Perturbation of hydrogen bonds in the adenine . thymine base pair by Na+: A quantum chemical study

Ab initio self-consistent field calculations with 4-31G and STO-3G basis sets show that Na+ are able to damage the H bonds in the formamidine . formamide complex, modeling the adenine . thymine base pair (both H bonds in the complex investigated are the same as in adenine . thymine). If a water molecule is placed between the complex and Na+, the H bonds of the model are fully protected. Covalent as well as noncovalent binding of polycyclic aromatic hydrocarbons to nucleic acids should decrease the local concentration of water as a result of the insertion of the hydrophobic hydrocarbon into the DNA and thereby increase the exposure of the DNA H bonds to Na+ attack. Thus, Na+ reaching the base pair could provoke or interfere with cell division.

Ab initio study of the (BH)2 dimer

The total interaction energy between two BH molecules was calculated as a sum of the SCF and correlation interaction energies. The latter was obtained either semiempirically or by the 2nd and 3rd order perturbation theory. It appeared to be the main contribution to the total interaction energy with some geometries. Important differences in the SCF interaction energy of different geometrical configurations of the dimer were explained by the utilization of higher terms of the Coulomb energy multipole expansion. Unexpectedly the geometry of highest stability does not correspond to the linear arrangement of the dimer but rather to the T-shaped structure.

Nature of stationary points on CNDO/2 energy hypersurfaces of van der Waals molecules formed by polar molecules

An attempt was made to find a complete set of stationary points on CNDO/2 energy hypersurface for five molecular complexes. Diagonalization of Hessian matrices served for analysis of the nature of stationary points which permits to distinguish between relative minima and saddle points. The total number of stationary points and real minima of the individual complexes is indicated in parentheses: (HF)2 (8, 1); (H2O)2 (7, 3); (LiF)2 (2, 1); (CH3OH)2 (6, 4) and CH3OH...HF (2, 1). CNDO/2 structural characteristics are compared with experimental values and with results of nonempirical calculations.

The dimer (HCl)2: Stationary points on the SCF 4-31G energy hypersurface and the role of entropy in the dimer formation

Two stationary points have been investigated on the 4-31G SCF energy hypersurface of (HCl)2. It has been shown, in agreement with experiment, that only the quasilinear structure satisfies all criteria required for a real minimum. Small heat of reaction and the crucial role of entropy in the (HCl)2 formation suggest that the dimer (HCl)2, in contrast to (HF)2, represents a true van der Waals molecule. A very small energy difference between the two stationary points (minimum and saddle point) suggests a very high rate of interconversion between two possible structures of the quasilinear form. Common features of and differences between (HCl)2 and (HF)2 are pointed out.

Molecular-orbital study of hydroxylation of collagenous proline and lysine

EHT and CNDO/2 types of calculations permit the interpretation of the course of hydroxylation of collagenous proline and lysine. Calculations were performed for the models of proline (I), zwitterion of proline (II), proline-containing peptide (III), and lysine (IV). The theoretical results are consistent with an electrophilic mechanism.