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.     

A Dynamic Analysis and Numerical Simulation of Explosive Development of an Extratropical Cyclone Over Land

The present paper has made a dynamic and diagnostic study of the process of explosive deepening of an extratropical cyclone over North China on April 25-26, 1983, in order to gain an insight into the physical mechanism of explosive development of cyclone over land. It turns out that this cyclone occurred in the strong baroclinic zone, and the vorticity and thermal advection triggered the initial development of the cyclone. Subsequently, as the rainfall increased, the effect of condensational heating became more and more important. During the time period of rapid intensification (from 1200GMT 25 to 0000GMT 26 April, 1983, the central surface pressure fell down from 998. 2 to 988. 3 hPa), the peak of diabatic heating profile continuously descended, leading to a rapid increase in heating amount in the lower troposphere. This condition is favorable to the explosive development of rotational circulation or vortex. The numerical simulations have further demonstrated the importance of the lowering of heating p     

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...     

Dynamic percolation transition induced by phase separation: A Monte Carlo analysis

The percolation transition of geometric clusters in the three-dimensional, simple cubic, nearest neighbor Ising lattice gas model is investigated in the temperature and concentration region inside the coexistence curve. We consider quenching experiments, where the system starts from an initially completely random configuration (corresponding to equilibrium at infinite temperature), letting the system evolve at the considered temperature according to the Kawasaki spinexchange dynamics. Analyzing the distributionn _l(t) of clusters of sizel at timet, we find that after a time of the order of about 100 Monte Carlo steps per site a percolation transition occurs at a concentration distinctly lower than the percolation concentration of the initial random state. This dynamic percolation transition is analyzed with finite-size scaling methods. While at zero temperature, where the system settles down at a frozen-in cluster distribution and further phase separation stops, the critical exponents associated with this percolation transition are consistent with the universality class of random percolation, the critical behavior of the transient time-dependent percolation occurring at nonzero temperature possibly belongs to a different, new universality class.     

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.     

乳液聚合共聚物玻璃化转变温度及其理论计算

从共聚单体的竞聚率、油相水相分布系数出发,通过动力学模拟计算了丙烯酸丁酯与醋酸乙烯酯乳液共聚物的链结构,并用Johnson公式对其玻璃化转变温度(T_g)进行了理论计算,给出了共聚物T_g及其对应聚合物的重量分布图。发现半连续共聚物有1个T_g,其值随共聚物组成而变化;但一步法共聚物有两个T_g:低温区T_g代表富丙烯酸丁酯共聚物,高温区T_g则代表PVA均聚物。计算结果与实验十分吻合。     

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.     

Fixed-bed adsorption of carbon dioxide/methane mixtures on silicalite pellets

The adsorption of carbon dioxide and methane on silicalite pellets packed on a fixed bed has been studied. Equilibrium and kinetic measurements of the adsorption of carbon dioxide and methane have been performed, and a binary adsorption isotherm for carbon dioxide/methane mixtures has been obtained. A model based on the LDF approximation for the mass transfer has been used to describe the breakthrough curves obtained experimentally. A PSA cycle has been proposed for obtaining methane with purity higher than 98% from carbon dioxide/methane mixtures containing 38% and 50% methane, and its performance has been simulated using the proposed model. The simulation results show that silicalite can be a suitable adsorbent for employment in a PSA separation process for carbon dioxide removal from coalseam and landfill gases.     

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.