1
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Yoshino ND, Wang LP. Two P, Ten P, White P, Red P: Mechanistic Exploration of the Oligomerization of Red Phosphorus from Diphosphorus with the Ab Initio Nanoreactor. Inorg Chem 2024; 63:19074-19086. [PMID: 39352782 DOI: 10.1021/acs.inorgchem.4c02299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
Phosphorus is critical to humans on many fronts, yet we do not have a mechanistic understanding of some of its most basic transformations and reactions─namely the oligomerization of white phosphorus to red. With heat or under ultraviolet (UV) exposure, it has been experimentally demonstrated that white phosphorus dissociates into diphosphorus units which readily form red phosphorus. However, the mechanism of this process is unknown. The ab initio nanoreactor approach was used to explore the potential energy surface of phosphorus clusters. Density functional theory and metadynamics simulations were used to characterize potential reaction pathways. A mechanism for oligomerization is proposed to take place via diphosphorus additions at π-bonds and weak σ-bonds through three membered ring intermediates. Downhill paths through P6 and P8 clusters eventually result in P10 clusters that can oligomerize into red phosphorus chains. The initial, rate limiting step for this process has an energy barrier of 24.2 kcal/mol.
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Affiliation(s)
- Nathan D Yoshino
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
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2
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Johansen S, Park H, Wang LP, Crabtree KN. Reactant Discovery with an Ab Initio Nanoreactor: Exploration of Astrophysical N-Heterocycle Precursors and Formation Pathways. ACS EARTH & SPACE CHEMISTRY 2024; 8:1771-1783. [PMID: 39318708 PMCID: PMC11418024 DOI: 10.1021/acsearthspacechem.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/09/2024] [Accepted: 07/30/2024] [Indexed: 09/26/2024]
Abstract
The incorporation of nitrogen atoms into cyclic compounds is essential for terrestrial life; nitrogen-containing (N-)heterocycles make up DNA and RNA nucleobases, several amino acids, B vitamins, porphyrins, and other components of biomolecules. The discovery of these molecules on meteorites with non-terrestrial isotopic abundances supports the hypothesis of exogenous delivery of prebiotic material to early Earth; however, there has been no detection of these species in interstellar environments, indicating that there is a need for greater knowledge of their astrochemical formation and destruction pathways. Here, we present results of simulations of gas-phase pyrrole and pyridine formation from an ab initio nanoreactor, a first-principles molecular dynamics simulation method that accelerates reaction discovery by applying non-equilibrium forces that are agnostic to individual reaction coordinates. Using the nanoreactor in a retrosynthetic mode, starting with the N-heterocycle of interest and a radical leaving group, then considering the discovered reaction pathways in reverse, a rich landscape of N-heterocycle-forming reactivity can be found. Several of these reaction pathways, when mapped to their corresponding minimum energy paths, correspond to novel barrierless formation pathways for pyridine and pyrrole, starting from both detected and hypothesized astrochemical precursors. This study demonstrates how first-principles reaction discovery can build mechanistic knowledge in astrochemical environments as well as in early Earth models such as Titan's atmosphere where N-heterocycles have been tentatively detected.
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Affiliation(s)
| | | | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Kyle N. Crabtree
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
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3
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Castiñeira Reis M, Martínez Núñez E, Fernández Ramos A. Comprehensive computational automated search of barrierless reactions leading to the formation of benzene and other C 6-membered rings. SCIENCE ADVANCES 2024; 10:eadq4077. [PMID: 39259783 PMCID: PMC11389753 DOI: 10.1126/sciadv.adq4077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 08/06/2024] [Indexed: 09/13/2024]
Abstract
We present the systematic exploration of various potential energy surfaces for systems with C6H6-x (x = 0, 1, 2, or 3) empirical formula using an automatic search approach. The primary objective of this study is to identify reaction pathways that lead to the creation of benzene, o-benzyne, and other rings. These pathways initiate with a barrierless recombination reaction and involve subsequent isomerization reactions with submerged transition states until the final product is reached. The reported reaction profiles are consistent with the existing conditions in the interstellar medium if the hot complex formed can cool down through radiative relaxation. Recent studies on the deactivation of polyaromatic hydrocarbons (PAHs) support the possibility of these reactions taking place. The C6-membered rings are considered precursors of PAHs, and our focus is on identifying pathways originating from the barrierless recombination of reactive molecules known to exist in the interstellar medium, with potential implications in other environments.
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Affiliation(s)
- Marta Castiñeira Reis
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Campus Vida, 15782, Universidade de Santiago de Compostela, C/Jenaro de la Fuente s/n, Santiago de Compostela, Spain
| | - Emilio Martínez Núñez
- Departamento de Química Física, Facultade de Química, Campus Vida, 15782, Universidade de Santiago de Compostela, Avda. das Ciencias s/n, Santiago de Compostela, Spain
| | - Antonio Fernández Ramos
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Campus Vida, 15782, Universidade de Santiago de Compostela, C/Jenaro de la Fuente s/n, Santiago de Compostela, Spain
- Departamento de Química Física, Facultade de Química, Campus Vida, 15782, Universidade de Santiago de Compostela, Avda. das Ciencias s/n, Santiago de Compostela, Spain
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4
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Rais N, Salta Z, Tasinato N. Theoretical investigation of the OH-initiated atmospheric degradation mechanism of CX 2CHX (X = H, F, Cl) by advanced quantum chemical and transition state theory methods. Phys Chem Chem Phys 2024; 26:19976-19991. [PMID: 38995148 DOI: 10.1039/d4cp01453g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Halogenated olefins are anthropogenic compounds with many industrial applications but at the same time raising many environmental and health concerns. Gas-phase electrophilic addition of the OH radical to the olefinic CC bond represents the primary sink for these chemicals in the atmosphere, with the degree and type of halogenation playing a significant role in their overall reactivity. In this work, we present a theoretical investigation of the reaction mechanisms and kinetics for the reactions between the OH radical and CH2CH2 (ethylene, ETH), CF2CHF (trifluoroethylene, TFE) and CCl2CHCl (trichloroethylene, TCE), simulated by state-of-the-art protocols and methods, with the aim of providing a detailed interpretation of the available experimental results, as well as new data of relevance to tropospheric chemistry. Specifically, potential energy surfaces (PESs) are obtained using the jun-Cheap (jChS) composite scheme, whereas temperature and pressure dependent rate coefficients and product distributions in the 100-600 K temperature range are calculated within the Rice-Ramsperger-Kassel-Marcus/master equation (RRKM/ME) framework. The rates for barrierless channels are obtained from variable reaction coordinate-variational transition state theory (VRC-VTST) combined with the two transition state model. While the reactions with ETH and TFE proceed mainly via the formation of addition adducts at P = 1 atm and T = 298 K, the dominant channel for TCE is the Cl-elimination reaction. Global rate constants for the two halogenated olefins, TFE and TCE, are found to be pressure-independent, contrary to the case of ETH. The computed rate constants, as well as their temperature and pressure dependence, are in remarkable agreement with the available experimental data, and they are used to derive atmospheric lifetimes (τ) for both TFE and TCE as a function of altitude (h) in the atmosphere, by taking into account variations in the rate coefficients (k (T, P)) and [OH] concentration.
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Affiliation(s)
- Nadjib Rais
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy.
- IUSS Scuola Universitaria Superiore, Piazza della Vittoria 15, I-27100, Pavia, Italy
| | - Zoi Salta
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy.
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126, Pisa, Italy.
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5
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Panadés-Barrueta RL, Duflot D, Soto J, Martínez-Núñez E, Peláez D. Automatic Determination of the Non-Covalent Stable Conformations of the NO 2-Pyrene Cluster in Full Dimensionality (81D) Using the vdW-TSSCDS Approach. Chemphyschem 2024; 25:e202301001. [PMID: 38662437 DOI: 10.1002/cphc.202301001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/27/2024] [Indexed: 05/24/2024]
Abstract
We present the detailed topographical characterisation (stationary points and minimum energy paths connecting them) of the full dimensional (81D) intermolecular potential energy surface associated with the non-covalent interactions between the NO2 radical and the pyrene (C16H10) molecule. The whole procedure is (quasi) fully automated. We have used our recent algorithm vdW-TSSCDS as implemented on the freely-available AutoMekin software package. To this end, a series of inexpensive classical trajectories using forces from a low-level (semi-empirical) theory are used to sample the configuration space of the system in the search for candidates to first order saddle points. These guess structures are determined by means of a graph-theory based algorithm using the concept of adjacency matrix. Low-level optimizations are followed by re-optimizations at a final high-level of theory (DFT and CCSD(T)-F12 in our case.). The resulting set of stationary points and paths connecting them constitutes the so-called reaction network. In the case of NO2-pyrene, this network exhibits four major basins which can be characterized by their point-group symmetry. A central one, of global C2 symmetry, comprises the global minimum (as well as all other permutationally related conformers) together with the corresponding C2v saddle points connecting them. This central basin is connected to three others of lower C1 symmetry. The latter can be distinguished by the projection of the position of the NO2 nitrogen atom on the pyrene plane in combination with the relative orientation of the oxygen pair pointing either inwards, outwards, upwards or downwards.
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Affiliation(s)
- Ramón L Panadés-Barrueta
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01069, Dresden, Germany
| | - Denis Duflot
- Univ. Lille, CNRS, UMR 8523, PhLAM - Physique des Lasers Atomes et Molécules, F-59000, Lille, France
| | - Juan Soto
- Departamento de Química Física, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Emilio Martínez-Núñez
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Daniel Peláez
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405, Orsay, France
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6
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Lupi J, Ayarde-Henríquez L, Kelly M, Dooley S. Ab Initio and Kinetic Modeling of β-d-Xylopyranose under Fast Pyrolysis Conditions. J Phys Chem A 2024; 128:1009-1024. [PMID: 38299300 PMCID: PMC10875674 DOI: 10.1021/acs.jpca.3c07063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Lignocellulosic biomass is an abundant renewable resource that can be upgraded to chemical and fuel products through a range of thermal conversion processes. Fast pyrolysis is a promising technology that uses high temperatures and fast heating rates to convert lignocellulose into bio-oils in high yields in the absence of oxygen. Hemicellulose is one of the three major components of lignocellulosic biomass and is a highly branched heteropolymer structure made of pentose, hexose sugars, and sugar acids. In this study, β-d-xylopyranose is proposed as a model structural motif for the essential chemical structure of hemicellulose. The gas-phase pyrolytic reactivity of β-d-xylopyranose is thoroughly investigated using computational strategies rooted in quantum chemistry. In particular, its thermal degradation potential energy surfaces are computed employing Minnesota global hybrid functional M06-2X in conjunction with the 6-311++G(d,p) Pople basis set. Electronic energies are further refined by performing DLPNO-CCSD(T)-F12 single-point calculations on top of M06-2X geometries using the cc-pVTZ-F12 basis set. Conformational analysis for minima and transition states is performed with state-of-the-art semiempirical quantum chemical methods coupled with metadynamics simulations. Key thermodynamic quantities (free energies, barrier heights, enthalpies of formation, and heat capacities) are computed. Rate coefficients for the initial steps of thermal decomposition are computed by means of reaction rate theory. For the first time, a detailed elementary reaction kinetic model for β-d-xylopyranose is developed by utilizing the thermodynamic and kinetic information acquired from the aforementioned calculations. This model specifically targets the initial stages of β-d-xylopyranose pyrolysis in the high-pressure limit, aiming to gain a deeper understanding of its reaction kinetics. This approach establishes a systematic strategy for exploring reactive pathways, evaluating competing parallel reactions, and selectively accepting or discarding pathways based on the analysis. The findings suggest that acyclic d-xylose plays a significant role as an intermediary in the production of key pyrolytic compounds during the pyrolysis of xylose. These compounds include furfural, anhydro-d-xylopyranose, glycolaldehyde, and dihydrofuran-3(2H)-one.
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Affiliation(s)
- Jacopo Lupi
- School of Physics, Trinity College Dublin, Dublin 2, Ireland
- AMBER, Advance Materials and BioEngineering Research Centre, Dublin 2, Ireland
| | - Leandro Ayarde-Henríquez
- School of Physics, Trinity College Dublin, Dublin 2, Ireland
- AMBER, Advance Materials and BioEngineering Research Centre, Dublin 2, Ireland
| | - Mark Kelly
- School of Physics, Trinity College Dublin, Dublin 2, Ireland
- AMBER, Advance Materials and BioEngineering Research Centre, Dublin 2, Ireland
| | - Stephen Dooley
- School of Physics, Trinity College Dublin, Dublin 2, Ireland
- AMBER, Advance Materials and BioEngineering Research Centre, Dublin 2, Ireland
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7
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Aboulfath Y, Bougueroua S, Cimas A, Barth D, Gaigeot MP. Time-Resolved Graphs of Polymorphic Cycles for H-Bonded Network Identification in Flexible Biomolecules. J Chem Theory Comput 2024; 20:1019-1035. [PMID: 38236138 DOI: 10.1021/acs.jctc.3c01031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
A novel approach based on a coarse-grained representation of topological graphs is proposed for the automatic analysis of molecular dynamics (MD) trajectories of hydrogen-bonded (H-Bonded) flexible biomolecules. Herein, our approach models an H-Bonded biomolecule by its H-Bonded cycles and its graph of cycles in which the vertices and links represent the intersections between these cycles. We propose a methodology in which each identified conformer/isomer from the MD is represented by a well-chosen set of H-Bonded cycles called a minimum cycle basis. The key component is the "polycycles" that distinguish the cycles that play the same polymorphic role in the molecule from the ones that lead to an actual conformational change of the molecule. The relevance of our proposed method is evaluated on MD trajectories of gas-phase biomolecules, for which the covalent bonds are unchanged over time and only the hydrogen bonds change over time. The polygraphs and their time evolution are shown to reveal the dynamicity of the metastructure(s) of the H-Bonded biomolecules while providing polymorphic information on the cycles. Such information on the dynamics and changes in the H-bond network, as some cycles change identity while retaining the same role in the overall structure, is not easily captured at the atomic level of representation. Such information can instead be captured by polymorphic cycles.
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Affiliation(s)
- Ylène Aboulfath
- Université Paris-Saclay, Univ Versailles Saint Quentin, DAVID, 78035 Versailles, France
| | - Sana Bougueroua
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Alvaro Cimas
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
| | - Dominique Barth
- Université Paris-Saclay, Univ Versailles Saint Quentin, DAVID, 78035 Versailles, France
| | - Marie-Pierre Gaigeot
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry-Courcouronnes, France
- Institut Universitaire de France (IUF), 75005 Paris, France
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8
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Kopp WA, Huang C, Zhao Y, Yu P, Schmalz F, Krep L, Leonhard K. Automatic Potential Energy Surface Exploration by Accelerated Reactive Molecular Dynamics Simulations: From Pyrolysis to Oxidation Chemistry. J Phys Chem A 2023; 127:10681-10692. [PMID: 38059461 DOI: 10.1021/acs.jpca.3c05253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Automatic potential energy surface (PES) exploration is important to a better understanding of reaction mechanisms. Existing automatic PES mapping tools usually rely on predefined knowledge or computationally expensive on-the-fly quantum-chemical calculations. In this work, we have developed the PESmapping algorithm for discovering novel reaction pathways and automatically mapping out the PES using merely one starting species is present. The algorithm explores the unknown PES by iteratively spawning new reactive molecular dynamics (RMD) simulations for species that it has detected within previous RMD simulations. We have therefore extended the RMD simulation tool ChemTraYzer2.1 (Chemical Trajectory Analyzer, CTY) for this PESmapping algorithm. It can generate new seed species, automatically start replica simulations for new pathways, and stop the simulation when a reaction is found, reducing the computational cost of the algorithm. To explore PESs with low-temperature reactions, we applied the acceleration method collective variable (CV)-driven hyperdynamics. This involved the development of tailored CV templates, which are discussed in this study. We validate our approach for known pathways in various pyrolysis and oxidation systems: hydrocarbon isomerization and dissociation (C4H7 and C8H7 PES), mostly dominant at high temperatures and low-temperature oxidation of n-butane (C4H9O2 PES) and cyclohexane (C6H11O2 PES). As a result, in addition to new pathways showing up in the simulations, common isomerization and dissociation pathways were found very fast: for example, 44 reactions of butenyl radicals including major isomerizations and decompositions within about 30 min wall time and low-temperature chemistry such as the internal H-shift of RO2 → QO2H within 1 day wall time. Last, we applied PESmapping to the oxidation of the recently proposed biohybrid fuel 1,3-dioxane and validated that the tool could be used to discover new reaction pathways of larger molecules that are of practical use.
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Affiliation(s)
- Wassja A Kopp
- Institute of Technical Thermodynamics, RWTH Aachen University, 52062 Aachen, Germany
| | - Can Huang
- Institute of Technical Thermodynamics, RWTH Aachen University, 52062 Aachen, Germany
| | - Yuqing Zhao
- Institute of Technical Thermodynamics, RWTH Aachen University, 52062 Aachen, Germany
| | - Peiyang Yu
- Institute of Technical Thermodynamics, RWTH Aachen University, 52062 Aachen, Germany
| | - Felix Schmalz
- Institute of Technical Thermodynamics, RWTH Aachen University, 52062 Aachen, Germany
| | - Lukas Krep
- Institute of Technical Thermodynamics, RWTH Aachen University, 52062 Aachen, Germany
| | - Kai Leonhard
- Institute of Technical Thermodynamics, RWTH Aachen University, 52062 Aachen, Germany
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9
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Zhang Y, Xu C, Lan Z. Automated Exploration of Reaction Networks and Mechanisms Based on Metadynamics Nanoreactor Simulations. J Chem Theory Comput 2023. [PMID: 38031422 DOI: 10.1021/acs.jctc.3c00752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
We developed an automated approach to construct a complex reaction network and explore the reaction mechanisms for numerous reactant molecules by integrating several theoretical approaches. Nanoreactor-type molecular dynamics was used to generate possible chemical reactions, in which the metadynamics was used to overcome the reaction barriers, and the semiempirical GFN2-xTB method was used to reduce the computational cost. Reaction events were identified from trajectories using the hidden Markov model based on the evolution of the molecular connectivity. This provided the starting points for further transition-state searches at the electronic structure levels of density functional theory to obtain the reaction mechanism. Finally, the entire reaction network containing multiple pathways was built. The feasibility and efficiency of the automated construction of the reaction network were investigated using the HCHO and NH3 biomolecular reaction and the reaction network for a multispecies system comprising dozens of HCN and H2O molecules. The results indicated that the proposed approach provides a valuable and effective tool for the automated exploration of the reaction networks.
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Affiliation(s)
- Yutai Zhang
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Chao Xu
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Zhenggang Lan
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
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10
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Li G, Li Z, Gao L, Chen S, Wang G, Li S. Combined molecular dynamics and coordinate driving method for automatically searching complicated reaction pathways. Phys Chem Chem Phys 2023; 25:23696-23707. [PMID: 37610711 DOI: 10.1039/d3cp02443a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The combined molecular dynamics and coordinate driving (MD/CD) method is updated and generalized in this work to broaden its applications in automatically searching reaction pathways for complicated reactions. In this updated version, MD simulations are performed with the GFN's family of methods to systematically sample conformers for almost any systems with atomic numbers Z ≤ 86. The improved CD procedure is greatly accelerated by applying a pre-screening stage at the semiempirical GFN2-xTB level. An automatic module based on the Marcus theory and its improved version (the Wolynes theory) is designed to include single electron transfer (SET) processes into reaction pathways. The capabilities of this method are demonstrated by exploring the most possible reaction pathways of three experimentally reported reactions: the organophosphine-catalyzed trans phosphinoboration, the Fe(II) complex-mediated C(sp2)-H borylation reaction, and the SET-triggered deaminative radical cross-coupling reaction. Comprehensive reaction networks are obtained for all three reactions with reasonable computational costs. Detailed mechanisms for these reactions can account for the reported experimental facts.
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Affiliation(s)
- Guoao Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| | - Zhenxing Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| | - Liuzhou Gao
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| | - Shengda Chen
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| | - Guoqiang Wang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| | - Shuhua Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
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11
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Ballotta B, Martínez-Núñez E, Rampino S, Barone V. New prebiotic molecules in the interstellar medium from the reaction between vinyl alcohol and CN radicals: unsupervised reaction mechanism discovery, accurate electronic structure calculations and kinetic simulations. Phys Chem Chem Phys 2023; 25:22840-22850. [PMID: 37584420 DOI: 10.1039/d3cp02571c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Vinyl alcohol (VyA) and cyanide (CN) radicals are relatively abundant in the interstellar medium (ISM). VyA is the enolic tautomer of acetaldehyde and has two low-lying conformers, characterized by the syn or anti placement of hydroxyl hydrogen with respect to the double bond. In this paper, we present a gas-phase model of the barrierless reactions of both VyA's conformers with CN employing accurate quantum chemical computations in the framework of a master equation approach based on the transition state theory. Our results indicate that both VyA conformers feature a similar reactivity with CN, starting with a barrierless addition to the double bond and followed by different isomerization, dissociation, and/or hydrogen elimination steps. The rate constants computed for temperatures up to 600 K show that several reaction channels are open even under the harsh conditions of the ISM, with the favoured one providing the first feasible formation route of a prebiotic molecule not yet detected in the ISM, namely cyanoacetaldehyde. This finding suggests looking for cyanoacetaldehyde in regions where both VyA and CN have already been detected, like, e.g., Sagittarius B2N or G+0.693-0.027.
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Affiliation(s)
- Bernardo Ballotta
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
| | - Emilio Martínez-Núñez
- Departamento de Química Física, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, Avenida das Ciencias s/n, 15782, Santiago de Compostela, Spain
| | - Sergio Rampino
- Università degli Studi di Padova, Dipartimento di Scienze Chimiche, Via Marzolo 1, 35131 Padova, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
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12
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Johnson MS, Gierada M, Hermes ED, Bross DH, Sargsyan K, Najm HN, Zádor J. Pynta─An Automated Workflow for Calculation of Surface and Gas-Surface Kinetics. J Chem Inf Model 2023; 63:5153-5168. [PMID: 37559203 DOI: 10.1021/acs.jcim.3c00948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Many important industrial processes rely on heterogeneous catalytic systems. However, given all possible catalysts and conditions of interest, it is impractical to optimize most systems experimentally. Automatically generated microkinetic models can be used to efficiently consider many catalysts and conditions. However, these microkinetic models require accurate estimation of many thermochemical and kinetic parameters. Manually calculating these parameters is tedious and error prone, involving many interconnected computations. We present Pynta, a workflow software for automating the calculation of surface and gas-surface reactions. Pynta takes the reactants, products, and atom maps for the reactions of interest, generates sets of initial guesses for all species and saddle points, runs all optimizations, frequency, and IRC calculations, and computes the associated thermochemistry and rate coefficients. It is able to consider all unique adsorption configurations for both adsorbates and saddle points, allowing it to handle high index surfaces and bidentate species. Pynta implements a new saddle point guess generation method called harmonically forced saddle point searching (HFSP). HFSP defines harmonic potentials based on the optimized adsorbate geometries and which bonds are breaking and forming that allow initial placements to be optimized using the GFN1-xTB semiempirical method to create reliable saddle point guesses. This method is reaction class agnostic and fast, allowing Pynta to consider all possible adsorbate site placements efficiently. We demonstrate Pynta on 11 diverse reactions involving monodenate, bidentate, and gas-phase species, many distinct reaction classes, and both a low and a high index facet of Cu. Our results suggest that it is very important to consider reactions between adsorbates adsorbed in all unique configurations for interadsorbate group transfers and reactions on high index surfaces.
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Affiliation(s)
- Matthew S Johnson
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States
| | - Maciej Gierada
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States
| | - Eric D Hermes
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States
| | - David H Bross
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Khachik Sargsyan
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States
| | - Habib N Najm
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States
| | - Judit Zádor
- Combustion Research Facility, Sandia National Laboratories, Livermore, California 94550, United States
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13
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Guerrero-Méndez L, Lema-Saavedra A, Jiménez E, Fernández-Ramos A, Martínez-Núñez E. Gas-phase formation of glycolonitrile in the interstellar medium. Phys Chem Chem Phys 2023; 25:20988-20996. [PMID: 37503548 DOI: 10.1039/d3cp02379f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Our automated reaction discovery program, AutoMeKin, has been utilized to investigate the formation of glycolonitrile (HOCH2CN) in the gas phase under the low temperatures of the interstellar medium (ISM). The feasibility of a proposed pathway depends on the absence of barriers above the energy of reactants and the availability of the suggested precursors in the ISM. Based on these criteria, several radical-radical reactions and a radical-molecule reaction have been identified as viable formation routes in the ISM. Among the radical-radical reactions, OH + CH2CN appears to be the most relevant, considering the energy of the radicals and its ability to produce glycolonitrile in a single step. However, our analysis reveals that this reaction produces hydrogen isocyanide (HNC) and formaldehyde (CH2O), with rate coefficients ranging from (7.3-11.5) × 10-10 cm3 molecule-1 s-1 across the temperature range of 10-150 K. Furthermore, the identification of this remarkably efficient pathway for HNC elimination from glycolonitrile significantly broadens the possibilities for any radical-radical mechanism proposed in our research to be considered as a feasible pathway for the formation of HNC in the ISM. This finding is particularly interesing given the persistently unexplained overabundance of hydrogen isocyanide in the ISM. Among the radical-molecule reactions investigated, the most promising one is OH + CH2CHNH, which forms glycolonitrile and atomic hydrogen with rate coefficients in the range (0.3-6.6) × 10-10 cm3 molecule-1 s-1 within the 10-150 K temperature range. Our calculations indicate that the formation of both hydrogen isocyanide and glycolonitrile is efficient under the harsh conditions of the ISM.
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Affiliation(s)
- Luis Guerrero-Méndez
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Avda. das Ciencias s/n 15782, Santiago de Compostela, Spain.
| | - Anxo Lema-Saavedra
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS), Universidade de Santiago de Compostela, C/Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain
| | - Elena Jiménez
- Departamento de Química Física, Facultad de Ciencias y Tecnologías Químicas, Universidad de Castilla-La Mancha, Avda. Camilo José Cela 1b, 13071, Ciudad Real, Spain
- Instituto de Investigación en Combustión y Contaminación Atmosférica (ICCA), Universidad de Castilla-La Mancha, Camino de Moledores s/n, 13071, Ciudad Real, Spain
| | - Antonio Fernández-Ramos
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Avda. das Ciencias s/n 15782, Santiago de Compostela, Spain.
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS), Universidade de Santiago de Compostela, C/Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain
| | - Emilio Martínez-Núñez
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Avda. das Ciencias s/n 15782, Santiago de Compostela, Spain.
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14
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Bougueroua S, Bricage M, Aboulfath Y, Barth D, Gaigeot MP. Algorithmic Graph Theory, Reinforcement Learning and Game Theory in MD Simulations: From 3D Structures to Topological 2D-Molecular Graphs (2D-MolGraphs) and Vice Versa. Molecules 2023; 28:molecules28072892. [PMID: 37049654 PMCID: PMC10096312 DOI: 10.3390/molecules28072892] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 04/14/2023] Open
Abstract
This paper reviews graph-theory-based methods that were recently developed in our group for post-processing molecular dynamics trajectories. We show that the use of algorithmic graph theory not only provides a direct and fast methodology to identify conformers sampled over time but also allows to follow the interconversions between the conformers through graphs of transitions in time. Examples of gas phase molecules and inhomogeneous aqueous solid interfaces are presented to demonstrate the power of topological 2D graphs and their versatility for post-processing molecular dynamics trajectories. An even more complex challenge is to predict 3D structures from topological 2D graphs. Our first attempts to tackle such a challenge are presented with the development of game theory and reinforcement learning methods for predicting the 3D structure of a gas-phase peptide.
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Affiliation(s)
- Sana Bougueroua
- Université Paris-Saclay, University Evry, CY Cergy Paris Université, CNRS, LAMBE UMR8587, 91025 Evry-Courcouronnes, France
| | - Marie Bricage
- Université Paris-Saclay, University Versailles Saint Quentin, DAVID, 78000 Versailles, France
| | - Ylène Aboulfath
- Université Paris-Saclay, University Versailles Saint Quentin, DAVID, 78000 Versailles, France
| | - Dominique Barth
- Université Paris-Saclay, University Versailles Saint Quentin, DAVID, 78000 Versailles, France
| | - Marie-Pierre Gaigeot
- Université Paris-Saclay, University Evry, CY Cergy Paris Université, CNRS, LAMBE UMR8587, 91025 Evry-Courcouronnes, France
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15
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García-Andrade X, García Tahoces P, Pérez-Ríos J, Martínez Núñez E. Barrier Height Prediction by Machine Learning Correction of Semiempirical Calculations. J Phys Chem A 2023; 127:2274-2283. [PMID: 36877614 PMCID: PMC10845151 DOI: 10.1021/acs.jpca.2c08340] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/19/2023] [Indexed: 03/07/2023]
Abstract
Different machine learning (ML) models are proposed in the present work to predict density functional theory-quality barrier heights (BHs) from semiempirical quantum mechanical (SQM) calculations. The ML models include a multitask deep neural network, gradient-boosted trees by means of the XGBoost interface, and Gaussian process regression. The obtained mean absolute errors are similar to those of previous models considering the same number of data points. The ML corrections proposed in this paper could be useful for rapid screening of the large reaction networks that appear in combustion chemistry or in astrochemistry. Finally, our results show that 70% of the features with the highest impact on model output are bespoke predictors. This custom-made set of predictors could be employed by future Δ-ML models to improve the quantitative prediction of other reaction properties.
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Affiliation(s)
| | - Pablo García Tahoces
- Department
of Electronics and Computer Science, University
of Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Jesús Pérez-Ríos
- Department
of Physics, Stony Brook University, Stony Brook, New York 11794, United States
- Institute
for Advanced Computational Science, Stony
Brook University, Stony
Brook, New York 11794-3800, United States
| | - Emilio Martínez Núñez
- Department
of Physical Chemistry, University of Santiago
de Compostela, Santiago
de Compostela 15782, Spain
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16
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Zhang G, Liang X, Li J, Liu Z. Heuristic-Based Alkaline Hydrolysis Mechanism of Nitrate Ester (Nitrocellulose Monomer) and Nitroamine (Hexogen) Compounds: Electrostatic Attraction Effect of the Nitro Group. J Phys Chem A 2023; 127:1609-1618. [PMID: 36780375 DOI: 10.1021/acs.jpca.2c08748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The alkaline hydrolysis reaction of energetic materials is important and complex. With improved performance, AMK_Mountain was used to systematically study the alkaline hydrolysis of the nitrocellulose monomer and hexogen. The reaction pathways showed that the nitrocellulose monomer produces the nitrate anion and nitrite anion differently, while hexogen only produces the nitrite anion. Electronic structure results at the M06-2X/6-311G(d,p)/PCM(Pauling) level showed that the nitrocellulose monomer and hexogen have a similar pathway in their main energy-releasing process (nitrite anion production): with electrostatic attraction effects after proton transfer, the nitrite anion dissociates from the original structure with a low barrier. Moreover, during the alkaline hydrolysis of the nitrocellulose monomer, the metastable intermediates after proton transfer may be directly generated following transition states that, structurally, tend to produce nitrite anions "proximal" to the proton transfer site and produce nitrate anions "distal" to the proton transfer site. Electronic structure analysis showed that representative metastable intermediates revealed that the charge transfer caused by electrostatic attraction may be the direct cause of these reactions.
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Affiliation(s)
- Guan Zhang
- School of Human Settlement and Civil Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xinxin Liang
- School of Human Settlement and Civil Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jin Li
- School of Human Settlement and Civil Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zongkuan Liu
- School of Human Settlement and Civil Engineering, Xi'an Jiaotong University, Xi'an 710049, China
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17
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A quantum-classical correspondence in the dynamics around higher order saddle points: a Bohmian perspective. Theor Chem Acc 2023. [DOI: 10.1007/s00214-023-02957-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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18
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Bougueroua S, Aboulfath Y, Barth D, Gaigeot MP. Algorithmic graph theory for post-processing molecular dynamics trajectories. Mol Phys 2023. [DOI: 10.1080/00268976.2022.2162456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Sana Bougueroua
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, Evry-Courcouronnes, France
| | - Ylène Aboulfath
- Université Paris-Saclay, Univ Versailles SQ, DAVID, Versailles, France
| | - Dominique Barth
- Université Paris-Saclay, Univ Versailles SQ, DAVID, Versailles, France
| | - Marie-Pierre Gaigeot
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, Evry-Courcouronnes, France
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19
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Komissarov L, Krep L, Schmalz F, Kopp WA, Leonhard K, Verstraelen T. A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part I: Force Field Development. Chemphyschem 2022; 24:e202200786. [PMID: 36585384 DOI: 10.1002/cphc.202200786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 01/01/2023]
Abstract
This work presents a novel parametrization for the ReaxFF formalism as a means to investigate reaction processes of chlorinated organic compounds. Force field parameters cover the chemical elements C, H, O, Cl and were obtained using a novel optimization approach involving relaxed potential energy surface scans as training targets. The resulting ReaxFF parametrization shows good transferability, as demonstrated on two independent ab initio validation sets. While this first part of our two-paper series focuses on force field parametrization, we apply our parameters to the simulation of chlorinated dibenzofuran formation and decomposition processes in Part II.
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Affiliation(s)
- Leonid Komissarov
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark - Zwijnaarde 46, B-9052, Ghent, Belgium
| | - Lukas Krep
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine - Westphalia, 52062, Aachen, Germany
| | - Felix Schmalz
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine - Westphalia, 52062, Aachen, Germany
| | - Wassja A Kopp
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine - Westphalia, 52062, Aachen, Germany
| | - Kai Leonhard
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine - Westphalia, 52062, Aachen, Germany
| | - Toon Verstraelen
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark - Zwijnaarde 46, B-9052, Ghent, Belgium
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20
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Krep L, Schmalz F, Solbach F, Komissarov L, Nevolianis T, Kopp WA, Verstraelen T, Leonhard K. A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part II: A ChemTraYzer Study of Chlorinated Dibenzofuran Formation and Decomposition Processes. Chemphyschem 2022; 24:e202200783. [PMID: 36511423 DOI: 10.1002/cphc.202200783] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/14/2022]
Abstract
In our two-paper series, we first present the development of ReaxFF CHOCl parameters using the recently published ParAMS parametrization tool. In this second part, we update the reactive Molecular Dynamics - Quantum Mechanics coupling scheme ChemTraYzer and combine it with our new ReaxFF parameters from Part I to study formation and decomposition processes of chlorinated dibenzofurans. We introduce a self-learning method for recovering failed transition-state searches that improves the overall ChemTraYzer transition-state search success rate by 10 percentage points to a total of 48 %. With ChemTraYzer, we automatically find and quantify more than 500 reactions using transition state theory and DFT. Among the discovered chlorinated dibenzofuran reactions are numerous reactions that are new to the literature. In three case studies, we discuss the set of reactions that are most relevant to the dibenzofuran literature: (i) bimolecular reactions of the chlorinated-dibenzofuran precursors phenoxy radical and 1,3,5-trichlorobenzene, (ii) dibenzofuran chlorination and pyrolysis, and (iii) oxidation of chlorinated dibenzofurans.
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Affiliation(s)
- Lukas Krep
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine-Westphalia, 52062, Aachen, Germany
| | - Felix Schmalz
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine-Westphalia, 52062, Aachen, Germany
| | - Florian Solbach
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine-Westphalia, 52062, Aachen, Germany
| | - Leonid Komissarov
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark-Zwijnaarde 46, B-9052, Ghent, Belgium
| | - Thomas Nevolianis
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine-Westphalia, 52062, Aachen, Germany
| | - Wassja A Kopp
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine-Westphalia, 52062, Aachen, Germany
| | - Toon Verstraelen
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark-Zwijnaarde 46, B-9052, Ghent, Belgium
| | - Kai Leonhard
- Institute of Technical Thermodynamics, RWTH Aachen University, North Rhine-Westphalia, 52062, Aachen, Germany
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21
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Hashemi A, Bougueroua S, Gaigeot MP, Pidko EA. ReNeGate: A Reaction Network Graph-Theoretical Tool for Automated Mechanistic Studies in Computational Homogeneous Catalysis. J Chem Theory Comput 2022; 18:7470-7482. [PMID: 36321652 DOI: 10.1021/acs.jctc.2c00404] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Exploration of the chemical reaction space of chemical transformations in multicomponent mixtures is one of the main challenges in contemporary computational chemistry. To remove expert bias from mechanistic studies and to discover new chemistries, an automated graph-theoretical methodology is proposed, which puts forward a network formalism of homogeneous catalysis reactions and utilizes a network analysis tool for mechanistic studies. The method can be used for analyzing trajectories with single and multiple catalytic species and can provide unique conformers of catalysts including multinuclear catalyst clusters along with other catalytic mixture components. The presented three-step approach has the integrated ability to handle multicomponent catalytic systems of arbitrary complexity (mixtures of reactants, catalyst precursors, ligands, additives, and solvents). It is not limited to predefined chemical rules, does not require prealignment of reaction mixture components consistent with a reaction coordinate, and is not agnostic to the chemical nature of transformations. Conformer exploration, reactive event identification, and reaction network analysis are the main steps taken for identifying the pathways in catalytic systems given the starting precatalytic reaction mixture as the input. Such a methodology allows us to efficiently explore catalytic systems in realistic conditions for either previously observed or completely unknown reactive events in the context of a network representing different intermediates. Our workflow for the catalytic reaction space exploration exclusively focuses on the identification of thermodynamically feasible conversion channels, representative of the (secondary) catalyst deactivation or inhibition paths, which are usually most difficult to anticipate based solely on expert chemical knowledge. Thus, the expert bias is sought to be removed at all steps, and the chemical intuition is limited to the choice of the thermodynamic constraint imposed by the applicable experimental conditions in terms of threshold energy values for allowed transformations. The capabilities of the proposed methodology have been tested by exploring the reactivity of Mn complexes relevant for catalytic hydrogenation chemistry to verify previously postulated activation mechanisms and unravel unexpected reaction channels relevant to rare deactivation events.
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Affiliation(s)
- Ali Hashemi
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
| | - Sana Bougueroua
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE) UMR8587, Universite Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, Evry-Courcouronnes 91025, France
| | - Marie-Pierre Gaigeot
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE) UMR8587, Universite Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, Evry-Courcouronnes 91025, France
| | - Evgeny A Pidko
- Inorganic Systems Engineering, Department of Chemical Engineering, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
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22
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Lavigne C, Gomes G, Pollice R, Aspuru-Guzik A. Guided discovery of chemical reaction pathways with imposed activation. Chem Sci 2022; 13:13857-13871. [PMID: 36544742 PMCID: PMC9710306 DOI: 10.1039/d2sc05135d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/09/2022] [Indexed: 11/12/2022] Open
Abstract
Computational power and quantum chemical methods have improved immensely since computers were first applied to the study of reactivity, but the de novo prediction of chemical reactions has remained challenging. We show that complex reaction pathways can be efficiently predicted in a guided manner using chemical activation imposed by geometrical constraints of specific reactive modes, which we term imposed activation (IACTA). Our approach is demonstrated on realistic and challenging chemistry, such as a triple cyclization cascade involved in the total synthesis of a natural product, a water-mediated Michael addition, and several oxidative addition reactions of complex drug-like molecules. Notably and in contrast with traditional hand-guided computational chemistry calculations, our method requires minimal human involvement and no prior knowledge of the products or the associated mechanisms. We believe that IACTA will be a transformational tool to screen for chemical reactivity and to study both by-product formation and decomposition pathways in a guided way.
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Affiliation(s)
- Cyrille Lavigne
- Department of Computer Science, University of Toronto214 College St.TorontoOntarioM5T 3A1Canada
| | - Gabe Gomes
- Department of Computer Science, University of Toronto214 College St.TorontoOntarioM5T 3A1Canada,Chemical Physics Theory Group, Department of Chemistry, University of Toronto80 St George StTorontoOntarioM5S 3H6Canada
| | - Robert Pollice
- Department of Computer Science, University of Toronto214 College St.TorontoOntarioM5T 3A1Canada,Chemical Physics Theory Group, Department of Chemistry, University of Toronto80 St George StTorontoOntarioM5S 3H6Canada
| | - Alán Aspuru-Guzik
- Department of Computer Science, University of Toronto214 College St.TorontoOntarioM5T 3A1Canada,Chemical Physics Theory Group, Department of Chemistry, University of Toronto80 St George StTorontoOntarioM5S 3H6Canada,Department of Chemical Engineering & Applied Chemistry, University of Toronto200 College St.OntarioM5S 3E5Canada,Department of Materials Science & Engineering, University of Toronto184 College St.OntarioM5S 3E4Canada,Vector Institute for Artificial Intelligence661 University Ave Suite 710TorontoOntarioM5G 1M1Canada,Lebovic Fellow, Canadian Institute for Advanced Research (CIFAR)661 University AveTorontoOntarioM5GCanada
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23
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Stan A, Esch BVD, Ochsenfeld C. Fully Automated Generation of Prebiotically Relevant Reaction Networks from Optimized Nanoreactor Simulations. J Chem Theory Comput 2022; 18:6700-6712. [PMID: 36270030 DOI: 10.1021/acs.jctc.2c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nanoreactor approach first introduced by the group of Martı́nez [Wang et al. Nat. Chem. 2014, 6, 1044-1048] has recently attracted much attention because of its ability to accelerate the discovery of reaction pathways. Here, we provide a comprehensive study of various simulation parameters and present an alternative implementation for the reactivity-enhancing spherical constraint function, as well as for the detection of reaction events. In this context, a fully automated postsimulation evaluation procedure based on RDKit and NetworkX analysis is introduced. The chemical and physical robustness of the procedure is examined by investigating the reactivity of selected homogeneous systems. The optimized procedure is applied at the GFN2-xTB level of theory to a system composed of HCN molecules and argon atoms, acting as a buffer, yielding prebiotically plausible primary and secondary precursors for the synthesis of RNA. Furthermore, the formose reaction network is explored leading to numerous sugar precursors. The discovered compounds reflect experimental findings; however, new synthetic routes and a large collection of exotic, highly reactive molecules are observed, highlighting the predictive power of the nanoreactor approach for unraveling the reactive manifold.
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Affiliation(s)
- Alexandra Stan
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Beatriz von der Esch
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany.,Max Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
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24
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Ismail I, Chantreau Majerus R, Habershon S. Graph-Driven Reaction Discovery: Progress, Challenges, and Future Opportunities. J Phys Chem A 2022; 126:7051-7069. [PMID: 36190262 PMCID: PMC9574932 DOI: 10.1021/acs.jpca.2c06408] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/22/2022] [Indexed: 11/29/2022]
Abstract
Graph-based descriptors, such as bond-order matrices and adjacency matrices, offer a simple and compact way of categorizing molecular structures; furthermore, such descriptors can be readily used to catalog chemical reactions (i.e., bond-making and -breaking). As such, a number of graph-based methodologies have been developed with the goal of automating the process of generating chemical reaction network models describing the possible mechanistic chemistry in a given set of reactant species. Here, we outline the evolution of these graph-based reaction discovery schemes, with particular emphasis on more recent methods incorporating graph-based methods with semiempirical and ab initio electronic structure calculations, minimum-energy path refinements, and transition state searches. Using representative examples from homogeneous catalysis and interstellar chemistry, we highlight how these schemes increasingly act as "virtual reaction vessels" for interrogating mechanistic questions. Finally, we highlight where challenges remain, including issues of chemical accuracy and calculation speeds, as well as the inherent challenge of dealing with the vast size of accessible chemical reaction space.
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Affiliation(s)
- Idil Ismail
- Department of Chemistry, University
of Warwick, CoventryCV4 7AL, United Kingdom
| | | | - Scott Habershon
- Department of Chemistry, University
of Warwick, CoventryCV4 7AL, United Kingdom
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25
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Field-Theodore TE, Taylor PR. Interstellar hide and go seek: C 3H 4O. There and back (again). Phys Chem Chem Phys 2022; 24:19184-19198. [PMID: 35730752 DOI: 10.1039/d2cp00995a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular species C3H4O represents a striking example of an astrochemical conundrum. With more than 60 structural isomers theoretically possible, to date only acrolein (CH2CHCHO) has been identified in the Sgr B2(N) region of the interstellar medium (ISM). The topography of the singlet potential energy surface is complicated, with three low-lying minima predicted to be almost isoenergetic: cis and trans-acrolein, and methylketene (CH3CHCO). Our CCSD(T)/cc-pVTZ calculations confirm that methylketene is energetically lower than cis-acrolein, lying only 1.9 kJ mol-1 above the trans-isomer, which is the global minimum. In this respect, methylketene is a promising candidate for interstellar observation. Unfortunately, however, despite several searches its astronomical detection has been unsuccessful. To this end, the key question is whether in fact methylketene exists as a discrete chemical entity in the ISM at all? In this paper, we present a detailed examination of the C3H4O potential energy surface, with specific focus on formation pathways. CCSD(T)/cc-pVTZ calculations enable a more elaborate interpretation of reaction mechanisms than was published hitherto. Our results show that gauche-propargyl alcohol and syn and anti-allenol emerge as interesting new targets for observational astronomers in TMC-1: given the recent discovery of the propargyl radical in this region, barrierless product channels involving OH˙ lend support to their candidacy as possible interstellar species. Finally, this work provides accurate spectral data of these three potential molecules, to be used for searches in interstellar space.
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Affiliation(s)
| | - Peter R Taylor
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China.
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26
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Ismail I, Robertson C, Habershon S. Successes and challenges in using machine-learned activation energies in kinetic simulations. J Chem Phys 2022; 157:014109. [DOI: 10.1063/5.0096027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The prediction of the thermodynamic and kinetic properties of chemical reactions is increasingly being addressed by machine-learning (ML) methods such as artificial neural networks (ANNs). While a number of recent studies have reported success in predicting chemical reaction activation energies, less attention has focused on how the accuracy of ML predictions filter through to predictions of macroscopic observables. Here, we consider the impact of the uncertainty associated with ML prediction of activation energies on observable properties of chemical reaction networks, as given by microkinetics simulations based on ML-predicted reaction rates. After training an ANN to predict activation energies given standard molecular descriptors for reactants and products alone, we performed microkinetics simulations of three different prototypical reaction networks: formamide decomposition, aldol reactions and decomposition of 3-hydroperoxypropanal. We find that the kinetic modelling predictions can be in excellent agreement with corresponding simulations performed with ab initio calculations, but this is dependent on the inherent energetic landscape of the networks. We use these simulations to suggest some guidelines for when ML-based activation energies can be reliable, and when one should take more care in applications to kinetics modelling.
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Affiliation(s)
| | | | - Scott Habershon
- Department of Chemistry, University of Warwick, United Kingdom
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27
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Garay-Ruiz D, Bo C. Chemical reaction network knowledge graphs: the OntoRXN ontology. J Cheminform 2022; 14:29. [PMID: 35637523 PMCID: PMC9153116 DOI: 10.1186/s13321-022-00610-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/11/2022] [Indexed: 11/10/2022] Open
Abstract
The organization and management of large amounts of data has become a major point in almost all areas of human knowledge. In this context, semantic approaches propose a structure for the target data, defining ontologies that state the types of entities on a certain field and how these entities are interrelated. In this work, we introduce OntoRXN, a novel ontology describing the reaction networks constructed from computational chemistry calculations. Under our paradigm, these networks are handled as undirected graphs, without assuming any traversal direction. From there, we propose a core class structure including reaction steps, network stages, chemical species, and the lower-level entities for the individual computational calculations. These individual calculations are founded on the OntoCompChem ontology and on the ioChem-BD database, where information is parsed and stored in CML format. OntoRXN is introduced through several examples in which knowledge graphs based on the ontology are generated for different chemical systems available on ioChem-BD. Finally, the resulting knowledge graphs are explored through SPARQL queries, illustrating the power of the semantic approach to standardize the analysis of intricate datasets and to simplify the development of complex workflows.
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Affiliation(s)
- Diego Garay-Ruiz
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007 Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel . lí Domingo s/n, 43007 Tarragona, Spain
| | - Carles Bo
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Països Catalans 16, 43007 Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel . lí Domingo s/n, 43007 Tarragona, Spain
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28
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Zhang G, Li J, Liang X, Liu Z. Automated reaction mechanisms and kinetics with the nudged elastic band method-based AMK_Mountain and its description of the preliminary alkaline hydrolysis of nitrocellulose monomer. J Comput Chem 2022; 43:1513-1523. [PMID: 35567577 DOI: 10.1002/jcc.26891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/18/2022] [Accepted: 04/27/2022] [Indexed: 11/08/2022]
Abstract
To improve the transition state (TS) search capability in complex chemical environments, AMK_Mountain is constructed based on the automated reaction mechanisms and kinetics (AutoMeKin) package. AMK_Mountain does not distinguish the reaction type of the TSs, which is beneficial to obtaining a more comprehensive reaction mechanism. In this study, the first step of the alkaline hydrolysis process of nitrocellulose monomer was adopted as the research object, and 730 possible initial configurations are constructed and 22 TSs pass high-level calculations. Energy difference and interaction region indicator reveal that the first step of alkaline hydrolysis is mainly the combination of nitrogen-containing functional groups at the positions α and β with hydroxide anions, followed by the formation of nitric acid and the further loss of protons to form nitrate. Overall, in combination with GFN2 -xTB and ORCA, the AMK_Mountain technique provides a reliable method for the location of the TSs in complex environments.
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Affiliation(s)
- Guan Zhang
- School of Human Settlement and Civil Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Jin Li
- School of Human Settlement and Civil Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Xinxin Liang
- School of Human Settlement and Civil Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Zongkuan Liu
- School of Human Settlement and Civil Engineering, Xi'an Jiaotong University, Xi'an, China
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29
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Two-state reactivity in the acetylene cyclotrimerization reaction catalyzed by a single atomic transition-metal ion: The case for V+ and Fe+. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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30
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Rimola A, Balucani N, Ceccarelli C, Ugliengo P. Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations. Int J Mol Sci 2022; 23:4252. [PMID: 35457069 PMCID: PMC9030215 DOI: 10.3390/ijms23084252] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 12/28/2022] Open
Abstract
Glycine (Gly), NH2CH2COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial laboratory experiments. Likewise, condensation of Gly to form peptides in scenarios resembling those present in a primordial Earth has been demonstrated experimentally. Thus, Gly is a paradigmatic system for biomolecular building blocks to investigate how they can be synthesized in astrophysical environments, transported and delivered by fragments of asteroids (meteorites, once they land on Earth) and comets (interplanetary dust particles that land on Earth) to the primitive Earth, and there react to form biopolymers as a step towards the emergence of life. Quantum chemical investigations addressing these Gly-related events have been performed, providing fundamental atomic-scale information and quantitative energetic data. However, they are spread in the literature and difficult to harmonize in a consistent way due to different computational chemistry methodologies and model systems. This review aims to collect the work done so far to characterize, at a quantum mechanical level, the chemical life of Gly, i.e., from its synthesis in the interstellar medium up to its polymerization on Earth.
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Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Catalonia, Spain
| | - Nadia Balucani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy;
- Osservatorio Astrosico di Arcetri, Largo E. Fermi 5, 50125 Firenze, Italy
| | - Cecilia Ceccarelli
- CNRS, Institut de Planétologie et d’Astrophysique de Grenoble (IPAG), Université Grenoble Alpes, 38000 Grenoble, France;
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS) Centre, Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy;
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31
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Chakraborty D, Hase WL. Direct dynamics simulation of the thermal O(
3
P) + dimethylamine reaction in the triplet surface. I. Rate constant and product branching. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Debdutta Chakraborty
- Department of Chemistry and Biochemistry Texas Tech University Lubbock Texas USA
- Department of Chemistry Birla Institute of Technology Mesra Ranchi India
| | - William L. Hase
- Department of Chemistry and Biochemistry Texas Tech University Lubbock Texas USA
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32
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Ríos-García M, Fernández B, Rodríguez-Otero J, Cabaleiro-Lago EM, Vázquez SA. The PM6-FGC Method: Improved Corrections for Amines and Amides. Molecules 2022; 27:molecules27051678. [PMID: 35268779 PMCID: PMC8924896 DOI: 10.3390/molecules27051678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/23/2022] [Accepted: 03/01/2022] [Indexed: 12/10/2022] Open
Abstract
Recently, we reported a new approach to develop pairwise analytical corrections to improve the description of noncovalent interactions, by approximate methods of electronic structures, such as semiempirical quantum mechanical (SQM) methods. In particular, and as a proof of concept, we used the PM6 Hamiltonian and we named the method PM6-FGC, where the FGC acronym, corresponding to Functional Group Corrections, emphasizes the idea that the corrections work for specific functional groups rather than for individual atom pairs. The analytical corrections were derived from fits to B3LYP-D3/def2-TZVP (reference). PM6 interaction energy differences, evaluated for a reduced set of small bimolecular complexes, were chosen as representatives of saturated hydrocarbons, carboxylic, amine and, tentatively, amide functional groups. For the validation, the method was applied to several complexes of well-known databases, as well as to complexes of diglycine and dialanine, assuming the transferability of amine group corrections to amide groups. The PM6-FGC method showed great potential but revealed significant inaccuracies for the description of some interactions involving the –NH2 group in amines and amides, caused by the inadequate selection of the model compound used to represent these functional groups (an NH3 molecule). In this work, methylamine and acetamide are used as representatives of amine and amide groups, respectively. This new selection leads to significant improvements in the calculation of noncovalent interactions in the validation set.
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33
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Krep L, Roy IS, Kopp W, Schmalz F, Huang C, Leonhard K. Efficient Reaction Space Exploration with ChemTraYzer-TAD. J Chem Inf Model 2022; 62:890-902. [PMID: 35142513 DOI: 10.1021/acs.jcim.1c01197] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of a reaction model is often a time-consuming process, especially if unknown reactions have to be found and quantified. To alleviate the reaction modeling process, automated procedures for reaction space exploration are highly desired. We present ChemTraYzer-TAD, a new reactive molecular dynamics acceleration technique aimed at efficient reaction space exploration. The new method is based on the basin confinement strategy known from the temperature-accelerated dynamics (TAD) acceleration method. Our method features integrated ChemTraYzer bond-order processing steps for the automatic and on-the-fly determination of the positions of virtual walls in configuration space that confine the system in a potential energy basin. We use the example of 1,3-dioxolane-4-hydroperoxide-2-yl radical oxidation to show that ChemTraYzer-TAD finds more than 100 different parallel reactions for the given set of reactants in less than 2 ns of simulation time. Among the many observed reactions, ChemTraYzer-TAD finds the expected typical low-temperature reactions despite the use of extremely high simulation temperatures up to 5000 K. Our method also finds a new concerted β-scission plus O2 addition with a lower reaction barrier than the literature-known and so-far dominant β-scission.
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Affiliation(s)
- Lukas Krep
- Institute of Technical Thermodynamics, RWTH Aachen University, Aachen 52062, Germany
| | - Indu Sekhar Roy
- Institute of Technical Thermodynamics, RWTH Aachen University, Aachen 52062, Germany
| | - Wassja Kopp
- Institute of Technical Thermodynamics, RWTH Aachen University, Aachen 52062, Germany
| | - Felix Schmalz
- Institute of Technical Thermodynamics, RWTH Aachen University, Aachen 52062, Germany
| | - Can Huang
- Institute of Technical Thermodynamics, RWTH Aachen University, Aachen 52062, Germany
| | - Kai Leonhard
- Institute of Technical Thermodynamics, RWTH Aachen University, Aachen 52062, Germany
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34
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Garay-Ruiz D, Álvarez-Moreno M, Bo C, Martínez-Núñez E. New Tools for Taming Complex Reaction Networks: The Unimolecular Decomposition of Indole Revisited. ACS PHYSICAL CHEMISTRY AU 2022; 2:225-236. [PMID: 36855573 PMCID: PMC9718323 DOI: 10.1021/acsphyschemau.1c00051] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The level of detail attained in the computational description of reaction mechanisms can be vastly improved through tools for automated chemical space exploration, particularly for systems of small to medium size. Under this approach, the unimolecular decomposition landscape for indole was explored through the automated reaction mechanism discovery program AutoMeKin. Nevertheless, the sheer complexity of the obtained mechanisms might be a hindrance regarding their chemical interpretation. In this spirit, the new Python library amk-tools has been designed to read and manipulate complex reaction networks, greatly simplifying their overall analysis. The package provides interactive dashboards featuring visualizations of the network, the three-dimensional (3D) molecular structures and vibrational normal modes of all chemical species, and the corresponding energy profiles for selected pathways. The combination of the joined mechanism generation and postprocessing workflow with the rich chemistry of indole decomposition enabled us to find new details of the reaction (obtained at the CCSD(T)/aug-cc-pVTZ//M06-2X/MG3S level of theory) that were not reported before: (i) 16 pathways leading to the formation of HCN and NH3 (via amino radical); (ii) a barrierless reaction between methylene radical and phenyl isocyanide, which might be an operative mechanism under the conditions of the interstellar medium; and (iii) reaction channels leading to both hydrogen cyanide and hydrogen isocyanide, of potential astrochemical interest as the computed HNC/HCN ratios greatly exceed the calculated equilibrium value at very low temperatures. The reported reaction networks can be very valuable to supplement databases of kinetic data, which is of remarkable interest for pyrolysis and astrochemical studies.
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Affiliation(s)
- Diego Garay-Ruiz
- Institute
of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science & Technology (BIST), Avinguda Països Catalans,
16, 43007 Tarragona, Spain,Departament
de Química Física i Inorgànica, Universitat Rovira i Virgili (URV), Marcel·lí Domingo s/n, 43007 Tarragona, Spain
| | - Moises Álvarez-Moreno
- Institute
of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science & Technology (BIST), Avinguda Països Catalans,
16, 43007 Tarragona, Spain
| | - Carles Bo
- Institute
of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science & Technology (BIST), Avinguda Països Catalans,
16, 43007 Tarragona, Spain,Departament
de Química Física i Inorgànica, Universitat Rovira i Virgili (URV), Marcel·lí Domingo s/n, 43007 Tarragona, Spain,
| | - Emilio Martínez-Núñez
- Departmento
de Química Física, Facultade de Química, Universidade de Santiago de Compostela, 15782 Santiago
de Compostela, Spain,
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35
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Cui Q, Peng J, Xu C, Lan Z. Automatic Approach to Explore the Multireaction Mechanism for Medium-Sized Bimolecular Reactions via Collision Dynamics Simulations and Transition State Searches. J Chem Theory Comput 2022; 18:910-924. [DOI: 10.1021/acs.jctc.1c00795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qinghai Cui
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Jiawei Peng
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Chao Xu
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
- Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education; School of Chemistry, South China Normal University, Guangzhou 510006, P. R. China
| | - Zhenggang Lan
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
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36
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Carrascosa E, Bull JN, Martínez-Núñez E, Scholz MS, Buntine JT, Bieske EJ. Photoisomerization of Linear and Stacked Isomers of a Charged Styryl Dye: A Tandem Ion Mobility Study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2842-2851. [PMID: 34787413 PMCID: PMC8640989 DOI: 10.1021/jasms.1c00264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/21/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
The photoisomerization behavior of styryl 9M, a common dye used in material sciences, is investigated using tandem ion mobility spectrometry (IMS) coupled with laser spectroscopy. Styryl 9M has two alkene linkages, potentially allowing for four geometric isomers. IMS measurements demonstrate that at least three geometric isomers are generated using electrospray ionization with the most abundant forms assigned to a combination of EE (major) and ZE (minor) geometric isomers, which are difficult to distinguish using IMS as they have similar collision cross sections. Two additional but minor isomers are generated by collisional excitation of the electrosprayed styryl 9M ions and are assigned to the EZ and ZZ geometric isomers, with the latter predicted to have a π-stacked configuration. The isomer assignments are supported through calculations of equilibrium structures, collision cross sections, and statistical isomerization rates. Photoexcitation of selected isomers using an IMS-photo-IMS strategy shows that each geometric isomer photoisomerizes following absorption of near-infrared and visible light, with the EE isomer possessing a S1 ← S0 electronic transition with a band maximum near 680 nm and shorter wavelength S2 ← S0 electronic transition with a band maximum near 430 nm. The study demonstrates the utility of the IMS-photo-IMS strategy for providing fundamental gas-phase photochemical information on molecular systems with multiple isomerizable bonds.
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Affiliation(s)
- Eduardo Carrascosa
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - James N. Bull
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
- School
of Chemistry, Norwich Research Park, University
of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Emilio Martínez-Núñez
- Departamento
de Química Física, Universidade
de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Michael S. Scholz
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jack T. Buntine
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Evan J. Bieske
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
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37
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Tsutsumi T, Ono Y, Taketsugu T. Visualization of reaction route map and dynamical trajectory in reduced dimension. Chem Commun (Camb) 2021; 57:11734-11750. [PMID: 34642706 DOI: 10.1039/d1cc04667e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the quantum chemical approach, chemical reaction mechanisms are investigated based on a potential energy surface (PES). Automated reaction path search methods enable us to construct a global reaction route map containing multiple reaction paths corresponding to a series of elementary reaction processes. The on-the-fly molecular dynamics (MD) method provides a classical trajectory exploring the full-dimensional PES based on electronic structure calculations. We have developed two reaction analysis methods, the on-the-fly trajectory mapping method and the reaction space projector (ReSPer) method, by introducing a structural similarity to a pair of geometric structures and revealed dynamic aspects affecting chemical reaction mechanisms. In this review, we will present the details of these analysis methods and discuss the dynamics effects of reaction path curvature and reaction path bifurcation with applications to the CH3OH + OH- collision reaction and the Au5 cluster branching and isomerization reactions.
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Affiliation(s)
- Takuro Tsutsumi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
| | - Yuriko Ono
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan. .,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
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38
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Gaigeot MP. Some opinions on MD-based vibrational spectroscopy of gas phase molecules and their assembly: An overview of what has been achieved and where to go. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119864. [PMID: 34052762 DOI: 10.1016/j.saa.2021.119864] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/13/2021] [Accepted: 04/18/2021] [Indexed: 06/12/2023]
Abstract
We hereby review molecular dynamics simulations for anharmonic gas phase spectroscopy and provide some of our opinions of where the field is heading. With these new directions, the theoretical IR/Raman spectroscopy of large (bio)-molecular systems will be more easily achievable over longer time-scale MD trajectories for an increase in accuracy of the MD-IR and MD-Raman calculated spectra. With the new directions presented here, the high throughput 'decoding' of experimental IR/Raman spectra into 3D-structures should thus be possible, hence advancing e.g. the field of MS-IR for structural characterization by spectroscopy. We also review the assignment of vibrational spectra in terms of anharmonic molecular modes from the MD trajectories, and especially introduce our recent developments based on Graph Theory algorithms. Graph Theory algorithmic is also introduced in this review for the identification of the molecular 3D-structures sampled over MD trajectories.
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Affiliation(s)
- Marie-Pierre Gaigeot
- Université Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, 91025 Evry-Courcouronnes, France.
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39
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Zhang G, Li J, Long B, Liu Z. Automated reaction mechanisms and kinetics based transition state search process AMK-gau_xtb and its application to the substitution reaction of the nitroso group in 2,4,6-trinitrotoluene by hydroxide anion in the aqueous phase. Phys Chem Chem Phys 2021; 23:23673-23683. [PMID: 34642711 DOI: 10.1039/d1cp02144c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The automated reaction mechanisms and kinetics (AutoMeKin) program evolved from a transition state search using chemical dynamics simulations (TSSCDS). It combines a series of empirical, semi-empirical and ab initio calculation methods to provide a two-step transition state search process from low-level calculation to high-level calculation. However, in this process, with the lack of solution keywords, low-level calculation has the problem of low accuracy or high computational cost. To address this problem, the gau_xtb interface that combines the high efficiency of xTB and the comprehensiveness of Gaussian09 was incorporated into the AutoMeKin2020 in this work and after adding some keywords, the AMK-gau_xtb software was obtained. Meanwhile, to adapt to the interface, the MD sampling results used Quadratic Synchronous Transit 3 (QST3) for the low-level transition state search. As an application, the reaction in which the nitroso group is replaced by hydroxide anion during the alkaline hydrolysis of 2,4,6-trinitrotoluene (TNT) in the water phase was studied with AMK-gau_xtb. The results of Intrinsic Reaction Coordinate (IRC) calculations revealed that the reactions on the front side and back side are different, with higher energy barriers obtained for the reactions on the front side. In addition, the hydrogen atom of the hydroxide anion has a slightly higher energy barrier for motion toward the inside of the benzene ring than for motion out of the benzene ring. Examination of the transition state structures of the low-level and high-level results showed that all reactions involve the stretching and restoration of the benzene ring. This process will lead to the incorrect identification of several transition states by the gau_xtb-based low-level calculation, while high-level calculation eliminates these incorrect results. The results of this research showed that AMK-gau_xtb has high efficiency and high fault tolerance, and has potential for use in large-scale system transition state searches.
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Affiliation(s)
- Guan Zhang
- School of Human Settlement and Civil Engineering, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Jin Li
- School of Human Settlement and Civil Engineering, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Bo Long
- School of Materials Science and Engineering, Guizhou Minzu University, Guiyang, 550025, China.
| | - Zongkuan Liu
- School of Human Settlement and Civil Engineering, Xi'an Jiaotong University, Xi'an 710049, China.
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40
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Perez-Mellor AF, Spezia R. Determination of kinetic properties in unimolecular dissociation of complex systems from graph theory based analysis of an ensemble of reactive trajectories. J Chem Phys 2021; 155:124103. [PMID: 34598552 DOI: 10.1063/5.0058382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In this paper, we report how graph theory can be used to analyze an ensemble of independent molecular trajectories, which can react during the simulation time-length, and obtain structural and kinetic information. This method is totally general and here is applied to the prototypical case of gas phase fragmentation of protonated cyclo-di-glycine. This methodology allows us to analyze the whole set of trajectories in an automatic computer-based way without the need of visual inspection but by getting all the needed information. In particular, we not only determine the appearance of different products and intermediates but also characterize the corresponding kinetics. The use of colored graph and canonical labeling allows for the correct characterization of the chemical species involved. In the present case, the simulations consist of an ensemble of unimolecular fragmentation trajectories at constant energy such that from the rate constants at different energies, the threshold energy can also be obtained for both global and specific pathways. This approach allows for the characterization of ion-molecule complexes, likely through a roaming mechanism, by properly taking into account the elusive nature of such species. Finally, it is possible to directly obtain the theoretical mass spectrum of the fragmenting species if the reacting system is an ion as in the specific example.
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Affiliation(s)
- Ariel F Perez-Mellor
- LAMBE UMR8587, Université d'Evry Val d'Essonne, CNRS, CEA, Université Paris-Saclay, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, 91025 Evry, France
| | - Riccardo Spezia
- Laboratoire de Chimie Théorique, Sorbonne Université and CNRS, F-75005 Paris, France
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41
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Field-Theodore TE, Taylor PR. Conjugation trumps cumulation: the global minimum on the C3H4O surface. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1979263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Terri E. Field-Theodore
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Peter R. Taylor
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, People's Republic of China
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42
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Pérez-Tabero S, Fernández B, Cabaleiro-Lago EM, Martínez-Núñez E, Vázquez SA. New Approach for Correcting Noncovalent Interactions in Semiempirical Quantum Mechanical Methods: The Importance of Multiple-Orientation Sampling. J Chem Theory Comput 2021; 17:5556-5567. [PMID: 34424696 PMCID: PMC8486165 DOI: 10.1021/acs.jctc.1c00365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
A new
approach is presented to improve the performance of semiempirical
quantum mechanical (SQM) methods in the description of noncovalent
interactions. To show the strategy, the PM6 Hamiltonian was selected,
although, in general, the procedure can be applied to other semiempirical
Hamiltonians and to different methodologies. A set of small molecules
were selected as representative of various functional groups, and
intermolecular potential energy curves (IPECs) were evaluated for
the most relevant orientations of interacting molecular pairs. Then,
analytical corrections to PM6 were derived from fits to B3LYP-D3/def2-TZVP
reference–PM6 interaction energy differences. IPECs provided
by the B3LYP-D3/def2-TZVP combination of the electronic structure
method and basis set were chosen as the reference because they are
in excellent agreement with CCSD(T)/aug-cc-pVTZ curves for the studied
systems. The resulting method, called PM6-FGC (from functional group
corrections), significantly improves the performance of PM6 and shows
the importance of including a sufficient number of orientations of
the interacting molecules in the reference data set in order to obtain
well-balanced descriptions.
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Affiliation(s)
- Sergio Pérez-Tabero
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Berta Fernández
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Enrique M Cabaleiro-Lago
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Emilio Martínez-Núñez
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Saulo A Vázquez
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
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43
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Martínez-Núñez E, Barnes GL, Glowacki DR, Kopec S, Peláez D, Rodríguez A, Rodríguez-Fernández R, Shannon RJ, Stewart JJP, Tahoces PG, Vazquez SA. AutoMeKin2021: An open-source program for automated reaction discovery. J Comput Chem 2021; 42:2036-2048. [PMID: 34387374 DOI: 10.1002/jcc.26734] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023]
Abstract
AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin.
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Affiliation(s)
- Emilio Martínez-Núñez
- Department of Physical Chemistry, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - George L Barnes
- Department of Chemistry and Biochemistry, Siena College, Loudonville, New York, USA
| | - David R Glowacki
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Sabine Kopec
- Institut de Sciences Moléculaires d'Orsay, UMR 8214, Université Paris-Sud - Université Paris-Saclay, Orsay, France
| | - Daniel Peláez
- Institut de Sciences Moléculaires d'Orsay, UMR 8214, Université Paris-Sud - Université Paris-Saclay, Orsay, France
| | - Aurelio Rodríguez
- Galicia Supercomputing Center (CESGA), Santiago de Compostela, Spain
| | | | - Robin J Shannon
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | | | - Pablo G Tahoces
- Department of Electronics and Computer Science, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Saulo A Vazquez
- Department of Physical Chemistry, University of Santiago de Compostela, Santiago de Compostela, Spain
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44
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Shannon RJ, Martínez-Núñez E, Shalashilin DV, Glowacki DR. ChemDyME: Kinetically Steered, Automated Mechanism Generation through Combined Molecular Dynamics and Master Equation Calculations. J Chem Theory Comput 2021; 17:4901-4912. [PMID: 34283599 DOI: 10.1021/acs.jctc.1c00335] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In many scientific fields, there is an interest in understanding the way in which chemical networks evolve. The chemical networks which researchers focus upon have become increasingly complex, and this has motivated the development of automated methods for exploring chemical reactivity or conformational change in a "black-box" manner, harnessing modern computing resources to automate mechanism discovery. In this work, we present a new approach to automated mechanism generation which couples molecular dynamics and statistical rate theory to automatically find kinetically important reactions and then solve the time evolution of the species in the evolving network. The key to this chemical network mapping through combined dynamics and ME simulation approach is the concept of "kinetic convergence", whereby the search for new reactions is constrained to those species which are kinetically favorable at the conditions of interest. We demonstrate the capability of the new approach for two systems, a well-studied combustion system and a multiple oxygen addition system relevant to atmospheric aerosol formation.
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Affiliation(s)
- Robin J Shannon
- School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K
| | - Emilio Martínez-Núñez
- Department of Physical Chemistry, University of Santiago de Compostela, Santiago de Compostela 15705, Spain
| | | | - David R Glowacki
- ArtSci International Foundation, 5th floor Mariner House, Bristol BS1 4QD, U.K
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45
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Moe MM, Tsai M, Liu J. Singlet Oxygen Oxidation of the Radical Cations of 8-Oxo-2'-deoxyguanosine and Its 9-Methyl Analogue: Dynamics, Potential Energy Surface, and Products Mediated by C5-O 2 -Addition. Chempluschem 2021; 86:1243-1254. [PMID: 34268890 DOI: 10.1002/cplu.202100238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/02/2021] [Indexed: 01/24/2023]
Abstract
8-Oxo-2'-deoxyguanosine (OG) is the most common DNA lesion. Notably, OG becomes more susceptible to oxidative damage than the undamaged nucleoside, forming mutagenic products in vivo. Herein the reactions of singlet O2 with the radical cations of 8-oxo-2'-deoxyguanosine (OG.+ ) and 9-methyl-8-oxoguanine (9MOG.+ ) were investigated using ion-molecule scattering mass spectrometry, from which barrierless, exothermic O2 -addition products were detected for both reaction systems. Corroborated by static reaction potential energy surface constructed using multi-reference CASPT2 theory and molecular dynamics simulated in the presence of the reactants' kinetic and internal energies, the C5-terminal O2 -addition was pinpointed as the most probable reaction pathway. By elucidating the reaction mechanism, kinetics and dynamics, and reaction products and energetics, this work constitutes the first report unraveling the synergetic damage of OG by ionizing radiation and singlet O2 .
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Affiliation(s)
- May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY, 11367, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY, 10016, USA
| | - Midas Tsai
- Department of Natural Sciences, LaGuardia Community College, 31-10 Thomson Ave., Long Island City, NY, 11101, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY, 11367, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY, 10016, USA
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46
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Makoś MZ, Verma N, Larson EC, Freindorf M, Kraka E. Generative adversarial networks for transition state geometry prediction. J Chem Phys 2021; 155:024116. [PMID: 34266275 DOI: 10.1063/5.0055094] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This work introduces a novel application of generative adversarial networks (GANs) for the prediction of starting geometries in transition state (TS) searches based on the geometries of reactants and products. The multi-dimensional potential energy space of a chemical reaction often complicates the location of a starting TS geometry, leading to the correct TS combining reactants and products in question. The proposed TS-GAN efficiently maps the space between reactants and products and generates reliable TS guess geometries, and it can be easily combined with any quantum chemical software package performing geometry optimizations. The TS-GAN was trained and applied to generate TS guess structures for typical chemical reactions, such as hydrogen migration, isomerization, and transition metal-catalyzed reactions. The performance of the TS-GAN was directly compared to that of classical approaches, proving its high accuracy and efficiency. The current TS-GAN can be extended to any dataset that contains sufficient chemical reactions for training. The software is freely available for training, experimentation, and prediction at https://github.com/ekraka/TS-GAN.
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Affiliation(s)
- Małgorzata Z Makoś
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA
| | - Niraj Verma
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA
| | - Eric C Larson
- Computer Science Department, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA
| | - Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, USA
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47
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48
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Borges R, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Quantum Chemistry Calculations for Metabolomics. Chem Rev 2021; 121:5633-5670. [PMID: 33979149 PMCID: PMC8161423 DOI: 10.1021/acs.chemrev.0c00901] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 02/07/2023]
Abstract
A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.
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Affiliation(s)
- Ricardo
M. Borges
- Walter
Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Sean M. Colby
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Susanta Das
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Arthur S. Edison
- Departments
of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate
Research Center and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Tobias Kind
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Jesi Lee
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Amy T. Merrill
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Thomas O. Metz
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Jamie R. Nunez
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Shunyang Wang
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Ryan S. Renslow
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
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49
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Takayanagi T. Application of Reaction Path Search Calculations to Potential Energy Surface Fits. J Phys Chem A 2021; 125:3994-4002. [PMID: 33915053 DOI: 10.1021/acs.jpca.1c01512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There has been significant progress in recent years in the use of machine learning techniques to model high-dimensional reactive potential energy surfaces using large-scale data obtained from ab initio electronic structure calculations. In these methods, the strategy used to gather data becomes a key issue as the molecular size increases. In this work, we examine the applicability of the reaction path search algorithm implemented in the Global Reaction Route Mapping (GRRM) code as a data-gathering approach. The electronic energies and gradients sampled by using the GRRM calculation are directly used in potential energy surface fitting to a permutationally invariant polynomial function. This simple approach was applied to the HNS and HCNO reaction systems, and we found that the fitted potential energy surfaces reasonably reproduce the features of the electronic structure calculations used in the GRRM calculations. This suggests that the GRRM sampling scheme can be used to construct an initial potential energy surface.
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Affiliation(s)
- Toshiyuki Takayanagi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Saitama City, Saitama 338-8570, Japan
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50
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