Chemistry Reference
In-Depth Information
Chapter 2
Basic Coordination Chemistry for Biologists
Introduction
21
Types of Chemical Bonds
21
Hard and Soft Ligands
23
Coordination Geometry
26
Redox Chemistry
28
INTRODUCTION
Biological inorganic chemistry is by its nature an interdisciplinary subject with linguistic and conceptual problems
that render it difficult for students who have a background uniquely in either biology or chemistry. The major
problem for the student with a background in biology is the understanding of the concepts inherent in the inter-
actions of chemical species (charged or uncharged) with each other. Such concepts involve electronic structure and
considerations of symmetry which in turn affect the bonding between them. In this chapter, we will lay out the
basics of such concepts with particular reference to the interactions of metal ions with organic molecules.
The electron in its simplest description can be considered as a negatively charged cloud that occupies a definite
but arbitrarily defined region of space relative to the nucleus. Such regions are called orbitals
1
and can contain
a maximum of 2 electrons of opposing spin. The s orbitals are spherical. The p orbitals are dumb-bell shaped and
there are three of them, each one lying across a Cartesian xyz-axes system. The d orbitals (apart from the d
z
2
) are
four-lobed and their orientation along a Cartesian xyz-axes system is shown in
Figure 2.1
. The f orbitals are seven
in number but their shape and orientation are beyond the scope of this topic.
TYPES OF CHEMICAL BONDS
Atoms within the same molecule or between different molecules interact and are held together by bonds formed by
electrons. The number of bonds that an atom can form is usually determined by its valency
the number of unpaired
electrons in its outer shell (the valency shell). Bonding results in each atom achieving the noble gas configuration.
2
e
Ionic Bonding
Electronegativity is the tendency of an atom to attract electrons in a molecule. Large differences in electroneg-
ativity between atoms in a given molecule often cause the complete transfer of an electron from the unfilled outer
1. Strictly speaking, an orbital is not a physical reality but refers to a particular solution of complicated wave equations associated with the
theoretical description of atoms and they are referred to by the initial letter of the terms describing the spectral lines: sharp, principal, diffuse,
and fundamental.
2. The noble gases of Group VIII of the Periodic Table (Figure 1.3) all contain eight electrons in their outer shell.
