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>

Molecular Dynamics Simulations of Diamond and Carbon Clusters

1993 ◽  
Vol 316 ◽  
Author(s):  
Bernard A. Pailthorpe
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Film Growth ◽  
Local Density ◽  
3D Structure ◽  
Three Dimensional ◽  
Carbon Clusters ◽  
Energy Structure ◽  
Dynamics Simulations

ABSTRACTThe synthesis of amorphous diamond thin films has been studied previously by classical molecular dynamics computer simulations utilising Stillinger Weber potentials, reparameterised to describe bonding in carbon. The simulations provided insight into the surface processes occuring during thin film growth and showed the role of stress and an energy window in promoting amorphous diamond formation from carbon ion beams. However, more realistic simulations require a full treatment of quantum effects to describe adequately chemical bonding and electronic properties. Local Density Functional theories and the Car-Parrinello molecular dynamics algorithm have proved to be successful and offer a route to first-principles materials design. We are using these techniques to investigate bonding and structure in small carbon clusters and to study doping of diamond required to fabricate electronic devices. Results are presented for a novel, three dimensional, neutral carbon-11 cluster which was studied by ab initio molecular dynamics simulations confirming that, while the 3D structure is stable, the ring is the lower energy structure. However, the 3D structure deforms rapidly to a more open structure of the same topology which is dynamically stable during simulated annealing up to 2000K. Higher quality calculations indicate that new, lower symmetry bonding arrangements form also. Attempts to enclose lithium or boron atoms within the Cl 1 cage caused heating and ultimate rupture into smaller fragments.

scholarly journals Machine Learning for Accurate Force Calculations in Molecular Dynamics Simulations

2020 ◽  
Author(s):  
Punyaslok Pattnaik ◽  
Shampa Raghunathan ◽  
Tarun Kalluri ◽  
Prabhakar Bhimalapuram ◽  
C. V. Jawahar ◽  
...  
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Time Scales ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Experimental Conditions ◽  
The Neural Network ◽  
Dynamics Simulations

<p>The computationally expensive nature of ab initio molecular dynamics simulations severely limits its ability to simulate large system sizes and long time scales, both of which are necessary to imitate experimental conditions. In this work, we explore an approach to make use of the data obtained using the quantum mechanical density functional theory (DFT) on small systems and use deep learning to subsequently simulate large systems by taking liquid argon as a test case. A suitable vector representation was chosen to represent the surrounding environment of each Ar atom, and a DNetFF machine learning model where, the neural network was trained to predict the difference in resultant forces obtained by DFT and classical force fields was introduced. Molecular dynamics simulations were then performed using forces from the neural network for various system sizes and time scales depending on the properties we calculated. A comparison of properties obtained from the classical force field and the neural network model was presented alongside available experimental data to validate the proposed method.</p>

Dissociation mechanism from highly charged bromophenol: ab initio molecular dynamics simulations

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Satoshi Ohmura ◽  
Kiyonobu Nagaya ◽  
Fuyuki Shimojo ◽  
Makoto Yao
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Electronic State ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Electronic Temperature ◽  
Multi Stage ◽  
Dissociation Mechanisms ◽  
Dynamics Simulations

AbstractDissociation mechanisms are studied by ab initio molecular dynamics simulations based on density functional theory for the highly charged bromophenol (C6H4OHBr)n+ (n ≤ 10) in the ground electronic state and in an electronic state which has a high electronic temperature Te characterized by Fermi–Dirac distribution. In the case of the ground state, the dissociation occurs through a sequential multi-stage process. At times shorter than 20 fs after the molecule is charged, hydrogens are dissociated from the molecule and, subsequently, the carbon ring breaks at about 150 fs In the case of an electronic state with high Te, the mechanism changes from a sequential dissociation process to a simultaneous process occurring at Te > 5 eV. To estimate the charge transfer time in a molecular bromide parent ion with +6 charge, which is generated through Auger cascades, we also performed nonadiabatic quantum-mechanical molecular dynamics (NAQMD) simulations that include the effects of nonadiabatic electronic transition with a surface-hopping approach.

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