1
|
Almazova N, Aubry S, Tsironis GP. Targeted Energy Transfer Dynamics and Chemical Reactions. ENTROPY (BASEL, SWITZERLAND) 2024; 26:753. [PMID: 39330086 PMCID: PMC11431403 DOI: 10.3390/e26090753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/29/2024] [Accepted: 08/31/2024] [Indexed: 09/28/2024]
Abstract
Ultrafast reaction processes take place when resonant features of nonlinear model systems are taken into account. In the targeted energy or electron transfer dimer model this is accomplished through the implementation of nonlinear oscillators with opposing types of nonlinearities, one attractive while the second repulsive. In the present work, we show that this resonant behavior survives if we take into account the vibrational degrees of freedom as well. After giving a summary of the basic formalism of chemical reactions we show that resonant electron transfer can be assisted by vibrations. We find the condition for this efficient transfer and show that in the case of additional interaction with noise, a distinct non-Arrhenius behavior develops that is markedly different from the usual Kramers-like activated transfer.
Collapse
Affiliation(s)
- Natalya Almazova
- Institute of Theoretical and Computational Physics, Department of Physics, University of Crete, 71003 Heraklion, Greece
| | - Serge Aubry
- Institute of Theoretical and Computational Physics, Department of Physics, University of Crete, 71003 Heraklion, Greece
| | - Giorgos P Tsironis
- Institute of Theoretical and Computational Physics, Department of Physics, University of Crete, 71003 Heraklion, Greece
| |
Collapse
|
2
|
Menon A, Pascazio L, Nurkowski D, Farazi F, Mosbach S, Akroyd J, Kraft M. OntoPESScan: An Ontology for Potential Energy Surface Scans. ACS OMEGA 2023; 8:2462-2475. [PMID: 36687109 PMCID: PMC9850739 DOI: 10.1021/acsomega.2c06948] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
In this work, a new OntoPESScan ontology is developed for the semantic representation of one-dimensional potential energy surface (PES) scans, a central concept in computational chemistry. This ontology is developed in line with knowledge graph principles and The World Avatar (TWA) project. OntoPESScan is linked to other ontologies for chemistry in TWA, including OntoSpecies, which helps uniquely identify species along the PES and access their properties, and OntoCompChem, which allows the association of potential energy surfaces with quantum chemical calculations and the concepts used to derive them. A force-field fitting agent is also developed that makes use of the information in the OntoPESScan ontology to fit force fields to reactive surfaces of interest on the fly by making use of the empirical valence bond methodology. This agent is demonstrated to successfully parametrize two cases, namely, a PES scan on ethanol and a PES scan on a localized π-radical PAH hypothesized to play a role in soot formation during combustion. OntoPESScan is an extension to the capabilities of TWA and, in conjunction with potential further ontological support for molecular dynamics and reactions, will further progress toward an open, continuous, and self-growing knowledge graph for chemistry.
Collapse
Affiliation(s)
- Angiras Menon
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Laura Pascazio
- CARES, Cambridge Centre for Advanced Research and Education
in Singapore, 1 Create
Way, CREATE Tower, #05-05, Singapore 138602
| | - Daniel Nurkowski
- CMCL
Innovations, Sheraton House, Castle Park, Cambridge CB3 0AX, U.K.
| | - Feroz Farazi
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Sebastian Mosbach
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
- CARES, Cambridge Centre for Advanced Research and Education
in Singapore, 1 Create
Way, CREATE Tower, #05-05, Singapore 138602
| | - Jethro Akroyd
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
- CARES, Cambridge Centre for Advanced Research and Education
in Singapore, 1 Create
Way, CREATE Tower, #05-05, Singapore 138602
| | - Markus Kraft
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
- CARES, Cambridge Centre for Advanced Research and Education
in Singapore, 1 Create
Way, CREATE Tower, #05-05, Singapore 138602
- School
of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459
- The
Alan Turing Institute, London NW1 2BD, United
Kingdom
| |
Collapse
|
3
|
Scivetti I, Sen K, Elena AM, Todorov I. Reactive Molecular Dynamics at Constant Pressure via Nonreactive Force Fields: Extending the Empirical Valence Bond Method to the Isothermal-Isobaric Ensemble. J Phys Chem A 2020; 124:7585-7597. [PMID: 32820921 DOI: 10.1021/acs.jpca.0c05461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Empirical Valence Bond (EVB) method offers a suitable framework to obtain reactive potentials through the coupling of nonreactive force fields. In this formalism, most of the implemented coupling terms are built using functional forms that depend on spatial coordinates, while parameters are fitted against reference data to model the change of chemistry between the participating nonreactive states. In this work, we demonstrate that the use of such coupling terms precludes the computation of the stress tensor for condensed phase systems and prevents the possibility to carry out EVB molecular dynamics in the isothermal-isobaric (NPT) ensemble. Alternatively, we make use of coupling terms that depend on the energy gaps, defined as the energy differences between the participating nonreactive force fields, and derive a general expression for the EVB stress tensor suitable for computation. Implementation of this new methodology is tested for a model of a single reactive malonaldehyde solvated in nonreactive water. Mass densities and probability distributions for the values of the energy gaps computed in the NPT ensemble reveal a negligible role of the reactive potential in the limit of low concentrated solutions, thus corroborating for the first time the validity of approximations based on the canonical NVT ensemble, customarily adopted for EVB simulations. The presented formalism also aims to contribute to future implementations and extensions of the EVB method to research the limit of highly concentrated solutions.
Collapse
Affiliation(s)
- Ivan Scivetti
- Daresbury Laboratory, Sc. Tech., Keckwick Lane, Daresbury, Warrington WA4 4AD, U.K.,Department of Chemistry, University of Liverpool, Liverpool L69 3BX, U.K
| | - Kakali Sen
- Daresbury Laboratory, Sc. Tech., Keckwick Lane, Daresbury, Warrington WA4 4AD, U.K
| | - Alin M Elena
- Daresbury Laboratory, Sc. Tech., Keckwick Lane, Daresbury, Warrington WA4 4AD, U.K
| | - Ilian Todorov
- Daresbury Laboratory, Sc. Tech., Keckwick Lane, Daresbury, Warrington WA4 4AD, U.K
| |
Collapse
|
4
|
Heidari M, Cortes-Huerto R, Kremer K, Potestio R. Concurrent coupling of realistic and ideal models of liquids and solids in Hamiltonian adaptive resolution simulations. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:64. [PMID: 29785645 DOI: 10.1140/epje/i2018-11675-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/03/2018] [Indexed: 05/27/2023]
Abstract
To understand the properties of a complex system it is often illuminating to perform a comparison with a simpler, even idealised one. A prototypical application of this approach is the calculation of free energies and chemical potentials in liquids, which can be decomposed in the sum of ideal and excess contributions. In the same spirit, in computer simulations it is possible to extract useful information on a given system making use of setups where two models, an accurate one and a simpler one, are concurrently employed and directly coupled. Here, we tackle the issue of coupling atomistic or, more in general, interacting models of a system with the corresponding idealised representations: for a liquid, this is the ideal gas, i.e. a collection of non-interacting particles; for a solid, we employ the ideal Einstein crystal, a construct in which particles are decoupled from one another and restrained by a harmonic, exactly integrable potential. We describe in detail the practical and technical aspects of these simulations, and suggest that the concurrent usage and coupling of realistic and ideal models represents a promising strategy to investigate liquids and solids in silico.
Collapse
Affiliation(s)
- Maziar Heidari
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | | | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Raffaello Potestio
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.
- Physics Department, University of Trento, via Sommarive, 14 I-38123, Trento, Italy.
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123, Trento, Italy.
| |
Collapse
|
5
|
Molecular Docking, Molecular Dynamics Simulations, Computational Screening to Design Quorum Sensing Inhibitors Targeting LuxP of Vibrio harveyi and Its Biological Evaluation. Appl Biochem Biotechnol 2016; 181:192-218. [DOI: 10.1007/s12010-016-2207-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 08/05/2016] [Indexed: 10/21/2022]
|