PAMAM树枝形分子与KALP肽相互作用的计算机模拟研究

采用粗粒化的分子动力学模拟研究了跨膜多肽,lysine-flanked peptide(KALP),对第四代聚酰胺-胺(PAMAM)树枝形分子形态结构的影响.考虑了中性和酸性两种不同pH环境下两个分子间的相互作用行为.计算了PAMAM分子的回转半径、非球形因子、相对于树枝形分子质心的径向密度分布函数,和两分子间的平均力势.模拟发现在两种pH环境下KALP多肽对树枝形分子的大小、形状及密度分布影响不大,证实了PAMAM树枝形分子内部有一定空间容纳KALP多肽分子.自由能的计算结果表明酸性pH环境中PAMAM分子排斥KALP肽,无法形成复合结构;在中性pH环境中,两种分子也不容易形成稳定的复合结构.     

丙烯热反应生成甲基环戊烷的理论探讨

在UHF／3-21G水平上,应用从头算分子轨道法和能量梯度技术,并用Mller-Plesset二级微扰理论对能量进行了相关能校正,研究了丙烯在800K热反应形成甲基环戊烷的反应机理．求得该反应分三步进行：（1）两分子丙烯相互作用产生1,4-双自由基中间体;（2）1,4-双自由基中间体经氢迁移过程生成1,5-双自由基中间体;（3）1,5-双自由基中间体闭环形成甲基环戊烷．理论计算所得的机理与实验工作者推测一致．     

气相中O3与HSO自由基间的氢键复合物

气相中O3与HSO自由基之间的相互作用及其反应在大气化学中非常重要.在DFT-B3LYP/6-311++G**和MP2/6-311++G**水平上求得O3+HSO复合物势能面上的稳定构型,B3LYP方法得到了三种构型(复合物Ⅰ,Ⅱ和Ⅲ),而MP2方法只能得到一种构犁(复合物Ⅱ).在复合物Ⅰ和Ⅲ中,HSO单元中的1H原子作为质子供体.与O3分子中的端基O原子作为质子受体相互作用,形成红移氢键复合物;而在复合物Ⅱ中,虽与复合物Ⅰ和Ⅲ中具有相间的质子供体和质子受体,却形成了蓝移氢键复合物.B3LYP/6-311++G**水平上计算的单体间相互作用能的计算考虑了基组重甍误差(BSSE)和零点振动能(ZPVE)校正,其值在-3.37到-4.55 kJ·mol-1之间.采用自然键轨道理论(NBO)对单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了三种复合物中氢键的电子密度拓扑性质.     

气相中O3与HSO自由基间的氢键复合物

气相中O3与HSO自由基之间的相互作用及其反应在大气化学中非常重要. 在DFT-B3LYP/6-311++G**和MP2/6-311++G**水平上求得O3+HSO复合物势能面上的稳定构型, B3LYP方法得到了三种构型(复合物I, II和III), 而MP2方法只能得到一种构型(复合物II). 在复合物I和III中, HSO单元中的1H原子作为质子供体, 与O3分子中的端基O原子作为质子受体相互作用, 形成红移氢键复合物; 而在复合物II中, 虽与复合物I和III中具有相同的质子供体和质子受体, 却形成了蓝移氢键复合物. B3LYP/6-311++G**水平上计算的单体间相互作用能的计算考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正, 其值在-3.37到-4.55 kJ·mol-1之间. 采用自然键轨道理论(NBO)对单体间相互作用的本质进行了考查, 并通过分子中原子理论(AIM)分析了三种复合物中氢键的电子密度拓扑性质.     

HOCl…HCOCl复合物的结构和电子性质

在DFT-B3LYP/6-311++G**水平上求得HOCl+HCOCl复合物势能面上的四种稳定构型(S1,S2,S3和S4).其中,在复合物S1和S3中,HOCl单体的5H原子作为质子供体,与HCOCl单体中作为质子受体的10原子相互作用,形成红移氢键复合物;在复合物S4中,HOCl单体的7Cl原子作为质子供体,与HCOCl单体中作为质子受体的IO原子相互作用,形成红移卤键复合物;而在复合物S2中,同时存在2C-3H…6O蓝移氢键和4Cl…5O相互作用.在MP2/6-311++G**水平上计算的单体间的相互作用能考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正,其值在-5.05与-14.76 kJ·mol-1之间.采用自然键轨道理论(NBO)对两种单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了复合物中氢键和卤键键鞍点处的电子密度拓扑性质.     

环状聚合物合成新路线:分子内受阻Lewis酸碱对催化下的高浓度合成

与传统线形聚合物的合成不同,环状聚合物的合成通常需要特殊的催化剂设计且容易引入主体单体以外的其他化学结构.最近,吉林大学张越涛团队将两分子硼路易斯酸(LA)与一分子磷路易斯碱(LB)以共价键相连,合成出分子内受阻路易斯酸碱对B-P-B三官能催化剂,通过分子内和分子间的双重协同作用实现了1+1>>2的催化效果,进而成功以γ-甲基-α-亚甲基-γ-丁内酯(MMBL)为单体合成了完全由一种丙烯酸酯类单体构成的环状聚合物c-PMMBL.值得指出的是,与合成环状聚合物的传统策略不同,该催化剂可以在较高浓度下简单快速地合成环状聚合物,开创了环状聚合物宏量高效合成的新路线.     

三唑酮分子印迹预组装体系的分子模拟与吸附性能

以三唑酮为模板分子, 以丙烯酰胺(AM)、 丙烯酸(AA)、 甲基丙烯酸(MAA)和三氟甲基丙烯酸(TFMAA)为功能单体预组装了分子印迹聚合物体系, 采用半经验法和从头算法, 利用Hyperchem软件模拟了三唑酮与4种功能单体所组成的分子印迹预组装体系的构型、 能量、 反应配比及复合反应的结合能, 选择复合物结合能最高的功能单体用于分子印迹聚合物的合成. 采用密度泛函方法计算了模板与单体在不同致孔剂中的溶剂化能. 结果表明, 三唑酮与三氟甲基丙烯酸所形成复合物的作用力最强, 在非极性溶剂中溶剂化能最弱. 由预组装体系的差示紫外光谱法研究发现, 一分子三唑酮可与两分子三氟甲基丙烯酸在氯仿中形成氢键复合物, 与分子模拟的结果一致. 在最佳模拟条件下, 合成了三唑酮的印迹聚合物, 利用吸附等温线Langmuir和Freundlich模型研究了印迹聚合物的吸附行为及识别机理. 上述方法对于分子印迹体系的筛选及分子印迹聚合物性能的预测有重要的意义.     

气相扩散法生长溶菌酶晶体的动态光散射研究

首次采用动态光散射研究了气相扩散法生长溶菌酶晶体.实验中采用了两种溶解溶菌酶的方法,所得实验结果是有区别的.这种区别表明了NaCl对溶菌酶分子间相互作用产生十分重要的影响.实验结果表明,晶体生长过程中,溶液中溶菌酶始终保持单分子与两分子聚集体的状态,这种状态是生长晶体的基础.     

超临界流体的共溶剂效应和混合流体研究进展

共溶剂的出现极大地拓展了超临界流体的应用范围，推动了超临界流体科学与技术的发展。本文从相行为和分子间相互作用热力学的角度，对相行为测定、量热技术、光谱技术和分子模拟等在超临界流体中共溶剂效应的研究作了综述，主要介绍超临界流体中共溶剂的作用机理和混合流体在临界点附近热力学性质研究，并对其未来发展方向进行了展望。     

基于金属配位和主客体相互作用分级自组装构筑超分子凝胶

将金属配位和主客体相互作用引入到同1个超分子体系中,设计合成了2个超分子单体1和2.通过这2个超分子单体分级自组装形成的交联网状超分子聚合物构建了一种多重刺激响应性和良好自修复性能的超分子凝胶.同时,进一步将具有聚集诱导发光性能的四苯乙烯引入到这种超分子体系中,以赋予超分子体系新颖的发光性能.单体分子1是由中间为双苯并24-冠-8的冠醚连接2个四苯基乙烯荧光生色团,两端为2个三联吡啶分子构成的1个主体分子.单体分子1两端的三联吡啶基团可以与过渡金属Zn(OTf)2进行金属配位形成线型超分子聚合物3;而中间的冠醚基团与双二级铵盐客体分子2通过主客体相互作用进一步形成交联超分子聚合物4.当该交联超分子聚合物的浓度达到30 mmol/L时,可形成荧光超分子聚合物凝胶.通过核磁共振(1H-NMR和DOSY)与黏度等测试方法,证明了线形和交联超分子聚合物的形成,并进一步通过流变的测试证明了超分子聚合物凝胶的形成及其良好的自修复性能.除此之外,由于引入的主客体相互作用以及金属配位固有的刺激响应性,该荧光超分子聚合物凝胶表现出对温度、p H值、K+离子和竞争配体的刺激响应性能.     

Relationships between three-body and two-body interactions in fluids and solids

Molecular dynamics data are reported for two-body and three-body interactions in noble gases at densities covering the gas, liquid, and solid phases. The data indicate that simple relationships exist between three- and two-body interactions in both fluid and solid phases. The relationship for liquids has a simple density dependence with only one external parameter. In contrast, the solid phase relationship depends both on density and on the square of density and requires the evaluation of two parameters. The relationships are tested for both system-size and temperature dependences. The values of the relationship parameters are only sensitive to system size when a small number of atoms are involved. For 500 or more atoms, they remain nearly constant. The relationships are valid for both subcritical and slightly supercritical temperatures. A practical benefit of the relationships is that they enable the use of two-body intermolecular potentials for the prediction of the properties of real systems without the computational expense of three-body calculations.     

Two- and three-body interactions among nanoparticles in a polymer melt

We perform direct three-dimensional density functional theory (DFT) calculations of two- and three-body interactions in polymer nanocomposites. The nanoparticles are modeled as hard spheres, immersed in a hard-sphere homopolymer melt of freely jointed chains. The two-particle potential of mean force obtained from the DFT is in near quantitative agreement with the potential of mean force obtained from self-consistent polymer reference interaction site model theory. Three-body interactions among three nanoparticles are found to be significant, such that it is not possible to describe these systems with a polymer-mediated two-body interaction calculated from the potential of mean force.     

水团簇(H2O)n中多体作用强度与水分子间距的关系

使用高精度从头算方法(含基组重叠误差校正)计算了水团簇(H₂O)_n (n = 8, 10, 16, 20, 22, 24)中的所有二体、三体和四体作用能,分析了水团簇中的多体效应.研究表明,二体作用对体系总作用能的贡献高达70%以上,三体作用对总作用能的贡献可高达25%,四体作用在总作用能中所占比例不超过3%,五体及以上多体作用能在总作用能中所占比例更小,不超过0.5%.本文研究还表明,两个水分子间距小于0.68 nm的二体作用、三个和四个水分子中最近的两个水分子间距小于0.31 nm的三体和四体作用对体系总作用能的贡献高达99.4%.因此,以生物体系为对象的分子模拟方法应该具备准确地模拟两个水分子间距小于0.68 nm的二体作用、三个和四个水分子中最近的两个分子间距小于0.31 nm的三体和四体作用的能力.     

Pairwise additivity of energy components in protein-ligand binding: the HIV II protease-Indinavir case

An energy expansion (binding energy decomposition into n-body interaction terms for n ≥ 2) to express the receptor-ligand binding energy for the fragmented HIV II protease-Indinavir system is described to address the role of cooperativity in ligand binding. The outcome of this energy expansion is compared to the total receptor-ligand binding energy at the Hartree-Fock, density functional theory, and semiempirical levels of theory. We find that the sum of the pairwise interaction energies approximates the total binding energy to ～82% for HF and to >95% for both the M06-L density functional and PM6-DH2 semiempirical method. The contribution of the three-body interactions amounts to 18.7%, 3.8%, and 1.4% for HF, M06-L, and PM6-DH2, respectively. We find that the expansion can be safely truncated after n=3. That is, the contribution of the interactions involving more than three parties to the total binding energy of Indinavir to the HIV II protease receptor is negligible. Overall, we find that the two-body terms represent a good approximation to the total binding energy of the system, which points to pairwise additivity in the present case. This basic principle of pairwise additivity is utilized in fragment-based drug design approaches and our results support its continued use. The present results can also aid in the validation of non-bonded terms contained within common force fields and in the correction of systematic errors in physics-based score functions.     

An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer

Different geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6-31++G** basis set. Three-body interaction energy has been obtained with the ab initio supermolecular approach at the levels of MP2/6-31++G**//B3LYP/6-31++G** and MP2/aug-cc-pVDZ//B3LYP/6-31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of C--H...O--N H-bond ranges from -9.0 to -12.4 kJ mol(-1) at the MP2/aug-cc-pVDZ//B3LYP/6-31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6-31++G**//B3LYP/6-31++G** calculated DeltaE(C) is within 2.5 kJ mol(-1) of the corresponding value at the MP4(SDTQ)/6-31G**//B3LYP/6-31++G** level. The analytic atom-atom intermolecular potential has been successfully regressed by using the MP2/6-31++G**//B3LYP/6-31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three-body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three-body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 A.     

Diffusion Monte Carlo study of the equation of state of solid ortho-D2

The authors present results of diffusion Monte Carlo calculations for a system of solid ortho-D2 at different densities, for pressure ranging from 0 up to 350 MPa. They compare the equation of state obtained using two of the most used effective intermolecular potentials, i.e., the Silvera-Goldman and the Buck potentials, with experimental data, in order to assess the validity of the model interactions. The Silvera-Goldman potential has been found to provide a satisfactory agreement with experimental results, showing that, as opposed to what recently found for p-H2, three-body forces can be efficiently accounted for by an effective two-body term.     

Monte Carlo liquid water simulation with four-body interactions included

A four-body interaction potential for water molecules is derived. The new terms are combined with previously developed two- and three-body potential terms and applied in a Metropolis—Monte Carlo simulation at 298 K for an (N, V, T) ensemble with 512 water molecules. Improvements, relative to the results using only two-body, or two- and three-body interactions, are reported for the correlation function g(OO), for the X-ray and neutron-beam scattering intensities, and for the enthalpy.     

Experimental method for wear assessment of sealing elastomers

Elastomeric dynamic seals are components to prevent or to limit lubricant leakage in machinery. Nevertheless, they wear away under certain working conditions. Mostly, wear exists by starvation of lubricant film (two-body abrasion) and interaction with hard debris (three-body abrasion). This work aims to propose a suitable test methodology toward determining two-body and three-body abrasive wear rates of elastomers by using a TE66 Micro-Scale Abrasion Tester. In the tests, sections of silicone rubber were used. The experiments were divided in two parts. Firstly, dry runs were carried out replicating the two–body abrasion mechanism. Secondly, trials were run using two different media (contaminated oil and slurry) to reproduce three-body abrasive wear. Large viscoelastic deformations were generated in the samples and then they were considered for the wear estimation. In conclusion, the method shows advantages which make it suitable as an alternative test to obtain the wear behavior of sealing elastomers.