GenIce is an efficient and user‐friendly tool to generate hydrogen‐disordered ice structures. It makes clathrate hydrate structures in various file formats. More than 100 kinds of are preset. Users can install their own crystal structures, guest molecules, formats as plugins. The algorithm certifies that the generated completely randomized networks obeying rule with zero net polarization. © 2017 Authors. Journal Computational Chemistry Published by Wiley Periodicals, Inc.

The adsorption of guest and kinetic inhibitor molecules on the surface methane hydrate is investigated by using molecular dynamics simulations. We calculate free energy profile for transferring a solute molecule from bulk water to various molecules. Spherical solutes with diameter ∼0.5 nm are significantly stabilized at surface, whereas smaller larger exhibit lower affinity than intermediate size. range attractive force subnanoscale, implying that this has no effect macroscopic mass transfer...

We investigate the dissociation of methane hydrate in liquid water using molecular dynamics simulations. As proceeds, molecules are released into aqueous phase and eventually they form bubbles. It is shown that this bubble formation, which causes change concentration phase, significantly affects kinetics hydrate. A large system size employed study makes it possible to analyze effects formation bubbles on detail. found rate decreases with time until then turns increase. also demonstrated can...

We report a molecular dynamics simulation demonstrating fast spontaneous liquid-liquid phase separation of water and subsequent slow crystallization to ice. It is found that supercooled separates rapidly into low- high-density domains so as reduce the surface energy in rectangular cell at certain thermodynamic states. The separation, which about two orders magnitude faster than crystallization, suggests possibility observe this phenomenon experimentally.

Bubble formation and the hydration free energy of methane play important roles in hydrate dissociation. The effects methanol NaCl on them are investigated using molecular dynamics simulations.

We investigate the mechanism of a typical kinetic hydrate inhibitor (KHI), polyvinylcaprolactam (PVCap), which has been applied to prevent plugs from forming in gas pipe lines, using molecular dynamics simulations crystal growth ethylene oxide hydrate. Water-soluble is chosen as guest species avoid problems associated with presence phase simulation cell such slow growth. A PVCap dodecamer adsorbs irreversibly on surface grows at supercooling 3 K when hydrophobic part two pendent groups are...

Molecular dynamics simulations of the dissociation methane hydrate in aqueous NaCl solutions are performed. It is shown that accelerated by formation bubbles both and pure water. We find two significant effects on kinetics NaCl. One slowing down an early stage before bubble formation, another swift enhances dissociation. These arise from low solubility solution, which gives rise to a nonuniform spatial distribution solvated phase. also demonstrate form near interface dense proceeds...

Most classical nonpolarizable ion potential models underestimate the solubility values of NaCl and KCl in water significantly. We determine Lennard-Jones parameters Na+, K+, Cl– that reproduce as well hydration free energy dilute aqueous solutions for three models, SPC/E, TIP3P, TIP4P/2005. The ion–oxygen distance solution cation–anion salt are also considered parametrization. In addition to target properties, enthalpy, entropy, self-diffusion coefficient, coordination number, lattice...

Tetrahydrofuran (THF) clathrate hydrate has been frequently used in experimental studies instead of gas hydrates because it forms at a temperature higher than the ice point under ambient pressure. In this paper, we compare crystal growth rates THF and using molecular dynamics simulations. It is demonstrated that much slower ice. The significantly deviate from standard kinetic model known as Wilson–Frenkel model, whereas reproduces dependence rate slow deviation are attributed to trapping...

We propose a model for slowing down of clathrate hydrate formation caused by kinetic inhibitors (KHIs) on the basis Gibbs–Thomson effect. The residence time inhibitor molecules bound to surface and intrinsic growth rate without KHIs are key ingredients model. binding free energies monomer, dimer, tetramer, octamer KHI, polyvinylcaprolactam (PVCap), calculated using molecular dynamics simulations estimate times, which far beyond feasible simulation time. Our accounts inhibition mechanism...

Clathrate hydrates of water-soluble guest molecules, such as ethylene oxide (EO) and tetrahydrofuran (THF), have been often investigated in experimental studies instead gas because their dissociation temperatures are higher than the ice point under ambient pressure. We examine formation mechanism EO THF using molecular dynamics simulations. The crystal growth rates determined by simulations hydrate/solution two-phase coexistence. It is found that rate hydrate an order magnitude hydrate....

Ice is different from ordinary crystals because it contains randomness, which means that statistical treatment based on ensemble averaging essential. structures are constrained by topological rules known as the ice rules, give them unique anomalous properties. These properties become more apparent when system size large. For this reason, there a need to produce large number of sufficiently homogeneously random and satisfy rules. We have developed an algorithm quickly generate containing ions...

Physical and chemical properties of liquid water are dominated by hydrogen bond structure dynamics. Recent studies on nonlinear vibrational spectroscopy intramolecular motion provided new insight into ultrafast However, our understanding intermolecular dynamics is still limited. We theoretically investigated the in terms two-dimensional infrared (2D IR) spectroscopy. The 2D IR spectrum frequency region (<1000 cm(-1)) calculated using equilibrium nonequilibrium hybrid molecular method. find...

Water is the most extensively studied of liquids because both its ubiquity and anomalous thermodynamic dynamic properties. The properties water are dominated by hydrogen bonds bond network rearrangements. Fundamental information on dynamics liquid has been provided linear infrared (IR), Raman, neutron-scattering experiments; molecular simulations have also insights. Recently developed higher-order nonlinear spectroscopies open new windows into study water. For example, vibrational lifetimes...

Many efforts have been devoted to elucidating the intra- and intermolecular dynamics of liquid water because their important roles in many fields science engineering. Nonlinear spectroscopy is a powerful tool investigate dynamics. Because nonlinear response functions are described by more than one time variable, it possible analyze static dynamic mode couplings. Here we review revealed recent linear spectroscopic experiments computer simulations. In particular, discuss population relaxation,...

More than 300 kinds of porous ice structures derived from zeolite frameworks and space fullerenes are examined using classical molecular dynamics simulations. It is found that a hypothetical zeolitic phase less dense more stable the sparse reported by Huang et al. [Chem. Phys. Lett. 671, 186 (2017)]. In association with structure, even structures, "aeroices," proposed. aeroices most solid phases water near absolute zero temperature under negative pressure.

We investigate high-pressure ice phases using molecular dynamics simulations. Spontaneous nucleation of a new crystalline solid, named T2, is observed in simulation TIP4P/2005 water at 260 K and 3.3 GPa. The phase diagram ices VI, VII, recently reported two other hypothetical ices, R T, determined the direct coexistence method Clausius-Clapeyron equation for TIP4P/2005, SPC/E, TIP5P water. It found that there exists least one pressure region which most stable ambient temperature with those...

We propose an efficient algorithm for generating hydrogen-disordered ice networks utilizing graph theory and the topological characteristic of network. The computational efficiency with new is much higher than conventional ones developed by Rahman Stillinger Buch et al. difference in time between our either two increases increasing system size.

We perform all-atom molecular dynamics simulations of the adsorption amino acid side-chain analogues on polymer brushes. The examined are nonpolar isobutane, polar propionamide, negatively charged propionate ion, and positively butylammonium ion. brushes consist a sheet graphene strongly hydrophilic poly(carboxybetaine methacrylate) (PCBMA) or weakly poly(2-hydroxyethyl (PHEMA). effective interactions between isobutane chains repulsive for PCBMA attractive PHEMA. Gibbs energy decomposition...

p H , with its well-known value of 7 at ambient condition, is a most basic property water, wide implications in chemistry and biology. The pH determined by the tendency autoionization water molecules into ion pairs, H+ OH−, expected to vary extensively which determines stability pairs. When temperature rises from normal supercritical region, experimentally exhibits complex, nonmonotonic dependence, that is, it first decreases then increases rapidly. Accurate theoretical evaluation...

We report a new ice phase that forms spontaneously at the interface between VII and liquid water in molecular dynamics simulations of TIP4P/2005 water. The is structurally quite similar to an originally found be precursor course homogeneous nucleation A part molecules these phases can rotate easily because number hydrogen bonds them less than four, thus they regarded as partial plastic phases. rough estimate suggests are thermodynamically more stable either VI or for 3 GPa < P 18 T = 300 K....

We theoretically investigate intermolecular motions in liquid water terms of third-order infrared (IR) spectroscopy. calculate two-dimensional (2D) IR spectra, pump-probe signals, and three-pulse stimulated photon echo signals from the combination equilibrium nonequilibrium molecular dynamics simulations. The 2D spectra peak shift exhibit that frequency correlation librational motion decays with a time scale 100 fs. two-color reveal energy transfer at 700 cm(-1) to low below 300 occurs 60 fs...

We present a novel method to investigate energy relaxation processes in condensed phases using nonequilibrium molecular dynamics simulations. This can reveal details of the time evolution like two-color third-order IR spectroscopy. Nonetheless, computational cost this is significantly lower than that response functions. apply intermolecular motions liquid water. show water characterized by four transfer processes. The structural changes associated with are also analyzed technique.

The χ(2) (second-order nonlinear optical susceptibility) spectrum of the water surface has been a matter debate for few decades. Here, we report that experimentally measured isotopic dilution dependence and theoretically reproduced it by employing quantum/classical mixed approach with new idea to subtract an artifact. present theoretical framework allows clarifying effects intramolecular, intermolecular, Fermi resonance couplings on OH-stretch vibrational spectra at as well in bulk.

We studied the concentration dependence of ν(C−H)'s in IR and 1J(C,H) NMR for binary water−tetrahydrofuran (THF) mixtures found different trends two types CH2 groups five-membered ring. The changes ν(C−O) spectra showed that complexes THF associated with water are formed, which number molecules increases concentration. suggested hydration proceeds through formation 1:1, 1:2 [THF:water] up to XH2O ≈ 0.9, where is mole fraction mixtures. carried out ab initio MO DFT calculations optimize...