Accurate Calculation of Chemical Shifts in Highly Dynamic H2@C60through an Integrated Quantum Mechanics/Molecular Dynamics Scheme

2011 ◽  
Vol 13 (10) ◽  
pp. 2528-2531 ◽  
Author(s):  
Gonzalo Jiménez-Osés ◽  
José I. García ◽  
Francisco Corzana ◽  
José Elguero
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Chemical Shifts ◽  
Accurate Calculation

ChemInform Abstract: Calculated and Experimental NMR Chemical Shifts of p-Menthane-3,9-diols. A Combination of Molecular Dynamics and Quantum Mechanics to Determine the Structure and the Solvent Effects.

ChemInform ◽  
2010 ◽  
Vol 32 (37) ◽  
pp. no-no
Author(s):  
Jordi Casanovas ◽  
Adriana M. Namba ◽  
Salvador Leon ◽  
Gilberto L. B. Aquino ◽  
Gil Valdo Jose da Silva ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Solvent Effects ◽  
Chemical Shifts ◽  
Nmr Chemical Shifts

Calculated and Experimental NMR Chemical Shifts ofp-Menthane-3,9-diols. A Combination of Molecular Dynamics and Quantum Mechanics to Determine the Structure and the Solvent Effects

2001 ◽  
Vol 66 (11) ◽  
pp. 3775-3782 ◽  
Author(s):  
Jordi Casanovas ◽  
Adriana M. Namba ◽  
Salvador León ◽  
Gilberto L. B. Aquino ◽  
Gil Valdo José da Silva ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Solvent Effects ◽  
Chemical Shifts ◽  
Nmr Chemical Shifts

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 Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation

2019 ◽  
Vol 116 (41) ◽  
pp. 20446-20452 ◽  
Author(s):  
Utsab R. Shrestha ◽  
Puneet Juneja ◽  
Qiu Zhang ◽  
Viswanathan Gurumoorthy ◽  
Jose M. Borreguero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Intrinsically Disordered Proteins ◽  
Chemical Shifts ◽  
Intrinsically Disordered Protein ◽  
Physical Models ◽  
Dynamics Simulation ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Eukaryotic Proteomes ◽  
Heterogeneous Ensemble

Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical to determine their configurational ensemble, i.e., the collection of 3-dimensional structures they adopt, and this remains an immense challenge in structural biology. Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. Here, by employing enhanced sampling MD we reproduce the experimental small-angle neutron and X-ray scattering profiles and the NMR chemical shifts of the disordered N terminal (SH4UD) of c-Src kinase without reweighting or constraining the simulations. The unbiased simulation results reveal a weakly funneled and rugged free energy landscape of SH4UD, which gives rise to a heterogeneous ensemble of structures that cannot be described by simple polymer theory. SH4UD adopts transient helices, which are found away from known phosphorylation sites and could play a key role in the stabilization of structural regions necessary for phosphorylation. Our findings indicate that adequately sampled molecular simulations can be performed to provide accurate physical models of flexible biosystems, thus rationalizing their biological function.

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.

Using 1H and 13C NMR chemical shifts to determine cyclic peptide conformations: a combined molecular dynamics and quantum mechanics approach

2018 ◽  
Vol 20 (20) ◽  
pp. 14003-14012 ◽  
Author(s):  
Q. Nhu N. Nguyen ◽  
Joshua Schwochert ◽  
Dean J. Tantillo ◽  
R. Scott Lokey
Keyword(s):  
Molecular Dynamics ◽  
Density Functional ◽  
Cyclic Peptide ◽  
Chemical Shifts ◽  
Low Energy ◽  
Functional Prediction ◽  
1H And 13C Nmr ◽  
New Approach ◽  
Solution Structures ◽  
Peptide Conformations

Conformational analysis from NMR and density-functional prediction of low-energy ensembles (CANDLE), a new approach for determining solution structures.

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