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

<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>

Bonded Force Constant Derivation of Advanced Glycation End-Products: DOGDIC, GODIC, and MODIC

10.26434/chemrxiv.5891602.v1 ◽

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 ◽

<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

Physical Chemistry Chemical Physics ◽

10.1039/d0cp06458k ◽

2021 ◽

Vol 23 (4) ◽

pp. 2964-2971

Author(s):

Bernadeta Jasiok ◽

Mirosław Chorążewski ◽

Eugene B. Postnikov ◽

Claude Millot

Keyword(s):

Molecular Dynamics ◽

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.

New Insights into the Jahn-Teller Effect through ab initio Quantum-Mechanical/Molecular-Mechanical Molecular Dynamics Simulations of CuII in Water

ChemPhysChem ◽

10.1002/cphc.200300659 ◽

2003 ◽

Vol 4 (9) ◽

pp. 931-943 ◽

Cited By ~ 56

Author(s):

Christian F. Schwenk ◽

Bernd M. Rode

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Teller Effect ◽

Quantum Mechanical ◽

Jahn Teller ◽

Jahn Teller Effect ◽

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

Journal of Molecular Liquids ◽

10.1016/j.molliq.2021.118240 ◽

2021 ◽

pp. 118240

Author(s):

Yanpeng Shang ◽

Reza Balali Dehkordi ◽

Supat Chupradit ◽

Davood Toghraie ◽

Andrei Sevbitov ◽

...

Keyword(s):

Molecular Dynamics ◽

Computational Study ◽

Nanofluid Flow ◽

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

Processes ◽

10.3390/pr7100699 ◽

2019 ◽

Vol 7 (10) ◽

pp. 699 ◽

Cited By ~ 2

Author(s):

Ma ◽

Zhong ◽

Liu ◽

Zhong ◽

Yan ◽

...

Keyword(s):

Molecular Dynamics ◽

Hydrogen Storage ◽

Density Functional ◽

Storage Capacity ◽

Computational Study ◽

Density Functional Theory Calculations ◽

Hydrogen Storage Capacity ◽

Large Cage ◽

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.

Characterization of a Catalytic Ligand Bridging Metal Ions in Phosphodiesterases 4 and 5 by Molecular Dynamics Simulations and Hybrid Quantum Mechanical/Molecular Mechanical Calculations

Biophysical Journal ◽

10.1529/biophysj.106.086835 ◽

2006 ◽

Vol 91 (5) ◽

pp. 1858-1867 ◽

Cited By ~ 32

Author(s):

Ying Xiong ◽

Hai-Ting Lu ◽

Yongjian Li ◽

Guang-Fu Yang ◽

Chang-Guo Zhan

Keyword(s):

Molecular Dynamics ◽

Metal Ions ◽

Quantum Mechanical ◽

Can’t we negotiate the importance of electron correlation? HF vs RIMP2 in ab initio quantum mechanical charge field molecular dynamics simulations of Cu+ in pure liquid ammonia

Journal of Molecular Liquids ◽

10.1016/j.molliq.2021.118286 ◽

2021 ◽

pp. 118286

Author(s):

Wahyu Dita Saputri ◽

Harno Dwi Pranowo ◽

Thomas S. Hofer

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Electron Correlation ◽

Liquid Ammonia ◽

Quantum Mechanical ◽

Pure Liquid ◽

Charge Field ◽

Dynamics Simulations ◽

Mechanical Charge

First-Principles-Based Interatomic Potential for SI and Its Thermal Conductivity

ASME/JSME 2011 8th Thermal Engineering Joint Conference ◽

10.1115/ajtec2011-44339 ◽

2011 ◽

Author(s):

Keivan Esfarjani ◽

Gang Chen ◽

Asegun Henry

Keyword(s):

Thermal Conductivity ◽

Molecular Dynamics ◽

Thermal Properties ◽

Force Field ◽

First Principles ◽

Density Functional ◽

Interatomic Potential ◽

Force Constants ◽

Based on first-principles density-functional calculations, we have developed and tested a force-field for silicon, which can be used for molecular dynamics simulations and the calculation of its thermal properties. This force field uses the exact Taylor expansion of the total energy about the equilibrium positions up to 4th order. In this sense, it becomes systematically exact for small enough displacements, and can reproduce the thermodynamic properties of Si with high fidelity. Having the harmonic force constants, one can easily calculate the phonon spectrum of this system. The cubic force constants, on the other hand, will allow us to compute phonon lifetimes and scattering rates. Results on equilibrium Green-Kubo molecular dynamics simulations of thermal conductivity as well as an alternative calculation of the latter based on the relaxation-time approximation will be reported. The accuracy and ease of computation of the lattice thermal conductivity using these methods will be compared. This approach paves the way for the construction of accurate bulk interatomic potentials database, from which lattice dynamics and thermal properties can be calculated and used in larger scale simulation methods such as Monte Carlo.