Contribution of Solvation Energy in Protein‐Peptide Recognition Systems

The contribution of solvation energy to guiding molecular recognition for six rigid protein‐peptide systems bad been evaluated by the variation in the number of the identified native‐like configurations and in the driving force of specific interaction resulting from the addition of the explicit solvation term in the force field function. The AMBER force field energy and the total energy including the force field energy and the WZS solvation energy were calculated for sampled configurations. The results obtained by the calculations of both force field and total energies were compared with each other. It suggests that the contribution of solvation energy is important to guiding the specific recognition of the systems in which the ligands possess larger hydrophobic or aromatic residues while the protein receptors provide the active surfaces with hydrophobic property.     

Phase equilibria and excess properties for binary systems in reactive distillation processes Part I. Methyl acetate synthesis

Isothermal vapor–liquid equilibrium (VLE) and excess enthalpy (H^E) data were measured for binary systems required for the design of reactive distillation processes for the methyl acetate production. The isothermal P–x data were measured with the help of a computer-operated static apparatus. A commercial isothermal flow calorimeter was used for the determination of the heats of mixing. Temperature-dependent interaction parameters for the UNIQUAC model were fitted simultaneously to the experimental data from this work and other authors.     

不同化学环境对Er^3＋离子的配位场能级结构的影响

首次在C3v点群对称汤中，运用双层点电荷配位场（DSCPCF）模型计算了CS3Y2I9晶体中Er^3 离子的59个配位场能级，与实验得到的能级比较，其均方根偏差为24．89cm^-1，而用点电荷配位场（PCF）模型计算的均方根偏差为29．08cm^-1，这说明双层点电荷配位场模型能更好地符合实验结果。同时，详细地分析CsLu2,Cs3Lu2Br9,Cs3Y2I9晶体中Er^3 离子能级结构的变化，由于Er^3 -X^-键共价性的增强，使Er^3 离子的能级重心发生红移，Cl→Br→I的配位场能级的分裂程序减小。     

Theoretical investigation of histidine-tryptophan preferential interactions

Several histidine-tryptophan complexes (either stacked or T-shaped), derived from the crystal structures available in the Brookhaven Protein Data Bank, have been examined with molecular mechanics (MM), using the Tripos force field with Gasteiger-Hückel charges, whose trend was found to be analogous to the AMBER or CHARMM ones. The MM results were compared to the ab initio MP2 results, with and without counterpoise (CP) correction, previously obtained using extended basis sets on 5-methylimidazole and indole as model systems. MM seems to underestimate the interaction energy between the two monomers when compared to the uncorrected MP2 results, while the agreement is much better after including the CP correction at the MP2 level in all cases. MM was thus used to qualitatively analyse the dependence of the stacking energy on the ring rotation at a variable distance and ring centroid displacement for these systems, while keeping the rings in parallel planes. An analogous study was carried out for a T-shaped adduct. Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 1 February 1999     

TeV能区物理的进展

综述近年各种TeV能量对撞机的计划和建造情况,TeV能区物理的理论研究进展和TeV能区物理的发展前景.     

Elemental Analysis of Cement by Calibration-Free Laser Induced Breakdown Spectroscopy (CF-LIBS) and Comparison with Laser Ablation – Time-of-Flight – Mass Spectrometry (LA-TOF-MS), Energy Dispersive X-Ray Spectrometry (EDX), X-Ray Fluorescence Spectroscopy (XRF), and Proton Induced X-Ray Emission Spectrometry (PIXE)

The purpose of the present study is to determine the elemental composition of Pakistani cement brands using calibration-free laser induced breakdown spectroscopy (CF-LIBS) and to compare the obtained results with the other analytical techniques such as, laser ablation – time-of-flight – mass spectrometry (LA-TOF-MS), energy dispersive X-ray spectrometry (EDX), X-ray fluorescence spectroscopy (XRF) and proton induced X-ray emission spectrometry (PIXE). Compositional results reveal that all the cement brands are mainly composed of calcium, silicon, iron, aluminum, magnesium, potassium, sodium, titanium, lithium and strontium with varying concentrations. The compositions obtained by LIBS and LA-TOF-MS are in good agreement with results obtained by the other standard techniques and demonstrate the potential use of LIBS for the online monitoring of industrial cement production.     

Performance of Pleurotus ostreatus Mushrooms and Spent Substrate for the Biosorption of Cd(II) From Aqueous Solution

The capacities of Pleurotus ostreatus mushroom and spent substrate were evaluated for the biosorption of cadmium (II) from aqueous solution in order to select the most efficient material for bioremediation. The optimum sorption conditions were optimized, including the pH of the aqueous solution, contact time, biomass dosage, initial metal concentration, and temperature. The sorption of cadmium on both biosorbents was also evaluated by several kinetic, equilibrium, and thermodynamic models. The possible heavy metal biosorption mechanisms were evaluated through point of zero charge (pH_pzc), Fourier-transform infrared (FTIR) spectroscopy and scanning electron microscopy coupled with energy dispersive X-ray microanalysis (SEM-EDX). Based on the results of column studies, the effectiveness of the P. ostreatus spent substrate was confirmed as a biosorbent for Cd(II) removal from aqueous solutions.     

Spin-inversion mechanisms in the reactions of transition metal cations (Sc+, Ti+, V+, Cr+, Mn+, Fe+, Co+, Ni+, and Cu+) with OCS in the gas phase: A perspective from automated reaction path search calculations

The mechanisms including spin-inversion have been systematically studied for the M⁺ + OCS → MS⁺ + CO/MO⁺ + CS (M denotes a transition metal from Sc to Cu) ion-molecule reactions using the automated reaction path search method. We used the lowest mixed-spin potential energy surface obtained from the diagonalization of the spin-coupled Hamiltonian matrix, whose diagonal elements are taken to be the lowest two spin states. This scheme can effectively locate approximate minimum energy crossing points between the two potential energy surfaces with different spin multiplicities. The spin-orbit couplings at spin-inversion points have been calculated to understand the efficiencies of nonadiabatic transitions. The obtained reaction pathways and the calculated spin-orbit couplings are employed to interpret previous experimental studies.     

Solvent effect on stabilization energy: An approach based on density functional reactivity theory

In the present article a formalism and the corresponding computational method is developed to take care of the variation of stabilization energy with solvent polarity in the process of adduct formation. For this purpose, a simple but physically insightful definition of “net desolvation energy” is proposed keeping in mind the sequence of events taking place in the process of adduct formation in a solvent. The approach used here is based on density functional reactivity theory (DFRT) and the representative samples chosen are adduct formation between (a) methyltrioxorhenium (MTO) and pyridine and (b) (azidomethyl)benzene and methylpropiolate. The generated data in case (a) is correlated with already known experimental parameter that is, formation constant (K_f). The observed trends claim that with the increase in solvent polarity interaction (or stabilization) energy becomes less negative which means that on increasing the solvent polarity the chances of adduct formation are less. This is further supported by calculating hardness values of adducts in different solvents which goes on decreasing with the increase in solvent polarity. Here, the computed data show that on increasing the polarity (i.e., dielectric constant) of the solvent, the “net desolvation energy” increases. Finally, when “net desolvation energy” is added to the stabilization energy obtained from DFRT the predicted trends are achieved.     

Computational chemistry in drug lead discovery and design

The main contributions of our group during the last 15 years developing and using biomolecular simulation tools in drug lead discovery and design, in close collaboration with experimental researchers, are presented. Special emphasis has been given to methodological improvements in the following areas: (1) target homology modeling incorporating knowledge about known ligands to accurately characterize the binding site; (2) designing alternative strategies to account for protein flexibility in high-throughput docking; (3) development of stochastic- and normal-mode-based methods to de novo design structurally diverse protein conformers; (4) development and validation of quantum mechanical semi-empirical linear-scaling calculations to correctly estimate ligand binding free energy. Several successful cases of computer-aided drug discovery are also presented, especially our recent work on viral targets.