Biomedical subjects

Sławomir M Cybulski

Publications and source records attributed to Sławomir M Cybulski.

3 recordsLinked to original sources

PubMed2005

An analysis of the electrostatic interaction between nucleic acid bases.

Results from several commonly used approximate methods of evaluating electrostatic interactions have been compared to the rigorous, nonexpanded electrostatic energies at both uncorrelated and correlated levels of theory. We examined a number of energy profiles for both hydrogen bonded and stacked configurations of the nucleic acid base pairs. We found that the penetration effects play an extremely important role and the expanded electrostatic energies are significantly underestimated with respect to the ab initio values. Apart from the inability to reproduce the magnitudes of the ab initio electrostatic energy, there are other problems with the available approximate electrostatic models. For example, the distributed multipole analysis, one of the most advanced methods, is extremely sensitive to the basis set and level of theory used to evaluate the multipole moments. Detailed ab initio results are provided that other researchers could use to test their approximate models.

Base Pairing↗

PubMed2005

Critical examination of the supermolecule density functional theory calculations of intermolecular interactions.

The results of calculations employing twelve different combinations of exchange and correlation functionals are compared with results of ab initio calculations for two different configurations of the water dimer and three different configurations of the thymine-adenine complex. None of the density functional theory (DFT) treatments could properly reproduce the results of coupled-cluster calculations for all configurations examined. The DFT approaches perform well when the interaction energy is dominated by the electrostatic component and the dispersion energy is less important. Two mechanisms that compensate for the missing dispersion component were identified. The first one is the decrease of the magnitude of the intermolecular exchange-repulsion and the second one is the increase of the magnitude of the attractive deformation energy. For some functionals both effects are observed together, but for some other ones only the second effect occurs. The three correlation functionals that were examined were found to make only very small contributions to the deformation energy. The examination of angular and distance dependence of the interactions shows that the currently available DFT approaches are not suitable for developing intermolecular potential energy surfaces. They could however be used to find global minima on potential energy surfaces governed by intermolecular electrostatic interactions. Additional single point ab initio calculations are recommended as the means of validating optimized structures.

Adenine↗

PubMed2004

New approximations for calculating dispersion coefficients.

Improved approaches for finding approximate values of dispersion coefficients are proposed. They are based on scaling the values of time-dependent Hartree-Fock (TDHF) dispersion coefficients by factors that use the ratio of the estimated true value and the TDHF value of static dipole polarizabilities. It is shown that for a set of 14 atoms and molecules the average absolute-value deviation of the estimated two-body isotropic dispersion coefficients with respect to the dipole oscillator strength distribution results is smaller than 1.0% for two of our approaches. For three-body isotropic dispersion coefficients the corresponding deviations are smaller than 1.2%. Our approximations work particularly well compared to approximations proposed by other researchers in cases where the TDHF results differ from the reference values by more than 10%.

Algorithms↗