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.     

Hydrogen Bonding between Metal‐Ion Complexes and Noncoordinated Water: Electrostatic Potentials and Interaction Energies

The hydrogen bonding of noncoordinated water molecules to each other and to water molecules that are coordinated to metal‐ion complexes has been investigated by means of a search of the Cambridge Structural Database (CSD) and through quantum chemical calculations. Tetrahedral and octahedral complexes that were both charged and neutral were studied. A general conclusion is that hydrogen bonds between noncoordinated water and coordinated water are much stronger than those between noncoordinated waters, whereas hydrogen bonds of water molecule in tetrahedral complexes are stronger than in octahedral complexes. We examined the possibility of correlating the computed interaction energies with the most positive electrostatic potentials on the interacting hydrogen atoms prior to interaction and obtained very good correlation. This study illustrates the fact that electrostatic potentials computed for ground‐state molecules, prior to interaction, can provide considerable insight into the interactions.     

Excitation Energies of Canonical Nucleobases Computed by Multiconfigurational Perturbation Theories

In this computational work, we assessed the performance of ab initio multireference (MR) methods for the calculation of vertical excitation energies of five nucleobases: adenine, guanine, cytosine, thymine and uracil. In total, we have studied 38 singlet and 30 triplet excited states. Where possible we used the multireference configuration interaction (MRCI) method as a reference for various flavors of multireference perturbation theory to second order. In particular, we have benchmarked CASPT2, NEVPT2 and XMCQDPT2. For CASPT2, we have analyzed the single‐state, multistate (MS) and extended MS variants. In addition, we have assessed the effect of the ionization potential electron affinity (IPEA) shift. For NEVPT2, we have used the partially and the strongly contracted variants. Further, we have tested the commonly used RI‐CC2, RI‐ADC2 and EOM‐CCSD methods. Generally, we observe the following trends for singlet excited states: NEVPT2 is the closest MR method to MRCISD+Q, closely followed by CASPT2 with the default IPEA shift. The same trend is observed for triplet states, although NEVPT2 and CASPT2‐IPEA are getting closer. Interestingly, the n, π* singlet excited states were described more accurately than π, π* excited states, while for triplet states the trend is inverted except for NEVPT2. This work is an important benchmark for future photochemical investigations.     

Transferability of Electronic Interaction Energies Between Localized Orbitals

Localized molecular orbitals have been shown to be transferable among structurally-related molecules. We further show that the electronic energies between localized orbitals are transferable and their magnitude can be estimated. A set of parameters of group interaction energies are established from the analysis of small molecules. Use of these parameters is demonstrated successfully for large molecules.     

Estimation of Exchange Energies in Two-Component Melts of Alkali Metals

An approach allowing establishment of the relationship between the energies of mixing in binary homovalent melts of metals and the corresponding values for halide salts (chlorides or fluorides) of these metals is proposed. The procedure given as an example for estimation of the exchange energies in liquid-phase systems formed by lithium and other alkali metals allows a considerable reduction in the number of experimentally complicated definitions for thermodynamic characteristics of similar systems. This revised version was published online in July 2006 with corrections to the Cover Date.     

Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies

The independent trajectory thermodynamic integration (IT-TI) approach (Lawrenz et. al J. Chem. Theory. Comput. 2009, 5:1106-1116(1)) for free energy calculations with distributed computing is employed to study two distinct cases of protein-ligand binding: first, the influenza surface protein N1 neuraminidase bound to the inhibitor oseltamivir, and second, the M. tuberculosis enzyme RmlC complexed with the molecule CID 77074. For both systems, finite molecular dynamics (MD) sampling and varied molecular flexibility give rise to IT-TI free energy distributions that are remarkably centered on the target experimental values, with a spread directly related to protein, ligand, and solvent dynamics. Using over 2 μs of total MD simulation, alternative protocols for the practical, general implementation of IT-TI are investigated, including the optimal use of distributed computing, the total number of alchemical intermediates, and the procedure to perturb electrostatics and van der Waals interactions. A protocol that maximizes predictive power and computational efficiency is proposed. IT-TI outperforms traditional TI predictions and allows a straightforward evaluation of the reliability of free energy estimates. Our study has broad implications for the use of distributed computing in free energy calculations of macromolecular systems.     

Modelling and Estimation of Measurement Errors

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完全活性空间组态相互作用能量的拟合和外推

完全活性空间组态相互作用计算与完全活性空间中的活性电子数和活性轨道数有关,但完全活性空间组态相互作用的能量不是活性电子数和活性轨道数的单调递减函数,因此活性轨道数和活性电子数不能用来外推完全活性空间组态相互作用的能量。为此,我们定义了一个新的变量:活性空间中的最大未占满轨道数。我们对一系列单重态、双重态和三重态分子进行了完全活性空间组态相互作用的计算,并利用活性空间中的活性电子数和最大未占满轨道数这两个变量,对这些基态能量进行了拟合和外推,拟合的均方根误差都在10~(-6)数量级。外推能量的精度优于MP4,对小分子体系,其精度高于CCSD。外推的完全的组态相互作用(FCI)能量值和实际计算的FCI值也很接近。另外,我们还利用外推能量来优化双原子分子的平衡键长,并计算谐振频率,其精度优于CASSCF。     

1,2,3-三氮杂苯-水复合物氢键相互作用

Density functional theory B3LYP method with 6-31++G** basis was used to optimize the geometries of the ground states for 1,2,3-triazine-(H2O)n (n=1,2,3) complexes. All calculations indicate that the 1,2,3-triazine-water complexes in the ground states have strong hydrogen-bonding interaction, and the complex having a N…H-O hydrogen bond and a chain of water molecules which is terminated by a O…H-C hydrogen bond is the most stable. The H-O stretching modes of complexes are red-shifted relative to that of the monomer. In addition, the Natural bond orbit (NBO) analysis indicates that the intermolecular charge transfer between 1,2,3-triazine and water is 0.0222e, 0.0261e and 0.0273e for the most stable 1:1, 1:2 and 1:3 complexes, respectively. The first singlet (n, π*) vertical excitation energy of the monomer 1,2,3-triazine and the hydrogen-bonding complexes of 1,2,3-triazine-(H2O)n were investigated by time-dependent density functional theory.     

可快速计算水团簇三体作用强度的新方法

将水分子视为由2个O—H键偶极构成, 再将水分子间的三体作用视为长程诱导作用和短程校正之和, 使用Thole模型计算长程诱导作用, 通过同时考虑不同水分子间的置换和同一个水分子中2个键偶极间的置换计算短程校正, 从而提出了一个可快速计算水团簇三体作用强度的新方法. 根据已报道的12347个水三聚体的结构和CCSD(T)三体作用能, 确定了该方法所需参数. 将该方法和所确定的参数应用于67个水团簇体系, 计算这些体系的三体作用能, 并与CCSD(T), MP2, M06-2X方法的计算结果进行比较. 结果表明, 相对于CCSD(T)方法的总三体作用能, 本文方法的均方根偏差(RMSD)仅为3.32 kJ/mol, 平均相对偏差(MRD)仅为2.43%; 对较大水团簇体系, 该方法计算精度稍优于MP2方法, 明显优于M06-2X方法, 并且更快捷高效.     

噻吩基钌配合物与酵母RNA的相互作用研究

通过紫外-可见吸收光谱和荧光光谱滴定、稳态荧光猝灭以及盐效应实验研究了噻吩基钌配合物[Ru(bpy)2(Htip)]Cl2(1)、[Ru(Htip)2(dppz)]Cl2(2)、[Ru(Htip)3]Cl2(3)和[Ru2(bpy)4(H2bipt)]Cl4(4){bpy=2,2'-联吡啶;Htip=2-噻吩咪唑[4,5-f][1,10]邻菲咯啉;H2bipt=2,5-二(2-咪唑[4,5-f][1,10]邻菲咯啉)噻吩;dppz=二吡啶并[3,2-a:2',3'-c]吩嗪}与酵母RNA(yeast-RNA)的相互作用,并比较了该类配合物与yeast-RNA和小牛胸腺DNA(ct-DNA)的键合性质。结果表明,该类噻吩基钌配合物是较强的RNA嵌入试剂,其中配合物2和3的RNA键合强度大于其DNA键合强度;此系列配合物在低盐和高盐浓度时均能与RNA较强地结合,即使在100 mmol/L Na Cl条件下仍具有较大的RNA键合常数;配合物1与RNA键合时荧光强度下降,配合物2在水溶液中以及与RNA键合时几乎无荧光,而它们与DNA作用时荧光强度明显增大,显示出良好的区分RNA和DNA的荧光特性。     

Synthesis of Cyclic Vinylidene Complexes and Azavinylidene Complexes by Formal [4+2] Cyclization Reactions

Reactions of the hydrido‐butenylcarbyne complex [OsHCl₂(≡CC(PPh₃)=CHEt)(PPh₃)₂]BF₄ ( 1 ) with nitriles RC≡N (R=2‐cyclopropyl‐2‐oxopropyl, 3‐amino‐2‐oxobutyl) lead to six‐membered cyclic vinylidene complexes 3 and azavinylidene complexes 4 , that is, iso‐osmapyridiniums. Treatment of 1 with excess 2‐formylbenzonitrile at reflux temperature in CHCl₃ in the presence of air produces a fused osmapyridinium 8 , which is first oxidized to the tricyclic iso‐osmapyridinium derivative 7 , then to iso‐osmapyridinium 9 , which contains a fused naphthalenone fragment. The conversion of iso‐osmapyridinium 9 (with a vinylidene segment) to the iso‐osmapyridinium compounds 10 and 11 (with azavinylidene segments) was achieved in the presence of a hydrogen halide, such as HCl or HI. The molecular structures of the complexes synthesized were confirmed by X‐ray studies. Moreover, the aromatic stabilization energy and nucleus‐independent chemical‐shift values of the osmapyridiniums and the strain in the iso‐osmapyridinium rings were investigated by DFT calculations.     

Cr3+离子配合物电子结构和d-d 跃迁谱的研究

建议了一种采用考虑重叠修正项的多重散射Ｘα自治场方法，结合不可约张量方法求解过渡金属配合物价电子体系多电子Ｓｃｈｒｏｄｉｎｇｅｒ方程的方法，并将其应用到Ｃｒ＾３＋配合物光谱的计算，其计算结果与实验结果的方均根偏差仅１．５ｋｃｍ＾－１，同时分析了Ｘα方法中重叠修正项对配合物电子结构以及光谱计算结果的影响，以及选用的组态对计算结果的影响。     

原子对作用能与有机红外光谱的相关性研究

将有机分子中的Ｃ和Ｈ、Ｃ和Ｃ、Ｃ和Ｏ、Ｃ和Ｎ间化学键的红外伸缩振动吸收峰位与ＭＮＤＯ法计算的原子对作用能相比较，找到了很好的相关性，并用最小二乘法拟合得到各自的回归线和回归方程，其相关系数均达到０．９７以上。运用二者相关性规律定量地解释了有机分子中Ｃ－Ｈ、Ｃ－Ｃ、Ｃ＝Ｃ、Ｃ≡Ｃ、Ｃ－Ｏ、Ｃ＝Ｏ、Ｃ－Ｎ、Ｃ＝Ｎ、Ｃ≡Ｎ键的伸缩振动吸收峰移动的影响因素，如不饱和性、诱导、中介、共轭、环张力等。     

Phosphate Transfer in Activated Protein Complexes Reveals Interaction Sites

For many proteins, phosphorylation regulates their interaction with other biomolecules. Herein, we describe an unexpected phenomenon whereby phosphate groups are transferred non‐enzymatically from one interaction partner to the other within a binding interface upon activation in the gas phase. Providing that a high affinity exists between the donor and acceptor sites, this phosphate transfer is very efficient and the phosphate groups only ligate to sites in proximity to the binding region. Consequently, such phosphate‐transfer reactions may define with high precision the binding site between a phosphoprotein and its binding partner, as well as reveal that the binding site in this system is retained in the phase transfer from solution to the gas phase.     

脯氨酸与Ag和Ag+相互作用及性质

用X3LYP杂化密度泛函方法在LACV3P^**++基组水平上对脯氨酸(Pro)的15种构象与Ag原子和Ag⁺离子形成多种配合物的几何结构、电子结构、振转光谱和能量学特征进行了计算研究, 结果得到17种Pro-Ag和23种Pro-Ag⁺稳定结构. 数据分析表明: (1) Pro-Ag配合物中仅有Pro的9种构象出现, 而Pro-Ag⁺配合物中则都涉及, 最稳定结构并不是能量最低的Pro构象与Ag或Ag⁺生成; (2) Pro与4d¹⁰5s¹组态的Ag结合主要是范德华作用力, 对Pro结构影响很小, 配合物中存在较弱的特殊O―H…Ag氢键. 外层5s5p全空的Ag⁺与配位原子间生成σ配位键. 前者以单配位最稳定, 后者以双配位最稳定; (3) Ag原子与Pro配位结合能小于-19 kJ·mol^-1, 而Ag⁺与Pro的结合能在-117 - -255 kJ·mol^-1范围, 形成热力学稳定体系Pro-Ag⁺; (4) 自然键轨道(NBO)布局分析显示 Pro-Ag和Pro-Ag⁺体系中Ag都获得少量负电荷, 配合物的前线轨道能量差(Δε)均比两个碎片的低. 配合物中O―H和N―H键的红移和蓝移都存在.     

Structural Distortion of Cycloalkynes Influences Cycloaddition Rates both by Strain and Interaction Energies

The reactivities of 2-butyne, cycloheptyne, cyclooctyne, and cyclononyne in the 1,3-dipolar cycloaddition reaction with methyl azide were evaluated through DFT calculations at the M06-2X/6-311++G(d)//M06-2X/6-31+G(d) level of theory. Computed activation free energies for the cycloadditions of cycloalkynes are 16.5–22.0 kcal mol⁻¹ lower in energy than that of the acyclic 2-butyne. The strained or predistorted nature of cycloalkynes is often solely used to rationalize this significant rate enhancement. Our distortion/interaction–activation strain analysis has been revealed that the degree of geometrical predistortion of the cycloalkyne ground-state geometries acts to enhance reactivity compared with that of acyclic alkynes through three distinct mechanisms, not only due to (i) a reduced strain or distortion energy, but also to (ii) a smaller HOMO–LUMO gap, and (iii) an enhanced orbital overlap, which both contribute to more stabilizing orbital interactions.     

Accurate Interaction Energies of CO2 with the 20 Naturally Occurring Amino Acids

We have performed a series of highly accurate calculations between CO₂ and the 20 naturally occurring amino acids for the investigation of the attractive noncovalent interactions. Different nucleophilic groups present in the amino acid structures were considered (α-NH₂, COOH, side groups), and the stronger binding sites were identified. A database of accurate reference interactions energies was compiled as computed by explicitly-correlated coupled-cluster singles-and-doubles, together with perturbative triples extrapolated to the complete-basis-set limit. The CCSD(F12)(T)/CBS reference values were used for comparing a variety of popular density functionals with different basis sets. Our results show that most density functionals with the triple-zeta basis set def2-TZVPP align with the CCSD(F12)(T)/CBS reference values, but errors range from 0.1 kcal/mol up to 1.0 kcal/mol.