Jakub Kaminský

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The conformational degrees of freedom for four amino acids in a model peptide environment have been sampled with density functional and second-order Møller-Plesset methods. Geometries have been optimized with an augmented double-ζ basis set and relative energies estimated by extrapolation of results using double, triple, and quadruple-ζ basis sets and(More)
Convergence patterns and limiting values of isotropic nuclear magnetic shieldings were studied for several small molecules (N2, CO, CO2, NH3, CH4, C2H2, C2H4, C2H6, and C6H6) in the Kohn-Sham limit. Individual results of calculations using dedicated families of Jensen's basis sets (pcS-n and pcJ-n) were fitted toward the complete basis set limit (CBS) using(More)
Rapid growth of nanoscience and nanotechnology requires new and more powerful modeling tools. Efficient theoretical modeling of large molecular systems at the ab initio and Density Functional Theory (DFT) levels of theory depends critically on the size and completeness of the basis set used. The recently designed variants of STO-3G basis set (STO-3Gel,(More)
For spectroscopic studies of peptide and protein thermal denaturation it is important to single out the contribution of the solvent to the spectral changes from those originated in the molecular structure. To obtain insights into the origin and size of the temperature solvent effects on the amide I spectra, combined molecular dynamics and density functional(More)
Hydration envelopes of metallic ions significantly influence their chemical properties and biological functioning. Previous computational studies, nuclear magnetic resonance (NMR), and vibrational spectra indicated a strong affinity of the Mg(2+) cation to water. We find it interesting that, although monatomic ions do not vibrate themselves, they cause(More)
Reliable modeling of protein and peptide circular dichroism (CD) spectra in the far UV presents a challenge for current theoretical approaches. In this study, the time-dependent density functional theory (TDDFT), configuration interaction with single excitation (CIS), and transition dipole coupling (TDC) were used to assess the most important factors(More)
Correlated ab initio wave function calculations have been performed, using nonrelativistic frozen core MP2 complete basis set extrapolation model chemistry. The calculations have been made for three test sets of gas-phase saccharide conformations to provide reference values for their relative energies. The remaining correlation effects are estimated from(More)
The Raman optical activity (ROA) spectroscopic technique has been applied in the past to many biologically relevant systems including peptides, proteins, sugars, and even viruses. However, theoretical interpretation of the spectra relies on lengthy quantum-chemical computations, which are difficult to extend to larger molecules. In the present study, ROA(More)
It is shown that a linear correlation exists between nuclear shielding constants for nine small inorganic and organic molecules (N(2), CO, CO(2), NH(3), CH(4), C(2)H(2), C(2)H(4), C(2)H(6) and C(6)H(6)) calculated with 47 methods (42 DFT methods, RHF, MP2, SOPPA, SOPPA(CCSD), CCSD(T)) and the aug-cc-pVTZ-J basis set and corresponding complete basis set(More)
Experimental and theoretical specific optical rotations (OR) of anhydro, epithio, and epiminoderivatives of methyl tetrofuranosides in chloroform solutions have been compared and used as a tool for exploring their conformational behavior. The potential energy surfaces of these saccharides with reduced flexibility were examined with the density functional(More)