Free energies of transfer of complexes of the type MCl2py4 between pyridine and other solvent media

Solubility isotherms are reported for the NiCl₂·4py, MnCl₂·4py, and MnCl₂·2py solid pyridinates in a number of pyridine+diluent mixtures at 25°C. Activity coefficients of the solvent components have been derived from the total vapor pressures measured by a static method. The standard free energies of transfer for the NiCl₂py₄ and MnCl₂py₄ complexes are the same, within the experimental error, in the pyridine+aprotic diluent mixtures, while marked differences are observed in the pyridine+chloroform mixtures. Marked deviations are observed for chloroform and 1,2-dichloroethane from a correlation between the standard free energy of transfer of the complexes, on one hand, and the Hildebrand's solubility parameter of the solvent, on the other, the latter correlation being roughly valid for aprotic solvents. The deviations are tentatively ascribed to hydrogen bond formation of the type H... between the protic solvents and the coordinated pyridine molecules, enhanced by the d electron delocalization.     

Double photoionisation spectra of small molecules and a new empirical rule for double ionisation energies

Complete double photoelectron spectra are presented for 18 small molecules where the location of charges in the cations and dications is relatively clearly defined. The data demonstrate the importance of a coulombic repulsion contribution to the double ionisation energies. Examination of data for a wide range of molecules leads to a new empirical rule to calculate double ionisation energies from the molecules’ single ionisation energies and maximum dimensions. Where single and double ionisation energies are known the rule allows the deduction of plausible intercharge distances.     

A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase

Summary A molecular dynamics/energy-minimisation protocol has been used to analyse the structural and energetic effects of functional group substitution on the binding of a series of C4-modified 2-deoxy-2,3-didehydro-N-acetylneuraminic acid inhibitors to influenza virus sialidase. Based on the crystal structure of sialidase, a conformational searching protocol, incorporating multiple randomisation steps in a molecular dynamics simulation was used to generate a range of minimum-energy structures. The calculations were useful for predicting the number, location, and orientation of structural water molecules within protein-ligand complexes. Relative binding energies were calculated for the series of complexes using several empirical molecular modelling approaches. Energies were computed using molecular-mechanics-derived interactions as the sum of pairwise atomic nonbonded energies, and in a more rigorous manner including solvation effects as the change in total electrostatic energy of complexation, using a continuum-electrostatics (CE) approach. The CE approach exhibited the superior correlation with observed affinities. Both methods showed definite trends in observed and calculated binding affinities; in both cases inhibitors with a positively charged C4 substituent formed the tightest binding to the enzyme, as observed experimentally.This paper is based on a presentation given at the 14th Molecular Graphics and Modelling Society Conference, held in Cairns, Australia, August 27–September 1, 1995.Presently on a visiting postdoctoral fellowship in the Department of Biomolecular Structure, Glaxo Research & Development Ltd, Greenford, Middlesex UB6 OHE, U.K.     

Theoretical investigation of isotopic scrambling mechanisms in 2-chloroethyl methyl sulfide

Ab initio and semiempirical molecular orbital calculations have been applied to study the concerted and stepwise isotopic scrambling mechanisms of 2-chloroethyl methyl sulfide in the gas phase and in aqueous solution. The calculations reveal the structural details of the reactants, transition structures, and intermediates involved in this reaction and provide relative energy estimates. The concerted mechanism is found to be competitive with the stepwise mechanism in the gas phase, but the stepwise mechanism is favored in aqueous solution as no true transition structure for the concerted mechanism could be found using the solvation models. A combined approach of evaluating solvation energies with the generalized-Bom-plus-surface-tensions SM _x solvation models of Cramer and Truhlar at ab initio optimized geometries is found to deliver the best agreement with experimentally determined reaction barriers. Together with the recent experimental results of McManus and co-workers, the present study provides insights into the controlling factors involved in the elementary reaction steps of sulfur mustards and a solid foundation for investigations into more complex reactions of related compounds.     

Inner shell structure of heavy atoms

The inner-shell structure of some heavy atoms is examined using a self-consistent relativistic local density method. Ar(K), Kr(K) and Xe (K,L ₁,L ₂ andL ₃) binding energies and {ie863-1} (hyper-satellite) energies of Tl, Hg and Tm are calculated. The results are compared with available experimental data. A part of this work was presented byMPD at the Trieste International Symposium on “Core level excitations in atoms, molecules and solids,” 22–26 June 1981, Extended Abstracts (ed.) E Tosatti, ICTP Report No. 89/81 p. 11.     

Degradation Kinetics of an Epoxy/Cycloaliphatic Amine Resin Under Isothermal and Non-isothermal Conditions

A study of an epoxy-cycloaliphatic amine system has been realized using a thermogravimetric technique (TG). Isothermal and non-isothermal (dynamic) methods were employed to determine the kinetic data of this system. Five methods were used for determining the activation energies of this system in the dynamic heating experiments. In two of them (Flynn-Wall-Ozawa, and Kissinger) it is not necessary to have a prior knowledge of the reaction mechanism of the degradation behaviour for this system. In the other ones (Coats and Redfern, Horowitz and Metzger, and Van Krevelen et al.) it is necessary to know this reaction mechanism, besides Criado et al. method was used for determining it. The results have shown that good agreement between the activation energies obtained from all methods can be achieved if it is assumed that the degradation behaviour of this system is of sigmoidal-rate type. This revised version was published online in August 2006 with corrections to the Cover Date.     

有机链状分子的定域分子轨道的研究

利用Foster-Boys定域化程序和STO-3G ab initio方法,对含有C、H、O、N原子的100多个有机链状分子进行了研究,得到定域分子轨道能量及其相互作用参数。应用这些参数和定域分子轨道模型,对于众多的含有C、H、O、N原子的有机链状分子,可得到相应的正则分子轨道能量及其与定域分子轨道的关系。以此预测它们的电离能,结果与实验值符合较好。     

Comprehensive DFT and MO studies on glyoxilic acid oxime and related ions in gas phase and solution: Conformations,basicities and acidities

Density functional (BLYP, B3LYP and BHLYP) and highly correlated MP2 and CCSD(T) calculations have been performed to investigate conformers, energy barriers, intramolecular H-bond strength, gas-phase basicity and deprotonation energies of glyoxilic acid oxime (gao) and related ions in gas phase and in aqueous solution (SCRF-PCM method). BHLYP/6-311G(d,p) and B3LYP/6-31++G(d) predictions for the global minimum conformer of gao were consistent with experiment. BLYP level overestimated the H-bond and stabilized incorrectly the H-bonded conformer. The calculations in solution indicated destabilization of H-bonded conformers due to the small polarizability and weaken of the H-bond. The same global minimum structures in gas phase and aqueous solution were found for gao-neutral (ectt) and gao-dianion (e⁻²), whereas they were different for gao-anion because of the strong decrease of the conformational energies in solution. The global minimum structures of the neutral, anion and dianion of gao, obtained in solution, are in agreement with experiment. The gas-phase basicity (GB) and molecular electrostatic potential (MEP) calculations revealed the same sites for electrophilic attack, supported by the nature of HOMO: the carbonylic oxygen for the neutral, the carboxylic oxygen for the anion and the oxime nitrogen for the dianion. MEP results in gas phase and in solution suggested a region between the two atoms, but not on one atom in accordance with bidentate binding of gao ions to a metal. The BHLYP/6-31++G(d,p) molecular properties of gao were in best consistent with CCSD(T) results. The thermodynamical properties (GB and bond deprotonation energy) of gao were better estimated at B3LYP level.     

Intramolecular proton transfer induced by divalent alkali earth metal cation in the gas state

Interactions between divalent alkali earth metal (DAEM) ions M (M?Be, Mg, Ca, Sr, Ba) and the second stable glycine conformer in the gas phase, which can transfer into the ground‐state glycine‐M²⁺ (except the glycine–Be²⁺) among each corresponding isomers when these divalent metal ions are bound, are studied at the hybrid three‐parameter B3LYP level with three different basis sets. Proton transfers from the hydroxyl to the amino nitrogen of the glycine without energy barriers have been first observed in the gas phase in these glycine–M²⁺ systems. The interaction between the glycine and these DAEM ions except beryllium and magnesium ion only create an amino hydrogen pointing to the original hydroxyl due to their weaker interaction relative to those divalent transition metal (DTM) ion‐bound glycine derivatives, being obviously different from that between the glycine and DTM ions, in which two amino hydrogens point to the original hydroxyl oxygen when these metal‐chelated glycine derivatives are produced. The interaction energy between the glycine and divalent magnesium would be the boundary of one or two amino hydrogens pointing to the hydrogyl oxygen, i.e., the ?170.3 kcal/mol of binding energy is a critical point. Similar intramolecular proton transfer has also been predicted for those DTM ion‐chelated glycine systems; however, that in the gas state has not been observed in the monovalent metal ion‐coordinated glycine systems. The binding energy between some monovalent TM ion and the glycine is similar to that of the glycine–Ba²⁺, which has the lowest binding strength among these DAEM–ion chelated glycine complexes. The difference among them only lies in the larger electrostatic and polarized effects in the latter, which favor the stability of the zwitterionic glycine form in the gas phase. According to these observations, we predict that the zwitterionic glycine would exist in the field of two positive charges in the gas phase. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 205–214, 2003     

Rapidly converging lattice sums for nonelectrostatic interactions

The relative energies of one-, two-, and three-dimensional Bravais lattice Lennard-Jones particles can be calculated by lattice sums. The expression of lattice sums over a Lennard-Jones potential can be manipulated into a form that converges rapidly. A formalism capable of calculating the lattice potential at arbitrary points of a completely general lattice has been developed. This method provides an alternative way to calculate the relative energies from the surface and the interior bulk sites of many chemical systems. The method is illustrated with application to hcp and fcc Lennard-Jonesium, both for the relative binding energy and for calculating the potential along the geometric diffusion pathway between tetrahedral and octahedral interstitial sites. Diffusion from the tetrahedral site to the octahedral site experiences a barrier of 752.600 in units of 4 epsilon. The reverse pathway experiences a barrier of 1035.614 in units of 4 epsilon.