Hiroko Fujita

Electronic structures of polymers using the tight‐binding approximation. III. Density matrix approach to poly‐L‐alanine and polyglycine‐water complex by the CNDO/2 method

In the present paper, formulas for calculating the electronic structure of polymers are derived in terms of the density matrix by the tight‐binding approximation using the CNDO/2 method. This formalism was successfully applied to poly‐L‐alanine, which was difficult to treat by the usual SCF procedure because of the divergent behavior of the iterative calculation. The obtained result indicates that the right‐handed α‐helical conformation is more stable than the left‐handed one and the planar one in agreement with experiments. The analysis of the total energy leads to the finding that the interaction between the methyl group and the carbonyl group is responsible for determining the relative stability of two α helices. Finally, the effect of water hydrogen‐bonded to polyglycine was studied from the view point of the polymer effect.

Electronic Structures of Polymers Using the Tight‐Binding Approximation. II. Polyethylene and Polyglycine by the CNDO Method

Formulas for the calculation of the electronic structure of polymers were derived by the tight‐binding approximation using the CNDO/2 method. This formalism was applied to the calculation of the electronic structure of polyethylene in the all‐trans conformation and polyglycine in the α‐helix form. For polyethylene, conformation analysis was carried out to obtain a fairly good agreement with the experimental results. The results of our conformation analysis were also in fair agreement with the calculation by the extended Huckel method which had already been published in this series of papers. The electronic structure of polyglycine was found to reflect the effect of the hydrogen bond formation in the α‐helix form.

A molecular orbital study of stability and the conformation of double-stranded DNA-like polymers

Abstract The stacking and hydrogen bonding energies between bases in the B form of DNA were calculated by a perturbation method using the wave functions by the CNDO and the P-P-P methods. The exchange energies were calculated by using the corresponding orbitals. The magnitudes of the sums of the average stacking and hydrogen bonding energies per base pair of double-stranded DNA-like polymers are in good parallel with the melting temperatures of the polymers. The polymers containing I-C pairs are exceptions to this relation. Intrastrand stacking bases have the potential minimum at the distances of 2·8–3·7 A. The minimum of stacking energy of double-stranded polymer for rotation of base pair around the helix axis exists near 36°. The deviation of the potential minimum from 36° seems to parallel the feature of the X-ray diffraction pattern of the polymer.

A molecular orbital study on the alkylation and depurination reactions of the base components of nucleic acids

Abstract Alkylation and depurination reactions of the bases of nucleic acids were investigated from the electronic structural point of view using the CNDO/2 method in which all valence electrons were taken into consideration. “Energy increment” due to the reaction was used as an index for the ease of reaction. With this index, the experimental fact was explained that among the available sites in bases the N-7 position of guanine is the most susceptible to the attack of alkylatiog agents. Energy increments in the depurination reaction for alkylated purines were calculated and were found to be smaller than those for non-alkylated purines —this is in agreement with the experiments. With regard to the mechanism of depurination, the calculation supported the S N 1 mechanism but not the S N 2 one. Calculated positive charge at the N-1 hydrogen of guanine was increased after alkylation at the N-7 position and this is in accord with the fact that the ionized form was increased by alkylation at the N-7 position in comparison with the non-alkylated base, and also with the supposition that alkylation would accelerate the proton transfer between the bases in DNA base-pairs.

A molecular orbital study on the incorporation of nucleotides into RNA

Stacking and hydrogen bond energies between bases are calculated by means of a molecular orbital method assuming the A form of DNA, and the results are compared with the values for the DNA B form. Based on the results of calculation that the stacking energies vary depending upon the base sequence, it is attempted to explain the experimental fact that incorporation of nucleotides into RNA by RNA polymerase depends on the base sequence of the template assuming two nucleotide binding sites in RNA polymerase. The incorporation process was assumed to be composed of two processes, the polymerization process and the translocation one. In the polymerization process, the stronger the stacking interaction of the substrate base with the base at the product terminus site and with the base(s) in the template and the hydrogen-bonding interaction with the complementary base are, the substrate seems to be more easily incorporated. While, in the systems involving the translocation process, when the difference in the stacking energies is relatively small and that in the hydrogen bond energies is large, the smaller the hydrogen bond energies are, the more the substrates seem to be incorporated. This result was consistently explained by assuming that the translocation process participates in determining the easiness of incorporation of the substrates in such a way that the less hydrogen bond energies are rather preferable. Good correlations between the calculated values of stacking and hydrogen bond energies and experimentally observed incorporation of nucleotides into RNA are obtained when the DNA B-like conformation was assumed at the incorporation region.