Nucleobases are the basic blocks in composing the double helix structures of DNA and RNA. The main ones are adenine, cytosine, thymine, guanine and uracil, abbreviated as A, C, T, G, and U, Figure 1.13a, respectively [87]. A, C, G. and T are called DNA bases because they are only found in DNA; while A, C. G and U are RNA bases in which uracil replaces thymine. Among the five bases, adenine and guanine belong to purines consisting of two hetrocyclic rings; the others are pyrimidines that are class of molecules composed of a single ring. One typical character of these bases is the tautomerism, arising from the shifting of one or two protons between different nitrogen atoms. In the two strands DNA structures, each type of base on one strand always connects with just one type of base on the other strand by double hydrogen bonds, forming base pairs, i.e. A-T and C-G pairs. However, mispairing may occur when one base is connected with a tautomeric form of the other bases, this is suspected to play an important role in spontaneous mutation in DNA replication [88].
Fig. 1.13:a) General structures of nucleic acid bases. b) The atom numbering of adenine and two preferential tautomeric structures of adenine.
Adsorption of nucleobases on surfaces has been well studied in recent years because it has been hypothesized that self-assembly of nucleic acid bases on inorganic surfaces may have had a role in the emergence of terrestrial life [11, 89]. In particular, more attention has been paid to adenine adsorbed on various substrates [22-35] because the molecule plays an essential role in the DNA replication in all known living systems [90]. Interaction of adenine molecules with metals may be influenced by such characters as the tautomerism, acidity and hydrogen bonds. Adenine can exist in twelve tautomers of which two energetically preferred tautomeric forms are: N9H and N7H, Figure 1.13b, arising from the migration of an H atom between the N9 and the N7 atoms. Generalized gradient approximation of density functional theory (DFT) calculations predicts that the N9H tautomer is 8.0 kcal mol-1 lower in energy than the N7H tautomer [91]. In gas phase, only the N9H tautomer is suggested by available experimental data [92-95]; mixture of both tautomers can exist in solvents [96, 97]. As for the acidity of gas phase adenine, it is revealed by calculations that the site N9 is about 19.0 kcal mol-1 more acidic than the amino site [98]. In addition to pairing with thymine in DNA structures, adenine also has strong ability to form various double hydrogen bonded pairs between themselves. The relatively strong intermolecular interactions play an important role in the formation of ordered molecular assemblies on surfaces.
1.5.2 Amino acids
Amino acids are the basic building blocks of proteins. The general molecular
formula of an α-amino acid is expressed as H2NCHRCOOH; its chemical structure is
shown in Figure 1.14a. The central carbon atom, usually referred as the α-carbon, is
linked to three functional groups in addition to an H atom: an amino group, a carboxylic group, and the third group, R, which acts as side chain varying for size and composition and is responsible for giving each amino acid its specific properties. All
amino acids with an exception are inherently chiral molecules in which the α-carbon,
called chiral center, is linked with four different groups. The one exception is glycine [99], the simplest amino acid, where R=H, making it achiral in the gas phase. An amino acid can display different ionized structures: the neutral ionic amino acid, namely zwitterion, existing in solid and at isoelectric point in solution, the anionic
form in basic pH value due to deprotonation of the carboxylate group, and the cationic form resulted from the protonation of the amino group in acidic solution, Figure 1.14b. Each of the three forms can be interconverted by changing the solution pH value. Anionic amino acids were also found upon metal surfaces because of strong coordination of the oxygen atoms of the carboxylic group with the substrate atoms [38, 45, 55-58].
Amino acids are essential for the human body and play an important function in metabolism [100]. Due to their importance in biochemistry, they have found wide applications in the food technology as flavour enhancers [92] and the synthesis of drugs and cosmetics [101]. In addition, amino acids can be used as chiral starting materials in the enantioselective synthesis [102] in the pharmaceutical industry. The development of amino acid based biomaterials is other research area of interest. Depending on the amino acid composition and any further chemical modification, the chemical and mechanical properties of these materials can be tailored for wide applications [103].
Fig. 1.14: a) General structure of an α-amino acid consisting of three functional groups: an amino
group, an carboxylate group, and a side chain R in addition to a H atom. b) Three different forms of ionized amino acid, the interconversion of them can be realized by mediating the solution pH value.