Pressure dependence of the liquid structure and the Raman noncoincidence effect of liquid methanol revisited

2004 ◽  
Vol 76 (1) ◽  
pp. 247-254 ◽  
Author(s):  
H. Torii
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Pressure Dependence ◽  
Md Simulations ◽  
Liquid Structure ◽  
Present Calculation ◽  
Number Density ◽  
Transition Dipole ◽  
Liquid Systems

Pressure dependence of the liquid structure and the Raman noncoincidence effect of liquid methanol is examined with the combination of molecular dynamics (MD) simulations and the intermolecular resonant vibrational interactions determined by the transition dipole coupling (TDC) mechanism (MD/TDC method). It is shown that the observed decrease of the Raman noncoincidence νNCE of the CO stretching band with increasing density reported in the literature is quantitatively reproduced by the present calculation. As the density increases, the hydrogen bonds get slightly shorter, but molecules belonging to different hydrogen-bond chains get closer to each other to a greater extent. This anisotropic change in the liquid structure is the reason for the behavior of νNCE. It is also shown that the concentration dependence of νNCE in the methanol/CCl4 binary mixtures reported in a previous study, and the pressure dependence of νNCE in methanol may be described in a consistent way as a function of the number density of methanol in the liquid systems.

scholarly journals Car–Parrinello and path integral molecular dynamics study of the intramolecular hydrogen bonds in the crystals of benzoylacetone and dideuterobenzoylacetone

2014 ◽  
Vol 16 (42) ◽  
pp. 23026-23037 ◽  
Author(s):  
Piotr Durlak ◽  
Zdzisław Latajka
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Path Integral ◽  
Molecular Crystal ◽  
Short Hydrogen Bond ◽  
Deuterated Analogue ◽  
Dynamics Simulations ◽  
Intramolecular Hydrogen

The dynamics of the intramolecular short hydrogen bond in the molecular crystal of benzoylacetone and its deuterated analogue are investigated using ab initio molecular dynamics simulations.

Influence of a Combined Low Dosage Gas Hydrate Inhibitor on Methane Hydrate Surface

2014 ◽  
Vol 1008-1009 ◽  
pp. 300-306
Author(s):  
Cui Ping Tang ◽  
Dong Liang Li ◽  
De Qing Liang
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Gas Hydrate ◽  
Methane Hydrate ◽  
Md Simulation ◽  
Side Group ◽  
Large Space ◽  
Surface Molecules ◽  
Low Dosage

According to analysis of the gas hydrate cage and structure of the inhibitor and simulation of molecular dynamics, the interaction between GHI1 and hydrates was discussed. The structure analysis indicated the side group of PVP can insert into the open hydrate cage, and force the hydrate growing along the polymer chain, which results in a large space resistance and inhibits gas hydrate agglomerating. The results of MD simulation show GHI1 can damage the surface cage in hydrate lattice; the hydrogen and oxygen in GHI1 can form hydrogen bonds respectively with oxygen and hydrogen in hydrates, which makes the surface molecules of the cages unstable and distorts the cages; Synergist diethylene glycol ether increases strength and range of length of hydrogen bond.

scholarly journals The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

2013 ◽  
Vol 9 ◽  
pp. 118-134 ◽  
Author(s):  
Jutta Erika Helga Köhler ◽  
Nicole Grczelschak-Mick
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Hydrogen Bonds ◽  
Md Simulations ◽  
Benzene Molecule ◽  
Glucose Unit ◽  
Hand Orientation ◽  
Different Temperatures ◽  
Dynamics Simulations ◽  
The Right

Four highly ordered hydrogen-bonded models of β-cyclodextrin (β-CD) and its inclusion complex with benzene were investigated by three different theoretical methods: classical quantum mechanics (QM) on AM1 and on the BP/TZVP-DISP3 level of approximation, and thirdly by classical molecular dynamics simulations (MD) at different temperatures (120 K and 273 to 300 K). The hydrogen bonds at the larger O2/O3 rim of empty β-CDs prefer the right-hand orientation, e.g., O3-H…O2-H in the same glucose unit and bifurcated towards …O4 and O3 of the next glucose unit on the right side. On AM1 level the complex energy was −2.75 kcal mol−1 when the benzene molecule was located parallel inside the β-CD cavity and −2.46 kcal mol−1 when it was positioned vertically. The AM1 HOMO/LUMO gap of the empty β-CD with about 12 eV is lowered to about 10 eV in the complex, in agreement with data from the literature. AM1 IR spectra displayed a splitting of the O–H frequencies of cyclodextrin upon complex formation. At the BP/TZVP-DISP3 level the parallel and vertical positions from the starting structures converged to a structure where benzene assumes a more oblique position (−20.16 kcal mol−1 and −20.22 kcal mol−1, resp.) as was reported in the literature. The character of the COSMO-RS σ-surface of β-CD was much more hydrophobic on its O6 rim than on its O2/O3 side when all hydrogen bonds were arranged in a concerted mode. This static QM picture of the β-CD/benzene complex at 0 K was extended by MD simulations. At 120 K benzene was mobile but always stayed inside the cavity of β-CD. The trajectories at 273, 280, 290 and 300 K certainly no longer displayed the highly ordered hydrogen bonds of β-CD and benzene occupied many different positions inside the cavity, before it left the β-CD finally at its O2/O3 side.

SIMULATION OF ENERGETIC CLUSTER IMPACTS ON METALLIC TARGETS

1991 ◽  
Vol 05 (05) ◽  
pp. 341-349 ◽  
Author(s):  
M.H. SHAPIRO ◽  
T.A. TOMBRELLO
Keyword(s):  
Molecular Dynamics ◽  
Recent Progress ◽  
Md Simulations ◽  
Cluster Ions ◽  
Confinement Time ◽  
Number Density ◽  
Metallic Surfaces ◽  
Energy Distributions ◽  
Highly Nonlinear

We review recent progress in the use of molecular dynamics (MD) simulations to study the energetic collisions of cluster ions with metallic surfaces. MD simulations have been used to predict the energy, number-density, and confinement-time properties of the highly nonlinear collision cascades initiated by cluster impacts; as well as to predict the yields, energy-distributions, and angle-distributions of ejected cluster-atoms and target-atoms.

Molecular dynamics simulations of N-methylacetamide (NMA) in water by the ABEEM/MM model

2009 ◽  
Vol 87 (12) ◽  
pp. 1738-1746 ◽  
Author(s):  
Ping Qian ◽  
Li-Nan Lu ◽  
Zhong-Zhi Yang
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Potential Model ◽  
Lone Pair ◽  
Static Properties ◽  
Range Interaction ◽  
Hydrogen Bond Interaction ◽  
Lone Pair Electron ◽  
Dynamics Simulations

The N-methylacetamide (NMA) is a very interesting kind of compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of peptides in aqueous solutions. We have carried out molecular dynamics (MD) simulations of a NMA molecule in water under 1 atm and 298 K. The simulations make use of the newly developed NMA–water fluctuating charge ABEEM/MM potential model ( Yang, Z. Z.; Qian, P. J. Chem. Phys. 2006, 125, 064311 ), which is based on the combination of the atom-bond electronegativity equalization method (ABEEM) and molecular mechanics (MM). This model has been successfully applied to NMA–water gas clusters, NMA(H2O)n (n = 1–6), and accurately reproduced many static properties. For the NMA–water ABEEM/MM potential model, two characters must be emphasized in the simulations. Firstly, the model allows the charges in system to fluctuate, responding to the ambient environment. Secondly, for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters klpO=,H and klpO–,HN–, respectively, which explicitly describe the short-range interaction of hydrogen bonds in the hydrogen bond interaction region. All sorts of properties have been studied in detail, such as, radial distribution function, energy distribution, ABEEM charge distribution and dipole moment, and so on. These simulation results show that the ABEEM/MM-based NMA–water potential model appears to be robust, giving the solution properties in excellent agreement with other dynamics simulations on similar systems.

scholarly journals Analyzing In Silico the Relationship Between the Activation of the Edema Factor and Its Interaction With Calmodulin

2020 ◽  
Vol 7 ◽  
Author(s):  
Irène Pitard ◽  
Damien Monet ◽  
Pierre L. Goossens ◽  
Arnaud Blondel ◽  
Thérèse E. Malliavin
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Md Simulations ◽  
Catalytic Site ◽  
Stacking Interactions ◽  
Long Distance ◽  
Edema Factor ◽  
Allosteric Communication ◽  
Network Of Hydrogen Bonds ◽  
The Relationship

Molecular dynamics (MD) simulations have been recorded on the complex between the edema factor (EF) of Bacilllus anthracis and calmodulin (CaM), starting from a structure with the orthosteric inhibitor adefovir bound in the EF catalytic site. The starting structure has been destabilized by alternately suppressing different co-factors, such as adefovir ligand or ions, revealing several long-distance correlations between the conformation of CaM, the geometry of the CaM/EF interface, the enzymatic site and the overall organization of the complex. An allosteric communication between CaM/EF interface and the EF catalytic site, highlighted by these correlations, was confirmed by several bioinformatics approaches from the literature. A network of hydrogen bonds and stacking interactions extending from the helix V of of CaM, and the residues of the switches A, B and C, and connecting to catalytic site residues, is a plausible candidate for the mediation of allosteric communication. The greatest variability in volume between the different MD conditions was also found for cavities present at the EF/CaM interface and in the EF catalytic site. The similarity between the predictions from literature and the volume variability might introduce the volume variability as new descriptor of allostery.

scholarly journals Molecular Dynamics Simulation of VEGFR2 with Sorafenib and Other Urea-Substituted Aryloxy Compounds

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Fancui Meng
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Md Simulation ◽  
Binding Mode ◽  
Dynamics Simulation ◽  
Dynamics Simulations ◽  
Simulation Time ◽  
Dynamics Method

The binding mode of sorafenib with VEGFR2 was studied using molecular docking and molecular dynamics method. The docking results show that sorafenib forms hydrogen bonds with Asp1046, Cys919, and Glu885 of VEGFR2 receptor. Molecular dynamics simulation suggests that the hydrogen bond involving Asp1046 is the most stable one, and it is almost preserved during all the MD simulation time. The hydrogen bond formed with Cys919 occurs frequently after 6 ns, while the bifurcated hydrogen bonds involving Glu885 occurs occasionally. Meantime, molecular dynamics simulations of VEGFR2 with 11 other urea-substituted aryloxy compounds have also been performed, and the results indicate that a potent VEGFR2 inhibitor should have lower interaction energy with VEGFR2 and create at least 2 hydrogen bonds with VEGFR2.

scholarly journals Dissolving Cellulose in 1,2,3-Triazolium- and Imidazolium-Based Ionic Liquids with Aromatic Anions

Molecules ◽  
2020 ◽  
Vol 25 (15) ◽  
pp. 3539 ◽  
Author(s):  
Martin Brehm ◽  
Julian Radicke ◽  
Martin Pulst ◽  
Farzaneh Shaabani ◽  
Daniel Sebastiani ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Ionic Liquids ◽  
Hydrogen Bonds ◽  
Md Simulations ◽  
Heterocyclic Carbenes ◽  
Quantitative Prediction ◽  
Lower Amount ◽  
New Class ◽  
Aromatic Anions ◽  
Lower Basicity

We present 1,2,3-triazolium- and imidazolium-based ionic liquids (ILs) with aromatic anions as a new class of cellulose solvents. The two anions in our study, benzoate and salicylate, possess a lower basicity when compared to acetate and therefore should lead to a lower amount of N-heterocyclic carbenes (NHCs) in the ILs. We characterize their physicochemical properties and find that all of them are liquids at room temperature. By applying force field molecular dynamics (MD) simulations, we investigate the structure and dynamics of the liquids and find strong and long-lived hydrogen bonds, as well as significant π–π stacking between the aromatic anion and cation. Our ILs dissolve up to 8.5 wt.-% cellulose. Via NMR spectroscopy of the solution, we rule out chain degradation or derivatization, even after several weeks at elevated temperature. Based on our MD simulations, we estimate the enthalpy of solvation and derive a simple model for semi-quantitative prediction of cellulose solubility in ILs. With the help of Sankey diagrams, we illustrate the hydrogen bond network topology of the solutions, which is characterized by competing hydrogen bond donors and acceptors. The hydrogen bonds between cellulose and the anions possess average lifetimes in the nanosecond range, which is longer than found in common pure ILs.

Molecular Dynamics Simulations of Ionic Liquids: Influence of Polarization on IL Structure and Ion Transport

2008 ◽  
Vol 1082 ◽  
Author(s):  
Oleg Borodin
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Ionic Liquids ◽  
Condensed Phase ◽  
Wide Class ◽  
Md Simulations ◽  
Liquid Structure ◽  
Many Body ◽  
Polarizable Force Field ◽  
Dynamics Simulations

ABSTRACTMany-body polarizable force field has been developed and validated for a wide class of ionic liquids. Classical molecular dynamics (MD) simulations have been performed on 29 ionic liquids. This presentation will focus on ability of developed force fields to predict condensed phase properties and on understanding the influence of many-body polarizable interactions on the ionic liquid structure and transport.

Sub-THz specific relaxation times of hydrogen bond oscillations in E.coli thioredoxin. Molecular dynamics and statistical analysis

2014 ◽  
Vol 171 ◽  
pp. 179-193 ◽  
Author(s):  
Tatiana Globus ◽  
Igor Sizov ◽  
Boris Gelmont
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Relaxation Time ◽  
Hydrogen Bonds ◽  
Spectral Resolution ◽  
Relaxation Times ◽  
Low Frequency ◽  
Thz Spectroscopy ◽  
Vibrational Modes ◽  
Covalent Bonds

Hydrogen bonds (H-bonds) in biological macromolecules are important for the molecular structure and functions. Since interactions via hydrogen bonds are weaker than covalent bonds, it can be expected that atomic movements involving H-bonds have low frequency vibrational modes. Sub-Terahertz (sub-THz) vibrational spectroscopy that combines measurements with molecular dynamics (MD) computational prediction has been demonstrated as a promising approach for biological molecule characterization. Multiple resonance absorption lines have been reported. The knowledge of relaxation times of atomic oscillations is critical for the successful application of THz spectroscopy for hydrogen bond characterization. The purpose of this work is to use atomic oscillations in the 0.35–0.7 THz range, found from molecular dynamic (MD) simulations of E.coli thioredoxin (2TRX), to study relaxation dynamics of two intra-molecular H-bonds, O⋯H–N and O⋯H–C. Two different complimentary techniques are used in this study, one is the analysis of the statistical distribution of relaxation time and dissipation factor values relevant to low frequency oscillations, and the second is the analysis of the autocorrelation function of low frequency quasi-periodic movements. By studying hydrogen bond atomic displacements, it was found that the atoms are involved in a number of collective oscillations, which are characterized by different relaxation time scales ranging from 2–3 ps to more than 150 ps. The existence of long lasting relaxation processes opens the possibility to directly observe and study H-bond vibrational modes in sub-THz absorption spectra of bio-molecules if measured with an appropriate spectral resolution. The results of measurements using a recently developed frequency domain spectroscopic sensor with a spectral resolution of 1 GHz confirm the MD analysis.

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