Constructing Potential Energy Surfaces for Polyatomic Systems: Recent Progress and New Problems

Espinosa‐García, J.; Monge‐Palacios, M.; Corchado, J. C.

doi:10.1155/2012/164752

Cited by 21 publications

(16 citation statements)

References 101 publications

(176 reference statements)

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“…Of the different methods developed in the literature for the construction of potential energy surfaces, a feasible alternative approach that has been extensively applied by our group is the construction of analytical potential energy surfaces based on known functional forms. 4,5 The title reaction has been little studied, whether experimentally or theoretically. This may be because the chemistry of the reaction of ammonia with chlorine atoms is very complex with many intermediate fast reactions being involved.…”

Section: Introductionmentioning

confidence: 99%

QCT and QM calculations of the Cl(2P) + NH3 reaction: influence of the reactant well on the dynamics

Monge‐Palacios

Yang

Espinosa‐García

2012

Phys. Chem. Chem. Phys.

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A detailed dynamics study, using both quasi-classical trajectory (QCT) and reduced-dimensional quantum mechanical (QM) calculations, was carried out to understand the reactivity and mechanism of the Cl((2)P) + NH(3)→ HCl + NH(2) gas-phase reaction, which evolves through deep wells in the entry and exit channels. The calculations were performed on an analytical potential energy surface recently developed by our group, PES-2010 [M. Monge-Palacios, C. Rangel, J. C. Corchado and J. Espinosa-Garcia, Int. J. Quantum. Chem., 2011], together with a simplified model surface, mod-PES, in which the reactant well is removed to analyze its influence. The main finding was that the QCT and QM methods show a change of the reaction probability with collision energy, suggesting a change of the atomic-level mechanism of reaction with energy. This change disappeared when the mod-PES was used, showing that the behaviour at low energies is a direct consequence of the existence of the reactant well. Analysis of the trajectories showed that different mechanisms operate depending on the collision energy. Thus, while at high energies (E(coll) > 5 kcal mol(-1)) practically all trajectories are direct, at low energies (E(coll) < 3 kcal mol(-1)) the trajectories are indirect, i.e., with the mediation of a trapping complex in the entry and/or the exit wells. The reactant complex allows repeated encounters between the reactants, increasing the reaction probability at low energies. The differential cross section results reinforce this change of mechanism, showing also the influence of the reactant well on this reaction. Thus, the PES-2010 surface yields a forward-backward symmetry in the scattering, while when the reactant well is removed with the mod-PES the shape is more isotropic.

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Section: Introductionmentioning

confidence: 99%

QCT and QM calculations of the Cl(2P) + NH3 reaction: influence of the reactant well on the dynamics

Monge‐Palacios

Yang

Espinosa‐García

2012

Phys. Chem. Chem. Phys.

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“… 15 All such strategies have positive sides and drawbacks, depending on the size of the system to be studied, the required simulation time, and the quality of the predictions. 1 , 16 , 17 …”

Section: Introductionmentioning

confidence: 99%

Thermal and Mechanochemical Tuning of the Porphyrin Singlet-Triplet Gap for Selective Energy Transfer Processes: A Molecular Dynamics Approach

Zapata

Nucci

Castaño

et al. 2021

J. Chem. Theory Comput.

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Molecular dynamics simulations provide fundamental knowledge on the reaction mechanism of a given simulated molecular process. Nevertheless, other methodologies based on the “static” exploration of potential energy surfaces are usually employed to firmly provide the reaction coordinate directly related to the reaction mechanism, as is the case in intrinsic reaction coordinates for thermally activated reactions. Photoinduced processes in molecular systems can also be studied with these two strategies, as is the case in the triplet energy transfer process. Triplet energy transfer is a fundamental photophysical process in photochemistry and photobiology, being for instance involved in photodynamic therapy, when generating the highly reactive singlet oxygen species. Here, we study the triplet energy transfer process between porphyrin, a prototypical energy transfer donor, and different biologically relevant acceptors, including molecular oxygen, carotenoids, and rhodopsin. The results obtained by means of nanosecond time-scale molecular dynamics simulations are compared to the “static” determination of the reaction coordinate for such a thermal process, leading to the distortions determining an effective energy transfer. This knowledge was finally applied to propose porphyrin derivatives for producing the required structural modifications in order to tune their singlet-triplet energy gap, thus introducing a mechanochemical description of the mechanism.

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“…As other authors have noted, such methods fall broadly into two categories: interpolation and fitting methods. 16,17 Interpolative methods include sparse interpolation based on the Smolyak algorithm with either a polynomial or trigonometric basis, 18,19 modified Shepard interpolation, 12,20−22 and (possibly local) interpolative moving least-squares (IMLS/L-IMLS). 23−25 Noninterpolative fittingbased methods include the (double) many-body expansion (MBE/DMBE), 26−28 moving least-squares (MLS) fitting, 29 permutationally invariant PES by least-squares fitting (PIP), 30−35 the valence bond (VB) functional form, 36−38 and neural network PESs (nn-PES).…”

Section: Introductionmentioning

confidence: 99%

Interpolation Methods for Molecular Potential Energy Surface Construction

et al. 2021

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The concept of a potential energy surface (PES) is one of the most important concepts in modern chemistry. A PES represents the relationship between the chemical system’s energy and its geometry (i.e., atom positions) and can provide useful information about the system’s chemical properties and reactivity. Construction of accurate PESs with high-level theoretical methodologies, such as density functional theory, is still challenging due to a steep increase in the computational cost with the increase of the system size. Thus, over the past few decades, many different mathematical approaches have been applied to the problem of the cost-efficient PES construction. This article serves as a short overview of interpolative methods for the PES construction, including global polynomial interpolation, trigonometric interpolation, modified Shepard interpolation, interpolative moving least-squares, and the automated PES construction derived from these.

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Constructing Potential Energy Surfaces for Polyatomic Systems: Recent Progress and New Problems

Cited by 21 publications

References 101 publications

QCT and QM calculations of the Cl(2P) + NH3 reaction: influence of the reactant well on the dynamics

QCT and QM calculations of the Cl(2P) + NH3 reaction: influence of the reactant well on the dynamics

Thermal and Mechanochemical Tuning of the Porphyrin Singlet-Triplet Gap for Selective Energy Transfer Processes: A Molecular Dynamics Approach

Interpolation Methods for Molecular Potential Energy Surface Construction

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