18 Possible extraterrestrial life: a quantum-chemical look on the silicon analogs of carbon biomolecules

The uniqueness of life on our planet has been an important topic of discussion in scientific literature for many decades. The most particular findings are in the fields of the structure of biomolecules and the mechanisms of their conformational and chemical transfers since they underlie all the biospheric processes of our planet. The compounds based on carbon are the subject of study of organic chemistry, which has an appropriate thoroughly developed classification of such substances; a number of approaches have been proposed for the analysis of composition and structure of the organic compounds, and a theoretical basis has been created, which describes the character of various chemical bonds involving carbon atoms. At the same time, since quite a while, there is a widely discussed hypothesis (Alison, 1968) concerning the possibility of existence of compounds, which are similar to organic, but are based on silicon atoms. Even in interstellar medium, among all the diversity of molecules detected, 84 are based on carbon, and 8 on silicon (Lazio, 2000), including four hybrid types, i.e. containing both silicon and carbon. According to approximate evaluations, the contents ratio of carbon to silicon in the space equals to 10:1, though the Earth’s crust consists of 87% of silicon in the form of oxides. In the Periodic Table, silicon is situated in the same group IV, like carbon. These two elements are largely similar in the structure of their valent electronic shells, and their noteworthy that previously it was stated (Lazio, 2000) that silicon-containing compounds are not as diverse in structure as carbon compounds. Despite having higher mass and radius, the atoms of silicon form double and triple covalent bonds (Wang et al., 2008). Therefore, the issue concerning the existence of silicon structures similar to carbon biomolecules, as well as the question of hypothetical “biochemical” processes involving non-carbonic analogs of aminoacids, carbohydrates, proteins, lipids, and other biomolecules, is still a matter of discussion in scientific and popular science literature. It is particularly notable that the modern methods of computational chemistry allow carrying out the estimating calculations of the structure and dynamics of such compounds, which is quite similar to the known approaches of substance modeling de novo in drug design. For instance, first by calculations (Nagase, Kudo, & Aoki, 1985), and later on experimentally (Abersfelder, White, Rzepa, & Scheschkewitz, 2010), aromaticity of cyclic carbohydrate-like derivatives of silicon was studied. In the present study, we used quantum-chemical semiempirical PM3 and ab initio B3LYP/6-311G(d,p) level of theory to investigate the peculiarities of several structural and thermodynamic parameters of molecules, which can be assumed as complete silicon analogs of carbonic L-amino acids and other biomolecules, so-called bricks of life: carbohydrates, nitrogenous bases, fatty acids, as well as vitamins and caffeine. The quantum-mechanical calculations that we made displayed that the molecules of silicon amino acids possess higher thermodynamic stability compared to carbon analogs. Thereby, silicon amino acids have a similar conformation freedom, increased values of dipole moment, as well as more pronounced electron-donor characteristics. Silicon analogs of carbohydrates, fatty acids, and nitrogenous bases are as well considered as heavier thermodynamically stable compounds, having special features in 3D-organization and worth further experimental study. The present work also deals with the question of the existence and stability of “alpha-helices” composed of silicon amino acids, because in the molecules of Si-analogs of aspartate and glutamate, we have discovered effective formation of intramolecular hydrogen bond (due to the side chain), which is highly important for Pauling–Corey alpha helix formation in natural L-amino acids (Kondratyev, Kabanov, & Komarov, 2010). Our estimations show that an “alpha helix” composed of 10 silicon alanine analogs is more stable in isolated state than a linear form of such macromolecule, which was not observed for a molecule of the same composition having a carbon backbone.