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Amino Acids

The amino acids are characterised by possessing acidic and basic groups on the same molecule. These are a carboxylic COOH and an amine $\mbox{NH}_{2}$ group respectively. In the so-called $\alpha $-amino acids, both functional groups are attached to the same carbon atom, the $\mbox{C}_{\alpha}$. A representative structure, that of alanine, is shown in figure 1.1.

Figure: Structure of alanine: the carboxylic and amine groups are common to all amino acids. The central carbon atom is the $\mbox{C}_{\alpha}$ atom.
\includegraphics[scale=0.7, angle=0]{fig_1a.eps}

In aqueous solutions and the solid state, these molecules often form dipolar ions, or zwitterions, whereby the carboxylic group donates a proton to the amine group. This leads to two oppositely charged functional groups on the same molecule. This is shown in figure 1.2. In the gaseous phase, zwitterionisation is energetically unfavourable, but the interactions present in solution and the solid state can act as a stabilising influence.

Figure 1.2: Structure of alanine: the effects of zwitterionisation. The molecule now has two oppositely charged functional groups.
\includegraphics[scale=1.5, angle=0]{zwitterion.eps}

The relevance of the amino acids lies in their biological importance; not only do they form the building blocks of peptides and proteins, all cellular tissue and fluid in living organisms contains a reservoir of free amino acids: an ``amino acid pool''. These take part in metabolic reactions, including the biosynthesis of polypeptides and proteins, and the synthesis of nucleotides.

The asymmetric carbon atoms present in all amino acids except for glycine leads to stereoisomerism: one may obtain optically active D- and L-amino acids, or optically inactive DL-amino acids. The majority of naturally occurring amino acids are of the L-type, for reasons that are unclear. However, the ratio of D- to L-type may alter naturally in archaeological samples via the process of racemisation; combined with the use of standard laboratory analytical techniques, this allows a method of dating samples other than $\mbox{C}_{13}$ dating [18].

Further interest can be motivated from potential technological applications of bio-organic molecules [19] such as the proposed use of DNA for creating electronic circuits [20] and the development of light-emitting organic polymers [21]. The importance of amino acids to the pharmaceutical industry and their useage in drug synthesis [18], coupled with the prospect of drug design from first principles, also provides a powerful motivation.

A more unexpected and perhaps quixotic motivation for examining the amino acids is in understanding the origins of life, and the possibilities of extra-terrestrial life, which may be aided by examining cool interstellar space for signs of biomolecules [22,23]. Traces of amino acids have been found on meteorites, whilst both glycine and alanine have been detected in lunar samples. Providing a satisfactory explanation for their presence requires a comprehensive knowledge of amino acid chemistry; ab initio techniques can serve as a useful companion to experimental approaches in such an endeavour.

A complete understanding of the role of amino acids in these important processes requires a thorough understanding of the underlying biochemistry, and consequently, a full and adequate treatment of the quantum mechanics underpinning this biochemistry is required. They are thus ideal candidates for the application of ab initio methods.

In light of the above, it is no surprise that a comprehensive body of ab initio work on amino acids already exists [22,24,25,26,27]. However, the majority of this work has concerned conformational analyses of a limited subset of the 20 naturally occurring $\alpha $-amino acids, in particular alanine and glycine. Numerous works also exist in which ab initio methodologies have been combined with Onsager models [28,29] in order to model the behaviour of amino acids in solution. Very little work has been carried out on determining the normal modes and dielectric behaviour. It is possible that this is due to the fact that the majority of work has been carried out using quantum chemical techniques such as restricted Hartree-Fock (RHF), methods which are not ideally suited to the study of large and complicated molecules. Less work exists concerning amino acids in the solid state, where they typically form molecular crystals. Indeed, this aspect has attracted surprisingly little interest from theorists, the only work in the literature appearing to concern the shielding tensors of carbon-13 [30,31].


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