Ilya I. Marochkin

From the determination of the accurate equilibrium structure of 1-methylthymine by gas electron diffraction and coupled cluster computations to the observation of methylation and flexibility effects in pyrimidine nucleobases.

1-Methylthymine is of particular interest because it can be considered as a simple model of thymidine, in which deoxyribose attaches to thymine precisely at the N1 atom. The structure of this molecule is still unknown and so far has been experimentally studied for the first time in this work. The semiexperimental equilibrium structural parameters (r(e)(se)/∠(e)(se)) of 1-methylthymine have been determined by the gas electron diffraction (GED) method, taking into account vibrational corrections calculated with the use of the anharmonic (cubic) MP2/cc-pVTZ force constants. The methyl torsion around the C–N bond has been treated as a large-amplitude motion. For the first time, the structure of this molecule has been optimized by the very time-consuming coupled-cluster method (CCSD(T)(ae)) with the triple-ζ (cc-pwCVTZ) basis set. The obtained results have been extrapolated to the quadruple-ζ basis set at the MP2 level. It has been revealed that the methylation of uracil, especially at the nitrogen atom, leads to an increase in the flexibility of the nucleobase as well as a noticeable deformation of the pyrimidine ring.

Interplay of Experiment and Theory: Determination of an Accurate Equilibrium Structure of 1-Methyluracil by the Gas Electron Diffraction Method and Coupled-Cluster Computations

As far as fundamental knowledge is concerned, the methyl derivatives of uracil can be considered as the simplest objects for studying the structural effects due to the substitution in the pyrimidyne nucleobases. From this point of view, 1-methyluracil is of special importance in biochemistry because uracil attaches ribose in ribonucleic acid (RNA) just precisely at the N1 atom. The semi-experimental equilibrium structure (r(e)(se)) of 1-methyluracil has been determined for the first time by the gas electron diffraction (GED) method taking into account rovibrational corrections to the thermal-average internuclear distances calculated with harmonic and anharmonic (cubic) MP2/cc-pVTZ force constants with consideration of the methyl torsion as a large-amplitude motion. For the first time, the structure of the molecule has been optimized by the very time-consuming coupled-cluster method with single and double excitations and perturbative treatment of connected triples using the correlation-consistent polarized weighted core-valence triple-ζ basis set with all electrons being correlated (CCSD(T)(all)/cc-pwCVTZ) and extrapolated to the complete basis set (CBS) with the help of the MP2 calculations. Small differences between similar bond lengths of equilibrium configurations were assumed in the GED analysis at the CCSD(T)(all)/CBS values. A remarkable agreement between the semi-experimental and computed equilibrium structures points out the high accuracy of both the GED determination and the coupled-cluster computations. The effect of methylation on the structure of uracil has been analyzed.

Experiment and theory at the convergence limit: accurate equilibrium structure of picolinic acid by gas-phase electron diffraction and coupled-cluster computations

The accurate molecular structure of picolinic acid has been determined from experimental data and computed at the coupled cluster level of theory. Only one conformer with the O[double bond, length as m-dash]C-C-N and H-O-C[double bond, length as m-dash]O fragments in antiperiplanar (ap) positions, ap-ap, has been detected under conditions of the gas-phase electron diffraction (GED) experiment (Tnozzle = 375(3) K). The semiexperimental equilibrium structure, rsee, of this conformer has been derived from the GED data taking into account the anharmonic vibrational effects estimated from the ab initio force field. The equilibrium structures of the two lowest-energy conformers, ap-ap and ap-sp (with the synperiplanar H-O-C[double bond, length as m-dash]O fragment), have been fully optimized at the CCSD(T)_ae level of theory in conjunction with the triple-ζ basis set (cc-pwCVTZ). The quality of the optimized structures has been improved due to extrapolation to the quadruple-ζ basis set. The high accuracy of both GED determination and CCSD(T) computations has been disclosed by a correct comparison of structures having the same physical meaning. The ap-ap conformer has been found to be stabilized by the relatively strong NH-O hydrogen bond of 1.973(27) Å (GED) and predicted to be lower in energy by 16 kJ mol-1 with respect to the ap-sp conformer without a hydrogen bond. The influence of this bond on the structure of picolinic acid has been analyzed within the Natural Bond Orbital model. The possibility of the decarboxylation of picolinic acid has been considered in the GED analysis, but no significant amounts of pyridine and carbon dioxide could be detected. To reveal the structural changes reflecting the mesomeric and inductive effects due to the carboxylic substituent, the accurate structure of pyridine has been also computed at the CCSD(T)_ae level with basis sets from triple- to 5-ζ quality. The comprehensive structure computations for pyridine as well as for carbon dioxide have been used to examine the convergence with respect to the basis set size.

Comparable study of the structure of 1,2-bis(2-acetamidoethyl) diaziridine and 3,3-diethyldiaziridine with structures of related compounds by X-ray diffraction analysis and quantum chemical calculations

The crystal structures of 1,2-bis(2-acetamidoethyl)diaziridine and 3,3-diethyldiaziridine have been determined by single-crystal X-ray diffraction study. The studied diaziridine molecules have C2 total group symmetry. The conformation of the studied molecules is similar to those of other diaziridines. A topological study within the framework of Bader’s atoms in molecule (AIM) theory was performed for these molecules, their analogs and related compounds. From AIM and natural bond orbital (NBO) analysis data, an influence of the intramolecular interaction on chemical bonds was described and quantified. It was found that the N-N bond length increases on going from acyclic to cyclic molecules in accordance with increasing p-character of σN-N bonding orbitals. The lengthening of N-N bond lengths in diaziridine molecules in most cases is accompanied with increasing of the bond ellipticities demonstrating the π-component contribution to these bonds.