Free energy perturbation approach to the critical assessment of selective cyclooxygenase-2 inhibitors

The discovery of selective cyclooxygenase-2 (COX-2) inhibitors represents a major achievement of the efforts over the past few decades to develop therapeutic treatments for inflammation. To gain insights into designing new COX-2-selective inhibitors, we address the energetic and structural basis for the selective inhibition of COX isozymes by means of a combined computational protocol involving docking experiment, force field design for the heme prothetic group, and free energy perturbation (FEP) simulation. We consider both COX-2- and COX-1-selective inhibitors taking the V523I mutant of COX-2 to be a relevant structural model for COX-1 as confirmed by a variety of experimental and theoretical evidences. For all COX-2-selective inhibitors under consideration, we find that free energies of binding become less favorable as the receptor changes from COX-2 to COX-1, due to the weakening and/or loss of hydrogen bond and hydrophobic interactions that stabilize the inhibitors in the COX-2 active site. On the other hand, COX-1-selective oxicam inhibitors gain extra stabilization energy with the change of residue 523 from valine to isoleucine because of the formations of new hydrogen bonds in the enzyme-inhibitor complexes. The utility of the combined computational approach, as a valuable tool for in silico screening of COX-2-selective inhibitors, is further exemplified by identifying the physicochemical origins of the enantiospecific selective inhibition of COX-2 by -substituted indomethacin ethanolamide inhibitors.     

扩散限制聚集与粘性指化图案的模拟研究

扩散限制聚集与粘性指化图案的模拟研究顾健德，田安民，鄢国森（四川大学化学系，成都，６１００６４）关键词ＤＬＡ，粘性指化，计算机模拟大自然经常以非常奇妙的方式向人们展示其魅力，吸引人们不断去思考和探索．四川大学图书馆文献阅览室的玻璃顶棚上出现的粘性指化...     

Cyclic Voltammetric Study of the Oxidation of Catechols in the Presence of Cyanide Ion

Electrochemical oxidation of catechols has been studied in the presence of cyanide ion as nucleophile in aqueous solution, by means of cyclic voltammetry and controlled‐potential coulometry. The results indicate that the participation of catechols in the Michael reaction with cyanide ion to form the corresponding o‐dihydroxybenzonitrile. Based on an EC mechanism, the homogeneous rate constants were estimated by comparing the experimental cyclic voltammetric responses with the digital simulated results.     

室温熔盐二(三氟甲基磺酸酰)亚胺锂-尿素体系的分子动力学模拟

应用分子动力学模拟了25 ℃和50 ℃时新型室温熔盐二(三氟甲基磺酸酰)亚胺锂[LiN(SO2CF3)2, LiTFSI]与尿素(摩尔比为1:3.6)体系的结构与动力学性质. 在两个温度下体系的微观结构基本相同, Li+的配位数约为5, 且都是与溶剂和阴离子中的氧原子发生配位. 对TFSI-的研究表明, 每个TFSI-只提供四个氧中的一个与Li+配位; 而且在Li+的配位层中, TFSI-具有顺、反和gauche 等不同的构象, 并且不同构象出现的几率会随着温度的改变而改变.     

Determination of molecular orientation distribution of a stable paramagnetic probe in oriented 4-cyano-4’-<Emphasis Type="Italic">n</Emphasis>-pentylbiphenyl

The molecular orientation distribution function of a stable radical 4-hydroxy-2,2,6,6-tetramethylpiperidine-1-oxyl in magnetic-field oriented 4-cyano-4’-n-pentylbiphenyl was determined from the angular dependence of the ESR spectra. The preferred molecular orientation of radical species in the liquid crystal matrix was determined. The temperature evolution of the orientation distribution function was studied.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 190–195, January, 2005.     

Hydrolysis and Condensation of Transition Metal Alkoxide: Experiments and Simulations

We present here an experimental and numerical study of the chemical and aggregative mechanisms for titanium alkoxide in a reverse micellar medium. NMR experiments were done to study the first step of the sol-gel process: hydrolysis of titanium isopropoxide. Light and X-ray scattering experiments were then conducted to characterize the clustering of aggregates and aggregation kinetics. Fractal dimension, measured by U.S.A.X.S., varies with the hydrolysis ratio and the hydration of the surfactant. This evolution was explained by polydispersity of the hydrolysis which depends on the surfactant concentration. This hypothesis was tested through a numerical simulation of irreversible aggregation using a chemically limited aggregation model. The hydrolyzed sites are distributed among the monomers by a random procedure governed by a polydispersity parameterp, varying from 0 to 1. The total number of hydrolyzed sites is governed by a parameterq belonging to the interval [0, 1]. Thep-q evolution of the fractal dimension coincides rather well with the experimental data in all the region of the two dimensional phase space.     

Lithium bromide in acetonitrile: Thermodynamics,theory, and simulation

A variety of methods has been used for the study of lithium bromide solutions in acetonitrile yielding by their combination reliable information on different levels of approximation. Osmotic coefficients based on precise vapor pressure measurements are reproduced by CM (chemical model) and HNC (hypernetted chain) calculations and by BD (brownian dynamics) simulations. The results of neutron scattering experiments are treated with the help of HNC and BD methods. Hartree-Fock calculations on isolated LiBr pairs and solvated lithium ions yield reliable particle distances and reveal the geometry of the lithium solvation sphere.     

Elastic behavior of non-Gaussian polymethylene chains

In this paper, elastic behaviors of non-Gaussian polymethylene (PM) chains with chain length N=100 are investigated by rotational isomeric state model. Here the tetrahedral lattice of PM chain and the non-local interaction of Sutherland potential are adopted. In the metropolis movement of PM chain, a four-bond movement model is used. The average energy and average Helmholtz free energy with various elongation ratios λ are calculated by Monte Carlo simulation method. The average energy increases with elongation ratio λ and the average Helmholtz free energy decreases with elongation ratio λ. The elastic force f and the energy contribution to elastic force f_u can be obtained from f=∂〈A〉/∂r and f=∂〈U〉/∂r. We find that the elastic force f increases with elongation ratio λ and the energy contribution f_u decreases with elongation ratio λ, and f_u is less than zero. The ratio f_u/f is close to −0.21 for λ?1.25, and −0.04 to −0.35 for λ>1.25 at T=364 K. In our calculation, the rubber elasticity may be discussed in terms of the chemical structure of polymer chains.     

Structural Analysis of Ti And Pb Citrate Using NMR and FT-Raman Signals and Quantum Mechanics Simulations

Titanium citrate and lead and titanium citrate were prepared by polymeric precursor method in aqueous solution. This citrate was analyzed by ¹H, ¹³C NMR and gHMBC–NMR (Hetero-nuclear multiple-bond correlation) to investigate the formation of the citrate complexs and influence of the Pb²⁺ ion in this complex. These complexs were characterized by interaction between Ti⁴⁺ ion and citric acid carboxyls. Quantum mechanic simulations in level ab initio were used to study the electronic structure and natural charges (NBO) to both the complexs. Such techniques indicated the formation of an octahedral complex with an arrangement similar to Ti atom in the crystalline structure of the PbTiO₃. A study using the technique FT-Raman made possible the confirmation of the interaction among the Ti⁴⁺ and Pb²⁺ ions with the citric acid carboxyls.