Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)

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 10:1, though the Earth’s crust consists on 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 its 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 et al., 1985), and later on experimentally (Abersfelder et al, 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 et al., 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.


    K. Abersfelder, A. J. P. White, H. S. Rzepa, D. Scheschkewitz (2010) A Tricyclic Aromatic Isomer of Hexasilabenzene. Science. 327. 564-566.

    A. Alison (1968) Possible Forms of Life. Journal of the British Interplanetary Society, 21, 48 (1968)

    M. S. Kondratyev, A. V. Kabanov, V. M. Komarov (2010) Modeling of helix formation in peptides containing aspartic and glutamic residues. Computer Research and Modeling. 2. 83–90. (Russian).

    J. Lazio (2000) Why do we assume that other beings must be based on carbon? Why couldn't organisms be based on other substances? Report based on a lecture by Alain Leger (IAS) at the SPIE Astronomical Telescopes and Instrumentation 2000 Conference.

    S. Nagase, T. Kudo and M. Aoki (1985) Hexasilabenzene (Si6H6). An ab initio theoretical study of its aromaticity and relative stability. J. Chem. Soc., Chem. Commun., 16, 1121-1122.

    Y. Wang, Y. Xie, P. Wei, R. B. King, H. F. Schaefer III, P. von R. Schleyer and G. H. Robinson (2008) A Stable Silicon (0) Compound with a Si=Si Double Bond. // Science, 321, 5892, 1069-1071.

Maxim S. Kondratyev
Artem V. Kabanov
Alexander A. Samchenko
Vladislav M. Komarov
Nikolay N. Khechinashvili

Institute of Cell Biophysics
Russian Academy of Sciences
Pushchino, Russia 142290

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