Calculation of the band structure of polyguanilic acid in the presence of water and Na+ ions.

Using the Hartree-Fock crystal orbital method with a combined symmetry (helix) operation, the band structure of polyguanilic acid was calculated in the presence of water and Na(+) ions. The water structure was optimized with the help of molecular mechanics. The obtained band structure shows that both the valence and conduction bands are purely guanine type. The three impurity bands in the 10.66 eV large gap are close to the conduction band and therefore cannot play any role in the assumed hole conduction of the system. Namely, according to detailed x-ray diffraction investigations of the nucleosomes in chromatin, there are possibilities of charge transfer from the negative sites of DNA to the positive ones in histones. Therefore most probably there is a hole conduction in DNA and an electronic one in the histone proteins.

Calculation of the charge-carrier mobility of polyguanylic acid: the simultaneous effect of stretching and twisting.

Charge-carrier (electron and hole) mobilities of polyguanylic acid have been computed using the deformation-potential approximation from ab initio Hartree-Fock band structure. Mobilities resulting from electron scattering on torsional acoustic phonons are calculated and compared to those obtained from a previous calculation [F. B. Beleznay et al., J. Chem. Phys. 119, 5690 (2003)] considering interaction with compressional phonons. The simultaneous effect of the two independent scatterings is also calculated.

Density functional study of infinite polyserine chains.

Two different helical conformations (alpha and 3-10 helices) of polyserine are studied using density functional theory. The infinite system characterized by exact translational-rotational symmetry is examined in vacuum using the BLYP exchange-correlation functional. Geometry analysis in terms of hydrogen bond strength and total energies of the different conformers are presented. The structural changes due to the presence of the serine side chain are identified comparing the polyserine and polyglycine chains. The rotational energy curves of the side chain are presented for both investigated helices. Band structures of polyserine and polyglycine conformers are also compared.

Relativistic Gaussian functions for atoms by fitting numerical results with adaptive nonlinear least-square algorithm.

The relativistic Gaussian basis set of Hg has been obtained by fitting the numerical relativistic atomic radial wave functions with the adaptive nonlinear least-square algorithm combined with the subset selection method. This fitting procedure and fitted results are presented. From this basis, in a further several-step procedure, we generated a new basis that gave reasonably good results for Hg, HgO, and a Se atom chain, respectively. The original fitted basis did not work, because the resulting overlap matrix was not positive definite. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 655-664, 1999.

Ab initio electronic structure calculation of a new gene system using the negative factor counting method.

We report a calculation of the electronic structure (density of states and molecular orbitals) of a new gene system-the plasmid shuttle vector pCRR1-performed at the ab initio Hartree-Fock level. To deal with the aperiodicity of the biopolymer, a vectorized version of a negative factor counting (NFC) program has been implemented. With this efficient tool, DNA molecules of up to 100 deoxynucleotides (approximately 10,000 basis functions at the ab initio level) can be calculated routinely. In our calculation the base sequence of the plasmid is explicitly taken into account and a standard helical structure is assumed. Minimum as well as 6-31G basis sets are used in the calculation, and solvation effects are explicitly included. The calculation shows that solvation does not have a significant effect on the electronic structure of the biopolymer. It is found that the frontier orbitals (HOMO and LUMO) are highly localized on the bases. The interpretation of this result in terms of the frontier molecular orbital theory is that the attack of radiation-induced radicals is mainly on the base moieties.

Theoretical investigations on oncogene activation by chemicals and antioncogene inactivation by radiation.

To activate the cancerous genetic information in the cell one has either to activate oncogenes or to inactivate antioncogenes (cancerous growth suppressing genes). These processes usually happen in the cell with the aid of external factors, especially chemical carcinogens' and radiations. It was shown with the aid of simple statistical considerations that both oncogene activation by chemical carcinogens and the double strand breakings due to ionizing radiations leading to antioncogene inactivation most probably are caused not only by local effects. Different mechanisms (like the change of the tertiary structure, the change of the dispersion and polarization forces between DNA and proteins due to charge transfer and different solution mechanisms) were investigated to prove the role of long-range effects of carcinogens in initiating the malignant transformation of an eucaryotic cell.

Theory of oncogene activation by chemicals and antioncogene inactivation by radiations - possible carcinogenic effect of power-lines.

To activate the cancerous information present in every cell one has either to activate oncogenes or to inactivate antioncogenes. This happens in the cell with the aid of external factors, especially chemical carcinogens and radiations. Simple statistical considerations have shown that both oncogene activation by chemical carcinogens and double strand breaks by ionizing radiations leading to antioncogene inactivation are not caused only by local effects. Different mechanisms were investigated to prove the role of long-range effects of carcinogens in initiating the malignant transformation of an eucaryotic cell. Finally, on the basis of very sound theoretical correlations it is shown that neither high voltage power lines nor TV sets, terminals and other electric household appliances are hazardous for human health (and they are not causing cancer).

Investigation of the possibility of solitary waves in the base stacks of DNA.

The possibility of the existence of solitary waves in DNA is investigated. On the basis of our classical model we do not find such a wave in a polynucleotide, but for a stack of adenine molecules without backbone we observe one. Possible extensions of the model for DNA are discussed. From our results we can conclude, that solitons exist in stacked systems without an additional backbone. At least the degree of freedom which couples a nucleotide base (pair) to the sugar-phosphate backbones (N-C stretching vibration) has to be treated with the help of the quantum equations of motion.

Long-range effects of direct-hit ultraviolet and particle radiation in oncogene activation.

A simple statistical analysis shows that the oncogene-activation effect of chemical carcinogens cannot be explained if one takes into account only short-range effects. As one of the most probable solid state physical long-range effects, the generation at the site of carcinogen binding of travelling solitary waves, which can interfere with DNA-blocking protein interactions, is discussed. It has been shown that the direct hit carcinogenic effects on DNA by ultraviolet--or particle radiation can also be explained by the generation of solitary waves (in the latter case the first step is a collective plasma oscillation which decays to individual local excitations and ionizations).