Computation of some thermodynamic properties of helium–neon and helium–krypton fluid mixtures using molecular dynamics simulation

We have performed molecular dynamics simulations to obtain internal energy and pressure of helium–neon and helium–krypton mixtures at different densities using accurate recently two-body ab initio potentials supplemented by quantum corrections following the Feynman–Hibbs approach. The significance of this work is that the three-body expression of Wang and Sadus [22] was used to improve prediction of the pressures and internal energies of helium + krypton and helium + neon mixtures without requiring an expensive three-body calculation. Our results show a good agreement with the corresponding experimental data.     

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.     

Molecular dynamics simulations of fluid methane properties using ab initio intermolecular interaction potentials

Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. The full potential curves of the methane dimer at 12 symmetric conformations were calculated by the supermolecule counterpoise‐corrected second‐order Møller‐Plesset (MP2) perturbation theory. Single‐point coupled cluster with single and double and perturbative triple excitations [CCSD(T)] calculations were also carried out to calibrate the MP2 potentials. We employed Pople's medium size basis sets [up to 6‐311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (cc‐pVXZ and aug‐cc‐pVXZ, X = D, T, Q). For each conformer, the intermolecular carbon–carbon separation was sampled in a step 0.1 Å for a range of 3–9 Å, resulting in a total of 732 configuration points calculated. The MP2 binding curves display significant anisotropy with respect to the relative orientations of the dimer. The potential curves at the complete basis set (CBS) limit were estimated using well‐established analytical extrapolation schemes. A 4‐site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen–hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show quantitative agreements on both the atom‐wise radial distribution functions and the self‐diffusion coefficients over a wide range of experimental conditions. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

The inclusion of electron correlation in intermolecular potentials: applications to the formamide dimer and liquid formamide

A test of the quality of the electrostatic properties and polarizabilities used in the nonempirical molecular orbital (NEMO) potential is carried out for formamide by calculating the molecular dipole moment and polarizability at the second-order M?ller–Plesset (MP2) level of theory. The molecular dipole moment is 11% lower at the MP2 level than at the Hartree–Fock (HF) level, whereas the isotropic part of the polarizability is increased by 36% by adding electron correlation and using a considerably larger basis set. The atomic charges, dipole moments and polarizabilities obtained at the HF level are rescaled to get the correct molecular properties at the MP2 level. The potential minimum for the cyclic dimer of formamide is −17.50 kcal/mol with the MP2-scaled properties and is significantly lower than other potentials give. Two intermolecular potentials are constructed and used in subsequent molecular dynamics simulations: one with the regular NEMO potential and the other with the rescaled MP2 properties. A damping of the electrostatic field at short intermolecular distances is included in the present NEMO model. The average energies for liquid formamide are lower for the MP2-scaled model and are in good agreement with experimental results. The lowering of the simulation energy for the MP2-scaled potential indicates the strong dispersive interactions in liquid formamide. Received: 20 March 2000 / Accepted: 18 April 2000 / Published online: 18 August 2000     

Structure,thermodynamics and diffusion in asymmetric binary mixtures: a molecular dynamics simulation study

Structural and thermodynamic properties as well as diffusion coefficients of binary fluid mixtures with asymmetry in mass, size, charge and their combinations have been studied using classical molecular dynamics simulations. The fluid mixture is modelled as spherical particles interacting via the Weeks–Chandler–Andersen and Coulomb potential. The diameter, charge and mass of the fluid particles are in the range 6–60 Å, 1–10e and 1—500 amu, respectively. Systematic variations in pair-correlation functions, thermodynamic properties as well as the self-diffusion coefficient are found with the size, charge and mass ratio of the particles. The self-diffusion coefficient for systems having more than one type of asymmetry is calculated and expressed in terms of diffusion coefficients of systems with only one type of asymmetry.     

Quantum control of a chiral molecular motor driven by femtosecond laser pulses: Mechanisms of regular and reverse rotations

Rotational mechanisms of a chiral molecular motor driven by femtosecond laser pulses were investigated on the basis of results of a quantum control simulation. A chiral molecule, (R)-2-methyl-cyclopenta-2,4-dienecarboaldehyde, was treated as a molecular motor within a one-dimensional model. It was assumed that the motor is fixed on a surface and driven in the low temperature limit. Electric fields of femtosecond laser pulses driving both regular rotation of the molecular motor with a plus angular momentum and reverse rotation with a minus one were designed by using a global control method. The mechanism of the regular rotation is similar to that obtained by a conventional pump–dump pulse method: the direction of rotation is the same as that of the initial wave packet propagation on the potential surface of the first singlet (nπ^*) excited state S₁. A new control mechanism has been proposed for the reverse rotation that cannot be driven by a simple pump–dump pulse method. In this mechanism, a coherent Stokes pulse creates a wave packet localized on the ground state potential surface in the right hand side. The wave packet has a negative angular momentum to drive reverse rotation at an early time.     

Molecular dynamics simulation of acetamide solvation using interaction energy components: Application to structural and energy properties

Molecular dynamics simulation of an aqueous solution of acetamide was performed using Lennard–Jones 12-6-1 potentials to describe the solute–solvent interactions, and TIP3P to describe the water–water interactions. The Morokuma decomposition scheme and the ESIE solute atomic charges were used to reproduce the molecular parameters of the solute–water interaction potential. The results showed that the functions that use the EX-PL-DIS-ES interaction model lead to good values of the structural and energy properties (in particular, the hydration shell and the solvation energies) when they are compared with those from using AMBER-derived parameters, and with the available theoretical and experimental data.     

A molecular dynamics approach to examine the kinetics of the capillary imbibition of a polymer at nanoscale

A molecular dynamics (MD) approach was employed to simulate the imbibition of a designed nanopore by a polymer. The length of imbibition as a function of time for various interactions between the polymer and the pore wall was recorded for this system (i.e., polymer and nanopore). By and large, the kinetics of imbibition was successfully described by the Lucas–Washburn (LW) equation, although deviation from it was observed in some cases. This nonuniformity contributes to the neglect of the dynamic contact angle (DCA) in the LW equation. Two commonly used models (i.e., hydrodynamic and molecular–kinetic models) were thus employed to calculate the DCA. It is demonstrated that none of the evaluated models is able to justify the simulation results in which are not in good agreement with the simple LW equation. Further investigation of the MD simulation data revealed an interesting fact that there is a direct relationship between the wall–polymer interaction and the speed of the capillary imbibition. More evidence to support this claim will be presented.     

Role of protein flexibility in the design of Bcl-XL targeting agents: insight from molecular dynamics

Detailed understanding of protein–ligand interactions is crucial to the design of more effective drugs. This is particularly true when targets are protein interfaces which have flexible, shallow binding sites that exhibit substantial structural rearrangement upon ligand binding. In this study, we use molecular dynamics simulations and free energy calculations to explore the role of ligand-induced conformational changes in modulating the activity of three generations of Bcl-X_L inhibitors. We show that the improvement in the binding affinity of each successive ligand design is directly related to a unique and measurable reduction in local flexibility of specific regions of the binding groove, accompanied by the corresponding changes in the secondary structure of the protein. Dynamic analysis of ligand–protein interactions reveals that the latter evolve with each new design consistent with the observed increase in protein stability, and correlate well with the measured binding affinities. Moreover, our free energy calculations predict binding affinities which are in qualitative agreement with experiment, and indicate that hydrogen bonding to Asn100 could play a prominent role in stabilizing the bound conformations of latter generation ligands, which has not been recognized previously. Overall our results suggest that molecular dynamics simulations provide important information on the dynamics of ligand–protein interactions that can be useful in guiding the design of small-molecule inhibitors of protein interfaces. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Local elevation: A method for improving the searching properties of molecular dynamics simulation

Summary The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.     

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.     

Discovery of potential inhibitor against human acetylcholinesterase: a molecular docking and molecular dynamics investigation

Alzheimer’s disease (AD) is a progressive neurodegenerative disease of central nervous system among elderly people. Human acetylcholinesterase (hAChE), an important enzyme in neuronal signaling, is responsible for the degradation of acetylcholine which in turn prevents the post synaptic signal transmissions. hAChE has been an attractive target of drug discovery for the search of therapeutics against AD. In the recent past hAChE has become hot target for the investigation of new potential therapeutics. We performed virtual screening of entire database against hAChE. Further, the extra precision molecular docking was carried out to refine the docking results and the best complex was passed for molecular dynamics simulations in order of understanding the hAChE dynamics and its behavior in complex with the ligand which corroborate the outcomes of virtual screening. This also provides binding free energy data that establishes the ligands efficiency for inhibiting hAChE. The computational findings discussed in this paper provide initial information of inhibitory effects of ligand, (drugbank entry DB00983), over hAChE.     

Proline-based chiral stationary phases: a molecular dynamics study of the interfacial structure

Proline chains have generated considerable interest as a possible basis for new selectors in chiral chromatography. In this article, we employ molecular dynamics simulations to examine the interfacial structure of two diproline chiral selectors, one with a terminal trimethylacetyl group and one with a terminal t-butyl carbamate group. The solvents consist of a relatively apolar n-hexane/2-propanol and a polar water/methanol mixture. We begin with electronic structure calculations for the two chiral selectors to assess the energetics of conformational changes, particularly along the backbone where the amide bonds can alternate between cis and trans conformations. Force fields have been developed for the two selectors, based on these ab initio calculations. Molecular dynamics simulations of the selective interfaces are performed to examine the preferred backbone conformations, as a function of end-group and solvent. The full chiral surface includes the diproline selectors, trimethylsilyl end-caps, and silanol groups. Connection is made with selectivity measurements on these interfaces, where significant differences are observed between these two very similar selectors.     

Liquid properties of dimethyl ether from molecular dynamics simulations using Ab Initio force fields

We have used molecular dynamic simulations to study the structural and dynamical properties of liquid dimethyl ether (DME) with a newly constructed ab initio force field in this article. The ab initio potential energy data were calculated at the second order Møller‐Plesset (MP2) perturbation theory with Dunning's correlation consistent basis sets (up to aug‐cc‐pVQZ). We considered 17 configurations of the DME dime for the orientation sampling. The calculated MP2 potential data were used to construct a 3‐site united atom force field model. The simulation results are compared with those using the empirical force field of Jorgensen and Ibrahim (Jorgensen and Ibrahim, J Am Chem Soc 1981, 103, 3976) and with available experimental measurements. We obtain quantitative agreements for the atom‐wise radial distribution functions, the self‐diffusion coefficients, and the shear viscosities over a wide range of experimental conditions. This force field thus provides a suitable starting point to predict liquid properties of DME from first principles intermolecular interactions with no empirical data input a priori. © 2012 Wiley Periodicals, Inc.     

Estimation and analysis of the rheological properties of a perfluoropolyether through molecular dynamics simulation

Equilibrium and non-equilibrium molecular dynamics simulations of a perfluoropolyether C₈F₁₈O₄ are reported using an atomistic interaction potential. The bulk rheological properties of the perfluoropolyether are investigated through molecular dynamics simulations as a function of both temperature and shear rate. The effect of molecular structure on viscosity is explored in detail. The rotational relaxation time is reported as a function of temperature. Structural properties, including the mean-square end-to-end chain length, the mean-square radius of gyration of chains, and the distribution functions of bond lengths, bond angles, and bond torsional angles are collected and analyzed as functions of shear rate. After an initial plateau, both mean-square end-to-end chain length and mean-square radius of gyration decrease monotonically with increasing shear rate. The behaviors of the rheological and structural properties are explained through an analysis of the individual contributions due to bond stretching, bond bending, and bond torsion, as well as both intramolecular and intermolecular non-bonded interactions. A further analysis is possible through a meticulous breakdown of each contribution into a specific type of mode; e.g., the total bond stretching is comprised of CC, CO, and CF bond stretching terms. In this way, one can relate the shear viscosity to the specific chemical structure of C₈F₁₈O₄.     

Multi-scale studies of glass transition and uniaxial tensile properties of a commercially available epoxy adhesive using experimental measurements and molecular dynamics simulation

In this study, the glass transition and uniaxial tensile properties of a commercially available epoxy adhesive were investigated using experimental measurements and molecular dynamics(MD) simulation. Differential scanning calorimetry(DSC) was used to study the change of glass transition temperature(T g) with cross-link density(CLD). Uniaxial tensile test was performed to measure the Young's modulus(E), Poisson's ratio(ν) and yielding strength(σY). In MD simulation, the complicated epoxy system was simplified as the mixture of two kinds of simple molecules, with the key information well preserved and the less important details omitted. The molecular model of the cross-linked epoxy network was constructed and its mechanical properties were calculated using MD simulation. Overall, the MD simulation results agreed with experimental ones, which proved the validity of the molecular model and justified the simplification method of the industrylevel epoxy system.     

A molecular dynamics simulation study of peptide deformylase from Leptospira interrogans complex：Exploring the closing mechanism of the substrate pocket

To explore the closing mechanism of the substrate pocket,we perform a 16,000 ps molecular dynamics simulation separately on the ligand-free and actinonin-bound peptide deformylase from Leptospira interrogans.Our results show that the CD-loop, hydrophilic inhibitor and hydrophobic cluster are necessary for the formation of semi-open conformation,and Tyr71 plays an important role in mediating the movements of CD-loop.The average MD structure of the actinonin-bound LiPDF complex approaches to the crystal structure.These are consistent with experiment very well.     

Molecular dynamics study of the tautomeric equilibrium in the 4-nitro- and 2,4,6-trichloro derivatives of 2-(N,N-dialkyloaminomethyl)phenol

 Molecular dynamics thermodynamic integration (MDTI) method and quantum chemical calculations at the density functional theory B3LYP 6-31+(d,p) level, which included the Tomasi model of the solvent reaction field, were applied to study the tautomeric equilibrium of Mannich base in methanol solution. The values obtained for the free-energy difference are in good agreement with experimental data. However, the results from quantum mechanical calculations were not as good as the results of MDTI simulations owing to inappropriate treatment of intermolecular hydrogen bonds between the solute molecule and the first shell of solvent molecules in the Tomasi model of the solvent reaction field. The radial distribution functions between solute atoms and solvent atoms confirmed the formation of hydrogen bonds between the solute molecule and surrounding methanol molecules and indicated that the zwitterionic form is associated more with an organized solvent structure at the level of the first solvation shell than is the molecular form. Received: 26 April 2002 / Accepted: 9 September 2002 / Published online: 31 March 2003     

Static and dynamic contact angles of water droplet on a solid surface using molecular dynamics simulation

The present study investigates the variation of static contact angle of a water droplet in equilibrium with a solid surface in the absence of a body force and the dynamic contact angles of water droplet moving on a solid surface for different characteristic energies using the molecular dynamics simulation. With increasing characteristic energy, the static contact angle in equilibrium with a solid surface in the absence of a body force decreases because the hydrophobic surface changes its characteristics to the hydrophilic surface. In order to consider the effect of moving water droplet on the dynamic contact angles, we apply the constant acceleration to an individual oxygen and hydrogen atom. In the presence of a body force, the water droplet changes its shape with larger advancing contact angle than the receding angle. The dynamic contact angles are compared with the static contact angle in order to see the effect of the presence of a body force.