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本文对HOC2H3F可能解离通道的势能面进行从头算CCSD(T)/CBS//B3LYP/6-311G(d,p)计算,同时对速率常数进行Rice-Ramsperger-Kassel-Marcus计算. 生成主要产物CH2CHO+HF最有利的反应途径是OHC2H3F→i2→TS14→i6→TS9→i3→TS3→CH2CHO+HF,其中速率决定步骤是HF通过TS11从CO桥接位置解离,能量比反应物高3.8 kcal/mol. 借助中间态TS14,F原子从Cα迁移到Cβ位置生成CH2O+CH2F,然后通过中间态TS16,H从O迁移到Cα位置;通过中间态TS5,C-C键断裂生成产物,其能量比反应物低1.8 kcal/mol,比TS11低4.0 kcal/mol.  相似文献   
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蛋白的离子选择性与蛋白的功能密切相关,而离子选择性本质上来源于蛋白分子与离子结合自由能的差别. 尽管近几十年来分子力场在描述蛋白体系相互作用方面取得了长足的进步,由于缺乏对静电极化和电荷转移效应显式的描述,传统的分子力场依然难以精确地描述金属蛋白体系中蛋白质与金属离子的相互作用. 量子化学方法非常适合于蛋白质与金属离子之间相互作用的描述. 但是在分子模拟中采用量子化学方法则太昂贵了. 近年来发展起来的参考势方法在保证计算精度的前提下兼顾效率,可以有效地解决这个窘境. 在这个方法中,动力学模拟的轨迹是在分子力场的精度下获得的. 随后,通过从分子力场到量子化学方法的矫正,从而获得在量子化学势函数级别下的自由能信息. 本文采用参考势函数方法研究了Parvalbumin B蛋白的结合口袋对钙、镁离子的选择性. 计算结果表明电荷转移效应非常重要,而量子化学方法可以比较精确地预测离子的选择性. 并且,量子化学区域的选择对于结果的可靠性也是非常重要的.  相似文献   
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如今碳捕获和储存技术已得到了迅速发展以减少对环境的二氧化碳排放. 研究发现胺基有机分子溶剂能有效地吸收二氧化碳,并通过氢键和二氧化碳形成的碳酸氢盐相互作用. 最近,实验报道了一种1,3-二苯基胍溶液,在室温条件下能捕获环境中的二氧化碳并将其转化为有价值的化学品. 然而,1,3-二苯基胍分子在溶液状态下如何与二氧化碳相互作用的机理仍不清楚. 在这项工作中,利用分子动力学方法模拟研究了溶液相中1,3-二苯基胍分子与二氧化碳的复杂作用细节. 模拟结果表明,质子化的1,3-二苯基胍分子和碳酸氢根离子倾向通过不同的双氢键模式作用形成稳定的复合物. 精确的密度泛函方法计算表明,这些双氢键复合物在热力学上相当稳定. 本研究有助于理解溶液相中1,3-二苯基胍分子中催化转化二氧化碳的机理.  相似文献   
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细胞周期依赖性激酶2(CDK2)是细胞周期调控中的关键大分子.在癌细胞中,CDK2常被过度表达,因此抑制CDK2的表达是治疗乳腺癌、白血病和淋巴瘤等多种癌症有效的方法,在分子水平上定量表征CDK2与其抑制剂之间的相互作用,可为药物开发提供更深入的蛋白质与抑制剂的相互作用机制和线索,本文采用计算丙氨酸扫描和相互作用熵方法,研究CDK2与13种抑制剂结合的微观机制,该方法得到的结合自由能与实验值之间的相关系数为0.76~0.83.计算结果揭示了这13种抑制剂中的两种结合模式,即范德华占优势和静电占优势.通过将总能量分解为每个残基的贡献,确定了结合过程中五个疏水残基为热点残基,同时发现了能够决定CDK2与抑制剂结合强度的残基.  相似文献   
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Estimation of protein-ligand binding affinity within chemical accuracy is one of the grand challenges in structure-based rational drug design. With the efforts over three decades, free energy methods based on equilibrium molecular dynamics (MD) simulations have become mature and are nowadays routinely applied in the community of computational chemistry. On the contrary, nonequilibrium MD simulation methods have attracted less attention, despite their underlying rigor in mathematics and potential advantage in efficiency. In this work, the equilibrium and nonequilibrium simulation methods are compared in terms of accuracy and convergence rate in the calculations of relative binding free energies. The proteins studied are T4-lysozyme mutant L99A and COX-2. For each protein, two ligands are studied. The results show that the nonequilibrium simulation method can be competitively as accurate as the equilibrium method, and the former is more efficient than the latter by considering the convergence rate with respect to the cost of wall clock time. In addition, Bennett acceptance ratio, which is a bidirectional post-processing method, converges faster than the unidirectional Jarzynski equality for the nonequilibrium simulations.  相似文献   
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Myoglobin has important biological functions in storing and transporting small diatomic molecules in human body. Two possible orientations of carbon monoxide (CO) in the heme distal pocket (named as B1 and B2 states) of myoglobin have been experimentally indicated. In this study, ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation of CO in myoglobin was carried out to investigate the two possible B states. Our results demonstrate that the B1 and B2 states correspond to Fe…CO (with carbon atom closer to iron center of heme) and Fe…OC (with oxygen atom closer to Fe), by comparing with the experimental infrared spectrum. QM electrostatic polarization effect on CO brought from the protein and solvent environment is the main driving force, which anchors CO in two distinctive orientations and hinders its rotation. The calculated vibrational frequency shift between the state B1 and B2 is 13.1 cm-1, which is in good agreement with experimental value of 11.5 cm-1. This study also shows that the electric field produced by the solvent plays an important role in assisting protein functions by exerting directional electric field at the active site of the protein. From residue-based electric field decomposition, several residues were found to have most contributions to the total electric field at the CO center, including a few charged residues and three adjacent uncharged polar residues (namely, HIS64, ILE107, and PHE43). This study provides new physical insights on rational design of enzyme with higher electric field at the active site.  相似文献   
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