Investigation of the molecular mechanisms of electronic decoherence within a quinone cofactor

2013 ◽  
Vol 91 (7) ◽  
pp. 628-636 ◽  
Author(s):  
Christophe Narth ◽  
Natacha Gillet ◽  
Bernard Lévy ◽  
Isabelle Demachy ◽  
Aurélien de la Lande
Keyword(s):  
Potential Energy Surfaces ◽  
Density Functional ◽  
Molecular Mechanisms ◽  
Tight Binding ◽  
Mass Effect ◽  
Methylamine Dehydrogenase ◽  
Molecular Systems ◽  
Tryptophan Tryptophylquinone ◽  
Dynamics Simulations ◽  
Energy Surfaces

The notion of decoherence is particularly adapted to discuss the quantum-to-classical transition in the context of chemical reactions. Decoherence can be modeled by computing the time evolution of nuclear wave packets evolving on distinct potential energy surfaces, here using density functional theory (DFT) and Born–Oppenheimer molecular dynamics simulations. We investigate a redox cofactor of biological interest (tryptophan tryptophylquinone, TTQ) found in the enzyme methylamine dehydrogenase. We also report the first systematic comparison of semi-empirical DFT (tight-binding DFT) and classical force field approaches for estimating decoherence in molecular systems. In the TTQ cofactor, we find that decoherence combines structural and dynamical aspects: it is initiated by the divergent motions of few atoms and then propagates dynamically to the remaining atoms. It is the mass effect of all the atoms that leads to decoherence within a few femtosecond.

scholarly journals Nonadiabatic Dynamics in Multidimensional Complex Potential Energy Surfaces

2020 ◽  
Author(s):  
Fábris Kossoski ◽  
Mario Barbatti
Keyword(s):  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Electron Attachment ◽  
Complex Surface ◽  
Nonadiabatic Dynamics ◽  
Surface Hopping ◽  
Molecular Systems ◽  
Out Of Plane ◽  
Dynamics Simulations ◽  
Energy Surfaces

<p>Despite the continuous development of theoretical methodologies for describing nonadiabatic dynamics of molecular systems, there is a lack of approaches for processes where the norm of the wave function is not conserved, i.e., when an imaginary potential accounts for some irreversible decaying mechanism. Current approaches rely on building potential energy surfaces of reduced dimensionality, which is not optimal for more involving and realistic multidimensional problems. Here, we present a novel methodology for describing the dynamics of complex-valued molecular Hamiltonians, which is a generalisation of the trajectory surface hopping method. As a first application, the complex surface fewest switches surface hopping (CS-FSSH) method was employed to survey the relaxation mechanisms of the shape resonant anions of iodoethene. We have provided the first detailed and dynamical picture of the p*/s* mechanism of dissociative electron attachment in halogenated unsaturated compounds, which is believed to underlie electron-induced reactions of several molecules of interest. Electron capture into the p* orbital promotes C=C stretching and out-of-plane vibrations, followed by charge transfer from the double bond into the s* orbital at the C-I bond, and, finally, release of the iodine ion, all within only 15 fs. On-the-fly dynamics simulations of a vast class of processes can be envisioned with the CS-FSSH methodology, including autoionisation from transient anions, core-ionised and superexcited states, Auger and interatomic Coulombic decay, and time-dependent luminescence.</p>

scholarly journals Nonadiabatic Dynamics in Multidimensional Complex Potential Energy Surfaces

2020 ◽  
Author(s):  
Fábris Kossoski ◽  
Mario Barbatti
Keyword(s):  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Electron Attachment ◽  
Complex Surface ◽  
Nonadiabatic Dynamics ◽  
Surface Hopping ◽  
Molecular Systems ◽  
Out Of Plane ◽  
Dynamics Simulations ◽  
Energy Surfaces

<p>Despite the continuous development of theoretical methodologies for describing nonadiabatic dynamics of molecular systems, there is a lack of approaches for processes where the norm of the wave function is not conserved, i.e., when an imaginary potential accounts for some irreversible decaying mechanism. Current approaches rely on building potential energy surfaces of reduced dimensionality, which is not optimal for more involving and realistic multidimensional problems. Here, we present a novel methodology for describing the dynamics of complex-valued molecular Hamiltonians, which is a generalisation of the trajectory surface hopping method. As a first application, the complex surface fewest switches surface hopping (CS-FSSH) method was employed to survey the relaxation mechanisms of the shape resonant anions of iodoethene. We have provided the first detailed and dynamical picture of the π*/σ* mechanism of dissociative electron attachment in halogenated unsaturated compounds, which is believed to underlie electron-induced reactions of several molecules of interest. Electron capture into the π* orbital promotes C=C stretching and out-of-plane vibrations, followed by charge transfer from the double bond into the σ* orbital at the C-I bond, and, finally, release of the iodine ion, all within only 15 fs. On-the-fly dynamics simulations of a vast class of processes can be envisioned with the CS-FSSH methodology, including autoionisation from transient anions, core-ionised and superexcited states, Auger and interatomic Coulombic decay, and time-dependent luminescence.</p>

scholarly journals Nonadiabatic Dynamics in Multidimensional Complex Potential Energy Surfaces

2020 ◽  
Author(s):  
Fábris Kossoski ◽  
Mario Barbatti
Keyword(s):  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Electron Attachment ◽  
Complex Surface ◽  
Nonadiabatic Dynamics ◽  
Surface Hopping ◽  
Molecular Systems ◽  
Out Of Plane ◽  
Dynamics Simulations ◽  
Energy Surfaces

<p>Despite the continuous development of theoretical methodologies for describing nonadiabatic dynamics of molecular systems, there is a lack of approaches for processes where the norm of the wave function is not conserved, i.e., when an imaginary potential accounts for some irreversible decaying mechanism. Current approaches rely on building potential energy surfaces of reduced dimensionality, which is not optimal for more involving and realistic multidimensional problems. Here, we present a novel methodology for describing the dynamics of complex-valued molecular Hamiltonians, which is a generalisation of the trajectory surface hopping method. As a first application, the complex surface fewest switches surface hopping (CS-FSSH) method was employed to survey the relaxation mechanisms of the shape resonant anions of iodoethene. We have provided the first detailed and dynamical picture of the π*/σ* mechanism of dissociative electron attachment in halogenated unsaturated compounds, which is believed to underlie electron-induced reactions of several molecules of interest. Electron capture into the π* orbital promotes C=C stretching and out-of-plane vibrations, followed by charge transfer from the double bond into the σ* orbital at the C-I bond, and, finally, release of the iodine ion, all within only 15 fs. On-the-fly dynamics simulations of a vast class of processes can be envisioned with the CS-FSSH methodology, including autoionisation from transient anions, core-ionised and superexcited states, Auger and interatomic Coulombic decay, and time-dependent luminescence.</p>

Impact of vibronic coupling effects on light-driven charge transfer in pyrene-functionalized middle and large-sized Metalloid Gold Nanoclusters from Ehrenfest dynamics.

2021 ◽  
Author(s):  
Adrian Dominguez-Castro ◽  
Thomas Frauenheim
Keyword(s):  
Molecular Dynamics ◽  
Charge Transfer ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Gold Nanoclusters ◽  
Tight Binding ◽  
Time Dependent ◽  
Effective Strategy ◽  
Dynamics Simulations ◽  
Dependent Density

Theoretical calculations are an effective strategy to comple- ment and understand experimental results in atomistic detail. Ehrenfest molecular dynamics simulations based on the real-time time-dependent density functional tight-binding (RT-TDDFTB) approach...

Mechanisms and kinetics of initial pyrolysis and combustion reactions of 1,1-diamino-2,2-dinitroethylene from density functional tight-binding molecular dynamics simulations

2019 ◽  
Vol 97 (11) ◽  
pp. 795-804 ◽  
Author(s):  
Dong Xiang ◽  
Weihua Zhu
Keyword(s):  
Activation Energy ◽  
Molecular Dynamics ◽  
Density Functional ◽  
Tight Binding ◽  
Combustion Process ◽  
Exponential Factor ◽  
Three Stages ◽  
Dynamics Simulations ◽  
Combustion Processes ◽  
Kinetics Of

The density functional tight-binding molecular dynamics approach was used to study the mechanisms and kinetics of initial pyrolysis and combustion reactions of isolated and multi-molecular FOX-7. Based on the thermal cleavage of bridge bonds, the pyrolysis process of FOX-7 can be divided into three stages. However, the combustion process can be divided into five decomposition stages, which is much more complex than the pyrolysis reactions. The vibrations in the mean temperature contain nodes signifying the formation of new products and thereby the transitions between the various stages in the pyrolysis and combustion processes. Activation energy and pre-exponential factor for the pyrolysis and combustion reactions of FOX-7 were obtained from the kinetic analysis. It is found that the activation energy of its pyrolysis and combustion reactions are very low, making both take place fast. Our simulations provide the first atomic-level look at the full dynamics of the complicated pyrolysis and combustion process of FOX-7.

scholarly journals The ANI-1ccx and ANI-1x Data Sets, Coupled-Cluster and Density Functional Theory Properties for Molecules

2020 ◽  
Author(s):  
Justin S. Smith ◽  
Roman Zubatyuk ◽  
Benjamin T. Nebgen ◽  
Nicholas Lubbers ◽  
Kipton Barros ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Potential Energy Surfaces ◽  
Density Functional ◽  
Atomic Charge ◽  
Density Functional Theory Calculations ◽  
Coupled Cluster ◽  
Data Sets ◽  
Data Set ◽  
Functional Theory ◽  
Energy Surfaces

<p>Maximum diversification of data is a central theme in building generalized and accurate machine learning (ML) models. In chemistry, ML has been used to develop models for predicting molecular properties, for example quantum mechanics (QM) calculated potential energy surfaces and atomic charge models. The ANI-1x and ANI-1ccx ML-based eneral-purpose potentials for organic molecules were developed through active learning; an automated data diversification process. Here, we describe the ANI-1x and ANI-1ccx data sets. To demonstrate data set diversity, we visualize them with a dimensionality reduction scheme, and contrast against existing data sets. The ANI-1x data set contains multiple QM properties from 5M density functional theory calculations, while the ANI-1ccx data set contains 500k data points obtained with an accurate CCSD(T)/CBS extrapolation. Approximately 14 million CPU core-hours were expended to generate this data. Multiple QM properties from density functional theory and coupled cluster are provided: energies, atomic forces, multipole moments, atomic charges, and more. We provide this data to the community to aid research and development of ML models for chemistry.</p>

scholarly journals Multiscale QM/MM Molecular Dynamics Simulations of the Trimeric Major Light-Harvesting Complex II

2021 ◽  
Author(s):  
Sayan Maity ◽  
Vangelis Daskalakis ◽  
Marcus Elstner ◽  
Ulrich Kleinekathöfer
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chlorophyll A ◽  
Density Functional ◽  
Light Harvesting ◽  
Higher Plants ◽  
Tight Binding ◽  
Spectral Densities ◽  
Light Harvesting Complex ◽  
Dynamics Simulations

Photosynthetic processes are driven by sunlight. Too little of it and the photosynthetic machinery cannot produce the reductive power to drive the anabolic pathways. Too much sunlight and the machinery can get damaged. In higher plants, the major Light Harvesting Complex (LHCII) efficiently absorbs the light energy, but can also dissipate it when in excess (quenching). In order to study the dynamics related to the quenching process but also the exciton dynamics in general, one needs to accurately determine the so-called spectral density which describes the coupling between the relevant pigment modes and the environmental degrees of freedom. To this end, Born–Oppenheimer molecular dynamics simulations in a quantum mechanics/molecular mechanics (QM/MM) fashion utilizing the density functional based tight binding (DFTB) method have been performed for the ground state dynamics. Subsequently, the time-dependent extension of the long-range-corrected DFTB scheme has been employed for the excited state calculations of the individual chlorophyll-a molecules in the LHCII complex. The analysis of this data resulted in spectral densities showing an astonishing agreement with the experimental counterpart in this rather large system. This consistency with an experimental observable also supports the accuracy, robustness, and reliability of the present multi-scale scheme. In addition, the resulting spectral densities and site energies were used to determine the exciton transfer rate within a special pigment pair consisting of a chlorophyll-a and a carotenoid molecule which is assumed to play a role in the balance between the light harvesting and quenching modes.

scholarly journals Migration of Zeolite-Encapsulated Pt and Au Under Reducing Atmospheres

2021 ◽  
Author(s):  
Dianwei Hou ◽  
Christopher Heard
Keyword(s):  
Monte Carlo ◽  
Potential Energy Surfaces ◽  
Density Functional ◽  
Noble Metals ◽  
Kinetic Monte Carlo ◽  
Pore System ◽  
Kinetic Monte Carlo Simulations ◽  
Zeolite Lta ◽  
Metal Migration ◽  
Energy Surfaces

Unbiased density functional global optimisation calculations, followed by kinetic Monte Carlo simulations are used to enumerate the potential energy surfaces for migration of noble metals Pt and Au inside the pore system of siliceous zeolite LTA. The effects of reducing adsorbates CO and H2 are determined. It is found that the two metals differ significantly in the strength and type of interaction with the framework, with strong, framework breaking interactions between Pt and and the zeolite, but only weak dispersive interactions between Au and the zeolite. Adsorbates are found to dramatically interfere with Pt-framework binding, leading to poorer atom-trapping, enhanced metal migration and faster equilibration.

scholarly journals Energetic Self-Folding Mechanism in α-Helixes

2019 ◽  
Author(s):  
Adolfo Bastida ◽  
José Zúñiga ◽  
Alberto Requena ◽  
Javier Cerezo
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy Surfaces ◽  
Reasonable Agreement ◽  
Dihedral Angles ◽  
Native Conformation ◽  
Experimental Values ◽  
Α Helix ◽  
Dynamics Simulations ◽  
Energy Surfaces ◽  
Large Peptide

A novel energetic route driving the folding of a polyalanine peptide from an extended conformation to its α-helix native conformation is described, supported by a new method to compute mean potential energy surfaces accurately in terms of the dihedral angles of the peptide chain from extensive Molecular Dynamics simulations. The Energetic Self-Folding (ESF) route arises specifically from the balance between the intrinsic propensity of alanine residues towards the α<sub>R </sub>conformation and two, opposite, effects: the destabilizing interaction with neighbor residues and the stabilizing formation of native hydrogen bonds, with the latter being dominant for large peptide lengths. The ESF mechanism provides simple but robust support to the nucleation-elongation, or zipper models, and offers a quantitative energetic funnel picture of the folding process. The mechanism is validated by the reasonable agreement between the computed folding energies and the experimental values.

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