Introduction

Types of Chemical Bonds

Hard and Soft Ligands

Coordination Geometry

Redox Chemistry

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 interactions 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 orbitals1 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 ) 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 book.

FIGURE 2.1 Graphic representation of the five d orbitals along a Cartesian xyz-axes system.

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

Hard and Soft Ligands

In 1923, the American chemist G.N. Lewis provided a broad definition of acids and bases which covered acid–base reactions not involving the traditional proton transfer: an acid is an electron pair acceptor (Lewis acid) and a base is an electron pair donor (Lewis base). The concept was extended to metal–ligand interactions with the ligand acting as donor, or Lewis base, and the metal ion as acceptor, or Lewis acid.

The metal ions can be empirically sorted into two groups on the basis of their preference for various ligands: the large and polarisable ions which prefer large, polarisable ligands and the smaller, compact, and less polarisable ones which prefer compact, less polarisable ligands. Such a correlation, coupled to the broader definition of acid–base, led to the concept of “hard” and “soft” acids and bases which can be useful in classifying and to some extent predicting the strength of metal–ligand bonds, and hence the stability of complexes.

The general characteristics of each group are summarised in Table 2.1 along with a classification of metal ions and ligands of importance in biological inorganic chemistry. In general, “hard” acids prefer “hard” ligands, whereas “intermediate” and “soft” acids form more stable complexes with “soft” bases. Hard–hard interactions will be primarily ionic in nature whereas soft–soft interactions will be governed by ‘orbital’ interactions.

TABLE 2.1. Classification of Biologically Important Metal Ions and Ligands According to the ‘Hard–Soft Acid–Base’ Concept and their General Characteristics

A number of more specific ligand–metal ion interactions are hidden within Table 2.1. For example, Mg2+ is often associated with phosphate ligands (Chapter 10); Ca2+ is most commonly coordinated by carboxylate ligands as in proteolytic enzymes of the blood coagulation cascade where Ca2+ is often bound to γ-carboxyglutamate residues; and Cu2+ is often bound to histidine residues. Nonbiological metal ions which are of importance in medicine or as environmental pollutants can also use the same ligands. Thus, Al3+ and Ga3+ fall into the ‘hard’ category, while Cd2+, Pt2+, Pt4+, Hg2+, and Pb2+ are classified as ‘soft’.

Ligands are also classified electronically (according to the number of electrons donated to the central atom) and structurally (by the number of connections they make to the central atom). The structural classification of the ligands refers to their denticity, i.e., the number of donor atoms from each molecule. A ligand attached by one atom is described as monodentate, by two bidentate, by three tridentate, and so on. Multidentate ligands bound directly to one atom are known as chelating agents and a central metal atom bound to one or more ligands is called a chelate.