Pharmaceutical Chemistry 125:

Pharmaceutical Organic
Chemistry 1
Robertson G. Rivera
Instructor
Outline
I. Review of General Chemistry
I. Structure of an atom
II. Ionic and covalent bonds
III. Periodic trends
IV. Representation of the structure of compounds
V. Atomic orbitals
VI. Molecular orbital theory
VII. Bond formation
VIII.Hybridization and geometry
IX. Dipole moments of molecules
Review on Atomic Structure
and Representation
Structure of an Atom
Atomic Representation
Review on Electron
Distribution
Distribution of Electrons
• Quantum Numbers
• Describe the energy levels of electrons and the shape of the orbitals that
describe distribution of electrons in space
• Atomic orbital
• Region of space in which the probability of finding electrons is high
Quantum Numbers
• Principal Quantum Number (n)
• Describes main energy level/ shell that an electron occupies
• Any positive integer
• n= 1, 2, 3, 4…
• Angular Momentum Quantum Number (l=n-1)
• Describes the shape of the subshell/sublevels present within a shell
• l= 0, 1, 2, … (n-1); s, p, d, f
Quantum Numbers
Quantum Numbers
Quantum Numbers
• Magnetic Quantum Number (ml)
• Designates a specific orbital within a subshell
• -l to +l
• Spin Quantum Number (ms)
• Spin of an electron/ orientation
• ms= +1/2 or -1/2
Quantum Numbers
Atomic Orbitals
• Degenerate orbitals
• Orbitals that have the same energy
• Ground-state electronic configuration
• Describes the orbitals occupied by the atom’s electrons when they are all in the
available orbitals with the lowest energy
• Excited-state electronic configuration
• When one or more electrons jump into a higher-energy orbital
Atomic Orbitals
• Core electrons
• Do not participate in chemical bonding
• Valence electrons
• Electrons in the outermost shell
• Have the greatest influence on the properties of elements
Rules in Filling Atomic Orbitals
• Aufbau Principle
• An electron goes into the available orbital with the lowest energy
• The closer the atomic orbital to nucleus, the lower its energy level
• 1s < 2s < 2p< 3s< 3p< 3d
• Pauli Exclusion Principle
• No more than 2 electrons can occupy each atomic orbital
• The two electrons must be of opposite spin
Rules in Filling Atomic Orbitals
• Hund’s Rule
• When there are two or more atomic orbitals with the same energy, an electron
will occupy an empty orbital before pairing up
• Minimization of repulsion.
Review on Periodic Trends
Periodic Trends
• Atomic radius
• Increases from top to bottom
• Generally decreases from left to right
Periodic Trends
• Ionization Energy
• Minimum amount of energy required to remove the most loosely bound electron
from an isolated gaseous atom to form an ion with a +1 charge
• Increase from left to right
• Decrease from top to bottom
Periodic Trends
• Electron affinity
• Energy change when an electron is added to an isolated gaseous form an ion
with a 1- charge
• Decrease from left to right
• Increase from top to bottom
Periodic Trends
• Electronegativity
• Increases from left to right
• Decreases from top to bottom
Review on Chemical Bonding
Chemical Bonding
• Ionic Bonding
• Attraction between ions of opposite charge
• Covalent Bonding
• Electron sharing between two nuclei
Writing Lewis Structures
• S= N-A
• S= shared electrons
• N= 8 x # of atoms + 2 x H atoms
• A= total electrons in the valence shells
Writing Lewis Structures
• F2
• S= 2(8)- 2(7)= 2 electrons
• 2 fluorine atoms; 8 electrons needed to complete octet of each atom
• 2 fluorine atoms; 7 electrons available in each of the valence shell
Writing Lewis Structures
• NH4+
• Needed= (1x8) + (4x2)= 16 electrons
• Available= (1x5) + (4x1)- 1(for +1 charge)= 8 electrons
• 8 electrons shared
Writing Lewis Structures
1. The least electronegative element is usually the central atom EXCEPT
hydrogen
• Example: CS2; Carbon is the central element
2. Max number of bonds in carbon and nitrogen : 4
3. Oxygen rarely bonds to each other except in: O2 and O3, peroxides
(O22-) and superoxides (O2-)
4. For ions or molecules that have more than one central atom, the most
symmetrical skeletons possible are used.
5. Use S= N-A
Examples
• Draw the Lewis formula for the following molecules:
A. CO32-
B. N2
C. CS2
Formal Charges
• Hypothetical charge on an atom in a molecule
• Most energetically favorable formula for a molecule is usually one in
which the formula charge in each atom is zero
• FC= group number- (number of bonds + number of lone pairs)
Formal Charges
• Negative formal charges are more likely to occur on the more
electronegative elements
• Lewis formulas in which adjacent atoms have formal charges of the
same sign are usually not accurate
Examples
• Draw the Lewis structure of NOCl (nitrosyl chloride)
Review on Molecular Orbital
Theory
MO Theory
• Lewis model + wavelike properties
• Assigns electrons to orbitals
• Covalent bonds result when atomic orbitals combine to form molecular
orbitals
MO Theory
• Orbitals are conserved
MO Theory
MO Theory
MO Theory
MO Theory
Electronic and Molecular
Geometry
Electronic Geometries and Hybridization
Bond Formation (Single Bond)
Single Bond Formation
• All single bonds are sigma bonds (head-on overlap)
• Single bonds are freely-rotating in space
Single Bond Formation
Single Bond Formation
Single Bond Formation
Single Bond Formation
• Methane
• 4 covalent bonds
Single Bond Formation
• Ethane
Bond Formation (Double
Bond)
Double Bond Formation
• Double bonds consist of one pi bond and one sigma bond
• Pi bonds are formed by side-to-side overlap of two orbitals
• Double bonds are planar, not rotatable
• Stronger than single bond
Double Bond Formation
• Ethene forms four bonds but with 3 atoms.
Double Bond Formation
Double Bond Formation
Double Bond Formation
Bond Formation (Triple Bond)
Triple Bond Formation
• Triple bond consists of 2 pi bonds and 1 sigma bond
• Strongest bond
• C has 4 bonds but only 2 atoms
Triple Bond Formation
Bonds in Methyl Cation,
Methyl Radical and Methyl
Anion
Methyl Cation
• CH3+
• Bonded to three atoms (1s, 2p)
• sp2
• Empty unhybridized p-orbital
Methyl Radical
• CH3●
• sp2 hybridized
Methyl Anion
• CH3-
• sp3 hybridized
Bonds in Ammonia and
Ammonium Ion
Bonds in Ammonia and Ammonium
• NH3– 3 covalent bonds

PROBLEM?
Bonds in Ammonia
Bonds in Ammonia
• Lone pair is more diffuse than a bonding pair that is shared by two
nuclei
Bonds in Ammonium
Bonds in Water and in
Hydrogen Halide
Bonds in Water
• Two covalent bonds
Bonds in Water
Bonds in Hydrogen Halide
Bonds in Hydrogen Halide
Summary: Hybridization, Bond
Lengths, Bond Strengths and
Bond Angles
Summary
Summary
Dipole Moments of Molecules
Dipole Moment
• Direction + magnitude of individual dipoles
• Towards the electronegative atom
Dipole Moment
End