A combined molecular dynamics+quantum mechanics method for investigation of dynamic effects on local surface structures

2004 ◽  
Vol 120 (10) ◽  
pp. 4939-4948 ◽  
Author(s):  
Björn Herschend ◽  
Micael Baudin ◽  
Kersti Hermansson
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Surface Structures ◽  
Dynamic Effects ◽  
Local Surface

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

scholarly journals Conformational energies and equilibria of cyclic dinucleotides in vacuo and in solution: computational chemistry vs. NMR experiments

2021 ◽  
Author(s):  
Ondrej Gutten ◽  
Petr Jurečka ◽  
Zahra Aliakbar Tehrani ◽  
Miloš Buděšínský ◽  
Jan Řezáč ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Computational Chemistry ◽  
Computational Error ◽  
Cyclic Dinucleotides ◽  
Error Bars ◽  
Conformational Energies

Computational “error bars” for modelling cyclic dinucleotides – NMR experiment vs. quantum mechanics and molecular dynamics.

scholarly journals Effects of applied voltage on water at a gold electrode interface from ab initio molecular dynamics

2021 ◽  
Vol 12 (16) ◽  
pp. 5865-5873
Author(s):  
Zachary K. Goldsmith ◽  
Marcos F. Calegari Andrade ◽  
Annabella Selloni
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Applied Voltage ◽  
Gold Electrode ◽  
Ab Initio Molecular Dynamics ◽  
Dynamic Effects ◽  
Electrode Interface

Ab initio molecular dynamics of an aqueous electrode interface reveal the electrostatic, structural, and dynamic effects of quantifiable voltage biases on water.

scholarly journals Computational Methods for Ab Initio Molecular Dynamics

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Eric Paquet ◽  
Herna L. Viktor
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Ab Initio ◽  
First Principles ◽  
Density Functional ◽  
Path Integrals ◽  
Ab Initio Molecular Dynamics ◽  
Molecular Systems ◽  
Hartree Fock ◽  
Computational Perspective

Ab initio molecular dynamics is an irreplaceable technique for the realistic simulation of complex molecular systems and processes from first principles. This paper proposes a comprehensive and self-contained review of ab initio molecular dynamics from a computational perspective and from first principles. Quantum mechanics is presented from a molecular dynamics perspective. Various approximations and formulations are proposed, including the Ehrenfest, Born–Oppenheimer, and Hartree–Fock molecular dynamics. Subsequently, the Kohn–Sham formulation of molecular dynamics is introduced as well as the afferent concept of density functional. As a result, Car–Parrinello molecular dynamics is discussed, together with its extension to isothermal and isobaric processes. Car–Parrinello molecular dynamics is then reformulated in terms of path integrals. Finally, some implementation issues are analysed, namely, the pseudopotential, the orbital functional basis, and hybrid molecular dynamics.

scholarly journals Dynamics and Temperature Simulation in Multi-Axis Milling

2008 ◽  
Vol 43 ◽  
pp. 89-96 ◽  
Author(s):  
Eduard Ungemach ◽  
Tobias Surmann ◽  
Andreas Zabel
Keyword(s):  
Surface Quality ◽  
Matrix Material ◽  
Ground Surface ◽  
Milling Process ◽  
Surface Structures ◽  
Dynamic Effects ◽  
Lightweight Construction ◽  
Surrounding Matrix ◽  
Simulation Systems ◽  
Very High

Lightweight extrusion profiles with reinforcement elements are promising news in the domain of lightweight construction. The machining of them suffers from several problems: Aside from the question of choosing a suitable tool, feed rate, and milling strategy, an excessive rise in temperature could lead to stress and even a distortion due to the differing thermal expansion of the reinforcement material and the surrounding matrix material. A simulation of the milling process could, in addition to force and collision calculations, recognize this case before manufacturing. For certain milling applications like seal surfaces, a certain roughness of the manufactured surface is necessary. In many other cases, a smooth surface of very high quality is desirable. Available simulation systems usually completely lack the simulation of dynamic effects, which have a great effect on the final surface quality, and therefore are not able to predict the resulting surface quality. In this paper simulation methods are presented that are capable of simulating the dynamic behavior of the tool in the milling process and the resulting flank and ground surface structures. Additionally, a fast temperature simulation for heterogeneous workpieces with reinforcement elements, which is based on the finite difference method and cellular automata, is introduced.

UNDERSTANDING DIFFERENT LCST LEVELS OF POLY(N-ALKYLACRYLAMIDE)S BY MOLECULAR DYNAMICS SIMULATIONS AND QUANTUM MECHANICS CALCULATIONS

2011 ◽  
Vol 10 (03) ◽  
pp. 359-370 ◽  
Author(s):  
JUAN PANG ◽  
HU YANG ◽  
JING MA ◽  
RONGSHI CHENG
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Aqueous Solutions ◽  
Molecular Dynamics Simulations ◽  
Steric Effect ◽  
Conformational Transition ◽  
Methyl Group ◽  
Branched Chain ◽  
Dynamics Simulations ◽  
Different Levels

Poly(N-alkylacrylamide) is a group of thermo-sensitive polymers that include poly (N-isopropylacrylamide), poly(N-n-propylacrylamide), poly(N-isopropylmethacryl-amide), and so on. The polymers exhibit different levels of lower critical solution temperatures (LCST) in aqueous solutions. In this article, their monomers and oligomers with 10 repeating units are selected, respectively, to demonstrate the cause of different LCST levels of the polymers in aqueous solutions using molecular dynamics simulations and quantum mechanics calculations. The monomers have functional groups of different steric volume that greatly affect the conformational transition of chains and LCST levels of the polymers. A branched chain of N-propyl group in N-isopropylacrylamide and an additional methyl group at α-carbon in N-isopropylmethacrylamide both increase the steric effect, making it more difficult for monomers to draw closer and resulting in higher LCST levels of the polymers. In addition, the simulated results from their corresponding oligomers exhibit the similar trend to those from the monomers.

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.

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