Andrzej Leś

The infrared spectra of matrix isolated uracil and thymine : an assignment based on new theoretical calculations

Abstract The IR spectra of uracil and thymine predicted theoretically at the ab initio Hartree-Fock level with 6-31G basis set are reported and compared with Ar matrix experimental spectra. The IR spectra computed at the SCF/6-31G level reproduce the experimental spectra with an accuracy which allows a reliable vibrational assignment. A split valence basis set, augmented with polarization functions on all atoms, was found to be quite sufficient for a reliable prediction and assignment of the IR absorption bands in the spectra of medium-sized molecules.

A molecular orbital study of the hydration of ions. The role of nonadditive effects in the hydration shells around Mg2+ and Ca2+

The role of divalent cations in biology, in particular Ca2+ and Mg2+, has led to many studies of the coordination of these ions. The existence of empirical rules serves to characterize these properties, however, a detailed quantum mechanical analysis of the fundamental causes which are responsible for the nature of such properties is lacking. Here, we perform a molecular orbital study of the interactions involved in the hydration scheme of the ions looking particularly into the role of nonadditive effects. Notable differences are found for the cases of Mg2+ and Ca2+.

Infrared spectra of 2-thiocytosine and 5-fluoro-2-thiocytosine; experimental and ab initio studies

Abstract IR absorption spectra of 2-thiocytosine and 5-fluoro-2-thiocytosine isolated in low-temperature, inert gas matrices and in thin polycrystalline films are reported. The spectra of amino-thiol tautomeric forms of the compounds were studied for matrix isolated species, whereas the spectra of amino-thione tautomeric forms were observed for polycrystalline films. The experimental spectra were compared with the spectra predicted with the ab initio SCF/6-31G** method. The observed IR absorption bands in the spectra of monomers (amino-thiol forms) were assigned to the theoretically calculated normal modes.

Non-additive effects in the first-order interaction energy of hydrogen atoms☆

Abstract First-order three- and four-body contributions to the interaction energy of 3 and 4 hydrogen atoms in their repulsive states of highest multiplicity have been calculated. In the case of H4 the multibody expansion of the interaction energy converges slower for a square than for a tetrahedral configuration of the atoms. Relations between various multibody terms and overlap integrals are discussed.

Theoretical and matrix-isolation experimental study of the infrared spectra of 5-azauracil and 6-azauracil

Abstract The infrared absorption spectra of 5-azauracil and 6-azauracil isolated in low-temperature Ar and N 2 matrices are reported. Within the limits of accuracy of spectroscopic measurements, both compounds appear to exist, in Ar and N 2 matrices, exclusively in dioxo tautomeric forms. An assignment of the observed infrared absorption bands is proposed based on the comparison of experimental frequencies and intensities with those calculated theoretically at ab initio Hartree-Fock level with 6-31G** basis set. Infrared spectra predicted at this level of theory reproduce the experimental spectra sufficiently accurately to enable a reliable assignment. Basis set dependency (6-31G**, 3–21G) of the theoretical result was also accounted for and it turned out that for accurate prediction of frequencies and intensities the use of basis set augmented with polarization functions is of crucial importance.

DFT study of B-like conformations of deoxydinucleoside monophosphates containing Gua and/or Cyt and their complexes with Na+ cation.

Abstract B-like minimum energy conformations of deoxydinucleoside monophosphate anions (dD-MPs) containing Gua and/or Cyt and their Na+ complexes have been studied by the DFT PW91PW91/DZVP method. The optimized geometry of the dDMPs is in close agreement with experimental observations and the obtained minimum energy conformations are consistent with purine-purine, purine-pyrimidine, and pyrimidine-purine arrangements in crystals of B-DNA duplexes. All the studied systems are characterized by pyramidalization of the amino groups, which participate in the formation of unusual hydrogen bond between the carbonyl oxygen of the second base in the dGpdC, dCpdG dDMPs, and their Na+ complexes. In all the obtained structures the bases assume a nearly parallel disposition to each other and this effect is independent on the degree of their spatial superposition. From this it is concluded that the parallel disposition of the bases in the B-like single-stranded conformations is dictated by the sugar-phosphate backbone. Correspondingly, the base-base interactions attain a secondary role in the formation of these spatial structures. The formation of a weak C6-H6…O5′ hydrogen bond between cytosine and the phosphate oxygen is reported, in agreement with experimental observations.

Thiophosphorylation of free amino acids and enzyme protein by thiophosphoramidate ions

In search of an activity-preserving protein thiophosphorylation method, with thymidylate synthase recombinant protein used as a substrate, potassium thiophosphoramidate and diammonium thiophosphoramidate salts in Tris- and ammonium carbonate based buffer solutions were employed, proving to serve as a non-destructive environment. Using potassium phosphoramidate or diammonium thiophosphoramidate, a series of phosphorylated and thiophosphorylated amino acid derivatives was prepared, helping, together with computational (using density functional theory, DFT) estimation of (31)P NMR chemical shifts, to assign thiophosphorylated protein NMR resonances and prove the presence of thiophosphorylated lysine, serine and histidine moieties. Methods useful for prediction of (31)P NMR chemical shifts of thiophosphorylated amino acid moieties, and thiophosphates in general, are also presented. The preliminary results obtained from trypsin digestion of enzyme shows peak at m/z 1825.805 which is in perfect agreement with the simulated isotopic pattern distributions for monothiophosphate of TVQQQVHLNQDEYK where thiophosphate moiety is attached to histidine (His(26)) or lysine (Lys(33)) side-chain.

The electronic and geometrical structure of aluminum fluoride anions AlF−n, n=1–4, and electron affinity of their neutral parents

The electronic and geometrical structure of AlF−, AlF−2, AlF−3, and AlF−4 as well as their neutral parents are determined at the unrestricted Hartree–Fock (UHF) and second‐order unrestricted Mo/ller–Plesset (UMP2) levels of theory. The results of the calculations are used for estimating the adiabatic electron affinity (E.A.) of the neutrals and fragmentation energies of both the neutrals and anions. All these characteristics were also recomputed using the UMP2/6‐31+G* geometry at the fourth‐order UMP4 level of theory. According to the results of the single‐, double, triple‐, and quadruple‐excitation fourth‐order Mo/ller–Plesset (MP4SDTQ) calculations, the AlF molecule in the ground state has no positive E.A., AlF2 possesses a rather high E.A. value of 1.90 eV, and AlF3 has a smaller E.A. of 0.93 eV, whereas the last member in the series AlF4 possesses an extremely high E.A. of 7.96 eV. Such a large value is related to high stability of the anion towards fragmentation opposite to the neutral AlF4 whose dis...

On the Interaction Energy Between Some Nematogenic Molecules

Abstract Calculation of the interaction energies between nematogenic MBBA and PAA molecules have been performed in the framework of the Rayleigh-Schrodinger perturbation theory, supplemented with the empirical repulsive term. The predominant role of dispersion interaction as well as negligibly small induction energy have been found. The electrostatic contribution to the interaction energy has been discussed. Some remarks relating to the possible mode of molecular motion have also been made.

Tautomerism of biologically important pyrimidines and purines: Part I. Theoretical predictions

Abstract An analysis of the tautomeric equilibrium corresponding to the gas phase and the aqueous solution has been carried out for cytosine, isocytosine and for some of their derivatives and also for uracil derivatives. The results of quantum-mechanical calculations available in the literature as well as those obtained in the present work have been used. The dominant tautomeric forms were predicted and compared with recent experimental data. The tautomerism of guanine, isoguanine, inosine and adenine corresponding to the gas phase is also discussed.