分子动力学模拟研究质子化态在HIV-1 Protease-Indinavir复合物中的作用

I型人体免疫缺陷病毒(HIV-1)蛋白酶中Asp25/Asp25'的质子化对于理论研究HIV-1蛋白酶和抑制剂的作用机制以及氨基酸变异对抗药性的影响有重要意义.分别对Protease-Indinavir(PR-IDV)复合物的六种可能的质子化态进行了5ns的分子动力学模拟,分析了不同状态对动力学特征和结构的影响,用molecular mechanics/Possion-Boltzman surfacearea(MM-PBSA)方法计算了PR和IDV在各种状态下的结合自由能.计算结果说明A链Asp25的OD2的质子化是最为可能的状态.对PR-IDV复合物中起到媒介作用的水分子与PR-IDV复合物形成的氢键进行了分析,分析结果说明不同的质子化态对水分子在PR-IDV复合物中所起的媒介作用没有影响,这一结果与我们先前对PR-BEA369复合物的研究不同.我们的研究结果为更高效的PR抑制剂的设计以及PR氨基酸变异对药物抗药性的研究提供了理论上的指导.

Excited-State Proton Transfer and Decay in Hydrogen-Bonded Oxazole System： MS-CASPT2//CASSCF Study

Herein we have employed high-level multi-reference CASSCF and MS-CASPT2 electronic structure methods to systematically study the photochemical mechanism of intramolecularly hydrogen-bonded 2-（2＇-hydroxyphenyl）-4-methyloxazole. At the CASSCF level, we have optimized minima, conical intersections, minimum-energy reaction paths relevant to the excited-state intramolecular proton transfer （ESIPT）, rotation, photoisomerization, and the excited-state deactivation pathways. The energies of all structures and paths are refined by the MS-CASPT2 method. On the basis of the present results, we found that the ESIPT process in a conformer with the OH... N hydrogen bond is essentially barrierless process; whereas, the ESIPT process is inhibited in the other conformer with the OH... O hydrogen bond. The central single-bond rotation of the S1 enol species is energetically unfavorable due to a large barrier. In addition, the excited-state deactivation of the S1 keto species, as a result of the ultrafast ESIPT, is very efficient because of the existence of two easily-approached keto S1/S0 conical intersections. In stark contrast to the S1 keto species, the decay of the S1 enol species is almostly blocked. The present theoretical study contributes valuable knowledge to the understanding of photochemistry of similar intramolecularly hydrogen-bonded molecular and biological systems.

Shallow Donor Impurity Ground State in a GaAs/AlAs Spherical Quantum Dot within an Electric Field

Using the configuration-integration methods （CI） [Phys. Rev. B 45 （1992） 19], we report the results of the Hydrogenie-impurity ground state in a GaAs/AIAs spherical quantum dot under an electric field. We discuss the variations of the binding energies of the Hydrogenic-impurity ground state as a function of the position of impurity D, the radius R of the quantum dot, and also as a function of electric field F. We find that the ground energy and binding energy of impurity placed anywhere depend strongly on the position of impurity. Also, electric field can largely change the Hydrogenic-impurity ground state only limiting to the big radius of quantum dot. And the differences in energy level and binding energy are observed from the center donor and off-center donor.

Variation in soil properties in a transformed ecosystem in Southwestern Nigeria

Variation in soil properties as a result of the conversion of the tropical rainforest to a monospecific plantation of teak, tectona grandis, was examined in Akure forest reserve in Southwestern Nigeria. Comparison was made in the active rooting zone of 50 cm soil depth. It was discovered that there were no significant differences in the physical properties except in the value of organic matter content at the top 10 cm layer but chemical properties such as the pH and organic carbon changed significantly at the top 10 cm layer. Differences in other chemical properties, such as the available P, exchangeable cations K, Ca and Mg, the exchangeable acidity and the cation exchange capacity were minor. This showed that no nutrient was limiting or was likely to be limiting in the soil for subsequent short rotation of plantation development.

High-entropy perovskite oxides: A versatile class of materials for nitrogen reduction reactions

Despite the intense research efforts directed to electrocatalytic nitrogen reduction reaction(eNRR),the NH_(3) yield and selectivity are still not up to the standard of practical application.Here,high-entropy perovskite oxides with composition Bax(FeCoNiZrY)_(0.2)O_(3−δ)(Bx(FCNZY)_(0.2)(x=0.9,1)are reported as eNRR catalysts.The eNRR activity of high-entropy perovskite oxide is enhanced by changing the nonstoichiometric metal elements at the A-site,thus generating additional oxygen vacancies.The NH_(3) yield and Faraday efficiency for B_(0.9)(FCNZY)_(0.2) are 1.51 and 1.95 times higher than those for B(FCNZY)_(0.2),respectively.The d-band center theory is used to theoretically predict the catalytically active center at the B-site,and as a result,nickel was identified as the catalytic site.The free energy values of the intermediate states in the optimal distal pathway show that the third protonation step(*NNH_(2)→*NNH_(3))is the rate-determining step and that the increase in oxygen vacancies in the high-entropy perovskite contributes to nitrogen adsorption and reduction.This work provides a framework for applying high-entropy structures with active site diversity for electrocatalytic nitrogen fixation.

Reductive dechlorination of polychlorinated biphenyls is coupled to nitrogen fixation by a legume-rhizobium symbiosis

Chlorinated persistent organic pollutants, including polychlorinated biphenyls （PCBs）, represent a particularly serious environmental problem and human health risk worldwide. Leguminous plants and their symbiotic bacteria （rhizobia） are important components of the biogeochemical cycling of nitrogen in both agricultural and natural ecosystems. However, there have been relatively few detailed studies of the remediation of PCB-contaminated soils by legume-rhizobia symbionts. Here we report for the first time evidence of the reductive dechlorination of 2,4,4＇-trichlorobiphenyl （PCB 28） by an alfalfa-rhizobium nitrogen fixing symbiont. Alfalfa （Medicago sativa L.） inoculated with wild-type Sinorhizobiurn meliloti had significantly larger biomass and PCB 28 accumulation than alfalfa inoculated with the nitrogenase negative mutant rhizobium SmY. Dechlorination products of PCB 28, 2,4＇-dichlorobiphenyl （PCB 8）, and the emission of chloride ion （C1-） were also found to decrease significantly in the ineffective nodules infected by the mutant strain SmY. We therefore hypothesize that N2-fixation by the legume-rhizobium symbiont is coupled with the reductive dechlorination of PCBs within the nodules. The combination of these two processes is of great importance to the biogeochemical cycling and bioremediation of organochlorine pollutants in terrestrial ecosystems.