用分子动力学模拟方法研究层孔与微孔磷酸铝化合 物中有机胺的模板作用: 指 导定向合成的有效途径

用分子动力学方法,研究了有机胺模板剂对二维层孔与三维微孔磷酸铝化合物的模板作用。依据主-客体间的非键相互作用能量,可以有效地预测出适于某一特定结构的有机胺模板剂。通过选择理论预测的有机胺分子作模板剂,在溶剂热体系中可以定向地合成出具有特定结构的化合物。这一工作对于微孔功能体系的分子工程学研究具有一定的指导意义。     

有机胺在离子热合成 LTA 型磷酸铝分子筛中的助模板作用

 在 1-丁基-3-甲基溴化咪唑 ([bmim]Br) 离子液体中引入有机胺合成了 LTA 型磷酸铝分子筛 (AlPO4-42), 采用热重分析、核磁共振光谱、红外光谱以及荧光光谱对所得晶化产物进行了表征, 并考察了体系的晶化动力学. 结果表明, 有机胺以特定的聚集形态协同离子液体阳离子起到助模板剂的作用, 并填充在 AlPO4-42 分子筛孔道中. 晶化产物随晶化时间的演变表明, 体系中有机胺浓度的变化改变了动力学路径. 高浓度有机胺所形成的聚集体组装周围的无机物种, 促进了 sod 或 lta 笼结构的形成, 并导致立方相的 LTA 骨架晶化.     

基于遗传编程方法的微孔磷酸铝的定向合成研究

根据微孔磷酸铝合成数据的特点,针对合成数据库中合成参数过多和交叉描述等问题,利用改进的遗传编程算法对具有(6,8)元环的微孔磷酸铝合成参数进行特征提取,优化出新的复合特征来更好地描述磷酸铝合成中溶剂和模板剂的特征,并通过参数进化过程的研究,考察了模板剂和溶剂对产物生成的具体影响,从而指导具有特定结构磷酸铝的定向合成.     

芳香胺对微孔层状磷酸铝材料的剥离与嵌入

用XRD和SEM研究了芳香胺对微孔层状磷酸铝 [Al3P4O16][CH3CH2NH3]3和[Al2P3O10(OH)2]•[C6NH8]的剥离和嵌入过程, 结果发现, 芳香胺本身的碱性大小是形成新的柱撑物的关键. 卞胺是碱性较强的芳香胺, 可以很好地将磷酸铝剥离并嵌入到层间形成新的层状化合物; 而碱性较弱的苯胺却无法做到. 新柱撑物形成的速度除与介质的介电常数和芳香胺的加入量有关外, 还取决于原有磷酸铝层板间相互作用的强弱.     

用计算模拟方法研究Al3P4O3-16计量比的二维层状磷酸铝中的有机胺模板能力

将快速Monte Carlo方法与分子动力学方法相结合, 研究了不同种类有机分子在Al3P4O3-16计量比的二维层状磷酸铝形成中的模板能力. 依据主-客体之间非键相互作用能(包括范德华能、氢键能和库仑能), 可合理地解释已知实验现象, 并能有效地预测出适于形成某一特定无机层结构的有机胺模板剂. 通过选择理论预测的有机胺分子作为模板剂, 成功地合成了二维层状磷酸铝化合物Al3P4O16*1.5H3NC6H10NH3.     

用计算模拟方法研究Al_3P_4O_(16)~(3-)计量比的二维层状磷酸铝中的有机胺模板能力

将快速 Monte Carlo方法与分子动力学方法相结合 ,研究了不同种类有机分子在 Al3P4 O3- 1 6 计量比的二维层状磷酸铝形成中的模板能力 .依据主 -客体之间非键相互作用能 (包括范德华能、氢键能和库仑能 ) ,可合理地解释已知实验现象 ,并能有效地预测出适于形成某一特定无机层结构的有机胺模板剂 .通过选择理论预测的有机胺分子作为模板剂 ,成功地合成了二维层状磷酸铝化合物 Al3P4 O1 6 · 1 .5 H3NC6 H1 0 NH3.     

定向合成具有AIPO-HDA骨架的微孔磷酸铝 Al4P5O20H·C4N3H15

用分子动力学方法,研究了不同种类的双胺和多胺与非等比三维微孔磷酸铝Al~4P~5O~2~0H·C~6N~2H~1~8(AlPO-HDA)的模板作用。依据主-客体的非键相互作用能量,有效地预测了可以诱导AlPO-HDA无机骨架生成的有机胺模板剂。选择理论预测的二乙烯三胺为模板剂,成功地合成了与AlPO-HDA同构的Al~4P~5O~2~0H·C~4N~3H~1~5(AlPO-DET),并对其进行了详细的结构表征。     

微孔层状磷酸铝材料的剥离与嵌入研究

用XRD和SEM等手段研究了微孔层状磷酸铝[Al₂P₃O₁₀(OH)₂][C₆NH₈]的剥离和嵌入过程,发现该材料在醇/水溶液中能很好地剥离,形成胶体溶液,并能在一定条件下再结晶形成C₂～C₁₂烷基胺嵌入的层状新材料.当嵌入达到饱和时,有机胺在层间呈双层排列,并与层板成42.6°倾斜角.磷酸铝剥离和嵌入的难易与其层板结构间相互作用的强弱直接相关.     

定向合成具有AIPO-HDA骨架的微孔磷酸铝 Al~4P~5O~2~0H·C~4N~3H~1~5

用分子动力学方法,研究了不同种类的双胺和多胺与非等比三维微孔磷酸铝Al~4P~5O~2~0H·C~6N~2H~1~8(AlPO-HDA)的模板作用。依据主-客体的非键相互作用能量,有效地预测了可以诱导AlPO-HDA无机骨架生成的有机胺模板剂。选择理论预测的二乙烯三胺为模板剂,成功地合成了与AlPO-HDA同构的Al~4P~5O~2~0H·C~4N~3H~1~5(AlPO-DET),并对其进行了详细的结构表征。     

开放骨架磷酸铝合成中F~-对有机胺结构导向效应的影响

研究了在开放骨架磷酸铝合成中氟离子对乙二胺(en)和二乙烯三胺(deta)的结构导向效应的影响.在水热条件下,以乙二胺为结构导向剂,分别从摩尔组成为n(Al2O3)∶n(P2O5)∶n(en)∶n(H2O)=1.0∶1.5∶18.0∶147和n(Al2O3)∶n(P2O5)∶n(en)∶n(HF)∶n(H2O)=1.0∶1.5∶18.0∶3.0∶147的初始混合物中晶化出二维层状磷酸铝Al2P2O9·NH3(CH2)2NH3(Ui O-13)和Al F(HPO4)·NH2(CH2)2NH2(1);以二乙烯三胺为结构导向剂,分别从摩尔组成为n(Al2O3)∶n(P2O5)∶n(deta)∶n(H2O)=1.0∶4.0∶3.0∶153和n(Al2O3)∶n(P2O5)∶n(deta)∶n(HF)∶n(H2O)=1.0∶4.0∶3.0∶3.0∶153的初始混合物中晶化出了三维开放骨架磷酸铝Al4P5O20(H2O)2·C4N3H16(Al PO-CJ31)和一维链状磷酸铝Al2P4O10(OH)3F·C4N3H15(2),表明凝胶中的F-显著改变了乙二胺和二乙烯三胺的结构导向效应.详细对比分析了Ui O-13和化合物1以及AlPO-CJ31和化合物2的结构,探讨了F-对乙二胺和二乙烯三胺的结构导向效应的影响及F-与有机胺的协同结构导向效应.     

Investigation of chiral recognition by molecular micelles with molecular dynamics simulations

Molecular dynamics simulations were used to characterize the binding of the chiral drugs chlorthalidone and lorazepam to the molecular micelle poly-(sodium undecyl-(L)-leucine-valine). The project’s goal was to characterize the nature of chiral recognition in capillary electrophoresis separations that use molecular micelles as the chiral selector. The shapes and charge distributions of the chiral molecules investigated, their orientations within the molecular micelle chiral binding pockets, and the formation of stereoselective intermolecular hydrogen bonds with the molecular micelle were all found to play key roles in determining where and how lorazepam and chlorthalidone enantiomers interacted with the molecular micelle.     

Understanding the adsorption of branched polyamine on surface of gold nanoparticles by molecular dynamics simulations

Molecular dynamics simulations were conducted to characterize the adsorption behavior of branched polyethylenimine (br‐PEI) on the surface of gold nanoparticles (AuNPs). We observed the preferential adsorption of br‐PEI on the [111] surface of AuNPs. Furthermore, br‐PEI maintained a flat arrangement on the surface and wrapped the AuNPs in a stable manner, thereby blocking the adsorption of H₂O molecules and other free br‐PEI molecules. The model and computational results provide theoretical support for relevant experiments. Copyright © 2016 John Wiley & Sons, Ltd.     

Force-field parametrization and molecular dynamics simulations of Congo red

Congo red, a diazo dye widely used in medical diagnosis, is known to form supramolecular systems in solution. Such a supramolecular system may interact with various proteins. In order to examine the nature of such complexes empirical force field parameters for the Congo red molecule were developed. The parametrization of bonding terms closely followed the methodology used in the development of the charmm22 force field, except for the calculation of charges. Point charges were calculated from a fit to a quantum mechanically derived electrostatic potential using the CHELP-BOW method. Obtained parameters were tested in a series of molecular dynamics simulations of both a single molecule and a micelle composed of Congo red molecules. It is shown that newly developed parameters define a stable minimum on the hypersurface of the potential energy and crystal and ab initio geometries and rotational barriers are well reproduced. Furthermore, rotations around C-N bonds are similar to torsional vibrations observed in crystals of diphenyl-diazene, which confirms that the flexibility of the molecule is correct. Comparison of results obtained from micelles molecular dynamics simulations with experimental data shows that the thermal dependence of micelle creation is well reproduced.     

Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry‐standard rendering techniques

Molecular dynamics (MD) simulations provide critical insights into many biological mechanisms. Programs such as VMD, Chimera, and PyMOL can produce impressive simulation visualizations, but they lack many advanced rendering algorithms common in the film and video‐game industries. In contrast, the modeling program Blender includes such algorithms but cannot import MD‐simulation data. MD trajectories often require many gigabytes of memory/disk space, complicating Blender import. We present Pyrite, a Blender plugin that overcomes these limitations. Pyrite allows researchers to visualize MD simulations within Blender, with full access to Blender's cutting‐edge rendering techniques. We expect Pyrite‐generated images to appeal to students and non‐specialists alike. A copy of the plugin is available at http://durrantlab.com/pyrite/ , released under the terms of the GNU General Public License Version 3. © 2017 Wiley Periodicals, Inc.     

Charge distributions for molecular dynamics simulations from self-consistent polarization method

Partial atomic charges are important force field parameters. They are usually computed by applying quantum-chemical calculations and the assumed population scheme. In this study polarization consistent scheme of deriving a charge distribution inside solute molecule is proposed. The environment effect is explicitly taken into account by distributing solvent molecules around the solute target. The performed analysis includes a few computational schemes (HF, MP2, B3LYP, and M026X), basis sets (cc-pvnz, n = 2, 3, …, 6), and electrostatically derived charge distributions (KS, CHELP, CHELPG, and HLY). It is demonstrated that the environment effect is very important and cannot be disregarded. The second solvation shell should be included to achieve the charge convergence. Huge corrections to charge distribution are due to induction and dispersion. The B3LYP/cc-pvqz level of theory is recommended for deriving the charges within self-consistent polarization scheme.     

The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations

Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used.     

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

MDAnalysis is an object‐oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance‐critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix‐based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com . © 2011 Wiley Periodicals, Inc. J Comput Chem 2011     

Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane–water partition coefficients

The importance of membrane‐water partition coefficients led to the recent extension of the conductor‐like screening model for realistic solvation (COSMO‐RS) to micelles and biomembranes termed COSMOmic. Compared to COSMO‐RS, this new approach needs structural information to account for the anisotropy of colloidal systems. This information can be obtained from molecular dynamics (MD) simulations. In this work, we show that this combination of molecular methods can efficiently be used to predict partition coefficients with good agreement to experimental data and enables screening studies. However, there is a discrepancy between the amount of data generated by MD simulations and the structural information needed for COSMOmic. Therefore, a new scheme is presented to extract data from MD trajectories for COSMOmic calculations. In particular, we show how to calculate the system structure from MD, the influence of lipid conformers, the relation to the COSMOmic layer size, and the water/lipid ratio impact. For a 1,2‐dimyristoyl‐sn‐glycero‐3‐phosphocholine (DMPC) bilayer, 66 partition coefficients for various solutes were calculated. Further, 52 partition coefficients for a 1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3‐phosphocholine (POPC) bilayer system were calculated. All these calculations were compared to experimental data. © 2013 Wiley Periodicals, Inc.     

Free energy calculations using flexible-constrained, hard-constrained and non-constrained molecular dynamics simulations.

A comparison of different treatments of bond-stretching interactions in molecular dynamics simulation is presented. Relative free energies from simulations using rigid bonds maintained with the SHAKE algorithm, using partially rigid bonds maintained with a recently introduced flexible constraints algorithm, and using fully flexible bonds are compared in a multi-configurational thermodynamic integration calculation of changing liquid water into liquid methanol. The formula for the free energy change due to a changing flexible constraint in a flexible constraint simulation is derived. To allow for a more direct comparison between these three methods, three different pairs of models for water and methanol were used: a flexible model (simulated without constraints and with flexible constraints), a rigid model (simulated with standard hard constraints), and an alternative flexible model (simulated with flexible constraints and standard hard constraints) in which the ideal or constrained bond lengths correspond to the average bond lengths obtained from a short simulation of the unconstrained flexible model. The particular treatment of the bonds induces differences of up to 2 % in the liquid densities, whereas (excess) free energy differences of up to 5.7 (4.3) kJ mol(-1) are observed. These values are smaller than the differences observed between the three different pairs of methanol/water models: up to 5 % in density and up to 8.5 kJ mol(-1) in (excess) free energy.     

Nonspecific interaction forces at water-membrane interface by forced molecular dynamics simulations

Nonspecific interactions are the main driving forces for the behavior of molecules with great affinity for biologic membranes. To investigate not only the molecular details of these interactions but to estimate their magnitude as well, the theoretical method of Forced Molecular Dynamics Simulations, based on the Atomic Force Spectroscopy experimental technique, was applied. In this approach, an additional one-dimensional elastic force, representing the cantilever probe, was incorporated to the force field of a Molecular Dynamics computational program. This force represents a spring fixed on one end to a selected atom of the molecule; the other end of the spring is displaced at constant velocity to pull the molecule out of the membrane. The force experimented by the molecule due to the spring, is proportional to the spring elongation relative to its equilibrium position. This value is registered during the entire simulation, and its maximum value will determine the molecule-membrane interaction force. Nonexplicit medium simulations were carried out. Polar and apolar media were considered according to their polarizability degree and a specific dielectric constant value was assigned. In this approach, the membrane was considered as the apolar region limited by two flat surfaces with a polar aqueous medium. The potential energy discontinuity at the interfaces was smoothed by considering the polarization-induced effects using the image method. The results of this methodology are presented using a small system, a single Alanine amino acid model, which enables extended simulations in a microsecond time scale. The confinement of this amino acid at the interface reduces its degrees of freedom and forces it to adopt one of the six defined conformations. A correlation between these stable structures at the water-membrane interface and the interaction force value was determined.