Simulation of proton transfer along ammonia wires: An “ab initio” and semiempirical density functional comparison of potentials and classical molecular dynamics

2002 ◽  
Vol 116 (6) ◽  
pp. 2572-2585 ◽  
Author(s):  
Markus Meuwly ◽  
Martin Karplus
Keyword(s):  
Molecular Dynamics ◽  
Proton Transfer ◽  
Ab Initio ◽  
Density Functional ◽  
Classical Molecular Dynamics

scholarly journals Ab initio molecular dynamics of hydrogen on tungsten surfaces

2021 ◽  
Author(s):  
Alberto Rodríguez-Fernández ◽  
Laurent Bonnet ◽  
Pascal Larrégaray ◽  
Ricardo Díez Muiño
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Dissociation Process ◽  
Functional Theory ◽  
Classical Molecular Dynamics ◽  
Hydrogen Molecules

The dissociation process of hydrogen molecules on W(110) was studied using density functional theory and classical molecular dynamics.

Effects of micro-hydration in proton transfer from H2S·NO+ complex to water: Ab initio and molecular dynamics study

2011 ◽  
Vol 76 (5) ◽  
pp. 585-603 ◽  
Author(s):  
Ivan Černušák ◽  
Jozef Federič ◽  
Pavel Jungwirth ◽  
Milan Uhlár
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Wave Function ◽  
Proton Transfer ◽  
Ab Initio ◽  
Density Functional ◽  
Binding Energies ◽  
Coupled Clusters ◽  
Functional Theory ◽  
Second Order Perturbation Theory

We have studied several microhydrated (H2O)n·NO+·H2S structures (n = 1–3) and their fragments using wave-function based approach (coupled-clusters including single, double and non-iterative triple substitutions – CCSD(T) and second-order perturbation theory – MP2) and also employing density functional theory (with BLYP and ωB97XD functional). MP2 energetics is very close to CCSD(T) one. Both functionals provide reasonable binding energies compared to MP2, the ωB97XD being superior to BLYP. The exploratory ab initio molecular dynamics performed on four- and five-body clusters revealed that the hydrogen bonds network and cooperativity in these systems play a crucial role in the proton transfer from H2S·NO+ to H2O and its conversion to thionitrous acid.

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.

Combined ab initio and classical molecular dynamics simulations of alkyl-lithium aggregates in ethereal solutions

2008 ◽  
Vol 121 (5-6) ◽  
pp. 321-326 ◽  
Author(s):  
Hassan K. Khartabil ◽  
Marilia T. C. Martins-Costa ◽  
Philippe C. Gros ◽  
Yves Fort ◽  
Manuel F. Ruiz-López
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations

scholarly journals Investigating Tunneling Controlled Chemical Reactions Through Ab-Initio Ring Polymer Molecular Dynamics

2021 ◽  
Author(s):  
Xinyang Li ◽  
Pengfei Huo
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Chemical Reaction ◽  
Quantum Tunneling ◽  
Quantum Dynamics ◽  
Density Functional ◽  
Molecular System ◽  
Ring Polymer ◽  
Ring Polymer Molecular Dynamics ◽  
Dynamics Simulations

<div>We use the ab-initio ring polymer molecular dynamics (RPMD) approach to investigate tunneling controlled reactions in methylhydroxycarbene. Nuclear tunneling effects enable molecules to overcome the barriers which can not be overcome classically. Under low-temperature conditions, intrinsic quantum tunneling effects canfacilitate the chemical reaction in a pathway that is neither favored thermodynamically nor kinetically. This</div><div>behavior is referred to as the tunneling controlled chemical reaction and regarded as the third paradigm of chemical</div><div>reaction controls. In this work, we use the ab-initio RPMD approach to incorporate the tunneling effects in our quantum dynamics simulations. The reaction kinetics of two competitive reaction pathways at various temperatures are investigated with the Kohn-Sham density functional theory (KS-DFT) on-the-fly molecular dynamics simulations and the ring polymer quantization of the nuclei. The reaction rate constants obtained here agree extremely well with the experimentally measured rates. We demonstrate the feasibility of using ab-initio RPMD rate calculations in a realistic molecular system, and provide an interesting and important example for future investigations on reaction mechanisms dominated by quantum tunneling effects.</div>

scholarly journals Solvent Effect on the Structure and Properties of RGD Peptide (1FUV) at Body Temperature (310 K) Using Ab Initio Molecular Dynamics

Polymers ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 3434
Author(s):  
Khagendra Baral ◽  
Puja Adhikari ◽  
Bahaa Jawad ◽  
Rudolf Podgornik ◽  
Wai-Yim Ching
Keyword(s):  
Molecular Dynamics ◽  
Body Temperature ◽  
Ab Initio ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Rgd Peptide ◽  
Ab Initio Molecular Dynamics ◽  
Quantum Mechanical ◽  
Aqueous Environment ◽  
Structure And Properties

The structure and properties of the arginine-glycine-aspartate (RGD) sequence of the 1FUV peptide at 0 K and body temperature (310 K) are systematically investigated in a dry and aqueous environment using more accurate ab initio molecular dynamics and density functional theory calculations. The fundamental properties, such as electronic structure, interatomic bonding, partial charge distribution, and dielectric response function at 0 and 310 K are analyzed, comparing them in dry and solvated models. These accurate microscopic parameters determined from highly reliable quantum mechanical calculations are useful to define the range and strength of complex molecular interactions occurring between the RGD peptide and the integrin receptor. The in-depth bonding picture analyzed using a novel quantum mechanical metric, the total bond order (TBO), quantifies the role played by hydrogen bonds in the internal cohesion of the simulated structures. The TBO at 310 K decreases in the dry model but increases in the solvated model. These differences are small but extremely important in the context of conditions prevalent in the human body and relevant for health issues. Our results provide a new level of understanding of the structure and properties of the 1FUV peptide and help in advancing the study of RGD containing other peptides.

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