用量子力学研究膦化三氢化铝储氢材料在磷化氢催化作用下的释氢反应机理

利用量子力学第一原理研究了储氢材料膦化三氢化铝(AlH3PH3)在催化剂膦(PH3)作用下的释氢反应机理;首先在MP2/aug-cc-pVDZ水平上计算了反应物、过渡态和产物的几何构型和频率,进而利用内禀反应坐标理论确定了反应的最小能量路径,随后在CCSD(T)/aug-cc-pVDZ水平上对基于MP2优化的几何构型进行了能量校正.结果表明,AlH3PH3释氢的能垒高于Al―P键的离解能,而催化剂PH3不能降低AlH3PH3的释氢能垒.因此,需要寻找其他的催化剂以使AlH3PH3成为一种合用的储氢材料.     

表皮生长因子受体和抑制剂之间分子对接的研究

研究了表皮生长因子受体(EGFR)和4-苯胺喹唑啉类抑制剂之间的相互作用模式，表皮生长因子受体的三维结构通过同源蛋白模建的方法得到，而抑制剂和靶酶结合复合物结构则通过分子力学和分子动力学结合的方法计算得到。从模拟结果得到的抑制剂和靶酶之间的相互作用模式表明范德华相互作用、疏水相互作用以及氢键相互作用对抑制剂的活性都有重要的影响，抑制剂的苯胺部分位于活性口袋的底部，能够与受体残基的非极性侧链产生很强的范德华和疏水相互作用，抑制剂双环上的取代基团也能和活性口袋外部的部分残基形成一定的范德华和疏水性相互作用，而抑制剂喹唑啉环上的氮原子能和周围的残基形成较强的氢键相互作用，对抑制剂的活性有较大的影响，计算得到抑制剂和靶酶之间的非键相互作用能以及抑制剂和靶酶之间的相互作用信息能够很好地解释抑制剂活性和结构的关系，为全新抑制剂的设计提供了重要的结构信息。     

单核锌双卟啉配合物构象平衡的理论研究及光谱分析

合成了一系列以不同长度柔韧链相连的p/p型单核锌双卟啉配合物。选用Tripos力场,利用分子动力学模拟退火和分子力学构象搜索相结合的方法对该系列双卟啉进行了能量优化和构象分析。理论计算结果表明:该类双卟啉稳定存在的最低能量构象为叠合式,最高能量构象为伸展式,并存在一系列的中间能量构象;双卟啉分子内π-π作用和能量转移与双卟啉存在的两种主要构象密切相关;分析了分子内π-π作用的本质。运用不同光谱测试手段验证了理论计算结果: 利用可见和相应二阶导数吸收光谱研究了双卟啉主要存在的叠合式和伸展式构象,通过红外光谱观察了对双卟啉构象和卟啉环间π-π作用较为敏感的吸收谱带;利用荧光光谱计算了双卟啉的分子内能量转移效率。     

超临界NaCl水溶液的分子动力学模拟

采用分子动力学模拟的方法对超临界NaCl水溶液的微观结构进行了研究.模拟发现在所研究超临界条件下,密度的变化比温度的变化对超临界NaCl水溶液的微观结构影响更大.温度及密度对Cl－ H2O径向分布函数的影响比对Na＋ H2O径向分布函数的影响要大.超临界条件下,各gNa＋－Cl－在0.261 nm处出现峰值,表明Na＋、Cl－之间发生了离子的缔合.超临界条件下,随温度增加,缔合作用增强；随密度增加,缔合作用减弱.本文工作为建立可适用于超临界条件下的电解质热力学模型提供了依据.     

Barriers to Internal Rotation and Conformational Behaviour of the MESO and D,L Isomers of Pt(II) Complexes with Antitumour Activity

Abstract

The conformational behaviour of a series of ring substituted (ortho-Cl, F and meta or para OH) Pt(II) complexes of general formula [(1,2-hydroxyphenyl)ethylenediamine]PtL₂ [L ? Cl, 1] has been studied by molecular mechanics (MM) methods. Preferred orientations of the phenyl rings, which are important for the complexes′ biological activity, were obtained by calculations of rotational energies about C_sp3?C_ar bonds for all theoretically possible isomers and conformers, meso-λ (R,S/S,R-λ), meso-δ (R,S/S,R-δ), d,l-δ (S,S/R,R-λ) and d,l-λ (S,S/R, R-δ). The influence of the ring substituents and the conformation type on the positions of the energy minima and barriers to rotations about C_sp3?C_ar and C_ar-O(H) bonds were investigated in detail. Theoretical predictions were compared with the experimental results where appropriate.     

Complete-active-space self-consistent-field/Amber parameterization of the Lys296–retinal–Glu113 rhodopsin chromophore-counterion system

A special hybrid quantum mechanics/molecular mechanics forcefield is defined, parameterized and validated for studying the photoisomerization path of the retinal chromophore in the rhodopsin protein. It couples a multireference ab initio Hamiltonian (CASSCF and second-order multireference many-body perturbation theory using a CASSCF reference) to describe the chromophore while the rest of the protein is approximated with the Amber forcefield. The frontier has been carefully parameterized in order to reproduce full quantum mechanics torsional energy profiles, for both the ground state and the first excited state. It is also shown that replacing the chromophore counterion with point charges is a valid approximation. This result is interpreted in terms of a cancellation effect for which a possible explanation is given.     

Extraction of kinetic information from single-molecule experiments.

We discuss two possible approaches for extracting kinetic information from single-molecule experiments. The first approach is based on computing correlation functions from measured fluorescence signals, and the second on studying the statistics of on and off times of the same fluorescence signal. We show that in both cases it is possible to extract kinetic information about the nature of intramolecular fluctuations of the single molecule. We show that for single-molecule kinetics the intramolecular fluctuations produce stochastic memory effects which lead to new dynamic features that do not exist in traditional chemical kinetics. In particular, we investigate a new type of chemical oscillations in correlation functions observed experimentally by Edman and Rigler (Proc. Natl. Acad. Sci. USA 2000, 97, 8266).     

Reverse-docking as a computational tool for the study of asymmetric organocatalysis

A novel methodology for 'reverse-docking' a cationic peptide-based organocatalyst to a rigid anionic transition state (TS) model for the conjugate addition of azide to alpha,beta-unsaturated carbonyl substrates is described. The resulting docking poses serve as simplified TS models for enantioselective catalysis. Molecular mechanics-based scoring and ranking of the docking poses, followed by clustering and structural analysis, reveal a clear energetic preference for docking to the S-enantiomeric azidation TS model, in agreement with experiment. Clear energetic trends emerged from docking the catalyst to both enantiomers of all six azidation TS models of this study. Structural analysis of the most favorable pose suggests a mechanism for enantioselective catalysis that is consistent with principles of molecular recognition, catalysis, and experimental data.     

Intramolecular charge transfer in pyrromethene laser dyes: photophysical behaviour of PM650.

Absorption and fluorescence (steady-state and time-correlated) techniques are used to study the photophysical characteristics of the pyrromethene 650 (PM650) dye. The presence of the cyano group at the 8 position considerably shifts the absorption and fluorescence bands to lower energies with respect to other related pyrromethene dyes; this is attributed to the strong electron-acceptor character of the cyano group, as is theoretically confirmed by quantum mechanical methods. The fluorescence properties of PM650 are intensively solvent-dependent. The fluorescence band is shifted to lower energies in polar/protic solutions, and the evolution of the corresponding wavelength with the solvent is analysed by a multicomponent linear regression. The fluorescence quantum yield and the lifetime strongly decrease in polar/protic solvents, which can be ascribed to an extra nonradiative deactivation, via an intramolecular charge-transfer state (ICT state), favoured in polar media.