基于ReaxFF力场的对硝基苯酚臭氧氧化分子动力学模拟

本文采用基于ReaxFF反应力场的分子动力学方法(ReaxFF MD),利用自主研发的国际首个基于GPU加速的ReaxFF MD程序系统GMD-Reax和独特的化学反应分析工具VARx MD,探索臭氧氧化对硝基苯酚的反应机理。通过模拟考察了300 K恒温条件下臭氧氧化水中对硝基苯酚的行为,获得了酚结构开环、CO_2生成、主要自由基(·OH、·O_2、·O)及团簇型自由基的数量演变趋势,并可定性描述六元环开环和CO_2生成均遵循伪一级反应动力学规律。反应机理分析表明酚类分子在水溶液中被臭氧氧化的路径主要经过攫氢、六元环开环、碳链的氧化分解三个阶段,也揭示了自由基和团簇型自由基在臭氧降解对硝基苯酚时所发挥的重要作用。本工作是应用ReaxFF MD分子模拟方法对常温水环境下臭氧降解酚类污染物反应机理研究的一个尝试,可为深入认识该机理及相关的实验、理论研究提供一定的参考。     

离聚体的结构表征——Ⅴ.含氟离聚体中离子微区稳定性的研究

本文用DSC方法研究了羟酸型含氟离聚体中不同金属离子种类、可离子化基团含量、配位结构单元构型及离子微区大小对离聚体中离子微区稳定性的影响。实验表明:离聚体中金属离子配位能力愈强,羟酸含量愈高,离子微区尺寸愈大,则相应离聚体中离子微区稳定性愈大。铅高聚体>锌离聚体>钙离聚体>钠离聚体。     

钙钛矿型CaSiO_3解压缩和重压缩过程的分子动力学模拟

用分子动力学模拟方法 (MD)研究了 3 0 0K时钙钛矿型CaSiO3 ,从高压到负压的解压缩过程 .MD模拟获得的P V关系与实验数据相近 ,与已报道的MD模拟数据基本一致 ,所得体积模量也在实验数据分布范围内 .减压缩和重压缩的MD模拟数据与实验结果相似 .钙钛矿型CaSiO3 解压缩成非晶态时 ,存在两个结构破坏阶段 :破坏硅氧八面体和破坏钙氧二十面体 .当钙氧二十面体被破坏后 ,重压缩不能得到钙钛矿型结构 .只要钙氧二十面体未被破坏 ,重压缩可恢复钙钛矿型结构 .本研究得到的结果尚未见相关报道 .由MD模拟数据计算了CaSiO3 系统的红外光谱 ,分析这些数据可知钙钛矿型CaSiO3 解压缩非晶化是一个二阶软模相变 .研究表明钙钛矿型CaSiO3 结构存在一个等容的亚稳极限 ,其解压缩非晶化是一个受动力学控制的亚稳状态 .     

两性聚电解质溶液的分子热力学模型和分子动力学模拟

从带电硬球混合物出发采用化学缔合理论建立了聚电解质和两性聚电解质溶液的分子热力学模型.用考虑溶剂的粘滞力和热浴随机力作用的分子动力学(MD)方法模拟了聚电解质和两性聚电解质溶液的渗透系数.对模型预测结果和MD模拟结果进行了比较,表明基于化学缔合理论的分子热力学模型可以用于聚电解质溶液和两性聚电解质溶液热力学性质的预测,对于均聚电解质溶液效果令人满意,对由直径不同的离子构成的聚电解质溶液,模型的预测效果变差,有待进一步改进.该模型对两性聚电解质溶液渗透系数的预测效果比对聚电解质溶液的预测效果更好.     

钙钛矿型CaSiO_3解压缩和重压缩过程的分子动力学模拟

用分子动力学模拟方法（MD）研究了300 K时钙钛矿型CaSiO_3，从高压到负压 的解压缩过程。MD模拟获得的P-V关系与实验数据相近，与已报道的MD模拟数据基 本一致，所得体积模量也在实验数据分布范围内。减压缩和重压缩的MD模拟数据与 实验结果相似。钙钛矿型CaSiO_3解压缩成非晶态时，存在两个结构破坏阶段：破 坏硅氧八面体和破坏钙氧二十面体。当钙氧二十面体被破坏后，重压缩不能得到钙 钛矿型结构。只要钙氧二十面体未被破坏，重压缩可恢复钙钛矿型结构。本研究得 到的结果尚未见相关报道。由MD模拟数据计算了CaSiO_3系统的红外光谱，分析这 些数据可知钙钛矿型CaSiO_3解压缩非晶化是一个二阶软模相变。研究表明钙钛矿 型CaSiO_3结构存在一个等容的亚稳极限，其解压缩非晶化是一个受动力学控制的 亚稳状态。     

功能性超薄有序分子沉积膜的制备及其结构研究

1991年G.Decher等首次探讨了阴阳离子与聚电解质交替沉积制备有机超薄膜的方法。我们在完善成膜技术和发展成膜基质的基础上,详细研究了其成膜过程与膜的结构,并定义这种新的自组装超薄有序膜为分子沉积膜——MD膜。MD膜是利用阴阳离子的静电吸附反应特性,通过相反离子体系的交替分子沉积制备的层状有序自组装多层超薄膜。需要指出的是,分子沉积既是有机超薄膜的制备技术,本身又是一种自组装超薄有序膜。MD膜制备工艺简单,热稳定性和长期稳定性好,不受基体形状与面积限制。     

基于基团贡献法和分子动力学预测聚间苯二甲酰对苯二胺的玻璃化转变温度

采用基团贡献法(GC)和分子动力学法(MD)模拟了聚间苯二甲酰间苯二胺纤维(MPDI)和聚对苯二甲酰对苯二胺(PPTA)的玻璃化转变温度, 并与实验值进行了对比. 结果表明, 使用基团贡献法和分子动力学法测得的MPDI和PPTA的玻璃化转变温度与实验值接近, 说明基团贡献法和分子动力学法可以用来预测芳香族聚酰胺的玻璃化转变温度. 在此基础上, 采用GC和MD预测了聚间苯二甲酰对苯二胺(PPIA)的玻璃化转变温度. 在MD模拟中, 对密度、 比体积、 回转半径和非键相互作用随温度的变化规律进行了分析. 结果表明, 自由体积理论能较好地解释PPIA的玻璃化转变现象, 其中非键相互作用随温度的变化是玻璃化转变的本质原因. PPIA的玻璃化转变温度介于MPDI和PPTA之间, 有望成为综合性能介于两者之间的另一种高性能聚酰胺.     

酚-胰岛素晶体生长体系的相关系研究

从三方二锌胰岛素晶体生长体系出发,以苯酚浓度为晶体生长条件的独立变元,对胰岛素晶体相变进行研究,获得该生长体系的相关系图,得到两个相变拐点。相变拐点Ⅰ指示二锌胰岛素晶体与四锌胰岛素晶体两相的转换,在苯酚浓度为0.028％—0.029％(g/ml)处两相短暂共存:相变拐点Ⅱ位于苯酚浓度为0.76％—0.77％(g/ml)处,指示三方晶相与单斜晶相间的相互转换,在苯酚浓度为0.76％—0.93％区域内两相或三相共存。研究过程中发现一种新的单斜相(B型单斜胰岛素晶体)。本文依据实验获得的相关系图,对胰岛素晶体的相变与苯酚浓度的依赖关系进行了分析和讨论。     

寡聚物在高分子母体中的扩散──分子动力学模拟研究

应用分子动力学模拟研究甲基丙烯酸甲酯寡聚物(从单聚体到十聚体)在高分子量的聚甲基丙烯酸甲酯母体中的扩散.随着寡聚物的聚合度的增加,发现其扩散系数从单聚体到三聚体迅速减小,而从四聚体到十聚体其扩散系数几乎保持不变,与实验得到的数值在趋势上符合得很好.     

水和甲醇混合溶剂氢键相互作用及对高分子链溶解能力的理论研究

用密度泛函理论对水和甲醇混合溶剂体系的氢键结构进行了详细研究.通过构象和频率分析发现在水团簇中五聚体和六聚体环状结构最为稳定,同时发现一个全新的特征,即甲醇分子能与水五聚体和六聚体形成双氢键.根据各相互作用的稳定化能,分析了水和甲醇混合溶剂对PNIPAM溶解能力的影响,并对实验现象给予了合理解释.     

Perfluoroalkyl chains direct novel self-assembly of insulin

The self-assembly of biopharmaceutical peptides into multimeric, nanoscale objects, as well as their disassembly to monomers, is central for their mode of action. Here, we describe a bioorthogonal strategy, using a non-native recognition principle, for control of protein self-assembly based on intermolecular fluorous interactions and demonstrate it for the small protein insulin. Perfluorinated alkyl chains of varying length were attached to desB30 human insulin by acylation of the ε-amine of the side-chain of LysB29. The insulin analogues were formulated with Zn(II) and phenol to form hexamers. The self-segregation of fluorous groups directed the insulin hexamers to self-assemble. The structures of the systems were investigated by circular dichroism (CD) spectroscopy and synchrotron small-angle X-ray scattering. Also, the binding affinity to the insulin receptor was measured. Interestingly, varying the length of the perfluoroalkyl chain provided three different scenarios for self-assembly; the short chains hardly affected the native hexameric structure, the medium-length chains induced fractal-like structures with the insulin hexamer as the fundamental building block, while the longest chains lead to the formation of structures with local cylindrical geometry. This hierarchical self-assembly system, which combines Zn(II) mediated hexamer formation with fluorous interactions, is a promising tool to control the formation of high molecular weight complexes of insulin and potentially other proteins.     

Changes of conformation and aggregation state induced by binding of lanthanide ions to insulin

To clarify the mechanism of lanthanide ions (Ln3+) on the across-membrane transport of insulin and subsequent reducing blood glucose, the interactions of Ln3+with Zn-insulin and Zn-free insulin are investigated by spectroscopic methods. The results reveal that the binding of Ln3+ to insulin can induce its structure changes from secondary to quaternary structure, depending on the Ln3+ concentration. In the lower concentration, it triggers the conformational changes of insulin monomer in the binding region with insulin receptor (B(24-30)). It would affect insulin-insulin receptor interaction. Moreover, Ln3+ binding promotes the assembly of insulin monomer from dimer to polymer. The potency of Ln3+ in inducing insulin's aggregation is stronger than that of Zn2+. Furthermore, the aggregation can be reversed partly by EDTA-treatment, indicating that it is not due to denaturation. Similar to Zn2+ effect, Ln3+ can stabilize insulin hexamer in a certain range of concentration, but is stronger than the former.     

Multimerization and aggregation of native-state insulin: effect of zinc

The aggregation of insulin is complicated by the coexistence of various multimers, especially in the presence of Zn(2+). Most investigations of insulin multimerization tend to overlook aggregation kinetics, while studies of insulin aggregation generally pay little attention to multimerization. A clear understanding of the starting multimer state of insulin is necessary for the elucidation of its aggregation mechanism. In this work, the native-state aggregation of insulin as either the Zn-insulin hexamer or the Zn-free dimer was studied by turbidimetry and dynamic light scattering, at low ionic strength and pH near pI. The two states were achieved by varying the Zn(2+) content of insulin at low concentrations, in accordance with size-exclusion chromatography results and literature findings (Tantipolphan, R.; Romeijn, S.; Engelsman, J. d.; Torosantucci, R.; Rasmussen, T.; Jiskoot, W. J. Pharm. Biomed. 2010, 52, 195). The much greater aggregation rate and limiting turbidity (τ(∞)) for the Zn-insulin hexamer relative to the Zn-free dimer was explained by their different aggregation mechanisms. Sequential first-order kinetic regimes and the concentration dependence of τ(∞) for the Zn-insulin hexamer indicate a nucleation and growth mechanism, as proposed by Wang and Kurganov (Wang, K.; Kurganov, B. I. Biophys. Chem. 2003, 106, 97). The pure second-order process for the Zn-free dimer suggests isodesmic aggregation, consistent with the literature. The aggregation behavior at an intermediate Zn(2+) concentration appears to be the sum of the two processes.     

The crystal structure of silver carp insulin at medium resolution

It is an important way of surveying the structure-function relationship of insulin to study insulins from different species. Based on the structure model of an orthorhombic crystal obtained by the molecular replacement method, the crystallographic refinement of a hexamer of silver carp insulin in an asymmetric unit has been carried out with 2.8 A resolution data using the restrained least-squares method. The comparisons of insulin structures have shown that the six silver carp insulin molecules have very similar but not identical three-dimensional structures which are similar to the known 2 Zn pig insulin structure but remarkably different in some local conformations.     

Forcefield evaluation and accelerated molecular dynamics simulation of Zn(II) binding to N-terminus of amyloid-β

We report conventional and accelerated molecular dynamics simulation of Zn(II) bound to the N-terminus of amyloid-β. By comparison against NMR data for the experimentally determined binding mode, we find that certain combinations of forcefield and solvent model perform acceptably in describing the size, shape and secondary structure, and that there is no appreciable difference between implicit and explicit solvent models. We therefore used the combination of ff14SB forcefield and GBSA solvent model to compare the result of different binding modes of Zn(II) to the same peptide, using accelerated MD to enhance sampling and comparing the free peptide simulated in the same way. We show that Zn(II) imparts significant rigidity to the peptide, disrupts the secondary structure and pattern of salt bridges seen in the free peptide, and induces closer contact between residues. Free energy surfaces in 1 or 2 dimensions further highlight the effect of metal coordination on peptide’s spatial extent. We also provide evidence that accelerated MD provides improved sampling over conventional MD by visiting as many or more configurations in much shorter simulation times.     

Predicting the coordination geometry for Mg2+ in the p53 DNA-binding domain: insights from computational studies

Zn(2+) in the tumor-suppressor protein p53 DNA-binding domain (DBD) is essential for its structural stability and DNA-binding specificity. Mg(2+) has also been recently reported to bind to the p53DBD and influence its DNA-binding activity. In this contribution, the binding geometry of Mg(2+) in the p53DBD and the mechanism of how Mg(2+) affects its DNA-binding activity were investigated using density functional theory (DFT) calculations and molecular dynamics (MD) simulations. Various possible coordination geometries of Mg(2+) binding to histidines (His), cysteines (Cys), and water molecules were studied at the B3LYP/6-311+g** level of theory. The protonation state of Cys and the environment were taken into account to explore the factors governing the coordination geometry. The free energy of the reaction to form the Mg(2+) complexes was estimated, suggesting that the favorable binding mode changes from a four- to six-coordinated geometry as the number of the protonated Cys increases. Furthermore, MD simulations were employed to explore the binding modes of Mg(2+) in the active site of the p53DBD. The simulation results of the Mg(2+) system and the native Zn(2+) system show that the binding affinity of Mg(2+)to the p53DBD is weaker than that of Zn(2+), in agreement with the DFT calculation results and experiments. In addition, the two metal ions are found to make a significant contribution to maintain a favorable orientation for Arg248 to interact with putative DNA, which is critically important to the sequence-specific DNA-binding activity of the p53DBD. However, the effect of Mg(2+) is less marked. Additionally, analysis of the natural bond orbital (NBO) charge transfer reveals that Mg(2+) has a higher net positive charge than Zn(2+), leading to a stronger electrostatic attractive interaction between Mg(2+) and putative DNA. This may partly explain the higher sequence-independent DNA-binding affinity of p53DBD-Mg(2+) compared to p53DBD-Zn(2+) observed in experiment.     

Rational syntheses of cyclic hexameric porphyrin arrays for studies of self-assembling light-harvesting systems.

Two new cyclic hexameric arrays of porphyrins have been prepared in a rational, convergent manner. The porphyrins in each cyclic hexamer are joined by diphenylethyne linkers affording a wheel-like array with a diameter of approximately 35 A. One array is comprised of five zinc (Zn) porphyrins and one free base (Fb) porphyrin (cyclo-Zn(5)FbU) while the other is comprised of an alternating sequence of two Zn porphyrins and one Fb porphyrin (cyclo-Zn(2)FbZn(2)FbU). The prior synthesis employed a one-flask template-directed process and afforded alternating Zn and Fb porphyrins or all Zn porphyrins. More diverse metalation patterns are attractive for manipulating the flow of excited-state energy in the arrays. The rational synthesis of each array employed three Pd-mediated coupling reactions with four tetraarylporphyrin building blocks bearing diethynyl, diiodo, bromo/iodo, or iodo/ethynyl groups. The final ring closure yielding the cyclic hexamer was achieved by reaction of a porphyrin pentamer + porphyrin monomer or the joining of two porphyrin trimers. In the presence of a tripyridyl template, the yields of the 5 + 1 and 3 + 3 reactions ranged from 10 to 13%. The 5 + 1 reaction in the absence of the template proceeded in 3.5% yield, thereby establishing the structure-directed contribution to cyclic hexamer formation. The 3 + 3 route relied on successive ethyne + iodo/bromo coupling reactions. One template-directed route to cyclo-Zn(2)FbZn(2)FbU employed a magnesium porphyrin, affording cyclo-Zn(2)FbZn(2)MgU from which magnesium was selectively removed. The arrays exhibit absorption spectra that are nearly the sum of the spectra of the component parts, indicating weak electronic coupling. Fluorescence spectroscopy showed that the quantum yield of energy transfer in toluene at room temperature from the Zn porphyrins to the Fb porphyrin(s) was 60% in cyclo-Zn(5)FbU and 90% in cyclo-Zn(2)FbZn(2)FbU. Two dipyridyl-substituted porphyrins, a Zn tetraarylporphyrin and a Fb oxaporphyrin, have been synthesized for use as guests in the cyclic hexamers, affording self-assembled arrays for light-harvesting studies.     

Exceptional thermodynamic stability of DNA duplexes modified by nonpolar base analogues is due to increased stacking interactions and favorable solvation: Correlated ab initio calculations and molecular dynamics simulations

The geometries of DNA hexamer (5'-GGAACC-3') and DNA 13-mer (5'-GCGTACACATGCG-3') have been determined by molecular dynamics (MD) simulations using an empirical force field. The central canonical base pair was replaced by a pair of nonpolar base analogues, 2,2'-bipyridyl and 3-methylisocarbostyril. The stabilization energy of the model system (model A) consisting of a central base pair (base-analogue pair) and two neighboring base pairs was determined by the RI-MP2 method using an extended aug-cc-pVDZ basis set. The geometry of the model was averaged from structures determined by MD simulations. The role of the solvent was covered by the COSMO continuum solvent model and calculations were performed for a larger model system (model B) which also contained a sugar-phosphate backbone. The total stabilization energies of the unperturbed system and the system perturbed by a base-analogue pair (model A) were comparable to the stability of both duplexes experimentally determined. This is due to large stacking interaction energy of the base-analogue self-pair which compensates for the missing hydrogen-bonding energy of the replaced adenine...thymine base pair. The selectivity of the base-analogue pair was reproduced (model B) when their desolvation energy was included with the interaction energy of both strands determined by the approximate SCC-DFTB-D method.     

Molecular dynamics simulation of structure H clathrate-hydrates of binary guest molecules

Molecular dynamics (MD) simulations are performed to study the stability of structure H clathrate-hydrates of methane+large-molecule guest substance (LMGS) at temperatures of 270, 273, 278 and 280 K under canonical (NVT-) ensemble condition in a 3×3×3 structure H unit cell replica with 918 TIP4P water molecules. The studied LMGS are 2-methylbutane (2-MB), 2,3-dimethylbutane (2,3-DMB), neohexane (NH), methylcyclohexane (MCH), adamantane and tert-butyl methyl ether (TBME). In the process of MD simulation, achieving equilibrium of the studied system is recognized by stability in calculated pressure for NVT-ensemble. So, for the accuracy of MD simulations, the obtained pressures are compared with the experimental phase diagrams. Therefore, the obtained equilibrium pressures by MD simulations are presented for studying the structure H clathrate-hydrates. The results show that the calculated temperature and pressure conditions by MD simulations are consistent with the experimental phase diagrams. Also, the radial distribution functions (RDFs) of host-host, host-guest and guest-guest molecules are used to analysis the characteristic configurations of the structure H clathrate-hydrate.     

Metal Ion Controlled Self-Assembly of a Chemically Reengineered Protein Drug Studied by Small-Angle X-ray Scattering

Precise control of the oligomeric state of proteins is of central importance for biological function and for the properties of biopharmaceutical drugs. Here, the self-assembly of 2,2'-bipyridine conjugated monomeric insulin analogues, induced through coordination to divalent metal ions, was studied. This protein drug system was designed to form non-native homo-oligomers through selective coordination of two divalent metal ions, Fe(II) and Zn(II), respectively. The insulin type chosen for this study is a variant designed for a reduced tendency toward native dimer formation at physiological concentrations. A small-angle X-ray scattering analysis of the bipyridine-modified insulin system confirmed an organization into a novel well-ordered structure based on insulin trimers, as induced by the addition of Fe(II). In contrast, unmodified monomeric insulin formed larger and more randomly structured assemblies upon addition of Fe(II). The addition of Zn(II), on the other hand, led to the formation of small quantities of insulin hexamers for both the bipyridine-modified and the unmodified monomeric insulin. Interestingly, the location of the bipyridine-modification significantly affects the tendency to hexamer formation as compared to the unmodified insulin. Our study shows how combining a structural study and chemical design can be used to obtain molecular understanding and control of the self-assembly of a protein drug. This knowledge may eventually be employed to develop an optimized in vivo drug release profile.