Study of thermodynamic properties of imidazolium-based ionic liquids and investigation of the alkyl chain length effect by molecular dynamics simulation

In this paper, structural and dynamical properties of five imidazolium-based ionic liquids (ILs) [amim]Br (a = methyl, ethyl, butyl, pentyl, hexyl) were studied by molecular dynamics simulations. United atom force field (UAFF) has been used for the representation of the interaction between ions. Good agreement with experimental data was obtained for the simulated density based on the UAFF. The calculated densities gradually decrease with an increase in the length of alkyl side chain, which is a result of weakening the electrostatic interaction between ions. The simulated heats of vaporisation are higher than that of non-ILs and decrease with an increase in temperature. Radial distribution function (RDF) was employed to analyse the local structure of ILs. Cation–anion RDFs show that the anions are well organised around the cation in two shells (0.41 and 0.6 nm). The velocity autocorrelation functions of the anion and cations show that the relaxation time increased with an increase in the length of the alkyl side chain. The diffusion coefficients of ions were calculated by mean square displacement of the centre of mass of the ions at 400 K. The calculated diffusion coefficients using UAFF agree well with other all atom force fields. Also diffusion coefficients decrease with an increase in the length of the alkyl side chain. The calculated transference numbers show that the cation contributes more than anion in the electrical current. The diffusion coefficients increase with temperature.     

A molecular dynamics study of liquid aliphatic alcohols: simulation of density and self-diffusion coefficient using a modified OPLS force field

A set of 13 aliphatic alcohols was modelled by molecular dynamics simulations at temperatures from 288 to 338 K using the optimised potential for liquid simulations (OPLS) united-atom force field, the OPLS all-atom force field and the OPLS all-atom force field with modified partial charges of the hydroxyl group. The set includes primary and secondary alcohols, and mono-, di- and trialcohols, and covers a broad range of polarities from log P = ? 0.74 (methanol) to log P = 2.9 (octanol). The density, the radial distribution function, the self-diffusion coefficient and the dielectric constant were evaluated. A long equilibration time of at least 50 ns and a large size of the molecular system of more than 75,000 atoms were used. Except for glycerol, the OPLS all-atom force field reliably reproduced the experimentally determined density with deviations of less than 4% over the whole temperature range. In contrast, the modelled self-diffusion coefficient deviated from its experimental value by up to 55%. To modify the force field, the partial charges of the hydroxyl group were varied by up to 3%. Using the modified OPLS force field, the deviation of the self-diffusion coefficients from their experimental values decreased to less than 19%, while the densities changed by less than 1%.     

Molecular dynamics simulation of hydrated Nafion with a reactive force field for water

We apply a newly parameterized central force field to highlight the problem of proton transport in fuel cell membranes and show that central force fields are potential candidates to describe chemical reactions on a classical level. After a short sketch of the parameterization of the force field, we validate the obtained force field for several properties of water. The experimental and simulated radial distribution functions are reproduced very accurately as a consequence of the applied parameterization procedure. Further properties, geometry, coordination, diffusion coefficient and density, are simulated adequately for our purposes. Afterwards we use the new force field for the molecular dynamics simulation of a swollen polyelectrolyte membrane similar to the widespread Nafion 117. We investigate the equilibrated structures, proton transfer, lifetimes of hydronium ions, the diffusion coefficients, and the conductivity in dependence of water content. In a short movie we demonstrate the ability of the obtained force field to describe the bond breaking/formation, and conclude that this force field can be considered as a kind of a reactive force field. The investigations of the lifetimes of hydronium ions give us the information about the kinetics of the proton transfer in a membrane with low water content. We found the evidence for the second order reaction. Finally, we demonstrate that the model is simple enough to handle the large systems sufficient to calculate the conductivity from molecular dynamics simulations. The detailed analysis of the conductivity reveals the importance of the collective moving of hydronium ions in membrane, which might give an interesting encouragement for further development of membranes. Figure: The structure of water in one pore of the highly hydrated Nafion membranes. Figure The structure of water in one of pore of the highly hydrated Nafion membrane Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Thermal expansion of ZnSe by molecular dynamics simulation

Thermal expansion of bulk ZnSe crystal, grown by physical vapour transport technique, is experimentally measured for various temperatures and molecular dynamics simulation using a three body Tersoff potential is also developed for the same. The resulting expansivity compares well with our experimental results and other reported values.     

Molecular dynamics simulation of liquid water under the influence of an external electric field

Molecular dynamics simulations of liquid water were performed at 258K and a density of 1.0?g/cm³ under various applied external electric field, ranging 0～10¹⁰?V/m. The influence of external field on structural and dynamical properties of water was investigated. The simple point charge (SPC) model is used for water molecules. An enhancement of the water hydrogen bond structure with increasing strength of the electric field has been deduced from the radial distribution functions and the analysis of hydrogen bonds structure. With increasing field strength, water system has a more perfect structure, which is similar to ice structure. However, the electrofreezing phenomenon of liquid water has not been detected since the self-diffusion coefficient was very large. The self-diffusion coefficient decreases remarkably with increasing strength of electric field and the self-diffusion coefficient is anisotropic.     

Calculation of diffusion coefficient for supercritical carbon dioxide and carbon dioxide+naphthalene system by molecular dynamics simulation using EPM2 model

NVT ensemble molecular dynamics (MD) simulation has been applied to calculate the self-diffusion coefficients of carbon dioxide and the tracer diffusion coefficients of naphthalene in supercritical carbon dioxide. The simulation was carried out in the pressure range from 8 to 40 MPa. The elementary physical model proposed by Harris and Yung was adopted for carbon dioxide and some approximation models were used for naphthalene. The systems of MD simulation for carbon dioxide consist of 256 particles. One naphthalene molecule was added for carbon dioxide+naphthalene system. The system can be assumed to be an infinite dilution condition for carbon dioxide+naphthalene system and the mutual diffusion coefficients are equal to the tracer diffusion coefficients of naphthalene. The self-diffusion coefficients of carbon dioxide and the tracer diffusion coefficients of naphthalene in supercritical carbon dioxide can be calculated by mean square displacement. The calculated results of diffusion coefficients showed good agreement with the experimental data without adjustable parameters.     

Investigating water and framework dynamics in pillared MOFs

In this work we highlight the use of molecular simulation to study the behaviour of water inside isostructural Zn-DMOF structures. Among the Zn-DMOF structures, the parent DMOF, and the DMOF-DM and DMOF-TF variants are known to be less stable than the DMOF-A and DMOF-TM structures in the presence of water. We apply tools such as radial distribution functions, rotational auto-correlation functions and the visualisation of adsorbate density distributions to investigate the differences in water behaviour within these structures. We also study properties that are inherent to the frameworks themselves such as thermal expansion and ligand flexibility. Our results indicate that water is only able to get 0.5 Å closer to the metal hydrolysis site in the water unstable structures than in the more water stable structures. The results can be somewhat sensitive to the details of the modelling of the electrostatic potential energy surface and, for dynamical properties, modelling of framework flexibility.     

Motion of groups of atoms in DNA studied by molecular dynamics simulation

The analysis of Molecular Dynamics simulations of two double stranded oligonucleotides is presented in terms of motions of quasi rigid subunits. First, a strategy is presented for grouping atoms submitted to concerted internal motions. The method is based on the analysis of the interatomic distance RMS matrix. It is found that each nucleotide can reasonably be decomposed into 3 or 4 rigid groups of atoms depending on the tolerance of the definition of a rigid body. In the second part, the different kinds of motions of the subunits (deformation, translation and rotation) are studied in terms of correlation using the canonical correlation analysis of data. It is shown that the residual deformation of any subunit does not influence the translational and rotational motions of the others, except perhaps for long time dynamics. Received: 3 October 1997 / Revised version: 22 December 1997 / Accepted: 23 December 1997     

On the structure of molecularly imprinted polymers by modifying charge on functional groups through molecular dynamics simulations

Molecularly imprinted polymers (MIPs) have been widely applied in many fields owing to their advantages. The recognition mechanism between target molecules and MIPs and the influence of dominant factor on the recognition process are still poorly understood. In this paper, a cubic methacrylate-based MIP model was constructed, and the charge on carboxyl group atoms was changed artificially to investigate the recognition process. It is found that the diffusion coefficients of the target molecules (cholesterol) are not affected by polymer network structure. The recognition process is mainly determined by the mesh sizes of the polymer network. In addition, the structure of modified MIP systems was also discussed from the viewpoints of radial distribution function and hydrogen bonds system. These results suggest that the polymer matrix structure would be enhanced with an increase in charge. Thus, it influences the structure of the water molecules in the system a little.     

Structure and dynamics of the antifungal molecules Syringotoxin-B and Syringopeptin-25A from molecular dynamics simulation

The phytopathogen Pseudomonas syringae pv. syringae produces toxic cyclic lipodepsipeptides (CLPs): nona-peptides and syringopeptins. All CLPs inhibit the growth of many fungal species, including human pathogens, although different fungi display different degrees of sensitivity. The best studied CLPs are Syringomycin-E (SR-E), Syringotoxin-B (ST-B) and Syringopeptin-25A (SP-25A). Their biological activity is affected by membrane composition and their structural differences. We previously (Matyus et al. in Eur Biophys J 35:459–467, 2006) reported the molecular features and structural preferences of SR-E in water and octane environments. Here we investigate in atomic detail the molecular features of the two other main CLP components, ST-B and SP-25A, in water and octane by 200 ns molecular dynamics simulations (MD), using distance restraints derived from NMR NOE data (Ballio et al. in Eur J Biochem 234:747–758, 1995). We have obtained three-dimensional models of ST-B and SP-25A CLPs in different environments. These models can now be used as a basis to investigate the interactions of ST-B and SP-25A with lipid membranes an important further step towards a better understanding of the antifungal and antibacterial activity of these peptides. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Dissolution of cellulose in ionic liquid and water mixtures as revealed by molecular dynamics simulations

Abstract

Increasing population growth and industrialization are continuously oppressing the existing energy resources, elevating the pollution and global fuel demand. Various alternate energy resources can be utilized to cope with these problems in an environment-friendly fashion. Currently, bioethanol (sugarcane, corn-derived) is one of the most widely consumed biofuels in the world. Lignocellulosic biomass is yet another attractive resource for sustainable bioethanol production. Pretreatment step plays a crucial role in the lignocellulose to bioethanol conversion by enhancing cellulose susceptibility to enzymatic hydrolysis. However, economical lignocellulose pretreatment still remains a challenging job. Ionic liquids (ILs), especially 1-ethyl-3-methylimidazolium acetate (EmimAc), is an efficient solvent for cellulose dissolution with improved enzymatic saccharification kinetics. To increase the process efficiency as well as recyclability of IL, water is shown as a compatible cosolvent for lignocellulosic pretreatment. The performance analysis of IL–water mixture based on the molecular level understanding may help to design effective pretreatment solvents. In this study, all-atom molecular dynamics simulation has been performed using EmimAc–water mixtures to understand the behavior of cellulose microcrystal containing eight glucose octamers at room and pretreatment temperatures. High-temperature simulation results show effective cellulose chain separation where cellulose–acetate interaction is found to be the driving force behind dissolution. It is also observed that pretreatment with 50 and 80% IL mixture is efficient in decreasing cellulose crystallinity. At a high IL concentration, water exists in a clustered network which gradually spans into the medium with increasing water fraction leading to loss of its cosolvation activity.

Communicated by Ramaswamy H. Sarma     

Molecular dynamics simulation on structural conformation of conjugated polymer-functionalised films for optimal fluorescent performance

The sensitive structure-related fluorescent properties of p-phenyleneethynylene (PPE)-functionalised fluorescent films with side chains and without side chains in different chemical environments are studied by molecular dynamics simulations. The calculations demonstrate that the structural change plays a crucial role in the fluorescent performance of PPE films, in which a major contribution is from the conformation of side chains. The PPE molecules with sides chains immobilised on SiO₂ substrate prefer to aggregate together in a dry state, but are more likely to stay in a monomolecular state in THF solvent. To an optimal concentration of the solvent molecules, the side chains are even perpendicular to the backbones of the molecules. The aggregation and separation of the PPE molecules with side chains are found to be controlled by the contraction and extension of the side chains connected to PPE. The van der Waals' force between the side chains is mainly responsible for these changes, which leads to a spreading out of the side chains in the presence of THF. All the results from the simulation studies can successfully explain the experimental observations.     

Adsorption and desorption surface dynamics of gaseous adsorbate on silicate-1 by molecular dynamics simulation

The dynamics of adsorption and desorption of gaseous molecules on the external surface of a crystal and a membrane of zeolite silicate-1 is investigated by molecular dynamics simulation. The gases are argon and three hydrocarbons, n-heptane, n-butane and ethylene. The sticking coefficient and the desorption coefficient are calculated for different coverages. The results clearly show that the desorption coefficients increase with the coverage contrary to the sticking coefficients. To have a better insight in the process, the desorption and adsorption time are computed, they are very similar and they show an increase with the coverage except for n-heptane which exhibit a specific decreasing behaviour at high loading.     

Calculation of the diffusion coefficient of thiophene oligomers using molecular dynamics

Electropolymerisation is a very useful methodology for conducting polymers synthesis. A total comprehension of this process will help on the designing of new materials with improved optical and electrical properties. In this sense, computational simulations can deliver important information at atomic scale. Within a kinetic Monte Carlo scheme, diffusion rates are crucial to obtain accurate predictions; however, experimental values of this dynamic property for different oligomers are very scarce among literature. In this study, the diffusion coefficient (D) of thiophene oligomers (1Th–6Th) has been calculated using molecular dynamics simulations coupled with the Einstein expression. Results are in the order of experimental values, demonstrating that this methodology is a fast and reliable alternative to calculate diffusion coefficients with low computational costs.     

Changes in the level of poly(Phe) synthesis in Escherichia coli ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus can be explained by structural changes in the peptidyltransferase center: a molecular dynamics simulation analysis

Data from polyphenylalanine [poly(Phe)] synthesis determination in the presence and in the absence of erythromycin have been used in conjunction with Molecular Dynamics Simulation analysis, in order to localize the functional sites affected by mutations of Thermus thermophilus ribosomal protein L4 incorporated in Escherichia coli ribosomes. We observed that alterations in ribosome capability to synthesize poly(Phe) in the absence of erythromycin were mainly correlated to shifts of A2062 and C2612 of 23S rRNA, while in the presence of erythromycin they were correlated to shifts of A2060 and U2584 of 23S rRNA. Our results suggest a means of understanding the role of the extended loop of L4 ribosomal protein in ribosomal peptidyltransferase center.     

Binding pattern analysis and structural insight into the inhibition mechanism of Sterol 24-C methyltransferase by docking and molecular dynamics approach

Sterol 24-C methyltransferase (SMT) plays a major role during the production of steroids, especially in the biosynthesis of ergosterol, which is the major membrane sterol in leishmania parasite, and the etiological basis of leishmaniasis. Mechanism-based inactivators bind irreversibly to SMT and interfere with its activity to provide leads for the design of antileishmanial inhibitors. In this study, computational methods are used for studying enzyme–inhibitor interactions. fifty-seven mechanism-based inactivators are docked using 3 docking/scoring approaches (FRED, GoldScore, and ChemScore). A consensus is generated from the results of different scoring functions which are also validated with already reported experimental values. The most active compound thus obtained is subjected to molecular dynamics simulation of length 20 ns. Stability of simulation is analyzed through root-mean-square deviation, beta factor (B-factor), and radius of gyration (Rg). Hydrogen bonds and their involvement in the structural stability of the enzyme are evaluated through radial distribution function. Newly developed application of axial frequency distribution that determines three-particle correlation on frequency distributions before and after simulation has provided a clear evidence for the movement of the inhibitor into active pocket of the enzyme. Results yielded strong interaction between enzyme and the inhibitor throughout the simulation. Binding of the inhibitor with enzyme has stabilized the enzyme structure; thus, the inhibitor has the potential to become a lead compound.     

Determinative factors in inhibition of aquaporin by different pharmaceuticals: Atomic scale overview by molecular dynamics simulation

The inhibition of water permeation through aquaporins by ligands of pharmaceutical compounds is considered as a method to control the cell lifetime. The inhibition of aquaporin 1 (AQP1) by bacopaside-I and torsemide, was explored and its atomistic nature was elucidated by molecular docking and molecular dynamics (MD) simulation collectively along with Poisson-Boltzmann surface area (PBSA) method. Docking results revealed that torsemide has a lower level of docking energy in comparison with bacopaside-I at the cytoplasmic side. Furthermore, the effect of steric constraints on water permeation was accentuated. Bacopaside-I inhibits the channel properly due to the strong interaction with the channel and larger spatial volume, whereas torsemide blocks the cytoplasmic side of the channel imperfectly. The most probable active sites of AQP1 for the formation of hydrogen bonds between the inhibitor and the channel were identified by numerical analysis of the bonds. Eventually, free energy assessments indicate that binding of both inhibitors is favorable in complex with AQP1, and van der Waals interaction has an important contribution in stabilizing the complexes.     

Understanding interaction and dynamics of water molecules in the epoxy via molecular dynamics simulation

The robust structural integrity of the epoxy plays an important role in ensuring the long-term service life of its applications, which is affected by the absorbed moisture. In order to understand the mechanism of the moisture effect, the knowledge of the interaction and dynamics of the water molecules inside the epoxy is of great interest. Molecular dynamics simulation is used in this work to investigate the structure and bonding behaviour of the water molecules in the highly cross-linked epoxy network. When the moisture concentration is low, the water molecules are well dispersed in the cross-linked structure and located in the vicinity of the epoxy functional groups, which predominantly form the hydrogen bond (H-bond) with the epoxy network, resulting in the low water mobility in the epoxy. At the high concentration, the water favourably forms the large cluster due to the predominant water–water H-bond interaction, and the water molecules diffuse primarily inside the cluster, which leads to the high water mobility and the accelerated H-bond dynamics. The variation of the bonding behaviour and dynamics of the water molecules reported here could be exploited to understand the material change and predict the long-term performance of the epoxy-based products during the intended service life.     

A molecular dynamics study of solvent behavior around a protein

The solvent structure and behavior around a protein were examined by analyzing a trajectory of molecular dynamics simulation of thetrp-holorepressor in a periodic box of water. The calculated selfdiffusion coefficient indicated that the solvent within 10 Å of the protein had lower mobility. Examination of the solvent diffusion around different atoms of different kinds of residues showed no general tendency. Thisfact suggested that the solvent mobility is not influenced significantly bythe kind of the atom or residue they solvated. Distribution analysis aroundthe protein revealed two peaks of water oxygen: a sharp one at 2.8 Å around polar and charged atoms and a broad one at ～3.4 Å aroundapolar atoms. The former was stabilized by water–protein hydrogen bonds, and the latter was stabilized by water-lwater hydrogen bonds, suggesting the existence of a hydrophobic shell. An analysis of protein atom–water radial distribution functions confirmed these shell structures around polar or charged atoms and apolar ones. © 1993 Wiley-Liss, Inc.     

Structure of hydration water in proteins: a comparison of molecular dynamics simulations and database analysis

Hydration layer water molecules play important structural and functional roles in proteins. Despite being a critical component in biomolecular systems, characterizing the properties of hydration water poses a challenge for both experiments and simulations. In this context we investigate the local structure of hydration water molecules as a function of the distance from the protein and water molecules respectively in 188 high resolution protein structures and compare it with those obtained from molecular dynamics simulations. Tetrahedral order parameter of water in proteins calculated from previous and present simulation studies show that the potential of bulk water overestimates the average tetrahedral order parameter compared to those calculated from crystal structures. Hydration waters are found to be more ordered at a distance between the first and second solvation shell from the protein surface. The values of the order parameter decrease sharply when the water molecules are located very near or far away from the protein surface. At small water-water distance, the values of order parameter of water are very low. The average order parameter records a maximum value at a distance equivalent to the first solvation layer with respect to the water-water radial distribution and asymptotically approaches a constant value at large distances. Results from present analysis will help to get a better insight into structure of hydration water around proteins. The analysis will also help to improve the accuracy of water models on the protein surface.