In order to examine the influence of the transition metal on the metal-silyl fragment MSiH3 and the metal-silicon bond, polarized Raman spectra of the complexes (C5R5)(CO)2FeSiH3 R = H (Cp) (1a), Me (Cp*) (1b)], (C5H5)(CO)(PPh3)FeSiH3 (1c), (C5Me5)(CO)2RuSiH3 (2), (C5R5)(CO)2(PMc3)MoSiH3 [R = H (3a), Me (3b)], and (C5R5)(CO)2(PMe3)WSiH3 [R = H(4a), Me (4b)] have been recorded. The spectral data have been evaluated and interpreted on the basis of a normal coordinate analysis of the MSiH3 core and the derived force constants and potential energy distributions were compared to results obtained for analogous halogen derivatives in the series XSiH3 [X = Br (5), I (6)]. 相似文献
A comparison has been made of conformational changes in the DNA molecule during its interaction in solution with different binuclear coordination compounds of platinum [Pt(NH3)2Cl-R-Pt(NH3)2Cl]Cl2 in cis and trans conformations, which contain cytosine, pyrazine, and carboxypyrazine as the common ligand (R). The influence of concentration of the components, and in particular, of ionic strength of the solution on the complexation process was studied. The influence of the nature of the common ligand, and of cis and trans conformations of coordination compounds on the character of their interaction with DNA was considered. A comparison was made between the structures of DNA complexes with mono-and binuclear compounds with the same set of ligands in the platinum coordination sphere. 相似文献
Novel ionic liquids with dual acidity, of which the cation contains Brφnsted acidity and anions contain Lewis acidity were synthesized. These ionic liquids obtained were identified by NMR, FF-IR, SDT and FAB-MS. Their acidities were determined by pyridine probe on IR spectrography. 相似文献
QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169-176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (approximately 16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 A) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product-reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute approximately 40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies. 相似文献
The diphosphate ester (ThDP) of thiamin (vitamin B1) is an important cofactor of enzymes within the carbohydrate metabolism. The initial reaction step shared by all ThDP-dependent enzymes is the deprotonation of the C2–H of the thiazolium ring. The replacement of the 4′-amino group by a hydroxyl one in the pyrimidine ring leads to the oxy-ThDP analogue which is known as an antagonist in thiamin catalysis.
Ab initio and DFT calculations on the MP2/6-31G* and B3LYP/6-31G* level were performed to study the proton relay function in thiamin and oxythiamin systems. Both MP2 and B3LYP calculations show significant differences of the reaction coordinate of the ylide formation in the systems. Tautomers, protonated and deprotonated species of both systems show different trends regarding their stability. The influence of correlation effects on the results is discussed by comparison with the HF-SCF/6-31G* data. Frequency calculations on the B3LYP/6-31G* level were performed to characterize the minima and transition state structures, respectively. 相似文献