Chapter 1 Bonding and Geometry

Organic Chemistry

• The study of the compounds of carbon.

• Over 10 million compounds have been identified.
– About 1000 new ones are identified each day!
• 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.
 Schematic View of an Atom

• A small dense nucleus, diameter 10-14 - 10-15 m,

which contains positively charged protons and
most of the mass of the atom.
• An extranuclear space, diameter 10-10 m, which
contains negatively charged electrons.
 Lewis Dot Structures
• Gilbert N. Lewis
• Valence shell:
– The outermost occupied electron shell of an atom.
• Valence electrons:
– Electrons in the valence shell of an atom; these electrons
are used to form chemical bonds and in chemical reactions.
• Lewis dot structure:
– The symbol of an element represents the nucleus and all
inner shell electrons.
– Dots represent electrons in the valence shell of the atom.
 Lewis Dot Structures

• Table 1.4 Lewis Dot Structures for Elements 1-18

1A 2A 3A 4A 5A 6A 7A 8A
H . He :
. . . . .
. N. :

: :
Li . Be : B : C:
. : O. : : ..F : :N e :

. . . P. : . .

: :
Na . Mg : Al : Si :
. . : S. : : Cl : :Ar :

:
 Lewis Model of Bonding
• Atoms interact in such a way that each participating atom
acquires an electron configuration that is the same as that
of the noble gas nearest it in atomic number.
– An atom that gains electrons becomes an anion. anion
– An atom that loses electrons becomes a cation.
cation
– The attraction of anions and cations leads to the formation of ionic
solids. This ionic interaction is often referred to as an ionic bond.
bond
– An atom may share electrons with one or more atoms to complete
its valence shell; a chemical bond formed by sharing electrons is
called a covalent bond.
bond Bonds may be partially ionic or partially
covalent; these bonds are called polar covalent bonds
 Electronegativity

• Electronegativity:
– A measure of an atom’s attraction for the
electrons it shares with another atom in a
chemical bond.
• Pauling scale
– Generally increases left to right in a row.
– Generally increases bottom to top in a column.
 Formation of Ions
A rough guideline:
• Ions will form if the difference in electronegativity between
interacting atoms is 1.9 or greater.
• Example: sodium (EN 0.9) and fluorine (EN 4.0)
• We use a single-headed (barbed) curved arrow to show
the transfer of one electron from Na to F.
•• ••
+ -
Na F Na F
•
•

•
•
•
•
+
•• ••
• In forming Na+F-, the single 3s electron from Na is
transferred to the partially filled valence shell of F.

Na(1 s22s22p63s1) + F(1s2 2s2 2p5 ) Na + (1s22s22p6) + F-(1s2 2s2 2p6 )

 Covalent Bonds
• The simplest covalent bond is that in H2
– The single electrons from each atom combine to form an electron
pair.

H• + •H H-H H0 = -435 kJ (-104 kcal)/mol

– The shared pair functions in two ways simultaneously; it is shared by
the two atoms and fills the valence shell of each atom.
• The number of shared pairs
– One shared pair forms a single bond
– Two shared pairs form a double bond
– Three shared pairs form a triple bond
 Polar and Nonpolar Covalent Bonds
• Although all covalent bonds involve sharing
of electrons, they differ widely in the degree
of sharing.
• We divide covalent bonds into nonpolar
covalent bonds and polar covalent bonds.
Difference in
Electronegativity
Between Bonded Atoms Type of Bond
Less than 0.5 Nonpolar covalent
0.5 to 1.9 Polar covalent
Greater than 1.9 Ions form
 Polar and Nonpolar Covalent Bonds
• An example of a polar covalent bond is that of H-Cl.
• The difference in electronegativity between Cl and
H is 3.0 - 2.1 = 0.9.

• We show polarity by using the symbols + and -,

or by using an arrow with the arrowhead pointing
toward the negative end and a plus sign on the tail
of the arrow at the positive end.

+ -
H Cl H Cl
 Polar Covalent Bonds
Bond dipole moment ():
• A measure of the polarity of a covalent bond.
• The product of the charge on either atom of a polar
bond times the distance between the two nuclei.
• Table 1.7
Bond Bond Bond
Dipole Dipole Dipole
Bond (D) Bond (D) Bond (D)

H-C 0.3 C-F 1.4 C-O 0.7

H-N 1.3 C-Cl 1.5 C=O 2.3
H-O 1.5 C-Br 1.4 C-N 0.2
H-S 0.7 C-I 1.2 --
C=N 3.5
 Lewis Structures
• To write a Lewis structure
– Determine the number of valence electrons.
– Determine the arrangement of atoms.
– Connect the atoms by single bonds.
– Arrange the remaining electrons so that each atom has a
complete valence shell.
– Show a bonding pair of electrons as a single line.
– Show a nonbonding pair of electrons (a lone pair) as a pair of
dots.
– In a single bond atoms share one pair of electrons, in a double
bond they share two pairs of electrons and in a triple bond they
share three pairs of electrons.
 Lewis Structures - Table 1.8
H
H-O-H H-N-H H-C-H H-Cl
H H
H2 O (8) NH3 (8) CH4 (8) HCl (8)
Water Ammonia Methane Hydrogen chloride
H H H O
C C H-C C-H C O H C H
O O
H H H
C2 H4 (12) C2H2 (10) CH2O (12) H2CO3 (24)
• In neutralAcetylene
Ethylene moleculesFormaldehyde Carbonic acid
– hydrogen has one bond.
– carbon has 4 bonds and no lone pairs.
– nitrogen has 3 bonds and 1 lone pair.
– oxygen has 2 bonds and 2 lone pairs.
– halogens have 1 bond and 3 lone pairs.
 Formal Charge
• Formal charge: The charge on an atom in a molecule or a polyatomic
ion.
• To derive formal charge
1. Write a correct Lewis structure for the molecule or ion.
2. Assign each atom all its unshared (nonbonding) electrons and one-half its
shared (bonding) electrons.
3. Compare this number with the number of valence electrons in the neutral,
unbonded atom.

Number of
4. Formal
The sum of all valence
formal charges Alltotal charge Oneonhalf
is equal to the
electrons the of
molecule
or ion. = unshared + all shared
charge in the neutral,
unbonded atom electrons electrons
 Formal Charge

• Example: Draw Lewis structures, and show

which atom in each bears the formal charge.
- - 2-
(a) NH2 (b) HCO3 (c) CO3
+ - -
(d) CH3 NH3 (e) HCOO (f) CH3 COO
Apparent Exceptions to the Octet Rule
• Molecules that contain atoms of Group 3A
elements, particularly boron and aluminum.

6 electrons in the
:

: F:

:
valence shells of boron : Cl :
and aluminum
: :

: :
:F B : Cl Al
:F: : Cl :
:

:
Boron trifluoride Aluminum chloride
Apparent Exceptions to the Octet Rule
• Atoms of third-period elements are often drawn
with more bonds than allowed by the octet rule.
• The P in trimethylphosphine obeys the octet rule
by having three bonds and one unshared pair.
• A common depiction of phosphoric acid, however,
has five bonds to P, which is explained by invoking
the use of 3d orbitals to accommodate the
additional bonds.
:
: Cl : :O:
: : : :

: : : :
: Cl Cl :
:

: :

:
CH3 -P- CH3 P H- O-P- O-H

:
CH3 : Cl Cl : O-H

:
Trimethyl- Phosphorus Phosphoric
phosphine pentachloride acid
Apparent Exceptions to the Octet Rule
• However, the use of 3d orbitals for bonding is in
debate.
• An alternative representation that gives P in
phosphoric acid an octet has four bonds and a
positive formal charge on P. The oxygen involved in
the double bond of the alternative depiction has one
bond and a negative formal charge.

O O formal
charges
P P
HO OH HO OH
OH OH
Apparent Exceptions to the Octet Rule
• Sulfur is commonly depicted with varying numbers of
bonds. In each of the alternative structures, sulfur
obeys the octet rule.
formal

:
:O : :O :
charges
: :

S S S
H H H 3C CH3 H 3C CH 3

:
:
Hydrogen Dimethyl sulfoxide
sulfide

:O : :
: O:
S +2
S formal
: :

: :
HO OH
: :

: :

HO OH charges
:O : :O :
:

Sulfuric acid
 Alcohols
• Contain an -OH (hydroxyl)
hydroxyl group bonded to a
tetrahedral carbon atom.
HH
:

-C-O-H H-C-C-O-H
:

HH
Functional Ethanol
group (an alcohol)

• Ethanol may also be written as a condensed

structural formula.
CH3 -CH2 -OH or CH3 CH2 OH
 Alcohols
• Alcohols are classified as primary (1°), secondary
(2°), or tertiary (3°) depending on the number of
carbon atoms bonded to the carbon bearing the
-OH group.
H H CH3
CH3 -C-OH CH3 -C-OH CH3 -C-OH
H CH3 CH3
A 1° alcohol A 2° alcohol A 3° alcohol
 Alcohols
There are two alcohols with molecular formula C3H8O

HHH
H-C-C-C-O-H or CH3 CH2 CH2 OH
H HH a 1° alcohol

H
HOH OH
H C-C-C-H or CH3 CHCH3
HH H a 2° alcohol
 Amines
• Contain an amino group;
group an sp3-hybridized
nitrogen bonded to one, two, or three carbon
atoms.
– An amine may by 1°, 2°, or 3°.

:
:

:
CH3 N H CH3 N H CH3 N CH3
H CH3 CH3
Methylamine Dimethylamine Trimethylamine
(a 1° amine) (a 2° amine) (a 3° amine)
 Aldehydes and Ketones

• Contain a carbonyl (C=O) group.

: O: O :O: O

C H CH3 -C- H C CH3 -C- CH3

Functional Acetaldehyde Functional Acetone

group (an aldehyde) group (a ketone)
 Carboxylic Acids

• Contain a carboxyl (-COOH) group.

O :O:

:
C O H CH3 -C-O-H o r CH3 COOH o r CH3 CO2 H
:
Functional Acetic acid
group (a carboxylic acid)
 Carboxylic Esters
• Ester: A derivative of a carboxylic acid in
which the carboxyl hydrogen is replaced by a
carbon group.
O O
C O CH3 - C-O- CH 2 -CH3
Functional Ethyl acetate
group (an ester)
 Carboxylic Amide
• Carboxylic amide,
amide commonly referred to as an amide:
amide A
derivative of a carboxylic acid in which the -OH of the
-COOH group is replaced by an amine.

O O
C N CH3 -C-N-H
H
Functional Acetamide
group
– The six atoms
(a 1° of the amide functional group lie in a
amide)
plane with bond angles of approximately 120°.
 VSEPR
• Based on the twin concepts that
– atoms are surrounded by regions of electron
density.
– regions of electron density repel each other.
H
4 regions of e- density

:
C N O
(tetrahedral, 109.5°) H H H
H H H H
H

3 regions of e- density H H H H H

:
(trigonal planar, 120°) C C C O C N

:
H H H H

2 regions of e- density
: :

O C O H C C H H C N
(linear, 180°)
:
 VSEPR Model

• Example: predict all bond angles for these

molecules and ions.

( a ) N H4 + ( b ) CH3 NH 2 ( d ) CH3 OH
( e ) CH 3 CH= CH 2 ( f ) H 2 CO 3 ( g ) HCO 3 -
( h ) CH3 CHO ( i) CH 3 COOH ( j) BF4 -
 Polar and Nonpolar Molecules

• To determine if a molecule is polar, we need

to determine
– if the molecule has polar bonds and
– the arrangement of these bonds in space.
• Molecular dipole moment (): The vector sum
of the individual bond dipole moments in a
molecule.
– reported in Debyes (D)
 Electrostatic Potential (elpot) Maps
• In electrostatic potential maps (elpots)
– Areas of relatively high calculated electron
density are shown in red.
– Areas of relatively low calculated electron
density are shown in blue.
– Intermediate electron densities are represented
by intermediate colors.
 Polar and Nonpolar Molecules
• These molecules have polar bonds, but each
molecule has a zero dipole moment.

F Cl

O C O B F C
F Cl Cl
Cl
Carbon dioxide Boron trifluoride Carbon tetrachloride
=0D =0D =0D
 Polar and Nonpolar Molecules
• These molecules have polar bonds and are polar
molecules.
direction O N direction
of dipole of dipole
H H H H
moment moment
H
Water Ammonia
 = 1.85D  = 1.47D
 Polar and Nonpolar Molecules
• Formaldehyde has polar bonds and is a polar
molecule.

direction O
of dipole C
moment H H
Formaldehyde
 = 2.33 D
 Shapes of Atomic s and p Orbitals
• All s orbitals have the
shape of a sphere with
the center of the
sphere at the nucleus.
Shapes of Atomic s and p Orbitals
– Figure 1.9 (a) 3D representations of the
2px, 2py, and 2pz atomic orbitals including
nodal planes.
Shapes of Atomic s and p Orbitals
• Figure 1.9(b) Cartoon representations of the
2px, 2py, and 2pz atomic orbitals.
 Molecular Orbital Theory
• MO theory begins with the hypothesis that
electrons in atoms exist in atomic orbitals and
electrons in molecules exist in molecular
orbitals.
 Molecular Orbital Theory
Rules:
• Combination of n atomic orbitals gives n MOs.
• MOs are arranged in order of increasing energy.
• MO filling is governed by the same rules as for atomic
orbitals:
• Aufbau principle: fill beginning with LUMO
• Pauli exclusion principle: no more than 2e- in a MO
• Hund’s rule: when two or more MOs of equivalent
energy are available, add 1e- to each before filling
any one of them with 2e-.
 Molecular Orbital Theory
• Figure 1.10 MOs derived from combination by (a)
addition and (b) subtraction of two 1s atomic
orbitals.
Covalent Bonding-Combined VB & MO
• Bonding molecular orbital: A MO in which
electrons have a lower energy than they
would have in isolated atomic orbitals.

• Sigma () bonding molecular orbital: A MO in

which electron density is concentrated
between two nuclei along the axis joining
them and is cylindrically symmetrical.
Covalent Bonding-Combined VB & MO

• Figure 1.11 A MO energy diagram for

H2. (a) Ground state and (b) lowest
excited state.
Covalent Bonding-Combined VB & MO

• Antibonding MO: A MO in which

electrons have a higher energy than
they would in isolated atomic orbitals.
 VB: Hybridization of Atomic Orbitals
• A principle of VB theory is that bonds are created by the overlap
of atomic orbitals.
– Therefore in VB theory, bonds are localized between adjacent atoms
rather than delocalized over several atoms as in MO theory.
– The VB model correlates with Lewis pictures where two electrons are
visualized between atoms as a bond.
– However, localization of bonds between atoms presents the following
problem.
– In forming covalent bonds, atoms of C, N, and O use 2s and 2p atomic
orbitals.
– If these atoms used these orbitals to form bonds, we would expect bond
angles of approximately 90°.
– However, we rarely observe these bond angles.
 VB: Hybridization of Atomic Orbitals
• Instead, we find bond angles of approximately
109.5° in molecules with only single bonds, 120° in
molecules with double bonds, and 180° in
molecules with triple bonds.
• Linus Pauling proposed that atomic orbitals for
each atom combine to form new atomic orbitals,
called hybrid orbitals, which form bonds by
overlapping with orbitals from other atoms.
• Hybrid orbitals are formed by combinations of
atomic orbitals by a process called hybridization.
VB: Hybridization of Atomic Orbitals
– The number of hybrid orbitals formed is equal to
the number of atomic orbitals combined.
– Elements of the 2nd period form three types of
hybrid orbitals, designated sp3, sp2, and sp.
– The mathematical combination of one 2s atomic
orbital and three 2p atomic orbitals forms four
equivalent sp3 hybrid orbitals.
2p
Energy

sp3
2s

sp3 Hybridization, with electron population for

carbon to form four single bonds
VB: Hybridization of Atomic Orbitals
• Figure 1.12 sp3 Hybrid orbitals. (a) Computed and
(b) cartoon three-dimensional representations. (c)
Four balloons of similar size and shape tied
together, will assume a tetrahedral geometry.
VB: Hybridization of Atomic Orbitals

• Figure 1.13 Orbital overlap pictures of

methane, ammonia, and water.
 VB: Hybridization of Atomic Orbitals
• The mathematical combination of one 2s atomic
orbital wave function and two 2p atomic orbital
wave functions forms three equivalent sp2 hybrid
orbitals.

2p 2p
Energy

sp2
2s

sp2 Hybridization, with electron

population for carbon to form double
bonds
 VB: Hybridization of Atomic Orbitals
• Figure 1.14 sp2 Hybrid orbitals and a single 2p
orbital on an sp2 hybridized atom.
 VB: Hybridization of Atomic Orbitals

• VSEPR tells us that

BH3 is trigonal planar,
with 120° H-B-H bond
angles. In BH3 the
unhybridized 2p orbital
is empty.
 VB: Hybridization of Atomic Orbitals
• The mathematical combination of one 2s
atomic orbital and one 2p atomic orbital gives
two equivalent sp hybrid orbitals.

2p 2p
Energy

sp
2s

sp Hybridization, with electron

population for carbon to form
triple bonds
 VB: Hybridization of Atomic
Orbitals
• Figure 1.16 sp Hybrid orbitals and two
2p orbitals on an sp hybridized atom.
 Combining VB & MO Theories
• VB theory views bonding as arising from electron
pairs localized between adjacent atoms. These
pairs create bonds.
• Further, organic chemists commonly use atomic
orbitals involved in three hybridization states of
atoms (sp3, sp2, and sp) to create orbitals to match
the experimentally observed geometries.
• How do we make orbitals that contain electrons that
reside between adjacent atoms? For this, we turn
back to MO theory.
 Combining VB & MO Theories
• To create orbitals that are localized between adjacent
atoms, we add and subtract the atomic orbitals on the
adjacent atoms, which are aligned to overlap with each
other.
• Consider methane, CH4. The sp3 hybrid orbitals of carbon
each point to a 1s orbital of hydrogen and, therefore, we
add and subtract these atomic orbitals to create
molecular orbitals.
• As with H2, one resulting MO is lower in energy than the
two separated atomic orbitals, and is called a bonding 
orbital. The other is higher in energy and is antibonding.
 Combining VB & MO Theories
• Figure 1.17 Molecular orbital mixing diagram for
creation of any C-C bond.
 Combining VB & MO Theories
• This approach is used to create C-H  bonds.
• CH3CH3 contains 1 C-C  bond and 6 C-H  bonds.
 Combining VB & MO Theories
• A double bond uses sp2 hybridization.
• In ethylene, C2H4. Carbon uses a combination of
sp2 hybrid orbitals and the unhybridized 2p orbital
to form double bonds.
 Combining VB & MO Theories
• Figure 1.21 MO mixing diagram for the
creation of any C-C  bond.
Combining VB & MO Theories

• A carbon-carbon
triple bond consists
of one  bond
formed by overlap of
sp hybrid orbitals
and two  bonds
formed by the
overlap of parallel 2p
atomic orbitals.
 Resonance
• For many molecules and ions, no single Lewis
structure provides a truly accurate representation.
: -

:
O: :O :
H3 C C and H3 C C
: O: O:
-
:

:
Ethanoate ion
(acetate ion)
 Resonance
• Linus Pauling - 1930s
– Many molecules and ions are best described by
writing two or more Lewis structures.
– Individual Lewis structures are called
contributing structures.
– Connect individual contributing structures by
double-headed (resonance) arrows.
– The molecule or ion is a hybrid of the various
contributing structures.
 Resonance

• Examples: equivalent contributing structures.

:
:O: - : O :-
:

:
O: O:
:N :N CH3 C CH3 C
O: :O :- O: : O :-
:

:
:
:

Nitrite ion Acetate ion

(equivalent contributing (equivalent contributing
structures) structures)
 Resonance
• Curved arrow: A symbol used to show the
redistribution of valence electrons.
• In using curved arrows, there are only two allowed
types of electron redistribution:
– from a bond to an adjacent atom.
– from a lone pair on an atom to an adjacent bond.
• Electron pushing is critical throughout organic
chemistry.
 Resonance

• All contributing structures must

1. have the same number of valence electrons.
2. obey the rules of covalent bonding:
– no more than 2 electrons in the valence shell of H.
– no more than 8 electrons in the valence shell of a 2nd
period element.
3. differ only in distribution of valence electrons; the
position of all nuclei must be the same.
4. have the same number of paired and unpaired
electrons.
 Resonance
• The carbonate ion
– Is a hybrid of three equivalent contributing
structures.
– The negative charge is distributed equally
among the three oxygens.
 Resonance

• Preference 1: filled valence shells

– Structures in which all atoms have filled valence
shells contribute more than those with one or
more unfilled valence shells.
+ •• +
CH3 O C H CH3 O C H
•• ••

H H
Greater contribution; Lesser contribution;
both carbon and oxygen have carbon has only 6 electrons
complete valence shells in its valence shell
 Resonance
• Preference 2: maximum number of covalent
bonds
– Structures with a greater number of covalent
bonds contribute more than those with fewer
covalent bonds.
+ •• +
CH3 ••O C H CH3 ••O C H

H H
Greater contribution Lesser contribution
(8 covalent bonds) (7 covalent bonds)
 Resonance

• Preference 3: least separation of unlike

charge
– Structures with separation of unlike charges
contribute less than those with no charge
separation.
:O: -
:

:
O:
CH3 -C- CH3 CH3 -C- CH3
Greater contribution Lesser contribution
(no separation of (separation of unlike
unlike charges) charges)
 Resonance
• Preference 4: negative charge on the more
electronegative atom.
– Structures that carry a negative charge on the
more electronegative atom contribute more than
those with the negative charge on a less
electronegative atom.

O O O
(1) (2)
C C C
H3 C CH3 H3 C CH3 H3 C CH3
(a) (b) (c)
Lesser Greater Should not
contribution contribution be drawn
Bond Lengths and Bond Strengths

Orbital Bond Length

Name Formula Bond Overlap (pm)

sp3-sp3
H H
C-C 153.2
Ethane H- C- C-H
C-H sp3-1s 111.4
H H

H H
C-C sp2-sp2, 2p-2p 133.9
Ethene C C

H H
C-H sp2-1s 110.0

C-C sp-sp, two 2p-2p 121.2

Ethyne H-C C-H
C-H
sp-1s 109.0
 1.10: Bond Lengths and
Strengths

• Alkyne C-C shorter than Alkene C-C

• Alkene C-C shorter than Alkane C-C
• Alkyne C-H shorter than Alkene C-H
• Alkene C-H shorter than Alkane C-H

• Shorter bonds are stronger

• But sigma bonds are stronger than pi
FAKTOR-FAKTOR YANG MENENTUKAN DENSITAS
ELEKTRON DALAM MOLEKUL ORGANIK

• Efek Induksi
• Mesomeri/delokalisasi elektron
• Resonansi
• Polarisabilitas
• Sterik/Ruang
 PEMAKSAPISAHAN
• Homolitik: menghasilkan radikal
• Heterolitik: menghasilkan karbokation
dan karboanion