scholarly journals In Silico Studies on Selected Neutral Molecules, CGa2Ge2, CAlGaGe2, and CSiGa2Ge Containing Planar Tetracoordinate Carbon

Atoms ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 65
Author(s):  
Prasenjit Das ◽  
Pratim Kumar Chattaraj
Keyword(s):  
Density Functional ◽  
Nbo Analysis ◽  
Ab Initio Molecular Dynamics ◽  
Structure Stability ◽  
Strong Electron ◽  
In Silico Studies ◽  
Natural Density ◽  
Dynamics Simulations ◽  
Electron Donation ◽  
Planar Geometries

Density functional theory (DFT) was used to study the structure, stability, and bonding in some selected neutral pentaatomic systems, viz., CGa2Ge2, CAlGaGe2, and CSiGa2Ge containing planar tetracoordinate carbon. The systems are kinetically stable, as predicted from the ab initio molecular dynamics simulations. The natural bond orbital (NBO) analysis showed that strong electron donation occurs to the central planar carbon atom by the peripheral atoms in all the studied systems. From the nucleus independent chemical shift (NICS) analysis, it is shown that the systems possess both σ- and π- aromaticity. The presence of 18 valence electrons in these systems, in their neutral form, appears to be important for their stability with planar geometries rather than tetrahedral structures. The nature of bonding is understood through the adaptive natural density partitioning analysis (AdNDP), quantum theory of atoms in molecules (QTAIM) analysis, and also via Wiberg bond index (WBI) and electron localization function (ELF).

Catalyzed β scission of a carbenium ion III — Scission observed in ab initio molecular dynamics simulations

2009 ◽  
Vol 87 (10) ◽  
pp. 1512-1520 ◽  
Author(s):  
Greg M. Berner ◽  
Allan L. L. East
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Time Windows ◽  
Three Dimensional ◽  
Ab Initio Molecular Dynamics ◽  
Catalytic Systems ◽  
Carbenium Ions ◽  
Carbenium Ion ◽  
Dynamics Simulations

The β scission (cracking) of branched carbenium ions have been observed in molecular dynamics simulations, possibly for the first time. Simulations were performed with molecular dynamics based on PW91 density functional theory, and which included three-dimensional periodic boundary replication of the unit cell to mimic long-range bulk effects. A rising-temperature algorithm was used to encourage reaction within the narrow time windows (∼10 ps) of the simulations. Twenty-eight simulations were performed, featuring alkyl ions in three different catalytic systems: the ionic liquid, [(C5H5NH+)5(Al2Cl7−)6]−, the chabazite zeolite, [AlSi23O48]−, and the chabazite zeolite, [Al4Si20O45(OH)3]−. Twenty-four runs began with unbranched sec-n-alkyl ions, but only one exhibited β scission, and only after branching to a tertiary ion and under extreme heating. In contrast, the four simulations that began with branched alkyl ions were all successful in demonstrating β scission at lower temperatures: 2,4,4-trimethyl-2-pentyl ion and 2,4-dimethyl-2-hexyl ion in each of the first two catalysts. The lifetimes of desorbed alkyl ions in the chabazite models were < 5 ps at 1000–1500 K. The β scission results support the classical Weitkamp et al. ( Appl. Catal. 1983, 8, 123 ) mechanism over the nonclassical Sie ( Ind. Eng. Chem. Res. 1992, 31, 1881 ) and the chemisorping Kazansky et al. ( J. Catal. 1989, 119, 108 ) mechanisms.

Ab-Initio Molecular Dynamics Simulations and Calculations of Spectroscopic Parameters in Hydrogen-Bonding Liquids in Confinement (Project 8)

2018 ◽  
Vol 232 (7-8) ◽  
pp. 973-987 ◽  
Author(s):  
Daniel Sebastiani
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Aqueous Mixtures ◽  
Functional Theory ◽  
Spatially Resolved ◽  
Local Strength ◽  
Dynamics Simulations

Abstract We investigate the effect of several nanoscale confinements on structural and dynamical properties of liquid water and binary aqueous mixtures. By means of molecular dynamics simulations based on density functional theory and atomistic force fields. Our main focus is on the dependence on the structure and the hydrogen-bonding-network of the liquids near the confinement interface at atomistic resolution. As a complementary aspect, spatially resolved profiles of the proton NMR chemical shift values are used to quantify the local strength of the hydrogen-bond-network.

scholarly journals Ab initio molecular dynamics studies of formic acid dimer colliding with liquid water

2018 ◽  
Vol 20 (36) ◽  
pp. 23717-23725 ◽  
Author(s):  
Vesa Hänninen ◽  
Garold Murdachaew ◽  
Gilbert M. Nathanson ◽  
R. Benny Gerber ◽  
Lauri Halonen
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Formic Acid ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Liquid Water ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Functional Theory ◽  
Dynamics Simulations

Ab initio molecular dynamics simulations of formic acid (FA) dimer colliding with liquid water at 300 K have been performed using density functional theory.

scholarly journals Stabilizing the Exotic Carbonic Acid by Bisulfate Ion

Molecules ◽  
2021 ◽  
Vol 27 (1) ◽  
pp. 8
Author(s):  
Huili Lu ◽  
Shi-Wei Liu ◽  
Mengyang Li ◽  
Baocai Xu ◽  
Li Zhao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Carbonic Acid ◽  
Topological Analysis ◽  
Density Functional Theory Calculations ◽  
Ab Initio Molecular Dynamics ◽  
Important Species ◽  
Good Thermal Stability ◽  
Dynamics Simulations

Carbonic acid is an important species in a variety of fields and has long been regarded to be non-existing in isolated state, as it is thermodynamically favorable to decompose into water and carbon dioxide. In this work, we systematically studied a novel ionic complex [H2CO3·HSO4]− using density functional theory calculations, molecular dynamics simulations, and topological analysis to investigate if the exotic H2CO3 molecule could be stabilized by bisulfate ion, which is a ubiquitous ion in various environments. We found that bisulfate ion could efficiently stabilize all the three conformers of H2CO3 and reduce the energy differences of isomers with H2CO3 in three different conformations compared to the isolated H2CO3 molecule. Calculated isomerization pathways and ab initio molecular dynamics simulations suggest that all the optimized isomers of the complex have good thermal stability and could exist at finite temperatures. We also explored the hydrogen bonding properties in this interesting complex and simulated their harmonic infrared spectra to aid future infrared spectroscopic experiments. This work could be potentially important to understand the fate of carbonic acid in certain complex environments, such as in environments where both sulfuric acid (or rather bisulfate ion) and carbonic acid (or rather carbonic dioxide and water) exist.

scholarly journals Methanol Carbonylation over Acid Mordenite: Insights from Ab Initio Molecular Dynamics and Machine Learning Thermodynamic Perturbation Theory

2021 ◽  
Author(s):  
Monika Gešvandtnerová ◽  
Dario Rocca ◽  
Tomas Bucko
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Perturbation Theory ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Thermodynamic Perturbation Theory ◽  
Dynamics Simulations ◽  
Thermodynamic Perturbation

<div>In this work we present a detailed \textit{ab initio} study of the carbonylation reaction of methoxy groups in the zeolite mordenite, as it is the rate determining step in a series of elementary reactions leading to ethanol. </div><div>For the first time we employ full molecular dynamics simulations to evaluate free energies of activation for the reactions in side pockets and main channels. Results show that the reaction in the side pocket is preferred and, when dispersion interactions are taken into account, this preference becomes even stronger. This conclusion is confirmed using multiple levels of density functional theory approximations with (PBE-D2, PBE-MBD, and vdW-DF2-B86R) or without (PBE, HSE06) dispersion corrections. These calculations, that in principle would require several demanding molecular dynamics simulations, were made possible at a minimal computational cost by using a newly developed approach that combines thermodynamic perturbation theory with machine learning.</div>

scholarly journals Ab initio molecular dynamics of atomic-scale surface reactions: insights into metal organic chemical vapor deposition of AlN on graphene

2018 ◽  
Vol 20 (26) ◽  
pp. 17751-17761 ◽  
Author(s):  
D. G. Sangiovanni ◽  
G. K. Gueorguiev ◽  
A. Kakanakova-Georgieva
Keyword(s):  
Molecular Dynamics ◽  
Density Functional ◽  
Surface Reactions ◽  
Chemical Vapor ◽  
Atomic Scale ◽  
Ab Initio Molecular Dynamics ◽  
Organic Chemical ◽  
Pristine Graphene ◽  
Metal Organic ◽  
Dynamics Simulations

Density-functional molecular dynamics simulations provide plausible interpretations of atomistic and electronic processes responsible for delivery of Al, C adatoms, and C–Al, CHx, AlNH2 admolecules on pristine graphene via precursor/surface reactions.

A DFT and HRTEM Study on MoS2/Co: Locating Promoters in Catalytic Nanostructures

2011 ◽  
Vol 1309 ◽  
Author(s):  
Manuel Ramos ◽  
Gilles Berhault ◽  
Jose Rurik Farias ◽  
Jose Trinidad Elizalde ◽  
Domingo Ferrer ◽  
...  
Keyword(s):  
Lower Energy ◽  
Density Functional ◽  
Population Analysis ◽  
Mulliken Population Analysis ◽  
Density Functional Theory Study ◽  
Mulliken Population ◽  
Strong Electron ◽  
Functional Theory ◽  
Electron Donation ◽  
Energy Package

ABSTRACTLocating cobalt promoters on catalytically MoS2 structures is a challenging task to achieve; this is due to the size on those MoS2 nanostructures. Previous reports in the literature indicate that specific locations for Co in MoS2 slabs are (1010)-plane creating either a sulfur-Co or Molybdenum-Co termination edge, due to lower energy required for the permutation Mo, S and Co to occur. We present results obtained from Density Functional Theory study done on the interface between MoS2 and Co9S8 crystal structures; the interface show an interesting thiocubane cluster and it is suspected to be the responsible for Mo-S-Co bonding to exist, along with HDS reaction. In order to understand electronic properties on thiocubane Density of States and Mulliken Population Analysis calculations were implemented using Cambridge Serial Total Energy Package (CASTEP). Results indicate a strong electron donation from Co to Mo through intermediate sulfur atom bonded to both metals while an enhanced metallic character is also found.

Interaction of CO with Gold Under Gas Phase and Electrochemical Environments

2020 ◽  
Author(s):  
Sudarshan Vijay ◽  
Thomas Vagn Hogg ◽  
Johan Ehlers ◽  
Henrik Høgh Kristoffersen ◽  
Yu Katayama ◽  
...  
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Co Adsorption ◽  
Density Functional Theory Calculations ◽  
Underpotential Deposition ◽  
Attenuated Total Reflection ◽  
Ab Initio Molecular Dynamics ◽  
Adsorption Sites ◽  
Temperature Programmed ◽  
Dynamics Simulations

<div> <div> <div> <p>We present a joint theoretical-experimental study of CO coverage on Au under both gas phase and electrochemical conditions. By analyzing temperature programmed desorption (TPD) spectra on (211) and (310) surface facets, we show that, under atmospheric CO pressure, the steps of both facets adsorb up to 0.7 ML coverage of *CO, while the terraces have close to zero coverage. We show this result to be consistent with density functional theory calculations of adsorption energies. Under electrochemical conditions on polycrystalline Au, we investigate the CO binding with in situ attenuated total reflection surface enhanced IR spectra (ATR-SEIRAS). We detect a CO band at 0.2V vs. SHE that disappears upon partial Pb underpotential deposition (facet selective), which suggests Pb blocks the CO adsorption sites. With Pb underpotential deposition on single crystals and theoretical surface Pourbaix analysis, we narrow down the possible adsorption sites of CO to open site motifs: (211) and (110) steps, as well as (100) terraces. Ab initio molecular dynamics simulations of explicit water at the Au surface, however, shows the adsorption of CO on (211) steps to be significantly weakened relative to the (100) terrace due to competitive water adsorption. This result suggests that CO is more likely to bind to the (100) terrace than steps in an electrochemical environment. The competition between water and CO adsorption can result in different binding sites for *CO on Au in gas phase and electrochemical environments. </p> </div> </div> </div>

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