Chapter 2

Basic Coordination Chemistry for Biologists

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

Ionic Bonding

Electronegativity is the tendency of an atom to attract electrons in a molecule. Large differences in electronegativity between atoms in a given molecule often cause the complete transfer of an electron from the unfilled outer shell of one atom to the unfilled shell of another. The resulting charged species (ions) are held together by electrostatic forces. Such bonds are highly polarised and are referred to as ionic bonds. Ionic bonding is the simplest type of chemical bonding encountered. NaCl, can be written as [Na+ Cl-], the sodium atom giving up one electron to resemble the stable neon atom, while the chlorine atom acquires an extra electron to resemble the stable argon atom. MgCl2 [Mg2+ ] and CoBr3 [Co3+ ] are other examples of ionic compounds.

Covalent Bonding

Orbital overlap, i.e., mutual sharing of one or more electrons, can occur when two atoms are in close proximity to each other. The bonding resulting from such overlap is referred to as covalent bonding. Most frequently, for a significant overlap and hence a more stable bond, either both atoms have half-filled valency orbitals as in the H2 molecule or one atom has a filled valency orbital not used for bonding and the other one a vacant valency orbital. Pure covalent bonding occurs in compounds containing atoms of the same element like H2. Most compounds, however, contain atoms of different elements, which have different electronegativities and, hence commonest type of bonding lies somewhere between purely ionic and purely covalent as in HCl.

Coordinate bonds are a special case of covalent bonds where the electrons for sharing are supplied by one atom. There is often a fractional positive charge on the donor atom and a fractional negative charge on the acceptor atom. CoBr3·3NH3 (Figure 2.2) exhibits this type of bonding and hence traditionally it is referred to as a coordination compound.

FIGURE 2.2 Structure of the coordination complex CoBr3·3NH3.

Coordination3 compounds consist of a central atom or ion, like Co3+, surrounded by electron-rich groups (ligands), like NH3. The ligands are directly bound (coordinated to) to the central atom or ion, they are usually between 2 and 9 in number and may be single atoms, ions, or molecules. The ligands directly bound to the metal are said to be in the inner coordination sphere, and the counter-ions that balance out the charge are said to be outer sphere ions. Coordination compounds are usually referred to as complexes, they can be charged or uncharged and their structure is defined by the coordination number (the number of ligand atoms bonded to the central atom) and their coordination geometry (the geometrical arrangement of the ligands and the symmetry of the entire complex). The central ion can be in any oxidation state, which remains unchanged in the coordination complex. We shall endeavour in what follows to explain some of the concepts of coordination chemistry and their relevance to biological inorganic chemistry.

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

High charge density

Small ionic radius

No easily excited outer shell electrons

Na+, K+,

Mg2+, Ca2+,

Cr3+, Fe3+, Co3+

Low polarisability

High electronegativity

Vacant, high-energy orbitals

Hard to oxidise

H2O, OH-, CO2-, , NO3-, ,

, , ,

ROH, RO-, R2O, NH3, RNH2, Cl-

Low charge density

Large ionic radius

Easily excited outer shell electrons

Cu+

High polarisability

Low electronegativity

Low energy vacant orbitals

Easily oxidised

RSH, RS-, CN-, CO

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 ?-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.

The Chelate Effect

Metal ions dissolved in water are effectively complexed to water molecules. Displacing the set of water ligands, partially or entirely by another set in such aqua...