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 Simplified Ab Initio Molecular Dynamics-Based Raman Spectral Simulations

2020 ◽  
Vol 74 (11) ◽  
pp. 1350-1357
Author(s):  
Edoardo Aprà ◽  
Ashish Bhattarai ◽  
Eric Baxter ◽  
ShanYi Wang ◽  
Grant E. Johnson ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Ab Initio Molecular Dynamics ◽  
Simplified Approach ◽  
Molecular Systems ◽  
Hartree Fock ◽  
Molecular Polarizabilities ◽  
Spectral Simulations ◽  
Tip Enhanced Raman Spectroscopy ◽  
Raman Spectral

We describe a simplified approach to simulating Raman spectra from ab initio molecular dynamics (AIMD) calculations. The protocol relies on on-the-fly calculations of approximate molecular polarizabilities using the well-known sum over orbitals (as opposed to states) method. This approach bypasses the more accurate but computationally expensive approach to calculating molecular polarizabilities along AIMD trajectories, i.e., solving the coupled perturbed Hartree–Fock/Kohn–Sham equations. We demonstrate the advantages and limitations of our method through a few case studies targeting molecular systems of interest to surface- and/or tip-enhanced Raman spectroscopy practitioners.

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.

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.

scholarly journals Unexpectedly Large Couplings Between Orthogonal Units in Anthraquinone Polymers

2019 ◽  
Author(s):  
Rocco Peter Fornari ◽  
Piotr de Silva
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Lone Pair ◽  
Localized States ◽  
Ab Initio Molecular Dynamics ◽  
Coupling Mechanism ◽  
Functional Theory ◽  
Pi Interactions

Directly linked polyanthraquinones have relatively large electronic couplings between charge-localized states despite near-orthogonality of the monomer units. By using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations, we investigate this unusual coupling mechanism and show that this is due to strong lone pair-pi interactions, which are maximized around orthogonal conformations. We find that such materials are largely resilient to dynamic disorder and are promising for organic electronics applications.

Ti and Zr Transition Metals Effect in the D03 Fe3Al by Ab Initio Study Approach

2014 ◽  
Vol 783-786 ◽  
pp. 1640-1645
Author(s):  
Jean Marc Raulot ◽  
S. Chentouf ◽  
T. Grosdidier ◽  
Hafid Aourag
Keyword(s):  
Molecular Dynamics ◽  
Transition Metals ◽  
Ab Initio ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Effect Of Temperature ◽  
Site Preference ◽  
Functional Theory ◽  
Study Approach

The effect of the Ti and Zr transition metals on the D03-Fe3Al intermetallic compounds has been investigated by means of ab initio Pseudo Potentials numerical simulations based on Density Functional Theory. Two main issues will be addressed the understanding of the role of these two transition metals in terms of stability of the bulk at the light of their site preference in the D03-Fe3Al structure the behaviour of Ti and Zr transition metals in the sigma 5 (310) [001] grain boundary and their effect on the structural stability of this interface. An important issue when studying these aspects is to take into accounts the effect of temperature. This requires a molecular dynamics treatment of the atoms in the supercell. The technique known as ab initio molecular dynamics (AIMD) solves these problems by combining ‘on the fly’ electronic structure calculations with finite temperature dynamics. Thus, our study was conducted both using the conventional static ab initio calculations (0K) as well as by taking into account the effect of temperature (Ab Initio Molecular Dynamics).

scholarly journals Ab initio and first principles theoretical investigations of triplet–triplet fluorescence in trimethylenemethane biradicals

RSC Advances ◽  
2016 ◽  
Vol 6 (87) ◽  
pp. 83668-83672 ◽  
Author(s):  
Yasunori Matsui ◽  
Kosuke Usui ◽  
Hiroshi Ikeda ◽  
Stephan Irle
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
First Principles ◽  
Density Functional ◽  
Theoretical Studies ◽  
Functional Theory ◽  
Hartree Fock ◽  
Theoretical Investigations

Theoretical studies on triplet–triplet (T1 → T0) fluorescence of the arylated trimethylenemethane (TMM) biradicals, 32˙˙, were carried out using post-Hartree–Fock ab initio and various first principles density functional theory methods.

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