硫团簇Sn(n=2～8)结构的朗之万分子动力学计算

引入第一原理密度泛函理论,即赝势密度泛函在实空间的有限差分方法和朗之万分子动力学退火技术,对硫团簇Sn(n=2～8)的结构等进行了计算.结果表明,S3,S4,S5,S6,S7和S8的结构对应为C2v,D2h,信封式Cs,D3d(或船式C2v),椅式C5和D4d的对称结构,其结构参数与有实验数据的S和S6-8吻合较好.从平均原子结合能看,原子数目越多,硫团簇越为稳定.     

On-the-Fly Ring-Polymer Molecular Dynamics Calculations of the Dissociative Photodetachment Process of the Oxalate Anion

The dissociative photodetachment dynamics of the oxalate anion, C₂O₄H⁻ + hν → CO₂ + HOCO + e⁻, were theoretically studied using the on-the-fly path-integral and ring-polymer molecular dynamics methods, which can account for nuclear quantum effects at the density-functional theory level in order to compare with the recent experimental study using photoelectron–photofragment coincidence spectroscopy. To reduce computational time, the force acting on each bead of ring-polymer was approximately calculated from the first and second derivatives of the potential energy at the centroid position of the nuclei beads. We find that the calculated photoelectron spectrum qualitatively reproduces the experimental spectrum and that nuclear quantum effects are playing a role in determining spectral widths. The calculated coincidence spectrum is found to reasonably reproduce the experimental spectrum, indicating that a relatively large energy is partitioned into the relative kinetic energy between the CO₂ and HOCO fragments. This is because photodetachment of the parent anion leads to Franck–Condon transition to the repulsive region of the neutral potential energy surface. We also find that the dissociation dynamics are slightly different between the two isomers of the C₂O₄H⁻ anion with closed- and open-form structures.     

乙醇-水分子团簇C2H5OH(H2O)n (n=1-9)稳定结构的量子化学研究

采用密度泛函理论B3LYP方法, 在B3LYP/6-311++G(2d,2p)//B3LYP/6-311++G(d,p)基组水平上对乙醇-水分子团簇(C₂H₅OH(H₂O)_n (n=1-9))的各种性质进行研究, 如: 优化的几何构型、结构参数、氢键、结合能、平均氢键强度、自然键轨道(NBO)电荷分布、团簇的生长规律等. 结果表明, 从二维(2-D)环状结构到三维(3-D)笼状结构的过渡出现在n=5的乙醇-水分子团簇中. 此外, 利用团簇结合能的二阶差分、形成能、能隙等性质, 发现在n=6时乙醇-水分子团簇的最低能量结构稳定性较好, 可能为幻数结构. 最后, 为了进一步探讨氢键本质, 将C₂H₅OH(H₂O)_n (n=2-9)最低能量结构的各种性质与纯水分子团簇(H₂O)_n (n=3-10)比较, 结果表明前者与后者中的水分子之间氢键相似.     

Theoretical Studies on the Stabilities and Hydrogen Bond Actions of （H2O）n Clusters

1 INTRODUCTION In the latest ten years, the structure and function of water clusters have captured the interest of chemists. One of the most important study objects in water cluster is to describe the behavior of water so- lution quantitatively at molecule level, which will pave the way for the solving of some environmental and other scientific problems, such as the formation of acid rain and nucleation mechanism of little water drop. Besides, weak interaction in water clusters could be al…     

ZIF-8材料中CH4/H2吸附与扩散的分子模拟

采用平衡分子动力学和巨正则系综蒙特卡洛模拟方法对多孔沸石咪唑酯骨架材料(ZIF-8)中CH4和H2分子的吸附与扩散特性进行了比较研究.结果表明,采用柔性力场能够很好地复制ZIF-8在不同压力或温度条件下的晶体结构,也能准确地计算不同温度下CH4和H2分子在ZIF-8中的扩散系数,特别是高温下CH4分子因能够摆脱ZIF-8骨架笼口的空间限制而使其扩散系数出现大幅提升.同时,该力场也能粗略地模拟CH4和H2分子在ZIF-8中的等温吸附曲线,通过自编程序得到吸附和扩散平衡时CH4和H2分子在ZIF-8单元晶胞内的几率密度分布数据,并利用VMD软件可视化.结果显示CH4和H2分子在ZIF-8中的优先吸附位置均在大孔中心靠近咪唑环的区域,但CH4分子的优先吸附位置有两个不同层次,而H2分子的优先吸附位置只有一个层次,说明CH4和H2分子在ZIF-8中存在着不同的吸附机理.     

Cover Feature: Ab Initio Molecular Dynamics Study of H2 Dissociation Mechanisms on Cu13 and Defective Graphene-supported Cu13 Clusters: Active Sites,Energy Barriers and Adsorption States (ChemPhysChem 19/2023)

Ab initio molecular dynamics calculations were performed to study H₂ dissociation mechanisms on Cu₁₃ and defective graphene-supported Cu₁₃ clusters. The study reveals that seven types of corresponding dissociation processes are found on the two clusters. The average dissociation energy barriers are 0.51 eV on the Cu₁₃ cluster and 0.12 eV on the defective graphene-supported Cu₁₃ cluster, which are lowered by ~19 % and ~81 % compared with the pristine Cu(111) surface, respectively. Furthermore, compared with the pure Cu₁₃ cluster, the average dissociation energy barrier on the defective graphene-supported Cu₁₃ cluster is substantially reduced by about 76 %. The preferred dissociation mechanisms on the two clusters are H₂ located at a top-bridge site with the barrier heights of 0.30 eV on the Cu₁₃ cluster and −0.31 eV on the defective graphene-supported Cu₁₃ cluster_. Analysis of the H−Cu bond interactions in the transition states shows that the antibonding-orbital center shifts upward on the defective graphene-supported Cu₁₃ cluster compared with the one on the Cu₁₃ cluster, which explains the reduction of the dissociation energy barrier. The average adsorption energy of dissociated H atoms is also greatly enhanced on the defective graphene-supported Cu₁₃ cluster, about twice that on the Cu₁₃ cluster.     

覆盖的氩原子簇过热的分子动力学模拟(英)

通过分子动力学模拟研究了覆盖较高熔点的原子的氩原子簇．原子族由177个氩原子和72个覆盖原子组成．覆盖原子的势能参数ε比氩原子大50％，该原子簇比纯氩原子簇熔点过热2K．模拟结果表明，覆盖的原子簇过热的原因是：在达到熔点之前，体系缺少氩原子构成的自由表面，仍然是覆盖原子的有序表面．     

Ab initio molecular dynamics studies of ionic dissolution and precipitation of sodium chloride and silver chloride in water clusters, NaCl(H2O)n and AgCl(H2O)n, n = 6, 10, and 14

An ab initio molecular dynamics method was used to compare the ionic dissolution of soluble sodium chloride (NaCl) in water clusters with the highly insoluble silver chloride (AgCl). The investigations focused on the solvation structures, dynamics, and energetics of the contact ion pair (CIP) and of the solvent-separated ion pair (SSIP) in NaCl(H(2)O)(n) and AgCl(H(2)O)(n) with cluster sizes of n = 6, 10 and 14. We found that the minimum cluster size required to stabilize the SSIP configuration in NaCl(H(2)O)(n) is temperature-dependent. For n = 6, both configurations are present as two distinct local minima on the free-energy profile at 100 K, whereas SSIP is unstable at 300 K. Both configurations, separated by a low barrier (<10 kJ mol(-1)), are identifiable on the free energy profiles of NaCl(H(2)O)(n) for n = 10 and 14 at 300 K, with the Na(+)/Cl(-) pairs being internally solvated in the water cluster and the SSIP configuration being slightly higher in energy (<5 kJ mol(-1)). In agreement with the low bulk solubility of AgCl, no SSIP minimum is observed on the free-energy profiles of finite AgCl(H(2)O)(n) clusters. The AgCl interaction is more covalent in nature, and is less affected by the water solvent. Unlike NaCl, AgCl is mainly solvated on the surface in finite water clusters, and ionic dissolution requires a significant reorganization of the solvent structure.     

Pu（^7Fg）＋H2（X^1∑g^＋,0,0）的分子反应动力学

基于PuH_2分子基态(X~7A_1)的分析势能函数，用准经典的Monte-Carlo轨线法 对Pu(~7Fg)+H_2(X~1∑_g~+，0，0)的分子反应动力学过程进行了计算。结果表明 ：Pu(~7F_g)与H_2(X~1∑_g~+，0，0)碰撞是弹性碰撞。     

Investigation of Thermodynamic,Dynamic, and Structural Properties of H2 Adsorption on a Ag–Au Nanoalloy with a Carbon Nanotube Support

We have performed MD simulations to investigate H₂ adsorption on Ag–Au nanoclusters with the different Au mole fractions supported on the carbon nanotubes with the different diameters. Our thermodynamic results shown that the saturation value of coverage and the enthalpy of adsorption increases as the mole fraction of Au is increased. Our structural results showed that the presence of the H₂ gas exerts a significant effect on the nanocluster surface atoms and tends to stabilize the surface atoms on the nanocluster. Also, the structural changes are irreversible in such a way that by gradually decreasing the pressure to zero, the nanocluster geometry is not reversed to its initial structure in vacuum conditions. We have also shown that the nanoclusters have smaller values of the self‐diffusion coefficients in presence of H₂ molecules than those values in the initial state (vacuum), which is due to the increasing of the interface structure between the nanocluster and the nanotube.     

Dissociative Adsorption of H2S on Li(110) Surface Using Density Functional Theory Calculations and Car-Parrinello Molecular Dynamics Simulations

The information concerning dissociative adsorption of H₂S on Li surface is inadequate and the mechanistic insight for its complete dissociation is yet to be explored. The present investigation aims to scrutinize the dissociative adsorption of H₂S on Li(110) surface using density functional theory calculations. The climbing image nudged elastic band calculation was employed to unveil the relative energy profiles for S−H dissociation. To elucidate the components of interaction energy responsible for stabilizing the adsorbed moieties on the surface, periodic energy decomposition analysis was performed. A Car-Parrinello molecular dynamics (CPMD) simulation was performed to understand the dynamic behaviour of H₂S on Li(110). Results vividly demonstrates: (i) partially dissociated product with perpendicular S−H is comparatively stable than the parallel SH, (ii) completely dissociated moieties H/H/S are the most stable among all, (iii) dissociation of first S−H is barrierless and the second S−H dissociation is a low energy barrier reaction, (iv) complete dissociation of H₂S occurs in a stepwise manner, (v) orbital and electrostatic contributions of the interaction energy plays a vital role in stabilizing the dissociated moieties, and (vi) stepwise dissociation of H₂S was further reinforced by CPMD.     

VEGFR-2 与抑制剂Sunitinib 的分子对接及分子动力学研究

用分子对接方法研究了VEGFR-2 和抑制剂Sunitinib 的相互作用模式, 并对其复合物进行了10 ns 的分子动力学(Molecular Dynamics, MD)模拟. 结果表明, 抑制剂Sunitinib 能与VEGFR-2 中位于活性空腔的Glu885, Ile888, His1026,Asp1028, Asp1046 五个氨基酸残基形成疏水作用; 另外, VEGFR-2 中His1026, Cys1024, Asp1046 三个氨基酸残基能与Sunitinib 形成三个作用强度不同的氢键. 这些基团之间的相互作用是Sunitinib 抑制VEGFR-2 活性的关键因素. 研究结果可为VEGFR-2 抑制剂的结构改良、分子设计、合成提供理论参考, 并有助于寻找活性更高、效果更好的抗肿瘤药物.     

CO2在氨基改性MIL-101(Cr)中吸附的分子模拟

采用实验与分子模拟结合的方法研究298 K下CO_2在氨基改性得到的MIL-101(Cr)-NH_2和MIL-101(Cr)-ED(ED:乙二胺)上的吸附性能。比较MIL-101(Cr)、MIL-101(Cr)-NH_2和MIL-101(Cr)-ED的吸附等温线与吸附热的结果,表明采用直接合成改性法得到的MIL-101(Cr)-NH_2比采用合成后再改性得到的MIL-101(Cr)-ED有更高的CO_2吸附容量。进一步比较密度分布图和径向密度分布曲线,分析CO_2在氨基改性MIL-101(Cr)中的吸附位,表明在低压下CO_2首先吸附在MIL-101(Cr)微孔的超级四面体中,随着吸附压力的增大逐渐填充到更大的孔中。氨基的存在增加了CO_2的吸附位点,使MIL-101(Cr)-NH_2具有较高CO_2吸附容量;同时MIL-101(Cr)-ED中的ED分子的存在增加了CO_2的吸附位点,使MIL-101(Cr)-ED也具有较高CO_2吸附容量;但是MIL-101(Cr)-ED中的ED分子占据了MIL-101(Cr)中Cr的吸附位点,使Cr对CO_2的吸附强度减弱,同时可吸附位点少于MIL-101(Cr)-NH_2,导致其对CO_2的吸附容量少于MIL-101(Cr)-NH_2。     

偏氟乙烯/三氟氯乙烯交替共聚物在TATB表面吸附的分子动力学模拟

采用COMPASS力场和NVT正则系综的动力学模拟方法, 搭建了聚合度分别为10, 50和100的偏氟乙烯(VDF)/三氟氯乙烯(CTFE)交替共聚物, 对交替共聚物在1,3,5-三氨基-2,4,6-三硝基苯(TATB)的(0,0,1)晶面上的吸附和结构进行了分子动力学(MD)模拟. 结果表明, 在300～320 K温区, 聚合度为100的VDF/CTFE交替共聚物链对TATB晶体有理想的表面活性和吸附能力, 以train型构象平铺于TATB表面. 通过对聚合度为10的交替共聚物的多链体系在TATB表面吸附的MD模拟, 表明了VDF/CTFE交替共聚物具有非凝聚吸附的高表面活性特征. 对搭建的乙酸乙酯溶剂化的聚合度为50的VDF/CTFE交替共聚物在TATB晶体表面吸附的模拟, 实验证明了溶剂小分子能够降低共聚物链的吸附能力, 且链以tail型构象吸附于TATB表面.     

CO2在氨基改性MIL-101(Cr)中吸附的分子模拟

采用实验与分子模拟结合的方法研究298 K下CO₂在氨基改性得到的MIL-101（Cr）-NH₂和MIL-101（Cr）-ED（ED：乙二胺）上的吸附性能。比较MIL-101（Cr）、MIL-101（Cr）-NH₂和MIL-101（Cr）-ED的吸附等温线与吸附热的结果,表明采用直接合成改性法得到的MIL-101（Cr）-NH₂比采用合成后再改性得到的MIL-101（Cr）-ED有更高的CO₂吸附容量。进一步比较密度分布图和径向密度分布曲线,分析CO₂在氨基改性MIL-101（Cr）中的吸附位,表明在低压下CO₂首先吸附在MIL-101（Cr）微孔的超级四面体中,随着吸附压力的增大逐渐填充到更大的孔中。氨基的存在增加了CO₂的吸附位点,使MIL-101（Cr）-NH₂具有较高CO₂吸附容量;同时MIL-101（Cr）-ED中的ED分子的存在增加了CO₂的吸附位点,使MIL-101（Cr）-ED也具有较高CO₂吸附容量;但是MIL-101（Cr）-ED中的ED分子占据了MIL-101（Cr）中Cr的吸附位点,使Cr对CO₂的吸附强度减弱,同时可吸附位点少于MIL-101（Cr）-NH₂,导致其对CO₂的吸附容量少于MIL-101（Cr）-NH₂。     

F-(H2O)n(n=1～4)体系的结构、偶极矩、极化率和一阶超极化率的从头计算

用MP2方法得到F^-(H₂O)_n(n=1～4)体系的优化几何结构.依据优化结构计算偶极矩μ₀、极化率α₀、各向异性极化率Δα和一阶超极化率β₀,研究了基组效应.讨论了溶剂水分子数、溶剂水分子排布及溶剂层数变化诸因素对体系超极化率等性质的影响.     

D_2在Ni(100)表面离解吸附的量子动力学研究

用量子含时波包法研究了Ｄ２在镍表面顶－桥位上离解吸附量子动力学．计算了不同入射动能及初始振转态的离解几率．讨论了分子的同核对称性、转动取向和振动激发对离解几率的影响，并与其他理论计算结果做了比较．     

螺环吲哚类MDM2抑制剂的分子对接、定量构效关系和分子动力学模拟

采用分子对接、三维定量构效关系(3D-QSAR)和分子动力学方法研究了21个螺环吲哚类化合物与MDM2蛋白的相互作用, 并建立了相关预测模型. 比较分子场分析法(CoMFA)和比较分子相似性指数分析法(CoMSIA)模型的交互验证相关系数q²分别为0.573 和0.651, 非交互验证相关系数r²分别为0.948和0.980. 分子对接得到的结合模式与分子动力学模拟得到的结果一致, 结合模式表明该类螺环吲哚化合物主要通过疏水相互作用和氢键与MDM2结合. 基于上述相互作用模型设计并合成了6个新结构螺环吲哚化合物, 并在MDM2高表达的前列腺癌LNCaP细胞株上测定其活性, 结果表明化合物5, 6的半数抑制浓度均低于1μg·mL^-1, 可作为新的抗肿瘤药物先导化合物进一步深入研究. 本研究对以MDM2为靶点的新结构螺环吲哚类抑制剂的开发提供了理论和实验依据.     

Cyclodextrin-supported Co(OH)2 Clusters as Electrocatalysts for Efficient and Selective H2O2 Synthesis

Co-based material catalysts have shown attractive application prospects in the 2 e⁻ oxygen reduction reaction (ORR). However, for the industrial synthesis of H₂O₂, there is still lack of Co-based catalysts with high production yield rate. Here, novel cyclodextrin-supported Co(OH)₂ cluster catalysts were prepared via a mild and facile method. The catalyst exhibited remarkable H₂O₂ selectivity (94.2 % ~ 98.2 %), good stability (99 % activity retention after 35 h), and ultra-high H₂O₂ production yield rate (5.58 mol g_catalyst⁻¹ h⁻¹ in the H-type electrolytic cell), demonstrating its promising industrial application potential. Density functional theory (DFT) reveals that the cyclodextrin-mediated Co(OH)₂ electronic structure optimizes the adsorption of OOH* intermediates and significantly enhances the activation energy barrier for dissociation, leading to the high reactivity and selectivity for the 2 e⁻ ORR. This work offers a valuable and practical strategy to design Co-based electrocatalysts for H₂O₂ production.