开发高效的催化剂用于催化还原CO₂转化为甲酸和它的盐类已经成为研究的热点，是因为将CO₂转化为C1产物不仅可以解决CO₂的含量升高带来的环境问题，还可以解决化石能源燃烧日趋严重的问题。贵金属配合物催化CO₂转化为甲酸和甲酸盐类是目前这类反应最有效的方式，尤其是Ru、Ir和Rh等贵金属。我们之前的研究结果表明Ir(Ⅲ), Ru(Ⅱ)类配合物催化还原CO₂转化为甲酸盐的活性是由配合物Ru―H键的成键性质决定的。它们能高活性的催化CO₂是由于它们都含有同一种特点的Ru―H键，是由Ru的sd²杂化轨道和H的1s轨道杂化而成的，而且这一特点可以被活性氢的对位配体显著影响。鉴于硼基配体具有强的对位效应，我们基于高活性的均相催化剂Ru(PNP)(CO)H₂ (PNP = 2, 6-二(二叔丁基磷甲基)-吡啶)设计了Ru-PNP-HBcat和Ru-PNP-HBpin，并计算了二者催化还原CO₂的活性。Bcat和Bpin配体是实验上常用的硼基配体。我们的计算结果表明Ru-PNP-HBcat和Ru-PNP-HBpin有比Ru-PNP-H₂更长的Ru―H键、亲核性更强的活性氢，其Ru―H键中的Ru原子的d轨道杂化成分的贡献也比Ru-PNP-H₂的更少。相应地Ru-PNP-HBcat和Ru-PNP-HBpin活化CO₂的能垒比Ru-PNP-H₂低。而且Ru-PNP-H₂、Ru-PNP-HBcat和Ru-PNP-HBpin催化CO₂转化为甲酸盐的能垒分别为76.2、67.8、54.4 kJ∙mol^-1，表明Ru-PNP-HBpin具有最高的催化活性。因此，钌配合物催化还原CO₂的活性可由硼基配体强的对位效应和Ru―H键的成键性质来调控。

Dye-sensitized solar cells (DSSCs) are one of the most promising renewable energy technologies. Charge transfer and charge transport are pivotal processes in DSSCs, which govern solar energy capture and conversion. These processes can be probed using modern electronic structure methods. Because of the heterogeneity and complexity of the local environment of a chromophore in DSSCs (such as solvatochromism and chromophore aggregation), a part of the solvation environment should be treated explicitly during the calculation. However, because of the high computational cost and unfavorable scaling with the number of electrons of high-level quantum mechanical methods, approaches to explicitly treat the local environment need careful consideration. Two problems must be tackled to reduce computational cost. First, the number of configurations representing the solvent distribution should be limited as much as possible. Second, the size of the explicit region should be kept relatively small. The purpose of this study is to develop efficient computational approaches to select representative configurations and to limit the explicit solvent region to reduce the computational cost for later (higher-level) quantum mechanical calculations. For this purpose, an ensemble of solvent configurations around a 1-methyl-8-oxyquinolinium betaine (QB) dye molecule was generated using Monte Carlo simulations and molecular mechanics force fields. Then, a fitness function was developed using data from inexpensive electronic structure calculations to reduce the number of configurations. Specific solvent molecules were also selected for explicit treatment based on a distance criterion, and those not selected were treated as background charges. The configurations and solvent molecules selected proved to be good representatives of the entire ensemble; thus, expensive electronic structure calculations need to be performed only on this subset of the system, which significantly reduces the computational cost.

针对铜表面化学反应，我们发展了一套铜-碳体系的密度泛函紧束缚(DFTB)参数。测试结果表明这套参数可以很好的描述吸附铜或碳原子前后铜表面的几何结构和能量。基于这套参数，我们对Cu(111)表面的碳二聚化过程进行了分子模拟研究。即使在高温下，直接的分子动力学模拟也很难观察到碳二聚体的形成。这是因为高温下铜表面显著的结构弛豫一定程度上阻止了二聚化。为了研究高温下铜表面碳二聚化的机理，我们进行了赝动力学模拟。发现在二聚化的过程中，碳原子形成C-Cu-C桥状结构以后，会绕中间Cu原子转动，最后形成碳二聚体。1300 K下碳二聚化的自由能垒约0.9 eV。

Ethylene carbonate (EC) liquid and its vapor-liquid interface were investigated using a combination of molecular dynamics (MD) simulation and vibrational IR, Raman and sum frequency generation (SFG) spectroscopies. The MD simulation was performed with a flexible and polarizable model of the EC molecule newly developed for the computation of vibrational spectra. The internal vibration of the model was described on the basis of the harmonic couplings of vibrational modes, including the anharmonicity and Fermi resonance coupling of C＝O stretching. The polarizable model was represented by the charge response kernel (CRK), which is based on ab initio molecular orbital calculations and can be readily applied to other systems. The flexible and polarizable model can also accurately reproduce the structural and thermodynamic properties of EC liquid. Meanwhile, a comprehensive set of vibrational spectra of EC liquid, including the IR and Raman spectra of the bulk liquid as well as the SFG spectra of the liquid interface, were experimentally measured and reported. The set of experimental vibrational spectra provided valuable information for validating the model, and the MD simulation using the model comprehensively elucidates the observed vibrational IR, Raman, and SFG spectra of EC liquid. Further MD analysis of the interface region revealed that EC molecules tend to orientate themselves with the C＝O bond parallel to the interface. The MD simulation explains the positive Im[$ \chi ^{(2)}$](ssp) band of the C＝O stretching region in the SFG spectrum in terms of the preferential orientation of EC molecules at the interface. This work also elucidates the distinct lineshapes of the C＝O stretching band in the IR, Raman, and SFG spectra. The lineshapes of the C＝O band are split by the Fermi resonance of the C＝O fundamental and the overtone of skeletal stretching. The Fermi resonance of C＝O stretching was fully analyzed using the empirical potential parameter shift analysis (EPSA) method. The apparently different lineshapes of the C＝O stretching band in the IR, Raman, and SFG spectra were attributed to the frequency shift of the C＝O fundamental in different solvation environments in the bulk liquid and at the interface. This work proposes a systematic procedure for investigating the interface structure and SFG spectra, including general modeling procedure based on ab initio calculations, validation of the model using available experimental data, and simultaneous analysis of molecular orientation and SFG spectra through MD trajectories. The proposed procedure provides microscopic information on the EC interface in this study, and can be further applied to investigate other interface systems, such as liquid-liquid and solid-liquid interfaces.

二维石墨烯纳米孔中气体分子的选择性渗透对多孔石墨烯分离膜非常重要。本文采用分子动力学方法研究了气体分子在氮氢修饰石墨烯纳米孔中的渗透特性，从分子的大小和结构、纳米孔的构型以及分子与石墨烯之间的作用强度等角度阐明了分子出现选择性渗透的原因。结果表明，不同分子的渗透率不同，即H₂O＞H₂S＞CO₂＞N₂＞CH₄。渗透率跟分子的质量和直径以及分子在石墨烯表面上的吸附密度有关；根据气体分子动理学理论，渗透率跟分子质量成反比关系；而分子在石墨烯表面上的高吸附密度对渗透起促进作用。对于H₂O和CH₄分子，分子直径起主导作用；H₂O分子直径最小，其渗透率最大；同理，CH₄分子的渗透率最小。对于H₂S和CO₂分子，H₂S分子的直径较大，但其与石墨烯之间的作用强度较大(吸附密度较高)，导致渗透率较高；对于CO₂和N₂分子，CO₂分子的直径较小，并且与石墨烯之间的作用强度较大，渗透率较高。同时发现，分子在纳米孔中的渗透使得其在石墨烯表面的密度分布极不均匀。纳米孔左右两侧的功能化氮原子使CH₄分子容易从孔两侧区域穿过，而其它分子由于直径较小在纳米孔中心区域穿过的概率最大。分子与石墨烯之间的作用越强，导致分子在石墨烯表面区域内停留的时间越长，最终使其在渗透纳米孔的过程中所经历的时间越长。本文所采用的氮氢修饰石墨烯纳米孔中，分子渗透速率达到~10^-3 mol·s^-1·m^-2·Pa^-1，并且其它分子相对于CH₄分子的选择性也很高，说明基于该类型纳米孔的多孔石墨烯分离膜在天然气处理等工业气体分离领域具有很好的应用前景。

由于在检测、药物输运、分子马达等领域具有广阔的应用前景，二维柔性响应Janus材料受到了广泛的关注。但遗憾的是，这些二维材料的响应形变的分子机理仍不明确。基于此，我们采用介观尺度的耗散粒子动力学模拟方法系统研究了Janus纳米片两侧接枝不同长度和不同溶剂相容性的高分子链对Janus纳米片形变的影响。我们发现由于构象熵和混合焓的共同作用，通过对接枝链长度和溶剂相容性的调整，Janus纳米片可以形成如反相包覆、信封装包覆和碗状等新奇的结构。我们的理论结果首次提供了对二维柔性Janus材料可控形变的基本认识，并预报了设计合成新型Janus纳米器件在药物和生物医学领域的潜在应用。

为探究固相CL-20热分解反应机理，本文采用反应分子动力学ReaxFF MD模拟研究了含有128个CL-20分子的超胞模型在800–3000 K温度下的热分解过程。借助作者所在课题组研发的反应分析及可视化工具VARxMD得到了热分解过程中多种反应中间物和较为全面的反应路径。氮氧化物是CL-20初始分解的主要中间产物，其中NO₂是数量最多的初始分解产物，观察到的中间物NO₃的生成量仅次于NO₂。统计CL-20初始分解的所有反应后发现，在所有考察温度下CL-20初始分解路径主要是N―NO₂断裂反应和C―N键断裂引起开环的单分子反应路径。N―NO₂断裂反应数量在高温下显著增多，而C―N键断裂引起的开环反应数量随温度升高变化不大。在低温热分解模拟中还观察到CL-20初始分解阶段生成的NO₂会发生双分子反应—从CL-20分子中夺氧生成NO₃。对CL-20热分解过程中环结构演化进行分析后发现，CL-20分解的早期反应中间物主要为具有3元或2元稠环结构的吡嗪衍生物，随后它们会分解形成单环吡嗪。吡嗪六元环结构在热分解过程中非常稳定，这一模拟结果支持Py-GC/MS实验中提出吡嗪存在的结论。CL-20中的咪唑五元环结构相对不稳定，在热分解过程中会发生开环分解而较早消失。由ReaxFF MD模拟得到的3000 K高温热分解产物N₂，H₂O，CO₂和H₂的数量与爆轰实验的测量结果定量吻合。本文获得的对CL-20热分解机理的认识表明ReaxFF MD结合VARxMD有可能为深入了解热刺激下含能材料复杂化学过程提供一种有前景的方法。

Surfactant molecules, when dispersed in solution, have been shown to spontaneously form aggregates. Our previous studies on molecular dynamics (MD) calculations have shown that ionic sodium dodecyl sulfate molecules quickly aggregated even when the aggregation number is small. The aggregation rate, however, decreased for larger aggregation numbers. In addition, studies have shown that micelle formation was not completed even after a 100 ns-long MD run (Chem. Phys. Lett. 2016, 646, 36). Herein, we analyze the free energy change of micelle formation based on chemical species model combined with molecular dynamics calculations. First, the free energy landscape of the aggregation, ΔG_i+j^†, where two aggregates with sizes i and j associate to form the (i + j)-mer, was investigated using the free energy of micelle formation of the i-mer, G_i^†, which was obtained through MD calculations. The calculated ΔG_i+j^† was negative for all the aggregations where the sum of DS ions in the two aggregates was 60 or less. From the viewpoint of chemical equilibrium, aggregation to the stable micelle is desired. Further, the free energy profile along possible aggregation pathways was investigated, starting from small aggregates and ending with the complete thermodynamically stable micelles in solution. The free energy profiles, G(l, k), of the aggregates at l-th aggregation path and k-th state were evaluated by the formation free energy $\sum\limits_i {{n_i}\left( {l, k} \right)G_i^\dagger } $ and the free energy of mixing $\sum\limits_i {{n_i}(l, k){k_B}Tln({n_i}(l, k)/n(l, k))} $, where n_i(l, k) is the number of i-mer in the system at the l-th aggregation path and k-th state, with $n\left( {l, k} \right) = \sum\limits_i {{n_i}\left( {l, k} \right)} $. All the aggregation pathways were obtained from the initial state of 12 pentamers to the stable micelle with i = 60. All the calculated G(l, k) values monotonically decreased with increasing k. This indicates that there are no free energy barriers along the pathways. Hence, the slowdown is not due to the thermodynamic stability of the aggregates, but rather the kinetics that inhibit the association of the fragments. The time required for a collision between aggregates, one of the kinetic factors, was evaluated using the fast passage time, t_FPT. The calculated t_FPT was about 20 ns for the aggregates with N = 31. Therefore, if aggregation is a diffusion-controlled process, it should be completed within the 100 ns-simulation. However, aggregation does not occur due to the free energy barrier between the aggregates, that is, the repulsive force acting on them. This may be caused by electrostatic repulsions produced by the overlap of the electric double layers, which are formed by the negative charge of the hydrophilic groups and counter sodium ions on the surface of the aggregates.

在分子尺度上构建光驱动的人工分子机器是超分子化学研究的一个热点。偶氮苯是一类具有双稳态的光致开关分子，能够完成高效、可逆的反式(E)$\to $顺式(Z)的光致异构化过程，因而可以作为人工分子机器的功能单元。本文采用密度泛函理论(DFT)和反应分子动力学(RMD)模拟，研究了含偶氮苯封端基团的互锁型超分子体系中冠醚主体与二烷基铵客体间结合强度，模拟了偶氮苯Z$\to $E异构化反应的动态过程，讨论了异构化反应对主客体分子构象的影响。在偶氮苯封端基团通过发生Z$\to $E异构化实现体系单向可控运动时，较强的主-客体间结合能力是保证互锁型超分子体系稳定的必要前提。顺式客体与主体大环氢键相互作用比反式客体更强，因此顺式复合异构体具有比反式异构体更大的结合强度。偶氮苯基团发生E$\to $Z光致异构化引入位阻效应，使得顺式复合物只能从环戊基准封端处进行脱环。主客体复合过程对偶氮苯基团的几何结构没有明显影响。偶氮苯光致异构化发生的速度快于客体脱环的速度是实现单向运动的动力学上的必要条件。在异构化反应后的500 ps内，大环会经历一个明显的结构驰豫过程。冠醚大环主体的柔性构象有助于实现在偶氮苯光致异构化发生过程中主客体间持续稳定的结合。各种超分子体系中，尽管客体组成各不相同，但是包含相似的主客体识别位点的超分子体系具有相似的结合能，显示了机械互锁型复合体系中各种功能性构建单元间主客体相互作用具有正交性。引入双稳态的偶氮苯功能基团对客体其他部分的几何结构影响很小。理论计算结果有助于理性设计更复杂的刺激响应性人工分子机器。

本文研究用温度副本交换分子动力学(T-REMD)和哈密顿副本交换分子动力学(H-REMD)方法模拟复杂化学反应的问题。使用具有不同活化能和反应能的简单置换反应模型，我们检验了上述两种方法用来预测反应平衡产物的效率和应用范围。T-REMD方法对具有适度活化能(约< 20 kcal·mol^-1)或者反应能量(< 3 kcal·mol^-1)的放热反应是有效的。由于在相空间的不完整采样，对于同时具有高活化能和反应能量的反应其模拟效率有严重障碍，并且对于吸热反应问题更为显着。另一方面，H-REMD对一系列具有不同活化能的反应能的模型表现出色，与T-REMD相比，H-REMD可以使用更少的副本获得优异的结果。