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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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2
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Steiner M, Reiher M. A human-machine interface for automatic exploration of chemical reaction networks. Nat Commun 2024; 15:3680. [PMID: 38693117 PMCID: PMC11063077 DOI: 10.1038/s41467-024-47997-9] [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: 08/31/2023] [Accepted: 04/15/2024] [Indexed: 05/03/2024] Open
Abstract
Autonomous reaction network exploration algorithms offer a systematic approach to explore mechanisms of complex chemical processes. However, the resulting reaction networks are so vast that an exploration of all potentially accessible intermediates is computationally too demanding. This renders brute-force explorations unfeasible, while explorations with completely pre-defined intermediates or hard-wired chemical constraints, such as element-specific coordination numbers, are not flexible enough for complex chemical systems. Here, we introduce a STEERING WHEEL to guide an otherwise unbiased automated exploration. The STEERING WHEEL algorithm is intuitive, generally applicable, and enables one to focus on specific regions of an emerging network. It also allows for guiding automated data generation in the context of mechanism exploration, catalyst design, and other chemical optimization challenges. The algorithm is demonstrated for reaction mechanism elucidation of transition metal catalysts. We highlight how to explore catalytic cycles in a systematic and reproducible way. The exploration objectives are fully adjustable, allowing one to harness the STEERING WHEEL for both structure-specific (accurate) calculations as well as for broad high-throughput screening of possible reaction intermediates.
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Affiliation(s)
- Miguel Steiner
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- ETH Zurich, NCCR Catalysis, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Markus Reiher
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
- ETH Zurich, NCCR Catalysis, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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3
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Harabuchi Y, Yokoyama T, Matsuoka W, Oki T, Iwata S, Maeda S. Differentiating the Yield of Chemical Reactions Using Parameters in First-Order Kinetic Equations to Identify Elementary Steps That Control the Reactivity from Complicated Reaction Path Networks. J Phys Chem A 2024; 128:2883-2890. [PMID: 38564273 DOI: 10.1021/acs.jpca.4c00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The yield of a chemical reaction is obtained by solving its rate equation. This study introduces an approach for differentiating yields by utilizing the parameters of the rate equation, which is expressed as a first-order linear differential equation. The yield derivative for a specific pair of reactants and products is derived by mathematically expressing the rate constant matrix contraction method, which is a simple kinetic analysis method. The parameters of the rate equation are the Gibbs energies of the intermediates and transition states in the reaction path network used to formulate the rate equation. Thus, our approach for differentiating the yield allows a numerical evaluation of the contribution of energy variation to the yield for each intermediate and transition state in the reaction path network. In other words, a comparison of these values automatically extracts the factors affecting the yield from a complicated reaction path network consisting of numerous reaction paths and intermediates. This study verifies the behavior of the proposed approach through numerical experiments on the reaction path networks of a model system and the Rh-catalyzed hydroformylation reaction. Moreover, the possibility of using this approach for designing ligands in organometallic catalysts is discussed.
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Affiliation(s)
- Yu Harabuchi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- JST, ERATO Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Tomohiko Yokoyama
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Wataru Matsuoka
- JST, ERATO Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Taihei Oki
- JST, ERATO Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Satoru Iwata
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- JST, ERATO Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- Department of Mathematical Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- JST, ERATO Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
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4
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Stan-Bernhardt A, Glinkina L, Hulm A, Ochsenfeld C. Exploring Chemical Space Using Ab Initio Hyperreactor Dynamics. ACS CENTRAL SCIENCE 2024; 10:302-314. [PMID: 38435517 PMCID: PMC10906254 DOI: 10.1021/acscentsci.3c01403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 03/05/2024]
Abstract
In recent years, first-principles exploration of chemical reaction space has provided valuable insights into intricate reaction networks. Here, we introduce ab initio hyperreactor dynamics, which enables rapid screening of the accessible chemical space from a given set of initial molecular species, predicting new synthetic routes that can potentially guide subsequent experimental studies. For this purpose, different hyperdynamics derived bias potentials are applied along with pressure-inducing spherical confinement of the molecular system in ab initio molecular dynamics simulations to efficiently enhance reactivity under mild conditions. To showcase the advantages and flexibility of the hyperreactor approach, we present a systematic study of the method's parameters on a HCN toy model and apply it to a recently introduced experimental model for the prebiotic formation of glycinal and acetamide in interstellar ices, which yields results in line with experimental findings. In addition, we show how the developed framework enables the study of complicated transitions like the first step of a nonenzymatic DNA nucleoside synthesis in an aqueous environment, where the molecular fragmentation problem of earlier nanoreactor approaches is avoided.
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Affiliation(s)
- Alexandra Stan-Bernhardt
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5, D-81377 München, Germany
| | - Liubov Glinkina
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5, D-81377 München, Germany
| | - Andreas Hulm
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair
of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstrasse 5, D-81377 München, Germany
- Max
Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
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5
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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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6
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McFarlane NR, Harvey JN. Exploration of biochemical reactivity with a QM/MM growing string method. Phys Chem Chem Phys 2024; 26:5999-6007. [PMID: 38293892 DOI: 10.1039/d3cp05772k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
In this work, we have implemented the single-ended growing string method using a hybrid internal/Cartesian coordinate scheme within our in-house QM/MM package, QoMMMa, representing the first implementation of the growing string method in the QM/MM framework. The goal of the implementation was to facilitate generation of QM/MM reaction pathways with minimal user input, and also to improve the quality of the pathways generated as compared to the widely used adiabatic mapping approach. We have validated the algorithm against a reaction which has been studied extensively in previous computational investigations - the Claisen rearrangement catalysed by chorismate mutase. The nature of the transition state and the height of the barrier was predicted well using our algorithm, where more than 88% of the pathways generated were deemed to be of production quality. Directly compared to using adiabatic mapping, we found that while our QM/MM single-ended growing string method is slightly less efficient, it readily produces reaction pathways with fewer discontinuites and thus minimises the need for involved remapping of unsatisfactory energy profiles.
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Affiliation(s)
- Neil R McFarlane
- Department of Chemistry, KU Leuven, B-3001 Leuven, Celestijnenlaan 200f, 2404, Belgium.
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, B-3001 Leuven, Celestijnenlaan 200f, 2404, Belgium.
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7
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Levine DS, Jacobson LD, Bochevarov AD. Large Computational Survey of Intrinsic Reactivity of Aromatic Carbon Atoms with Respect to a Model Aldehyde Oxidase. J Chem Theory Comput 2023; 19:9302-9317. [PMID: 38085599 DOI: 10.1021/acs.jctc.3c00913] [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: 12/27/2023]
Abstract
Aldehyde oxidase (AOX) and other related molybdenum-containing enzymes are known to oxidize the C-H bonds of aromatic rings. This process contributes to the metabolism of pharmaceutical compounds and, therefore, is of vital importance to drug pharmacokinetics. The present work describes an automated computational workflow and its use for the prediction of intrinsic reactivity of small aromatic molecules toward a minimal model of the active site of AOX. The workflow is based on quantum chemical transition state searches for the underlying single-step oxidation reaction, where the automated protocol includes identification of unique aromatic C-H bonds, creation of three-dimensional reactant and product complex geometries via a templating approach, search for a transition state, and validation of reaction end points. Conformational search on the reactants, products, and the transition states is performed. The automated procedure has been validated on previously reported transition state barriers and was used to evaluate the intrinsic reactivity of nearly three hundred heterocycles commonly found in approved drug molecules. The intrinsic reactivity of more than 1000 individual aromatic carbon sites is reported. Stereochemical and conformational aspects of the oxidation reaction, which have not been discussed in previous studies, are shown to play important roles in accurate modeling of the oxidation reaction. Observations on structural trends that determine the reactivity are provided and rationalized.
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Affiliation(s)
- Daniel S Levine
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, United States
| | - Leif D Jacobson
- Schrödinger, Inc., 101 SW Main Street, Suite 1300, Portland, Oregon 97204, United States
| | - Art D Bochevarov
- Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, United States
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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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Sabadell-Rendón A, Kaźmierczak K, Morandi S, Euzenat F, Curulla-Ferré D, López N. Automated MUltiscale simulation environment. DIGITAL DISCOVERY 2023; 2:1721-1732. [PMID: 38054103 PMCID: PMC10694852 DOI: 10.1039/d3dd00163f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/05/2023] [Indexed: 12/07/2023]
Abstract
Multiscale techniques integrating detailed atomistic information on materials and reactions to predict the performance of heterogeneous catalytic full-scale reactors have been suggested but lack seamless implementation. The largest challenges in the multiscale modeling of reactors can be grouped into two main categories: catalytic complexity and the difference between time and length scales of chemical and transport phenomena. Here we introduce the Automated MUltiscale Simulation Environment AMUSE, a workflow that starts from Density Functional Theory (DFT) data, automates the analysis of the reaction networks through graph theory, prepares it for microkinetic modeling, and subsequently integrates the results into a standard open-source Computational Fluid Dynamics (CFD) code. We demonstrate the capabilities of AMUSE by applying it to the unimolecular iso-propanol dehydrogenation reaction and then, increasing the complexity, to the pre-commercial Pd/In2O3 catalyst employed for the CO2 hydrogenation to methanol. The results show that AMUSE allows the computational investigation of heterogeneous catalytic reactions in a comprehensive way, providing essential information for catalyst design from the atomistic to the reactor scale level.
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Affiliation(s)
- Albert Sabadell-Rendón
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, (BIST) Av. Paisos Catalans 16 Tarragona 43007 Spain
| | - Kamila Kaźmierczak
- TotalEnergies, TotalEnergies One Tech Belgium Zone industrielle C, 7181 Feluy Belgium
| | - Santiago Morandi
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, (BIST) Av. Paisos Catalans 16 Tarragona 43007 Spain
- Department of Physical and Inorganic Chemistry, Universitat Rovira i Virgili Campus Sescelades, N4 Block, C. Marcel·lí Domingo 1 Tarragona 43007 Spain
| | - Florian Euzenat
- TotalEnergies Research and Technology Gonfreville, Route Industrielle, Carrefour 4, Port 4864 76700 Rogerville France
| | - Daniel Curulla-Ferré
- TotalEnergies, TotalEnergies One Tech Belgium Zone industrielle C, 7181 Feluy Belgium
| | - Núria López
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), The Barcelona Institute of Science and Technology, (BIST) Av. Paisos Catalans 16 Tarragona 43007 Spain
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10
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Rasmussen MH, Seumer J, Jensen JH. Toward De Novo Catalyst Discovery: Fast Identification of New Catalyst Candidates for Alcohol-Mediated Morita-Baylis-Hillman Reactions. Angew Chem Int Ed Engl 2023; 62:e202310580. [PMID: 37830522 DOI: 10.1002/anie.202310580] [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: 07/25/2023] [Revised: 09/15/2023] [Accepted: 10/13/2023] [Indexed: 10/14/2023]
Abstract
Recently we have demonstrated how a genetic algorithm (GA) starting from random tertiary amines can be used to discover a new and efficient catalyst for the alcohol-mediated Morita-Baylis-Hillman (MBH) reaction. In particular, the discovered catalyst was shown experimentally to be eight times more active than DABCO, commonly used to catalyze the MBH reaction. This represents a breakthrough in using generative models for catalyst optimization. However, the GA procedure, and hence discovery, relied on two important pieces of information; 1) the knowledge that tertiary amines catalyze the reaction and 2) the mechanism and reaction profile for the catalyzed reaction, in particular the transition state structure of the rate-determining step. Thus, truly de novo catalyst discovery must include these steps. Here we present such a method for discovering catalyst candidates for a specific reaction while simultaneously proposing a mechanism for the catalyzed reaction. We show that tertiary amines and phosphines are potential catalysts for the MBH reaction by screening 11 molecular templates representing common functional groups. The method relies on an automated reaction discovery workflow using meta-dynamics calculations. Combining this method for catalyst candidate discovery with our GA-based catalyst optimization method results in an algorithm for truly de novo catalyst discovery.
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Affiliation(s)
- Maria H Rasmussen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Julius Seumer
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Jan H Jensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
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11
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Hayashi H, Maeda S, Mita T. Quantum chemical calculations for reaction prediction in the development of synthetic methodologies. Chem Sci 2023; 14:11601-11616. [PMID: 37920348 PMCID: PMC10619630 DOI: 10.1039/d3sc03319h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/29/2023] [Indexed: 11/04/2023] Open
Abstract
Quantum chemical calculations have been used in the development of synthetic methodologies to analyze the reaction mechanisms of the developed reactions. Their ability to estimate chemical reaction pathways, including transition state energies and connected equilibria, has led researchers to embrace their use in predicting unknown reactions. This perspective highlights strategies that leverage quantum chemical calculations for the prediction of reactions in the discovery of new methodologies. Selected examples demonstrate how computation has driven the development of unknown reactions, catalyst design, and the exploration of synthetic routes to complex molecules prior to often laborious, costly, and time-consuming experimental investigations.
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Affiliation(s)
- Hiroki Hayashi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University Kita 21, Nishi 10, Kita-ku Sapporo Hokkaido 001-0021 Japan
- JST-ERATO, Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University Kita 21, Nishi 10, Kita-ku Sapporo Hokkaido 001-0021 Japan
- JST-ERATO, Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
- Department of Chemistry, Faculty of Science, Hokkaido University Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| | - Tsuyoshi Mita
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University Kita 21, Nishi 10, Kita-ku Sapporo Hokkaido 001-0021 Japan
- JST-ERATO, Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project Kita 10, Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
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12
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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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13
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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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14
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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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15
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Xu R, Meisner J, Chang AM, Thompson KC, Martínez TJ. First principles reaction discovery: from the Schrodinger equation to experimental prediction for methane pyrolysis. Chem Sci 2023; 14:7447-7464. [PMID: 37449065 PMCID: PMC10337770 DOI: 10.1039/d3sc01202f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/02/2023] [Indexed: 07/18/2023] Open
Abstract
Our recent success in exploiting graphical processing units (GPUs) to accelerate quantum chemistry computations led to the development of the ab initio nanoreactor, a computational framework for automatic reaction discovery and kinetic model construction. In this work, we apply the ab initio nanoreactor to methane pyrolysis, from automatic reaction discovery to path refinement and kinetic modeling. Elementary reactions occurring during methane pyrolysis are revealed using GPU-accelerated ab initio molecular dynamics simulations. Subsequently, these reaction paths are refined at a higher level of theory with optimized reactant, product, and transition state geometries. Reaction rate coefficients are calculated by transition state theory based on the optimized reaction paths. The discovered reactions lead to a kinetic model with 53 species and 134 reactions, which is validated against experimental data and simulations using literature kinetic models. We highlight the advantage of leveraging local brute force and Monte Carlo sensitivity analysis approaches for efficient identification of important reactions. Both sensitivity approaches can further improve the accuracy of the methane pyrolysis kinetic model. The results in this work demonstrate the power of the ab initio nanoreactor framework for computationally affordable systematic reaction discovery and accurate kinetic modeling.
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Affiliation(s)
- Rui Xu
- Department of Chemistry, The PULSE Institute, Stanford University Stanford CA 94305 USA
- SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
| | - Jan Meisner
- Department of Chemistry, The PULSE Institute, Stanford University Stanford CA 94305 USA
- SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
| | - Alexander M Chang
- Department of Chemistry, The PULSE Institute, Stanford University Stanford CA 94305 USA
- SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
| | - Keiran C Thompson
- Department of Chemistry, The PULSE Institute, Stanford University Stanford CA 94305 USA
- SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
| | - Todd J Martínez
- Department of Chemistry, The PULSE Institute, Stanford University Stanford CA 94305 USA
- SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo Park CA 94025 USA
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16
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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: 0] [Impact Index Per Article: 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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17
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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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18
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Zádor J, Martí C, Van de Vijver R, Johansen SL, Yang Y, Michelsen HA, Najm HN. Automated Reaction Kinetics of Gas-Phase Organic Species over Multiwell Potential Energy Surfaces. J Phys Chem A 2023; 127:565-588. [PMID: 36607817 DOI: 10.1021/acs.jpca.2c06558] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Automation of rate-coefficient calculations for gas-phase organic species became possible in recent years and has transformed how we explore these complicated systems computationally. Kinetics workflow tools bring rigor and speed and eliminate a large fraction of manual labor and related error sources. In this paper we give an overview of this quickly evolving field and illustrate, through five detailed examples, the capabilities of our own automated tool, KinBot. We bring examples from combustion and atmospheric chemistry of C-, H-, O-, and N-atom-containing species that are relevant to molecular weight growth and autoxidation processes. The examples shed light on the capabilities of automation and also highlight particular challenges associated with the various chemical systems that need to be addressed in future work.
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Affiliation(s)
- Judit Zádor
- Combustion Research Facility, Sandia National Laboratories, Livermore94550, California, United States
| | - Carles Martí
- Combustion Research Facility, Sandia National Laboratories, Livermore94550, California, United States
| | | | - Sommer L Johansen
- Combustion Research Facility, Sandia National Laboratories, Livermore94550, California, United States
| | - Yoona Yang
- Combustion Research Facility, Sandia National Laboratories, Livermore94550, California, United States
| | - Hope A Michelsen
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder80309, Colorado, United States
| | - Habib N Najm
- Combustion Research Facility, Sandia National Laboratories, Livermore94550, California, United States
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19
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Zhao Q, Savoie BM. Algorithmic Explorations of Unimolecular and Bimolecular Reaction Spaces. Angew Chem Int Ed Engl 2022; 61:e202210693. [PMID: 36074520 PMCID: PMC9827825 DOI: 10.1002/anie.202210693] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Indexed: 01/12/2023]
Abstract
Algorithmic reaction exploration based on transition state searches has already made inroads into many niche applications, but its potential as a general-purpose tool is still largely unrealized. Computational cost and the absence of benchmark problems involving larger molecules remain obstacles to further progress. Here an ultra-low cost exploration algorithm is implemented and used to explore the reactivity of unimolecular and bimolecular reactants, comprising a total of 581 reactions involving 51 distinct reactants. The algorithm discovers all established reaction pathways, where such comparisons are possible, while also revealing a much richer reactivity landscape, including lower barrier reaction pathways and a strong dependence of reaction conformation in the apparent barriers of the reported reactions. The diversity of these benchmarks illustrate that reaction exploration algorithms are approaching general-purpose capability.
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Affiliation(s)
- Qiyuan Zhao
- Davidson School of Chemical EngineeringPurdue UniversityWest LafayetteIN47906USA
| | - Brett M. Savoie
- Davidson School of Chemical EngineeringPurdue UniversityWest LafayetteIN47906USA
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20
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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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21
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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] [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
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. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13321-022-00610-x.
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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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22
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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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23
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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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24
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Chen X, Liu M, Gao J. CARNOT: a Fragment-Based Direct Molecular Dynamics and Virtual-Reality Simulation Package for Reactive Systems. J Chem Theory Comput 2022; 18:1297-1313. [PMID: 35129348 DOI: 10.1021/acs.jctc.1c01032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Traditionally, the study of reaction mechanisms of complex reaction systems such as combustion has been performed on an individual basis by optimizations of transition structure and minimum energy path or by reaction dynamics trajectory calculations for one elementary reaction at a time. It is effective, but time-consuming, whereas important and unexpected processes could have been missed. In this article, we present a direct molecular dynamics (DMD) approach and a virtual-reality simulation program, CARNOT, in which plausible chemical reactions are simulated simultaneously at finite temperature and pressure conditions. A key concept of the present ab initio molecular dynamics method is to partition a large, chemically reactive system into molecular fragments that can be adjusted on the fly of a DMD simulation. The theory represents an extension of the explicit polarization method to reactive events, called ReX-Pol. We propose a highest-and-lowest adapted-spin approximation to define the local spins of individual fragments, rather than treating the entire system by a delocalized wave function. Consequently, the present ab initio DMD can be applied to reactive systems consisting of an arbitrarily varying number of closed and open-shell fragments such as free radicals, zwitterions, and separate ions found in combustion and other reactions. A graph-data structure algorithm was incorporated in CARNOT for the analysis of reaction networks, suitable for reaction mechanism reduction. Employing the PW91 density functional theory and the 6-31+G(d) basis set, the capabilities of the CARNOT program were illustrated by a combustion reaction, consisting of 28 650 atoms, and by reaction network analysis that revealed a range of mechanistic and dynamical events. The method may be useful for applications to other types of complex reactions.
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Affiliation(s)
- Xin Chen
- Peking University Shenzhen Graduate School, Shenzhen, Guangdong 581055, China.,Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 581055, China
| | - Meiyi Liu
- Peking University Shenzhen Graduate School, Shenzhen, Guangdong 581055, China.,Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 581055, China
| | - Jiali Gao
- Peking University Shenzhen Graduate School, Shenzhen, Guangdong 581055, China.,Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 581055, China.,Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
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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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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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Ferro-Costas D, Cordeiro MNDS, Fernández-Ramos A. An integrated protocol to study hydrogen abstraction reactions by atomic hydrogen in flexible molecules: application to butanol isomers. Phys Chem Chem Phys 2022; 24:3043-3058. [DOI: 10.1039/d1cp03928h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This work presents a protocol designed to study hydrogen abstraction reactions by atomic hydrogen in molecules with multiple conformations.
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Affiliation(s)
- David Ferro-Costas
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - M. Natália D. S. Cordeiro
- LAQV@REQUIMTE, Department of Chemistry & Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Antonio Fernández-Ramos
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
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28
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Klippenstein SJ. Spiers Memorial Lecture: theory of unimolecular reactions. Faraday Discuss 2022; 238:11-67. [DOI: 10.1039/d2fd00125j] [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
One hundred years ago, at an earlier Faraday Discussion meeting, Lindemann presented a mechanism that provides the foundation for contemplating the pressure dependence of unimolecular reactions. Since that time, our...
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29
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Lucas K, Chen A, Schubmehl M, Kolonko KJ, Barnes GL. Exploring the Effects of Methylation on the CID of Protonated Lysine: A Combined Experimental and Computational Approach. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2675-2684. [PMID: 34677967 DOI: 10.1021/jasms.1c00225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report the results of experiments, simulations, and DFT calculations that focus on describing the reaction dynamics observed within the collision-induced dissociation of l-lysine-H+ and its side-chain methylated analogues, Nε-methyl-l-lysine-H+ (Me1-lysine-H+), Nε,Nε-dimethyl-l-lysine-H+ (Me2-lysine-H+), and Nε,Nε,Nε-trimethyl-l-lysine-H+ (Me3-lysine-H+). The major pathways observed in the experimental measurements were m/z 130 and 84, with the former dominant at low collision energies and the latter at intermediate to high collision energies. The m/z 130 peak corresponds to loss of N(CH3)nH3-n, while m/z 84 has the additional loss of H2CO2 likely in the form of H2O + CO. Within the time frame of the direct dynamics simulations, m/z 130 and 101 were the most populous peaks, with the latter identified as an intermediate to m/z 84. The simulations allowed for the determination of several reaction pathways that result in these products. A graph theory analysis enabled the elucidation of the significant structures that compose each peak. Methylation results in the preferential loss of the side-chain amide group and a reduction of cyclic structures within the m/z 84 peak population in simulations.
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Affiliation(s)
- Kenneth Lucas
- Department of Chemistry and Biochemistry, Siena College, 515 Loudon Road, Loudonville, New York 12211, United States
| | - Amy Chen
- Department of Chemistry and Biochemistry, Siena College, 515 Loudon Road, Loudonville, New York 12211, United States
| | - Megan Schubmehl
- Department of Chemistry and Biochemistry, Siena College, 515 Loudon Road, Loudonville, New York 12211, United States
| | - Kristopher J Kolonko
- Stewart's Advanced Instrumentation and Technology (SAInT) Center, Siena College, 515 Loudon Road, Loudonville, New York 12211, United States
| | - George L Barnes
- Department of Chemistry and Biochemistry, Siena College, 515 Loudon Road, Loudonville, New York 12211, United States
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