Molecular Dynamics Study of Water in Hydrogels

Abstract

Molecular dynamics simulations are performed for aqueous solutions of polymers: Poly (vinyl alcohol) (PVA), Poly (vinyl methylether) (PVME), and Poly (N-isopropyl acrylamide) (PNiPAM). The distributions and dynamics of hydrogen-bonds, the translational diffusion of water, and the orientational relaxation of water are analyzed to investigate the properties of water which is highly influenced by the surrounding polymer chains. The water molecules around the polymer chains are highly hindered by the chains.     

Molecular Dynamics Simulation of Protein Folding with Supersecondary Structure Constraints

We integrate molecular dynamics simulation methods with a newly developed supersecondary structure prediction method and compute the structure of a protein molecule, crambin. The computed structure is similar to the crystal structure with an rms error of 3.94 Å.     

Structural Transformations of Ice at High Pressures Via Molecular Dynamics Simulations

Abstract

A simple classical model is used for the study of the structural transformations of ice under high pressures, such as ice VIII to VII and X, via classical molecular dynamics (MD) simulation. In the present MD simulation, pair potentials of a simple form between pair of atoms and a thee-body potential representing the H-O-H angle dependence, originally developed by Kawamura et al., were used. Starting with a stable ice VIII at low pressure and low temperature, we have carried out two different MD runs, one with increasing pressure keeping the temperature constant (simulation I) and the other with increasing temperature under constant pressure (simulation II). From these MD simulations we have obtained the structural transformations from ice VIII to VII for both simulations; the former was finally transformed into ice X for the simulation I. The present results are compatible with recent experiments on high pressure ices.     

Imidacloprid and Related Compounds: Structure and Water Solubility of N-Alkyl Derivatives of Imidacloprid

An intramolecular hydrogen bond between NH???O₂N in insecticide, imidacloprid (1), and its nitromethylene analog 15 was proved by NMR and IR spectra. That electron delocalization over their planar moieties was disrupted by alkylation at the imidazolidine nitrogen atom is demonstrated by the hypsochromic shifts in UV and deshielding effect in NMR spectra. Interestingly, the N-alkyl derivatives (C1-5) had greater water solubility than 1, although increasing alkyl chain length decreased the solubility. The hydrophilicity of the alkyl derivatives would result from remote charge heads being formed as a result of the conjugation disruption by alkylation, while the hydrophobicity of 1 could be ascribed to the charge distribution over the conjugated system coupled with the intramolecular H-bonding. The greater water solubility of 15 than 1 and contrastively small solubility of the cyanoimine analogue are discussed based on the difference in their steric crowding.     

Molecular Dynamics Simulations of Zinc Ions in Water Using CHARMM

Molecular Dynamics simulations of a zinc ion with 123 and 525 TIP3P-water molecules were carried out with CHARMM using two different Lennard-Jones parameter sets for the Zn²⁺ ion. The results were compared to published experimental and simulation data. Good agreement was found for radial distribution functions, number of hydrogen bonds, and diffusion coefficients. Experimental radial distribution functions were better reproduced by the original CHARMM22 parameter set than by the parameter set modified by Stote and Karplus. Diffusion coefficients were found to depend on the system size rather than on the parameter set used and were better reproduced by the larger systems. The divalent zinc ion exerts a strong influence on its hydration shell as indicated by the high first peak of the radial distribution function. Water molecules in the vicinity of the zinc ion show a slight deformation of the O-H bond length and of the H-O-H bond angle as compared to pure water. No water molecules from the first hydration shell were exchanged during 1 ns of MD simulation.Electronic Supplementary Material available.     

Molecular Dynamics Study of the Structure,Flexibility and Dynamics of Thermostable L1 Lipase at High Temperatures

Molecular Dynamics (MD) simulations have been used to understand how protein structure, dynamics, and flexibility are affected by adaptation to high temperature for several years. We report here the results of the high temperature MD simulations of Bacillus stearothermophilus L1 (L1 lipase). We found that the N-terminal moiety of the enzyme showed a high flexibility and dynamics during high temperature simulations which preceded and followed by clear structural changes in two specific regions; the small domain and the main catalytic domain or core domain of the enzyme. These two domains interact with each other through a Zn²⁺-binding coordination with Asp-61 and Asp-238 from the core domain and His-81 and His-87 from the small domain. Interestingly, the His-81 and His-87 were among the highly fluctuated and mobile residues at high temperatures. The results appear to suggest that tight interactions of Zn²⁺-binding coordination with specified residues became weak at high temperature which suggests the contribution of this region to the thermostability of the enzyme. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Structure of Supercritical Fluid Krypton at Small Scattering Angle Using Parallel Molecular Dynamics Simulation

Abstract

We present a parallel algorithm for molecular dynamics involving short-range two- and three-body potentials and the pair-correlation function, g(r). The method is based on a spatial decomposition of the simulation box that takes advantage of a linked-cell list, and allows a load balanced partition of the computations of both the forces and g(r) over the processors. The tests of the program is conducted by evaluating the efficiency for both the thermalization phase and the production phase of the simulation. This method is successfully applied to the calculation of the direct correlation function of fluid krypton at small scattering angle along the T = 297 K supercritical isotherm.     

Molecular dynamics simulation of content of bound water in ethylene glycol and glycerol solution

In this paper, the content of bound water was studied to evaluate the cryoprotective properties of ethylene glycol and glycerol solution. Molecular dynamic models for the solution were built, the classification principle and statistical methods of water molecules in solutions were presented, respectively. The content of bound water with various hydroxyl molarity at different temperatures was obtained through molecular dynamic simulation. The results reveal that the content of bound water increases with increasing hydroxyl molarity, but decreases with increasing temperature. It was found that, the content of bound water in ethylene glycol solution is always slightly more than that in glycerol solution, regardless of whether the temperature increases or not.     

Molecular Dynamics Simulation of CaF2 Structure in Crystalline,Superionic and Molten Phases

Abstract

We describe here a number of molecular dynamics simulations on calcium fluoride over a range of temperatures spanning the transitions to the superionic and molten state. The simulation temperatures are 1400, 1590, 1800, 2000, 2200 K. By using the bond spherical harmonics method with equal neighbor number, we have studied the structure and bond orientation of cation sublattice and anion sublattice in superionic conductor CaF₂. The bond order parameters Q₁ have been calculated both for the computer generated instataneous configurations from the simulation system and for the standard configurations from the normal distribution model of bond orientation. The comparison of Q₁ between the molecular dynamics simulation and the normal distribution model shows that not only the cation sublattice but also the anion sublattice can be described by the normal distribution model. The cations keep their original fcc frame, but in the anion case there is a great deal of random distortions from the original anion sublattice.     

The self-diffusion and hydrogen bond interaction in neat liquid alkanols: a molecular dynamic simulation study

Self-diffusion of methanol, ethanol, 1-propanol and 2-propanol has been studied by molecular dynamics simulation in the temperature range between the melting pressure curve and 478 K at pressures up to 300 MPa. The simulation results on self-diffusion of methanol, ethanol and 2-propanol (for 2-propanol, at high temperatures) agree well with experiment, which suggests that the simulation method is a powerful tool to obtain self-diffusion coefficients over wide range of temperature and pressure, under which it is rather difficult for experiments. The local structures of methanol, ethanol and 2-propanol are investigated by calculating the radial distribution functions, H-bond numbers, coordination numbers and the ratios of H-bond number divided by coordination number. The correlation between self-diffusion and structural properties, and the influence of temperature and pressure on them are discussed. The degree of forming H-bond space network in methanol, ethanol and water is higher than that in 2-propanol, and they are all higher than those in ammonia and methylamine. The simulation results demonstrate that the effect of hydrogen bonding on the translational dynamics in methanol and ethanol is more pronounced than that in 2-propanol.     

Solution Conformation of [D-Pen2,D-Pen5]enkephalin in Water: A NMR and Molecular Dynamics Study

The solution conformation of [D -Pen²,D -Pen⁵] enkephalin (DPDPE), a highly potent δ-selective opioid agonist, was examined by means of NMR, molecular mechanics and molecular dynamics methods. The structural information in the solvent water was obtained employing one- and two-dimensional methods of ¹H and ¹³C-NMR spectroscopy. Based on the distance geometry technique using the ROE data as input, 400 conformers were obtained and considered in the structure analysis. Alternatively, about 2000 conformers were stochastically generated and related to the NMR data after energy minimization. The structure analysis provides one conformer in agreement with all NMR data, which belongs to the lowest energy conformation group. This structure may serve as a reference conformer for DPDPE analogues synthesized with the aim of activity increase.     

Union of Geometric Constraint-Based Simulations with Molecular Dynamics for Protein Structure Prediction

Although proteins are a fundamental unit in biology, the mechanism by which proteins fold into their native state is not well understood. In this work, we explore the assembly of secondary structure units via geometric constraint-based simulations and the effect of refinement of assembled structures using reservoir replica exchange molecular dynamics. Our approach uses two crucial features of these methods: i), geometric simulations speed up the search for nativelike topologies as there are no energy barriers to overcome; and ii), molecular dynamics identifies the low free energy structures and further refines these structures toward the actual native conformation. We use eight α-, β-, and α/β-proteins to test our method. The geometric simulations of our test set result in an average RMSD from native of 3.7 Å and this further reduces to 2.7 Å after refinement. We also explore the question of robustness of assembly for inaccurate (shifted and shortened) secondary structure. We find that the RMSD from native is highly dependent on the accuracy of secondary structure input, and even slightly shifting the location of secondary structure along the amino acid sequence can lead to a rapid decrease in RMSD to native due to incorrect packing.     

Structural Characteristics in Protein Hydration Investigated by Cryogenic X-ray Crystal Structure Analyses

Cryogenic X-ray crystallography has heen applied to investigate thehydration structures of proteins. The amount of hydration water moleculesidentified at cryogenic temperature is more than twice those at ambienttemperature, and the structural models of proteins with a lot of hydrationwater molecules have provided much information to elucidate the static anddynamical characteristics of hydration structures of proteins. On proteinsurface, hydration water molecules distribute non-randomly and stillretain the tetrahedral hydrogen-bond geometry as well as in bulk solvent.In addition, water molecules form clathrate-like arrangements to cover thehydrophobic residues exposed to solvent. The standard interaction geometryenables the three-dimensional extension of hydrogen-bond networks aroundprotein molecules and, simultaneously, ensures the concerted reorganizationof hydration structures during the dynamical motion of proteins at work.The hydration structure analyses at cryogenic temperatures may contributeto understanding physical principles governing the dynamics of `molecularmachines' in aqueous environment.     

Protein Surface Dynamics: Interaction with Water and Small Solutes

Previous time resolved measurements had indicated that protons could propagate on the surface of a protein, or a membrane, by a special mechanism that enhances the shuttle of the proton towards a specific site [1]. It was proposed that a proper location of residues on the surface contributes to the proton shuttling function. In the present study, this notion was further investigated using molecular dynamics, with only the mobile charge replaced by Na⁺ and Cl⁻ ions. A molecular dynamics simulation of a small globular protein (the S6 of the bacterial ribosome) was carried out in the presence of explicit water molecules and four pairs of Na⁺ and Cl⁻ ions. A 10 ns simulation indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. Yet it was noted that, close to some domains, the ions extended their duration near the surface, suggesting that the local electrostatic potential prevented them from diffusing to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed.     

Molecular Dynamics Simulation of Structural Phase Transition of AlPO4 Induced by Pressure

Abstract

The mechanism of pressure-induced phase transition of AlPO₄ has been investigated by means of a molecular dynamics method of constant temperature and pressure. A new crystalline phase with space group C2, which has not yet been experimentally found, appears by an instantaneous compression of 60, 70 and 80 GPa at 300 K. At high temperature (2500 K) and pressure (58 GPa), another new phase of AlPo₄ (y-phase), which is composed of PO₆ and AlO₆ octahedra, has been observed.     

The Structure of Liquid Methanol: A Molecular Dynamics Study Using Three-Site Models

Abstract

The structure of liquid methanol at 298.15 K is investigated by performing molecular dynamics (MD) simulations in NVE ensemble using two 3-site force field models. The simulated structural results are compared with the recent neutron diffraction (ND) results obtained at the partial pair distribution function (pdf) level by employing H/D substitution on the hydroxyl hydrogen, Ho. Overall agreement is found between the simulated and experimental total intermolecular radial distribution functions (rdfs). The ability of the 3-site model simulations to satisfactorily reproduce experimental X—X (X = C, O or H- a methyl hydrogen) intermolecular partial distribution function, dominated by contributions from the methyl group. demonstrates that the methyl group does not participate in any bonding in the liquid. However, a comparison between the simulated and experimental Ho—Ho and X—Ho functions reveals that discrepancies still exist at a quantitative level.     

Molecular Dynamics Study of BaB2O4 in Crystalline and Molten States

Abstract

Structural aspects of BaB₂O₄ liquids have been investigated by the molecular dynamics simulation including the determination on the parameters of the interatomic potential applicable to BaB₂O₄ in both crystalline and molten states. The structure and physical properties of BaB₂O₄ crystals were successfully reproduced by the MD simulation for both α and β phases. The simulated interference function in the liquid state was also in good agreement with the experimental one. Several interesting features on the relaxation phenomena just after melting were reproduced by the simulation that the structure factors of simulated liquid maintain the characteristic features of the original crystal structure for more than 40ps after melting, and the variation of the number of rings formed by B-O bondings was found to increase after melting.     

Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space

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