th nht vn c chn.
3. Nhp phi chut vo phn trng trn mn lm vic.
Vic ny gip ta hu b tt c cc la chn trc .
4. Nhp tri chut ln lt vo hai nguyn t khng lin kt.
Khong cch gia chng hin th trn dng hin trng.
Lin kt Hydro
gip ta xc nhn iu kin to lin kt hydro, HyperChem cho php ta
tnh ton v biu din lin kt ny.
Lin kt hydro c hnh thnh khi khong cch t hydro cho n nguyn t
nhn b hn 3,2 A0.
biu din lin kt hydro ta lm nh sau

1.
2.
3.
4.
Nhp tri chut vo cng c la chn trn thanh cng c.

Nhp phi chut vo vng trng trn trang lm vic.
Nhp tri chut tch vo Show Hydrogen Bonds trong Display menu.
Nhp tri chut chn Recompute H Bonds trong Display menu.
HyperChem s biu din cc lin kt hydro nu c di dng ng nt
t nh sau:
63

Lin kt hydro khng t ng tnh ton ng thi vi qu trnh ti u
hnh hc phn t. Do ta phi tnh lin kt hydro li mi khi cn thit.
Recompute Hydrogen Bonds

Tnh ton li lin kt hydro xc nh cc lin kt hydro gia cc phn t
chn hoc nu khng c s la chn, th n xc nh lin kt hydro gia tt
c cc nguyn t trong h phn t. HyperChem to ra cc lin kt hydro nu
khong cch gia cc hydro cho v nguyn t nhn b hn 3.2A0 v gc to
bi lin kt cng ho tr t hydro cho n cc nguyn t nhn ln hn 1500.
Tuy nhin ta cng c th thay i cc tiu chun ny.
Biu din momen lng cc

Khi ta tch chn Show Dipole Moment, HyperChem s biu din momen
lng cc tnh ton cho cc nguyn t c chn hoc cho c h phn t.
Show Dipole Moment ch hot ng sau khi ta thc hin tnh ton im n.
Momen lng cc biu din trn mn hnh dng ng nt t tm khi
ca cc nguyn t chn. Dng hin trng cho bit tng gi tr ca momen
lng cc v gi tr momen theo cc trc khc nhau theo n v Debye.
64
65
Bi 6. Databases Menu
To chui Polypeptide
Ni cc hp phn li vi nhau
Thm phn cn thiu cho chui
Thay i hp phn v tr c bit
S dng hp thoi la chn cc Amino Axit
Hp thoi la chn cha cc hp phn amino axit c cu trc ho hc chun.

Trong hp thoi ta chn cc cu hnh bc hai ca polypeptit (Xon apha,
mng beta hay cc kiu gc khc ta t: gc Phi, Psi v Omega). Ta chn
xy dng chui bt u t amino axit c im N cui (N-Terminus: ui
nit).
Trong hp thoi gm c:
20 amino axit chun.
Hai kiu trung tnh v mt kiu proton ho ca histidine (Hid, Hie v His).
pH sinh l, histidine c th mang in tch dng hoc trung ho tu
thuc vo mi trng.
Half-Cyx (bn Cystine) dng to lin kt ngang i sunfua.
Mt nhm c im N cui (N-teminal: Ace). N ch c dng lm hp
phn khi u cho chui.
Mt nhm c im C cui (C-teminal: Nme). N ch c dng kt thc
chui.
m hp thoi cch lm nh sau

1. Nhp tri chut vo Amino Acids trong Databases menu.
Hp thoi Amino axit xut hin nh sau:
66

Hp thoi Amino axit hin cho ti khi no ta nhp vo nt tt trn gc phi.
- Ala
Alanine, thuc cht bo trung tnh, khng cc.
- Gly
Glycine, trung tnh, c cc.
- Ser
Serine, trung tnh, c cc.
- Thr
Threorine, trung tnh, c cc.
- Leu
Leucine, trung tnh, thuc cht bo, khng cc.
- Ile
Isoleucine, trung tnh, thuc cht bo, khng cc.
- Val
Valine, trung tnh, thuc cht bo, khng cc.
- Asn
Asparagine, trung tnh, c cc.
- Gln
Glutamine, trung tnh, c cc.
- Arg
Arginine, tch in dng.
- Hid
Histidine, trung tnh, c hydro nit delta.
- Hie
Histidine, trung tnh, c hydro nit epsilon.
- Hip, His
Histidine, tch in dng, c hydro c nit delta v
epsilon.
- Trp
Tryptophan, vng thm trung tnh, khng cc.
- Phe
Phenylalanine, vng thm trung tnh, khng cc.
- Tyr
Tyrosine, vng thm trung tnh, c cc.
- Glu
Axit Glutamic, tch in m.
- Asp
Axit Aspartic, tch in m.
- Lys
Lysine, tch in dng.
- Pro
Proline, trung tnh, khng cc.
- Cys
Cysteine, trung tnh, c cc.
- Cyx
Bn Cystine, trung tnh, c cc. Nu ly t file PDB ta s
c hp phn Cystine y .
- Met
Methionine, trung tnh, khng cc.
- Ace
Acetyl, Nhm c im N cui (N-teminal).
- Nme
N-Methyl amino, Nhm c im C cui (C-teminal).
To dng v biu din chui Polypeptide

Cc chui Polypeptide thng c hnh dng rt phc tp. d dng trong
vic to dng v quan st ta phi la chn hnh dng biu din thch hp c
v mt ho hc ln kh nng quan st. Trong phn ny ta hc cch dng cu
trc bc hai ca polypeptide.
Ch : Ta khng thm bt hay sa i g cc hp phn bng cch dng cng
c v. sa i ta s hc cc bc sau (xem Thay th monome trong hp
phn bng amino axit khc; To ion lng cc).
67

HyperChem ni kt cc hp phn li vi nhau theo th t ta chn chng. Khi
nhp chn hp phn c C-teminal (cn gi l np bt: cap), n s ngn cn
khng cho ni thm cc hp phn khc vo chui. Nu ta chn tip th mt
chui khc s c hnh thnh.
Khi ko di chui, ta c th thay i cc thuc tnh ca cc hp phn tip
theo:
- Cu trc bc hai(xon alpha, mng beta, hay cc gi tr do ta t Other)
- Cu hnh ca lin kt peptit (Omega)
- ng phn L hoc D ca mi hp phn.
Cch lm nh sau:
1. Nhp tri chut chn Amino Acids trong Databaes menu.
2. Tch chn Beta sheet trong hp thoi Amino Acids.
iu ny gip biu din cc gc vn phi v psi 1800.
3. t gc vn omega l 1800.
To chui
1. Nhp tri chut ln lt vo cc amino axit m ta mun ni thm vo. V
d nh sau: Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg.
Ch : Ta khng s dng trnh xy dng (Model Builder) dng li
ton b cu trc chui. Trnh xy dng s lm hng cu trc ti u ca
phn t v khng th ly li chnh xc cu trc ban u. Tuy nhin ta c
th dng trnh xy dng i vi cc nguyn t c chn no .
Nu chui polypeptide khng c np bt, ta c th thm tip cc hp phn
n hp phn c C-teminus. Nu ta thc hin to ion lng cc (Make
Zwitterion), ta cng khng th thm cc hp phn c na, khi chn
thm hp phn th mt chui khc s c xy dng.
Hp phn ca chui c th c cu hnh bc hai khc nhau. Chui
polypeptide c th cng c cu trc xon alpha, cu trc gp beta cng
nh cc cu hnh chuyn ho khc.
68
Xon Alpha
(Alpha helix:
xon c alpha)
Mng beta
(Beta sheet)
t chun cc gc vn Phi v Psi l -58 v -470

cho xon alpha, cng vi lin kt peptit chuyn
tip (transpeptide) (Omega = 1800).
t chun cc gc Phi v Psi cng l 1800 v cng
t tm gp khc tm beta l 1800, cng vi mi
lin kt peptit chuyn tip (Omega = 1800).
Other Chp nhn gi tr khng chun cho cc gc vn Phi, Psi

v Omega.
Phi
Gc vn () ca C-N-C-C: Thay i t 360 n
+3600
Psi
Gc vn () ca N-C-C-N. Thay t 360 n
+3600.
Omega
Gc vn lin kt peptit (),thng thay i t 170 n
69
Isomer
1800. p dng cho hp phn amino axit tip theo. Thay

i t 360 n +3600.
Cho php ta chn ng phn lp th L thng thng
(Khng i xng S) hoc ng phn lp th D (khng
i xng R).
Ch : Ta c th dch chuyn hp thoi amino axit trn mn hnh

v s dng c cc cng c khc (v d nh
t nhn trong Display menu).
To ion lng cc (Make Zwitterion)

Trong dung dch c pH trung tnh, cc polypeptide tn ti di dng cc
ion lng cc, cha cc nhm ui l -NH3+ v -COO-. Thc hin to ion
lng tnh cho phn t polypeptide chn nhm chuyn cu trc theo file
d liu thnh ion lng tnh. Nu khng c polypeptide no c chn th
Make Zwitterion s thc hin cho tt c cc polypeptide trong h. Cc
polypeptide thc hin c Make Zwitterion phi c nhm ui thng
thng (-NH v -CO) ch khng phi l cc nhm np bt (cap: Ace v
Nme).
Khi ta dng chui peptit vi HyperChem, cc phn ui cha y (cn l
-N-H v -C-O). Make Zwitterion chuyn i cc phn ui thnh NH3+ v
-COO-.
Cch lm nh sau
1. Chn none ( phn Atoms) trong hp thoi Labels d nhn.
2. Dch chuyn v quay phn t polypeptide gip ta d quan st.
70
3. Nhp tri chut chn Make Zwitterion trong Databases menu.

HyperChem s thm vo oxi cn thiu trn nguyn t C.
HyperChem cng thm c cc proton cn thiu vo nguyn t N.
71

Ch : Cc hp phn amino axit trong file d liu (Trong Database hay
File PDB) bao gm cc nguyn t vi phn din tch ring. Khi thc hin
Make Zwitterion s lm thay i in tch nhm nguyn t ui
(Teminal). N khng lm thay i in tch ca cc nhm bin ca cc
amino axit (v d xem cc nhm bin axit, baz hay cc nhm imio
C3H4N2).
B Ion cc ui (Remove Ionic Ends)

B ion ui ngc li vi kt qu Make Zwitterion. iu ny tc l chuyn
cc nhm NH3+ v -COO- trong polypeptide thnh NH v -CO.
Thay th mt monome trong hp phn bng mt amino axit khc

Th t ca cc amino axit trong chui ng mt vai tr quan trng trong cu
trc chui. Mi s thay i th t hay thay th mt monome ny bng mt
monome khc u dn thay i cu trc v thuc tnh ca protein, do
cng thay i chc nng ca n.
72
Cch lm nh sau
Trc tin cn phi bit tn v v tr amino axit hp phn cn thay th.
1. Nhp tri chut vo Labels trong Display menu.
2. Nhp tri chut tch chn Name + seq trong hp thoi Labels. Nhp OK
mn hnh s hin ra nh sau.
3. Nhp tri chut tch chn Residues trong Select menu.

5. Nhp phi chut vo vng trng mn lm vic loi b tt c cc la
chn c th c trc .
6. Nhp tri chut vo PHE 5.
Hp phn ny s sng hn ln.
7. Nhp tri chut chn Mutate trong Databases menu.
73
Ch : Mutate s khng hot ng nu ta cha tch chn Residues trong

Select menu.
8. Trong hp thoi Mutate, ko thanh cun chn amino axit mun thay th.
V d chn Thr.
iu ny c ngha l phenylalanine c thay th bng threonine:
Ch : Nh lu tn phn t m bn mi to bng mt tn thch hp.

i vi nucleic axit ta cng lm tng t.
Cc Axit Nucleic
V c bn cch xy dng chui polycucleotide tng t nh cch xy dng
polypeptide trn.
Ta s dng cc Axit Nucleic xy dng chui polynucleotide (AND v
ARN). Cc hp phn ny c cu trc ho hc chun.
74

Trong hp thoi Nucleic Acids, ta c th chn cc cu trc bc hai cho cc
hp phn thm vo (A, B, Z hoc cc kiu gc cu hnh khc m ta t).
Ta c th to chui polynucleotide bt u t cc ui 5 hoc 3 bng cch
nhp chn cc hp phn axit nucleic ny:
- Bn deoxyribonucleotide (monophosphat)
- Bn ribonucleotide (monophosphat)
- Np bt (Cap) A 3 cn tr ko di chui thm.
- Np bt A 5 cn tr ko di chui thm.
Ch : Ta khng chnh sa cc hp phn bng cng c v. Ta c th
thm bt hay chnh sa cc hp phn nh trng hp Amino axit trn.
HyperChem ni kt cc hp phn li vi nhau theo th t ta chn cc hp
phn, bt u t phn ui 5. y l trt t t nhin ca qu trnh tng hp
AND v ARN. Nu ta mun xy dng chui bt u t ui 3 th phi tch
chn Backward (ngc) trong hp thoi.
Cc u bt (cap) ngn cn vic thm tip cc hp phn k c cc hp phn
ui 5 v 3. Sau khi thm mt u bt, vic chn thm hp phn mi s to
mt chui khc. Nu chui cha c u bt, ta c th thm c nhiu hp
phn na cho n khi c u bt.
Khi ko di chui, ta c th thay i thuc tnh ca cc hp phn tip theo
m ta thm vo:
- Cu hnh bc hai (A, B, Z hay cc kiu khc).
- K c kiu gp 2 Endo (gp ni) hay 3 Endo cho vng ng. Kiu
A ca AND thng cha ng deoxyribose dng C3-endo bn vng
hn. Kiu B ca AND cha ng C2-endo.
- Double-Stranded (Kt i thnh phn). Tch chn phn ny th khi
nhp chn axit, ngoi axit ta chn cn c thm baz lin hp ca chnh
n, gia chng c cu ni hydro vi nhau (Tch chn Recompute H
Bonds trong Display menu xem lin kt hydro). HyperChem quan
tm ch yu n cp baz; mt s lin kt trong hp phn lin hp c
di lin kt khng ng v mt s cp baz cng khng c cc gc
cun chnh xc. Ta cn phi ti u hnh hc li sa cc li trong
cu trc.
75

Ch : Khng s dng trnh xy dng (Model Builder) i vi
polynucleotide xy dng. Trnh xy dng s lm hng hnh hc ca
phn t v khng th xy dng li chnh xc c.
Cc la chn ta t c nh hng n cc hp phn sau cho n khi ta
thay i kiu la chn khc. Ta khng th thay i thuc tnh sau khi
tch chn hp phn .
Hp thoi Nucleic Acids c dng nh sau:
Cc kiu hp phn trong hp thoi nh sau:

- dA
Deoxyadenosine 5 monophosphate, hp phn ca
AND.
- dT
Deoxythymindine 5 monophosphate, hp phn ca
AND.
- dC
Deoxycytidine 5 monophosphate, hp phn ca
AND.
- dG
Deoxyguanosine 5 monophosphate, hp phn ca
DNA.
- rA
Adenosine 5 monophosphate, hp phn ca ARN.
- rU
Uridine 5 monophosphate, hp phn ca ARN.
- rG
Guanosine 5- monophosphate, hp phn ca ARN.
- rC
Cytidine 5 monophosphate, hp phn ca ARN.
- 5CAP
u bt kiu A (-OH) kt thc chui ui 5.
- 3CAP
u bt kiu A (-OH) kt thc chui ui 3.
Cc la chn cho hp phn nh sau:
Helix Form
t cu hnh bc hai cho cc hp phn ca chui.
(Kiu xon c) Mi dng xon c c gc vn, cun (s vng quay
ca mi phn) v cao (Chiu cao ca mt vng)
c trng ring.
A Form
Cu hnh xon phi trong AND kt i, kh nc, c
(Kiu A)
khong 11 hp phn mi vng.
76

B Form
(Kiu B)
Z Form
(Kiu Z)
Other
(Kiu khc)
Alpha
Beta
Gama
Chi
Delta
Epsilon
Zeta
Cu hnh xon phi trong AND kt i, kh nc,

vi khong 10 hp phn mi vng.
Cu hnh xon phi ca AND kt i, vi khong 12
hp phn mi vng. Xen k cc hp phn (c
nh s chn l: odd, even) trong mi phn ca Z
AND c cc gc vn khc nhau.
Nhn cc gi tr ta t cho gc vn trong lin kt
khung chui polynuleotide.
() Gc vn. Nhn gi tr t 360 n +3600.

() Gc vn. Nhn gi tr t 360 n +3600.
() Gc vn. Nhn gi tr t 360 n +3600.
() Gc vn. Nhn gi tr t 360 n +3600.
() Gc vn. Nhn gi tr t 360 n +3600.
() Gc vn. Nhn gi tr t 360 n +3600.
() Gc vn. Nhn gi tr t 360 n +3600.
77
- Sugar Form
2 Endo
3 Endo
- Double Strand
- Backward
Cu hnh ca vng ribo.

C2 l ngoi mt phng vng, trn cng mt phng
nh C5.
C3 l ngoi mt phng vng, trn cng mt phng
nh C5.
Khi phn ny c tch chn, HyperChem thm
hp phn lin hp ca chnh n, theo quy tc cp
baz ca Watson-Crick, v dng ln mt
polynucleotide khng song song. Ta c th tch
hoc khng tch dng cc phn t c baz kt
i mt phn.
Khi tch chn phn ny, HyperChem bt u xy
dng chui t phn ui 3, thm dn cc hp phn
n phn ui 5. iu ny ngc li vi qu trnh
tng hp AND v ARN thng thng. Vic t
nh vy nh hng n ton b chui, do ta
phi t n trc khi bt u xy dng chui.
Ch : Ta vn c th s dng cc cng c khc khi hp thoi Nucleic

Acids cn trn mn hnh.
Thm cc ion tri du (Add Counter Ions)
78

Add Counter Ions t mt ion natri gn mt nhm photphat trn khung lin
kt ca chui polynucleotide. Ion Na+ cch u mi oxy ca nhm photphat
mt khong 1.688A0.
Nu ta chn Add Counter Ions v sau thm cc hp phn khc, th ch cc

hp phn u mi c ion tri du. Ta phi chn li Add Counter Ions li
thm cc ion Na+ cho cc hp phn mi.
Ch : loi b cc ion Na+
ta s dng chn cc ion mun loi b v dng Clear hoc Cut trong Edit
menu. Nu ta lu h vo file HIN th cc ion tri du cng c lu.
Dng tinh th (Crystal Builder)
Crystal Builder l mt modun dng c, to v quan st cu trc tinh th
trong HyperChem. Cc cu trc tinh th c th c lu, chnh sa hoc tnh
ton nh bt k h no khc.
Crystal Builder c cc tnh nng nh sau:
- D dng xy dng cc tinh th nguyn t da trn cc kiu tinh th c
bn: lp phng, t din, trc thoi (orthorhombic), hnh lng din
(rhombohedral:c cc mt hnh thoi), su cnh, n t (monoclinic) v
tam t (triclinic)
- Cc cu trc mu nh l NaCl, CsCl, CaF2, PbS, MgO, ZnS
- C th hiu chnh d liu nguyn t nh l vi to ca chng trc khi
to tinh th.
- C kh nng quan st cc mt khc nhau ca tinh th, xc nh ch s
Miller.
79

- C kh nng c v vit cc file trong ngun d liu b tr bn ngoi.
Cc lnh s dng trong xy dng tinh th

File/new
Xo trng mn lm vic
File/Open
M file lu trc
File/save
Lu kt qu trn mn lm vic
None
Bt Stick trong Rendering
Xem dng a
Bt Disk trong Rendering
Xem dng cu
Bt Sphere trong Rendering
Xem b mt
tinh th
HyperChem/Get t t bo n v t HyperChem
HyperChem/Put Gi tinh th n HyperChem
Tm tr gip
To tinh th kim loi Natri

Phn ny minh ho cho ta cch to cu trc tinh th Natri
1. Khi ng HyperChem, tip theo tch chn Crystal trong Databases
menu.
2. Trong mc Crystal Type, tch vo Cubic (lp phng) chn t bo n
v dng lp phng.
80
3. Nhp s t bo n v: 3x3x3 bng cch nh gi tr 3 vo trong ba

tng ng.
4. Trong mc Unit Cell Parameters, nhp kch thc ca t bo cho Na:
4.225 cho u tin t a, b, c =. Gi tr ca b v c s c t ng
t l 4.225.
5. nh s th t ca cc nguyn t trong t bo n v Na (bcc): 2 cho
thch hp.
6. Nhp tri chut vo Edit Atom Date.. m hp thoi d liu nguyn t
(Atom Data).
7. Trong hp thoi nn biu din s th t nguyn t l 1. Thay i tn
nguyn t t - thnh NA1. i nguyn t thnh Na.
8. Nhn ln dng trn trong nt spin hoc nhp s 2 cho s th t nguyn t,
d liu ca 2 nguyn t s c biu din. Thay i a, b v c t 0 n 0.5.
Chuyn tn nguyn t t - thnh NA2. Nhp vo nt Close.
9. Nhp chn nt lnh: HyperChem/Put chuyn cu trc to c vo cho
HyperChem, hoc ln lt nhn nt Toolbar i n khi cc cht lng
mu xanh xut hin.
10. Tinh th natri 3x3x3 s xut hin trn mn lm vic ca HyperChem.
11. quan st mt phng tinh th [111], chn lnh View/Crystal Face trong
Crystal Builder hoc nhp vo nt View trn thanh cng c. Mt hp
thoi s xut hin. Nhp gi tr 1 cho cc h, k v l, nhp OK, v
HyperChem s quay tinh th v t ct mt phng nhm biu din cho ta
mt [111]. Dng lnh Display/Rendering trong HyperChem chuyn
dng biu din nguyn t sang dng cu.
12. Lu t bo n v bng cch nhp lnh File/Save as (Nhp Save as trong
File menu). nh tn mun lu vo mt file mi: NA.CSD. Nhp OK, v
t bo n v c lu vo kiu D liu tinh th Cambridge.
81

13. Lu ton b tinh th bng cch nhp vo ca s HyperChem v chn lnh
File/Save as... Lu file vi tn mi l: NA.HIN.
To tinh th NaCl
Phn ny ta s hc cch to tinh th ca natri clorua.
1. Tch chn Crystal Builder bng cch nhp Crystals.. trong Database
menu.
2. Nhn nt Samples.. vo hp thoi cu trc tinh th mu (Sample
Crystal Structure)
3. Chn kiu tinh th NaCl bng cch nhp vo nt thch hp v nhn OK
chn.
4. Nhp s t bo n v l: 3x3x3 bng cch nhp gi tr 3 vo trong ba
hiu chnh. Khng nn hiu chnh g n tham s t bo n v: Trnh xy
dng tinh th (Crystal Builder) t cc gi tr thch hp cho NaCl.
5. Chn lnh: HyperChem/Put gi cu trc cho HyperChem, hoc nhn
nt Toolbar i khi c dung dch mu xanh xut hin.
6. Tinh th NaCl 3x3x3 s xut hin trn mn lm vic.
7. quan st mt phng tinh th [111], chn lnh View/Crystal Face trong
Crystal Builder hoc nhp vo nt View trn thanh cng c. Mt hp
thoi s xut hin. Nhp gi tr 1 cho cc h, k v l, nhp OK, v
HyperChem s quay tinh th v t ct mt phng nhm biu din cho ta
mt [111]. Dng lnh Display/Rendering trong HyperChem chuyn
dng biu din nguyn t sang dng cu(nu mun).
Dng mt ct [111].
82
Xy dng phn t ng (Sugar Builder)

Trnh xy dng ng (Sugar Builder) cho php ta xy dng cu trc
polysaccharite tng t nh xy dng chui amino axi hay chui axit
nucleic. Ta c th to cc hp phn theo mun ch khng nht thit phi l
saccharite (sacarit), v dng Sugar Builder ni kt cc hp phn li vi
nhau.
Cc tnh nng ca Sugar Builder
- C 32 mu monosaccharite thng thng, bao gm c aldose v ketose,
k c dng D, L, alpha, beta v dng xp xon (acyclic).
- C kh nng thm cc nhm thng thng, k c OAc v Nac.
- C kh nng to chui t cc mono hnh thnh nn chui
polysaccharite.
- Tham s ho trng lc AMBER cho chui (aldose).
- C kh nng ni kt cc chui to cc nhnh.
- C kh nng thm ln n 21 hp phn ca ngi s dng vo file d
liu.
To chui
Phn ny minh ho cho ta cch to poly(1-4)--D-Glucose
1. Nhp tri chut chn Saccharides trong Database menu.
2. Dng lnh Add/Aldoses m hp thoi Aldoses.
3. Chn D v chn Dng phn D v anome .
4. Chn Glucoses to ra hp phn glucose trong HyperChem.
5. Chn kiu ni kt 1-4 bng cch chn n t list.
6. t v ln lt l 48.05 v -20.
7. Nhp tri chut lp i lp li vo Glucose cho n khi nhn c chui
mong mun.
8. Chuyn ra mn hnh HyperChem v quan st chui mi to.
83
Dng chui polymer

dng mt chui polyme, hy ch n kh nng xem phn t n trn
mn lm vic c kh nng to chui khng. Nhng vic cn lm l xc nh phn
u v phn ui ca phn t, ng thi xc nh gc vn, gc lin kt s c
dng ni kt lp i lp li u vi ui cho n khi to thnh chui vi di
mong mun.
Trnh xy dng polyme ch xy dng cu trc ca polyme, n khng phn tch
thuc tnh nh HyperChem thc hin i vi cc phn t khc. Khi cu trc
polyme vi kch thc nh sn xy dng c, n to nn mt phn t bnh
thng nh HyperChem quan tm.
nh r monome.
u v ui
cc monome c th dng xy dng chui phi c mt u, xem nh l a
v mt ui b. iu c ngha l monome phi c kiu, b-R-a. Bt k
phn t no c t nht ba nguyn t u c th l mt
monome.
Polyme ho bng s tch
Phn ng polyme ho l phn ng to ra
s tch (ngng t) ca a-b. l:
R-R-R-R bng cch lp i lp li
84
Nu gc vn R-R c xem l ngu nhin, khi u (a) v ui (b) phi

c xc nh xy dng chui.
Xc nh gc vn
Khi tch a v b, hnh hc bn trong ca R c xem nh khng i. Tuy
nhin, vn c s quay quanh lin kt R-R. C mt la chn cho qu trnh
polyme ho ngu nhin, nt nm ngay bn phi. Kh nng khc na l
gc c xc nh theo ngi s dng nh mt gi tr hng cho qu trnh ni
kt. Trong trng hp ny ta cn xem xt thm n hnh hc ca lin kt RR.
Tha nhn l a c ni vi nguyn t x ln lt ni vi x. Tng t,
nguyn t b ni vi y v y ni vi y. C th, s ngng t monome
l:
Trong trng hp, gc vn c xc nh l xon x-x-y-y. Mi nguyn t

ny, a, b, x, x, y, y, c xc nh trong monome bng cc phn la chn
c t tn. Nu chng khng c t tn, khi ta s thy dng bo li
sau xut hin:
V d:
Ta s xy dng mt polyme t monome 1-3 butadien. Phn t monome trng

nh sau, y ta dng custom labels v ch thch ch ra cc phn la
chn c t tn
85
Nu phn la chn c t tn ph hp c thc hin, khi nhp chn

Polymers trong Databases menu. Hp thoi la chn nh sau xut hin:
Nhng la chn phi c thc hin t ngu nhin cc gc x-x-y-y

hoc t cc gi tr hng xc nh. Hn na ta phi chn di ca chui
polyme mun xy dng.
Ch : Tch chn Branching Enabled ch khi cc nguyn t khc cng
c t tn tng ng. V d cnh b ta t b cnh a t a
Nu ta chn 300 cho gc xon v xy dng chui bng 20 n v. Ta s thu
c cu trc nh sau:
86
To polyme cho cc monome khc

Trong kiu mu trn ta c th s dng bt k monome no khc m ta mun
vi iu kin ta xc nh chnh xc cc nguyn t cn c, a, b, x, x, y v y.
Vi cc phn u v ui ngn, vic xc nh x v x c th trng vi vic
xc nh y v y nhng iu khng thnh vn vi iu kin a, x v x
(hoc b, y v y) xem nh l cc nguyn t lin kt ni tip nhau. Do , v
d, x v y hoc x v b c th l cng mt nguyn t. Cc phn la chn
c t tn a (hoc b) c th xem nh l mt nhm cc nguyn t, ch
khng phi l mt nguyn t n, vi iu kin cc nguyn t ny lin kt
vi x (hoc y) bng mt lin kt.
Cc bc tun t to Polyme nh sau (v d cho butadien)

1. V phn t Butadien ln mn lm vic.
87

2. Chn cng c la chn trn thanh cng c.
3. Chn nguyn t hydro u tin, tip theo chn Name Selection trong
Select menu.
4. Chn mc Other, ri nh b vo . Tip theo ln lt chn cc nguyn
t khc v nh tn theo th t nh hng dn trn.
5. Nhp chn Polymer.. trong Database menu, hp thoi la chn xut hin,
hy nhp cc gi tr nh gc vn, s monome n v.. thch hp:
6. Nhp OK thc hin to chui polyme.

Ch : Ta hon ton c th thc hin cc tnh ton kho st h
polyme m mnh va to ra. Tuy nhin do polyme l phn t ln nn
thng ngi ta ch kho st mt phn no ca h bng cch chn
phn v thc hin tnh ton nh i vi cc phn t nh khc.
88
Bi 7. La chn v biu din mt nhm cc nguyn t trn

mn lm vic
To vng xon c.
Chn nhm nguyn t.
t nhn v t mu nhm nguyn t.
To vng xon c alpha.

Ta hc cch to vng xon cho chui polypeptide.
Cch lm nh sau
1. Nhp tri chut chn Amino Acids trong Databases menu.
Hp thoi amino axit xut hin.
2. Nhp tri chut tch chn Alpha helix mc Conformation (hnh dng)
3. t gc Omega l 1800.
4. Nhp ln lt su ln tri chut vo Phe.
5. Nhp vo nt tt hp thoi.
Cu trc ca chui xut hin nh sau:
(Cu trc ny c tt Show Hydrogens trong Display menu v

c xoay n nh vy cho d nhn, vi cc bc trn ta s thu c
89

cng thc phn t nh vy nhng cha c xoay theo gc nhn thch
hp).
6. Nu cu trc xut hin vn cn biu din cc nguyn t hydro th hy
nhp tri chut b tch Show Hydrogens trong Display menu.
7. Xoay phn t n gc nhn thch hp.
t nhn cho u v ui chui

nhn c r hn ta nn t nhn cho cc nguyn t N v C cc ui
ca chui.
Cch lm nh sau
1. Nhp tri chut tch vo Atoms v Multiple Selections trong Select
menu.
3. Nhp tri chut nguyn t nit ui.
4. Nhp tri chut vo C ui cn li.
90
5. Nhp tri chut chn Labels trong Display menu.

Hp thoi Labels xut hin.
6. Nhp tri chut tch chn Symbol trong mc Atom ca hp thoi Labels
v nhp OK la chn.
Cc nguyn t N-ui v C-ui s c biu din di dng nhn biu
tng (symbol) nh sau:
Chn lin kt khung

nghin cu vng xon c alpha t nhin ca chui polypeptide, vic
chn ny gip ta hnh dung d dng hn.
91

Bc u tin chn lin kt khung, ta c th thc hin mt trong hai
cch sau:
- Chn ng ngn nht gia hai im chn lm ui.
- S dng Select Backbone (chn lin kt khung) trong Select menu.
Chn ng ngn nht gia hai ui chn.

1. Nu cn thit nhp b tch Show hydrogn trong Display menu.
3. Nhp tri chut vo nguyn t C-ui chn v r n nguyn t Nui chn ri nh chut.
S dng lnh Select Backbone:

1. u tin, nhp tri chut vo cng c la chn trn thanh cng c.
2. Nhp phi chut vo vng trng trn mn lm vic. Vic lm ny gip
loi b nhng la chn trc .
3. Nhp tri chut chn Select Backbone trong Select menu.
Hnh nh lin kt khung s xut hin nh sau:
92
T mu lin kt khung
t mu lin kt khung ta lm nh sau
1. Nhp tri chut chn Color trong Display menu.
Hp thoi la chn mu s xut hin.
2. Nhp tri chut chn mu m ta mun biu din, v d chn mu vng
(Yellow) v nhp OK chn.
3. Nhp phi chut vo vng trng mn lm vic.
HyperChem s biu din khung lin kt dng mu vng.
Ch biu din lin kt khung trn mn lm vic

biu din mi lin kt khung ta lm nh sau
1. Nhp tri chut chn Show Selection Only (ch biu din phn c
chn) trong Display menu.
Khi ch c phn lin kt khung v nhn ca n c biu din.
2. Nu mun khng xut hin c phn nhn th ta vo hp thoi Labels trong
Display menu v chn none mc Atom ri nhp OK chn.
Lc ny ch c lin kt khung c biu din trn mn lm vic.
Ch : Nu nh ta th thc hin v d ny ngay cho lin kt khung c
t mu trn th s khng cn g xut hin trn mn hnh, s d
nh vy v trong phn trn hin th mu ta nhp phi chut
ng ngha vi vic b tt c cc la chn.
Biu din lin kt nhnh (lin kt bin)

93
biu din lin kt nhnh ta lm nh sau

1. Quay v chuyn lin kt khung sao cho trc vng xon c lin kt khung
hng ra ngoi mt phng mn hnh.
2. Nhp tri chut chn Show All trong Display menu. Mn hnh s hin ra
nh sau:
Biu din cc nhm nguyn t khng chn

i khi ta mun chn v biu din cc phn cn li ca h phn t ch
khng phi l phn la chn hin ti. Ta c th s dng Complement
Selection (lu chn b xung) trong Select menu.
Cch lm nh sau
94

1. Nhp tri chut chn Complement Selection trong Select menu.
HyperChem s chn biu din tt c cc phn tr nhng phn c
chn trc s dng bnh thng.
2. Nu ta nhp tip tri chut chn Show Selection Only trong Display menu
th HyperChem s du lun phn lin kt chn trc.
Ch : a phn t v trng thi bnh thng ta nhp tri chut chn
Show All trong Display menu.
Chn theo hnh ch nht

chn cc nguyn t theo hnh ch nht ba chiu ta lm nh sau
1.
2.
3.
4.
Chn Show Hydrogens v chn Show All trong Display menu.

B tch nu c Select Sphere trong Select menu.
Nhp tri chut vo cng c la chn trn thanh cng c.
Nhp ng thi tri v phi chut gi nh vy v r ph ht nhng
nguyn t mun chn vo hnh ch nht.
95
5. Nh chut v tr thch hp th tt c cc nguyn t trong hnh ch nht

c chn s sng hn
Chn theo hnh cu

chn cc nguyn t trong mt hnh cu ta lm nh sau
2. Nhp phi chut vo khong trng trn mn lm vic b tt c cc la
chn trc .
3. Nhp tri chut tch chn Select Sphere trong Select menu.
4. t con tr la chn vo mt nguyn t no c chn lm tm hnh
cu
96
5. Nhp ng thi tri v phi chut, gi v r to mt hnh cu cha cc

nguyn t mun chn.
6. Nh chut th tt c cc nguyn t trong phn hnh cu s sng hn.
Ch : nu ta chn mt im trng no lm tm th khi nhp v r chut

s l kiu chn hnh ch nht ch khng phi kiu chn hnh cu.
t tn phn la chn
HyperChem gip ta d dng t tn cc phn la chn v th c th d dng
biu din li chng sau ny.
t tn phn la chn ta lm nh sau

1. Chn Name Selection trong Select menu.
Hp thoi Name Selection xut hin.
2. Nhp tri chut tch vo mc Other v nh tn ca nhm la chn ngay
trng cnh .
3. Nhp OK chn.
HyperChem s lu tt c phn la chn vi tn m ta nh vo, v d
y l n_sub.
4. Nhp phi chut vo vng trng trn mn lm vic loi b la chn.
5. Nhp tri chut chn Select trong Select menu.
97

Hp thoi Select s hin ra.
6. Nhp tri chut chn Named Selection trong mc By String.
7. Nhp tri chut chn n_sub trong list cc tn bn cnh, nhp OK
chn.
Phn la chn vi tn tng ng s c chn tr li.
Chn lin kt vng

chn vng lin kt ta lm nh sau
1. Nhp tri chut chn cng c la chn trn thanh cng c.
2. Nhp phi chut vo vng trng trn mn lm vic b tt c cc la
chn trc .
3. Nhp lin tip hai ln tri chut vo mt trong cc lin kt ca vng.
Vng lin kt s c chn.
Ch : Nu tch chn Multiple Selection trong Select menu th ta c th

chn c tt c cc lin kt vng.
98
Bi 8. Thao tc vi nhng phn t ln
c v m cc file PDB.
Biu din cc thuc tnh cu trc ca cc phn t ln.
Biu din lin kt hydro
Thay th cc monome.
Quay lin kt nhnh
Mt nt c trng quan trng ca HyperChem l kh nng thao tc
bng tay v tnh ton thuc tnh ca cc phn t ln, nh l cc protein v
nucleic acid.
Ngoi kh nng xy dng v nghin cu cc phn t nh. By gi chng
ta nghin cu cc phn t ln lu trong ngn hng d liu Protein
Brookhaven (Brookhaven Protein Data Bank, PDB).
Trong phn ny ta thc hnh trn trypsin, cht c ch tuyn tu (BPTI).
c ngun file d liu PDB .

Cc file (PDB) trong ngn hng d liu Protein Brookhaven c phn ui m
rng l .ent . HyperChem c th c cc file ny t cc ngun cung cp
khc nhau. Cc file ny trc tin phi c chuyn t ngun gc n
HyperChem.
m file PDB ta lm nh sau

1. Nhp tri chut chn Open trong File menu.
Hp thoi Open file xut hin.
2. Chuyn n th mc samples ca HyperChem.
3. Chn m th mc Pdb.
4. Chn phn ui m rng l Brookhaven PDB (*.ENT) trong mc Files of
type.
Cc file c ui ent hin ra.
5. Nhp tri chut chn pdb5pti.ent trong list file.
Dng ch gii bn di (Comment) s cho bit s qua v ngun gc ca
cht.
6. Nhp OK chn
Mn lm vic s xut hin phn t nh sau
99
Trong h c c cc phn t nc.

7. Nu cu trc xut hin c c nhn ca cc nguyn t th ta nn chn none
hp thoi Label trong Display menu d quan st.
8. Ta cng nn loi b biu din cc lin kt hydro tin quan st phn t.
Loi b cc phn t nc
Trong phn ny ta hc cch loi b cc phn t nc bao quanh phn t
BPTI (bovine pancreatic trypsin inhibitor) m ta ang nghin cu.
Cch lm nh sau
1. Nhp tri chut chn Molecules trong Select menu.
3. Nhp tri chut vo phn t BPTI chn phn t ny.
Phn t BPTI s sng hn ln
4. Nhp tri chut chn Complement Selection trong Select menu.
Vic ny gip ta ch la chn cc phn t nc.
5. Nhp tri chut chn Clear trong Edit menu.
Lc ny s c hp thoi hi ta c thc s mun xo cc nguyn t
chn xut hin
6. Chn Yes.
Cc phn t nc s b xo i v cu trc ca BPTI s xut hin trn mn
lm vic nh sau:
100
Ch : trnh trng hp mun kho st cu trc BPTI trn m li phi

loi b cc phn t nc khi m file PDB, ta nn lu cu trc hin ti vo
mt tn khc khi m sn c.
- Nhp tri chut chn Save as trong File menu.
- nh tn mun lu vo mc File name v chn phn ui m rng l
hin (HyperChem (*.HIN)).
- Nhp Save chn
HyperChem s lu li tn file m bn nh vo vi phn ui m rng
l hin.
Biu din cu trc phn t

Biu din cu trc chnh
Biu din cu trc chnh ca phn t ta lm nh sau
1. Nhp tri chut b tch Show Hydrogens trong Display menu.
iu ny gip ta d quan st phn t hn.
2. Nhp tri chut chn Backbone trong Select menu.
Lin kt khung s sng hn.
3. Nhp phm Spacebar trn bn phm.
iu ny gip cho phn t c biu din ph hp vi t l mn hnh v
cho php ta nhn r hn.
4. Nhp tri chut chn Show Selection Only trong Display menu.
101
Lc ny trn mn hnh ch biu din lin kt khung.

5. Nhp phi chut ln vng trng ca mn lm vic loi b la chn lin
kt khung.
Lin kt khung s tr v trng thi bnh thng.
Ch : biu din li cc lin kt nhnh ta nhp tri chut chn Show All
trong Display menu.
Biu din vng xon Alpha

biu din vng xon Alpha ta lm nh sau
1. Nhp tri chut tch chn Multiple Selections v Residues trong Select
menu.
2. Nhp tri chut chn Select trong Select menu.
Hp thoi Select xut hin.
3. Nhp tri chut tch chn Residue number trong mc By number.
4. nh s 47 vo mc value = v nhp OK chn.
iu ny ng ngha vi SER 47 c chn. Vi cch ny gip ta d
dng chn nhng monome hp phn c bit trong phn t.
5. Nhp tri chut chn Select trong Select menu m hp thoi Selecct
mt ln na v nhp chn Residue number vi s ch 55.
Ta thy trn mn hnh cc hp phn th 47 v 55 sng ln.
6. Nhp tri chut vo hp phn 47 v r n hp phn 55.
iu ny gip cho cc hp phn t 47 n 55 c chn.
Ta cng c th chn cc hp phn t 47 n 55 bng cch nh s 47 v
55 ln lt vo v tr value >= v <=.
7. Nhp tri chut chn Show Selection Only trong Display menu.
iu ny gip ta biu din nhng phn chn gn gh hn.
102

8. Nhp Spacebar HyperChem biu din phn la chn theo t l mn
lm vic.
9. Nhp phi chut vo vng trng mn lm vic loi b la chn cc
hp phn.
10. Chn Select Backbone trong Select menu, sau nhp chn Show
Selection Only trong Display menu.
HyperChem s biu din cc hp phn t 47 n 55. Nhng phn khng
c chn s khng xut hin trn mn hnh.
11. Chuyn v quay vng xon c Alpha sao cho trc ca n hng ra mt
phng mn hnh. Lc ny phn c chn s c dng biu din nh sau:
12. Nhp tri chut chn Show All v Scale to Fit biu din phn t theo
t l mn lm vic.
13. Nhp tri chut vo cng c la chn trn thanh cng c v nhp phi
chut vo vng trng mn lm vic loi b la chn.
Biu din cu ni i sunfua

Trong phn t PBTI c cha cc hp phn cystin (C6H12N2S2) to nn cc
hnh thc lin kt ngang dc theo lin kt khung ca chui peptit. Trong
phn ny ta hc cch phng to mt phn phn t xem biu din cc lin
kt ngang ny.
phng to phn c cu ni i sunfua ta lm nh sau

1. Nhp tri chut chn Show All trong Display menu sau nhp phm
Spacebar trn bn phm biu din ton b phn t theo t l mn lm
vic.
iu ny s gip biu din cu trc phn t vo tm mn lm vic.
103

3. Nhp ng thi tri v phi chut gi nh vy v r chn theo hnh ch
nht vng c hp phn xystin.
C th mt vi hp phn khc ln cn vi xystin cng c chn
Ch : HyperChem ngm nh mu ca lu hunh l mu vng, do c th
d dng pht hin ra hp phn xystin v tr no. Ta cng c th chn
xystin theo kiu hnh cu nh sau:
- Nhp tri chut tch chn Select Sphere.
- Nhp tri chut vo cng c la chn trn thanh cng c.
- Nhp ng thi tri v phi chut vo phn t lu hunh mun chn,
gi v r sao cho bn knh hnh cu tri rng ht vng ta mun chn.
4. Nhn vo dng hin trng lm vic bit chc chn hp phn CYX
c chn.
5. Nhp phm Spacebar biu din phn la chn vo tm theo t l mn
lm vic.
Hp thoi Labels hin ra.
7. Nhp tri chut tch chn Symbol trong mc Atoms sau nhp OK
chn.
8. Nhp tri chut b tch Show Hydrogens trong Display menu d quan
st.
9. Quay v phng to n khi c th quan st c cu ni S-S- mt cch
d dng.
104
10. Nhp tri chut vo cng c la chn trn thanh cng c sau nhp phi
chut vo vng trng trn mn lm vic b la chn.
Chn cu trc vng

Ta c th s dng tnh nng tm vng ca HyperChem biu din cc
hp phn hnh thnh nn vng trong protein.
biu din cu trc vng ta lm nh sau

1. Nhp tri chut chn Atoms trong Select menu.
3. Nhp lin tip hai ln tri chut vo lin kt S-S-.
4.
5.
6.
7.
8.
Vng lin kt c cha lin kt S-S- s c chn.

(Ta cng chn c vng nu nhp lin tip hai ln tri chut vo bt k
lin kt no thuc vng m ta bit)
Nhp phm Spacebar trn bn phm a vng lin kt chn vo tm
mn lm vic.
Nhp tri chut chn Show Selection Only trong Display menu.
Nhp tri chut chn Labels trong Display menu.
Nhp tri chut tch chn Name+Seq mc Residues trong hp thoi, sau
nhp OK chn.
HyperChem s biu din cc hp phn to nn vng v nhn tn km theo
ca chng.
Quay vng cho n khi c th nhn c r nh sau:
105
Biu din lin kt hydro

tnh ton v biu din lin kt hydro ta lm nh sau
1. Nhp tri chut vo cng c la chn trn thanh cng c, sau nhp
phi chut vo vng trng trn mn lm vic loi b nhng la chn
trc .
2. Nhp tri chut chn Show All v Scale to Fit trong Display menu biu
din ton b phn t vo tm theo t l mn lm vic.
4. Chn none trong tt c cc mc ca hp thoi ri nhp OK chn.
5. Nhp tri chut tch chn Show Hydrogen Bonds trong Display menu.
HyperChem s biu din ton b cc lin kt hydro c th c trong h.
6. Nhp tri chut chn Recompute H Bonds trong Display menu.
HyperChem biu din cc lin kt hydro dng ng nt t.
7. Nhn phm PgDn trn bn phm phng to cho n khi c th quan st
d dng cc lin kt hydro.
8. Nhn phm Spacebar trn bn phm chuyn phn t tr li tm theo t
l mn lm vic.
106
Ch : Nu ta thay i s sp xp ca cc phn t trong h hoc l

HyperChem thay i hnh dng trong qu trnh tnh ton, th ta nn chn
Recompute H Bonds li xem lin kt hydro.
Thay th hp phn v tr c bit

Trong bi 6 ta hc cch thay th cc hp phn cu trc bn trong. Trong
phn ny, ta s hc cch thay th cc hp phn cu trc ngoi.
thay th ta lm nh sau
1. Nhp tri chut b tch Multiple Selections trong Select menu.
3. Nhp tri chut tch chn Name+Seq mc Residues ri nhp OK
chn.
4. Nhp tri chut chn Select... trong Select menu.
Hp thoi Select xut hin.
5. Tch chn Residue number trong mc By number, tip theo nh s 58
vo phn value =.
6. Nhp OK chn.
Hp phn 58 s c chn.
7. Phng to phn c chn d quan st, cu trc phn t lc ny c
dng:
107
8. Khi hp phn ALA 58 cn ang c chn, nhp tri chut chn Mutate
trong Databases menu.
Hp thoi Mutate (thay th) xut hin.
9. Nhp tri chut chn VAL trong list cc hp phn ri nhp OK chn.
10. Tip tc dng hp thoi Select chn GLY 57 v thay th bng PHE.
Thay th 56 bng ALA v 55 bng VAL.
Ch : Ta c th thay th bng cc hp phn khc theo mnh.
Quay nhnh lin kt

Ta c th thay i gc vn ca cc nhnh bng vic la chn nhnh v chn
quay bn trong bng cng c quay theo trc Z.
quay nhnh lin kt ta lm nh sau

2. Nhp phi chut vo vng trng trn mn lm vic loi b cc la
chn trc .
3. Nhp tri chut tch chn Atoms trong Select menu.
4. Cu trc phn t v d c dng nh trn hnh
108
5. Nhp lin tip hai ln tri chut vo C trong lin kt C-C ca VAL
chn nhnh lin kt ny.
6. Nhp tri chut vo cng c quay theo trc Z trn thanh cng c.
7. a con tr chut vo mn lm vic, nhp tri gi v r sang bn phi
quay nhnh valin.
109
Ch : Vic dng cng c quay v thao tc quay bng tay l rt lu, v

thng l c phn t cng quay. thc hin ch quay nhnh ta nn dng
hp thoi quay theo trc chn gc quay thch hp theo mong mun.
Cch lm nh sau
- Nhp lin tip hai ln tri chut vo cng c quay theo trc Z.
Hp thoi la chn gc quay xut hin.
(Ta cng c th ly hp ny ra bng cch nhp tri chut vo Rotate trong
Edit menu.)
- Nhp tri chut tch chn trc Z (Z axis) trong hp thoi, tip theo tch
chn Molecules trong mc Apply to.
- nh gi tr gc m ta mun quay nhnh vo v tr Angle, nhp OK
chn.
Nhnh s quay mt gc m ta chn.
110
Bi 9. Cc tiu ho nng lng ca h.
Ti u ho hnh hc phn t theo phng php c hc phn t.

Tnh ton im n.
S dng lin kt xon bt buc.
o v so snh thuc tnh cu trc ca h.
S dng hnh nh phn chiu qua mt phng xc nh ca trnh xy
dng.
Lu vo trong log file kt qu tnh ton.
Trong bi ny, chng ta thc hin cc tiu ho nng lng ca xiclohexan s
dng trng lc AMBER. Trc khi thc hin ta nn hiu qua mt cht v s
cc tiu ho nng lng.
Cc tiu ho nng lng lm bin i hnh hc phn t n nhng mc h c
nng lng thp hn, v cui cng l to ra mt cu hnh n nh nht. Trong
qu trnh cc tiu ho, qu trnh i n cu trc phn t m nng lng
khng cn c th thay i vi phn c na. iu ny c ngha l bt ngun
t nng lng lin h theo cc to Decac, c gi l gradient, l gn nh
bng khng. y c bit l im dng (stationary point) trn mt th
nng.
Nu c s thay i no trong cc thng s hnh hc lm tng nng lng ca
phn t, cu hnh s nhanh chng sa i a v trng thi nng lng cc
tiu.
Mt h phn t c th c nhiu cc tiu nng lng. Nng lng c gi tr
thp nht c gi l cc tiu ton phn, nhng im cc tiu cn li gi l
cc tiu b phn.
Lu kt qu tnh ton vo Log file.

Dng hin trng bn di ca s HyperChem biu din nhng kt qa tnh
ton ph hp nht. Ta c th lu nhng kt qa ny km nhng thng tin tnh
ton lin quan vo trong mt Log file. iu ny thc hin c d dng nh
sau:
1. Nhp tri chute chn Start Log trong File menu.
Hp thoi Start Log xut hin vi tn ngm nh l chem.log.
2. nh tn file mun lu vo mc File name.
111

3. Nhp OK chn.
Log file s lu li tt c cc kt qu trong qu trnh tnh ton m ta tin
hnh.
4. Sau khi tnh ton xong ta nhp tri chut vo Stop log kho vic ghi
chp tip nhng sa i khng cn thit vo phn kt qu tnh ton.
Chn trng lc
Trc khi dng cu trc dng gh ca xiclohexan v tin hnh ti u theo
phng php c hc phn t, ta nn hc cch chn trng lc c hc phn t
do HyperChem cung cp. Trong phn ny ta s dng trng lc AMBER.
chn trng lc ta lm nh sau

1. Nhp tri chut chn Molecular Mechanics trong Setup menu.
2. Lc ny hp thoi la chn phng php xut hin, nhp tri chut chn
phng php AMBER.
3. Nhp vo nt Options m hp thoi la chn thm cho phng php.
4. Nhp tri chut chn Distance Dipendent (ph thuc khong cch) trong
mc Dielectric.
5. Chn Scale factor (h s t l) l 1.

6. t c hai h s Electrostatic (tnh in) ln van der Waals trong mc 1-4
Scale Factor l 0.5.
7. t none mc Cutoffs (lc b).
8. Nhp OK ng hp thoi.
9. Nhp tri chut chn Select Parameter Set trong Setup menu.
10. Hp thoi la chn xut hin, chn tham s thch hp m ta mong mun,
v d chn amber2.
11. Nhp OK ng hp thoi.
Dng cu trc dng gh ca Xiclohexan.

Cch lm nh sau
1. Nhp lin tip hai ln tri chut vo cng c v trn thanh cng c, hp
thoi la chn nguyn t hin ra.
112

2.
3.
4.
5.
6.
Chn nguyn t cacbon v ng hp thoi li.

Nhp tri chut tch chn Atoms trong Select menu.
Chn Labels trong Display menu v t Label l number.
Nhp tri chut b tch Exlicit Hydrogens nu c trong Build menu.
a chut ln mn hnh v v cu trc phn t:
7. Nhp tri chut chn Add H & Model Build trong Build menu thm
nhanh cc hydro cn thiu v biu din li phn t.
C th thc hin lnh ny bng cch nhp lin tip hai ln tri chut vo
cng c la chn trn thanh cng c.
8. Nhp tri chut b tch, nu c, Show Hydrogens trong Display menu.
9. Quay v chuyn cu trc n khi nhn c nh sau:
113
Trnh xy dng (Model Builder) dng cu trc dng gh ca xiclohexan nh

l mt cu trc ngm nh. Cu trc ny cha c ti u ho, nhng n
c t chun v chiu di lin kt, gc, v gc vn.
o thuc tnh cu trc dng gh ca xiclohexan.

By gi chng ta o cc thuc tnh cu trc theo cu trc ca trnh xy
dng nh sn ca HyperChem. Sau , ta em so snh gi tr o c vi
gi tr ca cu trc c ti u.
o thuc tnh cu trc ta lm nh sau

2. Nhp tri chut tch Atoms v b tch Multiple Selection trong Select
menu.
3. Chn mt vi lin kt, gc lin kt, gc vn xc nh gi tr ca
chng.
Cc gi tr nh sau s xut hin trn dng hin trng sau khi ta tin
hnh chn:
di lin kt: 1.54A0
Gc lin kt: 109.470.
Gc vn:
600.
4. Nhp phi chut b cc la chn.
Tnh ton im n
114

Tip theo, ta tin hnh tnh ton im n thu nng lng ton phn ca
cu hnh cha c ti u.
Cch lm nh sau
1. Nhp tri chut chn Single Point trong Cumpute menu.
Tnh ton im n biu din nng lng dng kcal/mol v cn bc hai
tng bnh phng trung bnh (RMS) gradient l kcal/mol.A0 cho cu hnh
ca cc nguyn t hin ti. Cc gi tr nng lng v gradient xut hin
trn dng hin trng
Ghi ch vo Log file

Ta c th ghi ch thm vo d liu tnh ton lu trong Log file. Tuy nhin
ghi ch ny ch thc hin c khi Start Log ang hot ng.
Cch lm nh sau
1. Nhp tri chut chn Log comments trong File menu.
Hp thoi Log comments xut hin:
2. nh ghi ch m ta mun vo vng trng, sau nhp OK chn.
Ti u ho cu trc
Tip theo ta hc cch cc tiu ho cu trc dng gh bng phng php ti
u c hc phn t. u tin l t cc bin s cc tiu ho, gm c hnh thc
cc tiu v tip theo l chy tnh ton.
t bin ti u
1. Nhp tri chut chn Geometry Optimization trong Computer menu.
Hp thoi xut hin:
115
Hp thoi la chn cho php ta chn thut ton ti u v tiu chun hi t

cho qu trnh cc tiu ho m ta tin hnh.
2. Nhp tri chut chn thut ton Polak-Ribiere.
Thut ton ny ni chung cho kt qu ti u tt.
3. Chn gi tr 0.1 kcal/A0mol cho RMS gradient v ngm nh gi tr ny
cho cc h khc.
Maximum cycles trong mc RMS gradient cho php ta t iu kin
kt thc tnh ton. Khi tnh ton t c mt trong cc tiu chun ny th
tnh ton s dng li.
Mc In vacuo (trong chn khng) c tch ngm nh sn nu ta khng
t Periodic Box trong Setup menu.
Hp thoi la chn ti u hnh hc l nh nhau i vi mi phng php.
HyperChem s dng cc thut ton tnh ton
cho h chn.
Steepest Descent Chuyn trc tip xung ng dc nht (ca lc
tng tc) trn mt th nng. Nu nng lng
ca h gim i, n tip tc thc hin nh vy
nhng vi bc nhy ln hn (tng thm 1.2 ln)
nu nng lng tng sau bc nhy, t l iu
chnh hnh hc gim xung: bc nhy tip theo
bng mt na bc nhy trc . Phng php
ny to ra cc in tch c gii hn cho h, dng
nhanh chng hiu chnh hnh hc khi u
km hoc loi b cc tip im km; n c tc
ng tt khi h cn xa so vi cc tiu. Tnh ton
khng sn sng hi t v c th dao ng.
Fletcher-Reeves y l phng php gradient lin hp, c ngha
l n chn hng gim ( c nng lng thp
hn) bng cch xt gradient hin ti, s lin hp
ca n, vi gradient ca bc trc . y l
Algorithm
116
Polak-Ribiere
EigenvectorFollow
Block Diagonal
Newton-Raphson
Conjugate
Dierections
Termination
condition
RMS gradient
max. Cycles
In vacuo
Periodic boudary
conditions
phng php c hi t tuyn tnh cao; n hi

t tt hn phng php trn.
y l phng php gradient lin hp s dng s
thm d mt chiu. N ci tin t phng php
Fletcher-Reeves cng bng cch xem xt hng
lin hp trc . L phng php nhanh hn
Fletcher-Reeves.
C gi tr cho cc ti u bn kinh nghim v
thun tu l thuyt; khng c gi tr cho ng
lc hc phn t.n dng cc vect c trng ca
ma trn cho ho Hesian xc nh hng ti
u cho s chuyn ng ca nguyn t. c on
ban u c tnh theo kinh nghim.
Ch c gi tr cho trng lc MM+. y ch l
phng php dng tnh trc tip cc o hm
bc hai, hoc cc hng s lc. y l phng
php c hiu qu trong vic xc nh cc tiu
nhng i hi hnh hc khi u hp l.
C gi tr cho tnh ton bn kinh nghim, thun
tu l thuyt v DFT. N ch dng nng lng
v o hm ca nng lng. Do n c th s
dng rng ri hn mc d n khng c kh nng
so snh vi cc phng php o hm. c th s
dng ti u hnh hc MP2 hay trng thi kch
thch hnh hc CI.
Dng cc hp thoi ny t cc iu kin kt
thc tnh ton.
Khi RMS gradient ca nng lng b hn gi tr
ny, tnh ton s dng li. Gi tr t thay i t
10-3 n 0.1. t gi tr b hn na c th my
s bo li. Ta c th t gi tr cao hn 0.1
tnh ton nhanh hn, nhng km chnh xc.
S vng tnh ton ti a. Ngm didnh bng 15
ln s nguyn t. Gi tr c th thay i t 100
n 1000.
Tch loi b cc iu kin bin tun hon
khi tnh ton. ch chn in vacuo nu h trong
mt hp tun hon.
y s dng iu kin bin tun hon thit
lp cho h tnh ton. ch c gi tr vi h
trong hp tun hon.
117

Variable Nhp nt la chn thm. cho php ta chonk
ti u nng lng SCF hay SCF + MP2 (ch
Ab initio) hoc nng lng trng thi kch thch
(cung cp cho tng tc cu hnh c chn
trc ).
Screen refresh y l tn s, trong cc vng ti u ho, biu
period din kt qu ln mn hnh.
Chy tnh ton

Sau khi t xong cc bin cho vic ti u, by gi ta bt u thc hin
tnh ton ti u .
1. Nhp tri chut chn OK ng hp thoi v HyperChem s bt u
tnh ton
Ti u ho bt u v hin trng tnh ton s hin trn dng hin trng.
Sau mt lc tnh ton hon thnh v gi tr nng lng ln gradient hin
ra trn dng hin trng.
o thuc tnh cu trc ca h ti u

By gi ta so snh thuc tnh cu trc ca cu trc c cc tiu ho vi cu
trc ca trnh xy dng trong HyperChem.
1. Chn o mt vi lin kt, gc lin kt, gc vn.
Cc gi tr o c xut hin trn dng hin trng nh sau:
di lin kt: 1.53A0.
Gc lin kt: 110.20
Gc vn:
58.00.
2. So snh cc gi tr ny vi cc gi tr ca cu trc cha c ti u.
di lin kt: 1.54A0
Gc lin kt: 109.40
Gc vn:
600
Ta thy cu trc c ti u gc lin kt tng ln mt t khi gc t din
v gc vn gim i hai .
Ch : Sau khi tnh ton xong ta c th xem thuc tnh ca h hay
mt phn la chn no bng cch nhp chn phn v chn
Propeties trong Compute menu xem thuc tnh.
118
Chuyn t xiclohexan dng gh sang dng thuyn

Trong phn ny ta s hc cch phn chiu (Reflect) mt ui ca phn t
to ra cu trc xiclohexan dng gh.
nh mt phng phn chiu ta lm nh sau

1. Nhp tri chut tch chn Multiple Selections trong Select menu.
3. Nhp lin tip hai ln tri chut vo cng c la chn to cu trc theo
trnh xy dng.
4. Nhp tri chut vo lin kt 1-2 v 4-5 chn lm mt phng phn
chiu.
5. Nhp tri chut chn Name Selection trong Select menu.

6. Nhp chn PLANE (mt phng) v nhp OK ng hp thoi.
phn chiu ui ca phn t ta lm nh sau
1. Nu cn thit, chn Show Hydrogens trong Display menu v dng cng
c phng to phng to thu nh phn t cho d nhn.
2. Nhp ng thi tri v phi chut, gi v r chn tt c cc nguyn t ta
mun phn chiu.
119
3. Nhp tri chut chn Reflect (phn chiu) trong Edit menu.
Cc nguyn t c chn s phn chiu theo mt mt phng to ra cu
trc xiclohexan dng thuyn.
4. Nhp phi chut vo vng trng trn mn lm vic b cc la chn.

Ch : Nu nh ta khng t Show Hydrogen trc khi la chn phn
chiu, ta s khng phn chiu c chng.
o khong cch gia cc Hydro trc
120
o khong cch gia cc hydro trc ta lm nh sau

1. Nhp tri chut tch chn Multiple Selections trong Select menu.
3. Nhp phi chut vo hai hydro trc.
Dng hin trng cho bit khong cch gia cc nguyn t l 1.84A0. gi tr
ny kh ph hp vi khong cch gia cc nguyn t khng lin kt.
Ti u ho cu trc xiclohexan dng thuyn

ti u ho cu trc dng thuyn ta lm nh sau
1. Nhp phi chut trn vng trng loi b tt c cc la chn trc .
2. Chn Geometry Optimization trong Cumputer menu.
3. Nhp OK bt u ti u, s dng nhng la chn ln trc.
Khi cu hnh c ti u ho xong, gi tr nng lng v gradient hin
trn dng hin trng.
o li khong cch gia cc Hydro trc

2. Nhp tri chut chn Multiple Selections trong Select menu.
3. Nhp tri chut vo hai hydro trc.
Dng hin trng biu din khong cch mi ca H-H (2.28A0). Cu trc
ti u c lm dt nh lm cho cc hydro trc dn xa nhau ra mt
trc.
121
To cu trc dng thuyn xon

Hnh thc th ba ca xiclohexan l cu trc dng thuyn xon. Cch n
gin to ra cu trc ny l thay i mt chc cu trc dng thuyn
bng cch xon cng bc lin kt.
xon cng bc ta lm nh sau.

1. Nhp phi chut ln vng trng loi b tt c nhng la chn trc .
2. Nhp tri chut b tch Show Hydrogens trong Display menu.
3. Chn gc vn gia bn nguyn t cc bon bng cch chn cc lin kt 61, 1-2 v 2-3.
Ta phi chn cc lin kt theo ng nh vy vn cng bc.

4. Nhp tri chut chn Constrain Bond Torsion trong Build menu, sau
nhp chn Other v nhp vo s 30 vn cng bc 300. Nhp OK
chn.
5. Nhp phi chut vo vng trng loi b tt c cc la chn trc .

Gc vn cng bc c thc hin.
xy dng li phn t vi lin kt c vn cng bc ta lm

nh sau
122
1. Nhp lin tip hai ln tri chut vo cng c la chn trn thanh cng c
gi trnh xy dng.
HyperChem s xy dng li cu trc vi s cng bc xon to ra cu
trc xon dng thuyn hp vi tiu chun.
Ti u ho cu trc xon dng thuyn

Cch lm nh nhng cu trc trn.
Ngng Log file

Sau khi tnh ton xong ta ngng Log file v kim tra kt qu bng Notepad
hoc Wordpad.
ngng Log (ghi) cng vic ta lm nh sau

1. Nhp tri chut vo Stop Log trong File menu.
kim tra kt qu tnh ton ta lm nh sau

1.
2.
3.
4.
M NotePad.
M tm file log m ta mun xem,v d chem.log
Xem kt qu tnh c.
ng NotePad khi xem xong kt qu.
123
Bi 10. C hc phn t
Xy dng v hiu chnh phn t

Ti u hnh hc theo c hc phn t
S dng iu kin bin chu k
Chng cht hai phn t
ng lc hc phn t
Biu din li ng lc hc phn t v tnh trung bnh.
ng lc hc Langevin v Monte Carlo
Trong phn ny ta s hc v chc nng v cch s dng cc phng php c

hc phn t ca HyperChem.
Cc tnh ton c hc phn t x l cc nguyn t nh s tng tc ca cc
ht Newton bng mt hm th nng. Cc th nng ph thuc vo di lin
kt, gc lin kt, gc vn v cc tng tc khng lin kt (gm c lc Van de
Waals, tng tc tnh in v cc lin kt hydro). Trong cc tnh ton ny,
lc tc dng ln nguyn t l hm v tr ca cc nguyn t.
Ch : Nu ch phn no ca h trn mn lm vic c chn, khi ch
cc tng tc lin quan n t nht mt nguyn t c chn mi c trong
cc tnh ton. Nhng tng tc lin quan n nhng nguyn t khng c
chn khng xut hin trong tnh ton. Vi tnh ton ti u ho cu trc, ch
nhng nguyn t c chn c php dch chuyn, trong khi cc phn
khng chn vn ng yn.
S dng trng lc AMBER ta s ti u ion lng tnh alanin dng c lp
v trong dung dch xc nh nh hng ca dung mi ln cu trc ti
u. Ta cng biu din ng lc hc phn t trong dung dch m phng tc
ng ca n vi cc h sinh hc.
Trong bi by c nm bi thc hnh:
Bi thc hnh 1: To ion lng tnh alanin c ti u ho s dng cc k
nng xy dng v hiu chnh nhng bi trc.
Bi thc hnh 2: S dng iu kin bin tun hon (periodic boundary
conditons) solvat ho ion lng tnh.
Bi thc hnh 3: S dng s chng cht so snh th gic phn t c lp
v phn t c solvat ho.
124
Bi thc hnh 4: S dng ng lc hc phn t tm dng c nng lng

thp nht.
Bi thc hnh 5: Dng ng lc hc Langevin m phng s c mt ca
dung mi trong qu trnh thc hin dao ng ng lc. Dng phng php
Monte Carlo ly mu cu hnh theo phn b Boltzmann.
Bi thc hnh 1: To ion lng tnh alanin c lp

Phc tho ion lng tnh alanin
Mc d ta c th d dng dng th vin amino axit ca HyperChem biu
din alanin, y ta s hc cch xy dng cu trc dng th ca n.
phc ho ion lng tnh alanin ta lm nh sau

1. Nhp lin tip hai ln tri chut vo cng c v trn thanh cng c.
Hp thoi la chn nguyn t hin ra.
2. Tch chn Allow Arbitrary Valence v Explicit hydrogens.
3. Chn cacbon v ng hp thoi li.
4. M hp thoi Label trong Display menu v t Symbol ri ng hp
thoi.
6. V phc ho nh sau:
Ch : Hydro lun t thm vo trong khi ta v.
125
Ch : C mt cacbon ch c hai hydro. Ta s hiu chnh cc hydro ny

thnh oxi.
Hiu chnh cu trc

Cu trc ny ch c hydro v cacbon, ta cn phi hiu chnh cu trc to
ra ion lng tnh alanin. c bit, ta cn chuyn mt s nguyn t thnh nit
hoc oxi v to lin hp trong nhm cacboxyl.
hiu chnh cu trc ta lm nh sau

1. Nhp lin tip hai ln tri chut vo cng c v m hp thoi cc
nguyn t, chn nit v ng hp thoi li.
2. Nhp tri chut vo cacbon nhm metyl chuyn n thnh nit nh sau:
126
3. M hp thoi la chn cc nguyn t v chn oxi.

4. Nhp tri chut vo hai nguyn t hydro chuyn chng thnh oxi.
5. Nhp lin tip hai ln tri chut vo cc lin kt cacbon-oxi chuyn
chng thnh lin kt lin hp.
6. Hnh v phc tho ca ta s trng nh sau:
t in tch nguyn t
Bc tip theo ta t in tch hnh thc cho mt s nguyn t biu din
mt cch xp x phn b in tch trn ion lng tnh hin ti. Ta c th tm
in tch nguyn t bng cc phng php sau vi HyperChem:
Nu mt phn t c xy dng t mt mu cho sn, nh PDB file,
mu cha sn in tch.
Bng tnh ton c hc lng t.
127

Bng cch ly xp x in tch.
Trong bi ny, ta t xp x n gin in tch ca nit l +1 v mi
nguyn t oxi l -0.5.
quy in tch cho cc nguyn t ta lm nh sau:

1.
2.
3.
4.
5.
Nhp tri chut tch chn Atoms trong Select menu.

nhp tri chut tch chn Multiple Selections trong Select menu.
Nhp tri chut chn cng c la chn trn thanh cng c.
Chn nguyn t nit.
Nhp tri chut chn Set Charge trong Build menu.
Hp thoi la chn xut hin, nhp in tch 1.0 v ng hp thoi li.
6. Nhp phi chut vo vng trng trn trang lm vic b la chn.
7. Chn c hai nguyn t oxi v quy cho in tch l - 0.5 cho mi nguyn
t.
8. Nhp phi chut vo vng trng b tt c cc la chn.
Chn trng lc
Tip theo y ta s hc cch chn trng lc. Ta nn chn trng lc trc
khi s dng n Trnh xy dng (Model Builder) bi v trnh xy dng quy
cho kiu nguyn t cho mi nguyn t theo trng lc m bn chn. Nh
mt s la chn, ta c th quy cho chnh xc cc kiu nguyn t bt k lc
no bng vic s dng hnh thc tnh ton (Calculate Types) trong Build
menu. Tuy nhin, cch n gin nht l quy cho trng lc chnh xc trc
khi ta s dng trnh xy dng.
Hp thoi trng lc c hc phn t biu din cc trng lc (hm

th) cho ta la chn tnh ton.
MM+
Pht trin cho cc phn t hu c. y l trng

lc ton b nguyn t. HyperChem b sung
trng lc MM2 bng cch cung cp thm cc
tham s (cc hng s lc). iu ny m rng
phm vi cho cc hp cht ho hc m MM+ c th
128

cung cp. MM+ cng cung cp cc gii hn cho
vic tnh ton cc tng tc khng lin kt, iu
kin bin tun hon v s hng gim bt s cng
lin kt nhm trnh lin kt qu di.
Pht trin cho cc protein v nucleic axit. Ta c
AMBER
th chn m phng nguyn t ton din (all-atom)
hay nguyn t hp nht (united-atom). La chn
United-atom x l cc nhm nguyn t nht nh
nh mt nguyn t, bng mt kiu nguyn t. Ta
cng c th chn t cc tp hp tham s khc
nhau hin hnh cho Amber.
BIO+(CHARMM) Pht trin cho cc phn t sinh hc ln. Ta c th
chn m phng all-atom hoc united-atom. La
chn united-tom x l nhm nguyn t nht nh
nh mt nguyn t, vi cng kiu nguyn t. Ta
c th chn cc tp hp tham s khc nhau.
Pht trin cho cc phn t protein v axit nucleic.
OPLS
N tng t nh AMBER nhng x l cc tng
tc khng lin kt chnh xc hn. Trng lc ny
ch cung cp kiu m phng united-atom.
Nhp tri chut la chn thm cho trng lc
Options
Nhp tri chut n cc thnh phn ca trng
Components
lc. iu ny cho php ta chn thnh phn no
ca trng lc c tnh n trong tnh ton.
chn trng lc ta lm nh sau

Hp thoi la chn trng lc xut hin.
2. Chn AMBER v nhp vo nt Options.
Hp thoi la chn thm cho trng lc xut hin.
3. S dng cc gi tr ngm nh ri nhp OK ng hp thoi ny li.
4. Chn OK ng hp thoi la chn trng lc.

5. Nu xut hin hp thoi nhc nh sau th nhp OK chn.
129
Ch : S dng hp thoi la chn trng lc t cc iu kin cho cc

trng lc c hc phn t AMBER, BIO+, v OPLS. HyperChem lu cc
thit lp la chn ny.
Dielectric
permittivity
(epsilon)
Constant
Distance
dependent
Scale factor
1-4 Scale factor

Electrostatic
Van de Waals
Cutoffs
Hng s hoc ph thuc khong cch xc nh

phng php tnh ton epsilon, h s gim bt cc
tng tc in tch-in tch (v th tnh in).
Epsilon l hng s in mi.
y lm cho epsilon l mt hng s. y l hnh
thc thch hp cho cc h trong pha kh hoc trong
mt dung mi r rng.
y lm cho epsilon t l vi s phn li tn ti gia
cc nguyn t. iu ny gn ng cho nh hng
ca dung mi khi thiu dung mi thch hp, v cho
php tnh ton nhanh hn. S dng Distance
dependent vi trng lc OPLS. Khi m phng ny
chn biu din cho mt dung mi, ta thng chn
Constant (hng s) khi dung mi hin din.
Vi hng s, epsilon = (hng s in mi ca
khong trng t do)x(H s t l). Vi ph thuc
khong cch, epsilon = (hng s in mi ca
khng gian t do)x(h s t l)x(s phn li gia cc
nguyn t). Scale factor (h s t l) phi 1. Ga tr
ngm nh l 1.0 l thch hp cho tt c cc h.
Cc tng tc khng lin kt (Van de Waals v tnh
in) gia cc nguyn t c tch t cc lin kt
ba c bi s bng h s ny.
y lm thay i ln tng tc in gia cc
nguyn t tch ra t cc lin kt ba. Thay i t 0
n 1. Vi AMBER v OPLS, s dng gi tr 0.5.
vi BIO+ s dng gi tr 1.0, 0.5, hoc 0.4
Lm thay i ln tng tc Van de Waals gia
cc nguyn t tch t cc lin kt ba. Thay i t 0
n 1. Vi AMBER dng 0.5. vi OPLS dng
0.125. vi BIO+ dng gi tr c nh l 1.
Cc la chn ny xc nh gii hn khong cch
cho vic tnh ton cc tng tc khng lin kt v
130

ng nht vi cc la chn trong MM+.
Hp thoi la chn MM+.
S dng hp thoi la chn MM+ t cc iu kin cho trng lc c hc
phn t MM+. HyperChem lu thit lp la chn ny, ngoi tr cc gii hn,
trong S ng k (Registry) hoc trong file chem.ini v s dng chng cho
cc phn HyperChem mi.
Cc tng tc tnh in khng lin kt c tnh

ton s dng cc tng tc lng cc lin kt hoc
mt phn in tch ca cc nguyn t.
Bond dipoles y s dng cc lng cc lin kt tnh ton cc
tng tc tnh in khng lin kt. Cc gi tr lng
cc lin kt ly t file tham s cng (stretch) MM+.
Atomic charges y s dng mt phn in tch nguyn t tnh
ton cc tng tc tnh in khng lin kt. Ta c
th quy in tch ny theo cch t in tch trong
Build hoc ta c th tnh ton bn kinh nghim hay
AB initio trc tnh in tch nguyn t vi mi
nguyn t s dng cc phn tch khu tr Muliken.
La chn ny xc nh khong cch gii hn cho
Cutoffs
vic tnh ton cc tng tc khng lin kt. Chn
Periodic Box trong Setup menu t ng thit lp
Switched (bt) vi cc gi tr ngm nh. Gii hn
l cn thit ngn vic tnh ton cc tng tc vi
cc hnh nh tun hon ln cn.
None Tnh ton tt c cc tng tc khng lin kt. None
ngm nh cho cc h in vacuo (chn khng).
Khng dung la chn ny cho cc iu kin bin
tun hon bi v n cho kt qu trong gii hn
khng m t hon ton v gy nn s gin on
trong mt th nng.
Electrostatics
131

Switched Mt hm trn, p dng cho bn knh trong n bn
knh ngoi (The inner radius to the outer radius),
gim t t cc tng tc khng lin kt n khng.
Nu h phn t trong mt hp tun hon,
HyperChem chn Switched (bt) v t Outer v
Inner Radius. Ta c th cng dng Shifted (tt).
Shifted Hm trn, p dng ln ton b khong cch khng
lin kt, t khng n bn knh ngoi, gim dn cc
tng tc khng lin kt n khng.
Outer radius bt (Switched) v tt (Shifted) cc gii hn, y
l khong cch cc tiu ti cc tng tc khng
lin kt c t l khng. y thng c t gi
tr t nht l 4A0, ln hn bn knh trong. Vi cc
iu kin bin tun hon, gi tr ny bng mt na
chiu nh nht ca hp tun hon.
Inner radius Ch bt gii hn, y l khong cch nh nht
gia cc nguyn t i vi cc tng tc khng lin
kt hon ton. Vi cc iu kin bin tun hon, gi
tr ny l 4A0, b hn mt na chiu nh nht ca
hp tun hon hoc c gi tr cc tiu l khng.
Ch : Cc gii hn c thit lp s tr v gi tr ngm nh khi ta
thit lp mt h phn t mi trn mn lm vic.
Cc thnh phn trng lc
S dng thnh phn trng lc t cc thnh phn ca trung lc MM+,

AMBER, BIO+ v OPLS lin quan n tnh ton ca ta. HyperChem lu s
thit lp cc thnh phn ny, p dng cho tt c cc trng lc, trong Registry
v s dng chng cho cc phn HyperChem mi.
132
Bond
Angle
Torsion
Non-Bonded
Electrosstatic
Hydrogen-Bonded
Thnh phn bao hm trong tt c cc s hng

trng lc kt hp vi s cng lin kt. Vi
MM+ y l s hng bao hm s hng cng
bc ba v s hng cng bnh thng.
Thnh phn ny bao hm tt c cc s hng
trng lc kt hp vi s un gc lin kt. Vi
MM+ y l s hng bao hm s hng uncng ngang v un mt phng ngoi cng nh
s hng un thng thng. Vi BIO+
(Charmm) n bao hm s hng Urey-Bradley
cng nh s hng un thng thng.
Bao hm tt c cc s hng vn, .v.v. s xon
thch hp v khng thch hp.
Bao hm tt c cc s hng kiu 6-12 van der
Waals gia cc nguyn t khng lin kt.
Bao hm tt c cc tng tc culomb v lng
cc (MM+).
Bao hm bt k s hng lin kt hydro nh s
bao hm trong cc phin bn trc ca Amber
v Charmm.
Dng v kho st cu trc 3D

Bn sn sng xy dng cu trc 3D cho alanin v quan st hnh dng
ca n.
xy dng v nh hng cu trc ta lm nh sau

thc hin dng cu trc theo trnh xy dng.
HyperChem xy dng v biu din gn ng bc nht cho ion lng tnh
alanin.
2. Quay v chuyn cu trc n khi hnh dng ca n trng nh sau:
133
Cu trc ca trnh xy dng ch l cu trc gn ng ca ion alanin.

3. M hp thoi Labels t Display menu v chn Chirality (tnh khng i
xng gng) cho cc nguyn t. Nu cacbon trung tm c gn nhn l
R ch khng phi l S, ta hy nhp tri chut vo cng c v, nhn phm
Shift v nhp tri chut vo cacbon trung tm.
Ta cng c th s dng nhn phm Shift v nhp tri chut quay hai
nguyn t bn cnh, theo thay i tnh i xng gng ca phn t.
4. i kiu nhn ca cc nguyn t tr li dng Symbol v nhp tri chut
bt li cng c la chn.
5. Lu cu trc vi tn l alaz.hin
o thuc tnh cu trc ca phn t ta lm nh sau:

2. Nhp tri chut vo nguyn t oxi gi v r chut n nguyn t oxi cn
li
Trnh xy dng dng gc O-C-O l 1200.
3. Nhp phi chut vo vng trng b la chn.
4. Nhp tri chut vo nguyn t oxi gi v r n nguyn t nit ri nh
chut.
134
Gc vn O-C-C-N l 600 hoc 1200, tu thuc vo th t m ta s

dng v cc nguyn t trong cu trc.
5. Nhp phi chut vo vng trng trn trang lm vic loi b cc la
chn gc.
biu din kiu nguyn t MBER ta lm nh sau:

1. M hp thoi Labels trong Display menu v kiu nhnh l Type.
Thc hin tnh ton im n cho phn t

By gi ta thc hin tnh ton im n tnh nng lng v gradient cho
phn t.
135
tnh ton im n ta lm nh sau:

1. Nhp tri chut chn Single Point trong Compute menu.
Sau mt lc tnh ton hon thnh dng hin trng xut hin kt qu nng
lng v gradient tnh ton c.
Ti u ho cu trc phn t c lp
Gi tr nng lng v gradient ln cho bit rng cu trc ca trnh xy dng
kh xa cu trc ti u. Sc cng ch yu ph thuc vo khong cch ca lin
kt C-N v C-O.
ti u ho cu trc ta lm nh sau
1. Nhp tri chut chn Geometry Optimization trong Compute menu.
Hp thoi la chn ti u hnh hc xut hin
2. Nhp cc gi tr nh trong hp thoi trn v nhp OK thc hin tnh

ton.
Sau mt lc, ti u ho hon thnh.
Trn dng hin trng xut hin kt qu v nng lng v gradient tnh
ton c.
3. Khi ti u hon thnh, tin hnh o gc O-C-O v gc vn O-C-C-N:
Gc O-C-O = 123.90.
Gc O-C-C-N = -510 v 990.
M li cu trc cha c ti u c gc O-C-O l 1200 v gc O-C-CN l 600 v 1200.
Cui cng trong bi ny ta s dng gc O-C-C-N biu din cc tnh
nng ca ng lc hc phn t ca HyperChem, v th hy lu gc ny.
Nhp tri, gi v r chn gc vn O-C-C-N.
Nhp tri chut chn Name Selection trong Select menu.
Tch chn Other, nhp tn ncco ri nhp OK chn.
136
4. Nhp phi chut vo vng trng b tt c cc la chn.
Lu cu trc
Ta nn lu cu trc alanin c lp ti u, nh th ta c th em so snh
n vi cu trc trong dung mi m ta s to ra bi tip theo.
Lu cu trc
1. Nhp vo Save trong File menu hoc nhp ng thi hai phm Ctrl v S
trn bn phm.
Hp thoi xut hin.
2. nh tn ala-gas vo mc File name.
3. Chn ui HIN trong mc Save as Type.
4. Nhp tri chut vo phn ghi ch v nh ch thch nh sau:
5. Nhp OK chn.
Bi thc hnh 2: Solvat ho h phn t
137

HyperChem cho php ta t h phn t trong mt hp tun hon ca cc
phn t nc m phng tc ng trong dung mi nc nh trong mt
h sinh hc. Trong bi ny ta solvat ho ion lng tnh alanin to bi 1.
Trc khi tip tc, hy lm theo cc bc sau

1. Nhp tri chut chn none v chn Labels trong Display menu v t
none, nhp OK chn.
2. Nhp trri chut chn Periodic Box trong Setup menu m hp thoi
la chn.
Ch c chc nng thng tin. X, Y, Z cho ta bit

kch c hp nh nht ta c th bao quanh h
phn t (cht tan). Hp thoi c kch c cc tiu
ny khng th iu tit s phn t nc trong h
v n ch c ngha tham kho.
Periodic box size Kch c cc chiu ca hp. Ta c th t li theo
mun.
Ch c ngha thng tin. N cho bit s phn t
Maximum
number of Water nc ti a trong hp.
molecules
Khong cch cc tiu gia cc phn t dung mi
Minimum
distance between v cht tan. Ngm nh l 2.3A0. C th t li
t 1-5A0.
solvent and
solute atoms
Smallest box
enclosing solute
t iu kin bin tun hon

solvat ho mt h bng HyperChem ta s dng mt hnh ch nht hoc
hnh lp phng cha cc phn t nc trng thi cn bng. Ta xc nh
cc chiu ca hp, t cht tan vo tm v xc nh khong cch cc tiu
138

gia cc nguyn t dung mi v cht tan. HyperChem s loi b tt c cc
phn t nc n gn phn t cht tan hn khong cch l thuyt.
Xc nh kch c hp tun hon

C nhiu yu t xem xt khi ta xc nh kch c ca hp tun hon. v d,
n phi ln hn hp nh nht cha c cht tan hin ra trong hp thoi la
chn.
Kch c ca hp t nht gp hai ln kch c ca cht tan ln nht trnh s
tng tc gia cht tan-cht tan khi s dng cc ngng gii hn ngm nh.
Tng tc gia cht tan-cht tan c th cng c trnh i vi hp nh hn
bng cch lm nh bn knh ngng sau khi solvat ho( v th kch c cht
tan ln nht bao gi cng b hn kch c ca hp nh nht). ln ln nht
ca cnh hnh lp phng l 56.10408A0, do ta khng th t kch thc
cc cnh ca hp bn ngoi gi tr nh nht v ln nht trong hp thoi la
chn.
Chn kch c hp
1. Ly kch thc hp theo cc chiu l 12.0, 10.0 v 12.0 A0, nh trnh by
trong minh ho sau:
2. Nhp OK chn.
iu ny c ngha la t cu trc vo tm ca hp bao quanh bi 40
phn t nc.
Biu din h solvat ha

1. Nhp tri chut chn Rendering trong Display menu.
2. Chn Sticks, m phn la chn Sticks tch chn Perspective (phi cnh)
ri nhp OK chn.
4. Chn vo lin kt hay mt nguyn t bt k thuc phn t alanin, quay h
cho n khi nhn c nh sau:
139
iu chnh cc gii hn v la chn cht in mi

Khi ta s dng iu kin bin tun hon, ta cn kim tra cc la chn i vi
cc gii hn v cht in mi trong hp thoi la chn trng lc.
kim tra la chn ngng v cht in mi ta lm nh sau

2. Chn Options m hp thoi la chn thm cho trng lc.
3. Nhn vo mc la chn Cutoff (ngng, gii hn) bn phi hp thoi.
Khi ta chn cc la chn trong hp thoi, HyperChem t ng thay i cc

la chn cho cc ngng ta la chn chnh xc ngng bn trong v bn
ngoi cho h c solvat ho. Ngng ngoi c t bng mt na kch
thc hp nh nht, ngng trong t b hn 4A0 bo m khng c
im khng lin tc trong mt th.
4. By gi nhn vo la chn Dielectric (cht in mi), trn nh ca hp
thoi
Khi ta s dng dung mi r rng, ta nn s dng hng s in mi.
5. Chn Constant (hng s) thay v Distance dependent (ph thuc khong
cch).
Ch : Hng s in mi khng t ng thay i bi v khi t mi n
c lu vo trong file Chem.ini.
140

6. Nhp OK ng ln lt cc hp thoi.
Ti u ho phn t c solvat ho
Tip theo y ta thc hin ti u h solvat ho s dng iu kin bin tun
hon. Bi trc phn t alanin c ti u hnh hc dng c lp. Trong
phn ny ta thc hin ti u ho di nh hng ca dung mi.
ti u phn t trong dung mi ta lm nh sau

2. Nhp phi chut vo vng trng loi b la chn trc .
Hp thoi la chn ti u hnh hc theo phng php c hc phn t xut
hin.
4. Nhp OK bt u ti u ho phn t alanin solvat ho, k c cc
phn t nc.
Tnh ton thc hin trong mt vi pht.
5. Khi tnh ton hon thnh, cc gi tr tnh c xut hin trn dng hin
trng.
6. Lu cu trc vi tn l ala-liq.hin.
Bi thc hnh 3: S dng s chng cht cc phn t

H ang biu din l h c cu trc c cc tiu ho ca ion lng tnh
alanin trong nc. Ta s dng n so snh vi cu trc c lp. Thay v so
snh cc phn t bng cch o thuc tnh cu trc ca tng phn t, ta s
dng tnh nng chng cht ca HyperChem so snh mt cch trc quan
hai cu trc bng vic chng cht cc phn t ln nhau.
Xo cc phn t nc
Trc khi tin hnh chng cht, ta cn xo cc phn t nc trong h.
xo cc phn t nc ta lm nh sau
3. Nhp tri chut vo alanin.
Phn t alanin s c chn.
141
4. Nhp tri chut chn Complement Selection trong Select menu

Thao tc ny gip ch chn cc phn t nc.
5. Nhp tri chut chn Clear trong Edit menu.
6. Nu hp thoi xut hin hi ta c mun xo cc nguyn t chn
khng, nhp Yes.
7. Nhp tri chut b tch Show Periodic box trong Display menu mn
hnh ch cn biu din phn t alanin.
8. Lu kt qu thc hin vo file tn l ala-sol.hin.
Hp nht hai h
Bc tip theo l hp nht h ny vi h c lp. Trc khi hp nht hai h, ta
nn chn h hin ti ta c th phn bit n trn mn hnh sau khi hp
nht.
hp nht hai h ta lm nh sau

1. Nhp tri chut chn alanin.
2. Nhp tri chut chn Name Selection trong Select menu, vo mc Other
v lu vi tn solvated ( solvat).
Thc hin iu ny tin li cho ta biu din li n v sau.
142

3. Nhp tri chut chn Merge trong File menu, hp thoi m file xut hin,
nhp m ala-gas.hin lu ln trc.
C hai cu trc c lp v cu trc c solvat ho by gi trng nh trn
mn hnh. Cu trc c solvat ho vn cn c chn nn sng hn.
4.
5.
6.
7.
8.
9.
Chng cht cho php ta kt hp h hin ti vi h khc c lu trc

. H kt hp tr thnh h ang lm vic trn mn hnh.
Nu cn thit, s dng cng c dch chuyn (Translation tool) dch
chuyn quan st cho r.
- Nhp tri chut vo cng c dch chuyn trn thanh cng c.
- Nhp phi chut gi v r, phn la chn s dch chuyn theo chiu
r chut.
Nhp tri chut chn Color trong Display menu, hp thoi la chn m
ra, chn Yellow ri nhp OK.
Mu ca phn la chn s biu din l mu vng nu ta b la chn i.
Nhng chng ta khoan hy b la chn.
Nu mun chn h c lp th nhp tri chut chn Complement Selection
trong Select menu.
H c solvat ho s b b la chn cn h c lp c chn.
Chn mu cho h c lp l mu ta (violet).
Nhp phi chut vo vng trng b la chn.
Chn Labels l symbol cho c h.
Chng cht cc phn t

Khi mt h c t nht hai phn t, nh trong v d ny, HyperChem c th
chng cht cc phn t. S chng cht da trn s la chn ba nguyn t
khng thng hng trong mi phn t. bt u, u tin chn cc
nguyn t trong mi phn t trng khp nhau. Tip theo, gia cc lin kt
143

la chn cc nguyn t u tin v th hai mi phn t phi thng hng.
Cui cng, la chn nguyn t th ba mi phn t phi t trn cng
mt phng.
thc hin chng cht ta lm nh sau

2. Nhp tri chut chn Atoms v tch chn Multiple Selections trong
Select menu.
3. Nhp tri chut v r chn gc lin kt N-C-C mi phn t. Ta c
th quay cc cu trc nhn c nh sau
4. Nhp tri chut chn Overlay (ph) trong Display menu.

5. Nhp phi chut vo vng trng loi b la chn.
6. Nhp phm Spacebar trn bn phm a cu trc chng cht vo
tm mn lm vic.
H lc ny s trng nh sau:
144
7. Lu kt qu lm vic vo file vi tn l ala-sup.hin.

Cc phn t hu nh trng kht vo nhau.
Bi thc hnh 4: Ti u m phng

M phng ng lc hc phn t kho st khng gian pha (vng xc nh
theo v tr v tc ca nguyn t) bng cch gii cc phng trnh chuyn
ng Newton. Khng nh tnh ton im n v ti u hnh hc, ng lc
hc phn t tnh ton cc chuyn ng nhit. Cc phn t c th c nhit
nng vt qua hng ro th. Tnh ton ng lc hc phn t cung cp cho
ta cc thng tin v cc cu hnh c th c, cc thuc tnh ng lc hc v
hot ng ng lc ca cc phn t.
Trong bi ny ta s dng ng lc hc ti u h nhm thu c nc c cc
tiu nng lng thp hn. u tin ta phi m li h ion lng tnh alanin
c solvat ho thc hin ng lc hc phn t vi n.
m li h c solvat ho ta lm nh sau
1. Nhp tri chut chn Open trong File menu.
2. Chn m file ala-liq trong hp thoi Open.
3. Nu cn thit nhp tri chut tch bt li Show Periodic Box trong Display
menu biu din hp tun hon gip ta xc nh d dng hn.
4. Nu cn thit chn li labels l none d nhn.
t m phng ng lc hc
1. Nhp tri chut chn Molecular Dinamics trong Compute menu.
145
Hp thoi la chn ng lc hc phn t xut hin cho php ta t cc la

chn cho tnh ton ng lc hc phn t
2.
3.
4.
5.
6.
7.
8.
9.
Chy tnh ng lc hc phn t c ba giai on la chn: nung nng,

chy v thi gian lm lnh. Giai on u tin xut hin giai on m
phng thi gian gia nhit, s dng nhit bt u t vn tc khi
u theo t l vi vn tc nhit tng ln n nhit m phng.
Giai on gia, vn tc c thay i ch khi nu hng s nhit c
chn.
Giai on cui cng xut hin qua giai on m phng thi gian lm lnh
vi s thay i vn tc t nhit tng thm n nhit cui cng.
t Heat time (thi gian gia nhit) l 0.1 pico giy.
t Temperature step (bc nhy nhit) l 30K.
Bi v gradient l rt nh lc h khi u, mt thi gian gia nhit ngn 0.1
pico giy dng tng nhit t 100K n nhit m phng l 300K
tng theo bc nhy nhit l 30K.
t thi gian chy l 0.5 pico giy.
Nhit c s dng y t vn tc nguyn t khi u hoc
iu chnh vn tc nguyn t. ng nng ny c th c bin i thnh
th nng trong qu trnh m phng, nguyn nhn do nhit tnh ton
c l gim xung. Nu nhit cui cng tng ln (nh trong v d
ny), c ngha l th nng ang chuyn thnh ng nng khi h
chuyn v cu hnh n nh hn.
Thc hin chc chn l iu kin bin tun hon trng thi bt.
La chn ny c HyperChem t ng bt khi iu kin bin tun hon
c s dng, nhng n c th b gt ra nu ta t In vacuo trong mc
Option.
t Step size (kch c bc) l 0.0005 pico giy.
t Data Collection period (giai on la chn d liu) l 4.
iu ny gip cho qu trnh tnh ton c nhanh hn.
B tch Constant Temperature tt nhit khng i.
t cc iu kin nh trong hp thoi sau
146
La kch c thi gian cho qu trnh m phng ng lc

hc v ng lc hc Langevin. Vi Monte Carlo, l s
bc trong mi pha, v s chuyn ng cc i ca
nguyn t trong mi bc. Giai on bt u v kt
thc u cng mt nhit .
La chn cho ng lc hc phn t (Molecular Dynamics ) v ng lc
hc Langevin (Langevin Dinamics).
Heat time Thi gian tnh bng poco giy (ps) cho qu trnh
chuyn nhit t lc bt u n nhit m phng.
Gi tr nn thay i t 0 n 10 ps
Run time Thi gian theo pico giy gi h nhit m
phng. Thay i t 0 n 103 ps.
Cool time Thi gian chuyn nhit t nhit m phng n nhit
cui cng. Thay i t 0 n 10 ps.
Step size Khong thi gian gia cc gi tr ca nng lng ton
phn v nhit ca h. Thay i t 10-4 n 10-3 ps,
v ln hn 0.
t cho Monte Carlo:
Heat S bc t nhit khi u n nhit m phng.
Run steps S bc thc hin tnh ton nhit m phng.
Cool S bc chuyn nhit m phng v nhit cui cng.
Max delta y l khong cch cc i (A0) m bt k nguyn t
no trong h s di chuyn trong mi bc theo tnh
ton. thay i t 0.01 n 0.1 A0. Ngm nh l
0.05A0.
Temperature Cc mc nhit m phng. Trong qu trnh nung nng
v lm lnh, HyperChem t nhit bng cch iu
chnh nh k cc vn tc. Trong qu trnh chy vi
nhit khng i, HyperChem iu chnh vn tc
mi bc thi gian. Nu hng s nhit khng tch, s
Times
147
Starting
temperature
Simulation
temperature
Final
temperature
Temperature
step
hiu chnh xut hin mt ln lc bt u m phng.

Nu thi gian gia nhit ln hn khng, vn tc ban
u ca nguyn t c hiu chnh n nhit ny.
gi tr thay i t 0 n 300 K.
Ti im khi u thi gian chy, vn tc nguyn t
c hiu chnh n nhit ny. nu ta mun nung
nng lc u trong qu trnh m phng, nhit ny
cn ln hn nhit khi u. Gi tr thay i t 0 n
300K.
Nu thi gian lm lnh ln hn khng, vn tc nguyn
t c hiu chnh n gn nhit ny im kt
thc ca thi gian lm lnh. Nu ta mun,
y dng t kch c bc nhy, theo K, cho qu
trnh nung nng v lm lnh. Gi tr thay i trong
khong 0 n 100K.
Options
In vacuo Tch chn khng tnh n iu kin bin tun hon
t trong tnh ton. Ta ch chn In vacuo (trong
chn khng) nu h c t hp tun hon, nu khng
th HyperChem ngm nh sn cho ta.
Periodic Tch chn phn ny bao gm c cc iu kin bin
boudary tun hon vo trong tnh ton. Vi iu kin h phi
conditions c t hp tun hon ta mi c th t la chn ny
c.
Constant Dng iu chnh nhit ca h phn t hng v
temperature nhit m phng, ch p dng trong qu trnh chy m
phng (Run time). iu ny to ra iu kin khng
cn bng; qu trnh m phng hiu chnh vn tc
nguyn t iu chnh nhit .
Bath Hng s thi gian dng cho qu trnh hiu chnh nhit
relaxation trong qu trnh chy. gi tr ny nh hng n
cng hiu chnh. Cc gi tr hng tng t nh
Step size (kch c bc nhy) gip cho qu trnh hiu
chnh tt hn, nhng lm cho h xa khi cn bng
hn. Thi gian ln nn t cho qu trnh hiu chnh
nh, nhng thng dng gi tr nhm chng li cc sai
s lm trn tch t trong qu trnh m phng lu. gi
tr ngm nh l 0.1 ps.
Random seed S ny l im khi u cho qu trnh to ra s ngu
nhin s dng m phng. N c dng xc
nh vn tc khi u cho cc nguyn t trong qu
148

trnh tnh ton ng lc hc phn t.
Friction La chn ny dng cho ng lc hc Langevin. N
coeficient m t h s ma st s dng cho vic m phng tng
tc ca dung mi. Gi tr ly c t 0 n v cng.
y l tn s, theo cc bc thi gian, qu trnh m
Data
phng a gi tr tnh ton c vo HyperChem . C
collection
th t t 1 n 32,767.
period
Screen refresh y l tn s, theo cc bc d liu, biu din kt qu
tnh ton ln mn lm vic. t c gi tr t 1 n
period
32,767.
Tch chn phn ny qu trnh m phng lu vo
Playback
mt file HIN cc nh chp nhanh (SNP). Nu mun
Playback li h phn t t file HIN ta phi trn m
lm vic.
Nu tch Playback, th ch c giai on tp hp d
liu, lm mi mn hnh, chp nh nhanh v tnh trung
bnh l c gi tr. Nhp tri chut vo Snapshots
xem hp thoi biu din li ng lc hc phn t.
Nhp vo Averages tnh trung bnh hoc v biu
cc gi tr trong qu trnh biu din li.
Nu Restart c tch chn, tnh ton thit lp vn tc
Restart
ban u ca nguyn t cho cc gi tr c xc nh
trc .
Nu Playback khng tch, khi chn, nt ny s biu
Snapshots
din hp thoi chp nh nhanh ng lc hc phn t.
Nu Playback tch chn, Snapshots biu din hp
thoi Playback ng lc hc phn t.
Biu din hp thoi tnh trung bnh ng lc hc phn
Averages
t, v th ta c th tnh trung bnh v v biu kt
qu tnh ton c. Dng hp thoi ny sau khi tnh
ton hoc chy li snapshots file. Tnh trung bnh ch
c gi tr cho ng lc hc phn t. Biu xut hin
trong hp thoi kt qu ng lc hc phn t.
Bt u tin hnh ng lc hc phn t, Monte Carlo
Proceed
hay l biu din li Snapshot file.
t biu din li ng lc hc
149

Bc tip theo ta s hc cch t biu din li ng lc hc. Biu din li
ng lc hc phn t l thch hp bi v n lu li thi gian m phng ng
lc khng nh trc ta phn tch sau ny.
ng lc hc phn t m phng din bin ca mt h theo thi gian, cho ta
bit c vn tc v v tr ca cc nguyn t (qu o ca n). Cc tnh ton
ny c th rt tn thi gian, v kt qu c ngha thng k, thi gian m
phng lu ph thuc vo hng nghn bc cn thit.
Thng ta s mun lu qu o tnh ton c biu din li v sau hoc
phn tch, hn l phi lp li m phng.
t biu din li ng lc hc
1. Nhp tri chut chn Snapshots (chp nh nhanh) y hp thoi la
chn ng lc hc phn t (Molecular Dynamics Option).
Hp thoi chp nh nhanh ng lc hc phn t xut hin (Molecular
Dynamics Snapshots) cho php ta nh tn v ghi ch cn thit vo file.
2. nh tn ala-run mc File name.
Mt file c tn ala-run.hin c lu li, l file HIN cha nh chp
nhanh. Mt file khc, ala-run.snp, l mt file nh nguyn cha ng thi
vn tc v to ca nguyn t.
3. t mc Snap Shot period gi tr 1.
4. Nhp OK tr v hp thoi la chn ng lc hc phn t.
5. Nhp Proceed tin hnh ng lc hc phn t.
Ch : Sau khi tin hnh ng lc hc phn t, nu mun xem li qu trnh
ng lc hc phn t thc hin ta li m hp thoi la chn Molecular
Dinamics trong Compute menu. Tch chn Playback, lc ny hp thoi la
chn biu din li ng lc hc s hin ra. Ta ch vic t nhng la chn
cn thit v nhp Nt Proceed nh trc xem biu din li qu trnh ng
lc hc.
150
Trajectory
Snapshot file
Step count
Step side
Start time
End time
AVI Movie
Create file
Movie file
Frame rate
Phn ny cho ta nhng thng tin v file snapshot,

v cho php ta xc nh biu din li tt c hay ch
mt phn.
Ch biu din file ngun. Bao gm ng dn.
Ch biu din s nh chp nhanh lu trong qu
trnh m phng.
Ch biu din khong thi gian gia cc nh
chp nhanh (theo ps).
Thi gian trong qu trnh m phng bt u
biu din li. Nhp gi tr t 0.000 (ngm nh)
n End time.
Thi gian trong qu trnh m phng kt thc
biu din li. Nhp s t Start time n gi tr
ngm nh (tng thi gian m phng).
Phn ny c cc la chn to ra mt phim AVI
t cc nh chp nhanh. C th xem t Multimedia
player hay cc trnh ng dng tng thch khc.
Nu la chn ny c tch, mt AVI movie s
c to ra.
nh tn file AVI ta mun to vo ny.
t t l hnh nh vo y.
t tnh trung bnh theo ng lc hc phn t

ng lc hc phn t thng c s dng thu nhng thng tin v m
bng cch ly mu m phng ln qua mt thi gian di. N cng hu dng
151

theo di s lng hnh hc v nng lng trong qu trnh m phng nhm
xem h c n nh cho vic ly mu c gi tr thng k hay khng.
Ch : Khi bt u tnh hm trung bnh, HyperChem to ra mt file vi phn
ui m rng l .csv trong th mc lm vic hin ti. Tuy nhin, nu ta ang
c file snapshot t CD, th mc hin ti trn CD; ta khng th to ra file
ny c. Ta cn copy file Snapshot vo cng ca my.
t tnh trung bnh

1. Nhp tri chut vo Averages y hp thoi la chn ng lc hc phn
t m hp thoi tnh trung bnh ng lc hc phn t.
2. Nhp tri chut vo EKIN, EPOT, ETOT v ncco trong mc Selecton, sau
nhp tri chut vo nt Add chuyn chng vo hp thoi Average
only.
3. Nhp tri chut chn EKIN, EPOT, ETOT v ncco trong mc Average
only, tip theo nhp vo nt Add chuyn chng vo mc Avg. &
graph.
152

iu ny gip cho vic lu d dng hn biu nng lng ton phn, th
nng, ng nng v gc vn vo phn la chn c t tn.
HyperChem to ra mt file vi tn l ala-run.csv (hoc chem.csv nu ta
khng t biu din li ng lc hc), ghi li nhng con s c tnh trung
bnh h biu din gip ta c c d dng bng biu hoc chng trnh
bng tnh phn tch.
y l list cc la chn, cng vi cc phn la chn
Selection
c t tn m HyperChem c th v biu v tnh
trung bnh.
EKIN ng nng (kcal/mol)
EPOT Th nng (kcal/mol)
ETOT Nng lng ton phn(kcal/mol)
TEMP Nhit (Kelvin)
ACCR T l chp nhn (ch c gi tr cho m phng Mote
Carlo)
Named Cc phn la chn c t tn cng c lit k trong
selections list.
D EKIN lch RMS so vi gi tr ng nng trung bnh.
D EPOT lch RMS so vi gi tr th nng trung bnh.
D ETOT lch RMS so vi gi tr nng lng ton phn trung
bnh.
D TEMP lch RMS so vi gi tr nhit trung bnh.
ACCR lch so vi t l chp nhn trung bnh (ch cho
Monte Carlo).
D Named lch RMS so vi trung bnh cc phn la chn c
selections t tn.
Average only y l list cc gi tr HyperChem tnh trung bnh khi
kt thc tnh ton ng lc hc phn t.
y l list bn gi tr HyperChem tnh trung bnh v v
Avg. &
biu trong qu trnh m phng ng lc hc phn t.
Graph
Biu din gi tr tnh trung bnh gn nht. na c ngha
Value
l cha tnh trung bnh.
Average/Gra y t khong cho d liu tnh trung bnh hay v
biu cho n.
ph period
Tin hnh ng lc hc
1. Nhp OK tr v hp thoi la chn ng lc hc phn t, tip theo
nhp vo nt Proceed bt u ng lc hc.
153

Hp thoi kt qu dng biu xut hin trn mn lm vic.
2. Di chuyn hp thoi sang mt bn c th nhn qu trnh m phng
c r hn.
Trong khi tnh ton ang chy, ta c th quay, dch chuyn hoc phng to
h quan st c r. Ta cng c th s dng cc ng dng khc ca
Window, nhng iu ny c th lm chm qu trnh m phng.
3. Khi qu trnh m phng vn ang tip tc, ta c th nhp vo nt Rescale
thay i t l cc gi tr ang v biu .
Khi giai on gia nhit hon thnh, (khi nng lng ang c thm vo)
nng lng ton phn vn l hng s, v ng nng phn nh th nng
ca h.
Cn trng: Ta khng th v li biu nu nhp tri chut vo Done.
v li biu ta phi thc hin li qu trnh ng lc hc.
Trong phn u lc chy v sau khi gia nhit th nng v nhit ca
h tr nn kh n nh, nhng khi nhit tng ln. Th nng trong
qu trnh chy cui cng gim xung ng k. ng lc hc phn t
nhit phng cho php h gii quyt hng ro nng lng trn mt th
v tm kim vng th nng thp hn khng c nghin cu bi thut
ton cc tiu. Khi chy ng lc hc hon thnh
ta c th ti u ho h xc nh cc tiu mi.
Sau khong 10 pht th vic chy s hon thnh.
Ti u ho li cu trc mi
By gi chy ng lc hc hon thnh, ta c th ti u ho cu trc
xc nh cc tiu b phn mi.
2. Nhp tri chut chn OK ti u ho bng phng php c hc phn t
theo nhng la chn trc.
Sau khi ti u hon thnh, dng hin trng cho bit cu trc c nng
lng thp hn cc tiu cu trc c solvat ho trc .
Trong hnh thc tnh ton ny, kch c hp v giai on m phng khng
quan trng bng khi ta tnh trung bnh kt qu so snh vi thc nghim.
Nh l ly mu nn bt u khi h c cn bng, thng c nh
154

gi theo th nng v ng nng dao ng trong khong gi tr thch hp
i vi giai on m phng di.
Bi thc hnh 5: M phng Langevin v Monte Carlo.

Trong phn ny ta s dng phng php m phng Langevin v Monte Carlo
kho st thm cc cu hnh ca h ion lng tnh alanin. Phng php
ng lc hc Langevin m phng chuyn ng ca cc phn t chu va chm
ngu nhin cng nh chu tc dng ca cc lc ma st v c th c dng
lm m hnh cho cc h c solvat ho khng bao gm cc phn t dung
mi.
Phn 1: ng lc hc Langevin
Cc phn t trong dung dch chu s va chm vi cc phn t khc v chu
tc dng ca cc lc ma st khi chng chuyn ng trong dung mi. Dng
ng lc hc Langevin, ta c th m hnh ho cc tc ng ny v nghin
cu v hot ng ng lc ca cc h phn t trong mi trng lng. Cc m
phng ny c th nhanh hn nhiu so vi m phng ng lc hc phn t.
Thay v bao hm c th cc phn t dung mi, phng php ng lc hc
Langevin m hnh ho cc nh hng qua cc lc ngu nhin tc dng ln
phn t c quan tm m phng cc va chm v lc ma st c thm
vo m hnh ho nng lng b mt i qua cc tng tc ny.
ng lc hc Langevin c th dng nghin cu cc vn ging nh
ng lc hc phn t: cc thuc tnh ph thuc vo thi gian ca h solvat
nhit khc khng. Do x l n dung mi, phng php ny c bit thch
hp cho vic nghin cu cc phn t ln trong dung dch.
M phng ng lc hc Langevin c thit lp ging nh m phng ng
lc hc phn t, nhng c s khc nhau nh tu thuc vo vic thm h s
ma st m t nh hng ca dung mi.
ng lc hc Langevin dng tnh ton cc thuc tnh ph thuc vo thi
gian ca phn t c lp. Tuy nhin, ngi ta thng quan tm n tnh cht
phn t ny nh hng n phn t khc. Vi HyperChem, ta cng c th
thm cc phn t dung mi, nhng vic thm nhiu phn t dung mi s lm
cho qu trnh m phng chm hn.
155

1. Khi phc li ion alanin trng thi kh, ta lu trong file ala-gas.hin t
trc.
2. t cc la chn trong hp thoi la chn ng lc hc Langevin nh
ng lc hc phn t bi trc.
3. t Friction coefficient l 0.05 ps-1.
Khi h s ma st c t l 0, HyperChem thc hin tnh ton s nh
ng lc hc phn t, v ta cng nn s dng time step (thi gian nhy)
thch hp cho phng php.Vi gi tr h s ma st ln hn, cc chuyn
ng xut hin qua mt thi gian ngn, thi gian nhy ln hn c th
c s dng.
4. t thi gian Time Step l 0.001 pico giy.
5. t Averages v Snapshots nh bi ng lc hc phn t trc.
6. Nhp tri chut vo nt Proceed bt u m phng ng lc hc
Langevin.
Nh vi k thut ng lc hc phn t, giai on nung nng v lm lnh
cng c thm vo m phng ng lc hc Langevin. Cn bng ca
h khng quyt nh cho vic xc nh thm cu trc c nng lng thp,
nhng n quan trng khi so snh gi tr c m phng vi cc thuc tnh
thc nghim.
Phn 2: M phng Monte Carlo

Phng php Monte Carlo kho st khng gian pha bng cch to ra cc cu
hnh ngu nhin t mt phn b Boltzmann nhit cho trc. Phng
php Monte Carlo c th c s dng tm nng lng trung bnh v
thuc tnh cu trc cn bng ca cc h tng tc phc tp. Phng php
Monte Carlo cung cp cch tip cn to ra cc cu hnh bn.
Thit lp m phng Monte Carlo

1. M li h ion lng tnh alanin c solvat ho m ta lu bi trc.
2. Nhp tri chut chn Monte Carlo trong Compute menu.
Hp thoi la chn xut hin cho php ta t cc tham s m phng
Monte Carlo. Trong v d ny chng ta s chy m phng nhit khng
i vi 1000 bc. i vi mt s h, c l nn thm giai on gia nhit
v lm lnh.
3. t Run Steps l 1000, t Heat v Cool steps l 0.
4. t kch c bc nhy cc i, Max Delta, l 0.05 A0.
y l t s di ch ti a ca cc nguyn t th.
5. t Simulation Temperature l 300K.
6. Tch chn Periodic boundary conditions.
156

7. t Data Collection period l 4 bc (steps).
t biu din li Monte Carlo

8. t file Snapshot, nu mun.
t tnh trung bnh theo Monte Carlo

9. t tnh trung bnh v v th nu mun. (nh bi thc hnh ng lc
hc phn t)
Tin hnh m phng v phn tch

Khng c s khc nhau ng k gia cc bc s dng HyperChem phn
tch m phng Monte Carlo v m phng ng lc hc phn t. Window c
th copy cc kt qu m phng Monte Carlo vo b nh tm thi v dn vo
trong cc ng dng khc.
Xem li kt qu
1. Theo nhng bc sau xem li ng lc hc:
M file ala-run.hin.
M hp thoi la chn ng lc hc phn t v tch chn Playback.
Chn Snapshots xc nh phn m phng lp li.
Chn Proceed bt u biu din li ng lc hc.
M phng s biu din li v cn bn l nhanh hn khi tnh ton
ng lc hc lc u.
2. To cc phn la chn t tn cho hai, ba hoc bn nguyn t v s dng
biu din li ng lc hc phn t v biu gi tr tnh c.
Bi cc phng php bn kinh nghim

Chn Semi-empirical s dng phng php tnh ton c hc lng t bn
kinh nghim. S tch chn ny hot ng mi cho n khi ta chn Molecular
Mechanics hay Ab initio. Ta c th dng mt phng php c hc lng t
bn kinh nghim cho tt c cc tnh ton trong Compute menu.
Cc tnh ton bn kinh nghim gii phng trnh Schrodinger, vi s xp x
no , nhm m t thuc tnh ca cc nguyn t v phn t. tnh nhanh
v n gin, cc phng php bn kinh nghim thc hin s n gin ho
nh sau: ch tnh cho cc electrong ho tr; b qua mt s tch phn tng
tc; s dng cc hm obital in t c bn chun, khng c ti u; dng
cc tham s xc nh t thc nghim. Cc tham s thc nghim loi b mt
157

lng tnh ton cn thit no v sa cc li kt qu thu c t s gn
ng.
Quan trng: Cc phng php bn kinh nghim trong HyperChem c th x
l tt c cc nguyn t nhm chnh, c tham s ho trong cc file tham s
x l n c xenon. Extended Huckel, ZINDO/1, ZINDO/S c th x l
hai hng kim loi chuyn tip u tin.
Tt c cc phng php bn kinh nghim hin hnh c thit lp nhm loi
b nhng tnh ton tn nhiu thi gian ca cc tch phn xen ph. Phng
php b qua xen ph vi phn khng tnh cc tch phn y c gi tr nh.
Hp thoi la chn phng php bn kinh nghim:
Extended
Huckel
CNDO
INDO
S dng tnh ton obital phn t ca cc phn t.

Khng c gi tr ti u hnh hc hoc tnh ton ng
lc hc phn t. Dng s ng gin ho mt electron
quy cho l khng c s tng tc r rng gia cc
electron. y khng phi l phng php trng t hp
(SCF)
B qua hon ton xen ph vi phn. y l phng php
trng t hp n gin nht. N c gi tr tnh cc
thuc tnh electron trng thi c bn ca cc h v h v
h v kn, dng ti u hnh hc, tnh nng lng ton
phn.
Gin tip b qua xen ph vi phn. Ci tin t CNDO
bng cch tnh n lc y mt tm gia cc electron
trong cng mt nguyn t. Dng tnh thuc tnh
electrong trng thi c bn ca h v h v v kn,
dng ti u hnh hc, tnh nng lng ton phn, y
158
MINDO3
MNDO
MNDO/d
AM1
PM3
ZINDO/1
ZINDO/S
l mt phng php SCF.

L phng php m rng t INDO bng cch s dng
cc tham s, thay v tnh ton i vi nhiu tng tc.
s dng cho cc phn t hu c ln, tnh ton thuc tnh
in t, ti u hnh hc, tnh nng lng ton phn. y
l phng php SCF.
S dng cho nhiu loi phn t hu c khc nhau c
cha cc nguyn t thuc hng 1 v 2 trong bng h
thng, khng c gi tr cho cc kim loi chuyn tip.
Loi b mt s sai s trong MINDO3. Tnh thuc tnh
in t, ti u hnh hc, nng lngt ton phn, v nhit
hnh thnh. y l phng php SCF.
L phin bn ca MNDO vi vic thm cho cc obital
d. S dng cho cc nguyn t nhm chnh c cc
obital-d ng vai tr quan trng (nh l Sunfua). c
tham s ho tt hn, dng cho cc kim loi chuyn tip.
Tnh ton thuc tnh in t, ti u hnh hc, nng
lng ton phn, nhit hnh thnh. y l phng php
SCF.
Ci tin t MNDO,v l phng php chnh xc nht.
Dng cho cc phn t hu c c cha cc nguyn t
thuc hng th nht v hng th hai trong bng h
thng, khng dng cho kim loi chuyn tip. C th
tnh tt hn MNDO cho cc hp cht cha c nit v
oxi. Tnh thuc tnh in t, ti u hnh hc, nng lng
ton phn, nhit hnh thnh. y l phng php SCF.
c tham s ho t AM1. PM3 khc AM1 ch cc
gi tr tham s. Cc tham s cho PM3 ly bng cch so
snh s lng ln v rng ri t thc nghim. Tiu biu,
cc tng tc khng lin kt t y hn trong PM3 so
vi AM1. PM3 u tin c s dng cho cc phn t
hu c, nhng n cng c s dng cho nhiu nguyn
t nhm chnh. y l phng php SCF.
S i t INDO m rng cho cc kim loi chuyn tip.
Tng ng vi phin bn gn y nht ca phng
php INDO/1, s khc u tin l s dng hng s
m obital. ZINDO/1 cho php ta tnh nng lng trng
thi chuyn tip, ti hu hnh hc ca cc phn t cha
kim loi chuyn tip.
L phng php INDO c tham s ho thm nhm
m phng s chuyn ph UV/Visible (t ngoi/kh
159
TNDO
Options..
kin) khi dng phng php CI n (tng tc cu hnh

n) dng e d on ph UV/Visible nhng khng
ph hp tnh ti u hnh hc hay ng lc hc phn
t.
L phng php b qua xen ph vi phn, bao gm cc
tham s khng ch cho s th t nguyn t m cn cho
kiu nguyn t. C gng thu c phng php bn
kinh nghim nng cao chnh xc nhiu hn. S dng
phng php ny nh mt cng c nghin cu cho mt
khong gii hn cc phn t c cc tham s c
pht trin v ang hin hnh.
Nhp tri chut biu din la chn bn kinh nghim
nhm thit lp cc iu kin tnh ton. C ba phin bn,
tu thuc vo phng php bn kinh nghim m ta
chn.
Phng php p dng cho cc nguyn t:

Cc bng sau y biu din cho ta bit cc nguyn t c x l theo cc
phng php bn kinh nghim khc nhau trong HyperChem. y biu
tng ca cc nguyn t x l theo mi phng php c t m:
Ch : Phng php Huckel m rng c th p dng cho tt c cc
nguyn t trong bng h thng, tp hp tham s ngm nh bao hm tt
c cc tham s cn thit
160
161
La chn bn kinh nghim cho phng php Huckel

Hp thoi ny dng t ring cho phng php Huckel. Tt c cc phng
php bn kinh nghim khc s dng hp thoi khc.
Total charge
Spin mutiplicity
in tch ht nhn d so vi in tch electron. N

bng khng i vi h trung ho, l gi tr nguyn
dng i vi cation v l gi tr nguyn m i
vi anion.
y l bi spin, 2S+1, y S l tng spin
electron ca h. Mi electron khng kt i c
tnh l 1/2. H v kn (singlet) c bi l 1.
Trng thi doublet (biu din hai mi tn hng
ln) v triplet (biu din ba mi tn hng ln) c
bi l 2 v 3. Ta c th thay i gi tr t 1 n
162

6.
Huckel Constant Hng s t l gia cc yu t ma trn khng cho
ho v cc yu t ca ma trn cho ho. Gi tr
thng l 1.75. Ga tr ln t cho trng lng ln
ng vai tr l xen ph obital nguyn t trong vic
xc nh nng lng. Gi tr nh t cho trong
lng ln nhm kt hp nng lng ca cc
electron trong cc obital nguyn t.
Unweighted Dng hng s Huckel khng sa i g.
constant
Weight Tng hng s Huckel bng mt h s c coi l
difuseness s khuch tn ca cc obital nguyn t. H s ny
ch c quy cho cc h phn t c cc obital
khuc tn rt khc nhau. iu ny him khi xut
hin i vi cc hp cht hu c v cc nguyn t
nhm chnh.
Tch chn thm cc obital d cho Si, P, S v Cl.
d orbitals
y l h s t l.
Scale Factor
Hp thoi la chn cho cc phng php bn kinh nghim khc

Total charge
Spin multiplicity
in tch ht nhn d so vi in tch electron.

Bng khng trong h trung ho, nguyn dng
trong cation v nguyn m trong anion.
L bi spin ton phn, 2S + 1, S l tng spin
electron ca h. Mi electron khng kt i
c tnh l 1/2. H v kn c bi l 1. H
v h c th c bi l 2, 3, 4 hoc cao hn.
Dng cc s nguyn thay i t 1 n 6.
163

State
Lowest
Next lowest
Convergence limit
Iteration limit
Accelerate
convergence
Spin pairing
UHF
RHF
Overlap Weighting
Factors
Sigma
Sigma
Pi-Pi
TNDO Version
M t trng thi kch thch ca cc electron

ho tr trong h.
Trng thi in t c nng lng thp nht
bi spin cho trc.
Trng thi kch thch in t u tin ca
bi spin cho trc. (singlet, doublet, triplet,
hoc quartet)
Kt thc tnh ton SCF khi s khc nhau v
nng lng sau hai ln lp li lin tip b hn
gi tr t. y l gii hn hi t cho nng
lng electron ton phn trong tnh ton SCF.
Ga tr cc i cho s lp li ca mt tnh ton
SCF. Tnh ton s ngng sau khi lp gi tr
ta t d cha n kt qa cui cng.
Tch chn t hi t nhanh hn cho qu
trnh lp SCF.
t cho phng php tnh ton cc kiu tc
ng spin. C hai kiu nh sau:
Phng php Hartree-Fock khng gii hn
cung cp cc obital c khng gian ring (alph
v beta) cho cc electron cng vi kiu spin.
Phng php ny dng cho cc h v h v v
kn.
Phng php Hartree-Fock gii hn i hi
spin cp i ca cc electron nh c trong
cng khng gian obital. L phng php dng
cho h v h v h v kn.
Tham s ho thm cho cc phng php
ZINDO nhm thay i phn ng gp trong
lin kt sigma v pi.
Hiu chnh xen ph obital nguyn t sigmasigma. Nn t cho ZINDO/1 gi tr 1, cho
ZINDOS gi tr 1.267.
Hiu chnh xen ph obital nguyn t pi-pi. Nn
t 1 cho ZINDO/1. Ngm nh 0.64 cho
ZINDOS l thch hp cho cc kim loi chuyn
tip, v gi tr 0.585 cho cc phn t hu c.
La chn chn hai phin bn TNDO ta
mun dng. La chn ny lp li cc h s
mc xen ph m t trn khi chn TNDO.
TNDO c ngun gc l CNDO v INDO v ta
164
Configuration
interaction
c th chn mt trong hai TNDO/1 hay

TNDO/2.
La chn ny t hot ng v t cc la
chn cho tnh ton tng tc cu hnh. iu
ny l cn thit nu ta mun tnh ph UV
visible.
La chn tng tc cu hnh

Cc tnh ton CI c th dng ci tin cht lng ca hm sng v trng
thi nng lng. Cc tnh ton trng t hp (SCF) da trn m hnh mt
electron, mi electron di chuyn trong trng trung bnh c to nn
bi n-1 electron cn li trong phn t. Thc t, cc electron tng tc ngay
tc thi v do c khuynh hng t nhin trnh xa electron khc, tho mn
nguyn l loi tr. S tng quan (tc ng qua li ln nhau) ny dn n kt
qu l lc y trung bnh gia cc electron thp hn v do c trng thi
nng lng thp hn.
C hai kiu tng quan electron: tnh v ng. Tng quan tnh c quy
cho l s suy bin gn trng thi cho trc; tng quan ng l s trnh xa
tc thi ca cc electron vi nhau.
Chn None, Singly Excited (kch thch n),
Microstate (vi trng thi)
None Chn None nu khng mun s dng tng tc cu
hnh.
Singly Excited Ch cc cu hnh kch thch n c tnh.
Microstate Gm nhiu trng thi kch thch, k c cc trng thi
kch thch n.
t phm vi cc obital v t cc electron c
Orbital
kch thch to ra mt tp hp cu hnh tng tc.
Criterion
CI Method
165

Occupied Phm vi ca cc obital nh c bt u t HOMO, t
cc electron c kch thch.
Unoccupied Phm vi ca cc obital o bt u t LUMO n khi
cc electron c kch thch ln.
L la chn cho Orbital Criterion, gi tr ny t
Energy
nng lng gii hn cho s to tp hp cc cu hnh
Criterion
tng tc.
Nng lng obital cao nht khc nhau (eV) gia cc
Maximum
obital nh c v khng nh c, c tnh trong tnh
Excitation
ton CI. Ni chung cc cu hnh c nng lng cao
khng tng tc mnh trong tnh ton ta ni y.
Tng thm nng lng cc i s lm tng thm s
tng tc cu hnh trong tnh ton CI.
166
Bi 11 Tnh ton Obital phn t
Tnh cc hm sng.
V biu th tnh in, mt in tch v obital phn t.
Tnh in tch nguyn t.
t cu trc thng trc.
Bi ny cho ta bit nhiu kiu tnh ton bn kinh nghim khc nhau m
HyperChem c th lm. Phn t ta s dng trong bi ny l nc.
To phn t nc
to phn t nc theo trnh xy dng ta lm nh sau
1. Nhp tri chut chn Show Hydrogens trong Display menu v b tch
Perpective nu c trong mc Sticks ca hp thoi la chn Rendering.
2. Nhp lin tip hai ln tri chut vo cng c v trn thanh cng c m
hp thoi la chn cc nguyn t.
3. B tch Explicit Hydrogens, nhp chn oxi ri ng hp thoi li.
4. Nhp tri chut vo cng c v, chuyn con tr ln mn lm vic v v
mt nguyn t oxi.
thm hydro cn thiu vo oxi.
HyperChem s t ng thm nhng hydro cn thiu v biu din phn t
nc theo trnh xy dng.
6. Nhp tri chut vo Labels trong Display menu v chn Symbol trong
hp thoi Labels mc Atoms, sau nhp OK chn.
Bc v ca ta s trng nh sau;
167
Gc lin kt ca cu trc theo trnh xy dng ny l gc t din 1090. Ta

c th ci tin cu trc ny, nhng vi bi tp ny ta thc hin tnh hm
sng cho cu trc ca trnh xy dng.
t cu trc thng trc

Trc khi tnh ton hm sng, ta t phn t vo nh hng chun bng
cch t thng trc qun tnh th hai ca nc (trc i xng trong mt
phng phn t) l trc y.
t thng cu trc ta lm nh sau

1. Nhp tri chut chn Align Molecules trong Edit menu.
2. Trong hp thoi la chn Align Molecules tch chn Secondary, trong
mc With chn Y Axit (trc Y).
3. B tch nu c mc Minor Axit; ta khng mun nh r s thng dc

theo trc th hai.
4. Nhp OK chn.
Phn t nc s c quay trn mn lm vic trng nh th ny:
168
5. Lu cu trc vi tn l h2o.hin.
Biu din in tch nguyn t

Trong bi 10 ta quy in tch nguyn t bng vic s dng Set Charges (t
in tch) trong Build menu. in tch c th c quy t ng nu phn t
ta ang dng c c t mt file mu, nh l file PDB.
Trong bi ny, ta thu c in tch nguyn t bng tnh ton c hc lng
t bn kinh nghim.
u tin, xem khng thy khng c in tch c quy cho phn t nc.
biu din in tch ta lm nh sau:

1. Nhp tri chut m hp thoi Labels trong Display menu.
2. Nhp tri chut tch chn Charge trong mc Atoms ca hp thoi Labels,
ri nhp OK chn.
Nhn cho bit l trn phn t khng c in tch c quy cho phn t
nc.
Tnh hm sng
Hm sng c lp nn t cc obital phn t v m t s phn b ca cc
electron trong phn t. Trong bi tp ny, ta tnh hm sng cho ton b phn
t nc. Sau trong bi 12, ta tnh hm sng cho phn c la chn trong
cu trc.
tnh hm sng ta lm nh sau

1. Nhp tri chut chn Semi-empirical trong Setup menu.
169

2. Nhp tri chut tch chn CNDO, ri nhp vo nt Options.
Ta cng c th chn mt trong cc phng php khc trong , nhng
v d ny s dng CNDO lm phng php tnh.
3. Dng cc gi tr nh sau t vo hp thoi la chn bn kinh nghim
(Semi-empirical Options):
Cc la chn ny t tnh Hartree-Fock gii hn (RHF) vi Convergence

limit (gii hn hi t trung bnh) l 0.0001, c ngha l tnh ton kt thc
khi s khc nhau v nng lng sau hai ln lp li lin tip b hn 0.0001
kcal/mol.
Gii hn lp li (Iteration limit), t l 50, l s ln lp li cc i c s
dng i n mt hm sng t hp. Total charge (in tch ton phn)
t l 0 v Spin multiplicity ( bi spin) t l 1.
Tnh ton c tin hnh trng thi thp nht khng c s gia tc hi t
c bit (b tch mc Acceleration convergence)
4. Nhp OK ng hp thoi la chn bn kinh nghim v nhp tip OK
ng hp thoi la chn phng php bn kinh nghim.
Kt qu nng lng, gradientv in tch nguyn t tnh c nh sau:
170

(Gi tr tnh ton ca bn c th khc mt cht)
V biu th tnh in
By gi ta tnh c hm sng, ta c th biu din bn th tnh
in. V biu th tnh in c l i hi nhiu thi gian hn tnh hm
sng c hc lng t. iu ny bi v cc gi tr phi c tnh lng ln
cc im k c c bn .
Bn th tnh in c ph ln trn trang lm vic ca HyperChem v
gi nguyn cho n khi ta dch chuyn hoc thay i phn t hoc biu
din bn khc.
Mt phng ca bn lun song song vi mt phng XY (Mt phng
mn lm vic).
v biu th tnh in ta lm nh sau

1. Chn none trong hp thoi Labels.
2. Nhp tri chut chn Plot Molecular Graphs trong Compute menu m
hp thoi la chn.
3. Nhp tri chut tch chn Electrostactic Potential trong mc Molecular
Properties v chn biu din trn khng gian hai chiu (2D Contour).
HyperChem s tnh ton v biu din biu th tnh in trn khng
gian hai chiu.
4. Nhp tri chut vo mc Contour Grid la chn biu din cc ng
biu trn mn hnh.
5. t Horizotal grid points l 60.
6. t Vertical grid points l 60.
7. t Contour levels l 30.
8. t Plane Offset l 0.5 .
9. Nhp OK bt u tnh ton.
10. Sau mt lc, th tnh in s c tnh ton v biu din trn mn lm
vic.
Ch : Biu m bn v c th khc vi biu in trong sch mt cht.
171
(Mu xanh th hin in tch dng, mu ta th hin mang in m, ta c

th t mu sc biu din trong mc Isosurface Color ca hp thoi
Preference )
11. M li hp thoi la chn v biu th tnh in v chn 3D isosurface
biu din biu trn khng gian ba chiu.
HyperChem s biu din li biu th tnh in trn khng gian ba
chiu (3D).
12. Nhp tri chut chn mc Isosurface Rendering. t gi tr Electrostatic
potential contour value l 0.1, v tnh chn Shaded surface .
Th tnh in s c biu din trn khng gian ba chiu, c t m v
khng c khong trng.
13. Nhp tri chut chn mc Isosurface Grid, tch chn Medium.
Mc ny cho php ta chn nn v b mt vi mt vi im (hnh v g
gh nhng v nhanh) hay l nhiu im (hnh v mn v v lu).
14. Nhp OK bt u tnh ton cho mt phng. iu ny s mt mt lc
tnh ton. Khi mt phng s biu din nh sau:
172
15. M li hp thoi la chn v biu th tnh in, tch chn 3D Mapped

Isosurface.
iu ny cho php biu din mt phng v vi gi tr c xc nh bng
tng mt in tch nhng t mu theo th tnh in.
16. Nhp tri chut chn mc Isosurface Rendering. nh gi tr 0.135 vo
mc Total charge density contour value, ri tch chn Gouraud shaded
surface.
Mt phng s biu din trn khng gian ba chiu mt in tch ton
phn. Mt phng s rt nhn.
17. Nhp tri chut chn mc Mapped Function. nh gi tr -1.0 vo
Minimum value v vo Maximum value l 1.0. Nhp tri chut tch chn
Display range legend.
Mt phng s c t mu theo th tnh in, mu sc thay i, mt ghi
ch c v km biu din s khc nhau v gi tri theo mu sc.
18. Nhp tri chut chn OK bt u tnh ton b mt. S mt mt lc
hon thnh. Khi b mt s c biu din nh sau:
173
Ch thch hp thoi v biu thuc tnh phn t

Ta dng hp thoi ny v biu cho nhiu thuc tnh khc nhau:
Property
Electrostactic
potential
Total spin
density
Total charge
density
Representation
Mc ny cho php ta la chn thuc tnh mun biu

din.
Chn v biu trng th tnh in theo s phn
b in tch in t v in tch ht nhn.
Chn v biu kh nng tm thy electron c
spin hng ln (electron alpha) nhiu hn electron
c spin hng xung im bt k trong khng
gian.
V biu hm mt in tch cho cc electron
ho tr ca phn t.
Mc ny cho php ta xc nh mun biu din biu
thuc tnh phn t dng no.
174

2D Contours
3D Isourface
3D Mapped
Isourface
La chn v biu dng ng vin hai chiu.

La chn v thuc tnh dng mt ba chiu.
V theo dng mt ba chiu kt hp vi mu sc biu
din thuc tnh c chn.
Mc la chn Isosurface Grid trong hp thoi

Ta dng la chn ny xc nh gi tr cho li 3D (3D Grid) dng biu
din mt ng hng (isosurface).
Grid Mesh Size
Grid Layout
Grid point step
size
Grid ponit counts
Spatial extents
Adjust points
Adjust Extents
Mc ny cho php chn kiu li Coarse (th),

Medium (trung bnh), hay Fine (p) hoc chn
theo mun sau xc nh cc kiu la chn
li c th ta mun v.
Dng la chn ny xc nh la chn cho li
3D.
Xc nh khong cch gia hai im d liu trong
li 3D, theo A0.
Kch c li 3D theo cc phng x, y, z, theo n
v s im li.
Kch c li 3D theo cc phng, theo n v A0.
Dng nt ny p dng s hiu chnh cho Grid
point counts
Dng nt ny p dng s hiu chnh cho
Spatial extents
Mc la chn Contour Grid

Dng mc ny t cc gi tr cho li 2D dng biu din cc ng
biu .
175
Horizontal grid
points
Vertical grid
points
Contour levels
Plane offset
Starting value
Default
Other
Increment
Default
Other
phn gii ngang ca cc ng biu . C th

thay i t 2 n 8,172.
phn gii thng ng ca cc ng biu .
Gi tr thay i t 2 n 8,172.
S ng ta mun dng v biu , gi tr thay
i t 1 n 32,767.
S mt phng ca tp hp cc ng dng v
biu , vung gc vi trc z ca ngi quan st.
Gi tr ca ng thp nht.
Gi tr khi u HyperChem tnh cho cc im
li v t ngm nh, (khi u tnh t trong ra
ngoi).
Gi tr ta mun thay i cho ng khi u.
Khong cch gia cc ng gn k.
Gi tr ngm nh tnh theo HyperChem.
Ga tr do ta t.
Mc Isosurface colors (mu sc th hin tnh m-dng trong biu )

Mc ny kh quan trng cho vic biu din biu cc thuc tnh khc nhau
ca h. Qua mu sc ta c th phn bit c phn no th hin tnh m
(negative), phn no th hin tnh dng (positive). Ta hon ton c th chn
cc mu sc biu din khc nhau tu theo s thch.
176
Cc mc cn li khng quan trng lm, c th tham kho trong HyperChem

reference, chng 7.
V bn mt in tch ton phn

Ta c th v biu dng ng cho mt in tch (electron) ton phn.
Khi phng php CNDO v cc phng php bn kinh nghim khc c hiu
lc trong HyperChem khng bao hm cc electron lp bn trong (v d,
electron 1s ca oxy trong nc), mt in tch biu din ch l mt
in tch cng ho tr.
v biu mt in tch ta lm nh sau

1. Nhp tri chut chn Plot Molecular graphs trong Compute menu.
2. Nhp tri chut chn 2D contour trong mc Molecular properties v nhp
chn Total Charge Density, sau nhp OK ng hp thoi.
Sau mt lc, biu mt in tch ton phn xut hin:
177
Mt in tch ton phn cng c th c v trn khng gian ba chiu.
V bn mt spin ton phn

Mt spin ton phn c th v biu c theo cng cch nh mt
in tch ton phn. Tuy nhin, trong trng hp phn t nc (v tt c cc
h khc trong tt c cc electron c ghp i), gi tr ca mt in
spin ton phn l 0 mi im, v khng c biu no c v. Mt
spin c th c tnh v biu din cho cc h ho hc c electron khng
ghp i.
V bn obital phn t ring

Ta c th v biu tt c cc obital ring l no. Obital c xc nh c
th l obital phn t nh c nng lng cao nht (HOMO) v obital phn t
khng nh c nng lng thp nht (LUMO).
Vi phn thc hnh ny, ta v obital phn t theo th t nng lng tng.
Vi nc, CNDO s dng tp hp ca su obital nguyn t c bn (2s, 2p
trn nguyn t oxi v 1s trn hai nguyn t hydro) v tnh ton cho su obital
phn t. Bn trong cc obital ny (2a1, 1b2, 3a1, v 1b1 bt u nng lng
thp nht) c nh c v hai obital (4a1 v 2b2) khng nh c. Obital phn t
nh c nng lng cao nht (HOMO) l 1b1, v obital phn t khng nh
c nng lng thp nht (LUMO) l 4a1. S thiu cc electron 1s lp v bn
trong ca oxi m t s thiu obital 1a1. Do obital u tin, 2a1 l HOMO3.
178
v biu obital phn t ring ta lm nh sau

1. Nhp tri chut chn cng c la chn trn thanh cng c v nhp phi
chut vo vng trng mn lm vic loi b cc la chn.
2. Nhp tri chut vo Obitals m hp thoi la chn trong Compute
menu.
3. Nhp tri chut chn HOMO-, tip theo nhp tri chut vo mc ghi ch
(text box) cho obital v t gi tr l 3.
iu ny gip chn obital thp th 3 theo th t sp xp nng lng ca
HOMO. Trong v d ny, n l obital c tnh l thp nht. Quan st
mc thp nht trong biu mc nng lng obital thay i mu sc. Ta
cng c th chn obital bng cch nhp tri chut vo mc obital c nng
lng thp nht trong biu .
4. Nhp tri chut tch chn 3D Isosurface.
5. B tch nu c Orbital Squared.
Hp thoi la chn v Obital c dng nh sau:
Pan
Thanh cun ln xung trong s nng lng

obital.
179

Orbital
Alpha
Beta
LUMO+
HOMONumber
Energy
Symmetry
Labels
Zoom Out
Orbital Plotting
2D Contours
3D Isosurface
Orbital squared
Cho bit thng tin v obital c chn.

Cho bit obital c chn c spin alpha hay khng.
Nu obital chn c spin beta, nhp tri chut
vo Alpha thay i la chn chuyn thnh obital
alpha. La chn ny ch hot ng sau khi ta tnh
ton bn kinh nghim UHF.
Cho bit obital c chn c spin beta hay khng.
Nu obital c chn c spin alpha, nhp tri chut
vo Beta chuyn s la chn v obital c spin
beta. La chn ny ch hot ng sau khi ta tnh
ton bn kinh nghim UHF.
Cho bit v tr obital la chn hin ti c lin quan
n LUMO. V d, khi ta chn obital LUMO
phn trn (ng gch) trong s nng lng, gi
tr +1 xut hin trong hp thoi ch s, ngc li
nu ta chn LUMO bn di, ch s 1 s xut
hin.
Tng t nh s la chn LUMO, nhng khc
ch ch s ngc vi LUMO.
Cho bit tr s tuyt i ca obital c chn, bt
u t obital nng lng thp nht (bn di). Vi
tnh ton UHF y c c hai ct obital alpha v
beta c biu din, s th t c thc hin phn
chia trong mi nhm.
Cho bit nng lng ca obital c chn theo n
v electron volt (ev).
Cho bit dng biu din ti gin ca obital c
chn.
Biu din electron nh c trong mi obital. Vi
tnh ton RHF s eletron nh c ti a trong mi
obital l 2, ngc li trong tnh ton UHF, s
electron nh c ti a l 1.
Sau khi ta phng to s nng lng (nhp tri
chut v r trong khung s ), chuyn tr li
dng ban u ta nhp vo nt ny.
Cung cp cho ta nhng la chn biu din biu
obital.
V biu obital trn khng gian hai chiu.
V biu obital trn khng gian ba chiu.
Khi chn, biu biu din bnh phng gi tr
obital trong mt phng xc nh.
180
Copy
Options Dng la chn thm cho dng biu din obital.

Plot Thc hin v biu obital chn.
Copy s nng lng vo trnh ng dng khc,
vo b nh tm thi.
6. Nhp OK thc hin v biu obital.

HyperChem v biu obital cho obital 2a1, v biu din hin trng cng
vic trn dng hin trng.
7. Nhp tri chut chn Isosurface trong Display menu, hoc nhn F4.
Hp thoi la chn Plot molecular properties xut hin.
8. Nhp tri chut tch chn Wire mesh (Li dy) trong mc Rendering
option, nh gi tr 0.05 vo Obital contour value, v nhp OK chn.
HyperChem biu din biu obital 2a1 nh sau:
9. M li hp thoi la chn v obital trong Compute menu, nh gi tr 1

vo number cho HOMO. Nhp vo nt Options v s dng nhng la
chn nh la chn th tnh in, nhng tch chn mc Rendering l
Jorgensen-Salem.
iu ny HyperChem s biu din obital 3a1:
181
C th dng cng c quay quay cu trc nhn cho r.

10. Lp li tnh ton v s dng gi tr 2 cho HOMO v chn Lines trong
mc Rendering.
HyperChem s biu din obital 1b2:
11. Nhp tri chut chn Rotate trong Edit menu.

12. Tch chn X Axis, nh gi tr Angle (gc) l 90, chn Apply to View,
ri nhp OK chn.
B tch Show isosurface hoc nhp F3 th HyperChem s khng biu din
obital phn t trn mn lm vic na. Tch li Show isosurface hoc nhp
F3 th HyperChem s biu din obital tr li.
13. Nhp tri chut m hp thoi Orbital trong Compute menu ly gi tr 0
cho HOMO.
182

14. Nhp vo nt Option, trong mc Isosurface Rendering chn Flat surface
v nh gi tr 0.05 vo Obital contour value, ri nhp OK chn.
HyperChem biu din obital phn t nh c cao nht ca nc cho 1b1:
15. Nhp tri chut chn Rotate trong Edit menu, nh gi tr Angle l -90,
ri nhp OK chn.
16. Nhp tri chut m hp thoi Obital trong Compute menu v tch chn
LUMO+, nh cc gi tr 0 v 1 biu din cc obital khng nh c.
V biu th nng mt chiu (1D) v hai chiu (2D)

Vi cc cng c la chn cho php tnh nng lng nh Amber94,
PM3, cho php ta tnh c cc gi tr v nng lng nh sau:
- Biu th nng mt chiu.
- Biu th nng hai chiu.
Biu th mt chiu biu din nng lng l hm ca mt s thay i. Biu
th hai chiu biu din nng lng l hm ca hai s thay i. Cc s thay
i ny c th l di lin kt, gc lin kt, gc vn.
Th mt chiu
Ta c th to ra th mt chiu mt cch d dng. u tin l chn kiu hm
nng lng s dng. C th chn l AMBER, PM3, STO-3G Sau
chn 2, 3 hoc 4 nguyn t trong mt lin kt, gc hay mt gc vn l nhng
thay i c lp.
Cc bc to th mt chiu nh sau:
1. Chn lin kt, hoc gc lin kt, gc vn mun v biu th.
183

2. Nhp chn Name Selection trong Select menu, tip theo tch chn mc
PLOT1, nhp OK chn.
3. Nhp chn Potetial trong Compute menu. Nu phn la chn ta vn t
ch chn th hp thoi sau xut hin:
Nu ta khng cn t ch chn phn la chn th hp thoi sau xut

hin:
t li cc gi tr v biu nu mun, hoc s dng ch ngm

nh.
4. Nhp OK thc hin tnh ton v biu . Trong phn ny ta chn v
biu th cho H2.
Cc la chn biu din biu th

Nhn nt Propeties m hp thoi la chn biu din biu :
184
Ta c th t cc la chn thch hp biu din th.
Th hai chiu
v biu th hai chiu ta phi t ng thi PLOT1 v PLOT2.
Phn la chn hin ti ch c th l mt s thay i do , ta phi t PLOT1
cho phn la chn u v PLOT2 cho bt k lin kt, gc lin kt hoc gc
vn no. S thay i hai khng cn thit l phi cng loi. Nhp vo
Rotential trong Compute menu to ra biu 3 chiu.
V d:
V biu th 2D cho cc gc vn C1-C2 v C2-C3 trong Pentan.
Ta t la chn v biu nh sau:
Tnh ton bng trng lc MM+. Cc tiu (mu ) xut hin gi tr gc 180, -60, 60 v 1800. Cc i xut hin cc gc -120, 0 v 1200.
185
Cng th nh quan st trn khng gian 3D s nh sau:
Lu phn t
Ta c th lu phn t nc tnh vo file water.hin.
C th s dng log file lu cc kt qu chi tit tnh ton c.
186
Bi 12: Tng tc ca nc vi N-metylaxetamit.
Dng gc xon cng bc

Ti u hnh hc cho mt tp hp con
S dng cc m phng dung mi
Tin hnh tnh ton hm sng tnh in tch nguyn t
Hp nht hai phn t vo mt h n
Trong bi ny, ta chy c tnh ton bn kinh nghim ln c hc phn t trong

HyperChem v tnh in tch nguyn t cho vic s dng tnh ton c hc
phn t tip theo.
u tin, ta to ra cu trc N-metylaxtamit (NMA) theo trnh xy dng, s
dng hnh hc cng bc thay i t kiu cis sang kiu trans, v dng li
phn t. Tip theo, ta tnh hm sng cho cu trc trc v sau khi ta solvat
ho phn t vi nc.
To ra phn t NMA
to N-metylaxetamit ta lm nh sau:
1. Chn New trong File menu.
2. M hp thoi Labels trong Display menu v t Symbol.
3. Trong hp thoi la chn cc nguyn t, b tch nu c Explicit
Hydrogens, v chn Carbon l nguyn t ngm nh.
4. Nhp tri chut vo cng c v trn thanh cng c v v lin kt khung
nh sau:
187
5. Chnh sa cu trc trng nh sau:
To lin kt i cho lin kt C-O.

6. Nhp lin tip hai ln tri chut vo cng c la chn trnh xy dng
xy dng li cu trc theo khng gian ba chiu v thm nhng hydro cn
thiu.
Chuyn dng cis- sang dng trans-NMA

Tu thuc vo vic ta v lin kt khung, trnh xy dng s xy dng li phn
t theo dng trans hay dng cis-NMA. Trnh xy dng dng gc nh din
dng trans- nh l gc ngm nh.
188

Nu ta v lin kt khung theo th t O-C-N-C hoc C-N-C-O, nguyn t ln
cn (O v C) s l trans v kt qu s l cis-NMA:
Nu ta v lin kt khung theo th t C-C-N-C hoc C-N-C-C, cc nguyn t

ln cn (C v C) s l trans v kt qu l trans-NMA:
1. Quay cu trc ca trnh xy dng v xc nh xem cu trc l dng cis

hay dng trans.
Nu dng cis nh trong v d u tin trn c biu din, ta cn
chuyn n v dng trans bng cch thm s xon lin kt bt buc v xy
dng li cu trc theo cc bc m t di y. Nu ta dng c cu
trc dng trans, gi nguyn n cho phn tip theo, Ti u ho cu trc
NMA.
189

chuyn cu trc dng cis v dng trans cho NMA ta lm nh sau:
1. Nhp tri chut chn cng c la chn trn thanh cng c, v tch chn
Atoms trong Select menu.
2. Nhp tri chut t nguyn t oxi, gi v r n nguyn t hydro ni vi
nit chn bn nguyn t nh sau:
3.
4.
5.
6.
Nhp tri chut chn Constrain Bond Torsion trong Build menu.
Tch chn Trans, ri nhp OK ng hp thoi.
Nhp phi chut vo vng trng loi b la chn.
Xy dng li phn t bng cch nhp lin tip hai ln tri chut vo cng
c la chn trn thanh cng c.
H phn t lc ny s biu din l dng trans-NMA.
Cc tnh ton sau tha nhn s nh hng ca nhm metyl nh l dng
trans i vi lin kt CO, nhng cis cho lin kt NH. S dng t gc vn
trong Edit menu thu c cu hnh cn thit.
Ti u ho cu trc NMA.
Trc khi tnh hm sng cho phn t, ta ti u cu trc phn t s dng
trng lc AMBER.
ti u cu trc ta lm nh sau:
Nu hp thoi cnh bo Recalculate atom types.. xut hin th nhp
chn OK.
2. Chn trng lc AMBER, v nhp vo nt Options.
3. S dng cc la chn ngm nh nh sau.
190
4. Nhp OK ng hp thoi la chn.

5. Nhp OK ng hp thoi la chn trng lc c hc phn t. C th s
c dng cnh bo Recalculate atom type . Nu th, nhp OK chn.
6. Nhp tri chut chn Select Parameter Set trong Setup menu.
7. Chn amber3, ri nhp OK.
8. Nu HyperChem hi ta c mun tnh li kiu nguyn t khng, nhp OK
chn.
10. Trong hp thoi, s dng cc la chn ngm nh, nhng t RMS
gradient l 0.001, ri nhp OK bt u tnh ton.
Sau mt lc, tnh ton hon thnh v HyperChem biu din kt qu trong
dng hin trng.
Tnh in tch nguyn t

Trong bi 11, ta thu c in tch cc nguyn t trong phn t nc bng
cch tnh hm sng. Trong phn thc hnh sau y, ta tnh in tch nguyn
t v s dng chng tnh ton c hc phn t cho NMA v nc v sau.
tnh in tch nguyn t ta lm nh sau:

1. u tin, ly Label l Charge (in tch) cho h.
HyperChem biu din tt c cc nguyn t c in tch l 0.00.
3. Tch chn CNDO v nhp OK ng hp thoi.
HyperChem biu din in tch nguyn t khi tnh ton hon thnh. Cc
gi tr in tch, nng lng, v gradient bn tnh c th sai khc vi gi
tr bn di mt cht:
191
5. Lu phn t ny vi tn l nma.hin.
Solvat ho nhm Cacbonyl
Hp nht hai cu trc

Trong bi ny, ta hp nht phn t NMA vi phn t nc trong bi 11 v
tnh ton tng tc ca chng.
biu din NMA v phn t nc nh mt h ta lm nh sau

1. Nhp tri chut chn Merge trong File menu.
2. Chn m file water.hin lu t trc.
Mn lm vic by gi biu din c NMA v nc.
Dch chuyn phn t nc

Tip theo ta dch chuyn phn t nc n v tr c kh nng to lin kt
hydro gia oxi ca nhm cacbonyl vi nguyn t hydro ca nc.
di chuyn phn t nc ta lm nh sau:

1. Nhp tri chut vo cng c la chn trn thanh cng c, ri nhp phi
chut vo vng trng loi b cc la chn trc .
2. Chn Symbol trong hp thoi Labels.
3. V tr ca phn t nc c di chuyn n nh minh ho di y.
Ch : di chuyn mt phn t ta lm nh sau
- Nhp tri chut vo cng c la chn trn thanh cng c.
192

-
Nhp tri chut tch chn Molecules trong Select menu.

Nhp tri chut vo phn t mun chn.
Nhp tri chut vo cng c dch chuyn trn thanh cng c.
Nhp phi chut vo phn t chn, gi v r n v tr mun
chuyn n.
- Nhp tri chut vo cng c la chn, ri nhp phi chut vo vng
trng loi b la chn.
Ti u mt tp hp con ca h
Trong bi thc hnh ny, ta ti u ho hnh hc ca nc s dng c hc
phn t.
Khi ta tin hnh ti u ho hnh hc ln mt h trong ch tp hp con
c chn chu tc ng ca php ti u, v tr ca cc nguyn t c chn
b thay i trong qu trnh ti u. iu ny c ngha l nu ta la chn ch c
phn t nc, khi ta ti u, phn t NMA gi nguyn khng i khi phn t
nc di chuyn n v tr thun li. iu ny ni chung nhanh hn cho php
tt c cc bc t do. Khi nc gn v tr thun li, ta c th ti u ton b
h, nu mun.
ti u tp hp con ta lm nh sau
2. Tch chn trng lc AMBER, nhp OK s dng cc la chn ngm
nh cho trng lc.
193

3. Chn phn t nc nu n cha c chn. Ta c th s nhn c li
cnh bo l kiu nguyn t s c tnh ton li, nu th nhp OK
chn.
5. S dng RMS gradient l 0.01.
6. Nhp OK bt u tnh ton.
7. Sau mt lc, tnh ton hon thnh.
Tnh ton li lin kt Hydro

tnh ton li lin kt hydro ta lm nh sau:
1. Nhp tri chut tch chn Show Hydrogen bonds v nhp tri chut vo
Recompute H bonds trong Display menu.
Cu hnh khi trng tng t nh sau:
Biu th c im ca h tng tc
gip biu th c im s solvat ho NMA, ta thc hin tnh ton c hc
lng t trn h tng tc. Ta khi c th so snh kt qu vi tnh ton cc
moneme (n th) ca nc v NMA trc .
tnh hm sng cho h ta lm nh sau:

2. Tch chn CNDO, ri nhp OK ng hp thoi.
iu ny gip tnh ton hm sng cho h lin kt.
4. Chn Charge trong hp thoi Labels biu din in tch nguyn t tnh
ton c.
194

Kt qu trnh by nh sau:
195
Bi 13: Thuc tnh in t ca Protein

Tnh mt in t
S dng cc bin lng t c in trong tnh ton
Tnh hm sng
Vi HyperChem, ta c th pha trn tnh ton c hc lng t vi tnh ton c
in cho cng mt h phn t. iu ny cho php ta nghin cu c hc lng
t trn cc phn ca cc phn t ln, nh l v tr hot ng ca enzim, khi
khng th tnh cho ton b h phn t.
Bi ny minh ho tnh ton mt in tch cho vng ui-N ca cht c
ch tripsin tuyn tu ca b (BPTI).
Tnh ton protein minh ho trong bi c thc hin ch yu cng cch nh
tnh ton c hc lng t bn kinh nghim ta thc hin trong bi 11 v 12,
ngoi tr bin gii (boundary) gia phn c in ca phn t vi phn
lng t ca phn t c nh r.
Trc khi ta bt u
Bi ny s dng file testbpti.hin, ta lu trong bi 8. Nu ta khng thc
hin bi 8, hy lm theo cc bc trong bi 8 li (bc m file PDB, v
xo cc phn t nc) trc khi thc hin bi 13 ny.
c v biu din phn t

c v quan st phn t BPTI ta lm nh sau
1. Nhp tri chut chn Labels trong Display menu, ri nhp OK ng
li.
Ta khng chn g v HyperChem gip ta t chn none cho labels.
2. M file tesbpti.hin.
Cu trc c lu trong bi 8.
3. Nu cu trc c biu din c hydro, b tch Show hydrogens trong
Display menu khng biu din hydro.
4. Nhp tri chut chn Rendering trong Display menu.
5. Biu din phn t dng cc la chn khc nhau ca hp thoi Rendering.
iu ny gip ta quan st phn t c d dng hn.
196

6. S dng cc cng c trong Select menu v Display menu biu din ch
lin kt khung ca phn t. (tham kho biu din lin kt khung cc
bi trc).
7. Dng cng c la chn, nhp phi chut vo vng trng loi b la
chn, nhp tri chut chn Riddbons (di) trong hp thoi Rendering
mc Sticks.
iu ny gip biu din cu trc bc hai ca phn t nh mt di ruy
bng.
8. Quay cu trc thu c s nh hng phn t nh sau:
9. M hp thoi Rendering trong Display menu, trong mc Sticks tch chn

thm Stereo.
iu ny gip biu din di dng lp th. Nu lt qua bng mt
chng cht cc hnh nh, hoc nu ta nhn bng knh nhn ni, th di s
xut hin dng ba chiu.
Chn vng ta quan tm

Bc tip theo l chn phn ca h ta mun m t theo c hc c in v
phn ta mun m t theo c hc lng t. thc hin iu ny ta chn mt
tp hp con ca h. Cc nguyn t chn cng thi im ta tin hnh tnh ton
c hc lng t l cc nguyn t m HyperChem tin hnh tnh ton c hc
lng t trn .
V d, ta s chn dng hnh cu cc nguyn t v xem xt ch cc nguyn t
trong vng bn knh chn. Ta cng c th la chn theo hnh ch nht.
Trong v d ny ta chn phn u thc hin tnh ton c hc lng t.
197
chn phn u Acginin ta lm nh sau

1. B tch Stereo, b la chn lin kt khung, v biu din ton b cc
nguyn t.
2. Nhp tri chut chn Select trong Select menu, trong mc By number tch
chn Residue number v ly gi tr l 1 value =.
iu ny ARG1 s c chn.
Phn ny ta s dng tnh c hc lng t.
3. Quay v chuyn phn t cho n khi trng c nh sau:
4. Nhn phm Spacebar a phn la chn vo tm mn lm vic. Khi

phn la chn trng c dng nh sau:
198
Chn bin c in lng t.

Phn tip theo l t chnh xc bin gii gia tnh ton c hc lng t v
tnh ton c in.
Vn tt l, y din t HyperChem gii quyt vn gii hn nh th no:
Mi nguyn t c chn s c x l bng c hc lng t v mi nguyn
t khng c chn, nhng c lin kt vi nguyn t c chn, c x l
nh mt nguyn t bin.
Cc nguyn t bin c t vo cho tnh ton c hc lng t bng cc
nguyn t flo gi.
t bin lng t c in ta lm nh sau

1. Nhp tri chut tch chn Extend to sp3 trong Select menu.
iu ny m rng la chn phn u acginin ti bin thch hp.
HyperChem x l cacbon lin kt vi bn nguyn t, nit lin kt vi ba
nguyn t, v oxi lin kt vi hai nguyn t.
Tnh hm sng
Tip theo, ta tnh hm sng. u tin, xc nh xem h c in tch in t
hnh thc khng, bng cch xem nhm nitro c b proton ho khng.
xem nhm nitro c c proton ho khng ta lm nh sau:

1. Biu din phn t c c hydro v chn Symbol trong hp thoi Labels.
199

C ba hydro c ni vi nit. Cng nh th, ui acginin, cacbon ni
vi ba nguyn t nit, hai nguyn t nit trong s c ni vi hai
nguyn t hydro, iu ny to nhm lin hp c in tch dng.
Khi ui nit (N-terminal) c ba nguyn t hydro, nit ny c in tch
hnh thc l +1. Theo phn c la chn tnh ton c hc lng t l
cation ho tr hai vi in tch l +2. Ta phi xc nh iu ny t
ng s electron trong tnh ton c hc lng t.
tnh hm sng ta lm nh sau

1. Chn none trong hp thoi Labels.
3. Trong hp thoi, tch chn phng php CNDO, v nhp tri chut vo
nt Options.
4. t gii hn hi t (Convergence limit) l 0.1.
Khi ta quan tm n in tch v hnh nh nh tnh ca obital ch khng
phi l nng lng, gii hn hi t t nghim ngt c s dng.
5. t Total charge l 2 nh r cation ho tr hai.
6. t cc la chn khc nh trnh by di y, khi nhp OK chn.
7. Nhp tri chut chn Single point trong Compute menu.

Nng lng v gradient xut hin trn dng hin trng tnh ton khi tnh
ton hon thnh.
8. Nhp tri chut chn Plot Molecular graphs trong Compute menu.
9. Tch chn Total Charge Density v chn biu din trn khng gian hai
chiu (2D Contour).
10. Chn mc Contour Grid, t Horizontal grid points v Vertical grid
points l 60, t Contour level l 30.
11. Nhp OK bt u v biu mt .
Khi tnh ton hon thnh, biu xut hin nh sau:
200
Nu v biu trn khng gian ba chiu (3D), s dng Gouraud Shading

v Total charge density contour value l 0.09 trong mc Isosurface
rendering, kt qu trng nh sau:
201
Phn tnh ton thun tu l thuyt (Ab Initio Calculations)

Bi Thit lp la chn tnh ton Ab Initio v Density
Functional
Tnh ton Ab Initio (thun tu l thuyt) v Density Functional (hm mt )
c rt nhiu im chung v v th ta m t c hai y. xc nh tnh
ton Ab initio ta c bn phi chn tp hp hm c bn. Vi tnh ton hm
mt ta cng phi chn tp hp hm, nhng phi chn thm mt hm
(functional). Cc phn SCF ca hai kiu tnh ton c bn tng t nhau.
Tnh ton Ab initio hay DFT tn nhiu thi gian hn cc phng php bn
kinh nghim. u tin ta nn chy ti u theo c hc phn t chuyn hnh
hc n mc ti u no , v ti u thm bng phng php bn kinh
nghim trc khi ti u hnh hc theo Ab initio. Ring vi cc cu trc v
c, ti u theo c hc phn t hay bn kinh nghim u cho kt qu km do
thiu cc tham s thch hp, nhng ta dng trnh xy dng (Model Builder)
cho cu trc v c s c c im khi u hp l hn.
Chn tp hm c bn
Chn tp hm c bn l cng vic quan trng i vi tnh ton Ab initio v
tnh hm mt . Bt k tp hm mt electron no u c th l tp hm c
bn trong php tnh gn ng LCAO. Tuy nhin, tp hm c bn tt s d
on c cc tnh cht ca in t, s dng cc s hng t hn so vi tp
hp hm khng tt. V th, chn tp hm c bn thch hp cho tnh ton Ab
initio v hm mt quyt nh n tnh thc t v chnh xc kt qu tnh
ton c.
Cc tp hm c trong la chn ca mi hp thoi u s dng c cho
phng php .
La chn cho phng php Ab initio v Density Functional

Hai hp thoi ca hai phng php kh ging nhau, ch khc mt s t chi
tit.
Ta c th dng nhiu tp hm c bn trong mt h phn t. Nt Apply Basis
Set trong hp thoi dng p dng tp hm la chn hin ti cho cc
nguyn t c chn hoc cho ton b cc nguyn t trong HyperChem nu
202

khng c s la chn no. V d, mt s nguyn t nng dng tp hm 631G (ch cho s v p) trong khi mt s nguyn t khc dng 6-31G* (c
cho obital d) (xem Basis set trong HyperChem computational chemistry).
Basis Set
No basis set
Minimal (STO3G)
Small (3-21G)
Medium (6-31G*)
Large (6-31G**)
Other
Assign Other
Basis Set..
Extra Basis
Function
Options
Advanced
Options
Apply Basis Set
Grid
Exchange
Xc nh tp hm cho phn la chn hoc c h

phn t.
Khng dng tp hm no c. La chn ny nn
dng ch khi p dng mt hm c bn ph cho cc
nguyn t.
t tp hm STO-3G
t tp hm 3-21g
t tp hm 6-31G*
t tp hm 6-31G**
Tch chn tp hm theo mun.
Nhp chut vo nt ny m hp thoi la chn
tp hm theo mun.
Tch chn hm c bn m rng, cho php ta
m rng hm c bn cho cc nguyn t chn.
t cc la chn thc hin tnh ton
t cc la chn cao cp cho tnh ton.
Nhp p dng tp hm hin ti cho cc nguyn
t chn.
(DFT) Nhp nt ny m hp thoi chn khung
li (grid) tch phn dng cho cc tnh phn s.
La chn n gin nht l Standard Grids. Nh
mt la chn, ta c th xc nh r rng
(DFT) Nhp chn hp thoi th tng quan
trao i nhm xc nh hm mt tng quan
203

Corelation
OK
Cancel
trao i dng cho tnh ton.

Lu thit lp hin ti, p dng cc hm cho phn
la chn v ng hp thoi li.
Thot khi hp thoi v khng lu thit lp hin
ti cng nh khng p dng tp hm hin ti cho
phn la chn.
Hp thoi la chn thm cho Ab initio v Density Functional

Dng hp thoi Otions chn cc la chn c bn cho tnh ton Ab initio
v Density Functional. Cc la chn ny c bn ging trong la chn bn
kinh nghim.
and Vng ny dng xc nh in tch thc trn h

phn t hin ti v xt xem h dng singlet, hay
doublet
Phn d in tch ca ht nhn so vi electron. Bng
Total charge
khng vi h trung ho, nguyn dng vi h cation,
nguyn m vi h anion.
bi spin dng cho h hin ti. H v kn c
Spin
bi spin l 1 (singlet), h v h c bi spin l 2,
Multiplicity
3, 4 hoc cao hn. gi tr c th thay i t 1 n 6.
Phn ny dng xc nh chnh xc mong mun
SCF controls
cho hm sng SCF v s lng lp li cc tiu n
chnh xc cho php.
t kt thc tnh ton SCF khi s khc nhau gia hai
Convergence
ln lp li lin tip b hn gi tr ta t.
limit
Iteration limit S ln lp li cc i.
Tch chn phn ny, HyperChem s thc hin nhanh
Accelerate
qu trnh tnh ton SCF.
convergence
Charge
spin
204

Point Phn ny xc nh xem c tnh ton gradient v
nng lng tng quan MP2 hay khng. La chn
ny ch dng cho tnh ton Single Point v b qua
bt k kiu tnh ton no khc.
Chn tnh gradient.
Gradient
Tch chn tnh nng lng tng quan.
MP2
correlation
energy
Phn ny chn phng php tnh cc tng tc
Spin pairing
spin.
Phng php Hartree-Fock khng gii hn. dng cho
UHF
h v h v v kn.
Phng php Hartree-Fock gii hn spin, i hi cc
RHF
electron c spin cp i trong mi khng gian obital
nh c. Ngi ta thng dng cho cc h v singlet
kn.
Tch chn t tng tc cu hnh.
Cl
Cp nhn s thay i thc hin trong hp thoi.
OK
Thot ht thoi, khng chp nhn s thay i no.
Cancel
Single
only
La chn cao cp cho Ab initio v Density Functional

Ta dng hp thoi Advanced options hiu chnh qa trnh tnh ton ab
initio.
iu khin tnh ton tch phn hai electron v

Two-electro
lu tr.
integral control
Cutoff Ch gi cc tch phn hai electron vi mt gi
tr hon ton ln hn hoc bng gi tr ny. gi
tr ngm nh l 10-10 Hartree.
Buffer size t kch c nh lu trn cng.
Integral format Xc nh kiu lu cc tch phn hai
205
Regular
Raffenetti
Direct SCF
calculation
Ghost-atoms
control
Use ghostatoms selection
MO initial guess
Core Hamiltonian
Projected CNDO
Projected INDO
Number of d
orbitals
Five
Six
OK
Cancel
electron.
Lu kiu nguyn bn.
Lu kiu Raffenetti tng tc hnh thnh
ma trn Fock.
Tnh trc tip SCF. Cc tch phn hai electron
c tnh trc tip. S chm hn tnh ton
thng thng, nhng khng mt nhiu a
trng v b nh. Dng cho cc phn t ln.
iu khin s dng phn la chn ghost
atoms.
Tch dng phn la chn ghost-atoms.
La chn ny c gi tr khi phn la chn c
t tn l ghost-atoms.
Xc nh c lng ban u cho cc h s
MO.
Chn nt ny dng cc h s MO thu c
t s cho ho Hamilton li.
Dng nt ny dng cc h s MO to ra t
tnh ton Huckel.
Dng nt ny dng cc h s MO to ra t
tnh ton INDO.
Xc nh s dng Gaussians Decac (6) hay
Gaussians Hermite (5)
Chn dng Gaussian Hermite bao gm nng
obital d: d0, d+1, d-1, d+2, d-2.
Chn dng Gaussian Decac bao gm su
obital d: dxx, dyy, dzz, dxy, dxz, dyz.
Chp nhn s thay i.
ng hp thoi, khng chp nhn s thay i.
La chn m rng hm c bn
Hp thoi ny cho php ta hiu chnh cc tp hp hm hin c bng cch
thm cc hm c bn m rng cho cc nguyn t. Nu ta mun thm hm
phn cc cho hydrogen hay hm khuch tn cho cc nguyn t nng.
Mt v ch mt v ph thm (kiu S, P, D, SP hay SPD) c th c p dng
cho bt k nguyn t no vi phin bn hin ti ca HyperChem. S khc
nhau gia cc v m rng l c th p dng c cho cc nguyn t khc
nhau nhng mi nguyn t ch nhn thm mt lp v m rng. Nu ta mun
206

thm v m rng cho nguyn t no, ta cn phi hiu chnh file tp hm c
bn v to ra mt tp hm mi.
Shell type
None
S
P
D
SP
SPD
Exponent
OK
Cancel
nh kiu v thm cho cc nguyn t chn,

hoc cho c h phn t.
Khng chn thm.
Thm hm c bn m rng kt hp vi kiu v S.
Thm hm c bn m rng kt hp vi kiu v P.
Thm hm c bn m rng kt hp vi kiu v D.
Thm hm c bn m rng kt hp kiu v SP.
Thm hm c bn m rng kt hp kiu v SPD.
t s m cho kiu hm chn.
Chp nhn cc la chn.
Khng chp nhn cc la chn.
207
Bi 14: S Proton ho ca nc
To h phn t tch mang in tch.
Chn tp hp hm c bn.
Chn cc la chn cho tnh ton im n thun tu l thuyt (Ab
initio) v ti u ho.
Kho st tnh ton nng lng tng tc MP2.
Phn hng dn ny s gii thiu cho ta nhng bc c bn cn thit thc
hin tnh ton thun tu l thuyt.
t v phn t
chun b v H3O vi cc nguyn t hydro c th ta lm nh sau:
1. Nhp tri chut tch chn Explicit Hydrogens trong Build menu.
2. Nhp tri chut tch chn Allow Arbitrary Valence trong Build menu.
Nu ta khng chn Allow Arbitrary Valence th s khng th v c ba
lin kt t nguyn t oxi khi m Oxi c ho tr thng thng l hai.
4. Chn Symbol trong hp thoi Labels v nhp OK ng hp thoi li.
5. Nhp tri chut chn Default Elemen trong Build menu, tch chn Oxi
trong hp thoi v ng hp thoi li.
By gi ta chun b sn sng v H3O+.
To H3O+
V H3O
1. Nhp tri chut vo mn lm vic to ra nguyn t oxi.
2. V ba lin kt t Oxi to H3O nh sau:
Chuyn hnh v thnh cu trc 3D

1. Nhp lin tip hai ln tri chut vo cng c la chn trn thanh cng c.
Thm in tch dng cho tnh ton c hc lng t.

1. Nhp tri chut chn Ab Initio trong Setup menu.
2. Nhp chut vo nt Options.
3. nh gi tr 1 cho Total charge v nhp tri chut vo nt OK ng
hp thoi la chn ring ny li.
208

4. Nhp tri chut vo nt OK ng hp thoi la chn phng php tnh
thun tu l thuyt.
Nh vy ta thm in tch +1 cho phn t thc hin tnh c hc
lng t, c bn gim s in t thnh mt. in tch ton phn c s
dng xc nh s electron s dng trong tnh ton c hc lng t.
Chn tp hp hm c bn tnh
chn tp hp hm c bn ta lm nh sau
1.
2.
3.
4.
Nhp tri chut chn Ab Initio trong Setup menu.

Tch chn Other trong phn Basis Set.
Nhn nt Assign Other Basis Set.
Chn 4-31G trong list v nhp OK chn.
iu ny gip thm tp hn c bn 4-31G cho list cc tp hp hm c
bn m ta c th nhanh chng chn n. Cc tp hp hm c bn xut hin
trong Assign Other Basis Set bao gm tt c cc tp hp hm c bn c
lit k trong file CHEM.INI theo tn file tp hp hm c bn c nh r
ca chng (*.BAS). Cc tp hp hm c bn do ta t c th c thm
cho list bng cch to file c ui .BAS mi v thm n vo cho file
CHEM.INI. Tuy nhin ta c th t cc tp hp khc theo yu cu kho
st phn t.
5. Tch chn Minimal (STO-3G) cho mc Basis set.
6. Nhp chut vo nt Apply Basis Set v nhp OK hoc ch cn nhp lun
OK ng hp thoi la chn phng php Ab Initio.
By gi ta chn tp hp hm c bn cho mi nguyn t ca phn t,
tp hp hm c bn cc tiu STO-3G. N c th la chn c th cc
nguyn t v s dng nt Apply Basis Set t tp hp hm c bn
chn ch trn cc nguyn t c chn vi s sp xp tip sau ca mt tp
hp hm c bn khc trn cc nguyn t c la chn khc. HyperChem
cho php t cc tp hp c s khc nhau cho cc nguyn t khc nhau.
xem tp hp hm c bn no c p dng cho mi nguyn t, ta c
th biu din cc nhn thch hp.
xem tp hp hm c bn p dng cho mi nguyn t ta lm nh

sau:
2. Chn Basis Set v nhp OK chn.
By gi ta s xem c nhn ca tp hp hm c bn p dng cho cc
nguyn t trn mn lm vic.
209
Cc tiu ho cu trc
tnh hnh hc ti u ca H3O+ ta lm nh sau:
1. Chn Ab Initio trong Setup menu.
2. t cc la chn thch hp ti u hnh hc bng cch nhp vo nt
Options v t cc gi tr nh sau: Total charge = 1, Spin multiplicity = 1,
Spin pairing = RHF, Convergence limit = 0.01, Iteration limit = 50, v
Accelerate convergence = Yes (3). Phn Single Point only khng c
chn s dng trong ti u hnh hc v c th c bt k gi tr no.
3. Nhp tri chut chn OK ng hp thoi Options v nhp tip OK
ng hp thoi la chn phng php.
5. Chn Polak-Ribiere cho phng php ti u v t RMS gradient l 0.1
ri nhp tri chut vo OK bt u ti u.
tnh nng lng ton phn ca H3O+ ti u k c nng lng

tng tc ta lm nh sau:
1. Chn Ab Initio trong Setup menu, nhn nt Options v chn tnh MP2
correlation energy, ri nhp OK ng hp thoi ny v nhp tip OK
ng hp thoi la chn phng php.
2. Chn Single point trong Compute menu.
Ta thy rng nng lng ton phn ca H3O+ vi tp hp hm c bn
STO-3G l -47270.57 kcal/mol mc SCF v l -47300.98 kcal/mol
mc MP2 khi ta bao gm c -30.50 kcal/mol nng lng tng tc tnh
ton c.
Nng lng Proton ho

tnh nng lng ti u theo STO-3G ca H2O + H+ ta lm nh
sau:
1. Nhp tri chut vo cng c v, v nhp phi chut vo mt hydro ca
H3O+ xo n v to thnh H2O.
Nng lng in t ca H+ l khng v th tnh nng lng proton ho
ca H2O ta ch cn tr nng lng tnh ton trc ca H3O+ cho nng
lng ng vi H2O.
2. Chn Ab Initio trong Setup menu v nhn nt Options chuyn Total
charge t 1 v 0. Khi nhp ln lt hai ln nt OK ng cc hp
thoi.
3. Chn Geometry Optimization trong Compute menu v ti u phn t
nc nh i vi H3O+.
210

4. Chn Single point trong Compute menu.
Ta thy rng nng lng ton phn ca H2O theo tp hp hm c bn
STO-3G l -47041.82 kcal/mol mc SCF v -47066.21 kcal/mol mc
MP2 khi ta bao gm c -24.45 kcal/mol ca nng lng tng tc tnh
c. Kt qu nng lng proton ho l 228.75 kcal/mol mc SCF hoc
234.77 kcal/mol mc MP2. nh hng ca s tng tc trong v d ny
l khng ln.
211
Bi 15: Dao ng v trng thi chuyn tip ca Amoni.
Phn tch dao ng.

Thm tng tc lp ph vo cc hm c bn.
Xc nh s i xng.
Tm trng thi chuyn tip theo vc t c trng hay phng php
chuyn ho ng thi.
Trong phn ny ta s kho st dao ng ca amoni v s khc nhau gia

dng hnh chp v dng phng ca amoni.
To Amoni
v amoni ta lm nh sau:
1. Nhp tri chut b tch Explicit Hydrogens trong Build menu.
2. Nhp chn Default Element trong Build menu m hp thoi la chn
cc nguyn t.
3. Nhp lin tip hai ln tri chut vo N (nit) chn nguyn t ny ng
thi ng hp thoi li.
4. Nhp tri chut chn cng c v trn thanh cng c.
5. Nhp tri chut mt ln vo mn lm vic to ra nguyn t nit n.
6. Chn Add H & Model Build trong Build menu to NH3 theo hnh hc
chun ca trnh xy dng.
Chn tp hp hm c bn
chn tp hp hm c bn ta lm nh sau:
1. Nhp tri chut tch chn Labels trong Display menu.
2. Chn Basis set v nhp OK ng hp thoi.
Nhn trn mi nguyn t by gi biu din l tp hp hm c bn cho
nguyn t . Lc ny l None.
3. Chn Ab Initio trong Setup menu.
4. Chn Small (3-21G) l tp hp hm c bn v nhp tri chut vo Apply
Basis Set, ri nhp OK ng hp thoi li.
By gi tp hp hm c bn trn mi nguyn t s l 3-21G.
5. Dng cng c la chn chn nit trong phn t amoni. (Tch chn
Atoms trong Select menu khi chn ch chn mt nguyn t mong
mun).
6. Nhp tri chut chn Ab Initio trong Setup menu.
212

7. Nhn nt Advanced Options v tch chn Six (su) trong phn Number of
d Orbitals ri nhp OK tr v hp thoi la chn phng php .
8. Nhn nt Extra Basis Function v chn D trong mc shell type (kiu v)
v t Exponent (s m) l 1.0 trong hp thoi Extra Basis Function. Tip
theo nhp ln lt hai ln OK ng cc hp thoi li.
9. Nhp phi chut vo vng trng b la chn. (Dng cng c la
chn).
By gi ta sn sng tnh ton Ab Initio i vi amoni bng tp hp
hm c bn va t.
Phn tch dao ng ca Amoni dng hnh chp, ph dao ng

Dng Vibrations tnh ton chuyn ng dao ng ca ht nhn, v dng
Vibrations Spetrum biu din dng biu cu trc ph ca cc dao
ng. Ta c th tnh dao ng bng cc phng php ab initio, DFT hay cc
phng php bn kinh nghim, ngoi tr phng php Huckel m rng.
thc hin phn tch dao ng ta lm nh sau:

1. Chn Geometry Optimization trong Compute menu v tin hnh ti u
theo Polak-Ribiere vi RMS gradient l 0.1. hi t SCF thch hp nn
s dng l 0.01. C l mt mt vi pht tnh ton tu thuc vo tc
my tnh ca ta.
Kt qu tnh ton v cu trc (gc H-N-H = 106.5 v di lin kt N-H
= 1.01A0) cho thy rt st vi gi tr thc nghim.
2. Chn Single Point trong Compute menu tnh nng lng ton phn bao
gm c nng lng tng tc MP2.
Nng lng ton phn mc SCF l -35086.49 kcal/mol v nng lng
ton phn k c nng lng tng tc MP2 l -35191.11 kcal/mol.
3. Chn Vibrations trong Compute menu tin hnh phn tch dao ng
trn hnh hc c ti u. Tnh ton ny i hi mt vi pht.
4. Nhp tri chut chn Vibrational Spectrum trong Compute menu biu
din ph dao ng nh trnh by di y:
213
Tn s c sp xp gim dn t tri qua phi.

5. Tch chn Animate Vibrations biu din. Tch vo dao ng nng
lng thp nht bn phi bn ph v nhn nt Apply. Dch chuyn
ca s bn ph n khi c th quan st c dao ng trong mn hnh
lm vic. Nu s dao ng qu nhanh, ta c th thay i gi tr mc
Frames iu chnh.
iu ny s biu din chuyn ng mt cch sinh ng vi tn s thp
cho amoni. N gi kiu i xng C3v v thay i ch yu l gc lin kt.
Ta c th quan st cc dao ng khc bng cch nhp chut trc tip vo
ph tng ng v nhn Apply.
Cc vch trn trong ca s biu din tt c cc mc chuyn dao ng,
cn dng di ca ca s biu din cc mc chuyn dao ng km theo
cng hng ngoi ca chng (cc mc chuyn thc t xy ra c).
Khi ta nhp vo mt vch, tn s (Frequency) v cng (intesity)
tng ng ca vch biu din gc tri ca ca s.
6. Chn mc chuyn nng lng thp nht ( pha bn phi) ln na. Nhn
vo nt Apply v nhp OK ng ca s ph dao ng li. Quay phn
t amoni bng cng c quay theo trc XY quan st c y dao
ng c tn s thp nht.
7. Nhp vo nt Cancel trn thanh cng c hoc nhn nt Esc ngng biu
din dao ng. Nhp tri chut chn Labels trong Display menu v nhp
OK khi hp thoi Labels m ra loi b nhn ang biu din. Nhp tri
chut chn Rendering trong Display menu. Trong mc Sticks tch chn
IR Vectors v nhp OK chn biu din cc vc t c trng ca kiu
dao ng. Quay phn t theo trc XY quan st y cc vc t IR
ca kiu dao ng th.
8. Nhp tri chut chn Vibrational Spectrum trong Compute menu biu
din li ph dao ng. Nhp vo vch c kiu dao ng th quan st
chuyn ng th km cc vc t IR ca n.
Ch : Lun cn phi thc hin ti u hnh hc to phn t c cc tr v
nng lng trc khi tnh ton phn tch dao ng.
Ti u amoni phng
By gi ta s to ra mt co trc amoni phng ti u nht. to cu trc
c bit ny ta s s dng cch cng bc. y ta dng gc vn khng
ng to ra amoni dng phng.
214
to amoni phng ta lm nh sau:

1. Loi b tt c cc nhn cng nh vect IR vn cn ang biu din.
2. Tch chn Multiple Selections trong Select menu. Tch chn Atoms trong
Select menu.
3. Nhp tri chut vo cng c la chn trn thanh cng c. Ln lt nhp
chn bn nguyn t hnh thnh nn phn t amoni.
4. Chn Name Selection trong Select menu. Tch chn Other, v nh vo
mt tn tu , chng hn nh l imptor. Nhp OK ng hp thoi
ny li.
By gi ta c th t nn to mt gc 1800 (1800 = phng) bng cch
thm lc nn cho gc. iu ny gip chuyn amoni v dng phng.
chn.
6. Chn Restraints (cng li) trong Setup menu. Chn 4-imptor (bn nguyn
t c chn c tn ta t l imptor) v nhn nt Add them phn
tn c chn ny vo list ca Restraints. Tch chn Other cho
Restrained Value (gi tr c cng li) v nh gi tr 180 cho gc vn
(torsion). Tch chn Other cho Force Constant v nh gi tr ln hp l,
500, bo m l amoni c gi phng. Nhp OK ng hp thoi
Restraints li.
7. Chn Geometry Optimization trong Compute menu ti u to ra cu
trc phng nht. Chn phng php Polak-Ribiere, chn RMS gradient l
0.1. Nhp OK bt u ti u.
8. Cu trc ti u ta thu c l phng vi di lin kt l 0.99A0.
9. Chn Single Point trong Compute menu tnh nng lng ca cu trc
phng bao gm c nng lng tng tc MP2.
Nng lng ton phn mc SCF l -35079.16 kcal/mol v nng lng
ton phn k c nng lng tng tc MP2 l -35183.80 kcal/mol. S
khc nhau gia nng lng ny v nng lng ti u ca amoni kiu chp
l hng ro nghch chuyn ca amoni. Gi tr SCF cho hng ro nghch
chuyn ny l 7.33 kcal/mol. nh hng ca nng lng tng tc i
vi hng ro nghch chuyn ny c d on l khng ng k c 0.05
kcal/mol.
Phn tch dao ng ca amoni phng

tin hnh phn tch dao ng ca amoni phng ta lm nh sau
1. Chn Restraints (cng li) trong Setup menu. Chn 4-imptor trong mc
Restraint v nhn nt Remove chuyn gc xon khng ng ny khi
list. Nhp OK ng hp thoi Restraint li.
215

Nu ta khng chuyn 4-imptor khi mc Restraint, phn tch dao ng s
bao gm c cc thnh phn dn xut bc hai theo lc km ch c hc phn
t v cn thm tnh ton thun tu l thuyt c hc lng t i vi
amoni phng.
2. Chn Vibrations trong Compute menu tin hnh phn tch dao ng
cho amoni phng c ti u. Tnh ton ny i hi tnh s cc dn
xut bc hai theo s thay i to Decac ca cc nguyn t v phi mt
mt vi pht tnh ton.
3. Kch c ca s HyperChem xp x bng mt phn ba mn hnh v ta hy
t n gc phi mn hnh.
4. Chn Vibrational Spectrum trong Compute menu biu din ph dao
ng nh bn di y:
Ch l dao ng c nng lng thp nht c tn s m. Thc t, gii cc

phng trnh bnh thng cho ta cc gi tr c trng l bnh phng ca cc
tn s dao ng. Khi mt trong cc bnh phng ny ca tn s dao ng l
m, HyperChem v biu cho n l cn bc hai ln ch khng phi nh
mt s o. Theo gi tr m ny, -, chnh xc c ngha l mt tn s dao
ng o. Tn s o n l vi tt c cc tn s cn li c ng r rng rng
cu trc phng l mt trng thi chuyn tip, ch khng phi l cu trc c
cc tiu nng lng, nh cu trc kiu chp ta nghin cu.
5. Nhp vo vch dao ng c tn s m v xem trng thi dao ng ca n.
Ta s thy rng kiu bnh thng ny tng t nh kiu th ca amoni.
y l ng phn ng lin hp vi trng thi chuyn tip. HyperChem
khng gii trc tip vi hnh hc cng bc cng nh vi cc to ni
cng bc, m n lm vic ch vi cc to Decac. Tuy nhin, n vn
c th, qua s cng bc, bng nhin tc ng khc thu c kt qu
qua to cng bc.
6. Nhp chut vo nt OK ng ca s Vibrational Spectrum v tip theo
l nhp Cancel ngng s dao ng. Chn New trong File menu xo
mn lm vic.
216
Tm trng thi chuyn tip theo vect c trng

Trong tnh ton ny ta s s dng phng php theo vect c trng
(Eigenvector Follow) tm kim trng thi chuyn tip tm trng thi
chuyn tip ca s nghch chuyn amoni chp, m khng cn cng bc
thm cu trc. Phng php ny c bit hu dng nu mt trong cc kiu
dao ng t nhin cu trc ca ta c hng chuyn n mt trng thi
chuyn tip.
Ta c th tm trng thi chuyn tip theo ab initio, DFT hay cc phng php
bn kinh nghim, tr phng php Huckel m rng.
1. M cu trc chp amoni ti u ta lu phn trc trong phn tch
dao ng amoni chp ln mn lm vic.
xy dng li cu trc theo trnh xy dng.
Ti u theo vect c trng khng lm vic tt c nu nh im khi
u l cu trc dng cc tiu no ; ngay c nu kiu dao ng i
theo c xc nh, cc chuyn ng nguyn t ti u dn dt t mt cc
tiu khng xc nh tt c.
3. Chn Transition State trong Compute menu.
4. Trong hp thoi m ra, chn Eigenvector following, v nhp OK chn.
Dng hin trng cho bit HyperChem ang tin hnh tnh ton dao ng.
Khi tnh ton hon thnh, hp thoi thm d trng thi chuyn tip xut
hin.
5. Nhp vo vect c trng c nng lng thp nht bn phi ca ph.

Nh trc, vct ny tng ng vi kiu th, tn s thp nht ca
amoni, trong s chuyn ng ca cc nguyn t trc tip dn n s
nghch chuyn ca amoni dng chp.
217

Dao ng c nng lng thp nht thng l kiu gn nht vi trng thi
chuyn tip.
6. t RMS gradient limit l 0.1 kcal/(A0 mol), v nhp OK chn.
HyperChem fm trng thi chuyn tip phng.
7. Trng thi chuyn tip l dng phng vi di lin kt l 0.99A0. Chn
ln lt t nguyn t N v ba nguyn t H xem gc xon khng ng
c trnh by trong dng hin trng. N rt gn vi 00 hoc 1800.
Tm trng thi chuyn tip bng s chuyn ho ng thi

Trong tnh ton ny ta s s dng phng php chuyn ho ng thi
(Synchronous Transit) tm trng thi chuyn tip tm trng thi chuyn
tip phng cho s nghch chuyn ca amoni chp, m khng cn cng bc
cu trc thm. Phng php ny cho php ta tnh cc trng thi chuyn tip
khi h cc cht phn ng v sn phm rt khc nhau, hoc nu ta mun xc
nh cn thn nh th no cc nguyn t c sp xp li qua trng thi
chuyn tip. Cc nguyn t ca cht phn ng v sn phm c lm cho
tng ng, v im bt u tm c ni suy t cc cu hnh ban u v
lc sau.
1. M li cu trc amoni m ta lu ln trc.
2. t Number hp thoi Labels trong Display menu.
3. Nhp tri chut vo cng c v trn thanh cng c, nhn phm Shift gi
nh vy v nhp tri chut vo nguyn t N.
Khi nh chut v nh phm ra, nguyn t H s chuyn n mt v tr
trng ca chp amoni, o chiu s khng i xng ca h c xt
n th t nguyn t. Thng thng ta s dng thao tc ny thay i
s ni khc nhau n tm bt i.
4. Ti u hnh hc ca h vi gradient l 0.1 kcal/(A0 mol) nh trc.
C tp hp nguyn t cht phn ng v sn phm c ti u trc khi ta
tm trng thi chuyn tip vi phng php i qua ng thi.
5. Nhp chn Merge trong File menu nhp m thm bn copy khc ca cu
trc amoni c ti u lu trc cho mn lm vic.
6. Nhp tri chut vo cng c la chn trn tranh cng c. Chn mt phn
t trn mn lm vic.
7. Nhp chn Name Selection trong Select menu, v nhp chn
REACTANT.
218
8. Nhp tri chut chn Complement Selection loi b s la chn phn

t th nht v chn phn t cn li.
9. Nhp vo Name Selection trong Select menu v tch chn PRODUCT.
chn.
11. Nhp chn Reaction Map trong Setup menu m hp thoi Transition
State Mapping.
12. Trong hp thoi chn nguyn t N t mc Reactant v nguyn t H trong
mc Product. Mi nguyn t trong list c nh r theo s th t ca n
trong phn t.
Khi ta chn mt nguyn t trong list, n s c sng hn trn mn lm
vic:
219

Bi v hai nguyn t ta chn khng tng ng vi nhau (Nguyn t N
trong cht phn ng khng th tr thnh nguyn t H trong sn phm),
nt Add s khng hot ng.
13. Chn li nguyn t N trong c list Reactant v Product.
Bi v cc nguyn t l tng ng, nt Add s hot ng.
14. Nhp tri chut vo nt Add.

Cc nguyn t c chuyn t list Reactant v Product thnh mt cp
tng ng trong list Map.
15. Chn nguyn t #2 trong list Reactant v Product v chuyn cp ny cho
list Map. Tng t lm cho cc cp nguyn t cn li.
Bi v ta ang tm cch nghch chuyn phn t amoni, do th t ca
cc nguyn t rt quan trng.
Khi tt c cc nguyn t c chuyn qua cho list Map, nhp OK
bt u thc hin cc bc cn thit tip theo.
16. t gi tr 0.49 cgi mc Lambda.
(Lambda) l tham s ni suy; gi tr ca n xp t 0 cho trng thi cht
phn ng n 1 cho trng thi sn phm. Bi v tp hp nguyn t cht
phn ng v sn phm l nh qua gng, gi tr ; 0.5 s cho mt im
khi u i xng tuyt i cho vic tm trng thi chuyn tip. S lm
vic khng c kt qu tt vi khi u i xng tuyt i. Gi tr 0.49
cho ta im khi u i xng va phi cho vic tm kim.
220
17. Nhp OK chn.

Cc nguyn t ca sn phm b xo i, v cc nguyn t ca cht phn
ng c gi li lm to cho im khi u ni suy cho vic tm kim
trng thi chuyn tip.
18. Nhn nt Spacebar a cu trc vo tm mn lm vic, v quay n sao
cho c th trng c d dng.
im khi u nn l cu trc phng.
19. Chn Transition State trong Compute menu.
Hp thoi la chn tm trng thi chuyn tip m ra.
Phng php ny cho php vect c trng ca kiu

dao ng tm kim trng thi chuyn tip. Nu ta chn
phn ny v nhp OK, HyperChem s thc hin tnh
ton dao ng v ra hp thoi n trng thi chuyn
tip cho php ta xc nh kiu dao ng no xy ra.
Phng php ny hu dng cho vic tm kim trng
thi chuyn tip theo kiu dao ng t nhin.
Phng php ny dng kiu chuyn ho ng thi,
Synchronous
thch hp cho vic tm kim trng thi chuyn tip
transit
trong phn ng ho hc.
Linear HyperChem dng php ni tuyn xc nh trng
thi ca cht phn ng v sn phm.
Quadratic HyperChem dng php ni suy ton phng xc
nh trng thi cht phn ng v sn phm.
Dng phn ny t cc iu kin kt thc tm trng
Synchronous
thi chuyn tip.
Transit
Termination
Eigenvector
following
221

Condition
RMS gradient Tnh ton s ngng khi RMS gradient ca nng lng
b hn gi tr ny. c th t gi tr thay i t 10-2
n 0.1, nu dng gi tr ln hn th tnh ton s
nhanh hn, nhng kt qu km hn.
S vng cc i dng tnh ton.
Max. cycles
20. t Synchronous Transit, tch chn Quadratic (bc hai), v RMS gradient
t chun l 0.1 kcal/(A0 mol). Nhp OK chn.
HyperChem thc hin tnh ton dao ng, chn cc vect c trng ca
n, v sau tm trng thi chuyn tip. Khi cng vic tm kim bt u
im khi u tt, n s tm ra trng thi chuyn tip mt cch nhanh
chng.
Ta cng c th s dng im khi u c ni suy t hp thoi Reaction
Map nh im khi u cho vic tm kim trng thi chuyn tip vi
phng php theo vect c trng.
222
Bi 16: Trng thi in t kch thch thp nht ca Etilen.
Nghin cu biu nng lng obital ca phn t.

Thc hin tnh ton tng tc cu hnh kch thch n.
Nghin cu ph in t ca phn t.
Tnh ton hnh hc vi trng thi kch thch triplet
Trong phn ny ta s kho st tnh ton ph kch thch in t, tho lun v

s chuyn mc vch ba -> * trong etilen.
Ti u trng thi c bn ca Etilen.

By gi ta s c mt cht kh khn trong vic tnh ton thun tu l thuyt,
v th phn ny s tm lc cho ta mt s ch dn.
to Etilen theo tp hp hm c bn STO-3G ta lm nh sau:

1. Nhp tri chut chn New trong File menu.
2. B tch Explicit Hydrogens trong Build menu.
3. Chn cacbon trong hp thoi la chn nguyn t v v to lin kt i C
= C.
4. Chn Add H & Model Build trong Build menu to ra etilen.
5. Chn Ab Initio trong Setup menu v chn Minimal (STO-3G) cho tp hp
hm c bn. t Total charge = 0, Spin multiplity = 1, Spin pairing =
RHF, Accelerate convergence = Yes (tch chn), v gi tr SCF
Convergence Limit t thch hp l 0.0001. Nhp nt CI (Cofiguration
Interaction) v t None ri nhp OK ln lt ng cc hp thoi.
ti u trng thi c bn ca etilen ta lm nh sau:

1. Chn Geometry Optimization trong Compute menu.
Tch chn phng php Polak-Ribiere v t gi tr 0.01 cho RMS
gradient. Nhp OK ng hp thoi v bt u ti u.
Ta s tm hnh hc c ti u ca etilen c di lin kt C-C l 1.31
A0, di lin kt C-H l 1.08 A0, v gc H-C-H l 115.70.
tnh nng lng tng tc ta lm nh sau:

1. Chn Ab Initio trong Setup menu, nhn nt Options, v chn MP2
correlation energy. Nhp OK ng hp thoi ny li tr v mn lm
vic.
2. Chn Single Point trong Compute menu.
223

Ta s tm nng lng SCF l -48364.64 kcal/mol v tng nng lng MP2
l -48438.61 kcal/mol trong bao gm c -74.97 kcal/mol nng lng
tng tc.
S khc nhau nh gia nng lng c ti u v nng lng tnh ton
theo Single Point i khi c th xy ra.
Obital trng thi c bn ca Etilen

quan st biu nng lng obital v cc obital ta lm nh sau:
1. Chn Orbitals trong Compute menu.
Nhp tri chut vo vng biu din cc vch mc nng lng obital, gi
v r phng to cho n khi c th nhn cc vch mc c nh sau:
C hai obital c quy cho l obital c in y (HOMO) v obital

* trng (LUMO) ca etilen. Cc trng thi kch thch thp nht ca etilen
tng ng vi s chuyn mt electron t obital p n obital *. C ngha
l t -> * (HOMO n LUMO) s chuyn dn n c hai trng thi
mc n b kch thch, y cc electron kiu i nhau, v mt trng
thi bi ba, y cc electron trong obital v * c spin song song.
2. Chn cc obital ny bng cch nhp tri chut vo n, v v biu
obital. nh hng phn t etilen sao cho c th quan st c nh trong
v d. y biu din obital *, sau khi phn t c t dc trc x bng
cng c hiu chnh Align Molecules trong Edit menu.
224
CI v ph in t ca Etilen
tnh ph ca Etilen ta lm nh sau
1.
2.
3.
4.
5.
6.
Nhp chn Ab Initio trong Setup menu.

Nhp chn Minimal (STO-3G).
Nhp vo nt Options.
Nhp vo nt CI (Configuration Interaction).
Tch chn Singly Excited.
Chn Energy Criterion (Chun nng lng). nh gi tr 1000 cho
Maximum Excitation Energy. Nhp ln lt OK tr li mn lm vic.
Khi tin hnh tnh ton tng tc cu hnh (CI) kch thch n, n trn s
lng ln cc th ca cc cu hnh. Cc cu hnh ny bao hm s kch
thch mt electron t mt obital nh c n mt obital trng. Cn thit
phi quyt nh c nhiu yu t nh th no lin quan n s trn. iu
ny c th thc hin trn c s ca tt c cc kch thch c lin quan bao
gm s lng c th cc obital khng nh c thp nht v obital nh c
cao nht hoc trn c s chun nng lng kt hp vi s khc nhau v
nng lng ca hai obital c lin quan.
Chn gi tr 1000 s cho kt qu trong bao gm tt c cc cu hnh
kch thch n trong CI (tng tc cu hnh).
7. Chn Single Point trong Compute menu. iu ny gip ta bt u tnh CI
kt hp vi tnh ton im n. Khi tnh ton hon thnh, mc Electronic
Spectrum s chuyn qua mu en v hot ng c.
8. Chn Electronic Spectrum trong Compute menu biu din ph nh
sau:
225
Vch cao nht l 52.7 nm v n khng lin h g vi s chyn -> *. Mc

chuyn nng lng thp nht (bc sng di nht) pha bn phi c bc
sng l 3.3.7 nm v l s chuyn bi ba (triplet) -> *. Tt nhin, y c s
cm (mt bng khng) khi tt c s chuyn l t singlet (bi mt, mc
n) n triplet. Nng lng thp nht cho php chuyn 106.4 nm l s
chuyn singlet -> *.
Wavelength
Zoom
Oscillator
Strength
Pan
Transition
Degeneracy
Spin
multiplicity
Wavelength
Oscillator
Strength
S ch gc cao bn tri v phi cho bit gii hn

ph ang c biu din.
Thanh trt phng to v thu nh gip d dng quan
st biu din ph.
T l ca cng dao ng (intensity).
Thanh trt h tr quan st.
Biu din s ca s chuyn, mc ca s chuyn c
chn. S chuyn theo th t t bc sng di nht
n bc sng ngn nht (tri qua phi). Ta c th
chn mt s chuyn bng cch nh vo s ca s
chuyn.
Xc nh s suy bin ca trng thi kch thch theo
s chuyn chn.
L bi spin ton phn, 2S+1, y S l tng spin
electron ca h. Mi electron khng kt i c spin
l 1/2,. H v kn (singlet) c bi l 1, trng thi
doublet, triplet ln lt c bi l 2 v 3.
Bc sng (nm) ca s chuyn c chn.
Lng khng th nguyn t l vi cng ca s
chuyn c chn.
226

Copy
Copy hnh nh hp thoi biu din ph vo trnh ng

dng khc, vo b nh tm thi.
Hnh hc v nng lng ca Etilen bi ba

Do trng thi kch thch thp nht ca etilen c trng thi spin khc (triplet)
ch khng phi trng thi c bn (singlet), vi HyperChem ta c th tnh d
dng v trc tip hm sng SCF ti u cho n. y khng phi l mt tnh
ton n gin khi trng thi b kch thch c s i xng spin nh trng thi
c bn v HyperChem hin ti khng c kh nng tnh trc tip trng thi
singlet b kch thch cho etilen, ngoi thng tin c gi tr phng php CI
cho trng thi c bn ra, nh l ta thc hin trn ra. Trng thi Triplet c
th tnh ton c bng trc tip bng tnh ton SCF yu t n.
tnh hnh hc cho trng Etilen bi ba ta lm nh sau:

1. To etilen chun theo trnh xy dng trn mn lm vic nu ta cha c.
Khi ta tin hnh ti u hnh hc, hnh hc khi u hin ti khng ti
hn v etilen ca ta c th l cu trc c ti u cho trng thi c bn
theo STO-3G thu c t trc.
2. Chn mt gc vn trong etilen phng v khi chn Set Bond Torsion
trong Edit menu i gc vn thnh 300.
Nhng ngi ti u dn xut u tin theo HyperChem c th khng d
dng tm thy s thun li ca s khng phng nu ta bt u vi mt cu
hnh phng cho mt phn t. Ta ang gip cho s ti u i lch hng so
vi mt cu trc khng phng.
3. Chn Ab Initio trong Setup menu v chn 3 (triplet) cho Spin Multiplicity
v t UHF cho Spin Pairing. iu ny s tnh ton cho trng thi triplet
electron khng cp i ch khng phi tnh bnh thng RHF cho trng
thi c bn singlet electron cp i. t 0.0001 cho SCF convergence. S
dng Minimal (STO-3G) Basis set v nhp OK tr li mn lm vic.
4. Chn Geometry optimization trong Compute menu. Tin hnh ti u vi
RMS gradient l 0.01.
S ti u mt mt lc kh lu. Tuy nhin kt qu l trng thi triplet c
kch thch c xon n 900 so vi trng thi c bn. Lin kt i C C
c dn rng n 1.49A0 so vi trng thi c bn l 1.31A0, ch yu,
l lin kt i c ph v v gi li gn vi lin kt n. Khong
cch C H cn li l 1.08A0 v gc H C H by gi l 117.80.
tnh nng lng kch thch on nhit ta lm nh sau:

227

1. Chn AbInitio trong Setup menu, nhn nt Options, tch chn MP2
correlation energy. Nhp OK ng hp thoi thot ra mn lm vic.
2. Chn Single Point trong Compute menu.
Nng lng SCF ca trng thi triplet kch thch c ti u l
-48328.65 kcal/mol cao hn 35.99 kcal/mol (794.4 nm) so vi trng thi
c bn singlet c ti u. y l nng lng kch thch on nhit o
c t cc tiu nng lng ca mi trng thi. Nng lng tng tc
MP2 trong trng thi triplet kch thch (-45.02 kcal/mol) b hn nhiu so
vi trng thi c bn (-74.43 kcal/mol) do , di nh hng ca s
tng tc, nng lng kch thch on nhit l 65.84 kcal/mol (434.3 nm).
Nhng con s ny c th so snh vi nng lng kch thch cc im
(91.14 kcal/mol hay 313.7 nm) tnh theo CI cho s chuyn ny. Nng
lng kch thch cc im (ging nh hnh hc ca trng thi kch thch
vi trng thi c bn) r rng cn phi ln hn nng lng kch thch
on nhit.
kho st obital ca trng thi triplet ta lm nh sau:

1. Chn Orbitals trong Compute menu. Phng to vo cc obital alpha
xem biu nh sau:
Ch rng hai obital nh c v * xuy bin. Nhp vo cc obital ny

chn v v biu tng ng kho st.
228
Bi 17 Kh nng phn cc DFT ca H2

Tnh hm mt
Chn hm tng tc trao i
Thm trng in v tnh kh nng phn cc
Thuyt hm mt (DFT) l phng php mi, n c nhiu im chung vi
cc phng php tnh ton thun tu l thuyt. Phng php ny dng thuyt
hm mt d on nng lng ph thuc vo mt . Phng php ny
thay th cc th Hartree-Fock ca tnh ton thun tu l thuyt bng th
tng tc trao i ca mt electron. L phng php chnh xc hn tnh
ton thun tu l thuyt.
Trong phn ny s gii thiu cho ta nhng bc c bn cn thit thc hin
tnh ton DFT.
To H2
v to phn t hydro ta lm nh sau:
1. Tch chn Explicit Hydrogens trong Build menu.
2. Chn Labels trong Display menu v tch chn Symbols.
3. Nhp tri chut vo cng c v trn thanh cng c v r v mt ng
trn mn lm vic. Nu v sai th dng phi chut xo hnh nh va
to.
4. Nhp tri chut vo Model Build trong Build menu to phn t hydro
theo trnh xy dng vi di lin kt l 0.74 A0 quay dc theo trc Y.
229
By gi ta c mt phn t thc hin tnh ton. Ta s tin hnh tnh ton

trn hnh hc ca trnh xy dng c di lin kt l 0.74 A0 mc d ta c
th ti u hnh hc nu ta mun.
Chn th tng tc trao i

biu th kiu tnh ton DFT ta mun thc hin cn lm nh sau:
1. Nhp chn Density Functional trong Setup menu.
2. Chn tp hp hm c bn 6-31G** nh trnh by di y. Kiu tp hp
hm c bn ny c thm hm phn cc kiu p cho cp tp hp hm c
bn zeta 6-31G kiu s cho H2.
3. Nhp vo nt Options v chn cc la chn ngm nh sn nh bn di

y:
Ring hi t ca SCF (1.0e-008) nn t nh hn bnh thng ( tnh kt

qu SCF c chnh xc hn) khi ta gi nguyn cc gi tr khc.
4. Nhp vo nt Grid trong hp thoi Density Functional Method v chn
Standard Grid #1 theo nh sn ca Pople v cc cng s.
230
Thuyt hm mt (DFT) i hi ta c lng cc yu t ma trn ca

ton t Hamilton trong bt k phng php c hc lng t no. Trong
trng hp DFT, cc s hng trong ton t Hamilton (cc th trao i v
tng tc) c hnh thc hm qu phc tp c th khai thc cc cng
thc gii tch cho cc tch phn thch hp. DFT ni chung i hi s tch
phn tnh ton cc tch phn ny v iu ny ch cho ta phi chn mt
li to biu din s tch phn ny.
Standard Grid #1 l mt s ho hp gia chnh xc v phc tp (s
cc im trn li). Nhiu im s cho cc tch phn chnh xc hn
nhng s i hi nhiu thi gian tnh ton.
5. Nhp vo nt Exchange Corelation v tch chn c hm trao i ln hm
tng tc. Chn phng php HCTH98 cho c hai.
Ta c th chn bt k hm trao i no kt hp vi bt k hm tng tc no

hoc c th chn c s lin h nh c ti u theo cc tc gi. Nhiu
trong s cc hm c pht trin vi s tha nhn chng s c s dng
thnh tng i xc nh mc d HyperChem khng i hi iu ny.
HyperChem cho php chn c lp cho trao i v chn c lp cho tng
tc. Trong trng hp ca ta ta s chn c hai hm trao i v tng tc nh
nhau (HCTH98) c nhm Handy thuc trng i hc Cambridge pht
trin. Mt cht kinh nghim c l c gi tr s dng ch cho mt trong cc
231

cp hm. C chng ngi ta c th pht trin mt th trao i ti u nht
trong chnh n m khng n s tng tc (hoc ngc li).
Chn None trn l xt on ton din cho th tng tc khi tnh ton
Hatree-Fock khng cha s tng tc. Tuy nhin chnj None chn s trao
i l c vn ng ng mc d n lin quan n tnh ton Hatree.
Tnh ton DFT im n trong trng in.

kho st ng dng ca trng in trn mn lm vic ta lm
nh sau:
1. Nhp chn Single Point tin hnh tnh ton DFT thiu s c mt ca
trng in 0.74 A0.
Ta thu c nng lng -743.850760 kcal/mol.
2. Nhp chn Show Dipole Moment trong Display menu.
Momen lng cc bng khng (hoc gn khng) nh mong i.
3. Nhp chn Set Finite Field trong Setup menu v thm gi tr 0.001 cho
trng in nh trnh by di y.
4. Nhp OK thm trng.

5. Nhp Single Point trong Compute menu tnh ton im n li nhng
by gi c thm trng in c p dng.
Ta thu c nng lng l -743.852747 kcal/mol b hn mt cht so vi
khng c trng in. Momen lng cc trong trng in s khng bng
khng.
6. Nhp vo Show Dipole Moment trong Display menu.
Kt qa momen lng cc dc theo trc y l 0.16096 Debye hay l
0.16096/2.541765 = 0.00633 a.u. S phn cc dn n kt qa c momen
lng cc theo trng p vo. Do , s phn cc dc theo trc y l
0.00633/0.001 = 6.33 n v nguyn t. Ta tin hnh tnh ton s lo
lng hn ch v s phn cc ca H2 bng hm DFT hcth98. Tuy nhin,
HyperChem cho php ta tnh trc tip s phn cc nh ta s thy sau y.
Tnh s cng phn cc
232
tnh s phn cc ta lm nh sau

1. Nhp chn Set Finite Field trong Setup menu v b tch Electric ta t
phn trc.
2. Nhp chn Density Functional trong Setup menu. Nhp vo nt Options
v nhp tip vo Polarizabilities. Ta by gi c th yu cu tnh phn cc
trong qu trnh tnh im n, t cc gi tr nh sau:
Dng gi tr 0.001 nh ta s dng trc y ch khng nn dng gi tr

ngm nh 0.0005. Ga tr ngm nh l s ho hp gia chnh xc ca s
thay i c th theo di c v gi tr chnh xc tuyt i ch trong gii hn
trng bng khng p vo.
3. Nhp chn Single Point trong Compute menu tnh im n li nhng
thi gian i hi nhiu hn.
Tnh ton i hi mt 6 ln thi gian tnh ton khng c tnh s phn cc
trong c tnh n c trng lc p vo cho cc trc X, Y v Z.
xem kt qa tnh ton sau khi tnh ton hon thnh, nhp vo
Properties trong Compute menu. Nhp vo Details xem y s
cng.
Ta thy rng hp phn YY ch c gi tr l 6.33 nh tnh ton phn

trn.
233
Bi 18 Ch thch
Thm ch thch cho phn t
Chn, chnh sa v dch chuyn ch thch
Th t lp ch thch theo trc Z, ghi ch thch vo lp ch thch.
Phn ny s gii thiu cho ta bn kiu ch thch c bn-kiu ghi, kiu ng
thng, elip (trn) v kiu ch nht. N gip ta lm cch no ghi ch v
sa i kch c, mu sc v cc thuc tnh khc.
To mt h phn t
to mt h phn t lm mu ta lm nh sau:
1. Chn Open trong File menu.
2. M chn file ethanol.hin m ta lu t trc (C th v trc tip trn
trang lm vic cng c).
Chn ball and cylinder mc Rendering ca Display menu.
Hnh nh biu din trn m lm vic s c dng nh sau:
Ch thch kiu ch nht

Ch thch kiu ch nht v elip c bn l nh nhau. Phn ny ch minh ho
cho kiu ch thch ch nht. Bn hy th li vi kiu elip.
to v thao tc vi ch thch kiu ch nht ta lm nh sau

1. Chn Options
mun:
trong Annotations menu v chn cc la chn mong
234
Tch chn nh trong hnh v.

2. Chn Color trong Annotations menu v chn mu xanh (blue). y s
l mu sc ca bt k ng thng, elip hay ch nht no m ta v ra sau
.
3. Nhp vo biu tng hnh ch nht trn thanh cng c. Ch l, sau khi
ta nhp vo biu tng ny th khi chuyn ln mn lm vic chut cng
c hnh dng ch nht.
4. t tr chut ln gc tri mn lm vic, nhp tri chut gi v r to hnh
ch nht nh mong mun ri nh chut ra. Ch thch kiu ch nht khi
xut hin nh sau:
Tt c phn t nm lp bn trong ri vi lp ch thch nm bn ngoi.

Chnh v chn Annotation Layer in Front nn phn t ca ta b che mt.
5. Chn Options trong Annotations menu v b tch Annotation Layer in
Front t lp ch thch ng sau, khi mn lm vic biu din nh
sau:
235
6. Nhp chn cng c la chn trn thanh cng c v nhp tri chut vo
ch thch ch nht chn ch thch ny. Ch nht ch thch s xut
hin ng vin la chn mu (ngm nh l mu xanh). Nu cn thit
loi b la chn ta ch vic nhp phi chut vo vng trng mn lm vic.
Tng t ta cng c th chn phn t nh nhng bi trc.
7. Dng cng c dch chuyn v phng to iu chnh kch c v v tr ph
hp. Ch , nu phn t cng c chn th n s c u tin i vi tc
ng ca cc cng c. Nu ch ch thch c chn, th n s chu tc
ng ca cng c phng to v cng c dch chuyn; cc cng c khc
khng c tc dng vi n.
8. Ch chn hnh ch nht.
9. Chn Options trong Annotations menu v b tch Fill Circles and
Rectangles. Nhp OK chn.
10. B la chn hnh ch nht. Ta s thy s lp y bin mt, thay vo l
hnh nh nh sau:
236

11. Chn hnh ch nht li ln na v nhp chn Options trong Annotaions
menu. Chn kiu ng thng (line type) l Dashed (Nt t). Ta s
thy hnh ch nht lin trn chuyn thnh hnh nt t.
Ch :
- Hide Annotation layer: giu ch thch.
- Fill Circles and Rectangles: Lm y ch thch (T y mu
la chn)
- Use Gravity on lines: Dng lc ht cho cc ng thng.
- Line Width: rng ca ng.
- Line type: Kiu ng: Solid (nt lin), Dashed (nt t),
Dotted (chm chm), DashDotted (gch chm),
DashDotDotted (gch chm chm).
Ch thch dng ng thng

Ch thch dng ng thng cng ging nh ch thch kiu elip v ch nht
nhng khng c ch lm y. Chng cng khc nhau v lc ht lm
cho cc ng ni c vi nhau.
Kho st ch thch kiu ng thng ta lm nh sau:
1. Chn cng c ch thch ng thng trn thanh cng c, v mt vi
ng, chn, t mu, dch chuyn v phng to nh ch thch kiu ch
nht trn.
Th kho st kh nng ht ca u mt cc ng khi v gn nhau bng
cch tch chn Use gravity in lines trong hp thoi Options ca
Annotation menu.
Ch thch kiu vn bn
Ghi ch bng t cng nh bng biu tng hu nh ging nhau ngoi tr
biu tng l mt k t n.
Ch thch kiu vn bn khc v mu sc so vi kiu ng, elip v kiu ch
nht. Mu chn cho kiu vn bn ch c 16 mu. Cng ch c duy nht
cc kiu phng ch, kch c ch cng nh mt s kiu biu din ch.
Kho st vic to v hiu chnh ch thch kiu vn bn ta lm nh

sau:
1. Nhp tri chut tch chn ch thch kiu vn bn trn thanh cng c.
237

2. Nhp tri chut ln gc trn bn tri hnh ch nht to trc (t
chut v tr mun ghi ch). Khi hp thoi la chn ghi ch kiu vn
bn xut hin:
3. Chn cc la chn nh trong hnh v, vit ch thch vo ca s trng bn

di, nhp OK th mn hnh s xut hin nh sau:
Ta c th thu c hnh nh sai khc mt cht nu cha chnh sa v hon

ton c th vit ting vit nu my tnh c ci phng ting vit.
238

4. Dng cng c la chn chn dng ch thch bng cch nhp chut vo
v tr thch hp trn dng . N s c vy li bng hp la chn ca
cng c la chn.
5. Chn Edit Text trong Annotations menu v thay i kch c ch t 40
v 30.
6. S dng cng c dch chuyn v dch chuyn dng ch thch n v tr
nh trnh by sau:
7. Chn Symbols (biu tng) trong Annotations menu v nhp vo mt

biu tng, v d nhp vo mi tn v nhp OK chn.
Tu thuc vo phng ta ci t trn my m ta s c kiu biu tng

khc.
Mu sc ngm nh ca biu tng l mu trng (mu ngm nh ca nn
HyperChem l mu en), do nu ta chn mu nn l mu trng th
khng th nhnh thy biu tng. Biu tng mi ly ra lun nm gc
239

trn bn tri mn lm vic, n vn cn ang c la chn v ta c th
dng cng c dch chuyn chuyn n n v tr cn thit.
8. Chn Edit Text trong Annotations menu v chn mu thch hp cho
biu tng mi ly. Ch , biu tng ta ly l mt k t trong phng
hin hnh trong hp thoi. Nhp OK chn.
9. Chuyn mi tn n nguyn t oxy. B la chn, ta c th b mi la

chn bng cch dng cng c la chn v nhp phi chut vo vng trng
trn mn lm vic.
10. Dng cng c ch thch dng vn bn to mt ch thch khc l
Oxygen Atom v t n vo v tr nh sau:
Nu ta lo lng v vic la chn cc ch thch ring th c th s dng

Select Next hay Select Previous trong Annotations menu. Ta ch c th s
dng chng khi mt ch thch c chn. Ta ch c th hiu chnh c
ch thch dng vn bn khi mt ch thch dng vn bn c chn.
240
Lu ch thch
Ch thch cng c HyperChem lu vo file HIN. Ta c th lu n vi h
phn t hoc khng cng c.
lu ch thch vo file HIN ta lm nh sau:
1. Lu phn t trn cng vi ch thch bng cch nhp chn Save trong
File menu.
2. Sau khi lu vo file HIN, chn New trong File menu.
3. Chn Open trong File menu v c file m ta mi lu. Ch thch s xut
hin nh ta biu din trc .
241
Bi 19 Cc File tham s TNDO

Tnh TNDO.
Hiu chnh trc tip tham s TNDO (V nhng phng php khc)
To cc tham s mi xc nh kiu
Phn ny s gii thiu cho ta nhng thao tc bng tay c bn v tnh ton
kiu b qua xen ph vi phn (TNDO). Ta s kho st tng c bn v kiu
nguyn t trong cc tnh ton bn kinh nghim v pht trin cc tham s mi
cho phng php TNDO.
Vi mt tp hp tham s ngm nh, TNDO ch l phng php CNDO
(hoc l INDO). Ta s kho st nh th no CNDO d on r rng di
lin kt C C trong etan v eten v pht trin cc tham s mi xc nh cho
cc h sp2 v sp3.
Tham s ngm nh CNDO/INDO.

kho st di lin kt CNDO ca etan v eten ta lm nh sau:
1. To mt phn t etan trn mn lm vic v p dng nhn (Labels) theo
kiu nguyn t (type).
2. Chn Semi-empirical trong Setup menu v chn TNDO s dng

phng php bn kinh nghim ny. Nhp vo nt Options v chn cc gi
tr ngm nh nh trnh by bn di:
242
c bit, khng chn Add INDO Terms. Khng tch chn phn ny, TNDO
tng ng vi CNDO (cng vi hoc khng cng vi cc tham s ring).
3. Chn Select Parameter Set trong Setup menu v chn tp hp tham s
ngm nh. Nhp OK ng hp thoi.
4. Dng Polak-Ribiere ti u cu trc ca Etan, t RMS gradient l
0.01. Ta nn thy rng di lin kt c ti u vo khong 1.457 A0.
Ta c th thch tnh ton li vi phng php CNDO. Lp li tnh ton
cho Eten v thu c di lin kt khong 1.310 A0.
Kim tra tham s TNDO

kim tra tham s TNDO ta lm nh sau:
1. Chn mt nguyn t cacbon ca etan v chn Edit Parameters trong Setup
menu. Hp thoi vi cc tham s TNDO ngm nh nh sau xut hin hon
ton ng nht vi cc tham s theo CNDO/INDO.
Trong TNDO cc tham s ny c kt hp vi mt kiu nguyn t ring

ch khng theo s th t nguyn t. Trong trng hp ny kiu l CT.
Ch c bit gi tr beta l 21. Lng beta ny l tham s c bn cho
di lin kt v cc yu t ngoi ng cho ca ma trn Fock. Gi tr beta
ln nn c t cho lin kt mnh hn v gi tr beta nh hn nn t cho
243

lin kt yu. Trc khi hiu chnh cc gi tr ngm nh ny ta nn to ra
mt file tham s mi th nghim vi n.
Ch : Ta cng c th kim tra cc tham s cho cc phng php bn kinh
nghim khc hoc phng php c hc phn t. Vi phng php c hc
phn t, ta s thy tham s khc pht trin da trn ta chn nguyn t, lin
kt, gc lin kt hay gc vn.
Copy tham s TNDO cho tp hp mi

copy tp hp tham s ngm nh cho tp hp vi tn tutorial s
dng cho th nghim.
1. Chn Select Parameter Set trong Setup menu nh trc xem cc tp
hp tham s TNDO. Chn tp hp ngm nh v nhp vo nt Copy.
HyperChem by gi s hi ta chn tn cho bn copy:
2. Tn tp hp tham s mi c nh vo l tutorial trong hp thoi hiu

chnh. Nhp OK. By gi ta s c th xem tp hp tham s mi ny m
t trong Registry nu ta mun.
Hiu chnh tham s TNDO

hiu chnh tp hp tutorial (t trn) ta lm nh sau:
1. Chn Select Parameter Set trong Setup menu v chn tp hp tham s
tutorial mi ca ta lm tp hp s dng.
2. Chn mt nguyn t cacbon ca etan v chn Edit Parameters trong Setup
menu.
3. Nhn nt Edit v nh vo gi tr mi cho Beta. Nhp vo OK. Th vi
cc gi tr khc ca beta v nh hng ca chng ln di lin kt C
C c ti u.
Ta nn c th cc gi tr beta b hn 21 xem ta c th ci tin di
lin kt C C t 1.457 A0 n gn vi 1.54A0. Ga tr CT cho beta vo
khong 16 s cho ta di lin kt tt hn nhiu.
244

4. Th vi eten. Ta s thy rng gi tr ngm nh cho beta 21 a n
di lin kt C=C l 1.310 A0 nh hn nhiu so vi 1.34 A0 c trng ca
lin kt i C=C.
5. Tham s beta CX mi khong 19 s cho di lin kt tt hn nhiu cho
eten.
Kt qu ca bi hc ny l ta s to ra c file tham s TNDO mi,
tutorial.abp, cha cc tham s beta mi cho lin kt n C-C sp3 sp2
(kiu CT-CT) v cho lin kt i C=C sp2-sp2 (kiu CX-CX). Ta by gi
c th th chng cho propen xem chng hot ng tt th no trong
tnh hung mi.
245
Ch gii
Glossary
Ab Initio. Hnh thc tnh ton c hc lng t trong mi obital c tnh l
tng ca mt tp hp cc hm hnh hc c bn (tp hm c bn). Bng cch tnh
ton s nh hng ca nhiu hm sng obital, cc tnh ton ab initio c th cho kt
qu rt chnh xc, phng php ny i hi nhiu phn a trng ghi v thi gian
tnh ton rt lu.
AM1. M hnh Austin. L phng php SCF, bn kinh nghim, dng cho tnh ton
ho hc. L mt trong cc phng php MOPAC [Stewart, J.J.P., J. Comp.-Aided
Molec. Thit k 4(1):1-108, 1990]. Phng php ny ci tin t phng php
MNDO. N c dng tnh cho cc phn t hu c c cha cc nguyn t kim
loi. Ni chung n l phng php bn kinh nghim chnh xc nht trong
HyperChem. Tnh ton cc thuc tnh in t, hnh hc ti u, nng lng ton
phn v nhit hnh thnh. Tham kho: Dewar, M.J.S., et at., J. Am. Chem. Soc. 107:
3902, 1985.
ALL atom. L mt phng php tnh ton c hc phn t trong mi nguyn t
c biu din nh mt ht ring bit. Tri ngc vi united atom.
AMBER. L phng php c hc phn t, hay cn gi l phng php trng
lc(force field), dng tnh ton ho hc. Phng php ny c thit lp tnh
ton cho cc protein v cc nucleic axit. Trng lc ny cung cp cho c hai hnh
thc tnh all atom v united atom. Tham kho: Weiner, S.J., et al., J. Comp.
Chem. 7:230-252, 1986.
Atom type. Kiu nguyn t biu din cc loi mi trng ho hc quy cho mi
nguyn t s dng trong tnh ton trng lc. Cc tnh cht ca mi trng gm c
s lai ho, in tch hnh thc v cc lin kt trc tip bn cnh. V d, kiu nguyn
t AMBER ca C biu din l mt cacbon cacbonyl sp2, kiu CT biu din l mt
cacbon t din, v kiu CH l s biu din nguyn t cacbon c lai ho sp3 cng
vi mt nguyn t hiro. Mi trng lc c mt tp hp cc kiu nguyn t khc
nhau. HyperChem c th quy kiu nguyn t cho mt h nguyn t bng vic dng
cc quy tc trong chem.rul.
Backbone (Lin kt khung). L mch lin kt cng ho tr lin tc trong mt phn
t. Vi polypeptide, lin kt khung bao gm tt c cc lin kt peptide, xen k gia
cc cacbon alpha cng vi cu ni isunfua. Vi polynucleotide, lin kt khung
bao gm tt cc cc lin kt photpho ieste, ln lt gia cc cacbon C3-C4 trong
phn t ng (ribo hoc deoxyribose).
246
Back end. Phn mm tnh ton HyperChem. HyperChem c thit k thnh cc

modul, vi phn mm front-end chy trn mt PC v phn mm back-end chy
trn cng PC hoc trn mt my tnh khc. Back-end gm c HyperNewton
(AMBER, BIO+, v OPLS), HyperMM+ (MM+), HyperGauss (Ab Initio),
HyperEHT (Extended Huckel), v HyperNDO (CNDO, INDO, MINDO/3, MNDO,
AM1, v PM3).
Bio+. B xung thm cho trng lc CHARMM (Chemistry at HARvard
Macromolecular Mechanics), do nhm Martin Karplus thuc trng i hc
Harvard pht trin ln. L phng php c hc phn t, cn gi l force field
(trng lc), dng cho tnh ton ho hc. Dng tnh ton cho cc phn t
protein. Tham kho: Brook, B.R., ET AL., J. Comp. Chem. 4:187-217, 1983;
Reiher, W.E., II, Theoretical Studies of Hydrogen Bonding, Ph. D. thesis, Harvard
University, 1985.
Bitmap. Bc nh mn lm vic to nn t tp hp cc im (dots). Bc nh c
phn gii nh trn mn hnh.
Brookhaven Protein Data Bank (PDB). L d liu v cc cu trc ca protein v
cc nucleic axit. Thng tin v mi cu trc phn t gm c to nguyn t, kh
nng lin kt ca nguyn t v nhng vn lin quan khc. HyperChem c th
c v gii thch tt c cc file PDF cng vi nhng thng tin v to hoc kh
nng lin kt ca nguyn t. Cc file PDF c ui m rng l .ent.
Charge density. S phn b mt in tch electron trong phn t. Hnh dng
ca phn t thng kt hp vi b mt in tch c mt khng i. HyperChem
tnh ton mt in tch bng tng ca cc mt obital phn t, l tng bnh
phng ca cc hm sng obital.
Clipboard. Vng nh tm thi cho d liu v th do Window cung cp. Lnh
Cut v Copy trong HyperChem s t mt m t dng vn bn vo trong b nh
tm thi. Copy nh trong HyperChem s t hnh nh vo trong b nh tm thi. Ta
c th xem nhng g c trong b nh tm thi bng cch s dng trnh Clipboard
trong nhm trnh ng dng chnh ca Window.
Click. Nhn v gii phng nt chut mt cch nhanh chng.
Clipping. Biu din mt phn trong h phn t trn mn lm vic (Workspace)
ca HyperChem. Giu nhng nguyn t cn cnh v cc nguyn t pha sau khng
cn thit v th ta c th tp trung vo vng cn quan tm. Phn quan tm c gi
247

l clipping slab. y l hp thoi hnh ch nht c th iu chnh chiu su, chiu
cao v chiu rng bng chiu cao v chiu rng mn lm vic ca HyperChem.
Xem clipping planes.
Clipping planes. Cc bin trc v sau ca mt mt ct, c th iu chnh ring t
0 A0 n mt s no theo Angstrom tu theo kch c v phng i ca h
phn t.
Clipping slab. Phn hnh ch nht trong mt h phn t c gii hn bi hai mt
phng ct c th iu chnh c.
Closed-shell. Phn t khng c cc electron k i.
CNDO. Hon ton b qua xen ph vi phn (xem NDO). y l phng php SCF
n gin nht trong cc phng php tnh ton c hc lng t bn kinh nghim.
N thch hp cho tnh ton thuc tnh in t trng thi c bn cc h v kn v
v h, ti u hnh hc v tnh ton nng lng ton phn. HyperChem s dng
CNDO/2. Tham kho: Pople, J.A. and Beveridge, DL., Approximate Molecular
Orbital Theory, McGraw-Hill, 1970.
Connectivity. Thng tin v s hnh thnh lin kt cng ho tr ca nguyn t vi
cc nguyn t ln cn. File PDF c th cha cc thng tin ny trong cc tp
CONECT. Cc file HIN c cha cc thng tin ny cui cc tp ghi nguyn t,
trong dng <nbor#nbor-bonds>.
Constraint. Cng bc gi tr ca Model Build (trnh xy dng) ph hp vi
ca cc cu trc thc khi xy dng cu trc 3D gn ng.
Convergence. Tiu chun kt thc mt tnh ton ho hc. Tnh ton c hc SCF
bn kinh nghim hi t (kt thc) khi s khc nhau v nng lng sau hai ln lp
li lin tip b hn gii hn hi t (ngm nh l 0.01kcal/mol) hoc tnh ton t
n gii hn lp (ngm nh l 50). Vi tnh ton ti u hnh hc phn t, gii hn
hi t l s vng tnh ton (s ngm nh bng 15 ln s nguyn t) hoc l
gradient RMS ca h phn t (ngm nh 0.1 kcal/Angstrom mol).
Coordinate system. Khng gian ba chiu (3D) cha cc to Decac x, y v z ca
mi nguyn t trong h. HyperChem c h to ca ngi quan st v h to
ca phn t. T h ta ca ngi quan st ta c th dch chuyn, quay h phn t
n v tr quan st thch hp. Quay v dch chuyn theo h to phn t s lm
thay i v tr ring ca cc nguyn t.
248

Correlation Energy. Nng lng m phng php Hartree-Fock m t nng lng
c c t s tng tc theo v tr c th ca cc electron, ch khng phi l t v
tr trung bnh ca chng. Cc tnh ton Ab initio c th tnh ton nng lng tng
tc theo thuyt Moller-Plesset bc hai (MP2). Thuyt hm mt (DFT) s l nng
lng tng tc theo thuyt trng t hp cng vi cc phng trnh (Cc phng
trnh Kohn-Sham) tng t nh cc phng trnh Hartree-Fock. Cc phng trnh
Kohn-Sham i hi mt hm trao i v mt hm tng quan (tng tc qua li).
Chng chuyn thnh thuyt Hartree-Fock khi hm trao i l hm Hartree-Fock v
hm tng quan coi nh b b qua.
CPK. Cc k t u ca Corey-Pauling-Koltun; quy cho tp hp nguyn t ph
bin radii dng miu t khng gian nhiu hnh nh hay xy dng cc m
hnh cht do.
Cursor keys. (Phm tr chut) l cc phm
. S dng ring tng
phm ny, cng vi phm Shift, hoc kt hp vi phm Ctrl+Shift quay hoc dch
chuyn cc phn t trn mn lm vic (Workspace).
Cursor. im tr chut hoc cng c trn mn hnh m ta dch chuyn khi dng
chut. S dng im tr chut chn cc mc t cc menu, dng v v dch
chuyn cc phn t, dng thc hin cc la chn trong hp thoi v hiu
chnh.
Cycle. Trong qu trnh ti u hnh hc (Geometry optimization), s vng (cycle)
ch ra s ln tnh ton trn mt th nng xc nh im cc tiu. Mi vng c
mt hoc nhiu im, dng tnh ton nhm c lng nng lng v gradient
trong qu trnh tnh ton. HyperChem cho bit s vng v s im tnh ton trn
dng hin trng.
DDE. Trao i d liu ng lc hc. Mt h dng trao i d liu gia
HyperChem v cc ng dng Window khc. HyperChem th hin nh mt trnh
phc v (server): n cung cp thng tin ch khi mt trnh ng dng khch (client)
yu cu d liu ring.
Default element. Nguyn t cng c v ca HyperChem dng xy dng cc
phn t. N c th ch l mt nguyn t ngm nh thi im no , v ta c th
thay i n khi cn thit.
Density functional. S ph thuc ca nng lng vo mt hm (mt electron).
Cc hm khc nhau m t s ph thuc khc nhau vo mt electron. Thuyt hm
249

mt m t phng php tnh ton nng lng tp trung vo mt electron ch
khng phi vo hm sng.
Desktop. Mn biu din Microsoft Window dng biu din cc ca s v cc
biu tng.
Dialog box. Kiu ca s dng chp nhn thng tin hoc biu din thng tin. S
biu din cc hp thoi lm cn tr cc chc nng khc ca HyperChem. Ta phi
ng cc hp thoi ny HyperChem hot ng tr li. Cc hp thoi lin tc (v
d: hp thoi Amino Axit) khng lm cn tr cc chc nng ca HyperChem.
Dielectric constant. H s (epsilon) dng hiu chnh cc tng tc trong qu
trnh tnh ton c hc phn t. Khi thiu dung mi, hng s in mi ph thuc
khong cch tc l hng s in mi c gi tr ln hn 1 m phng s c mt
ca dung mi. Khi biu din dung mi, nh l trong hp tun hon hyrat ho,
hng s in mi l mt hng s ch ph thuc vo khong cch. Hng s in
mi, epsilon = (hng s in mi trong khng gian t do)x((h s t l). Vi hng
in mi ph thuc khong cch, epsilon = (hng s in mi trong khng gian t
do)x(h s t l)x(h s phn ly gia cc nguyn t). Xem electrostatic potential.
Drag. Dch chuyn mt vt th trn mn hnh bng cch gi mt nt chut trong
khi ch chuyn chut. Cc vt th c th l cc phn t hoc cc mc trong mt
menu. Khi ta hon thnh qu trnh chuyn, gii phng nt chut. V d: ta c th
dch chuyn mt phn t c chn bng cch r (drag) cng c dch chuyn trn
mn lm vic ca HyperChem trong qu trnh ta phi gi nt phi chut. Ta c
th gi nt tri chut v dch chuyn n biu tng no trn menu mun chn.
Gii phng nt chut chn biu tng .
Dynamic Data Exchange. Xem DDE.
Electrostatic potential. Th nng mi im trong khng gian xut hin do s
phn b ca cc nguyn t tch in. Th tnh in )U) khong cch r so vi in
tch im c xc nh theo nh lut Coulomb: U = Cq/(r), y C l hng s
(ph thuc vo cc n v) v l hng s in mi (hay epsilon). Vi nhiu in
tch trong khng gian 3D (k c cc in tch ht nhn v cc electron trong cc
obital phn t), phng trnh ny tr thnh h phc tp. HyperChem tnh ton th
tnh in nh th nng ca mt n v in tch dng tng tc vi h phn t.
Trong qu trnh tnh ton tng tc vi cc electron trong cc obtal phn t,
HyperChem b qua cc hp phn tu thuc vo s xen ph vi phn gia cc
nguyn t (xem NDO). HyperChem tnh ton v v biu th tnh in t cc kt
250

qu tnh ton im n, tnh ton c hc lng t bn kinh nghim. Ta c th s
dng cc kt qu ny d on v tr tn cng ca cc proton v cc ion khc
trong qu trnh phn ng.
Exchange Functional. S ph thuc ca nng lng trao i vo mt electron.
Cch thc lin h mt electron l nng lng trao i. Thuyt hm mt
xut phng php tnh nng lng trao i v nng lng tng quan t mt
electron.
Explicit hydrogens. Khi Explicit hydrogent hot ng trong qu trnh v,
HyperChem mong mun tt c cc nguyn t hydro c v. Cc nguyn t ch vi
mt lin kt c v l hydro ch khng nh default element. iu ny tri ngc
vi vic thm cc nguyn t hydro bng Model Builder sau khi cc nguyn t nng
hn c v.
Force constant. S hng trong mi phng trnh ca mt trng lc l s chuyn
cc d liu t to nguyn t thnh gi tr th nng. V d, nng lng cng lin
kt: Ebond = K r (r r0 ) 2 , y E l th nng, r l di lin kt, r0 l di lin
bonds
kt trng thi cn bng (strain-free), v Kr l hng s lc. Vi mi trng lc,

mt hay nhiu tp hp tham s xc nh cc hng s lc v cc hnh hc cn bng
(v d, r0).
Force field. L phng php c hc phn t dng tnh ton ho hc. Cc tnh
ton ny c th l tnh im n, ti u hnh hc, hay ng lc hc phn t.
HyperChem cung cp bn trng lc: MM+, AMBER, BIO+ v OPLS. Mi trng
lc c ba thnh phn: cc phng trnh xc nh th nng ca mt h phn t l
hm to ca cc nguyn t, cc kiu nguyn t (atom types) v cc tp tham s
ph hp cho cc phng trnh ly t d liu thc nghim. Xem u vo khc nhau
gia atom type v parameter set.
Front end. Xem back end.
Geometry optimization. L mt tnh ton, dng cho c phng php c hc phn
t ln c hc lng t, tm cu hnh c nng lng cc tiu (bn vng) ca mt
h phn t. Tnh ton iu chnh cc to nguyn t tng bc tm mt cu
hnh trong cc tc ng thc ln mi nguyn t c gim n khng. y
thng l mt cc tiu a phng local minimum) trn mt th, khng nht thit
phi l cc tiu ton phn (global minimum).
Global minimum. Cu hnh ca mt h phn t c th nng thp nht.
251
Gradient. Tc bin i (xut pht im u tin) ca nng lng mt h phn

t, l hm cc v tr ca nguyn t. bin thin (gradient) bng khng cho bit
cu hnh vi nng lng cc tiu l cc tiu a phng hay cc tiu ton phn
hoc l trng thi chuyn tip. Khi HyperChem bo mt gi tr n ca Gradient,
l RMS gradient ca cc lc trong ton b cc nguyn t.
Ground state. Trng thi in t c nng lng thp nht. Xem lowest state.
Group selection. Mt la chn mt tp hp con cc nguyn t, cc hp phn hoc
cc phn t trong mt h phn t. La chn cc nguyn t, cc hp phn hay cc
phn t trong Select menu hiu chnh mc nhm la chn. Cng vi cng c
la chn ng hot ng, ta la chn nhm bng cch r mt ng bin bao
quanh cc cu trc phn t mun chn, kt hp vi vic nhn ng thi c nt tri
v nt phi chut (nhn nt tri trc nt phi). La chn cu (Select Sphere) trong
Select menu nhm vo qu trnh la chn nhm 2D hay 3D. La chn 2D bao
gm tt c cc nguyn t nh ra trong mt hnh ch nht hai chiu c chn. La
chn 3D bao gm tt c cc nguyn t trong mt hnh cu ly tm trn mt nguyn
t.
HIN. File u vo ca HyperChem. y l kiu file c bn HyperChem dng
lu cc h phn t. cc file c phn m rng l .hin.
HOMO. Obital phn t nh c c nng lng cao nht. iu ny cho bit tt c
cc obital phn t khc u c v tr di obital ny trong biu nng lng.
Cc obital phn t l t hp tuyn tnh ca cc obital nguyn t (LCAO).
Huckel method. Phng php n gin v gn ng dng cho cc tnh ton c hc
lng t bn kinh nghim. Phng php Huckel m rng dng trong HyperChem
ch c tc dng cho tnh ton im n (single point), khng dng ti u hnh
hc hoc tnh ton ng lc hc phn t. Cc tnh ton Huckel m rng cho nhng
m t nh tnh hoc bn nh lng cc obital phn t v thuc tnh ca in t (v
d, in tch thc ca nguyn t v phn b spin). y khng phi l phng php
trng t hp (Self-Consistent Field: SCF). Tham kho: Hoffman, R., J. Chem.
Phys. 39(6):1397-1412, 1963.
Icon. Biu tng hnh hc nh biu din mt cng c hay mt chng trnh ng
dng.
INDO. Gin tip b qua xen ph vi phn (xem NDO). L phng php SCF dng
tnh ton c hc lng t bn kinh nghim. N ci tin t CNDO bng cch tnh
252

ton cc tng tc y mt tm c th gia cc electron trong cng nguyn t.
Dng cho tnh ton cc thuc tnh in t trng thi c bn ca cc h v h v
v kn, ti u hnh hc v tnh ton nng lng ton phn. Tham kho: Pople, J. A.
and Beveridge, D.L., Approximate Molecular Orbital Theory, McGraw-Hill, 1970.
Improper torsion. Gc vn (gc nh din) khng c hnh thnh do s ni tip
ca ba lin kt. Mt s trng lc c hc phn t dng cc gc nh th trong cc s
hng nng lng duy tr mt phng hoc ngn s nghch chuyn ca cc
carbon t din c mt hydrogen biu din kiu nguyn t lin kt (united atom).
Inertial axes. (Trc qun tnh) c ba trc (trc th nht, th hai v th ba) kt hp
vi cc momen qun tnh ca mt h phn t hay mt h con c chn. Cc trc
l cc hm v tr v khi lng ca nguyn t. chng ph thuc vo h v khng
ph thuc vo h to phn t hay h to ca ngi quan st. Trc qun tnh
th nht thng biu th di nht qua h phn t, trc th ba thng biu din
di ngn nht.
Isosurface. (ng mt) Mt ba chiu biu din trong khng gian ba chiu, tnh
cht c nh ngha theo gi tr cho trc; n nh l lp da ca mt vt th rn. V
d, i vi hm ton hc s = x2 + y2 + z2, biu ng mt (isosurface plot) vi s =
1 s l mt mt cu vi bn knh l 1; cc biu ng mt vi cc gi tr khc ca
s s l cc mt cu vi cc kch c khc nhau.
Interation. Trong mt phng php c hc lng t SCF, mi tnh ton cc obital
phn t bt u cng s phng on v kiu ca cc obital. Mi th nghim (hay
interaction: s lp li) lc ra s phng on cho th nghim tip theo. Khi s khc
nhau gia hai ln lp li lin tip b hn gii hn hi t (do ta t), th tnh ton
SCF i n hi t (convergence).
Label. Thng tin v cc hp phn ca mt h phn t HyperChem c th biu din
cng h. Nhn (Label) cng c p dng cho nguyn t hay cc phn d
(residue). Nhn nguyn t l Symbol (biu tng) (ho hc), Name (tn) (theo file
PDB thch hp), Number (s ca v tr ni), Type (Atom type), Basis Set, Mass,
Charge, hay Chirality (R hay S). Nhn Residue l Name, Sequence, hay
Name+Sequence. HyperChem gn cc nhn cho la chn hin hnh.
LINE. Gii hn trc, Named selection nhn bit cc nguyn t trong phn la
chn, cng vi trc qun tnh chnh ca cc nguyn t c chn. (Trc qun tnh
chnh tng ng vi gi tr c trng nh nht ca moment ma trn qun tnh.) Mt
h phn t c th ch c mt la chn LINE ring bit.
253

Local minimum. Mt cc tiu trn mt nng lng i vi h phn t biu din
cu hnh th nng thp. Cc mt nng lng phn t c th c nhiu cc tiu a
phng (local minimum), cc tiu a phng nh nht l global minimum (cc
tiu ton phn). Cc tnh ton Geometry optimization c th a n mt cu trc
cc tiu a phng.
Log. Mt file cha kt qu tnh ton ho hc v nhng li ch gii. HyperChem t
ng tp hp nhng thng tin ny nu ta chn Start Log trong Menu File (xem
Start Log). Tn file (filename) ngm nh l chem.log v file thng c phn m
rng l .log.
Lowest state. Trng thi in t thp nht ca bi spin ring bit; nht thit
khng phi l ground state.
LUMO. Orbital phn t khng nh c thp nht. iu ny c dng nh mt
im ch dn miu t v tr ca bt k orbital phn t no bng hay trn orbital
ny. Cc orbital phn t l mt t hp tuyn tnh ca cc orbital nguyn t
(LCAO).
Metafile. Hnh nh bao gm cc lnh v. S chuyn mt hnh metafile khng ph
thuc vo mn hnh (monitor), v l s chuyn ca thit b u ra. V d, nu ta in
mt metafile bng my in laser, s chuyn l 300 dpi.
MINDO/3. B qua c mc cc xen ph vi phn trung gian, phin bn 3. y l
mt phng php SCF ca tnh ton c hc lng t bn kinh nghim. M rng t
INDO, MINDO/3 dng cc tham s thch hp cho kt qu thc nghim, thay v tnh
ton chnh xc. Dng cho cc phn t hu c ln, cation, v cc hp cht polynitro.
Tnh ton cc thuc tnh in t, ti u hnh hc v nng lng ton phn. Tham
kho: Dewar, M.J.S. et al., J. Am. Chem. Soc. 97: 1285, 1975.
MM+. Phng php chung nht i vi cc tnh ton c hc phn t, pht trin cho
cc phn t hu c. y l mt trng lc all atom. MM+ da trn cc hm MM2
(77), tc gi l Dr. Norman Allinger thuc i hc Georgia. HyperChem n nh
cc kiu nguyn t v cc tham s khng c gi tr thng thng l MM2, m rng
phm vi ca cc hp cht ho hc m trng lc ny c th thch nghi. MM+ m
rng MM2 cho php cc la chn nh l cc iu kin bin tun hon v ng
lc hc phn t chung vi cc trng lc khc. Tham kho: Allinger, N.L., J. Am.
Chem. Soc. 99:8127-8134, 1977.
254

MNDO. Gim bt s b qua xen ph hai nguyn t. y l phng php SCF i
vi cc tnh ton c hc lng t bn kinh nghim. Dng cho cc hp cht hu c
khc nhau cha cc nguyn t t dng 1 v 2 ca bng h thng tun hon, tr kim
loi chuyn tip. Loi b mt s li trong MINDO/3. Tnh ton cc thuc tnh in
t, ti u hnh hc, nng lng ton phn, v nhit hnh thnh. Tham kho: Dewar,
M.J.S. v Theil, W., J. Am. Chem. Soc. 99:4899, 1977.
Model Builder. Trnh thun tin trong HyperChem dng dng m hnh 3D ca
cc cu trc ho hc t hnh v 2D. HyperChem dng cc quy tc gn lin quy
nh di lin kt, gc lin kt, gc xon v ho lp th chun. Trnh xy dng
(Model Builder) cng quy nh kiu nguyn t i vi force field ang hot ng,
v c th t ng thm cc nguyn t hydrogen tho mn ho tr cn thit. C cc
cu trc gn ng v c th cn lc bng geometry optimization.
Moleculer dynamics. Tnh ton m phng chuyn ng ca mi nguyn t trong
h phn t nng lng c nh, nhit c nh, hay vi s bin i nhit c
iu khin. Kt qu tnh ton ng lc hc phn t c gi l trajectory (qu
o). HyperChem c th dng c hc phn t hay phng php c hc lng t bn
kinh nghim tnh qu o ng lc hc phn t. Ta c th dng tnh ton ny
nhn c mt s ln cc tnh cht v cu trc v tnh cht v nhit ng lc hc,
bao gm ln lt cc local minimum, nng lng khc nhau gia cc cu hnh
khc nhau, v c ch cng nh ng phn ng.
Molecular mechanics. Cc phng php khc nhau tnh ton th nng ca cc
h phn t nh hm to ca cc ht nhn nguyn t, b qua x l cc electron.
Tc ng ca in t c ngm nh trong cc kiu hm gii tch v qu trnh
tham s ho. Tt c cc phng php dng d liu kinh nghim xc nh cc
hng s lc ring (v d, cc hng s cng lin kt) v thng bng (cng t do
strain-free) cc gi tr i vi mi i lng hnh hc (v d, di lin kt).
HyperChem cung cp cc phng php sau: MM+, AMBER, BIO+ v OPLS.
Multiplicity. bi spin ton phn l 2S + 1, y S l tng spin electron ca h.
Mi electron khng cp i tnh c spin l +1/2. Cc electron cp i c spin thc
l khng (+1/2 -1/2 = 0). Mt h v kn (closed-shell) c bi l 1 (singlet
mc n). Mt h v h (open-shell) c th c bi l 2, 3, 4 (doublet, triplet,
quartet tng ng), hay cao hn. Dng cc gi tr nguyn t 1 n 6 trong
HyperChem.
Named selection. Mt tp hp cc nguyn t c n nh tn, nh gii hn
(POINT, LINE, hay PLANE) hay tn khc di n 19 k t. Ta c th dng cc
phn la chn c t tn lp li phn la chn hay chuyn n nhng qu
255

trnh c bit (v d, nghch chuyn-inversion, phn chiu-reflection, quay-rotation,
tnh trung bnh-averaging v v th trong ng lc hc phn t, hay t kim ch
(restraints) trong tnh ton).
NDO. B qua xen ph vi phn. i vi cc tnh ton c hc lng t bn kinh
nghim, y l s n gin ho loi tr nhiu tch phn m t tng tc ca cc
electron. Phng php CNDO b qua vic tnh ton tt c cc tch phn xen ph vi
phn. Cc phng php NDO khc (INDO, MNDO/3, MNDO v AM1) b qua mt
s tch phn.
Open shell. Mt h phn t cha cc electron cha kt i.
OPLS. Cc th c ti u ho i vi cc m phng cht lng. Mt phng php
c hc phn t, hay force field, tnh ton ho hc. Pht trin cho cc protein v
nucleic acid. N tng t AMBER nhng xem xt cc tng tc khng lin kt
chnh xc hn. Trng lc ny ch cung cp cho miu t united atom (nguyn t
lin kt).
Orbital. Hm m t s phn b trong khng gian ca mt electron. Cc orbital
nguyn t m t cc electron trong cc nguyn t. Orbital phn t, bt ngun l s
t hp tuyn tnh ca cc orbital nguyn t (LCAO), m t cc electron trong phn
t.
Parameter set. i vi cc trng lc c hc phn t, kinh nghim hay l thuyt
nhn c t cc hng s lc v cc gi tr cu trc p dng cho cc t hp lin kt
xc nh ca cc nguyn t (mi m t bng mt atom type). Mi trng lc c
th c nhiu hn mt tp hp tham s, nhng ta c th ch dng mt tp hp ring
bit. Vi MM+, HyperChem cung cp cc tham s khi chng khng c sn trong
tp tham s MM2.
Vi cc tnh ton bn kinh nghim, cc file tham s (c phn m rng l .abp) cha
cc gi tr kinh nghim cho cc tch phn trong tnh ton.
PDB. Xem Brookhaven Protein Data Bank.
Periodic box/ boundary conditions. Hp tun hon l mt hnh lp phng bao
quanh h phn t. HyperChem thm cc phn t nc chun (TIP3P, cn bng
300K v 1 atmosphere) hp, cung cp mt hng s t trng dung mi. Trong cc
tnh ton c hc phn t, hp c xem nh l c bao quanh bng 26 hp ging
ht nhau (hnh nh), mi hp cha cc phn t ging ht nhau. Cc nguyn t trong
mi hnh chu cng cc lc (biu l cc chuyn ng nh nhau) nh cc phn t
256

trong hp trung tm. Nu trong qu trnh tnh ton, cc phn t chuyn ng ra
ngoi hp, mt ht ging ht vo t hp ln cn. Cc iu kin bin tun hon
ny m phng mt h lin tc vi mt hng t trng ca cc phn t. Ta c th tch
loi cc phn t nc, nhng gi nguyn hp tun hon v cc iu kin bin, m
phng mng tinh th.
Vi cc iu kin bin tun hon ca HyperChem, mt nguyn t ch tng tc vi
hnh nh gn nht ca cc nguyn t khc v khng bao gi vi hnh nh ca chnh
n trong cc tnh ton c hc phn t.
PLANE. Xc nh trc, named selection ng nht cc nguyn t trong phn la
chn, cng vi mt phng hnh thnh bi trc qun tnh th nht v th hai ca cc
nguyn t c chn. Mt h phn t c th ch c mt la chn PLANE ring
bit.
Potential (energy) surface. Mt biu nhiu chiu ca th nng mt h phn t
l hm ca tt c cc bin s (cc t do) trong h (v d, cc gc lin kt). Mt
th nng ca phn t khng thng c N nguyn t (ln hn 2) c 3N 6 t do
c lp (6 = ba duy tr s quay v ba cho s chuyn dch ca ton b h phn
t). Cc mt th nng thng c v biu ch trong mt hoc hai chiu. Mt th
1D biu din nng lng lin kt theo di. Mt th 2D biu din biu ng
vin nng lng l hm ca hai gc xon. Nhng nt quan trng trong mt th nng
l cc cc tiu vi HyperChem c th nh v bng ti u hnh hc v cc tnh
ton ng lc hc phn t - v cc im yn nga, biu din cu trc cc trng thi
chuyn tip.
Quantum mechanics. Thuyt nng lng c hp th hay pht x trong cc phn
ri rc, gi l cc lng t. Kt qu l cc electron di chuyn trong mt s orbital
gii hn quanh ht nhn nguyn t, v mi orbital c trng bng mt nng lng
xc nh. S chuyn ng ca cc electron c tnh cht ca ht v sng. Phng
trnh Schrodinger v cc o hm ca n m t hon ton hot ng ca cc
electron v ht nhn, v do tc ng ca cc hp cht ho hc.
Cc tnh ton bn kinh nghim trong HyperChem tha nhn cc ht nhn ng yn
v gii gn ng phng trnh Schrodinger, cng vi d liu kinh nghim (cc tham
s), d on tnh cht ca cc electron ca h phn t.
Cc tnh ton ab initio ca HyperChem gii cc phng trnh Roothaan (xem
computationa Chemistry ) m khng c s gn ng no thm ngoi vic dng mt
tp hm hn ch xc nh. Chng bao gm nhiu hm gn ng vi li gii phng
trnh Schrodinger hn cc phng php bn kinh nghim.
257
Rendering. Biu din kiu nhn mt h phn t di cc hnh thc. Phin bn

HyperChem ny cung cp nm kiu: Sticks, Disks, Spheres (CDK kiu m
hnh), Dots, v Sticks & Dots.
RHF. Thuyt Hartree-Fock gii hn. Biu din hm sng cng vi cc electron c
spin cp i (hng ln v hng xung) hn ch c ng cc orbital phn t cng
khng gian. Mi orbital khng gian c th cng cha cc electron n (spin hng
ln hay spin hng xung).
RMS gradient. Gradient ( dc) nng lng ton phn c tnh bng gi tr cn
bc hai bnh phng trung bnh. Gradient (G) l tc bin thin (o hm u
tin) nng lng ton phn (E) xem xt n s chuyn di ca mi nguyn t theo
cc hng x, y v z. T nguyn t 1 n n,
GRMS
2
2
2
1 n E E E
=
+ +
3n i =1 xi yi zi
n v l kcal/mol Angstrom. HyperChem bo gi tr ny cho tnh ton geometry

optimization v single point. Gradient RMS l khng c ngha cu trc mt
local minimum hay im yn nga trong mt th nng, khng nht thit cu trc
v trng thi nng lng thp nht (global minimum).
Restraint. Restraint tnh ton mnh cng vi hon li cc lc cho cc nguyn t
c chn. Kim ch (restraint) p dng cho khong cch nguyn t (mt hoc hai
nguyn t), gc lin kt (ba nguyn t), v gc xon (bn nguyn t).
Scale to fit. Mt mc trong Display menu (biu din) ly t l cc nguyn t v
phn t nhn thy thch va vi workspace (mn lm vic). Nu c phn la chn,
cc nguyn t c chn c chim y mn lm vic. Khng c phn la chn,
HyperChem t ton b h phn t va vi mn lm vic.
SCF. Trng t hp (Self-Consistent Field). y l mt phng php lp, dng
trong tt c cc phng php tnh ton c hc lng t NDO, semi-empirical. N
gii thch nng lng y ca electron trong cc li gii phng trnh Schrodinger.
Phng php SCF hay Hartree-Fock n gin ho bi ton ny bng vic tha nhn
s chuyn ng ca cc electron l c lp v mt electron tng tc vi mt
trng trung bnh ca cc electron khc trong phn t. Trong HyperChem, tt c
cc phng php c hc lng t bn kinh nghim, ngoi tr phng php Huckel
m rng, u l cc phng php SCF.
258
Mt tnh ton SCF bt u bng vic c lng hm sng m t cc orbital electron

v cc tng tc y electron. Da trn c on ny, HyperChem tnh ton mt
hm sng mi v so snh kt qu vi kt qu c on. HyperChem lp li qu
trnh ny cho n khi gi tr c on v kt qu hi t tr thnh t hp. Mi s
lp li ci tin cc orbital cho n khi kt qu t n gii hn hi t
(convergence).
Script. Mt tp hp cc d liu, lu trong mt file vi phn m rng l .scr,
chy HyperChem. Tng t nh mt chng trnh ln p dng. HyperChem vit
tp hp hay c cc bin s, truyn cc lnh, v lm hot ng cc mc menu.
Dng mt trnh thu thp ch to ra file script, sau dng menu Script trong
HyperChem chy mt Script.
Self-consistent field method. Xem SCF.
Semi-empirical. Kiu tnh ton ho c hc lng t dng cc tham s xut pht t
thc nghim n gin ho qu trnh tnh ton.
Single point. Mt tnh ton xc nh nng lng ton phn (theo kcal/mol) v
gradient ca mt h phn t hay ca cc nguyn t c chn. Bng phng php
c hc lng t, tnh ton im n cng xc nh s phn b electron (in tch)
trong h. Tnh ton ch biu din cu hnh phn t hin ti, mt im n trn mt
th i vi h phn t.
Snapshot. Ghi im n theo thi gian trong mt m phng molecular dynamic.
Ta c th ch th HyperChem thc hin chp nh nhanh (snapshot) cc khong
thi gian khng i trong qu trnh m phng. To v vn tc i vi mt h
phn t c lu trong cc file SNP. Ta c th biu din li sau cc nh chp
nhanh xem s bin thin cu hnh ca h, v biu cc gi tr d liu, v tnh
trung bnh cc gi tr d liu. D liu chn bin s (nh l nng lng ton phn
hay gc xon) c lu trong file CSV.
Spin density. Kh nng tm thy nhiu electron c spin hng ln hn cc electron
c spin hng xung mt im trong khng gian. i vi h v kn, mt spin
(spin density) l bng khng mi im. HyperChem c th v biu mt
spin ton phn cho mt h phn t sau khi thc hin tnh im n, tnh ton c
hc lng t bn kinh nghim hay ab initio. Ta c th dng cc biu mt
spin ht nhn d on kt qu ph cng hng spin electron (ESR). Xem Spin
pairing v multiplicity.
259

Spin multiplicity. Xem multiplicity.
Spin pairing. Hai electron c ng cng orbital phi c cp i v c cc spin i
nhau, mt spin hng ln v mt spin hng xung. Cc h v knh ch cha cc
electron kt i. Cc h v h cha cc electron khng kt i.
Status line. Dng y ca s HyperChem biu din thng tin v d liu.
3D surface. Xem isosurface.
Tool. Con tr thc hin cc nhim v, nh l v hay dch chuyn, trong
workspace ca HyperChem. Biu tng cng c (Tool icon) trong mt ct hay
mt hng v tr bn trn hay bn tri ca s HyperChem. Nhp tri chut (Lclick) vo biu tng cng c chuyn tr chut thnh cng c.
Trajectory. Lch s ca chuyn ng nguyn t theo thi gian. Thut ng ny
thng c p dng cho m phng ng lc hc phn t (molecular
dynamics). C th lu c trong file snapshot.
Translation. Dch chuyn phn t m khng quay.
Type rules. Quy tc i vi mi force field, tm trong file chem.rul (hay ng
lng nh phn ca n, typerule.bin), n nh kiu nguyn t cho cc nguyn t
hay nhm nguyn t ring.
UHF. Phng php Hartree-Fock khng gii hn. Biu din hm sng cung cp
cc orbital khng gian tch ri vi cc electron c spin hng ln () v spin hng
xung (). Mi orbital v c th khng cha hoc cha mt electron. Ta c th
dng cc tnh ton UHF tnh ton cc phn ng phn tch ca cc h v h.
United atom. S n gin ho force field xem xt cc nhm nguyn t c th (cc
nguyn t nng nh C v N v cc lin kt hydrogen ca chng) l mt nguyn t
n. T hp nguyn t (united atom) i hi x l cc kiu nguyn t kt hp cc
tnh cht ca cc nguyn t hp phn v cc kiu quy tc bng s ch nh cc kiu
ny. Biu din t hp nguyn t l cc la chn vi AMBER v MM+, t ng quy
cho nhiu nguyn t vi OPLS, v biu din ngm nh cho BIO+. Thut ng khc
i vi t hp nguyn t l nguyn t m rng. Ln lt cho cc t hp l all
atom, biu din mi nguyn t tch ring, vi atom type ring.
Wave function. Xem orbital.
260
Window. Vng lm vic trn mn hnh cha chng trnh phn mm (nh l
HyperChem). Mt ca s c mt thanh tiu trn nh, cha tn ca chng
trnh. Ch mt ca s c th hot ng mi thi im. Ca s hot ng nhn d
liu u vo t chut v bn phm. Mt hp thoi l mt kiu ca s.
Workspace. Vng ca s cha d liu; vi HyperChem, l mt h phn t.
Z Clipping. Xem clipping.
Zoom. Hm HyperChem phng to hay thu nh kch c h phn t trong mn lm
vic.
Zwitterion. Mt phn t c cc vng tnh in m v in dng hnh thc. y l
trng thi bnh thng ca polypeptide pH trung tnh trong dung dch, vi cc
nhm tn cng lNH3+ v -COO-. Polypeptide c xy dng t d liu
HyperChem cha hon thnh, on cui khng tch in (-N-H v -C-O), tr phi
cc nhm tn cng c s dng.
261
Bi 1 Bt u s dng phn mm.........................................................................1

Thanh tiu (title bar) .....................................................................................1
Thanh cng c la chn (menu bar) ..................................................................1
Thanh biu tng cng c (tool bar)..................................................................1
Mn lm vic (workspace) .................................................................................1
Dng hin trng tnh ton (status line) ..............................................................2
Tr gip (help) ...................................................................................................2
Cch s dng chut:...........................................................................................2
S dng bn phm...............................................................................................2
Cc phm tt khc: .............................................................................................3
Cc cng c quan trng trn thanh cng c.......................................................3
Cc thao tc trn HyperChem ................................................................................4
M mt file v d: V d m file c ui HIN...................................................4
Cch s dng Display Settings...............................................................................6
S dng nhn (Labels) .......................................................................................6
Hnh thc biu din phn t:..............................................................................8
Thay i hnh thc biu din: ............................................................................8
t mu nn trang lm vic ...................................................................................9
t mu sc lin kt trong phn t ......................................................................10
Mu sc ca nguyn t.........................................................................................11
t ch Copy hnh nh....................................................................................12
Thot khi HyperChem....................................................................................15
Bi 2. V v hiu chnh
16
V nguyn t v lin kt ......................................................................................16
Chn nguyn t (Selecting Atoms) ......................................................................18
Chn nguyn t ....................................................................................................20
Chn nhm nguyn t..........................................................................................21
Chn thm mt nhm nguyn t..........................................................................21
Chn cc hp phn (Residures) ...........................................................................21
Chn c phn t (Molecules) ...............................................................................22
Loi b la chn...................................................................................................23
Mu sc biu din khi la chn ...........................................................................23
Chn phn b (Complement Selection) ...............................................................24
Chn theo chui (String) ......................................................................................26
Chn theo s.........................................................................................................26
Tn phn la chn (Name Selection) ...................................................................26
Xo nguyn t ......................................................................................................27
Xo nhiu nguyn t ........................................................................................27
Copy nguyn t vo b nh tm thi (Clipboard)................................................28
t in tch hnh thc cho nguyn t trong h...................................................28
262

t in tch thc.................................................................................................29
t khi lng nguyn t ....................................................................................29
t di lin kt................................................................................................29
t xon lin kt ..................................................................................................30
t nhn ring......................................................................................................30
t kiu nguyn t (Atom Type) .........................................................................30
Thay i cc thuc tnh hnh hc.........................................................................30
Cng bc hnh hc .............................................................................................30
Cng bc di lin kt ....................................................................................32
Cng bc gc lin kt ........................................................................................32
Cng bc lin kt xon ......................................................................................33
Bi 3. To nhng phn t nh trong khng gian hai chiu (2D) v ba chiu (3D).
35
V phn t trn khng gian hai chiu ..................................................................35
Lu bc v vo trong mt File .............................................................................36
Thay i hnh thc lin kt ..................................................................................36
Biu din nguyn t di cc dng nhn khc nhau............................................38
Chnh sa cc nguyn t ......................................................................................39
Thm nhanh hydro cn thiu ...............................................................................40
Bi 4. Dch chuyn, quay v biu din h phn t theo t l mn lm vic. .....42
H to trong HyperChem ................................................................................42
H to ca ngi quan st...........................................................................43
H to ca phn t ......................................................................................43
Trc qun tnh ......................................................................................................44
t ch lm vic cho cc cng c...................................................................46
Nghch chuyn (Invert: chuyn (ho) thnh).......................................................47
Phn chiu (Reflect).............................................................................................48
Dch chuyn phn t theo trc xy ........................................................................49
Dch chuyn theo trc Z ......................................................................................51
S dng cng c phng to....................................................................................51
t phn t tr li tm v biu din theo t l.....................................................53
Quay phn t theo phng XY ............................................................................53
Quay phn t theo trc Z .....................................................................................54
Ct phn t thnh tng lt nh theo trc Z ..........................................................55
Cch lm nh sau
56
Dng cc dng nm (Wedge) biu din lin kt trong khng gian ................58
Bi 5. Xem thuc tnh cu trc phn t..............................................................60
Xem thuc tnh ca nguyn t .............................................................................60
o di lin kt.................................................................................................60
o gc lin kt .....................................................................................................61
o gc vn ...........................................................................................................62
263

o khong cch khng lin kt ...........................................................................63
Lin kt Hydro .....................................................................................................63
Recompute Hydrogen Bonds ...........................................................................64
Biu din momen lng cc.................................................................................64
Bi 6. Databases Menu
66
To chui Polypeptide..........................................................................................66
S dng hp thoi la chn cc Amino Axit .......................................................66
To dng v biu din chui Polypeptide ............................................................67
To chui..............................................................................................................68
To ion lng cc (Make Zwitterion)..................................................................70
B Ion cc ui (Remove Ionic Ends) .................................................................72
Thay th mt monome trong hp phn bng mt amino axit khc .....................72
Cc Axit Nucleic..................................................................................................74
Thm cc ion tri du (Add Counter Ions) ..........................................................78
Dng tinh th (Crystal Builder)............................................................................79
Cc lnh s dng trong xy dng tinh th ...........................................................80
To tinh th kim loi Natri...............................................................................80
To tinh th NaCl .............................................................................................82
Xy dng phn t ng (Sugar Builder) ............................................................83
Dng chui polymer ............................................................................................84
To polyme cho cc monome khc..................................................................87
Cc bc tun t to Polyme nh sau (v d cho butadien).............................87
Bi 7. La chn v biu din mt nhm cc nguyn t trn mn lm vic .......89
To vng xon c alpha. ......................................................................................89
t nhn cho u v ui chui...........................................................................90
Chn lin kt khung .............................................................................................91
T mu lin kt khung .........................................................................................93
Ch biu din lin kt khung trn mn lm vic ..................................................93
Biu din lin kt nhnh (lin kt bin) ...............................................................93
Biu din cc nhm nguyn t khng chn.........................................................94
Chn theo hnh ch nht ......................................................................................95
Chn theo hnh cu ..............................................................................................96
t tn phn la chn ..........................................................................................97
Chn lin kt vng ...............................................................................................98
Bi 8. Thao tc vi nhng phn t ln ...............................................................99
c ngun file d liu PDB . ...............................................................................99
Loi b cc phn t nc ...................................................................................100
Biu din cu trc phn t..................................................................................101
Biu din cu trc chnh.................................................................................101
Biu din vng xon Alpha............................................................................102
Biu din cu ni i sunfua............................................................................103
264

Chn cu trc vng ............................................................................................105
Thay th hp phn v tr c bit.....................................................................107
Quay nhnh lin kt ...........................................................................................108
Bi 9. Cc tiu ho nng lng ca h............................................................ 111
Lu kt qu tnh ton vo Log file.....................................................................111
Chn trng lc..................................................................................................112
Dng cu trc dng gh ca Xiclohexan. ..........................................................112
o thuc tnh cu trc cu trc dng gh ca xiclohexan.................................114
Tnh ton im n ............................................................................................114
Ghi ch vo Log file ..........................................................................................115
Ti u ho cu trc ............................................................................................115
t bin ti u................................................................................................115
Chy tnh ton ................................................................................................118
o thuc tnh cu trc ca h ti u .............................................................118
Chuyn t xiclohexan dng gh sang dng thuyn............................................119
o khong cch gia cc Hydro trc..............................................................120
Ti u ho cu trc xiclohexan dng thuyn .....................................................121
o li khong cch gia cc Hydro trc............................................................121
To cu trc dng thuyn xon ..........................................................................122
Ti u ho cu trc xon dng thuyn...............................................................123
Ngng Log file...................................................................................................123
Bi 10. C hc phn t
124
Bi thc hnh 1: To ion lng tnh alanin c lp .......................................... 125
Phc tho ion lng tnh alanin..........................................................................125
Hiu chnh cu trc ............................................................................................126
t in tch nguyn t......................................................................................127
Chn trng lc..................................................................................................128
Cc thnh phn trng lc .................................................................................132
Dng v kho st cu trc 3D ............................................................................133
Thc hin tnh ton im n cho phn t.........................................................135
Ti u ho cu trc phn t c lp.....................................................................136
Lu cu trc .......................................................................................................137
Bi thc hnh 2: Solvat ho h phn t ........................................................... 137
t iu kin bin tun hon .............................................................................138
Xc nh kch c hp tun hon.....................................................................139
Biu din h solvat ha ......................................................................................139
iu chnh cc gii hn v la chn cht in mi .......................................140
Ti u ho phn t c solvat ho ...................................................................141
Bi thc hnh 3: S dng s chng cht cc phn t ...................................... 141
Xo cc phn t nc.........................................................................................141
Hp nht hai h ..................................................................................................142
265

Chng cht cc phn t ......................................................................................143
Bi thc hnh 4: Ti u m phng.................................................................. 145
t biu din li ng lc hc ...........................................................................149
t tnh trung bnh theo ng lc hc phn t ..................................................151
Tin hnh ng lc hc......................................................................................153
Ti u ho li cu trc mi ................................................................................154
Bi thc hnh 5: M phng Langevin v Monte Carlo................................... 155
Phn 1: ng lc hc Langevin.........................................................................155
Phn 2: M phng Monte Carlo.........................................................................156
Xem li kt qu ..................................................................................................157
Bi cc phng php bn kinh nghim ........................................................... 157
Phng php p dng cho cc nguyn t:..........................................................160
Hp thoi la chn cho cc phng php bn kinh nghim khc .....................163
La chn tng tc cu hnh..............................................................................165
Bi 11 Tnh ton Obital phn t...................................................................... 167
To phn t nc................................................................................................167
t cu trc thng trc.......................................................................................168
Biu din in tch nguyn t ............................................................................169
Tnh hm sng....................................................................................................169
V biu th tnh in.....................................................................................171
Ch thch hp thoi v biu thuc tnh phn t ........................................174
Mc la chn Isosurface Grid trong hp thoi ..............................................175
Mc la chn Contour Grid ...........................................................................175
Mc Isosurface colors (mu sc th hin tnh m-dng trong biu ) ......176
V bn mt in tch ton phn ...............................................................177
V bn mt spin ton phn.......................................................................178
V biu th nng mt chiu (1D) v hai chiu (2D).....................................183
Th mt chiu ................................................................................................183
Cc la chn biu din biu th ................................................................184
Th hai chiu..................................................................................................185
Lu phn t ........................................................................................................186
Bi 12: Tng tc ca nc vi N-metylaxetamit. ......................................... 187
To ra phn t NMA ..........................................................................................187
Chuyn dng cis- sang dng trans-NMA...........................................................188
Ti u ho cu trc NMA. .................................................................................190
Tnh in tch nguyn t ....................................................................................191
Solvat ho nhm Cacbonyl.................................................................................192
Dch chuyn phn t nc .................................................................................192
Ti u mt tp hp con ca h...........................................................................193
Tnh ton li lin kt Hydro ...............................................................................194
Biu th c im ca h tng tc ....................................................................194
266

Bi 13: Thuc tnh in t ca Protein............................................................ 196
Trc khi ta bt u ...........................................................................................196
c v biu din phn t ...................................................................................196
Chn vng ta quan tm ......................................................................................197
Chn bin c in lng t. ..........................................................................199
Tnh hm sng....................................................................................................199
Phn tnh ton thun tu l thuyt (Ab Initio Calculations) ........................... 202
Bi Thit lp la chn tnh ton Ab Initio v Density Functional .................. 202
Chn tp hm c bn..........................................................................................202
La chn cho phng php Ab initio v Density Functional ............................202
Hp thoi la chn thm cho Ab initio v Density Functional .........................204
La chn cao cp cho Ab initio v Density Functional .....................................205
La chn m rng hm c bn ..........................................................................206
Bi 14: S Proton ho ca nc ...................................................................... 208
t v phn t ...............................................................................................208
Chn tp hp hm c bn tnh.......................................................................209
Cc tiu ho cu trc..........................................................................................210
Nng lng Proton ho ......................................................................................210
Bi 15: Dao ng v trng thi chuyn tip ca Amoni. ................................ 212
To Amoni
212
Chn tp hp hm c bn...................................................................................212
Phn tch dao ng ca Amoni dng hnh chp, ph dao ng ........................213
Ti u amoni phng ...........................................................................................214
Phn tch dao ng ca amoni phng ................................................................215
Tm trng thi chuyn tip theo vect c trng ...............................................217
Tm trng thi chuyn tip bng s chuyn ho ng thi................................218
Bi 16: Trng thi in t kch thch thp nht ca Etilen............................. 223
Ti u trng thi c bn ca Etilen. ...................................................................223
Obital trng thi c bn ca Etilen ....................................................................224
CI v ph in t ca Etilen...............................................................................225
Hnh hc v nng lng ca Etilen bi ba .........................................................227
Bi 17 Kh nng phn cc DFT ca H2 .......................................................... 229
To H2 ................................................................................................................229
Chn th tng tc trao i................................................................................230
Tnh ton DFT im n trong trng in.......................................................232
Tnh s cng phn cc........................................................................................232
Bi 18 Ch thch
234
To mt h phn t.............................................................................................234
Ch thch kiu ch nht .................................................................................234
Ch thch dng ng thng ..............................................................................237
Ch thch kiu vn bn.......................................................................................237
267

Lu ch thch .....................................................................................................241
Bi 19 Cc File tham s TNDO ...................................................................... 242
Tham s ngm nh CNDO/INDO. ...................................................................242
Kim tra tham s TNDO....................................................................................243
Copy tham s TNDO cho tp hp mi...............................................................244
Hiu chnh tham s TNDO ................................................................................244
Ch gii
246
268

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Huong Dan Hyperchem

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Hng dn s dng HyperChem 7.

Thanh tiu (title bar)

Thanh cng c la chn (menu bar)

Thanh biu tng cng c (tool bar)

Hng dn s dng HyperChem 7.04

Dng hin trng tnh ton (status line)

Cch s dng chut:

Hng dn s dng HyperChem 7.04

Cc cng c quan trng trn thanh cng c

Hng dn s dng HyperChem 7.04

Cc thao tc trn HyperChem

3. Nhp tri chut vo Open. Mn hnh s hin ra nh sau:

Hng dn s dng HyperChem 7.04

4. Nu mn hnh list vn cn cc cht khc, c th ko thanh trt tm

Trn mn hnh s hin ra phn t cha trong file

Hng dn s dng HyperChem 7.04

Cch s dng Display Settings

S dng nhn (Labels)

Hng dn s dng HyperChem 7.04

Hng dn s dng HyperChem 7.04

Hnh thc biu din phn t:

Thay i hnh thc biu din:

Hng dn s dng HyperChem 7.04

Ch : HyperChem cn c cc kiu biu din khc:

Hng dn s dng HyperChem 7.04

t mu sc lin kt trong phn t

Hng dn s dng HyperChem 7.04

2. Chn mc Bond Color trong hp thoi Preferences. Tch chn mu m ta

Ch : Tu theo ta chn mu no, lin kt s c biu din theo

Hng dn s dng HyperChem 7.04

Ta c th t li mu sc biu din cc nguyn t theo su mu chun, cng

t mu mi cho nguyn t ta lm nh sau:

Hng dn s dng HyperChem 7.04

2. t cc la chn nh trn hnh v. Nhp OK chn.

Hng dn s dng HyperChem 7.04

Ch : HyperChem cho ta nhiu la chn copy hnh nh.

Hng dn s dng HyperChem 7.04

Thot khi HyperChem

Hng dn s dng HyperChem 7.04

C hai cch thc hin iu ny

Bng la chn cc nguyn t hin ra nh sau:

Sau khi la chn nguyn t mun v, nhp tri chut ln mn lm vic ta

Hng dn s dng HyperChem 7.04

3. Mun v lin kt ta ch vic nhn nt tri chut v r t v tr ny n v

4. v phn t dng vng ta nhn v r chut ni cc nguyn t vi nhau.

Hng dn s dng HyperChem 7.04

5. To lin kt i, ba bng cch nhp tri chut vo chnh lin kt .

Chn nguyn t (Selecting Atoms)

t cc hnh thc chn c mt s bc sau:

Hng dn s dng HyperChem 7.04

2. Nu cc nguyn t cha c chn th hy nhp chut tri vo Atoms

Hng dn s dng HyperChem 7.04

Ch : nguyn t c la chn c m t trn dng hin trng:

Hng dn s dng HyperChem 7.04

Chn nhm nguyn t

Chn thm mt nhm nguyn t

Chn cc hp phn (Residures)

Hng dn s dng HyperChem 7.04

chn hp phn ta c cc cch sau:

Chn c phn t (Molecules)

Hng dn s dng HyperChem 7.04

Mu sc biu din khi la chn

Ch : Khi ta chn cc mu khc th khi la chn phn la chn s c

Hng dn s dng HyperChem 7.04