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.     

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.     

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.     

钡原子对Ru（0001）表面氮分子吸附和解离过程的影响

采用密度泛函理论方法研究了钡原子对Ru（0001）表面氮分子解离过程的影响.计算结果表明：在Ru（0001）表面,钡原子失去电子后形成Ba（1＋δ）＋阳离子.表面转移电荷增强了衬底钌原子d轨道和氮分子π轨道间的杂化作用以及氮分子内的库仑排斥作用,减弱了氮分子键.在钡原子的作用下,γ态氮分子键键长从0.113 nm增加到...     

放射性碘分子在Cu2O表面的吸附:第一性原理密度泛函研究

采用第一性原理密度泛函计算方法和周期性平板模型系统研究了放射性碘分子在Cu₂O三个低指数表面的吸附行为。通过计算若干平衡吸附构型的结构参数和吸附能评估了不同特征吸附位的作用。构型优化计算表明所选晶面存在适度的结构弛豫。计算结果表明,与Cu₂O（110）表面相比,Cu₂O（100）和（111）晶面表现出更高的碘分子吸附反应活性。其中,表面氧原子位（O_S）和配位未饱和铜原子位（Cu_CUS）分别为Cu₂O（100）和（111）晶面的能量最优吸附位点。此外,针对几种典型吸附结构计算分析了其电子结构信息,以进一步阐明吸附体系之间的相互作用机理。     

分子亲脂-亲水性的量子化学描述(Ⅰ)——分子的亲脂和亲水表面

给出基于分子结构的“启发式”亲脂-亲水势HMLP(Heuristic molecular lipophilicity-hydrophilicity potential)的理论分析和有说服力的算例.用量子化学计算其分子表面的静电势V(r)的分布,通过与周围原子表面静电势的比较,构造表达分子静电势的极性和大小的函数L(r).亲脂势L(r)保留了静电势V(r)描述分子静电作用的能力,并把应用范围扩展到疏水性的描述.HMLP不使用原子的经验参数,但在L(r)的构造中使用了经验的函数形式.经参数化和指标化后,HMLP有望用于蛋白质结构与功能的研究和药物分子配体与生物大分子受体结合自由能的估算.     

应用ABEEM/MM蛋白质力场模型研究半胱氨酸二肽构象的性质

ABEEM/MM蛋白质力场模型是应用于蛋白质体系的原子-键电负性均衡方法(ABEEM)与力场(MM)相结合的浮动电荷模型.该模型能够准确地描述分子在环境变化时的静电极化,并能快速计算气态和溶液多肽的结构和能量.首次应用ABEEM/MM蛋白质力场模型研究半胱氨酸二肽构象的性质,如构象能、氢键等.此外,应用从头计算HF/6-31G**方法对其性质进行计算.ABEEM/MM蛋白质力场模型可以快速准确地得到半胱氨酸二肽分子不同稳定构象的性质,其结果可以和从头计算相媲美.以上研究有助于加深对半胱氨酸二肽构象性质的了解,从而也为进一步验证ABEEM/MM蛋白质力场模型的正确性以及参数的合理性提供可靠的依据.     

沥青质杂环模型分子间相互作用及溶剂化效应的理论研究

重质油中沥青质组分易发生聚沉形成团簇,严重影响重质油的加工和利用效率,但目前对于沥青质聚沉的研究较少,其机理尚不明确。本文采用理论计算对沥青质杂环模型分子间相互作用和溶剂化效应进行研究,以此为重质油沥青质聚沉现象的研究及聚沉抑制剂的研发提供一定的数据和理论支持。(1)在M062X/6-31G(d)水平上,计算得到了11种由沥青质杂环分子片段组成的二元体系的全优化稳定构型,讨论分析了构型的几何结构、NBO电荷、Mulliken重叠布居、相互作用能和分子轨道能,得到了最稳定的两种构型。(2)在B3LYP/6-31G(d)水平上,运用SMD模型对沥青质大分子在13种溶剂中进行溶剂化效应的建模和理论计算,通过对静电溶剂化自由能(ΔGelec)、非静电溶剂化自由能(ΔGnonelec)、总溶剂化自由能(ΔGsolv)的分析可知,沥青质溶解性大小的关键在于溶剂对它的远程静电作用的大小。     

CO和H2分子在Cu(111)面的吸附和溶剂化效应

采用广义梯度近似(GGA)密度泛函理论(DFT)的PW91方法结合周期性模型, 在DNP基组下, 利用Dmol3模块研究了CO和H2在真空和液体石蜡环境下在Cu(111)表面上不同位置的吸附. 计算结果表明, 溶剂化效应对H2和CO的吸附结构参数和吸附能的影响非常显著. 在液体石蜡环境下, H2平行吸附在Cu(111)表面是解离吸附, 而CO 和H2在两种环境下的垂直吸附都是非解离吸附. 相比真空环境吸附, 在液体石蜡环境中, Cu(111)吸附CO时, 溶剂化效应能够提高CO吸附的稳定性, 同时有利于CO的活化. 在真空中, H2只能以垂直方式或接近垂直方式吸附在Cu(111)表面. 当Cu(111)顶位垂直吸附H2, 相比真空环境吸附, 溶剂化效应能够提高H2吸附的稳定性, 但对H2的活化没有明显影响. Cu(111)表面的桥位或三重穴位(hcp和fcc)垂直吸附H2时, 溶剂化效应能明显提高H2的活化程度, 但降低H2的吸附稳定性; 在液体石蜡中, 当H2平行Cu(111)表面吸附时, 溶剂化效应使H—H键断裂, 一个H原子吸附在fcc位, 另一个吸附在hcp位.     

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.     

EGFR和4-苯胺喹唑啉类抑制剂之间相互作用模式的研究

采用分子动力学和MM/PBSA相结合的方法预测了表皮生长因子受体和4-苯胺喹 啉类抑制剂的相互作用模式。在分子动力学采样的基础上,采用MM/PBSA的方法分 别预测了四种可能结合模式下表皮生长因子受体和4-苯胺喹唑啉类抑制剂间的结合 自由能。在MM/PBSA计算中,受体和抑制剂之间的非键相互作用能采用分子力学 (MM)的方法得到;溶剂效应中极性部分对自由能的贡献通过解Possion- Boltzmanne (PB)方程的方法得到;溶液效应中非极性部分对自由能的贡献则通过 分子表面积计算(SA)的方法得到。计算表明,在四种结合模式下,表皮生长因子受 体和4-苯胺喹唑啉类抑制剂之间的结合自由能有较大的差别。在最佳的相互作用模 式中,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。抑制剂喹唑啉环上的N(1)原子能够和Met-769上的 NH形成稳定的氢键,而抑制剂上的N(3)原子则和周围的一个水分子形成氢键。同时 ,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 水相互作用。最佳结合模式能够很好地解释已有抑制剂结构和活性间的关系。     

Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf

Estimating protein-protein interaction energies is a very challenging task for current simulation protocols. Here, absolute binding free energies are reported for the complex H-Ras/C-Raf1 using the MM-PB(GB)SA approach, testing the internal consistency and model dependence of the results. Averaging gas-phase energies (MM), solvation free energies as determined by Generalized Born models (GB/SA), and entropic contributions calculated by normal mode analysis for snapshots obtained from 10 ns explicit-solvent molecular dynamics in general results in an overestimation of the binding affinity when a solvent-accessible surface area-dependent model is used to estimate the nonpolar solvation contribution. Applying the sum of a cavity solvation free energy and explicitly modeled solute-solvent van der Waals interaction energies instead provides less negative estimates for the nonpolar solvation contribution. When the polar contribution to the solvation free energy is determined by solving the Poisson-Boltzmann equation (PB) instead, the calculated binding affinity strongly depends on the atomic radii set chosen. For three GB models investigated, different absolute deviations from PB energies were found for the unbound proteins and the complex. As an alternative to normal-mode calculations, quasiharmonic analyses have been performed to estimate entropic contributions due to changes of solute flexibility upon binding. However, such entropy estimates do not converge after 10 ns of simulation time, indicating that sampling issues may limit the applicability of this approach. Finally, binding free energies estimated from snapshots of the unbound proteins extracted from the complex trajectory result in an underestimate of binding affinity. This points to the need to exercise caution in applying the computationally cheaper "one-trajectory-alternative" to systems where there may be significant changes in flexibility and structure due to binding. The best estimate for the binding free energy of Ras-Raf obtained in this study of -8.3 kcal mol(-1) is in good agreement with the experimental result of -9.6 kcal mol(-1), however, further probing the transferability of the applied protocol that led to this result is necessary.     

Calculations of the free energy of interaction of the c-Fos-c-Jun coiled coil: effects of the solvation model and the inclusion of polarization effects

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein-protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson-Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos-c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos-c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.     

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     

QM/MM-PBSA method to estimate free energies for reactions in proteins

We have developed a method to estimate free energies of reactions in proteins, called QM/MM-PBSA. It estimates the internal energy of the reactive site by quantum mechanical (QM) calculations, whereas bonded, electrostatic, and van der Waals interactions with the surrounding protein are calculated at the molecular mechanics (MM) level. The electrostatic part of the solvation energy of the reactant and the product is estimated by solving the Poisson-Boltzmann (PB) equation, and the nonpolar part of the solvation energy is estimated from the change in solvent-accessible surface area (SA). Finally, the change in entropy is estimated from the vibrational frequencies. We test this method for five proton-transfer reactions in the active sites of [Ni,Fe] hydrogenase and copper nitrite reductase. We show that QM/MM-PBSA reproduces the results of a strict QM/MM free-energy perturbation method with a mean absolute deviation (MAD) of 8-10 kJ/mol if snapshots from molecular dynamics simulations are used and 4-14 kJ/mol if a single QM/MM structure is used. This is appreciably better than the original QM/MM results or if the QM energies are supplemented with a point-charge model, a self-consistent reaction field, or a PB model of the protein and the solvent, which give MADs of 22-36 kJ/mol for the same test set.     

Prediction of molecular solvation free energy based on the optimization of atomic solvation parameters with genetic algorithm

We propose an improved solvent contact model to estimate the solvation free energy of an organic molecule from individual atomic contributions. The modification of the solvation model involves the optimization of three kinds of parameters in the solvation free energy function: atomic fragmental volume, maximum atomic occupancy, and atomic solvation parameters. All of these atomic parameters for 24 atom types are developed by the operation of a standard genetic algorithm in such a way as to minimize the difference between experimental and calculated solvation free energies. The data set for experimental solvation free energies is divided into a training set of 131 compounds and a test set of 24 compounds. Linear regressions with the optimized atomic parameters yield fits with the squared correlation coefficients (r2) of 0.89 and 0.86 for the training set and for the test set, respectively. Overall, the results indicate that the improved solvent contact model with the newly developed atomic parameters would be a useful tool for rapid calculation of molecular solvation free energies in aqueous solution.