高分子材料模拟中的分子力学法和力场

比较了分子模拟中两种基本方法 :量子力学法和分子力学法。详细介绍了在高分子模拟中应用较多的分子力学法和力场 。

人血清白蛋白与氯氰菊酯相互作用的分子模拟研究

运用分子对接、分子动力学、结合自由能计算和丙氨酸扫描等分子模拟方法,研究了人血清白蛋白（human serum albumin,HSA）与氯氰菊酯的结合模式。结果表明：氯氰菊酯与HSA结合形成了稳定的复合物,与其氨基酸残基Arg209形成1个氢键,结合自由能为–83.43 kJ/mol,其中范德华力是结合的主要驱动力,极性溶剂化能是主要抑制力。丙氨酸突变扫描结果显示,氨基酸残基Lys199的ΔΔG_（bind）值为16.78 kJ/mol,是HSA和氯氰菊酯结合的关键氨基酸。该研究结果为阐明氯氰菊酯在人体内的代谢机制提供了理论参考。

顺式环十二碳烯的构象

用分子力学法(MMX程序)计算了15-苯基双环[10,3,0]十五碳-1(12)-烯-13-酮,其分子中环十二碳烯部分的构象为能量最低的[l_(ene)2333],与X衍射结果吻合.同时,还计算了15个顺式环十二碳烯的构象,求出了它们的能量及结构参数,讨论了影响构象稳定性的因素.

甜菜夜蛾细胞色素P450(CYP9A11)与3种杀虫剂的结合机理研究

细胞色素P450(以下简称CYP)与昆虫的抗药性密切相关。本研究运用Auto Dock分子对接技术和分子力学泊松-波尔兹曼表面积法(molecular mechanics Poisson-Boltzmann surface area,MM-PBSA)结合自由能计算方法,分析了甜菜夜蛾CYP9A11与3种杀虫剂结合的作用位点、作用力类型和大小。结果表明:CYP9A11与毒死蜱结合形成两个氢键,有8个氨基酸残基参与形成疏水作用力,二者结合自由能为–3 659.80 k J/mol;CYP9A11与灭多威结合形成5个氢键,有3个氨基酸残基形成疏水作用力,结合自由能为–470.92 k J/mol;CYP9A11中有7个氨基酸残基与氯氰菊酯结合形成疏水作用力,结合自由能为–473.44 k J/mol。范德华力是CYP9A11与毒死蜱结合的主要驱动力,极性溶剂化能是CYP9A11与氯氰菊酯和灭多威结合的主要驱动力,这些结果为阐明甜菜夜蛾CYP9A11与3种杀虫剂的结合机理提供了参考。

Non-isothermal thermal decomposition kinetics of high iron gibbsite ore based on Popescu method

The thermal decomposition kinetics of high iron gibbsite ore was investigated under non-isothermal conditions.Popescu method was applied to analyzing the thermal decomposition mechanism.The results show that the most probable thermal decomposition mechanism is the three-dimensional diffusion model of Jander equation,and the mechanism code is D3.The activation energy and pre-exponential factor for thermal decomposition of high iron gibbsite ore calculated by the Popescu method are 75.36 kJ/mol and 1.51×10-5 s-（-1）,respectively.The correctness of the obtained mechanism function is validated by the activation energy acquired by the iso-conversional method.Popescu method is a rational and reliable method for the analysis of the thermal decomposition mechanism of high iron gibbsite ore.

Simulation study on non-linear effects of initial melt temperatures on microstructures during solidification process of liquid Mg_7Zn_3 alloy

The non-linear effects of different initial melt temperatures on the microstructure evolution during the solidification process of liquid Mg7Zn3 alloys were investigated by molecular dynamics simulation, The microstructure transformation mechanisms were analyzed by several methods. The system was found to be solidified into amorphous structures from different initial melt temperatures at the same cooling rate of 1×10^12 K/s, and the 1551 bond-type and the icosahedron basic cluster （12 0 12 0 ） played a key role in the microstructure transition. Different initial melt temperatures had significant effects on the final microstructures. These effects only can be clearly observed below the glass transition temperature Tg; and these effects are non-linearly related to the initial melt temperatures, and fluctuated in a certain range. However, the changes of the average atomic energy of the systems are still linearly related with the initial melt temperatures, namely, the higher the initial melt temperature is, the more stable the amorphous structure is and the stronger the glass forming ability will be.

Anisotropy of Thermal-expansion for β-Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine： Quantum Chemistry Calculation and Molecular Dynamics Simulation

Molecular dynamics simulations on octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine （HMX） at 303-383 K and atmospheric pressure are carried out under NPT ensemble and COMPASS force field, the equilibrium structures at elevated temperatures were obtained and showed that the stacking style of molecules don＇t change. The coefficient of thermal expansion （CTE） values were calculated by linear fitting method. The results show that the CTE values are close to the experimental results and show anisotropy. The total energies of HMX cells with separately increasing expansion rates （100%-105%） along each crystallographic axis was calculated by periodic density functional theory method, the results of the energy change rates are anisotropic, and the correlation equations of energy change-CTE values are established. Thus the hypostasis of the anisotropy of HMX crystal＇s thermal expansion, the determinate molecular packing style, is elucidated.

A Modified Molecular Structural Mechanics Method for Analysis of Carbon Nanotubes

A modified molecular structural mechanics method, based on molecular mechanics and similar to the finite element method, was developed. The energy of a system was expressed by the force field functions of the molecular mechanics. Under the small deformation assumption and by the principle of minimum potential energy, the system function was established. The properties of tension and bending of single-walled carbon nanotubes were analyzed. The Young＇s modulus is about 0.36 TPa nm, which agrees perfectly with the results of previous analysis by other researchers. It is found, for the first time, that the Young＇s moduli, for Zigzag nanotubes, are different from each other when the system energy was expressed as the sum of two or three individual energy terms in molecular mechanics. Whereas, the Young＇s moduli were the same for the Armchair nanotubes. It is found, when simulating the bending, that the deflections are closer to the theoretical ones, of the classical elasticity, when the diameter of the carbon nanotube increases.

Molecular Dynamics Study of Interaction between Acrylamide Copolymers and Alumina Crystal

Four acrylamide polymer flocculants, anionic polyacrylamide P（AA-co-AM）, cationic poly- acrylamide P（DMB-co-AM）, nonionic polyacrylamide P（AM）, and hydrophobical polyacry- lamide P（OA-co-AM） have been prepared by copolymerizing with acrylic acid, cationic monomer dimethylethyl （acryloxyethyl） ammonium bromide （DMB） and hydrophobical monomer octadecyl acrylate with acrylamide. The interactions between the flocculants with the （012） surface of alumina crystal （A1203） have been simulated by molecular dynamics method. All the polymers can bind tightly with A1203 crystal, the interaction between the O of polymers and A1 of the （012） surface of A1203 is significantly strong. The order of binding energy is as follows： P（DMB-co-AM）〉P（OA-co-AM）〉P（AA-co-AM）〉P（AM）, implying a better flocculation performance of P（DMB-co-AM） than the others. Analy- sis indicates that binding energy is mainly determined by Coulomb interaction. Bonds are found between the O atoms of the polymers and the A1 atoms of A1203. The poly- mers＇ structures deform when they combine with A1203 crystal, but the deformation en- ergies are low and far less than non-bonding energies. Flocculation experiments in sus- pension medium of l%Kaolin show a transmittancy of 90.8% for 6 mg/L P（DMB-co-AM） and 73.0% for P（AM）. The sequence of flocculation performance of four polymers is P（DMB-co-AM）〉P（OA-co-AM）〉P（AA-co-AM）〉P（AM）, which is in excellent agreement with the simulation results of binding energy.

QM/MM Study on Enzymatic Mechanism in Sinigrin Biosynthesis

As the major and abundant type of glucosinolates(GL)in plants,sinigrin has potential functions in promoting health and insect defense.The final step in the biosynthesis of sinigrin core structure is highly representative in GL compounds,which corresponds to the process from 3-methylthiopropyl ds-GL to 3-methylthiopropyl GL catalyzed by sulfotransferase(SOT).However,due to the lack of the crystallographic structure of SOT complexed with the 3-methylthiopropyl GL,little is known about this sulfonation process.Fortunately,the crystal structure of SOT 18 from Arabidopsis thaliana(At SOT18)containing the substance(sinigrin)similar to 3-methylthiopropyl GL has been determined.To understand the enzymatic mechanism,we employed molecular dynamics(MD)simulation and quantum mechanics combined with molecular mechanics(QM/MM)methods to study the conversion from ds-sinigrin to sinigrin catalyzed by AtSOT18.The calculated results demonstrate that the reaction occurs through a concerted dissociative mechanism.Moreover,Lys93,Thr96,Thr97,Tyr130,His155,and two enzyme peptide chains(Pro92-Lys93 and Gln95-Thr96-Thr97)play a role in positioning the substrates and promoting the catalytic reaction by stabilizing the transition state geometry.Particularly,His155 acts as a catalytic base while Lys93 acts as a catalytic acid in the reaction process.The presently proposed concerted dissociative mechanism explains the role of At SOT18 in sinigrin biosynthesis,and could be instructive for the study of GL biosynthesis catalyzed by other SOTs.

Molecular Dynamics Investigation of Differences in Melting Behaviors of Cu57 and Cu58 Clusters

Within the framework of the embedded-atom method, we performed molecular-dynamics calculations to investigate the structural transformation during melting of two copper clus- ters containing 57 and 58 atoms. The simulation results reveal how their different structural changes can strongly influence internal energy and radial distribution functions. The local structural patterns of different regions during the temperature increase, determined by atom density profiles, are identified for the melting of each cluster. The simulations show sensi- tivities of the structural changes for these two small size clusters with different structures.

Selectivity of Parvalbumin B Protein Binding to Ca^(2+) and Mg^(2+) at an Ab Initio QM/MM Level Using the Reference-Potential Method

Ion selectivity in protein binding sites is of great significance to biological functions.Although additive force fields have been successfully applied to various protein-related studies,it is difficult to well capture the subtle metal-protein interaction for the prediction of ion selectivity,due to the remarkable polarization and charge transfer effect between the metals and the surrounding residues.Quantum mechanics-based methods are well-suited for dealing with these systems,but they are too costly to apply in a direct manner.In this work,the reference-potential method(RPM)was used to measure the selectivity for calcium and magnesium cations in the binding pocket of parvalbumin B protein by calculating the free energy change associated with this substitution reaction at an ab initio quantum mechanics/molecular mechanics(QM/MM)level.The alchemical transformations were performed at the molecular mechanics level,and the relative binding free energy was then corrected to the QM/MM level via thermodynamic perturbation.In this way,the free energy change at the QM/MM level for the substitution reaction was obtained without running the QM/MM simulations,thus remarkably enhancing the efficiency.In the reweighting process,we found that the selection of the QM region greatly affects the accuracy of the QM/MM method.In particular,the charge transfer effect on the free energy change of a reaction cannot be neglected.

Study on Application of Hypervirial Therem in the Variational Method

We discuss a methodology problem which is crucially important for solving the Sch?dinger equation in terms of the variational method. We present a complete analysis on the application of the hypervirial theorem for judging the quality of the trial wavefunction without invoking the precise solutions.

Extensive Numerical Tests of Leapfrog Integrator in Middle Thermostat Scheme in Molecular Simulations

Accurate and efficient integration of the equations of motion is indispensable for molecular dynamics(MD)simulations.Despite the massive use of the conventional leapfrog(LF)integrator in modern computational tools within the framework of MD propagation,further development for better performance is still possible.The alternative version of LF in the middle thermostat scheme(LFmiddle)achieves a higher order of accuracy and efficiency and maintains stable dynamics even with the integration time stepsize extended by several folds.In this work,we perform a benchmark test of the two integrators(LF and LF-middle)in extensive conventional and enhanced sampling simulations,aiming at quantifying the time-stepsizeinduced variations of global properties(e.g.,detailed potential energy terms)as well as of local observables(e.g.,free energy changes or bondlengths)in practical simulations of complex systems.The test set is composed of six chemically and biologically relevant systems,including the conformational change of dihedral flipping in the N-methylacetamide and an AT(AdenineThymine)tract,the intra-molecular proton transfer inside malonaldehyde,the binding free energy calculations of benzene and phenol targeting T4 lysozyme L99A,the hydroxyl bond variations in ethaline deep eutectic solvent,and the potential energy of the blue-light using flavin photoreceptor.It is observed that the time-step-induced error is smaller for the LFmiddle scheme.The outperformance of LF-middle over the conventional LF integrator is much more significant for global properties than local observables.Overall,the current work demonstrates that the LF-middle scheme should be preferably applied to obtain accurate thermodynamics in the simulation of practical chemical and biological systems.

Separation of Variable Treatment for Solving Time—Dependent Potentials

We use the separation of variable treatment to treat some time-dependent systems, and point out that the condition of separability is the same as the condition of existence of invariant, and the separation of variable treatment is interrelated with the quantum-invariant method and the propagator method. We directly use the separation of variable treatment to obtain the wavefunctions of the time-dependent Coulomb potential and the time-dependent Hulthén potential.

Fluid-Solid Interaction Analysis of Drug Delivery Mechanism to Damaged Cancer Cellules in the Shape of Single-Walled Carbon Nanocone by Molecular Mechanics Approach

Drug delivery systems able to deliver the required dose of the drug to the target level use active or passive nano metric designed systems. In the earlier researches, carbon nanocones are used for transferring the serum to damaged proteins and damaged cancer cellules. In this lecture, stability analysis of drug delivery to damaged cancer cellutes is studied in the shape of single-walled carbon nanocone. In this method, each atom is considered as node and interactions between them are supposed as 3D-beam elements. By supposing that potential energy in macro relations is equal to the nano relations, nano-drug characteristics can be calculated. Then shape functions can be extracted to use in blood＇s FEM model and using reduced-order method, divergence velocities of carbon nanocone can be found. In this lecture, carbon nanocones are modeled with different dimensions and boundary conditions and stability of them in blood flow is studied and optimized carbon nanocone is selected in blood flow. Results show that conical nano-drug structures have more efficiency in blood flow rather than tube nano-drug structures and by increasing length of carbon nanocones, dimensionless stability parameter decreased and by increasing declination angle of carbon nanocones, dimensionless stability parameter increased.

Computational Characterization of Nanosystems

Nanosystems play an important role in many applications.Due to their complexity,it is challenging to accurately characterize their structure and properties.An important means to reach such a goal is computational simulation,which is grounded on ab initio electronic structure calculations.Low scaling and accurate electronic-structure algorithms have been developed in recent years.Especially,the efficiency of hybrid density functional calculations for periodic systems has been significantly improved.With electronic structure information,simulation methods can be developed to directly obtain experimentally comparable data.For example,scanning tunneling microscopy images can be effectively simulated with advanced algorithms.When the system we are interested in is strongly coupled to environment,such as the Kondo effect,solving the hierarchical equations of motion turns out to be an effective way of computational characterization.Furthermore,the first principles simulation on the excited state dynamics rapidly emerges in recent years,and nonadiabatic molecular dynamics method plays an important role.For nanosystem involved chemical processes,such as graphene growth,multiscale simulation methods should be developed to characterize their atomic details.In this review,we review some recent progresses in methodology development for computational characterization of nanosystems.Advanced algorithms and software are essential for us to better understand of the nanoworld.

Clustering Algorithms to Analyze Molecular Dynamics Simulation Trajectories for Complex Chemical and Biological Systems

Molecular dynamics （MD） simulation has become a powerful tool to investigate the structure- function relationship of proteins and other biological macromolecules at atomic resolution and biologically relevant timescales. MD simulations often produce massive datasets con- taining millions of snapshots describing proteins in motion. Therefore, clustering algorithms have been in high demand to be developed and applied to classify these MD snapshots and gain biological insights. There mainly exist two categories of clustering algorithms that aim to group protein conformations into clusters based on the similarity of their shape （geometric clustering） and kinetics （kinetic clustering）. In this paper, we review a series of frequently used clustering algorithms applied in MD simulations, including divisive algorithms, ag- glomerative algorithms （single-linkage, complete-linkage, average-linkage, centroid-linkage and ward-linkage）, center-based algorithms （K-Means, K-Medoids, K-Centers, and APM）, density-based algorithms （neighbor-based, DBSCAN, density-peaks, and Robust-DB）, and spectral-based algorithms （PCCA and PCCA＋）. In particular, differences between geomet- ric and kinetic clustering metrics will be discussed along with the performances of diflhrent clustering algorithms. We note that there does not exist a one-size-fits-all algorithm in the classification of MD datasets. For a specific application, the right choice of clustering algo- rithm should be based on the purpose of clustering, and the intrinsic properties of the MD conformational ensembles. Therefore, a main focus of our review is to describe the merits and limitations of each clustering algorithm. We expect that this review would be helpful to guide researchers to choose appropriate clustering algorithms for their own MD datasets.

The Buckling Behavior of Boron Nitride Nanotubes under Bending： An Atomistic Study

In this paper, the buckling behavior of zigzag BN （Boron Nitride） nanotubes under bending is studied through molecular dynamics finite element method with Tersoff potential. The tube with namely （15, 0） BN zigzag tube is investigated. The critical bending buckling angle, moment and curvature are studied and examined with respect to the tube length-diameter ratios from 5 to 30. Effects of a SW （Stone-Wales） defect in the middle tube on the bending behavior are also discussed. The results show that the tube length affects significantly the bending behavior of these tubes. All tubes exhibit brittle fracture under bending. The buckling takes place at the middle in the compressive side of these tubes. These results are important information on the buckling behaviors of pristine and Stone-Wales BN nanotubes, which will be useful for their future applications.

Atomistic Model of Uranium

The electronic state and potential data of U2 molecules are performed by first principle calculations with B3LYP hybrid exchange-correlation functional, the valence electrons of U atom are treated with the （5s4p3d4f）/[3s3p2d2f] contraction basis sets, and the cores are approximated with the relativistic effective core potential. The results show that the ground electronic state is x^9∑g＋. The pair potential data are fitted with a Murrell-Sorbie analytical potential function. The U-U embedded atom method （EAM） interatomic potential is determined based on the generalized gradient approximation calculation within the framework of the density functional theory using Perdew-Burke-Ernzerhof exchange-correlation functional at the spin-polarized level. The physical properties, such as the cohesive energy, the lattice constant, the bulk modulus, the shear modulus, the sc/fec relative energy, the hep/fce rela- tive energy, the shear modulus and the monovacaney formation energy are used to evaluate the EAM potential parameters. The U-U pair potential determined by the first principle calculations is in agreement with that defined by the EAM potential parameters. The EAM calculated formation energy of the monovacancy in the fee structure is also found to be in close agreement with DFT calculation.