铜锌金属天然酶活性中心量子化学计算

以菠菜叶中天然超氧化物歧化酶（SOD）铜锌活性中心及人为去掉金属锌的活 性中心为模板，运用Gaussian 94量子化学程序，在B3LYP/LANL2DZ基组水平上进行 了计算，获得了分子轨道能量、电荷分布以及原子轨道对前沿分子轨道贡献的信息 。结果表明，金属铜对于催化歧化超氧阴离子O_2~-具有至关重要的作用，而金属 锌起到稳定结构和促成构建活性中心的作用。     

氧电催化材料的多自由度思考

氧电催化反应的活性与析氧反应和氧还原反应的热动力学驱动机制密切相关。从多自由度角度考虑，包括系统自由度和量子自由度两方面。系统自由度包括形貌工程、晶格工程和配位工程等，量子自由度包括电子自旋、轨道耦合和分子键自由度等，本质均是调节活性中心和中间体分子的轨道耦合强度。因此，突破中间体自身吸附自由能的线性关系，寻找新的氧耦联路径是提高氧电催化反应活性的一个关键方向。同时，控制活性中心和惰性中间体的分子轨道，实现质子化和脱质子化的过程也是提高反应活性的有效途径。这些新思路将有助于设计高效的催化剂，为能源领域的可持续发展做出贡献。     

芬太尼及其哌啶季铵离子的电子结构研究

改进了CNDO/2计算机程序,可减少对高速内存的要求,从而实现在65K内存的计算机上对价轨道在150个以内的大药物分子的半经验自洽场计算。对芬太尼分子及其哌啶季铵离子进行了CNDO/2半经验分子轨道计算,讨论了它们的电子结构特征,指出了它们与受体作用时可能的活性中心及其作用性质。     

过渡金属化合物的CNDO计算(Ⅱ)——α-Fe吸附分子氮的活性中心模型

本文采用自旋非限制的CNDO-SCF方法研究了α-Fe吸附分子氮的活性中心模型,讨论了各种吸附模型的N_2活化程度,以及各种原子簇模型的费米能级、分子轨道系数等。     

负载型钯催化剂的硫中毒机理—硫对催化剂上CO吸附性质的影响

制备了负载型Pd/Al_2O_3和Pd/MgO催化剂,借助于CO探针分子,用原位FT-IR研究了不同状态的硫对催化剂上活性组分的影响,结果表明,吸附在多位活性中心上的硫(一般是不可逆吸附硫)除了屏蔽本身所在的活性点外,对周围单活性中心还具有电子效应;吸附在单活性中心上的硫(主要为可逆吸附硫),主要以屏蔽效应影响催化剂的性质,载体上的硫对活性组分的电子状态具有一定的影响。     

α,β-不饱和羰基化合物抗菌作用和机理的研究

采用全略微分重叠法对丁烯二酸及其酯类的量子化学参数进行了计算，并对该类化合物的分子结构特征与抗菌活性间的关系进行了相关分析．结果表明，丁烯二酸及其酯类抗菌活性依分子流水性能增强而提高，依分子内基团间作用力的增强而降低；随分子最低空轨道能量的降低，抗菌生物活性极显著上升（p＜0．01），抗代谢性能显著提高（p＜0．02）．α，β-不饱和羰基结构是该类化合物的抗菌功能域，其活性中心在β-碳和羰基氧。     

1-(2-羟乙基)-2-烷基-咪唑啉缓蚀剂缓蚀机理的理论研究

采用量子化学计算、分子动力学模拟和分子力学相结合的方法, 对6种不同烷基链长的1-(2-羟乙基)-2-烷基-咪唑啉缓蚀剂抑制H2S腐蚀的缓蚀机理进行研究, 并对其缓蚀性能进行评价. 前线轨道分布和Fukui指数表明, 6种缓蚀剂分子的反应活性区域均集中在分子的咪唑环上, 3个反应活性中心分别位于咪唑环上的N(4), N(7)和C(8)原子, 可使咪唑环在金属表面形成多中心吸附. 分子的反应活性及活性区域分布对烷基链长并不敏感. 单分子吸附能、膜的内聚能、吸附角和链间距的计算数据显示, 缓蚀剂膜的稳定性以及膜与金属基体的结合强度随链长的增加而增大; 当正构烷基碳链长度大于13时, 缓蚀剂可在金属表面形成一层高覆盖度、致密的疏水膜, 能有效阻碍溶液中的腐蚀介质向金属表面扩散, 从而达到阻碍或延缓腐蚀的目的.     

α，β－不饱和羰基化合物的分子结构特性与抗菌活性间的关系

采用全略微分重叠法计算了丁烯二酸及其酯类的量子化学参数，并对该类化合物的分子结构特征与抗菌活性间的关系进行了相关分析，结果表明，丁烯二酸及其酯类抗菌活性依分子疏水性能增强而提高，依分子内基团间作用力的增强而减小，随分子最低空轨道能量的降低，抗菌生物活性极显著上升（ρ＜０．０１），抗代谢性能显著增加（ρ＜０．０２）。α，β－不饱和羰基结构是该类化合物的抗菌功能域，其活性中心在β－碳和羰基氧。     

CaO·Al_2O_3、CaO·2Al_2O_3和CaO·6Al_2O_3水化活性的SCC-DV-X_α方法研究

用量子化学的SCC－DV－Xα方法分别对铝酸盐水泥熟料矿物CaO·Al2O3、CaO·2Al2O3和CaO·6Al2O3的价键结构与水化活性的关系进行了研究．从Ca—O键级、最低空分子轨道与最高占据分子轨道能级差及总能量状态密度等方面解释了以上三种水泥矿物的水化活性依序降低的理论原因．     

金属碳、卡宾阳离子[M—X]~+(M=Au,Ag,Cu;X=C,CH2)与甲烷反应机制研究

在CCSD(T)-REL//B2GP-PLYP水平下构建[Au(CH_2)]~+与甲烷反应的可靠反应势能面,分析了C—H键活化过程中的几何结构变化情况;对反应IRC路径上关键点进行自然键轨道(NBO)电荷和分子轨道分析,从理论上推定该氢转移过程属于氢负离子(H~-)转移.对[M—X]+(M=Au,Ag,Cu;X=C,CH_2)与甲烷反应进行对比,分析了甲烷作为氢供体反应过程的内在影响因素.M—X键能和反应活性中心C上直接参与反应的低能轨道对反应活性均起重要作用,两者协同调控微观反应机制.     

Quantum chemistry investigation on the active site of Mn-SOD

In this paper, we carried out a theoretical study on the active site structures of the Mn-SOD with ab initio Hartree–Fock SCF method, and analyzed the molecular orbital energies, charges and atomic orbital contribution to the frontier molecular orbital.     

A theoretical study on the reaction pathways of peroxynitrite formation and decay at nonheme iron centers

A computational study based on density functional theory was undertaken to identify possible reaction pathways for the formation and decomposition of peroxynitrite at models of the active sites of the nonheme superoxide scavenging enzymes superoxide reductase (SOR) and iron superoxide dismutase (FeSOD). Two peroxynitrite isomers and their possible protonated states were investigated, namely Fe? OONO^?, Fe? N(O)OO^?, Fe? OONOH, and Fe? N(O)OOH. Peroxynitrite formation at the active sites was assumed by either the interaction of a peroxynitrite cis/trans anion with the pentacoordinated iron active site or the interaction between a nitric oxide bound adduct and superoxide; both scenarios were found to be facile for all models investigated. The ferrous adducts of the Fe? OONO^?isomer were found to undergo instant heterolytic cleavage of the O? ONO bond to yield nitrite, whereas for the ferric adducts, the homolytic cleavage of the O? ONO bond to yield nitrogen dioxide was found to be energetically facile. For the Fe? N(O)OO^? isomer, the active site models of FeSOD and SOR were only able to accommodate the cis isomer of peroxynitrite. Ferric adducts of the cis Fe? OONO^? isomer were found to be energetically more stable than their trans counterparts and were also more stable than the cis adducts of the Fe? N(O)OO^? isomer; conversely, the protonated forms of all adducts of the Fe? OONOH isomer were found to be lower in energy than their equivalent Fe? N(O)OOH adducts. Multiple reaction pathways for the decomposition of the formed peroxynitrite adducts (whether the anions or the protonated forms) were proposed and explored. The energy requirements for the decomposition processes ranged from exothermic to highly demanding depending on the peroxynitrite isomer, the type of model (whether an SOR or FeSOD active site), and the oxidation state of iron. © 2014 Wiley Periodicals, Inc.     

Ab Initio Study on the Anti-HIV Activities of Hydroxyflavones

1 INTRODUCTION AIDS, in other words, Acquired Immunodefici-encysyndrome, is a viral contagious disease withhigh death rate. However, effective treatment againstit has not appeared so far. At present, about 100kinds of natural compounds that could be extractedfrom natural products or artificially synthesized havebeen found to have anti-HIV activities to some ex-tent. They belong to flavonoid, terpenoid, steroid, cou-marin, peptide, alkaloid etc., respectively. Previousstudies show that…     

The Exact Icosahedral Symmetry Relations for Atomic Overlaps,Molecular Orbitals and Vibrational Species of C60 Buckyballs

A computer adapted vector method and Euler angle transformation procedures are used to generate the relationship between the atomic orbitals of icosahedral C₆₀ Buckminsterfullerene cluster and to produce symmetry adapted molecular orbitals and vibrational species. The atomic overlaps based on the orientational relationship of the orbitals are used to compute the approximate molecular orbital energies and normalization constants. One of the vibrations of A_u, symmetry is used to interpret the isomeric (dyotropic) rearrangement that breaks and forms two bonds to change two pentagons to two hexagons and vice versa.     

Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation

Summary Molecular dynamics (MD) simulations of 100 ps have been carried out to study the active-site behaviour of the Cu,Zn superoxide dismutase dimer (SOD) in water. The active site of each subunit was monitored during the whole simulation by calculating the distances between functional residues and the catalytic copper. The results indicate that charge orientation is maintained at each active site but the solvent accessibility varies. Analysis of the MD simulation, carried out by using the atomic displacement covariance matrix, has shown a different intra-subunit correlation pattern for the two monomers and the presence of inter-subunit correlations. The MD simulation presented here indicates an asymmetry in the two active sites and different dynamic behaviour of the two SOD subunits.     

Structure-Activity Relationship of Fluoroquinolones Against K:pneumoniae

The structure-activity relationship of °uoroquinolones, which show anti-K. pneumoniae activity, was studied by using principal component analysis (PCA) and hierarchical cluster analysis (HCA). The PCA results showed that the lowest unoccupied molecular orbital energy, energy difference between the highest occupied and the lowest unoccupied molecular orbital, dipole moment, net atomic charge on atom I, molecular polarizability, partition coe±cient and molecular refractivity of these compounds are responsible for the separation between high-activity and low-activity groups. The HCA results were similar to those obtained with PCA. By using the chemometric results, four synthetic compounds were analyzed through PCA and HCA, and three of them are proposed as active molecules against K. pneumoniae which is consistent with the results of clinical experiments. The methodologies of PCA and HCA provide a reliable rule for classifying new °uoroquinolones with anti-K. pneumoniae activity.     

Transferability of modified atomic orbitals

The modified atomic orbital basis set determined for molecular orbital calculations on a given molecule is shown to be transferable to other molecules. This transferability is examined using the modified atomic orbital basis set determined for the carbon atom in methane for calculations on ethane, propane, butane, cyclohexane, acetylene, ethylene and benzene.     

Interaction of gas phase atomic hydrogen with Pt(111):Direct evidence for the formation of bulk hydrogen species

Employing hot tungsten filament to thermal dissociate molecular hydrogen,we generated gas phase atomic hydrogen under ultra-high vacuum(UHV)conditions and investigated its interaction with Pt(111) surface.Thermal desorption spectroscopy(TDS)results demonstrate that adsorption of molecular hy- drogen on Pt(111)forms surface Had species whereas adsorption of atomic hydrogen forms not only surface Had species but also bulk Had species.Bulk Had species is more thermal-unstable than surface Had species on Pt(111),suggesting that bulk Had species is more energetic.This kind of weakly- adsorbed bulk Had species might be the active hydrogen species in the Pt-catalyzed hydrogenation reactions.