Trajectory Simulations of Molecular Collisions: Classical Treatment

Thompson, Donald L.

doi:10.1002/0470845015.cca021

Cited by 6 publications

(5 citation statements)

References 207 publications

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“…The transition states for the OCCO molecule in singlet and triplet states were studied with the computational package Gaussian 09 40 using the DFT 41,42 with the generalized gradient approximation (GGA) in the Perdew−Burke−Ernzerhof (PBE) exchange−correlation scheme 43 with the 6-31G* basis set, 44 and the atom centered density matrix propagation (ADMP) option. 45 For the adsorption study, we placed the OCCO molecule on a defective graphene supercell of 6 × 6, at a distance of 2.5 Å. We made a systematic search of the ground-state configuration, see Figure 1, placing the adsorbed molecule in several positions and orientations; top-site (over a C atom); a bridge-site (over a C−C bond); and in the middle of a hexagonal ring.…”

Section: Computational Methodologymentioning

confidence: 99%

“…The transition states for the OCCO molecule in singlet and triplet states were studied with the computational package Gaussian 09 using the DFT , with the generalized gradient approximation (GGA) in the Perdew–Burke–Ernzerhof (PBE) exchange–correlation scheme with the 6-31G* basis set, and the atom centered density matrix propagation (ADMP) option …”

Section: Computational Methodologymentioning

confidence: 99%

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Adsorption of Ethene-1,2-Dione on Materials Based on Graphene

2019

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We study the adsorption of ethene-1,2-dione or ethylene-dione (OCCO) on defective graphene sheets with nitrogen. The principal motivation is to determine the feasibility of the OCCO molecule as an intermediate state in the transformation of CO 2 into hydrocarbons. We observed that defective graphene systems present weak interactions with the adsorption of OCCO molecules, in the physisorption range. The most stable configuration is the pyridinic-N-OCCO system, which presents p-type doping, donating electrons to the adsorbed molecules. Also, this system has the best electronic transport, inducing substantially free states in the Fermi-energy level and the virtual zone of the local density of states, while increasing the reactivity of the system. The increment of available states in the Fermi-energy level and thermic stability at room temperature makes the pyridinic-N system an excellent candidate to stabilize the OCCO molecule.

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Section: Computational Methodologymentioning

confidence: 99%

Section: Computational Methodologymentioning

confidence: 99%

Adsorption of Ethene-1,2-Dione on Materials Based on Graphene

2019

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“…All activation free energies are quoted relative to infinitely separated reagents. Classical molecular dynamics trajectory calculation, using the atom-centred density matrix propagation (ADMP), on TS was initialized in the region of the PES near to the TS and performed using Gaussian 09 in the presence of implicit solvation model (SMD/t-BuOH) and under standard conditions (T = 298.15 K and 1 atm) [50,51]. The TS was initiated into forward and backward propagations showing the product and reactants (aldehyde and chlorous acid), in which a time step of 1.0 fs was used over periods of 300.0 fs.…”

Section: Computational Detailsmentioning

confidence: 99%

Mechanistic investigations on Pinnick oxidation: a density functional theory study

et al. 2020

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A computational study on Pinnick oxidation of aldehydes into carboxylic acids using density functional theory (DFT) calculations has been evaluated with the (SMD)-M06-2X/aug-pVDZ level of theory, leading to an important understanding of the reaction mechanism that agrees with the experimental observations and explaining the substantial role of acid in driving the reaction. The DFT results elucidated that the first reaction step (FRS) proceeds in a manner where chlorous acid reacts with the aldehyde group through a distorted six-membered ring transition state to give a hydroxyallyl chlorite intermediate that undergoes a pericyclic fragmentation to release the carboxylic acid as a second reaction step (SRS). 1 H NMR experiments and simulations showed that hydrogen bonding between carbonyl and t -butanol is unlikely to occur. Additionally, it was found that the FRS is a rate-determining and thermoneutral step, whereas SRS is highly exergonic with a low energetic barrier due to the Cl(III) → Cl(II) reduction. Frontier molecular orbital analysis, intrinsic reaction coordinate, molecular dynamics and distortion/interaction analysis further supported the proposed mechanism.

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“…The reaction path from reactants through intermediates (if any) to products describes the reaction mechanism 41. A more detailed description of a reaction can be obtained by classical trajectory calculations42–45 that simulate molecular dynamics by integrating the classical equations of motion for a molecule moving on a potential energy surface. Photochemistry involves motion on multiple potential energy surfaces and transitions between them (see Ref 46).…”

Section: Potential Energy Surfacesmentioning

confidence: 99%

Geometry optimization

Schlegel

2011

WIREs Comput Mol Sci

330

349

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Geometry optimization is an important part of most quantum chemical calculations. This article surveys methods for optimizing equilibrium geometries, locating transition structures, and following reaction paths. The emphasis is on optimizations using quasi‐Newton methods that rely on energy gradients, and the discussion includes Hessian updating, line searches, trust radius, and rational function optimization techniques. Single‐ended and double‐ended methods are discussed for transition state searches. Single‐ended techniques include quasi‐Newton, reduced gradient following and eigenvector following methods. Double‐ended methods include nudged elastic band, string, and growing string methods. The discussions conclude with methods for validating transition states and following steepest descent reaction paths. © 2011 John Wiley & Sons, Ltd. WIREs Comput Mol Sci 2011 1 790–809 DOI: 10.1002/wcms.34 This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods

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Trajectory Simulations of Molecular Collisions: Classical Treatment

Cited by 6 publications

References 207 publications

Adsorption of Ethene-1,2-Dione on Materials Based on Graphene

Adsorption of Ethene-1,2-Dione on Materials Based on Graphene

Mechanistic investigations on Pinnick oxidation: a density functional theory study

Geometry optimization

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