Guest-specific diffusion anisotropy in nanoporous materials: Molecular dynamics and dynamic Monte Carlo simulations

For anisotropic nanoporous materials, guest diffusion is often reflected by a diffusion tensor rather than a scalar diffusion coefficient. Moreover, the resulting diffusion anisotropy may notably differ for different guest molecules. As a particular class of such systems, we consider an array of two types of channels, mutually intersecting each other, where the rates of diffusion in the different directions depend on the nature of the guest molecules. The simultaneous adsorption of two types of guest molecules is considered, as in technical applications of porous materials such as catalysis. A case study is presented in which atomistic molecular dynamics (MD) and coarse-grained dynamic Monte Carlo (DMC) simulations are compared and shown to yield qualitatively similar results for non-steady-state diffusion. The two techniques are complementary. MD simulations are able to predict the details of molecular propagation over distances of a few unit cells, whereas the evolution of sorption profiles over distances comparable with entire crystallites can be studied with DMC simulations. Consideration of these longer length and time scales is necessary for applications of such systems in chemical separations and heterogeneous catalysis.     

The effect of corrugation of pore wall on the thermal diffusion in nanopores by molecular dynamics simulations

In this work we have studied the effect of corrugation on the thermal diffusion (soret effect) in isotopic and non-isotopic fluid mixtures confined in a slit pore. We used a boundary driven non-equilibrium molecular dynamics to simulate thermal diffusion in Lennard–Jones (LJ) binary mixtures confined in structureless Steele 10-4-3 and atomistic Lennard–Jones pore walls. The results showed that for the isotopic mixture thermal diffusion factor for both wall types agrees and the corrugation of the LJ wall has no effect in isotopic mixture. However, for non-isotopic mixture confined in atomistic LJ pore the component with stronger attraction adsorbs more to the wall than the structureless Steele wall. The effect of corrugation of pore wall on the thermal diffusion is noticeable in narrow slit pore and mixture with large difference in molecular attraction parameter of components.     

基于分子对接的thanatin与NDM-1分子动力学模拟研究

耐碳青霉烯类抗生素的超级细菌给人类健康带来了严重威胁,其所携带的金属 β-内酰胺酶编码基因是耐药性的主要来源。NDM-1作为其中传播最广、活性最强的 β-内酰胺酶,其抑制剂的研发刻不容缓。具有广谱作用的抗菌肽thanatin对NDM-1展现出了较好的抑制效果,但抑制机理并不清楚。本文使用HPEPDOCK与Rosetta FlexPepDock服务器,将thanatin与NDM-1进行了分子对接,并使用Desmond软件包对对接模型进行了分子动力学模拟。结果表明,thanatin与NDM-1活性中心的Zn2+ 并无直接相互作用,而作为竞争性抑制剂结合于NDM-1的活性口袋,阻止抗生素分子进入活性口袋与Zn2+ 结合,从而抑制NDM-1的水解活性。本文为研发有效的NDM临床抑制剂探索了可行的方法。     

Dynamic viscosity estimation of hydrogen sulfide using a predictive scheme based on molecular dynamics

An approach based on molecular dynamics results on Lennard–Jones spheres is proposed to model the viscosity of hydrogen sulfide, H₂S. The molecular parameters, that have a strong physical meaning, are the depth of the potential, and the length at which the potential is null (the “molecular diameter”), which take into account the dipolar moment of the hydrogen sulfide through an isotropic dipolar approximation. The interest of the method is that the adjustment does not involve any viscosity data because only density values have been used in order to estimate the molecular parameters. Consequently, the model is entirely predictive. A comparison between the data generated by our model, REFPROP7 and REFPROP8 database and the few available experimental viscosity data (dilute gas and saturated liquid) is performed and it clearly demonstrates the performance of this predictive model. It is even shown that this model is, without fitting, slightly better than REFPROP7 and REFPROP8 which uses viscosity experimental database to adjust their parameters. In addition, in typical petroleum reservoirs conditions, it is shown that non-negligible deviations appear when comparing results predicted by REFPROP7, REFPROP8 and the model proposed. Due to its predictive nature, we believe that the values evaluated by the proposed model make sense in such reservoir conditions, at least for industrial purposes. Moreover, the scheme proposed is shown to be very easily extended to deal with mixtures involving H₂S with the limit that the Lennard–Jones fluid model is appropriate for the other species of the mixtures.     

Effect of acetone accumulation on structure and dynamics of lipid membranes studied by molecular dynamics simulations

The modulation of the properties and function of cell membranes by small volatile substances is important for many biomedical applications. Despite available experimental results, molecular mechanisms of action of inhalants and organic solvents, such as acetone, on lipid membranes remain not well understood. To gain a better understanding of how acetone interacts with membranes, we have performed a series of molecular dynamics (MD) simulations of a POPC bilayer in aqueous solution in the presence of acetone, whose concentration was varied from 2.8 to 11.2 mol%. The MD simulations of passive distribution of acetone between a bulk water phase and a lipid bilayer show that acetone favors partitioning into the water-free region of the bilayer, located near the carbonyl groups of the phospholipids and at the beginning of the hydrocarbon core of the lipid membrane. Using MD umbrella sampling, we found that the permeability barrier of ∼0.5 kcal/mol exists for acetone partitioning into the membrane. In addition, a Gibbs free energy profile of the acetone penetration across a bilayer demonstrates a favorable potential energy well of −3.6 kcal/mol, located at 15–16 Å from the bilayer center. The analysis of the structural and dynamics properties of the model membrane revealed that the POPC bilayer can tolerate the presence of acetone in the concentration range of 2.8–5.6 mol%. The accumulation of the higher acetone concentration of 11.2 mol% results, however, in drastic disordering of phospholipid packing and the increase in the membrane fluidity. The acetone molecules push the lipid heads apart and, hence, act as spacers in the headgroup region. This effect leads to the increase in the average headgroup area per molecule. In addition, the acyl tail region of the membrane also becomes less dense. We suggest, therefore, that the molecular mechanism of acetone action on the phospholipid bilayer has many common features with the effects of short chain alcohols, DMSO, and chloroform.     

Prediction of microscopic structure and physical properties of complex fluid mixtures based on molecular simulation

Molecular simulation calculations are presented for two types of complex fluid mixtures, namely elastomer polymer mixtures and water–1-octanol binary and ternary mixtures. Elastomer polymers are used widely as membrane materials for gas separation. In this respect, the solubility and diffusion coefficient of gases need to be known accurately. Predictions for both properties are presented here. Water–1-octanol mixture is a widely used prototype system used to assess the partitioning of various chemical compounds with applications to chemical industry, biotechnology, etc. The microscopic structure of the water–1-octanol mixture is examined and the Gibbs free energy of solvation of four organic solutes is calculated. In all cases, detailed atomistic force fields are used to account for inter- and intra-molecular interactions. Simulation results are shown to be in excellent agreement with literature experimental data.     

Spontaneous formation of annular structures observed in molecular dynamics simulations of polyglutamine peptides

Annular structures have been observed experimentally in aggregates of polyglutamine-containing proteins and other proteins associated with diseases of the brain. Here we report the observation of annular structures in molecular-level simulations of large systems of model polyglutamine peptides. A system of 24 polyglutamine chains 16 residues long at a concentration of 5 mM spontaneously formed large beta sheets which curved to form tube-like annular structures that resemble beta barrels. This work was accomplished by extending the PRIME model to polyglutamine. PRIME is an off-lattice, unbiased, intermediate-resolution protein model based on an amino acid representation of between three and seven united atoms depending on the residue being modeled. Our results are interesting not only because of the recent discovery of tubular protofibrils in experiments on aggregation of mutant huntingtin fragments containing expanded polyglutamine tracts but also because Perutz predicted that polyglutamine forms water filled nanotubes.     

Steered molecular dynamics simulations of protein-ligand interactions

Molecular recognition and specific protein-ligandinteractions are central to many biochemical processes,such as enzyme catalysis, assembly of organelles, en-ergy transduction, signaling, diverse control functions,and replication, expression and storage of the geneticmaterial[1]. Moreover, protein-ligand interactions pro-vide the mechanism of many drug therapies and un-derstanding of such interactions is thus significant forrational drug design[1,2]. For the experimental studiesof protein-ligan…     

Rational optimization of the Whelk-O1 chiral stationary phase using molecular dynamics simulations

Rational in silico optimization of the Whelk-O1 chiral stationary phase (CSP) has been carried out based on the chiral recognition mechanism extracted from previous molecular dynamics simulations [C.F. Zhao, N.M. Cann, Anal. Chem. 80 (2008) 2426] of this CSP. Three modified CSPs have been examined. The first two are designed to increase selectivity by reducing the docking probability of the less retained analyte. The third modified selector reverses the amide bridge to introduce a structural motif found in the popular carbamate-derivatized polysaccharide CSPs [Y. Okamoto, M. Kawashima, K. Hatada, J. Am. Chem. Soc. 106 (1984) 5357]. For each modified selector, an atomistic model has been obtained through extensive ab initio calculations. The effect of selector modification is then evaluated via simulations of the modified interface in the presence of target analytes. Simulation results show that the separation factors are increased for the modified CSPs but in some cases elution orders are reversed. The Whelk-O1 CSP was originally designed to separate naproxen [W.H. Pirkle, C.J. Welch, B. LAmm, J. Org. Chem. 57 (1992) 3854]. With this in mind, molecular dynamics simulations of naproxen are compared for the original, and the modified, selectors.     

Synthesis and antimicrobial bioassays of 1,3,4-thiadiazole sulfone derivatives containing amide moiety: A study based on molecular dynamics (MD) simulations,MM/GBSA,and molecular docking

The backbone structure (1,3,4-thiadiazole sulfone derivatives containing amide moiety) of target compounds was determined by modification and optimization of the theoretical design based on commercial chemical carboxin, including molecular docking, scaffold hopping, ligand expansion, etc.In this paper, 23 target compounds were synthesized by the combination of theoretical design and chemical synthesis, and characterized by ¹H NMR, ¹³C NMR and HR MS. Addtionally, the antibacterical bioassay showed that most target compounds performed excellent inhibition on Xanthomonas axonopodis pv. citri (Xac) and Xanthomonas oryzae pv. oryzae (Xoo) in vitro. Meanwhile, molecular docking, molecular dynamics (MD) simulations, and studies on ligand/protein (carboxin/2FBW and 4n/2FBW) complex systems were displayed, and the interaction patterns of ligand/protein complex system were predicted by molecular docking. Besides, the ligand/protein complex system was subject to MD simulation. The analysis of molecular dynamics such as RMSD values suggested that compound/2FBW complexes were stable. MM/GBSA (Molecular mechanics generalized born surface area) dynamic binding affinity results revealed that the active residues (TYR58, HIS26, ARG43, SER39, etc.) played an essential part in the binding of the compound(s) to form a stable low-energy ligand/protein complex, while the MD trajectories demonstrated that the interactions of drugs with 2FBW affected the tertiary structure and increased the stability of protein. Besides, compound 4n also showed control efficacies (curative and protective) on Xoo in vivo, where the curative efficacy was 35.91% and the protective efficacy was 18.97%. In a word, this study showed that 1,3,4-thiadiazole sulfone derivatives containing amide moiety designed based on the structure of carboxin were promising agricultural antibacterial agents, featuring certain stability of binding affinity to proteins and carboxin.     

Application of molecular dynamics simulations in molecular property prediction II: diffusion coefficient

In this work, we have evaluated how well the general assisted model building with energy refinement (AMBER) force field performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, five organic compounds in aqueous solutions, four proteins in aqueous solutions, and nine organic compounds in nonaqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned errors and the root mean square errors are 0.137 and 0.171 × 10(-5) cm(-2) s(-1), respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for eight organic solvents with experimental data (R(2) = 0.784), four proteins in aqueous solutions (R(2) = 0.996), and nine organic compounds in nonaqueous solutions (R(2) = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide, and cyclohexane have been studied. The major molecular dynamics (MD) settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution.     

Enthalpies of mixing predicted using molecular dynamics simulations and OPLS force field

Enthalpy of mixing (EOM) is one of the most basic thermodynamic properties of mixtures. To assess feasibility of predicting EOM using force field simulation methods, fifteen (15) representative binary mixtures were investigated using MD simulations based on OPLS and TIP4P force fields. The simulation conditions and errors were carefully examined. The precision level of 0.04 kJ/mol was obtained for calculated EOM data. However, the predictions, measured by deviations from experimental data, were only qualitatively correct. Among various factors influencing the accuracy of predictions, force field quality representing interactions among different molecules plays the most significant role. Using methanol/benzene and ethanol/benzene as examples, we demonstrated that non-additive interaction terms between polarizable atoms can be used to significantly improve the quality of predictions. In addition, it appears that charge-dependent LJ parameters are required in order to represent the polarization effects accurately.     

An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: application to water

An efficient parallelization scheme for classical molecular dynamics simulations with flexible, polarizable empirical potentials is presented. It is based on the standard Ewald summation technique to handle the long-range electrostatic and induction interactions. The algorithm for this parallelization scheme is designed for systems containing several thousands of polarizable sites in the simulation box. Its performance is evaluated during molecular dynamics simulations under periodic boundary conditions with unit cell sizes ranging from 128 to 512 molecules employing two flexible polarizable water models [DC(F) and TTM2.1-F] containing 1 and 3 polarizable sites, respectively. The time-to-solution for these two polarizable models is compared with the one for a flexible, pairwise-additive water model (TIP4F). The benchmarks were performed on both shared and distributed memory platforms. As a result of the efficient calculation of the induced dipole moments, a superlinear scaling as a function of the number of the processors is observed. To the best of our knowledge, this is the first reported results of parallel scaling and performance for simulations of liquid water with a polarizable potential under periodic boundary conditions.     

Atomic-scale investigation of the interaction between coniferyl alcohol and laccase for lignin degradation using molecular dynamics simulations and spectroscopy

The interaction between coniferyl alcohol (CA) and laccase (LAC) was investigated using molecular dynamics (MD) simulations and spectral experiments. The mode of interaction between CA and LAC was established by MD simulations. The micro-environmental changes, stability and rigidity of the LAC-CA system were assessed by relevant parameters. These parameters include root mean square deviation (RMSD), root mean square fluctuation (RMSF) and radius of gyration (Rg). The calculated binding free energy (ΔG_binding=??19.99?kcal·mol.^?1), the van der waals (VDW) contribution (ΔG_vdw=?23.99?kcal·mol^?1) and the electrostatic energy (ΔG_ele=?23.09?kcal·mol^?1) of LAC-CA system demonstrated that the interaction of LAC-CA was a spontaneous process and the main interaction forces were van der Waal's and electrostatic forces. The values of ΔG_vdw and ΔG_ele were negative, which demonstrated that VDW interactions and electrostatic interactions were favorable for the binding of CA and LAC. The binding constants, thermodynamic parameters, molecular force types and binding distances confirmed the interaction between CA and LAC and further verified the rationality of the theoretical model by spectral experiments. The MD simulations and experimental approaches provide clues for the discovery of new mediators and useful references for the mechanism of microbial degradation of lignin and industrialization of lignocellulose.     

Computation of some thermodynamic properties of nitrogen using a new intermolecular potential from molecular dynamics simulation

A new pair-potential energy function of nitrogen has been determined via the inversion of reduced viscosity collision integrals and fitted to obtain an analytical potential form. The pair-potential reproduces the second virial coefficient, viscosity, thermal conductivity, self-diffusion coefficient, and thermal diffusion factor of nitrogen in a good accordance with experimental data over wide ranges of temperatures and densities. We have also performed the molecular dynamics simulation to obtain pressure, internal energy, heat capacity at constant volume, and self-diffusion coefficient of nitrogen at different temperatures and densities using our calculated pair-potential and some other potentials. The molecular dynamics of the nitrogen molecules has been also used to determine nitrogen equation of state in two (low and high) pressure ranges. Our results are in a good agreement with experiment and literature values.     

Evaluation of the binding ability of a macrobicyclic receptor for anions by potentiometry and molecular dynamics simulations in solution

The macrobicycle derived from bis-tren and containing diphenoxy groups as spacers, L¹, was synthesized and used as receptor for anions. The binding ability of the new receptor for some aromatic carboxylates [phthalate (ph²⁻), isophthalate (iph²⁻), terephthalate (tph²⁻), benezenetricarboxylate (btc³⁻), and the herbicide 4-amino-3,5,6-trichloro-2-pyridinecarboxylate (ATCP⁻)], and the aliphatic cyclohexanetricarboxylate (ch³⁻) anions was evaluated by potentiometric measurements and molecular dynamic simulation in solution. The association constants were determined by potentiometry in H₂O/MeOH (1:1 v/v) at 298.2 K and 0.10 mol dm⁻³ in KCl. The strongest association was found with btc³⁻ anion and the effective binding constants at pH 5.5 follow the order: btc³⁻>tph²⁻>ph²⁻≈iph²⁻>ch³⁻≈ATCP⁻. Molecular dynamics simulations carried out for the associations of (H₆L¹)⁶⁺ with btc³⁻, tph²⁻ and iph²⁻ in the same mixture of solvents indicated that these anions interact with the receptor by a combination of electrostatic and multiple N-H?OC hydrogen bond interactions. It was also verified that in the recognition process the tph²⁻ remained encapsulated over the entire time of simulation while the btc³⁻ is partially inserted into the receptor cavity with one carboxylate group largely exposed to water solvent molecules, and iph²⁻ anion exhibited an intermediate binding behaviour. The free energy difference between btc³⁻ and iph²⁻ associations estimated by free energy calculations is in excellent agreement with the difference found from the experimental values for the corresponding association constants, which indicates that the unconstrained molecular dynamics simulations carried out with these two anions are realistic pictures of their molecular recognition processes.     

Experimental,Monte Carlo and molecular dynamics simulations to investigate corrosion inhibition of mild steel in hydrochloric acid solutions

The efficiency of three furan derivatives, namely 2-(p-toluidinylmethyl)-5-methyl furan (Inh. A), 2-(p-toluidinylmethyl)-5-nitro furan (Inh. B) and 2-(p-toluidinylmethyl)-5-bromo furan (Inh. C), as possible corrosion inhibitors for mild steel in 1.0 M HCl, has been determined by weight loss and electrochemical measurements. These compounds inhibit corrosion even at very low concentrations, and 2-(p-toluidinylmethyl)-5-methyl furan (Inh. A) is the best inhibitor. Polarization curves indicate that all compounds are mixed-type inhibitors, affecting both cathodic and anodic corrosion currents. Adsorption of furan derivatives on the mild steel surface follows the Langmuir adsorption isotherm, and the calculated Gibbs free energy values confirm the chemical nature of the adsorption. Monte Carlo simulations technique incorporating molecular mechanics and molecular dynamics can be used to simulate the adsorption of furan derivatives on mild steel surface in 1.0 M HCl.     

Multibaric-multithermal ensemble molecular dynamics simulations

We present new generalized-ensemble molecular dynamics simulation algorithms, which we refer to as the multibaric-multithermal molecular dynamics. We describe three algorithms based on (1) the Nosé thermostat and the Andersen barostat, (2) the Nosé-Poincaré thermostat and the Andersen barostat, and (3) the Gaussian thermostat and the Andersen barostat. The multibaric-multithermal simulations perform random walks widely both in the potential-energy space and in the volume space. Therefore, one can calculate isobaric-isothermal ensemble averages in wide ranges of temperature and pressure from only one simulation run. We test the effectiveness of the multibaric-multithermal algorithm by applying it to a Lennard-Jones 12-6 potential system.     

Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems

A systematic analysis is performed on the effectiveness of removing degrees of freedom from hydrogen atoms and/or increasing hydrogen masses to increase the efficiency of molecular dynamics simulations of hydrogen-rich systems such as proteins in water. In proteins, high-frequency bond-angle vibrations involving hydrogen atoms limit the time step to 3 fs, which is already a factor of 1.5 beyond the commonly used time step of 2 fs. Removing these degrees of freedom from the system by constructing hydrogen atoms as dummy atoms, allows the time step to be increased to 7 fs, a factor of 3.5 compared with 2 fs. Additionally, a gain in simulation stability can be achieved by increasing the masses of hydrogen atoms with remaining degrees of freedom from 1 to 4 u. Increasing hydrogen mass without removing the high-frequency degrees of freedom allows the time step to be increased only to 4 fs, a factor of two, compared with 2 fs. The net gain in efficiency of sampling configurational space may be up to 15% lower than expected from the increase in time step due to the increase in viscosity and decrease in diffusion constant. In principle, introducing dummy atoms and increasing hydrogen mass do not influence thermodynamical properties of the system and dynamical properties are shown to be influenced only to a moderate degree. Comparing the maximum time step attainable with these methods (7 fs) to the time step of 2 fs that is routinely used in simulation, and taking into account the increase in viscosity and decrease in diffusion constant, we can say that a net gain in simulation efficiency of a factor of 3 to 3.5 can be achieved. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 786–798, 1999     

Poisson-Boltzmann calculations versus molecular dynamics simulations for calculating the electrostatic potential of a solvated peptide

We performed a very long molecular dynamics simulation of a peptide in explicit water molecules and ions and averaged the electrostatic potential caused by peptide, water and ions at eight points in the vicinity of the peptide. These electrostatic potential values were directly compared to the potential calculated by solving the non-linear Poisson-Boltzmann equation for the system, which describes the solvent using continuum electrostatics. We analyze the contribution of dielectric constant, conformational flexibility and solvation effects on the electrostatic potential at these eight points. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 23 November 1998