基于分子表面的水化自由能预测方法

报导了一种基于加权原子表面的水合自由能预测（SAWSA）.对于不同原子类型的溶剂化参数，其参数化分为三个步骤：首先用SMARTS 语言确定不同的原子类型；然后计算每个原子的溶剂可及化表面；最后用遗传算法来优化不同原子类型的溶剂化参数.采用该模型，计算了18个蛋白质分子的水合自由能，预测结果和PB/SA的计算结果呈现了很好的线性关系（r=0.99).计算表明，SAWSA模型对有机小分子和生物大分子都具有很好的预测能力.     

基于几何约束的蛋白质-配体准确结合自由能计算

蛋白质-配体的结合过程伴随着复杂的结构变化,在分子模拟可及的时间尺度内难以完全捕获,这使得准确估计蛋白质-配体的结合自由能十分困难.一种有效的解决途径是采用几何约束减小需要采样的构象空间,再通过后处理方式扣除约束的影响.本文综述了三种几何约束策略——漏斗状约束、球形约束和七自由度约束与自由能计算算法结合准确计算结合自由能的原理和进展,重点概述理论严谨的七自由度约束的最新进展以及与Alchemistry或重要性采样方法的联用策略,最后,讨论了如何针对不同体系选择合适的计算策略以及蛋白质-配体准确结合自由能计算在药物设计等领域中的挑战和前景,并提出了将上述方法进一步运用于研究更复杂的蛋白质-蛋白质问题的可能性.     

低自由能固体表面的制备及其应用

低自由能表面具有一些独特的性能,在工业和日常生活中具有广泛的应用,本文就低自由能表面的制备及其发展概况进行综述,共引用文献83篇。     

一种可溶性低表面自由能聚合物的制备及其表面性质

用全氟辛酸和甲基丙烯酸羟丙酯 (HPMA)为原料 ,合成了具有低表面自由能 ( 1 4 2mN m)的聚合物聚甲基丙烯酸全氟辛酰氧丙基酯 (PFPMA) ,接触角的测定表明聚合物具有较好双疏性 (疏水 疏油性 ) ,其对水的接触角高达 1 1 5°,对正十六烷的接触角为 75°.     

一组和AMBER力场配合的普适波恩模型参数

提出了一套和AMBER力场相匹配的普适波恩模型参数.新的参数集包含21种原子类型的初始半径和屏蔽因子.参数通过遗传算法拟合359个小分子水合自由能的实验值得到.采用新的参数，预测了44个小分子的水合自由能，预测值和实验值能很好地吻合，而且大大优于采用Jayaram参数得到的结果.此外，采用新的参数，还预测了15个蛋白质的水合自由能，预测值和PB/SA预测得到的结果能很好地吻合.     

二元表面活性剂溶液表面吸附层分子交换能的研究

由于分子间存在的相互作用,表面活性剂混合体系通常比单一表面活性剂更能降低溶液的表面能,该现象称为协同效应或复配增效^[1,2]。由于多元体系组成复杂,迄今仅能用正规溶液理论导出的非理想性参数（又称分子相互作用参数βs）来表征^[3-5],βs愈负,复配增效效果愈好。但如何从分子水平去理解βs至今尚不清楚。本文用二维晶格模型得出协同效应可用溶液表面层的分子交换能来描述,并推导出由βs计算该交换能的相应公式。     

关于表面张力和表面自由能的讨论

简要地回顾了表面物理化学中表面张力和表面吉布斯自由能(以下简称为表面自由能)两个基本概念的发展历史,讨论了表面张力和表面自由能形成的机制,以及键能与表面张力的关系,最后指出了尽管表面相可以在理论上抽象为几何面,但它是真实存在的独立相,而且由于表面自由能的原因它始终处于亚稳定状态.     

接触角法研究医用聚醚聚氨酯材料表面自由能与界面自由能

<正> 表面性质在医用材料与生物体的相互作用中起着至关重要的作用,如血液相容性材料的表面对血细胞具有吸附、变形、凝血、溶血等作用。表面能和界面能是医用材料的重要研究内容之一,材料的表面能及其极性与非极性分量在影响或控制材料与生物体的相互作用之面一直是医用材料的重要课题。Raier曾提出当材料的临界表面张力在20-30erg/cm~2时,血液相容性好,也有人认为,血液与材料的界面自由能趋于零时,才能     

Co(Ⅱ)和Ni(Ⅱ)在北山花岗岩上的吸附：表面配位模型及线性自由能关系

用批式法研究了Co(Ⅱ)和Ni(Ⅱ)在北山花岗岩(BS03, 600 m)上的吸附. Co(Ⅱ)和Ni(Ⅱ)在北山花岗岩上的吸附分配比(K_d)均随pH值、离子强度和吸附质浓度的变化而变化; 在低pH值范围, Co(Ⅱ)和Ni(Ⅱ)的K_d 值随离子强度的增大显著减小, 而在高pH值范围,离子强度对K_d的影响较小; Co(Ⅱ)和Ni(Ⅱ)在北山花岗岩上的吸附作用可以分别用1个离子交换反应和2个内层表面配位反应进行定量描述. 建立了表面配位反应平衡常数(K)与过渡金属二价离子水解常数(^OHK)之间的线性自由能关系(LFER),据此对Pb(Ⅱ)和Cu(Ⅱ)在花岗岩上的吸附进行了预测,并与实验结果进行了对比,获得了较好的一致性.     

热解条件对LiFePO4/C表面自由能的影响

以葡萄糖为碳前驱体对水热合成的磷酸铁锂粉末进行碳包覆.测定磷酸铁锂粉末与三种探测液的接触角,并据此通过Young方程采用Wu方法计算了粉末的表面自由能.研究了表面自由能与电导率、放电比容量的关系及对工业化涂布性能的影响.结果表明,在电导率相同的前提下,粉末表面自由能中色散分量与极性分量的比值(γd/γp)对低倍率放电性能没有影响,但对高倍率放电性能影响较大.提高热解温度和延长热解时间可使γd/γp值增加,这有利于粉体与聚偏氟乙烯(PVdF)的粘合和高倍率放电容量的提高.     

Hybrid Solvation Model with First Solvation Shell for Calculation of Solvation Free Energy

We present a hybrid solvation model with first solvation shell to calculate solvation free energies. This hybrid model combines the quantum mechanics and molecular mechanics methods with the analytical expression based on the Born solvation model to calculate solvation free energies. Based on calculated free energies of solvation and reaction profiles in gas phase, we set up a unified scheme to predict reaction profiles in solution. The predicted solvation free energies and reaction barriers are compared with experimental results for twenty bimolecular nucleophilic substitution reactions. These comparisons show that our hybrid solvation model can predict reliable solvation free energies and reaction barriers for chemical reactions of small molecules in aqueous solution.     

基于分子动力学模拟和连续介质模型的自由能计算方法*

近些年,基于分子动力学模拟和连续介质模型的自由能计算方法受到了越来越多的关注,其中MM/PBSA就是最具代表性的方法.在MM/PBSA中,体系的焓变采用分子力学(MM)的方法计算得到;溶剂效应中极性部分对自由能的贡献通过解Poisson-Boltzmann(PB)方程的方法计算得到;溶液效应中非极性部分对自由能的贡献则通过分子表面积(SA)计算得到.本文结合我们科研组的工作,就近几年MM/PBSA方法的最新进展做了较为详细的阐述,同时对MM/PBSA的发展前景进行了展望.     

Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy

The generalized Born/surface area (GB/SA) continuum model for solvation free energy is a fast and accurate alternative to using discrete water molecules in molecular simulations of solvated systems. However, computational studies of large solvated molecular systems such as enzyme-ligand complexes can still be computationally expensive even with continuum solvation methods simply because of the large number of atoms in the solute molecules. Because in such systems often only a relatively small portion of the system such as the ligand binding site is under study, it becomes less attractive to calculate energies and derivatives for all atoms in the system. To curtail computation while still maintaining high energetic accuracy, atoms distant from the site of interest are often frozen; that is, their coordinates are made invariant. Such frozen atoms do not require energetic and derivative updates during the course of a simulation. Herein we describe methodology and results for applying the frozen atom approach to both the generalized Born (GB) and the solvent accessible surface area (SASA) parts of the GB/SA continuum model for solvation free energy. For strictly pairwise energetic terms, such as the Coulombic and van-der-Waals energies, contributions from pairs of frozen atoms can be ignored. This leaves energetic differences unaffected for conformations that vary only in the positions of nonfrozen atoms. Due to the nonlocal nature of the GB analytical form, however, excluding such pairs from a GB calculation leads to unacceptable inaccuracies. To apply a frozen-atom scheme to GB calculations, a buffer region within the frozen-atom zone is generated based on a user-definable cutoff distance from the nonfrozen atoms. Certain pairwise interactions between frozen atoms in the buffer region are retained in the GB computation. This allows high accuracy in conformational GB comparisons to be maintained while achieving significant savings in computational time compared to the full (nonfrozen) calculation. A similar approach for using a buffer region of frozen atoms is taken for the SASA calculation. The SASA calculation is local in nature, and thus exact SASA energies are maintained. With a buffer region of 8 A for the frozen-atom cases, excellent agreement in differences in energies for three different conformations of cytochrome P450 with a bound camphor ligand are obtained with respect to the nonfrozen cases. For various minimization protocols, simulations run 2 to 10.5 times faster and memory usage is reduced by a factor of 1.5 to 5. Application of the frozen atom method for GB/SA calculations thus can render computationally tractable biologically and medically important simulations such as those used to study ligand-receptor binding conformations and energies in a solvated environment.     

Solvation free energies calculated using the GB/SA model: Sensitivity of results on charge sets,protocols, and force fields

The sensitivity of aqueous solvation free energies (SFEs), estimated using the GB/SA continuum solvent model, on charge sets, protocols, and force fields, was studied. Simple energy calculations using the GB/SA solvent model were performed on 11 monofunctional organic compounds. Results indicate that calculated SFEs are strongly dependent on the charge sets. Charges derived from electrostatic potential fitting to high level ab initio wave functions using the CHELPG procedure and “class IV” charges from AM1/CM1a or PM3/CM1p calculations yielded better results than the corresponding Mulliken charges. Calculated SFEs were similar to MC/FEP energies obtained in the presence of explicit TIP4P water. Further improvements were obtained by using GVB/6-31G** and MP2/6-31+G** (CHELPG) charge sets that included correlation effects. SFEs calculated using charge sets assigned by the OPLSA* force field gave the best results of all standard force fields (MM2*, MM3*, MMFF, AMBER*, and OPLSA*) implemented in MacroModel. Comparison of relative and absolute SFEs computed using either the GB/SA continuum model or MC/FEP calculations in the presence of explicit TIP4P water showed that, in general, relative SFEs can be estimated with greater accuracy. A second set of 20 mono- and difunctional molecules was also studied and relative SFEs estimated using energy minimization and thermodynamic cycle perturbation (TCP) protocols. SFEs calculated from TCP calculations using the GB/SA model were sensitive to bond lengths of dummy bonds (i.e., bonds involving dummy atoms). In such cases, keeping the bond lengths of dummy bonds close to the corresponding bond lengths of the starting structures improved the agreement of TCP-calculated SFEs with energy minimization results. Overall, these results indicate that GB/SA solvation free energy estimates from simple energy minimization calculations are of similar accuracy and value to those obtained using more elaborate TCP protocols. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 769–780, 1998     

CO在Ni(100)面吸附模式的研究

本文首次将McGreery的推广LEPS法用于异核双原子分子的吸附势能面.设CO在Ni面上的吸附位置有3种(图1).取Sato参数为0.5,所得典型的势能面示于图2、图3.当C—O键平行于表面并接近Ni面上的3种吸附位置时,各势能面均与图2类似,先进入一势阱,然后越过势垒进入第二势阱.发生解离型C及O的原子吸附时,共有4种模式.各势能面上表征吸附的参数列于表1,吸附模式见图1.在4种吸附模式中最稳定的是C模式,即对角相邻5CN上的解离双原子吸附,R_(c-o)=6.65a.u.,它是R_(c-o)(平衡)=2.17a.u.的三倍多.当CO键与表面垂直且接近Ni面上3种吸附位置时所得势     

Chiral recognition by enantioselective liquid chromatography: Mechanisms and modern chiral stationary phases

An overview of the state-of-the-art in LC enantiomer separation is presented. This tutorial review is mainly focused on mechanisms of chiral recognition and enantiomer distinction of popular chiral selectors and corresponding chiral stationary phases including discussions of thermodynamics, additivity principle of binding increments, site-selective thermodynamics, extrathermodynamic approaches, methods employed for the investigation of dominating intermolecular interactions and complex structures such as spectroscopic methods (IR, NMR), X-ray diffraction and computational methods. Modern chiral stationary phases are discussed with particular focus on those that are commercially available and broadly used. It is attempted to provide the reader with vivid images of molecular recognition mechanisms of selected chiral selector–selectand pairs on basis of solid-state X-ray crystal structures and simulated computer models, respectively. Such snapshot images illustrated in this communication unfortunately cannot account for the molecular dynamics of the real world, but are supposed to be helpful for the understanding. The exploding number of papers about applications of various chiral stationary phases in numerous fields of enantiomer separations is not covered systematically.