scholarly journals Computational Study on Homogeneous Melting of Benzene Phase I

Crystals ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 84 ◽  
Author(s):  
Kenji Mochizuki
Keyword(s):  
Phase I ◽  
Computational Study ◽  
Transient State ◽  
Defect Migration ◽  
Melting Temperatures ◽  
Liquid Phases ◽  
Dependent Potential ◽  
Higher Temperature ◽  
Induction Times ◽  
Dynamics Simulations

Molecular-dynamics simulations are used for examining the microscopic details of the homogeneous melting of benzene phase I. The equilibrium melting temperatures of our model were initially determined using the direct-coexistence method. Homogeneous melting at a higher temperature is achieved by heating a defect- and surfacefree crystal. The temperature-dependent potential energy and lattice parameters do not indicate a premelting phase even under superheated conditions. Further, statistical analyses using induction times computed from 200 melting trajectories were conducted, denoting that the homogeneous melting of benzene occurs stochastically, and that there is no intermediate transient state between the crystal and liquid phases. Additionally, the critical nucleus size is estimated using the seeding approach, along with the local bond order parameter. We found that the large diffusive motion arising from defect migration or neighbor-molecule swapping is of little importance during nucleation. Instead, the orientational disorder activated using the flipping motion of the benzene plane results in the melting nucleus.

Bonded Force Constant Derivation of Lysine-Arginine Cross-linked Advanced Glycation End-Products

2018 ◽  
Author(s):  
Anthony Nash ◽  
Nora H de Leeuw ◽  
Helen L Birch
Keyword(s):  
Molecular Dynamics ◽  
Force Constant ◽  
Computational Study ◽  
Force Constants ◽  
Quantum Mechanical ◽  
Advanced Glycation ◽  
Partial Charges ◽  
Cross Links ◽  
Complete Set ◽  
Dynamics Simulations

<div> <div> <div> <p>The computational study of advanced glycation end-product cross- links remains largely unexplored given the limited availability of bonded force constants and equilibrium values for molecular dynamics force fields. In this article, we present the bonded force constants, atomic partial charges and equilibrium values of the arginine-lysine cross-links DOGDIC, GODIC and MODIC. The Hessian was derived from a series of <i>ab initio</i> quantum mechanical electronic structure calculations and from which a complete set of force constant and equilibrium values were generated using our publicly available software, ForceGen. Short <i>in vacuo</i> molecular dynamics simulations were performed to validate their implementation against quantum mechanical frequency calculations. </p> </div> </div> </div>

Liquid dibromomethane under pressure: a computational study

2021 ◽  
Vol 23 (4) ◽  
pp. 2964-2971
Author(s):  
Bernadeta Jasiok ◽  
Mirosław Chorążewski ◽  
Eugene B. Postnikov ◽  
Claude Millot
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Thermophysical Properties ◽  
Computational Study ◽  
Thermal Expansivity ◽  
Dynamics Simulations ◽  
Isobaric Thermal Expansivity

Thermophysical properties of liquid dibromomethane are investigated by molecular dynamics simulations between 268 and 328 K at pressures up to 3000 bar. Notably, the isotherms of the isobaric thermal expansivity cross around 800 bar.

Melting of Aromatic Compounds: Molecular Dynamics Simulations

1995 ◽  
Vol 408 ◽  
Author(s):  
P. W.-C. Kung ◽  
J. T. Books ◽  
C. M. Freeman ◽  
S. M. Levine ◽  
B. Vessali ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Crystal ◽  
Constant Pressure ◽  
Molecular Crystals ◽  
Melting Transition ◽  
Melting Temperatures ◽  
Molecular Dynamics Calculations ◽  
Dynamics Simulations ◽  
Experimental Melting Point ◽  
Experimental Melting

AbstractWe have used constant pressure molecular dynamics calculations to explore the behavior at various temperatures of two molecular crystals: benzene and a brominated phenyl compound. We observed a melting transition by heating the crystals from a low temperature. In the case of benzene, we performed one heating run of about 1 ns and obtained agreement with the experimental melting point to within some 8%. We have also simulated the melting of a more complex molecular crystal that contains bromine and phenyl groups. We performed four heating runs, with different rates of heating. For total simulation times of about 100, 220, 770, and 1 I50ps, the heating runs predicted melting temperatures that differed from the experimental melting temperature by 53%, 33%, 25%, and 9% respectively.

The Computational Study of Microchannel Thickness Effects on H2O/CuO Nanofluid Flow with Molecular Dynamics Simulations

2021 ◽  
pp. 118240
Author(s):  
Yanpeng Shang ◽  
Reza Balali Dehkordi ◽  
Supat Chupradit ◽  
Davood Toghraie ◽  
Andrei Sevbitov ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Computational Study ◽  
Nanofluid Flow ◽  
Dynamics Simulations

Effect of Tensile Strain on Performance Parameters of Different Structures of MoS2 Monolayer

2021 ◽  
Author(s):  
Priya kaushal ◽  
Tarun Chaudhary ◽  
Gargi Khanna
Keyword(s):  
Tensile Strain ◽  
Computational Study ◽  
Level Structure ◽  
Charge Carriers ◽  
Performance Parameters ◽  
Mos2 Monolayer ◽  
Higher Temperature ◽  
Silicon Doped ◽  
The Impact ◽  
Biaxial Tensile Strain

Abstract The present work is based on the computational study of MoS2 monolayer and effect of tensile strain on its atomic level structure. The bandgap for MoS2 monolayer, defected MoS2 monolayer and Silicon-doped monolayer are 1.82 eV (direct bandgap), 0.04 (indirect bandgap) and 1.25eV (indirect bandgap), respectively. The impact of tensile strain (0-0.7%) on the bandgap and effective mass of charge carriers of these three MoS2 structure has been investigated. The bandgap decrease of 5.76%, 31.86% and 6.03% has been observed in the three structures for biaxial strain while the impact of uniaxial strain is quite low. The impact of higher temperature on the bandgap under biaxial tensile strain has been also analyzed in this paper. These observations are extremely important for 2D material-based research for electronic applications.

scholarly journals The Intramolecular Pressure and the Extension of the Critical Point’s Influence Zone on the Order Parameter

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Jose Luis Rivera ◽  
Homero Nicanor-Guzman ◽  
Roberto Guerra-Gonzalez
Keyword(s):  
Transition Temperature ◽  
Critical Temperature ◽  
Liquid Phase ◽  
Order Parameter ◽  
Bulk Liquid ◽  
Influence Zone ◽  
Molecular Potential ◽  
Liquid Phases ◽  
Dynamics Simulations ◽  
Wide Zone

The critical point affects the coexistence behavior of the vapor-liquid equilibrium densities. The length of the critical influence zone is under debate because for some properties, like shear viscosity, the extension is only a few degrees, while for others, such as the density order parameter, the critical influence zone covers up to hundreds of degrees below the critical temperature. Here we show that, for ethane, the experimental critical influence zone covers a wide zone of tens of degrees (below the critical temperature) down to a transition temperature, at which the apparent critical influence zone vanishes, and the transition temperature can be predicted through a pressure analysis of the coexisting bulk liquid phase, using a simple molecular potential. The liquid phases within the apparent critical influence zone show low densities, making them behave internally like their corresponding vapor phases. Therefore, Molecular Dynamics simulations reveal that the experimentally observed wide extension of the critical influence zone is the result of a vapor-like effect due to low bulk liquid phase densities.

scholarly journals Molecular Insights into Cage Occupancy of Hydrogen Hydrate: A Computational Study

Processes ◽  
2019 ◽  
Vol 7 (10) ◽  
pp. 699 ◽  
Author(s):  
Ma ◽  
Zhong ◽  
Liu ◽  
Zhong ◽  
Yan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Storage ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Storage Capacity ◽  
Computational Study ◽  
Density Functional Theory Calculations ◽  
Hydrogen Storage Capacity ◽  
Large Cage ◽  
Dynamics Simulations

Density functional theory calculations and molecular dynamics simulations were performed to investigate the hydrogen storage capacity in the sII hydrate. Calculation results show that the optimum hydrogen storage capacity is ~5.6 wt%, with the double occupancy in the small cage and quintuple occupancy in the large cage. Molecular dynamics simulations indicate that these multiple occupied hydrogen hydrates can occur at mild conditions, and their stability will be further enhanced by increasing the pressure or decreasing the temperature. Our work highlights that the hydrate is a promising material for storing hydrogen.

scholarly journals Prediction of Second Melting Temperatures Already Observed in Pure Elements by Molecular Dynamics Simulations

Materials ◽  
2021 ◽  
Vol 14 (21) ◽  
pp. 6509
Author(s):  
Robert F. Tournier ◽  
Michael I. Ojovan
Keyword(s):  
Glass Transition ◽  
Heating Rate ◽  
Homogeneous Nucleation ◽  
Glassy State ◽  
Singular Values ◽  
Md Simulations ◽  
Melting Temperatures ◽  
Heating And Cooling ◽  
Dynamics Simulations ◽  
Universal Law

A second melting temperature occurs at a temperature Tn+ higher than Tm in glass-forming melts after heating them from their glassy state. The melting entropy is reduced or increased depending on the thermal history and on the presence of antibonds or bonds up to Tn+. Recent MD simulations show full melting at Tn+ = 1.119Tm for Zr, 1.126Tm for Ag, 1.219Tm for Fe and 1.354Tm for Cu. The non-classical homogeneous nucleation model applied to liquid elements is based on the increase of the Lindemann coefficient with the heating rate. The glass transition at Tg and the nucleation temperatures TnG of glacial phases are successfully predicted below and above Tm. The glass transition temperature Tg increases with the heating rate up to Tn+. Melting and crystallization of glacial phases occur with entropy and enthalpy reductions. A universal law relating Tn+ and TnG around Tm shows that TnG cannot be higher than 1.293Tm for Tn+= 1.47Tm. The enthalpies and entropies of glacial phases have singular values, corresponding to the increase of percolation thresholds with Tg and TnG above the Scher and Zallen invariant at various heating and cooling rates. The G-phases are metastable up to Tn+ because the antibonds are broken by homogeneous nucleation of bonds.

scholarly journals Influence of Br − /S 2− site-exchange on Li diffusion mechanism in Li 6 PS 5 Br: a computational study

2021 ◽  
Vol 379 (2211) ◽  
Author(s):  
Marcel Sadowski ◽  
Karsten Albe
Keyword(s):  
Rotation Axis ◽  
Computational Study ◽  
Diffusion Mechanism ◽  
Range Transport ◽  
Site Exchange ◽  
Dynamics Simulations ◽  
Low Degrees ◽  
Fast Ion ◽  
Free Material ◽  
Superionic Conduction

We investigate how low degrees of Br − / S 2 − site-exchange influence the Li + diffusion in the argyrodite-type solid electrolyte Li 6 PS 5 Br by ab initio molecular dynamics simulations. Based on the atomic trajectories of the defect-free material, a new mechanism for the internal Li + reorganization within the Li + cages around the 4 d sites is identified. This reorganization mechanism is highly concerted and cannot be described by just one rotation axis. Simulations with Br − / S 2 − defects reveal that Li + interstitials ( L ii . ) are the dominant mobile charge carriers and originate from Frenkel pairs. These are formed because B rS . defects on the 4 d sites donate one or even two L ii . to the neighbouring cages. The L ii . then carry out intercage jumps via interstitial and interstitialcy mechanisms. With that, one single B rS . defect enables Li + diffusion over an extended spatial area explaining why low degrees of site-exchange are sufficient to trigger superionic conduction. The vacant sites of the Frenkel pairs, namely V Li   ′ , are mostly immobile and bound to the B rS . defect. Because S Br ′ defects on 4 a sites act as sinks for L ii . they seem to be beneficial only for the local Li + transport. In their vicinity T4 tetrahedral sites start to get occupied. Because the Li + transport was found to be rather confined if S Br ′ and B rS . defects are direct neighbours, their relative arrangement seems to be crucial for effective long-range transport. This article is part of the Theo Murphy meeting issue ‘Understanding fast-ion conduction in solid electrolytes’.

scholarly journals Computational investigation on the role of C-Terminal of human albumin on the dimerization of Aβ1-42 peptide

2020 ◽  
Vol 10 (1) ◽  
pp. 4944-4955 ◽  
Keyword(s):  
Computational Study ◽  
Binding Free Energy ◽  
Conformational Dynamics ◽  
Human Albumin ◽  
Potential Of Mean Force ◽  
Amber Force Field ◽  
Aβ Aggregation ◽  
The Difference ◽  
Dynamics Simulations

Alzheimer’s disease (AD) is characterized by the presence of Amyloid-beta (Aβ) peptide, which has the propensity to fold into β-sheets under stress forming aggregated amyloid plaques. Nowadays many studies have focused on the development of novel, specific therapeutic strategies to slow down Aβ aggregation or control preformed aggregates. Albumin, the most abundant protein in the cerebrospinal fluid, was reported to bind Aβ impeding its aggregation. Recently, it has been reported that C-terminal (CTerm) of Human Albumin binds with Aβ1-42, impairs Aβ aggregation and promotes disassembly of Aβ aggregates protecting neurons. In this computational study, we have investigated the effect of CTerm on the conformational dynamics and the aggregation propensity of Aβ1-42 peptide. We have performed molecular dynamics simulations on the Aβ1-42-Aβ1-42 homodimer and Aβ1-42-CTerm of albumin heterodimer using the AMBER force field ff99SBildn. From the Potential of mean force (PMF) study and Binding free energy (BFE) analysis, we observed the association of Aβ1-42 peptide monomer with itself in the form of homodimer to be stronger than its association with the CTerm in the heterodimer complex. The difference in the number of residues in the Aβ1-42 peptide monomer (42 AAs) and CTerm (35 AAs) may be probable reason for the difference in association between the monomeric units in corresponding homodimer and heterodimer complexes. But even then CTerm shows a significant effect on the dimerization of Aβ1-42 peptide. Our findings therefore suggest that CTerm can be used for the disassembly of Aβ1-42 peptide monomer.

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