I HC QUC GIA TP.

H CH MINH
TRNG I HC KHOA HC T NHIN

______

PHNG PHP TNH TON LNG T V M PHNG TRONG QUANG PH

PGS. TS. Hunh Thnh t (ch bin) PGS. TS. L Vn Hiu

Tp. HCM, thng 12-2004 Chng 1

M U
I. PHNG PHP HO HC TNH TON Phng php ho hc tnh ton m phng cc cu trc v phn ng ho hc bng s da vo nhng nh lut ca vt l. N gip chng ta nghin cu cc hin tng bng cc tnh ton trn my tnh thay cho vic kho st thc nghim. C th ni rng ho hc tnh ton khng i hi s chun b mu, k thut phn tch, c lp; khng cn quang ph k hoc bt c s o lng vt l no. Mt vi phng php c th c s dng xy dng m hnh khng nhng cho cc phn t n nh m cn cho c nhng sn phm trung gian c thi gian sng ngn, khng n nh, ngay c nhng trng thi chuyn di. Theo cch ny, chng ta s c c nhng thng tin v phn t, qu trnh phn ng m chng ta khng th thu c t vic quan st. Do , phng php ho hc tnh ton va l mt lnh vc nghin cu c lp va b sung cho nhng nghin cu thc nghim cho nhng nh ha hc, vt l hc, quang ph hc... Ho hc tnh ton c hai phng php ph bin : (1) C hc phn t v (2) l thuyt cu trc in t. C hai u thc hin nhng loi tnh ton ging nhau: Tnh nng lng ca phn t ring l v nhng tnh cht lin quan; thc hin ti u ha cu trc; tnh ton tn s dao ng phn t. I.1. Phng php c hc phn t MM (Molecular Mechanics) Phng php c hc phn t MM s dng nhng nh lut vt l c in d on cc tnh cht v cu trc phn t. C nhiu phng php c hc phn t ty thuc vo trng lc ca n. Phng php ny c s dng trong cc chng trnh my tnh nh MM3, HyperChem, Quanta, Sybyl v Alchemy. C nhiu phng php c hc phn t khc nhau. Mi phng php c c trng bi trng lc ring ca n.

Tnh ton bng phng php c hc phn t MM khng quan tm cc in t trong h phn t, m cc tnh ton ny c thc hin da vo s tng tc gia cc ht nhn. Cc hiu ng do in t c th hin thng qua cc trng lc. Mt trng lc bao gm cc thnh phn sau : (1) (2) Mt tp hp cc phng trnh nh ngha th nng ca mt phn t bin i nh th no theo v tr ca cc nguyn t trong h. Mt chui cc mu nguyn t xc nh cc c trng ca mt nguyn t trong mt iu kin ha hc ring bit no . Mu nguyn t quy nh nhng c trng v tnh cht khc nhau i vi mt nguyn t ph thuc vo mi trng ca n. V d, mt nguyn t carbon trong nhm carbonyl (C=O) c xem l khc vi nguyn t carbon lin kt vi ba nguyn t hydro. Mu nguyn t ph thuc vo s lai ha, in tch v loi ca ca cc nguyn t lin kt vi n. Mt hoc nhiu tp hp cc thng s m chng c nhim v lm cho khp (fit) cc phng trnh v mu nguyn t vi cc d liu thc nghim. Cc tp hp thng s xc nh cc hng s lc m chng l cc gi tr c s dng trong cc phng trnh lin kt cc c trng nguyn t vi cc thnh phn nng lng v cc d liu cu trc nh di lin kt v gc lin kt.

(3)

Phng php c hc phn t MM l phng php bn c in hay cn gi l phng php kinh nghim, da trn trng lc c tham s ha m khng phi l hm sng v cc vn o phn t. Phng trnh ca phng php MM c bn cht c in v trng lc nhn chung c xc nh t cc d liu ph. Tuy nhin cc d liu nhn c t cc tnh ton ab anitio cng c th s dng cho phng php ny. Phng php MM l phng php tnh ton rt nhanh v s dng tt cho vic ti u ha hnh hc, c bit l cc phn t ln, cc nucleotide, protein,..m cc phng php ab anitio hay cc phng php bn kinh nghim khc khng th thc hin c. Cc hng s lc trong phng php MM xc nh c t o hm bc hai ca chui Taylor khai trin th nng V xung quanh v tr cn bng:
V 1 2V q i q j + ... qi + V = V0 + q 2 i , j q i j i i 0 0

y {qi} l cc ta v tr. Trong phng trnh, o hm bc 1 bng 0 v V0 c chn ty , thng thng c chn l 0. V vy:

V=

3 1 2V qiq j + 1 V 2 i , j q i j 6 i , j,k q i q j q k 0

q i q j q k + ... 0

{qi} c chn nh l s chuyn dch so vi mt v tr i chng. q i = (r-r0), ( - 0), ( - 0)ng vi lin kt, gc lin kt v gc xon trong phn t. Vi cc m hnh n gin khai trin c ngt n bc hai. Tuy vy vi kh nng ca my tnh ngy nay khai trin n cc s hng bc bn l ph bin v cc tnh ton tr nn chnh xc hn nhiu. Th nng ca h l tng ca tt c cc loi tng tc bao gm c nhng tng tc cong kiu bt cho v cc phn t khng nm trn ng cho (i j).
V total = V(r ) + V() + V() + V(r, ) + ...

Vi chuyn ng vn, thng thng th nng V() c tnh theo khai trin chui Fourier.
V(( = 1 { V1i (1 + cos i ) + V2i (1 + cos2 i ) + V3i (1 + cos3 i ) + ...} 2

y, Vki c xc nh t cc d liu ph khc nhau c th m t tt ni ng lc ca h (internal strain). Phng php c hc phn t MM ph hp vi nhng h ln cha hng ngn nguyn t. Tuy nhin, n cng c mt s hn ch nh : (1) (2) Mi mt trng lc ch thu c kt qu tt i vi mt gii hn cc phn t. Khng c trng lc tng qut cho tt c cc h phn t. Vic b qua cc in t lm cho phng php c hc phn t khng th th hin c nhng tnh cht ha hc do in t to nn, chng hn nh chng khng th m t qu trnh to lin kt hay ph v lin kt.

I.2. Phng php cu trc in t (electronic structure) Phng php cu trc in t s dng cc nh lut c hc lng t thay cho vt l c in lm c s tnh ton. Nng lng v cc tnh cht lin quan c th thu c bng cch gii phng trnh Schrdinger : H = E (1.1)

Tuy nhin, ngoi tr nhng h nh, vic gii phng trnh Schrdinger thu nghim chnh xc l rt phc tp, khng thc t. Cc phng php cu trc
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in t c c trng bng phng thc tnh ton gn ng ca chng. C hai phng thc ch yu : a) Phng thc bn thc nghim Cc phng thc tnh ton bn thc nghim, chng hn nh AM1, ZINDO/1, ZINDO/s, MINDO/3, PM3,...c s dng trong cc b phn mm MOPAC, AMPAC, HyperChem v Gaussian. Cc phng thc ny s dng cc thng s c rt ra t cc d liu thc nghim nhm n gin ho vic tnh ton. Phng thc ny thc hin tng i nhanh, cung cp nhng kt qu nh lng c th chp nhn c v nhng d on nh lng kh chnh xc v nng lng v cu trc cho h trong iu kin l cc thng s ph hp tt vi h kho st. Tc gi ng ng Vn ng dng phng thc ZINDO/1 chy trn b phn mm HyperChem kho st cu trc ca phc Nb(V) vi 4-(2-Pyriddylazo)rezocsin. Kt qu thu c ph hp vi thc nghim. b) Phng thc tnh ton lng t ab initio Ab initio l t Latin, c ngha l t ban u (from the beginning) v c s dng trong nhiu ng cnh khc nhau. Trong khoa hc, c bit l trong ha hc v vt l, n c ngha l t nhng nguyn l ban u. Mt tnh ton c gi l ab initio nu n da trn nhng nh lut c bn v c kim chng. D kin thc nghim u vo ca tnh ton ab initio ch yu l cc hng s vt l c bn. Khng ging nh phng php c hc phn t hay phng thc bn thc nghim, phng thc lng t ab initio khng s dng cc thng s thc nghim, thay vo , cc tnh ton ny da ch yu vo cc nh lut c hc lng t v mt s hng s vt l nh vn tc nh sng; khi lng, in tch ca in t v ht nhn; hng s Planck. Phng thc lng t ab initio s c s dng ch yu tnh ton trong ti liu ny trn c s b phn mm Gaussian. Phng thc lng t ab initio tnh ton nghim ca phng trnh Schrdinger bng cch s dng mt s php gn ng nh php gn ng BornOppenheimer v gn ng vn o (orbital). Php gn ng Born-Oppenheimer Hamilton y cho mt h phn t l:

H = T elec( r ) + T nucl ( R ) + V elec nucl (R , r ) + V elec( r ) + V nucl ( R )

Php gn ng Born Oppenheimer c s dng n gin ha vic gii phng trnh Schrdinger. V khi lng ca ht nhn ln hn hng ngn ln khi lng in t do ht nhn chuyn ng rt chm so vi in t. C th ni rng, ng vi mt sp xp xc nh ca cc ht nhn ti mt thi im bt k, h lun c th t ti nng lng cc tiu bng cch sp xp li cc in t ca n. V vy, h c th c tch thnh hai phn: phn chuyn ng ca ht nhn v phn chuyn ng ca cc in t. Do , mt cch tng ng c th tch ton t Hamilton ton phn (1.1) thnh hai phn, mt cho chuyn ng ca ht nhn v mt cho chuyn ng ca in t, tc l cho php ha phn ca bi ton c gii mt cch c lp. Do , xy dng mt ton t Hamilton in t m n b qua s hng ng nng ca cc ht nhn:

H elec =

n N N Z Z 1 n 2 n N Zs 1 i + + Is J 2 i=1 s =1 i =1 ris i< j rij I J < I R IJ

Php gn ng Born-Oppenheimer xem cc in t chuyn ng trong trng ht nhn tnh (ng nng ht nhn bng khng), lc s hng tng tc tnh in gia cc ht nhn nguyn t Vnucl l hng s, nn c th tch s hng ny khi ton t Hamilton ca in t. Lc ny ton t Hamilton tr thnh:

elec

n 1 n 2 n N Zs 1 = i + 2 i=1 s =1 i =1 ris i < j rij

Trong , N l s ht nhn, n s in t trong h, Zs l in tch ht nhn, ris l khong cch t in t i n ht nhn s, r ij l khong cch gia hai in t i v j. Phng trnh Schrdinger tr thnh : Hel =Eel (1.2)

y el l hm sng in t. Mc ch ch yu ca ha hc tnh ton l gii phng trnh (1.2), nn y c th s dng k hiu thay el trong phng trnh ny. Thuyt vn o phn t phn tch hm sng ton phn trong phng trnh (1.2) thnh s kt hp tuyn tnh ca cc hm sng n in t 1, 2,... n vi gia thit rng cc in t chuyn ng hon ton c lp nhau. Hm sng tng c dng:
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 = 1(1) 2(2)... n(n)

(1.3)

Tch trong (1.3) l tch Hartree-Fock, trong i uc gi l cc vn o. Nhng v cc in t l cc fermion, ngha l c spin bng , nn vi h n in t, hm sng ton phn (1.3) c vit thnh: = 1(1) 2(2) ... n(n) (1.4)

Trong i l cc vn o spin vi i(i) = i(i)(), vi () l hm sng spin () hoc () tu thuc vo s lng t spin ms bng hay -. Trn c s hai php gn ng ni trn, phng trnh Schrdinger c gii thng qua vic gii phng trnh Roothaan (ng vi cu hnh b hn ch v ng) v phng trnh Pople - Nesbet (ng vi cu hnh khng hn ch) theo quy trnh gii lp trng t hp Hartree-Fock HF - SCF (Hartree-Fock Self-Consitent-Field). B phn mm Gaussian 98 m chng ta s dng s thc hin quy trnh gii lp ny vi iu kin hi t thng l 10-6 Hartree (1 Hartree = e2/a0 vi e in tch ca in t, a0 bn knh Bohr). Nu hi t th ra khi vng lp v tnh cc tnh cht ca h theo yu cu ca ngi s dng. Phng thc lng t ab initio trong b phn mm Gaussian 98 c kh nng tnh ton d on nhiu tnh cht ca phn t v nhng qu trnh lin quan, c th nh sau : (1) (2) (3) (4) (5) (6) (7) (8) (9) Nng lng v cu trc phn t; Nng lng v cu trc ca cc trng thi chuyn tip; Nng lng lin kt v phn ng; Vn o phn t; Momen lng cc; in tch v th tnh in nguyn t; Tn s dao ng; Ph IR v Raman; Ph cng hng t ht nhn (NMR);

(10) H s phn cc; (11) Cc tnh cht nhit ha; (12) Cc ng phn ng.
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Vi phng thc ny, c th kho st cc h pha kh, pha lng, trong dung mi, trng thi c bn hay trng thi kch thch. Trong ti liu ny, v mc ch ca chng ta l kho st, phn tch ph, cho nn khng s dng ht 12 kh nng tnh ton nu trn, m ch yu s dng cc kh nng (1), (5), (7), (8) v (10). I.3. M hnh ho hc tnh ton (model chemistry) B phn mm Gaussian tnh ton da trn nhiu m hnh l thuyt khc nhau, thng c gi l m hnh ha hc. M hnh ho hc ny c c trng bi phng php l thuyt v h hm c s. a) Phng php l thuyt B phn mm Gaussian cha mt h thng t thp n cao cc th tc tnh ton tng ng vi cc phng php gn ng khc nhau, cn c gi l mc l thuyt. B phn mm Gaussian c s dng tnh ton trong phng php ho hc tnh ton xut hin t nhng nm 70. B u tin l Gaussian 70 v sau ngy cng c hon thin hn vi Gaussian 76, Gaussian 76, Gaussian 80, Gaussian 82, Gaussian 86, Gaussian 88, Gaussian 92, Gaussian 94, Gaussian 98 v hin nay l Gaussian 2003. Di y l mt s phng php thng c s dng : (1) Phng php Trng t hp Hartree-Fock (HF); (2) Phng php l thuyt hm mt 3 thng s loi Becke (B3LYP); (3) Phng php l thuyt nhiu lon Moller-Plesset bc 2 (MP2); (4) Phng php l thuyt nhiu lon Moller-Plesset bc 4 (MP4); ... Phng php no s c chn s dng trong tnh ton ty thuc vo h kho st, mc ch tnh ton, yu cu v chnh xc. Phng php (1) c s dng ch yu tnh ton trong ti liu ny, do thi gian tnh ton hp l v chnh xc chp nhn c. b) H hm c s H hm c s l s biu din ton hc ca cc vn o phn t (molecular orbitals) trong mt phn t. Mt h hm c s c th c xem nh l s gii hn tng in t vo mt vng khng gian ring bit. H hm c s cng ln th cc in t cng t b gii hn v v tr khng gian v do , cc vn o phn t c m t cng chnh xc.
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Cc h hm c s s dng cho phng php tnh ton cu trc in t da trn s kt hp tuyn tnh ca cc hm Gaussian xy dng cc vn o phn t. B phn mm Gaussian cha nhiu h hm c s, m n c th c phn loi theo s v loi ca hm c s (basis function) cha trong chng. Cc h hm c s n nh mt nhm cc hm c s cho mi nguyn t trong mt phn t m t cc vn o ca n. Cc hm c s ny c to nn t s k hp tuyn tnh ca cc hm Gaussian. Mt vn o phn t ring l c nh ngha nh sau:

i = ci
=1

(1.5)

Biu thc (1.5) c gi l biu thc t hp tuyn tnh cc vn o nguyn t LCAO (Linear Combination of Atomic Orbitals), trong ci l cc h s khai trin vn o phn t. Cc hm c s 1... N l cc hm c chun ha. B phn mm Gaussian v cc chng trnh tnh ton bng phng php cu trc in t ab initio s dng cc hm nguyn t loi Gaussian nh l cc hm c s. Cc hm Gaussian c dng tng qut nh sau :
g(, r ) = cx n y m z l e
r 2

Trong r l cha cc thnh phn x, y, z; l hng s xc nh kch thc ca hm; n, l, m l cc s lng t. n = 1, 2, 3... l = 0, 1, 2,...n-1 m = -l, ...,0,...l s lng t chnh s lng t moment gc s lng t t
2

Trong mt hm Gauss, e r c nhn vi cc ly tha ca x, y, z v mt hng s chun ha c, sao cho :

toan khong gian

=1

Do , c ph thuc vo , l, m v n. Di y l ba hm Gaussian ban u (primitive) in hnh tng ng vi loi s (l=0), py (l=1) v dxy (l=2) :

l=0 :vn o s; l = 1: vn o p (px, py, pz); l=2: vn o d (dxy, dyz, dyz, dx2-y2, dz2)

 2 gs (, r) =

3/ 4

er
1/ 4

108 5 gy (, r) = 3

yer
1/ 4

(1.6)
2

2048 7 gxy (, r) = 3

xyer

S kt hp tuyn tnh cc hm Gaussian ban u nh trong (1.6) c s dng xy dng cc hm c s thc s v thng c gi l hm Gaussian rt gn, c dng :
= d p g p
p

(1.7)

Trong dp l hng s trong h hm c s cho trc. Tp hp cc hm (1.7) c gi l h hm c s. Theo phng trnh (1.5), vn o phn t l s kt hp tuyn tnh cc hm c s (1.7):

i = ci = ci dpgp =1 =1 p

(1.8)

Cc h hm c s c phn loi theo s lng v loi hm c s cha trong chng. Di y l mt s loi h hm c s c bn hay c s dng trong tnh ton lng t ab initio : b.1. H hm c s ti thiu: STO-2G, STO-3G, STO-6G,... H hm c s ti thiu cha mt s ti thiu cc hm c s cn thit cho mi nguyn t. Nh trong v d di y vn o ca hydro v carbon c biu din nh sau: H : 1s C : 1s, 2s, 2px, 2py, 2pz Tn chung ca h hm c s ti thiu l STO-nG (trong n l s nguyn>1) l s hm Gaussian ban u trong mt hm c s n. H hm ny s dng cc vn o kiu nguyn t c kch thc c nh. V d, h hm c s STO10

(Cu hnh in t ca carbon l 1s2 2s2 2p2)

2G l mt h hm c s ti thiu, s dng 2 hm Gaussian ban u cho mt hm c s. iu ny gii thch s hng "2G" trong tn ca n. "STO" l vit tt ca "Slater -type orbitals", ngha l h hm c s STO-3G xy dng cc vn o Slater vi cc hm Gaussian. b.2. H hm c s ho tr chia tch (split-valence): 3-21G, 6-31G, 6-311G... Cch u tin lm tng ln ca mt h hm c s l tng s hm c s cho mt nguyn t. H hm c s ha tr tch i, chng hn nh 3-21G, 6-31G c hai loi hm c s c kch thc khc nhau cho mi vn o ha tr. V d, hydro v carbon c biu din nh sau : H : 1s, 1s C : 1s, 2s, 2s, 2px, 2py, 2pz, 2px, 2py, 2pz. K hiu x-yzG c hiu l: mi hm c s ca vn o nguyn t li c biu din bng x hm Gaussian ban u; Cn y v z ch ra rng mi vn o nguyn t ha tr bao gm 2 hm c s, hm c s th nht l s k hp tuyn tnh ca y hm Gaussian ban u, hm c s th hai l s k hp tuyn tnh ca z hm Gaussian ban u.Trong trng hp ny, s hin din ca hai con s sau du gch ni ngm hiu l h hm c s ny l h hm c s ha tr tch i. H hm c s tch ba, tch bn cng c thc hin ging nh th, k hiu l x-yxwG, xyzwvG,...v d h hm c s 6-311G l h hm c s ha tr tch ba. Ch l cc vn o c du phy v cc vn o khng c du c kch thc khc nhau. b.3. H hm c s phn cc: 6-31G(d), 6-31G(d,p),... Cc h hm c s tch ha tr nh trn cho php thay i kch thc vn o nhng khng thay i c hnh dng. H hm c s phn cc loi b hn ch ny bng vic b sung vo cc vn o s hng momen gc. V d, h hm c s phn cc b sung cc hm d vo cc nguyn t carbon v cc hm f vo cc nguyn t kim loi chuyn tip v i khi b sung cc hm p vo nguyn t hydr. Xt h hm c s 6-31G(d). H hm c s ny chnh l h hm c s 6-31G vi cc hm d c b sung vo cc nguyn t nng. H hm c s ny rt ph

Vn o nguyn t li c hnh thnh bi cc in t li - in t khng tham gia lin kt, v d cc in t trong vn o 1s ca carbon l in t li. Vn o nguyn t ha tr c hnh thnh bi cc in t ha tr - in t tham gia lin kt, v d cc in t trong cc vn o 2s22p2 ca carbon l in t ha tr.

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bin cho vic ton hu ht i vi cc h c kch thc trung bnh. Mt h hm c s phn cc kh thng dng na l 6-31G(d,p), n b sung cc hm d vo cc nguyn t nng v cc hm p cho nguyn t hydr. b.4. H hm c s phn cc khuch tn: 6-31+G(d), 6-31++G(d,p),... Cc hm c s khuch tn l cc phin bn c kch thc ln ca cc hm loi s v loi p. Chng cho php cc vn o chim mt vng khng gian ln hn. Cc h hm c s vi vi cc hm khuch tn l rt quan trng i vi cc h m cc in t nm tng i xa cc ht nhn: cc phn t c cp in t cha lin kt, cc anion v cc h khc vi in tch m, h trong trng thi kch thch, h vi th oxy ha thp,... H hm c s 6-31+G(d) l h hm c s 6-31G(d) vi cc hm khuch tn c b sung vo cc nguyn t nng. Phin bn hai cng 6-31++G(d) c b sung thm cc hm khuch tn vo nguyn t hydr. Hm khuch tn trong nguyn t hydr ni chung lm tng rt t chnh xc ca tnh ton. b.5. H hm c s cho cc nguyn t c ht nhn ln Ring i vi nhng nguyn t c ht nhn rt ln (nhng nguyn t nm chu k 4 tr i trong bng phn loi tun hon), th cc in t gn ht nhn uc xt mt cch gn ng qua cc th li hiu dng (ECP). Trong trng hp ny h hm c s LanL2DZ (cho cc nguyn t H, Li-Ba, La-Bi), LanL2MB (cho cc nguyn t H-Ba, La-Bi) thng c s dng nhiu nht. Tt nhin, h hm c s ny cng c th s dng cho nhng trng hp nguyn t c ht nhn nh. Ty thuc vo tnh cht, kch thc h kho st, mc ch tnh ton m h c s hm c chn cho ph hp. Trong ti liu, chng ta s s dng mt s h hm c s tnh ton theo yu cu ca tng trng hp c th, chng hn nh s dng h hm c s ti thiu STO-3G cho phn t c kch thc ln nh fullerene C60, h hm c s khuch tn - phn cc 6-31+G(d) cho ion, h hm c s LanL2DZ cho phn t c nguyn t nng nh HgI2, XeF4,.... c) Thng s c trng ca phn t Cc thng s c trng ca phn t ch loi, v tr, di lin kt, gc gia cc lin kt ca nguyn t trong phn t. B phn mm Gaussian cn cc thng s ny thc hin tnh ton. Cc d liu ny c th c a vo theo mt trong 3 dng: (1) To Descartes;
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(2) Ma trn Z (to ni); (3) Dng hn hp c to ni v to Descartes. Cc d liu tnh ton c th c nhp vo mt cch trc tip hoc thng qua s h tr ca b phn mm HyperChem, GaussView. Di y l ma trn Z ca ion phosphate (hnh bn) c a vo tnh ton bng b phn mm Gaussian.

P O,1,R2 O,1,R3,2,A3 O,1,R4,2,A4,3,D4,0 O,1,R4,2,A4,3,-D4,0 Variables: R2=1.79 R3=1.78951893 R4=1.79058342 A3=109.48798702 A4=109.47593348 D4=119.99746943

5 1 4 3 2 :P :O

Trong , R2, R3, R4, R5 l khong cch t cc nguyn t O n nguyn t P; A3, A4, A5 l gc gia cc lin kt : O3-P-O2, O4-P-O2, O5-P-O2; D4, D5 l cc gc nh din : O4-P-O2 -O3, O5-P-O2 -O3. Tnh ton bng phng php ab initio ny trong nhiu trng hp c th mang n nhng kt qu ng tin cy m khng th thc hin c bng phng php khc. Mc ch chnh ca s tnh ton ph dao ng bng phng php ny khng ch d on tn s v cng , bi v chng c th c xc nh mt cch chnh xc hn bng thc nghim, m cn gii on ph, tnh ton trng lc, nng lng phn t v cc thng s quan trng khc. Cc thng s k trn khng th c c ch t ph thc nghim, c bit i vi nhng phn t c kch thc ln vi 3N-6 tn s chun tc c xc nh bng (3N)2 gi tr hng s lc. d) Nhp d liu tnh ton Cng nh cc chng trnh tnh ton khc, b phn mm Gaussian 03 cn cc th tc v cc d liu cn thit, c gi chung l d liu nhp (input) thc hin tnh ton. Cc d liu c a vo cc vng (section) tng ng ca chng trnh.
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Sau y chng ta s thc hin cc bc cn thit thc hin vic tnh ton bng Gaussian (13 bc c bn). II. CC BC CN LM THC HIN VIC TNH TON BNG GAUSSIAN 1. Khi ng chng trnh (thao tc 1-2) 2. Np hoc nhp d liu nhp (thao tc 3-11) 3. Thc hin vic tnh ton (thao tc 12) 4. Xem xt v din gii d liu xut (thao tc 13) II.1 Khi ng chng trnh 1. Bt u chng trnh: Nhp kp biu tng ca Gaussian 03 (hnh 1.1), ca s chnh ca chng trnh gm nhiu mc s xut hin trn mn hnh.

Hnh 1.1. Biu tng Gaussian 03

2. Cc mc trong ca s chnh (hnh 1.2): Menu bar (thanh n lnh) Job control icons (cc biu tng kim sot php tnh) Job progress display (trnh by qu trnh tnh ton) Gaussian output area (vng d liu xut) Editing icons (biu tng son tho) Status line (dng trng thi) Out put filename (tp tin xut) Chng ta s xem xt ln lt cc mc trn. thc hin vic tnh ton cn cung cp cc d liu cn thit cho chng trnh. n lnh File c dng to mt tp tin nhp mi hoc sa i mt tp tin c. n lnh File gm cc lnh:
-

New: to tp tin nhp mi v m ca s Job Entry.

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Open: np mt tp tin nhp c hoc chuyn i mt cu trc phn t. Modify: bin tp tp tin nhp hin ang c np. Preferences: dng ch r cc sp xp mc nh.

Exit: thot khi Gaussian.

Hnh 1.2. Ca s chnh ca chng trnh

II.2 Np hoc nhp d liu

3. Chn New t n lnh File to mt tp tin nhp mi, ca s Job Entry

s xut hin vi nhng vng chnh nh trong hnh 1.3:

-

%Section: ghi tn file kim tra (v d: %Chk=toluene). Route Section: ghi cch thc, h hm c s, t kha dng cho tnh ton. Title Section: ghi ta , m t s lc php tnh. Charge&Multipl. : ghi in tch v i bi spin ca phn t.

bi spin ca phn t c cho bi cng thc 2S+1, trong S l spin tng ca phn t. Cc in t cp i khng ng gp vo i lng ny. Chng c spin tng cui cng bng 0 v in t c spin l v in t c spin l -. Mi in t khng cp i ng gp gi tr vo i lng S. Do : + Trng thi singlet - mt h khng c in t cp i s c bi spin l 1 (S=0); + Trng thi doublet - mt h c mt in t khng cp i s c bi spin l 2 (S= );
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+ Trng thi triplet - mt h c hai in t khng cp i ging spin s c bi spin l 3 (S=1).

-

Molecule Specification: cha thng tin v cu trc phn t nh ma trn Z (hoc ta Descartes hoc hn hp), cc bin v cc d liu v tham s cn thit khc.

Hnh 1.3. Ca s Job Entry

Con tr c di chuyn gia cc vng bng cch n phm Tab - sang vng sau; Shift+Tab - v vng trc, hay nhp chut thng vo vng mun chuyn n. Sau y, chng ta s in d liu nhp vo ca s Job Entry tnh nng lng ca phn t nc (H2O).
4. Chuyn con chy n vng Route Section. Vng ny cha cc lnh thc

hin vic tnh ton.

5. in dng sau y vo vng Route Section:

#T RHF/6-31G(d) Test xc nh phng php tnh ton v hm c s dng cho php tnh ny. Cc t kha c ghi trong bng 1.1. Bng 1.1 T kha RHF ngha Restricted Hartree-Fock (restricted: khng c cc in
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6-31G(d)

t khng cp trong phn t) Dng h hm c s 6-31G(d) (l h hm c s hu hiu v thng c s dng)

Vi dng trn xc nh php tnh s dng l RHF vi h hm c s 631G(d). Cc dng trong Route Section bt u vi du #: - #T : yu cu ch c nhng kt qu chnh c in m thi.
-

#N (hoc khng km k t no khc): xut d liu bnh thng.

- #P: xut ti a cc d liu. Vng Route Section phi gm: T kha ch phng php tnh; T kha ch h hm c s. Cc t kha ph xc nh thm loi php tnh mong mun v cc nhim ph. T kha Test cho bit y l mt php tnh th nghim v kt qu tnh ton khng c lu tr vo h s.
6. Chuyn con tr n vng Title Section, vng ny cha thng tin ngn gn

(thng ch c mt hng) m t php tnh. Th d: nhp cu sau y vo Title Section: My first job: water single point energy Cc ni dung trong Title Section xut hin trong d liu xut v c lu trong mc lu tr ca Gaussian v khng c dng trong chng trnh.
7. Chuyn con tr n vng Charge&Multipl.

Vng ny v vng k tip (Molecular Specification) xc nh cu trc ca phn t cn kho st. in tch v bi ca phn t c ghi trong vng ny di dng cc s nguyn cch nhau bi mt hay nhiu khong cch. V nc l phn t trung ha nn in tch bng 0. bi tng ng vi cch sp xp ca cc in t trong phn t. Nc khng c cc in t khng ghp i v vy phn t ny trng thi singlet vi bi spin l 1.
8. Nhp cc gi tr sau vo vng Charge&Multipl. : 0 1

Vng Molecular Specification ghi loi v v tr ca tng nguyn t trong phn t (ta Descartes c dng trong php tnh ny).
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9. Nhp cc d liu sau y vo vng Molecular Specification: O H H -0.464 -0.464 0.441 0.177 1.137 -0.143 0.0 0.0 0.0

Cc d liu cn thit cho php tnh c cung cp v mn hnh s c dng nh hnh 1.4.

Hnh 1.4. Ca s son tho (Existing File Job Edit)

Ba biu tng bn cnh phi ca s dng tr v n lnh chnh theo ba cch khc nhau nh trong bng 1.2. Bng 1.2 Icon Tc dng Tr v n lnh chnh v bt u thc hin php tnh Tr v n lnh chnh B d liu nhp v tr v n lnh chnh n lnh file Exit & Run Exit Abandon Data

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10. Chn Save Job hay Save Job As t n lnh File lu d liu nhp vo mt

tp tin. Cn chn th mc v tn tp tin (.gif, gaussian job file).

11. Chn Exit t n lnh File hay nhp chut ln icon Exit tr v ca s

chng trnh chnh. Lu l trong vng Output file lc ny c tn tp tin m d liu tnh c s c lu vo (water.out). D liu xut cng s xut hin trong ca s ln, di dng ch Run Progress. C th bt u php tnh bng mt trong hai cch sau: Chn icon Run; Chn Begin Processing t n lnh Process. II.3. Thc hin vic tnh ton
12. Bt u thc hin php tnh bng mt trong hai cch ni trn. Khi php tnh

c thc hin, vng Run Progress s cho bit din tin ca qu trnh tnh ton. Th d: Dng trn cho bit rng php tnh hin ang thc hin Link 302 (mi phin bn Gaussian u c chia thnh khong 75 Link c chc nng tnh ton ring). Ngoi ra, trong dng trng thi cnh di mn hnh s xut hin thng tin v Link ang thc hin. Th d:

C th cho php tnh tm dng hay chm dt vic tnh ton bng cc mc trong n lnh Process hay cc icon tng ng (Bng 1.3). Bng 1.3 Icon Tc dng Tm ngng tc khc Tm ngng sau khi Link hin hnh kt thc Bt u li php tnh b tm dng Chm dt php tnh hin hnh n lnh Process Pause Pause @ Next Link Resume Kill Job

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D liu xut c trnh by trong vng Output Display. Vng ny c th cun ln hay ko xung xem khi mun. Khi php tnh chm dt, vng Run Progress c thng bo:

Khi y trong ca s Output vn cn cha d liu xut t php tnh. II.4. Xem xt v din gii d liu xut 13. Xem xt d liu xut phn d liu xut s thy thng bo c dng:
SCF Done: E(RHF) = -76.0098706218 A.U. after 6 cycles

Cho bit nng lng ca h thng tnh theo cch RHF. gn cui ca ca s output c thng tin, nh:
Job CPU time: O days O hours Int=1 0 minutes D2E=0 12.6 seconds Scr=0

Files lengths (Mbytes): RWF=5

Chk=1

Normal termination of Gaussian 98.

Cho bit php tnh c thc hin tt v cung cp mt s d liu thng k v php tnh. III. XY DNG MA TRN Z III.1. Mc ch Mc ch ca phn ny l trnh by cch xy dng ma trn Z biu din phn t. III.2. Dng ta ni Mi hng ca ma trn Z ghi ta ni ca mt nguyn t trong phn t. C nhiu dng ma trn Z, dng thng dng nht c cu trc nh sau:
K hiu nguyn t, nguyn t 1, chiu di ni, nguyn t 2, gc ni, nguyn t 3, gc nh din

y, cc du phy (,) c dng phn cch cc s hng, nhng ty trng hp, cc du khc nh khong trng, du gch,cng c th c dng. K hiu nguyn t: l chui k t cha hoc k hiu ha hc hoc bc s nguyn t. Nu l k hiu ha hc, c th km theo cc ch s nh danh nguyn t tng ng (th d C1, C2, O1, O2, N1,).

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Nguyn t 1, nguyn t 2, nguyn t 3: l k hiu ca cc nguyn t ( c xc nh ri) v c dng xc nh v tr ca nguyn t ang xt. C th s dng th t dng ca mt nguyn t trong vng Molecule Specification Section thay cho k hiu ca nguyn t tng ng (dng cha in tch v bi l dng 0). V tr ca nguyn t ang xt c xc nh qua chiu di ni ca n vi nguyn t 1; gc to thnh bi ni trn v ni gia nguyn t 1 v nguyn t 2; gc nh din (gc xon) to bi mt phng cha nguyn t 1, nguyn t 2 v nguyn t 3 vi mt phng cha nguyn t ang xt, nguyn t 1 v nguyn t 2. Lu l 00 < gc ni < 1800 v 00 gc nh din 1800. Th d : Phn t hydroperoxide H2O2 (hnh 1.5)
H1 O2 O3 H4
Khong cch: O2-H1 = H4-O3 = 0.9 Gc: O3-O2-H1 = H4-O3-H2 = 105
0

H1 O2 H4
O3-O2 = 1.4 H4-O3-O2-H1 = 1200

Hnh 1.5. Phn t Hydroperoxide

Ma trn Z c dng:
H O O H 1 2 3 0.9 1.4 0.9 1 2 105.0 105.0

120.

- Dng 1 ca ma trn Z xc nh mt nguyn t hydro. - Dng 2 xc nh mt nguyn t oxy, cch nguyn t hydro (xc nh dng 1) mt khong cch 0.9 . - Dng 3 xc nh mt nguyn t oxy, cch nguyn t oxy xc nh dng 2 mt khong 1.4 v to mt gc O-O-H (vi nguyn t c xc nh dng 2 v 1) l 105 . - Dng 4 xc nh mt nguyn t hydro, cch nguyn t oxy xc nh dng 3 mt khong 0.9 , to mt gc H-O-O (vi nguyn t xc nh dng 3 v 2) l 150 v to mt gc nh din H-O-O-H (vi nguyn t xc nh dng 1, 2 v 3) l 120 .

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Dng tng ng:

H O O H B1 B2 1 A B1 2 A Variables: B1=0.9 B2=1.4 A =105.0 D =120.0 1 2 3

Cc rng but v tnh i xng th hin r qua ta ni. Hai di H-O c ch nh bi cng mt bin s, hai gc H-O-O cng th. Khi ma trn Z ny c dng trong vic ti u ha cu trc (Opt=Z-matrix), gi tr ca cc bin s s c ti u ha cho ra cu trc c nng lng thp nht. Trong tnh ton ti u y (Fopt), cc bin s cn phi c lp tuyn tnh vi nhau v bao gm mi t do trong phn t. Trong cc tnh ton ti u mt phn (Popt), cc bin xut hin trong vng sau t kha Constants c gi khng i.
Variables: B1=0.9 c B2=1.4 c A=105.0 c Constants: D=120.0 c ti u ha ti u ha ti u ha gi khng i

Th d 2: Phn t ethane. Phn t ny c cu trc nh hnh 1.6 di y:

Hnh 1.6. Phn t ethane

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Ma trn Z ca ethane c cc dng sau: Dng ta Descartes:

C C H H H H H H 0.00 0.00 1.02 -0.51 -0.51 -1.02 0.51 0.51 0.00 0.00 0.00 -0.88 0.88 0.00 -0.88 0.88 0.00 1.52 -0.39 -0.39 -0.39 1.92 1.92 1.92

Dng ta ni:

C C,1,B1 H,1,B2,2,A1 H,1,B3,2,A2,3,120. H,1,B4,2,A3,3,-120. H,2,B5,1,A4,3,180. H,2,B6,1,A5,6,120. H,2,B7,1,A6,6,-120. Variables: B1=1.54272583 B2=1.08415609 B3=1.08415609 B4=1.08415609 B5=1.08415609 B6=1.08415609 B7=1.08415609 A1=110.77945879 A2=110.77945879 A3=110.77945879 A4=110.77945879 A5=110.77945879 A6=110.77945879

III.3. Dng nguyn t gi (dummy atoms) Trong phn ny s minh ha vic s dng nguyn t gi trong ma trn Z. Nguyn t gi c k hiu bi mu t X. Th d sau y trnh by vic s dng mt nguyn t gi xc lp trc i xng bc ba C3 trong phn t Amoniac NH3 c nhm i xng im l C3v (hnh 1.7).

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N1 H3 X2

H5 H4 H5 H3 N1 H4

Hnh 1.7. Phn t amoniac

Ma trn Z nh sau:
N X H H H 1. nh 2 hnx nh 2 hnx 3 120.0 nh 2 hnx 3 -120.0 Variables: nh 1.0 hnx 70.0 1 1 1 1

V tr ca nguyn t gi trn trc l khng quan trng lm, khong cch 1 vi nguyn t N c th thay bi mt s dng khc. Cn hnx = 70 0 l gc gia trc i xng bc ba C3v v lin kt NH. Th d: Phn t Oxirane CH4O (hnh 1.8). V d ny minh ha hai im. im th nht, mt nguyn t gi c t gia ca lin kt C-C bt buc tam gi CCO l tam gi cn. OX vung gc vi C-C v do gc OXC c gi 900. im th hai l c mt vi s hng ca bin gc nh din (hcco) trong ma trn Z l m.
O C1 H1 H2 C1 H1 H2 O X C2 H3 H4 H3 O C4 H4

Hnh 1.8. Phn t Oxirane

Ma trn Z ca Oxirane c dng nh sau:

X C1 O C2 H1 X X X C1 halfcc ox halfcc ch C1 O X 90. 90. hcc 24

C1 180.0 O hcco

H2 H3 H4

C1 ch C2 ch C2 ch Variables: halfcc 0.75 ox 1.0 ch 1.08 hcc 130.0 hcco 130.0

X X X

hcc hcc hcc

O O O

-hcco hcco -hcco

Th d: Phn t NCH. Trong trng hp ny gc lin kt l 1800 (hnh 1.9). V d ny minh ha vic s dng cc nguyn t gi kho st cc lin kt thng hng vi nhau. Vic ti u ha cu trc theo ta i ni l khng th thc hin vi cc gc lin kt 180 0 trong nhng phn thng ca phn t, chng hn nh acethylene hoc chui C4 trong butatriene. Kh khn cng c th gp phi trong trng hp gn thng nh nhm ethylene (-C2H5) trong nhng phn t khng i xng. Kh khn ny cng c th khc phc c bng vic t cc nguyn t gi ln ng phn gic v s dng gc mt na (half-angle) nh l bin hay l hng s.
X3 N cn C ch H N1 C2 H4

Hnh 1.9. Phn t NCH

Ma trn Z ca phn t NCH c dng nh di y:

N C 1 cn X 2 1. 1 90. H 2 ch 3 90. 1 180. Variables: cn 1.20 ch 1.06

Th d: Phn t NC-OH (hnh 1.10).

H N C O X3 N1 C2 H O4

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Hnh 1.10. Phn t NCOH

Mt cch tng t, trong ma trn Z dnh cho vic ti u ha cu trc, half l mt na gc NCO m n khuynh hng tin ti gc 1800. Nh vy, gi tr ca half phi nh hn 900. Ma trn Z ca NC-OH trong trng hp ny c dng nh di y:
N C X O H cn 1.0 1 co 3 oh 2 Variables: cn = 1.20 co = 1.30 oh = 1.0 half = 80.0 coh =105. 1 2 2 4 half half 1 coh 3

180. 0.

______________

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