Pseudobond ab initio QM/MM approach and its applications to enzyme reactions

This perspective article mainly focuses on the development and applications of a pseudobond ab initio QM/MM approach to study enzyme reactions. The following aspects of methodology development are discussed: the approaches for the QM/MM covalent boundary problem, an efficient iterative optimization procedure, the methods to determine enzyme reaction paths, and the approaches to calculate free energy change in enzyme reactions. Several applications are described to illustrate the capability of the methods. Finally, future directions are discussed.     

The importance of nonconventional structures in the binding of Ni<Superscript>+</Superscript> to ethynylsilanes and ethynylgermanes

The influence of the nature of the heteroatom on the Ni⁺ gas-phase binding energies of HCC–XH₃ (X is C, Si, or Ge) compounds has been investigated through the use of high-level density functional theory methods. The structures of the corresponding Ni⁺ complexes were optimized at the B3LYP/6-311G(d,p) level of theory. Final energies were obtained in single-point B3LYP/6-311+G(2df,2p) calculations. Nonconventional complexes, in which the metal cation interacts simultaneously with the CC system and with one of the X–H bonds of the substituent XH₃ group, play a significant role in the binding of Ni⁺ to HCC–XH₃ (X is Si or Ge) derivatives. Conversely, such nonconventional complexes are not local minima of the propyne–Ni⁺ potential-energy surface. This establishes a clear distinction between unsaturated carbon derivatives and the Si- and Ge-containing analogues as far as bonding to transition-metal monocations is concerned. Actually, the attachment of Ni⁺ to HCC–XH₃ (X is Si or Ge) compounds in the gas phase yields a mixture of conventional and nonconventional complexes. These agostic-type interactions can be viewed as a dative bond from the X–H bonding orbital toward the empty s orbital of the metal, and a back-donation from the valence electron pairs of the metal into the X–H antibonding orbital of the neutral species.Proceedings of the 11th International Congress of Quantum Chemistry satellite meeting in honor of Jean-Louis Rivail     

Interaction of (1-phenylethyl)indole-2-carbonitrile with C-nucleophiles

Methods of obtaining ketones and enamino esters have been developed on the basis of reactions of 1-(1-phenylethyl)indole-2-carbonitrile with organomagnesium and organozinc compounds. Removal of a benzyl group from the indole nitrogen atom by the Grignard reagent has been discovered. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 8, pp. 1179–1183, August, 2006.     

Steric control over hydrogen bonding in crystalline organic solids: a structural study of N,N'-dialkylthioureas

Hydrogen bonding in crystalline N,N'-dialkylthioureas was examined with the help of single-crystal X-ray diffraction, DFT calculations, and Cambridge Structural Database (CSD) analysis. A CSD survey indicated that unlike the related urea derivatives, which persistently self-assemble into one-dimensional hydrogen-bonded chains, the analogous thioureas can form two different hydrogen-bonding motifs in the solid state: chains, structurally similar with those found in ureas, and dimers, that further associate into hydrogen-bonded layers. The formation of one motif or another can be manipulated by the bulkiness of the organic substituents on the thiourea group, which provides a clear example of steric control over the hydrogen bonding arrangement in crystalline organic solids.     

Investigation of solution and solid-state properties of poly(R,R,4,4-cyclohexylidene diphenylene diphenyl-4,4-disulfonate)

Solution and solid-state properties of poly(R,R^′,4,4^′-cyclohexylidene diphenylene diphenyl-4,4^′-disulfonate) (PS-6: R=R^′=H; PS-7: R=CH₃, R^′=H; PS-8: R=R^′=Cl; PS-9: R=CH₃, R^′=Cl and PS-10: R=R^′=Br) have been determined and discussed in terms of nature of the substituents. Ultrasonic velocity (2 MHz) and acoustical parameters of PS-7 and PS-9 solutions in chloroform, 1,2-dichloroethane and tetrahydrofuran (THF) at 30, 35 and 40 °C have been evaluated to understand the effect of methyl and chlorine groups, concentration, and temperature on molecular interactions. The data are interpreted in light of solvent-polymer and polymer-polymer interactions. Predominant solvation is observed in THF system and the least in chloroform system at all three temperatures. The structural change is observed above 2%. Both the polymers possess structure-forming tendency and it is supported by positive values of S_n.The densities of PS-7 and PS-9 determined by floatation method are in excellent agreement with calculated values but those determined by specific volume method differ remarkably from calculated values due to solvation effect. PS-7 and PS-9 possess respectively tensile strength of 38.4 and 1.1 N/mm²; electric strength of 16.2 and 25.0 kV/mm and volume resistivity of 5.7×10¹⁶ and 1.0×1017Ωcm. The low tensile strength of PS-9 is due to low molecular weight, rigid and brittle nature of the polymer chains. PS-6 to PS-9 are thermally stable up to about 349-379 °C while PS-10 up to about 279 °C and involved two-step degradation. DTA thermograms indicated T_g at about 204-226 °C. High activation energy indicated rigid nature of the polymer chains and the positive magnitudes of ΔS* indicated less ordered transition state. The nature of the substituents (CH₃, Cl and Br) affected thermal, mechanical and electrical properties.     

DNA codes for nanoscience

The nanometer scale is a special place where all sciences meet and develop a particularly strong interdisciplinarity. While biology is a source of inspiration for nanoscientists, chemistry has a central role in turning inspirations and methods from biological systems to nanotechnological use. DNA is the biological molecule by which nanoscience and nanotechnology is mostly fascinated. Nature uses DNA not only as a repository of the genetic information, but also as a controller of the expression of the genes it contains. Thus, there are codes embedded in the DNA sequence that serve to control recognition processes on the atomic scale, such as the base pairing, and others that control processes taking place on the nanoscale. From the chemical point of view, DNA is the supramolecular building block with the highest informational content. Nanoscience has therefore the opportunity of using DNA molecules to increase the level of complexity and efficiency in self-assembling and self-directing processes.     

Structures of terminal heterocyclic groups and fluorescence-spectral properties of polymethine dyes

The fluorescence and absorption bands of carbocyanines containing pyrylium or benzoxazolium groups, their nitrogen-, sulfur-, and selenium-containing analogs, their benzohomologs, or isomeric analogs of pyrylium as terminal groups were mathematically processed using the method of moments. The regularities in the displacement of the absorption and fluorescence bands following the replacement of the heteroatom and variations of the positions of substituents in the terminal groups were explained using perturbation theory. Based on quantum-chemical calculations, the changes in the bond orders in the ground and excited states of the dyes were studied. The correlations between the moments of the experimental absorption and fluorescence bands and the frequency and the form of the chromophore vibrations were analyzed. The transition from pyrylo-4-cyanines to isomeric pyrylo-2-cyanines leads to substantial broadening of the bands, an increase in the Stokes shifts, decreases in the coefficients of asymmetry, kurtosis, and fine structure of the bands, as well as a decrease in the quantum yield of fluorescence.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 2194–2203, September, 1996.     

Osmotic and activity coefficients at 25°C for tetraalkylammonium bromides in deuterium oxide

Earlier work by Lindenbaum and Boyd has demonstrated the important role of hydrophobic interactions involving the water solvent in determining the osmotic coefficients and properties of aqueous solutions of the tetraalkylammonium halides. Osmotic coefficients of solutions of tetramethyl-, tetraethyl-, tetrapropyl-, and tetrabutylammonium bromides in the more highly structured solvent D₂O have now been determined by the gravimetric isopiestic method, using reference solutions of NaCl in D₂O. The data were fitted to the Rush-Johnson and Pitzer equations. Satisfactory agreement with the results for aqueous solutions at comparable concentrations indicates that the solution chemistry of these quaternary ammonium bromides is not highly dependent on the degree of structure of the pure solvents. Supplementary data for mixtures of Me₄NBr with Et₄NBr, Pr₄NBr, or Bu₄NBr in both H₂O and D₂O are consistent with this conclusion.On leave 1980–82 from Banaras Hindu University, India     

Elution order in gas chromatography

The retention behavior of a heterogeneous group of solutes has been examined on seven different stationary phases under isothermal and temperature-programmed conditions. Both ΔH_v (enthalpy of solute vaporization from the stationary phase) and ΔS_v (entropy of solute vaporization from the stationary phase) values were determined for each solute – stationary phase combination under isothermal conditions. Both program rate and carrier gas velocity were shown to affect solute elution order. Unless these and other experimental factors discussed are controlled, column equivalency studies based on solute elution order have dubious value.