Ab initio simulation of the structure and dynamics of white phosphorus (P4) at low temperatures

1995 ◽  
Vol 73 (11-12) ◽  
pp. 710-717 ◽  
Author(s):  
P. Jeffrey Ungar ◽  
Kari Laasonen ◽  
Michael L. Klein
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Density Functional ◽  
Local Density ◽  
Orientational Order ◽  
Intermolecular Forces ◽  
White Phosphorus ◽  
Basis Set ◽  
Cell Parameters ◽  
Ab Initio Simulations

Ab initio simulations of low-temperature white phosphorus (β-P4) were performed using Car–Parrinello density-functional-theory molecular dynamics and a plane-wave basis set. Gradient corrections to the local density approximation were used to obtain a better description of the weak intermolecular forces. Starting with unit-cell parameters and atomic coordinates recently verified using neutron scattering, molecular dynamics trajectories over 9–10 ps were obtained for temperatures of 50 and 145 K. The computations show that the distortions from ideal tetrahedral P4 molecules found in the reduction of the neutron data may be a finite-temperature effect and not an artifact of the data analysis. Examination of the molecular reorientational dynamics shows that orientational order persists throughout the simulations, which suggests that β-P4 is an orientational crystal.

AB-INITIO MOLECULAR DYNAMICS IN THE FULL-POTENTIAL LMTO METHOD: DERIVATION OF A PRACTICAL FORCE THEOREM

1993 ◽  
Vol 07 (01n03) ◽  
pp. 262-265 ◽  
Author(s):  
M. METHFESSEL ◽  
M. VAN SCHILFGAARDE
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Local Density ◽  
Basis Set ◽  
Ab Initio Molecular Dynamics ◽  
Basis Sets ◽  
Full Potential ◽  
Major Advance ◽  
First Results ◽  
Lmto Method

A major advance in electronic structure calculations was the combination of local-density techniques with molecular dynamics by Car and Parrinello seven years ago. Unfortunately, application of the Car-Parrinello scheme has been limited essentially to sp materials because only in the plane-wave pseudopotential method forces are trivial to calculate. We present a systematic approach to derive force theorems with desired characteristics within complicated basis sets, which are applicable to all elements of the periodic table equally well. Application to the LMTO basis set yields an accurate force theorem, quite distinct from the Hellman-Feynman form, which is exceptionally insensitive to errors in the trial density. The forces were implemented in a new full-potential LMTO method which is suited to arbitrary geometries. First results for ab-initio molecular dynamics and simulated annealing runs are shown for some random small molecules and small clusters of silver atoms.

scholarly journals Acceleration vs Accuracy: Influence of Basis Set Quality on the Mechanism and Dynamics Predicted by Ab Initio Molecular Dynamics

2019 ◽  
Author(s):  
Sharma Yamijala ◽  
Zulfikhar A. Ali ◽  
Bryan Wong
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Density Functional ◽  
Single Point ◽  
Basis Set ◽  
Ab Initio Molecular Dynamics ◽  
Energy Calculation ◽  
Shift Reaction ◽  
The Impact

<p>Ab initio molecular dynamics (AIMD) is an indispensable tool for understanding the mechanistic details of externally-energy mediated chemical reactions. In this work, we show that the predicted thermodynamic and catalytic properties of certain reactions using AIMD simulations critically depend on the quality of the employed basis set. To this end, we have examined the reactants and products of the water-gas shift reaction (viz., CO, CO<sub>2</sub>, H<sub>2</sub>, and H<sub>2</sub>O) and studied their interaction with the ZnO(101̄0) surface using density functional theory (DFT) and Born Oppenheimer Molecular Dynamics (BOMD) simulations. By merely increasing the quality of the basis, from double zeta (commonly used in most calculations of these systems) to triple zeta, we surprisingly find that the reaction outcome of an H<sub>2</sub>O molecule colliding with a ZnO surface pre-covered with carbon monoxide gives qualitatively different results. These surprising results are shown to be robust with similar trends that are also obtained with other software packages. Furthermore, we show that the calculated adsorption energies can vary by as much as 380 meV (which is an order of magnitude larger than room temperature) by simply changing the basis set. Using electron density difference maps, we present mechanistic insight into the origin of these changes. Finally, we propose a simple diagnostic test that uses a single-point binding energy calculation to estimate the impact of basis-set quality, which can be used before carrying out a computationally-expensive BOMD simulation.</p>

scholarly journals Acceleration vs Accuracy: Influence of Basis Set Quality on the Mechanism and Dynamics Predicted by Ab Initio Molecular Dynamics

2019 ◽  
Author(s):  
Sharma Yamijala ◽  
Zulfikhar A. Ali ◽  
Bryan Wong
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Density Functional ◽  
Single Point ◽  
Basis Set ◽  
Ab Initio Molecular Dynamics ◽  
Energy Calculation ◽  
Shift Reaction ◽  
The Impact

<p>Ab initio molecular dynamics (AIMD) is an indispensable tool for understanding the mechanistic details of externally-energy mediated chemical reactions. In this work, we show that the predicted thermodynamic and catalytic properties of certain reactions using AIMD simulations critically depend on the quality of the employed basis set. To this end, we have examined the reactants and products of the water-gas shift reaction (viz., CO, CO<sub>2</sub>, H<sub>2</sub>, and H<sub>2</sub>O) and studied their interaction with the ZnO(101̄0) surface using density functional theory (DFT) and Born Oppenheimer Molecular Dynamics (BOMD) simulations. By merely increasing the quality of the basis, from double zeta (commonly used in most calculations of these systems) to triple zeta, we surprisingly find that the reaction outcome of an H<sub>2</sub>O molecule colliding with a ZnO surface pre-covered with carbon monoxide gives qualitatively different results. These surprising results are shown to be robust with similar trends that are also obtained with other software packages. Furthermore, we show that the calculated adsorption energies can vary by as much as 380 meV (which is an order of magnitude larger than room temperature) by simply changing the basis set. Using electron density difference maps, we present mechanistic insight into the origin of these changes. Finally, we propose a simple diagnostic test that uses a single-point binding energy calculation to estimate the impact of basis-set quality, which can be used before carrying out a computationally-expensive BOMD simulation.</p>

scholarly journals Molecular structure investigation by ab initio, DFT and X-ray diffraction of thiazole-derived compound

2014 ◽  
Vol 70 (a1) ◽  
pp. C1234-C1234
Author(s):  
Manel Boulakoud ◽  
Abdelkader Chouaih ◽  
Fodil Hamzaoui
Keyword(s):  
Molecular Structure ◽  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Intermolecular Hydrogen Bond ◽  
Basis Set ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
Cell Parameters

We report here the synthesis of Z-3-(2-Ethoxyphenyl)-2-(2-Ethoxyphenyl)-1,3-Thiazolidin-4-one compound. The crystal structure has been determined by X-ray diffraction. The compound crystallizes in the monoclinic system with space group P21/n and cell parameters: a = 9.4094(10), b = 9.3066(10), c = 20.960(2) Å, β=99.0375(10)0, V = 1812.7(3)Å3 and Z = 4. The structure has been refined to a final R = 0.05 for 2083 observed reflections. The refined structure was found to be significantly non planar. The molecule exhibits intermolecular hydrogen bond of type C–H...O, C–H...N and C–H...S. Ab initio calculations were also performed at Hartree–Fock and density functional theory levels. The full HF and DFT geometry optimization was carried out using 6-31G(d,p) basis set. The observed molecular structure is compared with that calculated by both HF and density functional theory methods. The optimized geometry of the title compound was found to be consistent structure determined by X-ray diffraction.

scholarly journals ON THE APPLICABILITY OF THE JELLIUM MODEL TO THE DESCRIPTION OF ALKALI CLUSTERS

2003 ◽  
Vol 12 (01) ◽  
pp. 81-107 ◽  
Author(s):  
ANTON MATVEENTSEV ◽  
ANDREY LYALIN ◽  
ILIA A. SOLOV'YOV ◽  
ANDREY V. SOLOV'YOV ◽  
WALTER GREINER
Keyword(s):  
Ab Initio ◽  
Density Functional ◽  
Local Density ◽  
Binding Energies ◽  
Jellium Model ◽  
Hartree Fock ◽  
Ab Initio Simulations ◽  
Theoretical Approaches ◽  
Cluster Shape ◽  
Cluster Properties

This work is devoted to the elucidation of the applicability of the jellium model to the description of alkali cluster properties. We compare the jellium model results with those derived within ab initio theoretical approaches and with experiments. On the basis of Hartree–Fock and local-density approximations we have calculated the binding energies per atom, ionization potentials, deformation parameters and optimized values of the Wigner–Seitz radii for neutral and singly charged sodium clusters with the number of atoms N ≤ 20. The characteristics calculated within the framework of the deformed jellium model are compared with the results derived from ab initio simulations of cluster electronic and ionic structure based on density functional theory and systematic post Hartree–Fock many-body perturbation theory accounting for all electrons in the system. The comparison performed demonstrates the great role of the cluster shape deformations in the formation cluster properties and quite reasonable level of applicability of the deformed jellium model. This elucidates the similarities of atomic cluster physics with the physics of atomic nuclei.

scholarly journals Density Functional Theory and Complete Basis Set Ab Initio Computational Study of Five-, Six-, Seven- and Eight-hydrogen Coordinated Carbon Cations

1999 ◽  
Vol 23 (8) ◽  
pp. 502-503
Author(s):  
Branko S. Jursic
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Computational Study ◽  
Basis Set ◽  
Functional Theory ◽  
Complete Basis ◽  
Complete Basis Set ◽  
High Level

High level ab initio and density functional theory studies are performed on highly protonated methane species.

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 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.

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