All lectures Bio-organic Chemistry for Life Sciences

Lecture 1
Bio-organic Chemistry for Life Sciences
Chapter 1
Structure and Bonding
Acids and Bases


All organic compounds contain the element carbon.

 Bonds to other carbons to create chains and rings
 Not all carbon compounds are derived from living organisms
 >99% of 37 million known compounds contain carbon

Atomic Structure
Nucleus
 Positively charged
 Made up of protons (positively charged) and neutrons (neutral)
 Small (10-14 to 10-15m in diameter)
 Contains essentially all the mass of the atom

Electron cloud
 Negatively charged electrons in clous around nucleus
 Atomic diameter is about 2 Angstroms (A) = 2 x 10-10m

,Orbitals
 Orbital describes volume of space around the nucleus that the electron is
most likely to occupy
 This space can be calculated with a wave function (Quantum mechanical
model)

Four different kinds of orbitals for electrons (s, p, d and f)
 s and p orbitals most important in organic chemistry
o s orbitals are spherical
o p orbitals are dumbbell-shaped




p Orbital
 There are three equal, mutually perpendicular p orbitals: px, py and pz
 Lobes of p orbitals are separated by region of zero electron density: a node




Orbitals
- contain zero one or two electrons
- are grouped in electron shells of increasing size/energy

,Electron Shell
 First shell contains one s orbital, denoted 1s -> holds two electrons
 Second shell contains four orbitals, one s orbital (2s) and three p orbitals
(2p) -> holds a total of eight electrons
 Third shell contains nine orbitals, one s orbital (3s), three p orbitals (3p), and
five d orbitals (3d) -> holds a total of 18 electrons




Ground-state electron configuration
 Most stable, lowest energy electron configuration of an atom

Three rules:
1. Lowest-energy orbitals fill first:
1s → 2s → 2p → 3s → 3p → 4s → 3d
2. Electron spin can have only 2 orientations: up  and down 
 A maximum of two electrons can occupy an orbital, and they must be of
opposite spin
1. If two or more empty orbitals of equal energy are available, electrons occupy
each orbital with parallel spins until all orbitals have one electron

Chemical bonding
Atoms bond because the compound that results is more stable and lower in energy
than the separate atoms
• Energy is released from the chemical system when a bond forms
• Energy is consumed by the system when a bond breaks

, Valence shell
= Outer most electron shell of an atom
 Eight electrons in valence shell (an electron octet) impart special stability to
noble-gas elements
 Other elements have a tendency to take on electron configuration of the
nearest noble gas

Ionic compounds
 Some elements achieve an octet configuration by gaining or losing
electrons
 Ions form when an electron is gained or lost form a neutral atom
 Ions are held together by electrostatic attraction forming an ionic bond




Covalent compounds
 Covalent Bond = bond formed by sharing electrons between atoms
 Molecule = neutral collection of atoms held together by covalent bonds
 Carbon achieves an octet configuration by sharing electrons

Lewis structures (electron dot structures)
 Valence shell electrons of an atom are represented as dots




Kekulé structures (line bond structures)
 Two-electron covalent bond is represented by a line




Lone-pair electrons
= Valence-shell electron pairs not used for bonding

Octet rule
Number of covalent bonds depends on how many additional valence electrons
needed to reach noble-gas configuration
 H (1s) needs one more electron to attain (1s2) and forms one bond
 N (2s22p3) needs three more electrons to attain (2s22p6) and forms three
bonds