Scaled in Cartesian Coordinates Ab Initio Molecular Force Fields of DNA Bases: Application to Canonical Pairs.

The model of Regularized Quantum Mechanical Force Field (RQMFF) was applied to the joint treatment of ab initio and experimental vibrational data of the four primary nucleobases using a new algorithm based on the scaling procedure in Cartesian coordinates. The matrix of scaling factors in Cartesian coordinates for the considered molecules includes diagonal elements for all atoms of the molecule and off-diagonal elements for bonded atoms and for some non-bonded atoms (1-3 and some 1-4 interactions). The choice of the model is based on the results of the second-order perturbation analysis of the Fock matrix for uncoupled interactions using the Natural Bond Orbital (NBO) analysis. The scaling factors obtained within this model as a result of solving the inverse problem (regularized Cartesian scale factors) of adenine, cytosine, guanine, and thymine molecules were used to correct the Hessians of the canonical base pairs: adenine-thymine and cytosine-guanine. The proposed procedure is based on the block structure of the scaling matrix for molecular entities with non-covalent interactions, as in the case of DNA base pairs. It allows avoiding introducing internal coordinates (or coordinates of symmetry, local symmetry, etc.) when scaling the force field of a compound of a complex structure with non-covalent H-bonds.

Electronic excitation of [(µ4-η2-alkyne)Rh4(CO)8(µ-CO)2]: an in situ UV/Vis spectroscopy, spectral reconstruction and DFT study.

Reactions of three alkynes, namely, 1-heptyne, 3-hexyne and 1-phenyl-1-butyne, with [Rh(4)(CO)(9)(µ-CO)(3)] are performed in anhydrous hexane under argon atmosphere with multiple perturbations of alkynes and [Rh(4)(CO)(9)(µ-CO)(3)]. The reactions are monitored by in situ UV/Vis spectroscopy, and the collected electronic spectra are further analyzed with the band-target entropy minimization (BTEM) family of algorithms to reconstruct the pure component spectra. Three BTEM estimates of [(µ(4)-η(2)-alkyne)Rh(4)(CO)(8)(µ-CO)(2)], in addition to that of [Rh(4)(CO)(9)(µ-CO)(3)], are successfully reconstructed from the experimental spectra. Time-dependent density functional theory (TD-DFT) predicted spectra at the PBE0/DGDZVP level are consistent with the corresponding BTEM estimates. The present study demonstrates that: 1) the BTEM family of algorithms is successful in analyzing multi-component UV/Vis spectra and results in good spectral estimates of the trace organometallics present; and 2) the subsequent DFT/TD-DFT methods provide an interpretation of the nature of the electronic excitation and can be used to predict the electronic spectra of similar transition organometallic complexes.

Effect of a pH change on the conformational stability of the modified nucleotide queuosine monophosphate.

The naturally occurring modified nucleotide queuosine 5'-monophosphate (QMP) related to biochemical regulatory pathways in the cell was investigated using quantum chemical approaches. The relative stability of biologically relevant conformations of QMP in solvent under a pH change was predicted at the BVP86/TZVP and MP2/TZVP levels of theory. Hydrogen bonding in QMP was studied using Bader's approach. The acidity constants of QMP were estimated using the COSMO-RS theory. It has been found that the neutral and anionic forms of QMP are the most stable in the physiological pH range. These forms correspond to the anti/north conformation and exist as zwitterionic tautomers having a negatively charged phosphate group (-1 for neutral and -2 for anionic) and a positively charged secondary amine group in the side chain. It was also found that QMP possesses the syn conformation in the cationic state at pH < 5.0 and undergoes syn to anti conformation transition when the pH increases, remaining in the anti conformation at the higher pH values. The marker IR bands specific for the anionic and neutral QMP forms in the 2300-2700 cm(-1) region were assigned to H-bonded NH groups of the QMP side chain. The bands between 800 and 1300 cm(-1) of the "fingerprint" (400-1500 cm(-1)) region were assigned to the vibrations of the ribose ring, the phosphate group and the side chain of QMP. The predicted IR spectra can be useful for the assignment of vibration bands in the experiential spectra of QMP or identification of the QMP forms. The revealed peculiarities of the QMP conformation sensitivity to a pH change as well as additional formed H-bonds could be responsible for specific nucleotide interactions with enzymes.