Organic Chemistry

Organic Chemistry: Originally defined as study of compounds from living things / organisms (compounds from nature). Later, chemists made (synthesized) compounds in the laboratory NOW: Organic chemistry is the study of compounds containing carbon. However, Biochemistry is the study of the chemicals and processes that sustain life (the life on Earth that is based on carbon compounds). Biochemistry is based on and overlapped with Organic Chemistry.
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Organic Chemistry
Over 10 million organic compounds have been identified about 1000 new ones are discovered or synthesized and identified each day! Unlimited number of organic compounds are possible
Why?

C is a small atom it forms single, double, and triple bonds it is intermediate in electronegativity (2.5) it forms strong bonds with C, H, O, N, and some metals.

Chapter 1. Bonding and Isomerism

1.1 The Review of Atomic Structure

Atom

nucleus electron(s)

proton(s) neutron(s)

no. of protons = atomic number

Atomic weight = no. of proton(s) + no. of neutron(s)

Electrons are located in orbitals

possibility of electrons around the nucleus

Quantum Numbers
n - principal quantum number, n = 1, 2, 3, 4, l - azimuthal (angular momentum) quantum number, l < n (1, , n 1) ml - magnetic quantum number, total ml values = 2l + 1 (-l,, 0, , l) ms electron spin quantum number, ms values = +, or -. One orbital can only hold up to two electrons (Pauli Exclusion Principle).

Orbitals are grouped in electron shells (based on n values).

Different orbitals have different shapes (based on l values). e.g. s sphere, l= 0; p dumbbell, l= 1.
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Table 1.1 Numbers of orbitals and electrons in the first three shells

Shapes of Atomic Orbitals

A p- orbital consists of two lobes arranged in a straight line with the center at the nucleus. All s orbitals have the shape of a sphere, with its center at the nucleus. Of the s orbitals, 1s is the smallest, 2s is larger, and a 3s is even larger, etc.

Aufbau principle for filling electrons on atomic orbitals

Finish here

Energy of the atomic orbitals

Start here
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Type of Orbitals

No. of Orbitals

No. of Electrons

Shell Number

Max. No. of Electrons on the shell

Orbitals (No.)
1s (1) 2s 2p (4) 3s 3p 3d (9) 4s 4p 4d 4f (16)

s (l=0) p (l=1) d (l=2) f (l=3) l

1 =(2 x 0+1) 3 =(2 x 1+1) 5 =(2 x 2+1) 7 =(2 x 3+1) (2l +1)

2 6 10 14 2(2l +1)

1 2 3 4 n

2 (2 x 12) 8 (2 x 22) 18 (2 x 32) 32 (2 x 42) 2n2

n2

Electron configuration and Periodic Table inner electrons See Table 1.3 on pg. 8 12 6C e.g. Carbon 6 electrons: 1s22s22p2 Kernel of the atom --- nucleus + inner electrons

valence electrons

valence shell --- the outermost shell

Valence (shell) electrons: the electrons in the valence shell to form chemical bonding
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Lewis symbol a dot for each valence electron

So the Lewis symbol for carbon element --- C

chemical symbol with valence electron(s)

1.2 Review of Chemical Bonding

Only exist in metal elements

Chemical bonding: ionic, covalent, and metallic (1) Ionic bond --- electrostatic interaction between cations and anions. Atoms lose the electron(s) --- cations --- positive charge(s) electropositive atoms, e.g. Na Na+ + eAtoms gain the electron(s) --- anions --- negative charge(s) electronegative atoms, e.g. Br + e- Br
Na +

Br Na+ Br

used for transfer of one electron

ionic compound contains ions

and structure see Figure 1.1 next slide Normally across the row (period): left right electronegative electropositive down the column (group): up down electronegative electropositive Ion charges: In the periodic table, group1 1+, group2 2+, group3 3+, group 6 2-, group7 1-, Other ions: H+ , Ag+, Zn2+, Cu+ / Cu2+, Fe2+ / Fe3+, etc.

Polyatomic ions: NH4+, OH, NO3, CO32, MnO4, SO42, CN, PO43 etc. The total charge in an ionic compound is zero. e.g. Ca2+ and OH form ionic compound. Write its empirical formula. 9

Figure 1.1 Sodium chloride is an ionic crystal

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Table 1.4 Electronegativities of some common elements

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(2) Covalent bond --- shared electron pair(s) between atoms For atoms like Carbon (in group 4), neither strongly electronegative nor strongly electropositive, they tend to share electron pairs to form a molecule by covalent bonds. H H :C: + 4H H C H H or CH4
covalent bond

molecule or molecular compound

H C H H

H + H H : H or H2 or H H pure covalent: electron pair equally distributed between two identical atoms In general, two atoms have similar electronegativity /electropositivity and they form covalent bond. Like in CH4 molecule, the electron pair between C and H are quite evenly shared, so 4 C H bonds are covalent bonds. For atoms with different electronegativity /electropositivity, they form polar covalent bond. Like in H2O, the electron pairs between O and H are not equally shared, so 2 O H bonds are polar covalent bonds.
-

H
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+ H

Dipole using symbol arrow toward to more electronegative atom

Polar covalent bonds

Figure 1.3 The molecular orbital

representation of covalent bond formation

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Figure 1.4 Orbital overlap to form s bonds

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Chapter 1, Page 29 p+p = bond

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Bond energy (BE) and Bond length are used to evaluate the strength of covalent Bond. See definitions on pg. 11 in the textbook. BE (stronger) Bond length (shorter) one electron pair shared between two atoms single bond __ e.g. C C two electron pairs shared between two atoms double bond = e.g. C C three electron pairs shared between two atoms triple bond e.g. C C BE: single bond < double bond < triple bond Bond length: single bond > double bond > triple bond Organic Chemistry is the study of compounds containing carbon, so in Organic Chemistry we mainly study covalent bonding molecules.

Structural formula and Isomerism

Using Lewis structures, we can write the structural formulas of different molecules. e.g. C2H6O Molecular formula gives information the types and numbers of atoms in the compound. Structural formula gives the types and numbers of atoms as well as the arrangement of these atoms in the compound. H H H H Isomerism: O C H One molecular formula may have more H C C O and H C than one structural formulas, which H H H H H correspond to different molecules. ethanol dimethyl ether Isomerism 16 is a characteristic of Organic Chemistry

Isomers --- molecules that have the same kinds and numbers of atoms but different atomic arrangements. Structural or constitutional isomers --- molecular compounds with same molecular formula but different structural formulas. They are different compounds and they differ in physical and chemical properties because of different structures. e.g. ethanol, CH3__CH2__OH and dimethyl ether CH3__O__CH3 are structural isomers. Here, we abbreviate the structural formulas by omitting the C __ H single bonds. Even more abbreviated structures can be written as CH3CH2OH and CH3OCH3 The use of lines to represent carbon backbone or framework is often common in Organic Chemistry. e.g. CH3CH2CH2CH3

CH3CH=CHCH3
Stereoisomers will be studied in later chapters

Formal Charge (FC) and Resonance (Review)

Using formal charge can help you to write correct structures. For certain atom in the molecule, VE valence electrons of the atom FC = VE CB USE CB covalent bonds around the atom USE unshared electrons around the atom 17

Resonance Structures Resonance is the use of two or more Lewis structures that differ only in the distribution of the valence electrons in representing the bonding in a species. The skeleton structure does not change; only the placement of bonds is different. We indicate resonance structures with a double-headed arrow. e.g. the Lewis structure of CO32O 2O O C O 2O O C O 2-

O O C O

2-

* C O O

Calculate the formal charges of C and O atoms in CO32FC (C) = 4 4 0 = 0 FC (O*) = 6 2 4 = 0 FC(O) = 6 1 6 = -1

These Lewis structures ------ resonance structures The real molecule or ion is described by an average of these resonance structures.
Benzene, C6H6

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1.5 Symbols used in Organic Chemistry

(1) Curved arrows curved arrow --- used for transferring a pair of electrons fishhook or half-headed curved arrow --- used for transferring one electron (2) Straight arrows straight arrow --- used for pointing from reactants to products in a chemical equation double headed straight arrow --- used for converting resonance structures half headed straight arrow --- used for a reversible chemical reaction or an equilibrium

1.6 Hybridization and / bonds (Review)

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Linus Pauling proposed the theory of orbital hybridization. (a) Hybrid orbitals can be formed by mixing s, p and / or d orbitals on an atom in order to form bonds in the molecules. (b) Hybrid orbitals have an orientation in space that matches the geometry of a molecule. (c) The number of hybrid orbitals formed is the same as the number of atomic orbitals used for the hybridization.

Hybridization involving s and p atomic orbitals (a) sp3 CH4 molecule C atom Energy 2p 2s sp3 hybridization

4 sp3 hybrid orbitals

Carbons four sp3 hybrid orbitals and 4 hydrogens1s orbitals form 4 C-H bonds. They are equivalent. H 109.5 C + 4 H tetrahedral C H H H H NH3 molecule H2O molecule N O H H H H
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(b) sp2
BF3 molecule B atom

Energy

2p
2s

sp2 hybridization

2p 3 sp2 hybrid orbitals

+3

F
B 120 trigonal planar

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H
C C

H H2C=CH2 molecule H

1 bond --- overlapping 2 sp2 hybrid orbitals C=C double bond 1 bond --- overlapping 2 2p orbitals H 2 orbitals 1 bond --overlapping 2 sp C=O 1 bond --- overlapping 2 2p orbitals C O molecule H2C=O: H O atom also uses sp2 hybridization, 1 sp2 orbital is used to form bond by overlapping with Cs sp2 orbital; two lone pair electrons occupy the other 2 sp2 orbitals; 1 unhybridized 2p orbital overlaps with a 2p orbital of Cs to form a bond.
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Benzene molecule --- C6H6 (Delocalized Bonding) All six carbon atoms are sp2 hybridized. Benzene molecule is a planar ring structure. Each carbon has one 2p orbital left. Six 2p orbitals overlap with each other to form a big bond with 6 electrons. So the six C-C bonds are equivalent. So are the six C-H bonds
H H H C C C C H
H

H C C H H H H C C C C H C C H H H C C H

H C C H
H H

H C C H

H H

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(b) sp
Be atom Energy 2p 2s +3 Cl BeCl2 molecule y sp hybridization x 2p

2 sp hybrid orbitals
Cl Be linear Cl

Be

HCCH molecule CC triple bond

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1 bond --- overlapping 2 sp hybrid orbitals 1 bond --- overlapping 2 2p orbitals 1 bond --- overlapping 2 2p orbitals

Table 1.6 The main functional groups

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1.7 Classifications of Organic Compounds

(1) Classification Based on Molecular Framework Acyclic Compounds: unbranched chain and branched chain Carbocyclic Compounds: ring structures Heterocyclic Compounds: at least one atom in the ring is a heteroatom, (ie., not a carbon atom) See examples in the textbook, pg. 33-35 (2) Classification Based on functional groups (see Table 1.6 on pg. 36-37) (a) Hydrocarbons (only contain C and H atoms): CC single bond --- alkane C=C double bond --- alkene CC triple bond --- alkyne (b) Functional Groups Containing Oxygen only CO single bond OH --- alcohol COC --- ether only C=O double bond (C=O)H (CHO) --- aldehyde >C=O --- ketone both CO single bond and (CO)OH --- carboxylic acid C=O double bond (CO)OR --- ester (c) Functional Groups Containing Nitrogen CNH2 --- amine (primary) 26 CN --- nitrile

(c) Functional Groups Containing both Oxygen and Nitrogen (CO)NH2 --- amide (primary) (d) Functional Groups Containing Sulfur SH --- thiol (also mercaptane) CSC ---- thioether (also disulfide)

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Figure 1.11 Examples of natural acyclic compounds

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Figure 1.12 Examples of natural carbocyclic compunds with rings of various sizes and shapes

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Figure 1.13 Examples of natural heterocyclic compounds

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