丙氨酸晶体太赫兹振动光谱的实验和理论研究

利用太赫兹时域光谱和低频拉曼光谱仪研究了丙氨酸晶体在0.2-2.6 THz 范围内的太赫兹吸收和拉曼散射光谱. 研究表明: 在该低频范围有四个振动模式, 其中两个只具有拉曼活性, 其余两个同时具有红外和拉曼活性. 基于B3LYP杂化密度泛函的自洽场晶体轨道法对丙氨酸周期性结构进行了理论研究和光谱计算. 通过比较实验和理论结果, 指认了实验光谱特征峰所属的不可约表示. 通过理论计算得到的图形, 得出在此低频范围的振动模式主要包含分子间氢键的扭转和摇摆运动.     

ABEEM方法预测响应函数

在密度泛函理论和原子-键电负性均衡模型基础上,定义了与化学键有关的响应函数以及化学键区域的Fukui函数,建立了一套快速确定分子中各区域(包括原子区域和化学键区域)响应函数的新方法.对大量分子的响应函数的计算结果表明,该方法得到的响应函数可以较好地预测分子中各点的反应活性,并更加快捷省时,展示了原子-键电负性均衡模型的广阔应用前景.     

建立短肽抑制剂与酶识别的模式──基于表面静电互补和溶剂化能的Docking计算方法

提出了把简化的接触表面静电互补模型与溶剂化能模型相结合的新的Docking计算方法.编写了计算模拟程序ESCOLD,并用于酶-短肽体系的Docking计算.对3个已知X射线晶体结构的酶-抑制剂肽链复合物中的六肽用ESCOLD重新进行了Docking计算.用溶剂化能作为评价函数,正确地预测出接近实验结果的六肽取向.     

水及有机溶剂中离子溶剂化焓的理论计算

离子溶剂化热力学的理论研究是一项令人感兴趣的工作.在Born理论的基础上人们先后提出了多种较详细的计算离子溶剂化热力学量的模型或公式,并对离子在不同溶剂中的溶剂化自由能进行了理论计算.本文从离子-溶剂间的相互作用力出发,分别考虑了离子溶剂化过程中造腔作用、静电吸引、静电排斥及非静电相互作用对离子溶剂化焓的贡献,得到了一个具有一定意义的、计算离子溶剂化焓的理论公式。     

La(Ⅲ)-乙醇溶液微团簇理论和光谱研究

利用分子光谱和基于密度泛函理论的第一性原理,采用改进的TPSSTPSS泛函方法对C、H、O原子用6-31G基组并添加极化和弥散函数,对La原子选用Def2-SV(P)赝势基组,研究La3+/乙醇溶液微团簇构型。优化计算La3+在水溶液中的溶剂化结构,得出气相中的优化结果可以近似代替液相结果的结论;理论优化计算La3+/乙醇溶液可能存在的结构构型的结果表明,溶剂化数n=6时结构最稳定。采用荧光光谱和核磁共振实验对结果进行了验证,表明La3+的加入使荧光强度显著增强,在高浓度时生成的团簇构型比较稳定,且随着溶剂化数目的增加,O—H键长增大,La3+使其附近的质子产生强大的屏蔽效应,化学位移向高场移动,溶剂化数n=6时绝对误差最小,最稳定,与理论计算结论相吻合。     

二价离子溶剂化自由能的计算—玻恩方程的应用

离子溶剂化自由能是一个很重要的热力学参数,求得溶剂化自由能后,不仅可以了解离子溶剂化的性质,而且由此还可以计算其它热力学函数。由于单个离子不能独立存在,所以不能由实验直接测得单个离子的溶剂化自由能。1920年,玻恩根据静电模型,提出计算单个离子溶剂化自由能的公式如下:     

非平衡溶剂效应的约束平衡理论及在电子转移中的应用

基于经典热力学约束平衡方法,采用新非平衡溶剂化理论研究了Np O+2-Np O2+2体系电子转移反应的溶剂重组能,采用限制密度泛函理论实现电荷定域,用积分方程可极化连续介质模型获得水溶液中极化电荷.计算结果表明,新双球模型和数值解都给出了一致的溶剂重组能理论计算值.     

非平衡溶剂化新理论在有机染料电子光谱中的应用

总结了非平衡溶剂化新理论和在量子化学软件Q-Chem中基于含时密度泛函理论(TD-DFT)实现溶剂效应下计算电子吸收和发射光谱的数值解方法.采用该方法计算了染料敏化太阳能电池(DSSCs)中三苯胺型有机染料■在真空和乙腈溶剂中的电子结构与光谱性质,研究发现,π共轭桥上碳碳双键的个数和溶剂效应会促进光电转换.     

用离散-连续模型计算NH2-,NH3和NH4+的溶剂化自由能

通过理论计算推测NH2-,NH3和NH4+在水溶液第一溶剂化层中与之直接作用的水分子分别为2,4和4个,并采用离散-连续模型计算了NH2-,NH3,NH3和NH4+在水溶液中的溶剂化自由能.结果表明,由于离散-连续模型在从头算水平考虑了溶质分子与第一溶剂化层溶剂分子之间的作用,能更准确地描述溶剂化作用.此外,采用更加符合溶液中真实情况的溶剂化构型,能得到更准确的溶剂化性质.     

生物分子的微溶剂化过程*

研究分子的微溶剂化动力学过程是一个热点课题。应用各种光谱、质谱等实验技术并与从头计算和密度泛函等计算方法相结合,通过对生物分子和溶剂分子在气相中形成的分子团簇的研究,可以使我们了解溶剂分子对生物分子的结构和构型的影响。本文首先介绍了一些先进的实验技术及其应用于溶剂化团簇的研究,综述了近年来发展的几种主要理论计算和溶剂化模型方法。文中介绍了氨基酸分子与水、甲醇等发生微溶剂化过程的最新研究进展,然后分别综述了核酸碱基和碱基对、糖类、神经传递分子的溶剂化团簇的最新研究进展。最后,对该领域的研究前景进行了展望。     

Ionic and dipolar solvation dynamics in liquid water

The solvation time correlation function for solvation in liquid water was measured recently. The solvation was found to be very fast, with a time constant equal to 55 fs. In this article we present theoretical studies on solvation dynamics of ionic and dipolar solutes in liquid water, based on the molecular hydrodynamic approach developed earlier. The molecular hydrodynamic theory can successfully predict the ultrafast dynamics of solvation in liquid water as observed from recent experiments. The present study also reveals some interesting aspects of dipolar solvation dynamics, which differs significantly from that of ionic solvation. Dedicated to Prof. C N R Rao on his 60th birthday     

The influence of chain dynamics on the far-infrared spectrum of liquid methanol-water mixtures

Far-infrared-absorption spectroscopy has been used to study the low-frequency (相似文献   

Generalized Langevin theory on the dynamics of simple fluids under external fields

A theory on the time development of the density and current fields of simple fluids under an external field is formulated through the generalized Langevin formalism. The theory is applied to the linear solvation dynamics of a fixed solute regarding the solute as the external field on the solvent. The solute-solvent-solvent three-body correlation function is taken into account through the hypernetted-chain integral equation theory, and the time correlation function of the random force is approximated by that in the absence of the solute. The theoretical results are compared with those of molecular-dynamics (MD) simulation and the surrogate theory. As for the transient response of the density field, our theory is shown to be free from the artifact of the surrogate theory that the solvent can penetrate into the repulsive core of the solute during the relaxation. We have also found a large quantitative improvement of the solvation correlation function compared with the surrogate theory. In particular, the short-time part of the solvation correlation function is in almost perfect agreement with that from the MD simulation, reflecting that the short-time expansion of the theoretical solvation correlation function is exact up to t(2) with the exact three-body correlation function. A quantitative improvement is found in the long-time region, too. Our theory is also applied to the force-force time correlation function of a fixed solute, and similar improvement is obtained, which suggests that our present theory can be a basis to improve the mode-coupling theory on the solute diffusion.     

Exploration of the secondary structure specific differential solvation dynamics between the native and molten globule states of the protein HP-36

Recent experiments have shown that the time dependence of fluorescence Stokes shift of a chromophore is substantially different when the chromophore is located in a molten globule (MG) state and in the native state of the same protein. To understand the origin of this difference, particularly the role of water in the differential solvation of the protein in the native and the MG states, we have carried out fully atomistic molecular dynamics simulations with explicit water of a partially unfolded MG state of the protein HP-36 and compared the results with the solvation dynamics of the protein in the folded native state. It is observed that the polar solvation dynamics of the three helical segments of the protein is influenced in a nonuniform heterogeneous manner in the MG state. While the equilibrium solvation time correlation function for helix-3 has been found to relax faster in the MG state as compared to that in the native state, the decay of the corresponding function for the other two helices slows down in the MG state. A careful analysis shows that the origin of such heterogeneous relative solvation behavior lies in the differential location of the polar probe residues and their exposure to bulk solvent. We find a significant negative cross-correlation between the contribution (to the solvation energy of a tagged amino acid residue) of water and the other groups of the protein, indicating a competing role in solvation. The sensitivity of solvation dynamics to the secondary structure and the immediate environment can be used to discriminate the partially unfolded and folded states. These results therefore should be useful in explaining recent solvation dynamics experiments on native and MG states of proteins.     

Site-specific solvation determined by intermolecular nuclear Overhauser effect--measurements and molecular dynamics

Site-specific solvation has been determined by intermolecular NOE measurements between solvent and solute. The experimental effect is shown on the four compounds 2-butanol, L-alanyl-L-tryptophan (Ala-Trp), adenosine and the disodium salt of adenosine 5'-monophosphate (5'-AMP) in the two solvents water and dimethyl sulfoxide (DMSO). The strength of NOE transfer correlates with the average distribution of solvent molecules around the corresponding solvation sites represented by the number of solvent molecules in a first solvation sphere, which can be obtained from molecular dynamics simulations in water. Saturation transfer between exchanging protons explains some deviations from this correlation. The NOE transfer measurements provide information on specific solute-solvent interactions and contribute to a better understanding of solvation phenomena. On the basis of a distinct relationship between steric solvation hindrance and the strength of NOE transfer, the application of such measurements for conformational analysis has been demonstrated for the first time.     

Sensitivity of polar solvation dynamics to the secondary structures of aqueous proteins and the role of surface exposure of the probe

The structure and dynamics of water around a protein is expected to be sensitive to the details of the adjacent secondary structure of the protein. In this article, we explore this sensitivity by calculating both the orientational dynamics of the surface water molecules and the equilibrium solvation time correlation function of the polar amino acid residues in each of the three helical segments of the protein HP-36, using atomistic molecular dynamics simulations. The solvation dynamics of polar amino acid residues in helix-2 is found to be faster than that of the other two helices (the average time constant is smaller by a factor of 2), although the interfacial water molecules around helix-2 exhibit much slower orientational dynamics than that around the other two helices. A careful analysis shows that the origin of such a counterintuitive behavior lies in the dependence of the solvation time correlation function on the surface exposure of the probe-the more exposed is the probe, the faster the solvation dynamics. We discuss that these results are useful in explaining recent solvation dynamics experiments.     

Be2+在水、甲醇和乙醇中结构性质的从头算分子动力学模拟

采用Car-Parrinello分子动力学(CPMD)方法分别研究了Be²⁺在水、甲醇和乙醇中的溶剂结构性质, 并对Be²⁺的第一溶剂壳结构的实验及理论结果进行了比较. 所得第一溶剂壳结构与已报道的实验和理论结果较为一致. 对径向分布函数、配位数以及角度分布等进行了详细的分析. 结果表明: 在水、甲醇和乙醇中, Be²⁺第一溶剂壳为稳定理想的四面体结构. 在本文的模拟时间尺度内,没有观察到第一溶剂壳中的分子与第二溶剂壳中的分子进行交换, 进一步证明Be²⁺第一溶剂壳为稳定的四配位结构. 根据计算得到的空间分布函数, Be²⁺在溶剂分子的等高面上主要集中分布在溶剂分子接受氢键的方向. 根据氧原子在Be²⁺周围的分布, 壳层分子主要集中分布在Be²⁺周围的四个区域, 进一步证实溶剂壳为四面体对称.     

Polar solvation dynamics in supercritical fluids: a mode-coupling treatment

A mode-coupling treatment of polar solvation dynamics in supercritical fluids is presented. The equilibrium solvation time correlation function for the solute fluctuating transition frequency is obtained from the mode-coupling theory method and from molecular-dynamics simulations. The theory is shown to be in good agreement with the simulation. The solvation time correlation function exhibits three distinct time scales, with rapid initial decay, followed by a recurrence at intermediate times, and a slowly decaying long-time tail. Our theoretical analysis shows that the short-time decay arises from the coupling of the solute energy gap to the solvent polarization modes, the recurrence at intermediate times is due to the energy modes, while the slow long-time decay reflects the coupling to the number density modes.