Reaction Field Effects on the Simulated Properties of Liquid Water

Abstract

The effects of including a reaction field contribution on the structure and dynamics of liquid water have been investigated using molecular dynamics simulations. Reaction field effects are determined for two models of water, the simple point charge (SPC) model and the extended simple point charge (SPC/E) model, and at two temperatures (277 K and 300 K). Inclusion of the reaction field leads to a reduced system density, an increase in translational diffusion, which is model dependent, an increase in internal energy, and an increase in rotational diffusion rates, in addition to the large (known) changes in the dielectric properties of liquid water. It is concluded that continued use of the reaction field technique should involve a reparameterization of the water model and not merely a merging with the original model parameters.     

Influence of Cooperativity on Hydrogen Bond Networks

Abstract

Cooperative effects are known to strongly affect the geometrical, energetic and vibrational properties of hydrogen bonded systems. In particular, such effects strongly favor molecular arrangements where each molecule is simultaneously a donor and an acceptor of hydrogen bonds (HBs), regardless of the chemical nature of the monomer subunits. In the particular case of water systems, it has been shown that the more a molecule is a proton donor in HBs, the more the HBs where it is a proton acceptor are reinforced. Such a property could be at the origin of the equilibrium between the two species of hydrogen bonded water molecules in liquid water (one with a strong hydrogen bonding character, and one with a weaker one), as experimentally evidenced and as a molecular dynamic study of the small (H₂O)₂₄ cluster clearly suggests.     

On the Implementation of Friedman Boundary Conditions in Liquid Water Simulations

Abstract

We have applied the image approximation to the reaction field as suggested by H.L. Friedman [Mol. Phys., 29, 1533 (1975)] by investigating appropriate cavity sizes and system parameters for use in molecular simulations. The energy of and the structure around a central simple point charge (SPC) water molecule in a dielectric cavity was found to be in good agreement with the properties of a liquid sample. To confine the water molecules within the cavity, we introduced a short-range repulsion between a real charge and its image as the Lennard-Jones repulsive potential between oxygen atoms of the SPC potential. For a system of 65 water molecules a cavity radius of 10.45 Å is appropriate; this radius is altered to 12.00 Å for a cavity surrounding 113 molecules. The effect of the boundary is restricted to the outer-most water layer which is in contact with the dielectric continuum.     

Why Structured Water Causes Sharp Absorption by DNA at Microwave Frequencies

Abstract

Aqueous solutions of oligopolymer DNA have been observed by G.S. Edwards, C.C. Davis, M.L. Swicord and J.D. Saffer, Phys. Rev. Lett. 53, 1284(1984) to show structured absorption of microwave energy in the region of several gigahertz, characteristic of an ordered series of compressional normal mode vibrations propagating on the polymer chain. Although hydrodynamic coupling of such vibrations to the surrounding solvent would preclude the existence of sharp resonances, the molecular nature of the solvent in the near neighborhood of the polymer and - paradoxically- the strong water/polymer interactions provide a means for effectively decoupling the polymer motion from the dissipation of the liquid. Recent measurements of DNA/water relaxation times allow estimating numerical values in a parameterization of the decoupling effect. The resulting predicted frequency dependence explains many of the smaller features of Edwards' experiment as well as theoverall anomaly. A simple model gives a surprisingly complete account of the features of the data using only values determined from other experiments.     

Radio-frequency capacitive discharge with flowing liquid electrodes at reduced gas pressures

Results are presented from experimental studies of the electrophysical and spectral characteristics of the low-temperature plasma of a radio-frequency capacitive discharge excited between two flowing liquid electrodes at gas pressures of 10³?10⁵ Pa. The plasma composition, the electron density, and the vibrational and rotational temperatures of gas molecules are estimated. The types and shapes of discharge are described, and the thermal and gas-hydrodynamic processes in the discharge zone are analyzed.     

Methane in Water: An Ab Initio Study

Abstract

In preceding publications we discussed some properties of pure water in condensed phases using an ab initio approach. Here this study is used as a basis of comparison for analysing the behaviour of water as a solvent in the presence of an apolar molecule. Our analysis is focused on the process of organization of the hydrogen bonding network around the solute. For this purpose we perform some ab initio calculations for a system of 32 water molecules and one methane molecule at 300 K; in particular, the average molecular dipole moment of water is determined and the result is compared with that of pure water. Next the attention is switched to the methane molecule; related properties such as excluded volume and sphericity of its shape are illustrated and discussed. A comparison with results obtained using classical approaches suggests that some classical models of water can be considered to be still valid when they are used to analyse the water-methane system.     

Ab initio study of phenyl benzoate: structure,conformational analysis,dipole moment,IR and Raman vibrational spectra

The molecular structure (bond distances and angles), conformational properties, dipole moment and vibrational spectroscopic data (vibrational frequencies, IR and Raman intensities) of phenyl benzoate were calculated using Hartree–Fock (HF), density functional (DFT), and second order Møller–Plesset perturbation theory (MP2) with basis sets ranging from 6-31G* to 6-311++G**. The theoretical results are discussed mainly in terms of comparisons with available experimental data. For geometric data, good agreement between theory and experiment is obtained for the MP2, B3LYP and B3PW91 levels with basis sets including diffuse functions. The B3LYP/6-31+G* theory level estimates the shape of the experimental functions for phenyl torsion around the Ph–O and Ph–C bonds well, but reproduces the height of the rotational barriers poorly. The B3LYP/6-31+G* harmonic force constants were scaled by applying the scaled quantum mechanical force field (SQM) technique. The calculated vibrational spectra were interpreted and band assignments were reported. They are in excellent agreement with experimental IR and Raman spectra.Figure Calculated and experimental (GED) potential energy functions for torsional motion of phenyl benzoate relative to the minimum value. a The potential function for torsion about the O₃–C₄ bond. b The potential function for torsion about the C₂–C₁₀ bond.     

Proton Transfer in Liquid Water II; A Semiempirical Method to Describe Chemical Reactions

Abstract

A new semiempirical method is developed to deal with the proton transfer in liquid water. In the previous work, we have shown that two- and three-body charge transfer interactions and electrostatic interactions are the most important factors to describe the potential energy surfaces (PES) of the proton transfer in liquid water [Chemical Physics 180, 239–269, 1994], In order to take account of these factors, we develop a semiempirical method imposing the principle of electronegativity equalization to the Atoms in Molecule (AIM) method. The method is free from the well-known discrepancy of the traditional AIM methods, that is, the fractional molecular charges at large molecular separation, and thus can be applied to the charge transfer reactions. Intra- and intermolecular physical quantities, such as total energies, force vectors, dipole moment vectors and intermolecular charge transfer, obtained by the present method are found to be in good agreement with those by ab initio calculation.     

Rearrangement of the Hydrogen-Bonded Network of the Clathrate Hydrates Encaging Polar Guest

Abstract

Rearrangement process of the hydrogen-bonded network of clathrate hydrate of the polar guest ethylamine is examined by the molecular dynamics simulation. The hydrogen-bonded network rearrangements with reorientation of water or migration of water are observed in the 10 ns trajectories and analyzed in term of a representative connectivity pattern of a time zone longer than a time scale of vibrational motion of molecules. The most frequent rearrangement is the reorientation of single water molecule rotating 180° around its twofold axis in the network unlike Bjerrum's picture of molecular rotation in ice. Migration of water in the host lattice rarely occurs and very long time (several hundred pico second) is required to complete the rearrangement process since cooperative reorientation of many neighboring water is necessarily accompanied. The correlation of reorientational motion of water appears to decay not with the Debye type but rather with a power-law behavior.     

Vibrational spectra of deuterated methane and water molecules in structure I clathrate hydrate from ab initio MD simulation

The deuteration of the lattice molecules in clathrate hydrates is a widely used experimental technique to clearly separate the vibrational modes. However, the effect of the deuteration on the vibrational spectra and molecular motions is not fully understood. Since the guest–host coupling may change the vibrational spectra, a detailed analysis of the vibrational spectra of deuterated clathrate hydrate is significant in the understanding of the mechanism of the vibrational shift. In this study, the vibrational spectra of the deuterated methane hydrates were calculated by ab initio molecular dynamics simulation. The intramolecular vibrational frequency of the methane in D₂O lattice and deuterated methane in H₂O lattice was calculated and compared with the pure methane hydrate. The bending, rocking and overtone of the bending mode was also reported. The effect of coupling of the rattling motions of guest and host molecules on the vibrational spectra was revealed.     

Resolving the kinetics of lipid,protein and peptide diffusion in membranes

Abstract

Recent developments in the understanding of molecular diffusion phenomena in membranes are reviewed. Both model bilayers and biological membranes are considered in respect of lateral diffusion, rotational diffusion and transverse diffusion (flip-flop). For model systems, particular attention is paid to recent data obtained using surface-specific techniques such as sum frequency generation vibrational spectroscopy on supported lipid bilayers, and fluorescence correlation spectroscopy on giant unilamellar vesicles, both of which have yielded new insights into the intrinsic rates of diffusion and the energetic barriers to processes such as lipid flip-flop. Advances in single-molecule and many-molecule fluorescence methodologies have enabled the observation of processes such as anomalous diffusion for some membrane species in biological membranes. These are discussed in terms of new models for the role of membrane interactions with the cytoskeleton, the effects of molecular crowding in membranes, and the formation of lipid rafts. The diffusion of peptides, proteins and lipids is considered, particularly in relation to the means by which antimicrobial peptide activity may be rationalized in terms of membrane poration and lipid flip-flop.     

Leapfrog Rotational Algorithms

Abstract

A new implicit rotational integrator for the orientation of rigid molecules is introduced, and compared with an existing explicit integrator. Both algorithms are categorised as leapfrogs since the quantities saved between time steps are on the on-step orientation and the mid-step angular momentum. Orientations may be expressed in terms of principal axis vectors or, as in the implementations used here, quaternions. Thermostatted versions of the algorithms as well as conventional energy-conserving versions are described. The algorithms are extensively tested in simulations of liquid water, the aim being to study the effect of increased time steps on a range of measured properties. The implicit algorithm is superior to the explicit algorithm, and can be used with time steps up to 3 fs with energy-conserving dynamics. When thermostatted, it may be used with time steps up to at least 6 fs.     

Molecular Dynamics Studies of Electrolyte Solution/Metal Interfaces

Abstract

The results of Molecular Dynamics simulations of pure water near a Pt(100) and a mercury surface as well as an aqueous LiI solution in contact with the Pt(100) surface are reported. The flexible BJH water model is employed in the simulations and the metal-water, ion-water and platinum-ion potentials are derived from molecular orbital calculations. It is shown that the structural and dynamical properties of water and the ions in the adsorbed water layer are significantly different from those in the bulk region.     

Interpretation of DNA vibration modes: I-The guanosine and cytidine residues involved in poly(dG-dC)·poly(dG-dC) and d(CG)3·d(CG)3

Abstract

A normal coordinate analysis has been carried out on guanosine and cytidine residues appearing in oligo and polynucleotides by using a simplified valence force field that allows the vibrational spectra of 5′-dGMP and 2′-deoxycytidine molecules to be reproduced. The role of both C2′-endo and C3′-endo conformations on sugar pucker, as well as that of glycosidic torsion angle (χ), on several characteristic vibration modes of these residues have been studied. The present calculations based on a non-redundant set of internal coordinates preserving the harmonic approximation of the potential field, allows us to explain quite satisfactorily the modifications of the vibrational spectra in the 1550-1250 cm^?1 and 785-500 cm^?1 regions, when the right → left-handed conformational transition occurs.     

Contribution of changes in translational, rotational, and vibrational degrees of freedom to the energy of complex formation of aromatic ligands with DNA

A method for calculation and analysis of the contribution of changes in translational, rotational, and vibrational degrees of freedom to the energy of complex formation of aromatic compounds with DNA duplex has been developed. The results of calculations of the thermodynamic parameters (ΔG, ΔH, ΔS) indicate that changes in the translational and rotational degrees of freedom destabilize, and changes in the vibrational degree of freedom stabilize the complexes, the energy contribution from the movements under consideration being predominantly of entropic character. It is shown that the energy components of changes in translational, rotational, and vibrational degrees of freedom are in the main comparable with the experimentally determined thermodynamic parameters, which requires consideration of these components in the energy analysis of complex formation of aromatic molecules with DNA. It has been found that the total contribution of changes in translational, rotational, and vibrational degrees of freedom to the Gibbs energy of complexing of aromatic molecules with DNA can be assumed to be on the average the same for different ligands and equal to 8.2 kcal/mol.     

Role of chemical short-range order in atomic dynamics decoupling

Abstract

Using molecular dynamics simulation, α-relaxation times τ_α and self-diffusion coefficients D for Al₉₀Fe₁₀, Al₈₀Fe₂₀, Al₇₀Fe₃₀, Al₆₀Fe₄₀ and Al₈₀Ni₂₀ (as a contrast system) melts have been systematically computed over a wide temperature range (1000–2000 K). The computed results reveal that τ_Fe/τ_Al (or D_Al/D_Fe) for the Al₉₀Fe₁₀ and Al₈₀Fe₂₀ melts exhibit an accelerating increase with cooling at temperatures lower than 1400 K, implying a clear decoupling of dynamics of Al and Fe (here referred to as component decoupling). This component decoupling diminishes in Al₇₀Fe₃₀ melt and disappears in Al₆₀Fe₄₀ melt. We simultaneously checked the relaxation decoupling (i.e. the decoupling between α-relaxation and diffusion). The relaxation decoupling is clear in Al₆₀Fe₄₀ melt, less clear in Al₇₀Fe₃₀ melt and not shown in Al₈₀Fe₂₀ and Al₉₀Fe₁₀ melt. It exhibits a tendency counter to that of component decoupling with changing composition, arguing that relaxation decoupling does not necessarily lead to component decoupling. This finding is contradicted against the conventional view that component decoupling is believed as a result of relaxation decoupling. We further attributed such a contradiction to the difference in the degree of chemical short-range order (CSRO) in melts. The existence of CSRO can increase the cooperativity in dynamics of different components. So it is better to consider component decoupling as a combined effect of relaxation decoupling and CSRO. This work would be helpful in improving our understanding of the relationship between the two kinds of decoupling.     

Understanding the thermal properties of amorphous solids using machine-learning-based interatomic potentials

Abstract

Understanding the thermal properties of disordered systems is of fundamental importance for condensed matter physics - and for practical applications as well. While quantities such as the thermal conductivity are usually well characterised experimentally, their microscopic origin is often largely unknown - hence the pressing need for molecular simulations. However, the time and length scales involved with thermal transport phenomena are typically well beyond the reach of ab initio calculations. On the other hand, many amorphous materials are characterised by a complex structure, which prevents the construction of classical interatomic potentials. One way to get past this deadlock is to harness machine-learning (ML) algorithms to build interatomic potentials: these can be nearly as computationally efficient as classical force fields while retaining much of the accuracy of first-principles calculations. Here, we discuss neural network potentials (NNPs) and Gaussian approximation potentials (GAPs), two popular ML frameworks. We review the work that has been devoted to investigate, via NNPs, the thermal properties of phase-change materials, systems widely used in non-volatile memories. In addition, we present recent results on the vibrational properties of amorphous carbon, studied via GAPs. In light of these results, we argue that ML-based potentials are among the best options available to further our understanding of the vibrational and thermal properties of complex amorphous solids.     

VCD Robustness of the Amide‐I and Amide‐II Vibrational Modes of Small Peptide Models

The rotational strengths and the robustness values of amide‐I and amide‐II vibrational modes of For(AA)_nNHMe (where AA is Val, Asn, Asp, or Cys, n = 1–5 for Val and Asn; n = 1 for Asp and Cys) model peptides with α‐helix and β‐sheet backbone conformations were computed by density functional methods. The robustness results verify empirical rules drawn from experiments and from computed rotational strengths linking amide‐I and amide‐II patterns in the vibrational circular dichroism (VCD) spectra of peptides with their backbone structures. For peptides with at least three residues (n ≥ 3) these characteristic patterns from coupled amide vibrational modes have robust signatures. For shorter peptide models many vibrational modes are nonrobust, and the robust modes can be dependent on the residues or on their side chain conformations in addition to backbone conformations. These robust VCD bands, however, provide information for the detailed structural analysis of these smaller systems. Chirality 27:625–634, 2015 © 2015 Wiley Periodicals, Inc.     

Protein Linewidth and Solvent Dynamics in Frozen Solution NMR

Solid-state NMR of proteins in frozen aqueous solution is a potentially powerful technique in structural biology, especially if it is combined with dynamic nuclear polarization signal enhancement strategies. One concern regarding NMR studies of frozen solution protein samples at low temperatures is that they may have poor linewidths, thus preventing high-resolution studies. To learn more about how the solvent shell composition and temperature affects the protein linewidth, we recorded ¹H, ²H, and ¹³C spectra of ubiquitin in frozen water and frozen glycerol-water solutions at different temperatures. We found that the ¹³C protein linewidths generally increase with decreasing temperature. This line broadening was found to be inhomogeneous and independent of proton decoupling. In pure water, we observe an abrupt line broadening with the freezing of the bulk solvent, followed by continuous line broadening at lower temperatures. In frozen glycerol-water, we did not observe an abrupt line broadening and the NMR lines were generally narrower than for pure water at the same temperature. ¹H and ²H measurements characterizing the dynamics of water that is in exchange with the protein showed that the ¹³C line broadening is relatively independent from the arrest of isotropic water motions.     

Effect of the Vibrational/Rotational Energy Partitioning on the Energy Transfer in Atom–Triatomic Molecule Collisions

The effect of the initial partitioning of the molecular energy between vibrational and rotational modes of a triatomic molecule on the collisional energy transfer is studied for a model atom–triatomic molecule system. We considered the collisions of thermal bath Ar atoms with SO2 molecules, and used the trajectory calculations for determining the energy transfer for three different samplings of initial conditions of the molecule. The first sampling method generated the microcanonical distribution over all states, entering into the vibrational and rotational manifolds, while two others produced distributions with relatively lower values of the rotational energies. It is shown that both the average energy transfer per collision and the mechanism of the energy exchange are significantly affected by the vibrational/rotational energy partitioning before the collisions. Relative decrease in the rotational energy results in the decrease of the averaged energy transfer and progressively emphasizes the role of active rotation as the gateway for translation-vibration energy exchange.