Theoretical investigation of cooperative effects of H-bonds in biomolecular systems

Abstract

Streffer, Friedrich Theoretical Investigation of Cooperative Effects of H-Bonds in Biomolecular Systems The present work investigates signatures of cooperative effects of H-bonds especially in DNA with statistical and quantum chemical methods. Part I investigates results of information-theoretical analyses of DNA sequences of living organisms, which are tested qualitatively and quantitatively with respect to their biological aspects and/or implications. The results concern ’long-range correlations’ and ’fractals’ in intron-containing DNA sequences, their possible ’linguistic’ structure, and other related aspects. The investigations demonstrate that the findings a ’fractal’ structure in DNA are trivially equivalent to variations of the base pair composition, or patchiness, of different regions in a natural DNA sequence. It is explicitly shown that neither a well-defined ’scaling’ or ’fractal’ exponent, nor a well-defined Zipf exponent of the ’linguistic’ test does exist. The biological origins of such variations are discussed. Quantitative comparisons of natural DNAs with computer-generated, artificial sequences are made. But the present work shows that certain natural DNA sequences (especially those with compact genomes) do have certain stochastic characteristics (say, pseudo-fractal exponents, averaged Zipf slopes, etc.) which are intrinsically different from artificial sequences. To shed more light on this point, investigations concerning the short range correlation of base pair, which may be caused by short-lived quantum entanglement of protons, are presented. The most striking finding is that quantum entanglement appears preferably between the third base of a codon and the first base of the following one. Results on a large number of DNA sequences of various types and from widely different taxa are reported. Additionally, results of current investigations concerning the so-called ’detrended fluctuation analysis’ and the ’Kullback information measure’ of DNA sequences are reported. Part II deals with quantum chemical investigations of the AT, GC and the artificial κχ base pair. Different levels of theory have been applied with full geometry optimization and the ’frozen-core’ approximation; among them are B3LYP/6-31G** and MP2/6-31G**. The calculations in the ’frozen-core’ approximation confirm the double well character of all investigated potential energy surfaces, with a decreased energy of the transition states on the inclusion of the electron correlation effects. Couplings of the different proton transfer reactions are discussed, testing quantitavely the assumptions of a quantum mechanical Jordan-Block structure found in the GC pase pair. The geometry optimization of the relevant stationary points of the double proton transfer reactions in the AT and GC base pair has been performed at the B3LYP/6-31G** level of theory. The most striking finding is found during the normal mode analysis of the vibrations. A vibrational mode involving the relevant protons for the double proton transfer does exist in the GC base pair and all tautomers, whereas the AT base pair does not have such a vibrational mode. Implications are discussed. Finally, two experiments are proposed to test the findings.