51
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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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52
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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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53
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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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54
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Li B, Chen H. Prediction of Compound Synthesis Accessibility Based on Reaction Knowledge Graph. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27031039. [PMID: 35164303 PMCID: PMC8838603 DOI: 10.3390/molecules27031039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/19/2022] [Accepted: 02/01/2022] [Indexed: 11/16/2022]
Abstract
With the increasing application of deep-learning-based generative models for de novo molecule design, the quantitative estimation of molecular synthetic accessibility (SA) has become a crucial factor for prioritizing the structures generated from generative models. It is also useful for helping in the prioritization of hit/lead compounds and guiding retrosynthesis analysis. In this study, based on the USPTO and Pistachio reaction datasets, a chemical reaction network was constructed for the identification of the shortest reaction paths (SRP) needed to synthesize compounds, and different SRP cut-offs were then used as the threshold to distinguish a organic compound as either an easy-to-synthesize (ES) or hard-to-synthesize (HS) class. Two synthesis accessibility models (DNN-ECFP model and graph-based CMPNN model) were built using deep learning/machine learning algorithms. Compared to other existing synthesis accessibility scoring schemes, such as SYBA, SCScore, and SAScore, our results show that CMPNN (ROC AUC: 0.791) performs better than SYBA (ROC AUC: 0.76), albeit marginally, and outperforms SAScore and SCScore. Our prediction models based on historical reaction knowledge could be a potential tool for estimating molecule SA.
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Affiliation(s)
- Baiqing Li
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510663, China;
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health-Guangdong Laboratory), Guangzhou 510530, China
| | - Hongming Chen
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510663, China;
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health-Guangdong Laboratory), Guangzhou 510530, China
- Guangzhou Laboratory, Guangzhou International Bio Island, No. 9 XinDaoHuanBei Road, Guangzhou 510005, China
- Correspondence:
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55
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Steiner M, Reiher M. Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis. Top Catal 2022; 65:6-39. [PMID: 35185305 PMCID: PMC8816766 DOI: 10.1007/s11244-021-01543-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 12/11/2022]
Abstract
Autonomous computations that rely on automated reaction network elucidation algorithms may pave the way to make computational catalysis on a par with experimental research in the field. Several advantages of this approach are key to catalysis: (i) automation allows one to consider orders of magnitude more structures in a systematic and open-ended fashion than what would be accessible by manual inspection. Eventually, full resolution in terms of structural varieties and conformations as well as with respect to the type and number of potentially important elementary reaction steps (including decomposition reactions that determine turnover numbers) may be achieved. (ii) Fast electronic structure methods with uncertainty quantification warrant high efficiency and reliability in order to not only deliver results quickly, but also to allow for predictive work. (iii) A high degree of autonomy reduces the amount of manual human work, processing errors, and human bias. Although being inherently unbiased, it is still steerable with respect to specific regions of an emerging network and with respect to the addition of new reactant species. This allows for a high fidelity of the formalization of some catalytic process and for surprising in silico discoveries. In this work, we first review the state of the art in computational catalysis to embed autonomous explorations into the general field from which it draws its ingredients. We then elaborate on the specific conceptual issues that arise in the context of autonomous computational procedures, some of which we discuss at an example catalytic system.
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Affiliation(s)
- Miguel Steiner
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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56
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Xu M, Li Y, Ma Y. Materials by design at high pressures. Chem Sci 2022; 13:329-344. [PMID: 35126967 PMCID: PMC8729811 DOI: 10.1039/d1sc04239d] [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: 08/03/2021] [Accepted: 12/08/2021] [Indexed: 01/29/2023] Open
Abstract
Pressure, a fundamental thermodynamic variable, can generate two essential effects on materials. First, pressure can create new high-pressure phases via modification of the potential energy surface. Second, pressure can produce new compounds with unconventional stoichiometries via modification of the compositional landscape. These new phases or compounds often exhibit exotic physical and chemical properties that are inaccessible at ambient pressure. Recent studies have established a broad scope for developing materials with specific desired properties under high pressure. Crystal structure prediction methods and first-principles calculations can be used to design materials and thus guide subsequent synthesis plans prior to any experimental work. A key example is the recent theory-initiated discovery of the record-breaking high-temperature superhydride superconductors H3S and LaH10 with critical temperatures of 200 K and 260 K, respectively. This work summarizes and discusses recent progress in the theory-oriented discovery of new materials under high pressure, including hydrogen-rich superconductors, high-energy-density materials, inorganic electrides, and noble gas compounds. The discovery of the considered compounds involved substantial theoretical contributions. We address future challenges facing the design of materials at high pressure and provide perspectives on research directions with significant potential for future discoveries.
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Affiliation(s)
- Meiling Xu
- Laboratory of Quantum Functional Materials Design and Application, School of Physics and Electronic Engineering, Jiangsu Normal University Xuzhou 221116 China
| | - Yinwei Li
- Laboratory of Quantum Functional Materials Design and Application, School of Physics and Electronic Engineering, Jiangsu Normal University Xuzhou 221116 China
| | - Yanming Ma
- State Key Laboratory of Superhard Materials & International Center for Computational Method and Software, College of Physics, Jilin University Changchun 130012 China
- International Center of Future Science, Jilin University Changchun 130012 China
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57
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Baiardi A, Grimmel SA, Steiner M, Türtscher PL, Unsleber JP, Weymuth T, Reiher M. Expansive Quantum Mechanical Exploration of Chemical Reaction Paths. Acc Chem Res 2022; 55:35-43. [PMID: 34918903 DOI: 10.1021/acs.accounts.1c00472] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Quantum mechanical methods have been well-established for the elucidation of reaction paths of chemical processes and for the explicit dynamics of molecular systems. While they are usually deployed in routine manual calculations on reactions for which some insights are already available (typically from experiment), new algorithms and continuously increasing capabilities of modern computer hardware allow for exploratory open-ended computational campaigns that are unbiased and therefore enable unexpected discoveries. Highly efficient and even automated procedures facilitate systematic approaches toward the exploration of uncharted territory in molecular transformations and dynamics. In this work, we elaborate on such explorative approaches that range from reaction network explorations with (stationary) quantum chemical methods to explorative molecular dynamics and migrant wave packet dynamics. The focus is on recent developments that cover the following strategies. (i) Pruning search options for elementary reaction steps by heuristic rules based on the first-principles of quantum mechanics: Rules are required for reducing the combinatorial explosion of potentially reactive atom pairings, and rooting them in concepts derived from the electronic wave function makes them applicable to any molecular system. (ii) Enforcing reactive events by external biases: Inducing a reaction requires constraints that steer and direct elementary-step searches, which can be formulated in terms of forces, velocities, or supplementary potentials. (iii) Manual steering facilitated by interactive quantum mechanics: As ultrafast quantum chemical methods allow for real-time manual interactions with molecular systems, human-intuition-guided paths can be easily explored with suitable human-machine interfaces. (iv) New approaches for transition-state optimization with continuous curve representations can provide stable schemes to be driven in an automated way by allowing for an efficient tuning of the curve's parameters (instead of a manipulation of a collection of structures along the path), and (v) reactive molecular dynamics and direct wave packet propagation exploit the equations of motion of an underlying mechanical theory (usually, classical Newtonian mechanics or Schrödinger quantum mechanics). Explorative approaches are likely to replace the current state of the art in computational chemistry, because they reduce the human effort to be invested in reaction path elucidations, they are less prone to errors and bias-free, and they cover more extensive regions of the relevant configuration space. As a result, computational investigations that rely on these techniques are more likely to deliver surprising discoveries.
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Affiliation(s)
- Alberto Baiardi
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Stephanie A. Grimmel
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Miguel Steiner
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Paul L. Türtscher
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Jan P. Unsleber
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Thomas Weymuth
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Markus Reiher
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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58
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Pazdera TM, Wenz J, Olzmann M. The unimolecular decomposition of dimethoxymethane: channel switching as a function of temperature and pressure. Faraday Discuss 2022; 238:665-681. [DOI: 10.1039/d2fd00039c] [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
Branching ratios of competing unimolecular reactions often exhibit a complicated temperature and pressure dependence that makes modeling of complex reaction systems in the gas phase difficult. In particular, the competition...
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59
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Affiliation(s)
- Markus Reiher
- ETH Zürich, Laboratorium für Physikalische Chemie Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
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60
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Lanrezac A, Férey N, Baaden M. Wielding the power of interactive molecular simulations. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- André Lanrezac
- CNRS, Laboratoire de Biochimie Théorique Université de Paris Paris France
| | - Nicolas Férey
- CNRS, Laboratoire interdisciplinaire des sciences du numérique Université Paris‐Saclay Orsay France
| | - Marc Baaden
- CNRS, Laboratoire de Biochimie Théorique Université de Paris Paris France
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61
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Chantreau Majerus R, Robertson C, Habershon S. Assessing and rationalizing the performance of Hessian update schemes for reaction path Hamiltonian rate calculations. J Chem Phys 2021; 155:204112. [PMID: 34852478 DOI: 10.1063/5.0064685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The reaction path Hamiltonian (RPH) can be used to calculate chemical reaction rate constants, going beyond transition-state theory in taking account of recrossing by providing an approximation to the dynamic transmission coefficient. However, the RPH necessitates the calculation of the Hessian matrix at a number of points along the minimum energy path; the associated computational cost stands as a bottleneck in RPH calculations, especially if one is interested in using high-accuracy electronic structure methods. In this work, four different Hessian update schemes (symmetric rank-1, Powell-symmetric Broyden, Bofill, and TS-BFGS updates) are assessed to see whether or not they reliably reproduce calculated transmission coefficients for three different chemical reactions. Based on the reactions investigated, the symmetric rank-1 Hessian update was the least appropriate for RPH construction, giving different transmission coefficients from the standard analytical Hessian approach, as well as inconsistent frequencies and coupling properties. The Bofill scheme, the Powell-symmetric Broyden scheme, and the TS-BFGS scheme were the most reliable Hessian update methods, with transmission coefficients that were in good agreement with those calculated by the standard RPH calculations. The relative accuracy of the different Hessian update schemes is further rationalized by investigating the approximated Coriolis and curvature coupling terms along the reaction-path, providing insight into when these schemes would be expected to work well. Furthermore, the associated computational cost associated with the RPH calculations was substantially reduced by the tested update schemes. Together, these results provide useful rules-of-thumb for using Hessian update schemes in RPH simulations.
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Affiliation(s)
- R Chantreau Majerus
- Molecular Analytical Science Centre for Doctoral Training, Senate House, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - C Robertson
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - S Habershon
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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62
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Sharma S, Arya A, Cruz R, Cleaves II HJ. Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives. Life (Basel) 2021; 11:1140. [PMID: 34833016 PMCID: PMC8624352 DOI: 10.3390/life11111140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
Prebiotic chemistry often involves the study of complex systems of chemical reactions that form large networks with a large number of diverse species. Such complex systems may have given rise to emergent phenomena that ultimately led to the origin of life on Earth. The environmental conditions and processes involved in this emergence may not be fully recapitulable, making it difficult for experimentalists to study prebiotic systems in laboratory simulations. Computational chemistry offers efficient ways to study such chemical systems and identify the ones most likely to display complex properties associated with life. Here, we review tools and techniques for modelling prebiotic chemical reaction networks and outline possible ways to identify self-replicating features that are central to many origin-of-life models.
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Affiliation(s)
- Siddhant Sharma
- Blue Marble Space Institute of Science, Seattle, WA 98154, USA; (S.S.); (A.A.); (R.C.)
- Department of Biochemistry, Deshbandhu College, University of Delhi, New Delhi 110019, India
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Aayush Arya
- Blue Marble Space Institute of Science, Seattle, WA 98154, USA; (S.S.); (A.A.); (R.C.)
- Department of Physics, Lovely Professional University, Jalandhar-Delhi GT Road, Phagwara 144001, India
| | - Romulo Cruz
- Blue Marble Space Institute of Science, Seattle, WA 98154, USA; (S.S.); (A.A.); (R.C.)
- Big Data Laboratory, Information and Communications Technology Center (CTIC), National University of Engineering, Amaru 210, Lima 15333, Peru
| | - Henderson James Cleaves II
- Blue Marble Space Institute of Science, Seattle, WA 98154, USA; (S.S.); (A.A.); (R.C.)
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
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63
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Abstract
We demonstrate that a program synthesis approach based on a linear code representation can be used to generate algorithms that approximate the ground-state solutions of one-dimensional time-independent Schrödinger equations constructed with bound polynomial potential energy surfaces (PESs). Here, an algorithm is constructed as a linear series of instructions operating on a set of input vectors, matrices, and constants that define the problem characteristics, such as the PES. Discrete optimization is performed using simulated annealing in order to identify sequences of code-lines, operating on the program inputs that can reproduce the expected ground-state wavefunctions ψ(x) for a set of target PESs. The outcome of this optimization is not simply a mathematical function approximating ψ(x) but is, instead, a complete algorithm that converts the input vectors describing the system into a ground-state solution of the Schrödinger equation. These initial results point the way toward an alternative route for developing novel algorithms for quantum chemistry applications.
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Affiliation(s)
- Scott Habershon
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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64
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Gertig C, Fleitmann L, Hemprich C, Hense J, Bardow A, Leonhard K. CAT-COSMO-CAMPD: Integrated in silico design of catalysts and processes based on quantum chemistry. Comput Chem Eng 2021. [DOI: 10.1016/j.compchemeng.2021.107438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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65
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Bi K, Zhang S, Zhang C, Li H, Huang X, Liu H, Qiu T. Knowledge expression, numerical modeling and optimization application of ethylene thermal cracking: From the perspective of intelligent manufacturing. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2021.03.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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66
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Automated Construction and Optimization Combined with Machine Learning to Generate Pt(II) Methane C–H Activation Transition States. Top Catal 2021. [DOI: 10.1007/s11244-021-01506-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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67
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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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68
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Barone V, Puzzarini C, Mancini G. Integration of theory, simulation, artificial intelligence and virtual reality: a four-pillar approach for reconciling accuracy and interpretability in computational spectroscopy. Phys Chem Chem Phys 2021; 23:17079-17096. [PMID: 34346437 DOI: 10.1039/d1cp02507d] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The established pillars of computational spectroscopy are theory and computer based simulations. Recently, artificial intelligence and virtual reality are becoming the third and fourth pillars of an integrated strategy for the investigation of complex phenomena. The main goal of the present contribution is the description of some new perspectives for computational spectroscopy, in the framework of a strategy in which computational methodologies at the state of the art, high-performance computing, artificial intelligence and virtual reality tools are integrated with the aim of improving research throughput and achieving goals otherwise not possible. Some of the key tools (e.g., continuous molecular perception model and virtual multifrequency spectrometer) and theoretical developments (e.g., non-periodic boundaries, joint variational-perturbative models) are shortly sketched and their application illustrated by means of representative case studies taken from recent work by the authors. Some of the results presented are already well beyond the state of the art in the field of computational spectroscopy, thereby also providing a proof of concept for other research fields.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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69
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Barber VP, Green WH, Kroll JH. Screening for New Pathways in Atmospheric Oxidation Chemistry with Automated Mechanism Generation. J Phys Chem A 2021; 125:6772-6788. [PMID: 34346695 DOI: 10.1021/acs.jpca.1c04297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In the Earth's atmosphere, reactive organic carbon undergoes oxidation via a highly complex, multigeneration process, with implications for air quality and climate. Decades of experimental and theoretical studies, primarily on the reactions of hydrocarbons, have led to a canonical understanding of how gas-phase oxidation of organic compounds takes place. Recent research has brought to light a number of examples where the presence of certain functional groups opens up reaction pathways for key radical intermediates, including alkyl radicals, alkoxy radicals, and peroxy radicals, that are substantially different from traditional oxidation mechanisms. These discoveries highlight the need for methods that systematically explore the chemistry of complex, functionalized molecules without being prohibitively expensive. In this work, automated reaction network generation is used as a screening tool for new pathways in atmospheric oxidation chemistry. The reaction mechanism generator (RMG) is used to generate reaction networks for the OH-initiated oxidation of 200 mono- and bifunctionally substituted n-pentanes. The resulting networks are then filtered to highlight the reactions of key radical intermediates that are fast enough to compete with traditional atmospheric removal processes as well as "uncanonical" processes which differ from traditionally accepted oxidation mechanisms. Several recently reported, uncanonical atmospheric mechanisms appear in the RMG dataset. These "proof of concept" results provide confidence in this approach as a tool in the search for overlooked atmospheric oxidation chemistry. Several previously unreported reaction types are also encountered in the dataset. The most potentially atmospherically important of these is a radical-carbonyl ring-closure reaction that produces a highly functionalized cyclic alkoxy radical. This pathway is proposed as a promising target for further study via experiments and more detailed theoretical calculations. The approach presented herein represents a new way to efficiently explore atmospheric chemical space and unearth overlooked reaction steps in atmospheric oxidation.
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Affiliation(s)
- Victoria P Barber
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - William H Green
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jesse H Kroll
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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70
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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: 9] [Impact Index Per Article: 3.0] [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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71
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Zhao Q, Savoie BM. Simultaneously improving reaction coverage and computational cost in automated reaction prediction tasks. NATURE COMPUTATIONAL SCIENCE 2021; 1:479-490. [PMID: 38217124 DOI: 10.1038/s43588-021-00101-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 06/18/2021] [Indexed: 01/15/2024]
Abstract
Automated reaction prediction has the potential to elucidate complex reaction networks for applications ranging from combustion to materials degradation, but computational cost and inconsistent reaction coverage are still obstacles to exploring deep reaction networks. Here we show that cost can be reduced and reaction coverage can be increased simultaneously by relatively straightforward modifications of the reaction enumeration, geometry initialization and transition state convergence algorithms that are common to many prediction methodologies. These components are implemented in the context of yet another reaction program (YARP), our reaction prediction package with which we report reaction discovery benchmarks for organic single-step reactions, thermal degradation of a γ-ketohydroperoxide, and competing ring-closures in a large organic molecule. Compared with recent benchmarks, YARP (re)discovers both established and unreported reaction pathways and products while simultaneously reducing the cost of reaction characterization by nearly 100-fold and increasing convergence of transition states. This combination of ultra-low cost and high reaction coverage creates opportunities to explore the reactivity of larger systems and more complex reaction networks for applications such as chemical degradation, where computational cost is a bottleneck.
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Affiliation(s)
- Qiyuan Zhao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA
| | - Brett M Savoie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN, USA.
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72
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Xu J, Cao XM, Hu P. Perspective on computational reaction prediction using machine learning methods in heterogeneous catalysis. Phys Chem Chem Phys 2021; 23:11155-11179. [PMID: 33972971 DOI: 10.1039/d1cp01349a] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Heterogeneous catalysis plays a significant role in the modern chemical industry. Towards the rational design of novel catalysts, understanding reactions over surfaces is the most essential aspect. Typical industrial catalytic processes such as syngas conversion and methane utilisation can generate a large reaction network comprising thousands of intermediates and reaction pairs. This complexity not only arises from the permutation of transformations between species but also from the extra reaction channels offered by distinct surface sites. Despite the success in investigating surface reactions at the atomic scale, the huge computational expense of ab initio methods hinders the exploration of such complicated reaction networks. With the proliferation of catalysis studies, machine learning as an emerging tool can take advantage of the accumulated reaction data to emulate the output of ab initio methods towards swift reaction prediction. Here, we briefly summarise the conventional workflow of reaction prediction, including reaction network generation, ab initio thermodynamics and microkinetic modelling. An overview of the frequently used regression models in machine learning is presented. As a promising alternative to full ab initio calculations, machine learning interatomic potentials are highlighted. Furthermore, we survey applications assisted by these methods for accelerating reaction prediction, exploring reaction networks, and computational catalyst design. Finally, we envisage future directions in computationally investigating reactions and implementing machine learning algorithms in heterogeneous catalysis.
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Affiliation(s)
- Jiayan Xu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Centre for Computational Chemistry and Research Institute of Industrial Catalysis, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China. and School of Chemistry and Chemical Engineering, Queen's University Belfast, Belfast BT9 5AG, UK
| | - Xiao-Ming Cao
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Centre for Computational Chemistry and Research Institute of Industrial Catalysis, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China.
| | - P Hu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Centre for Computational Chemistry and Research Institute of Industrial Catalysis, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P. R. China. and School of Chemistry and Chemical Engineering, Queen's University Belfast, Belfast BT9 5AG, UK
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73
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Brunken C, Reiher M. Automated Construction of Quantum–Classical Hybrid Models. J Chem Theory Comput 2021; 17:3797-3813. [DOI: 10.1021/acs.jctc.1c00178] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Christoph Brunken
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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74
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Chen S, Peterson CW, Parker JA, Rice SA, Ferguson AL, Scherer NF. Data-driven reaction coordinate discovery in overdamped and non-conservative systems: application to optical matter structural isomerization. Nat Commun 2021; 12:2548. [PMID: 33953159 PMCID: PMC8099877 DOI: 10.1038/s41467-021-22794-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
Optical matter (OM) systems consist of (nano-)particle constituents in solution that can self-organize into ordered arrays that are bound by electrodynamic interactions. They also manifest non-conservative forces, and the motions of the nano-particles are overdamped; i.e., they exhibit diffusive trajectories. We propose a data-driven approach based on principal components analysis (PCA) to determine the collective modes of non-conservative overdamped systems, such as OM structures, and harmonic linear discriminant analysis (HLDA) of time trajectories to estimate the reaction coordinate for structural transitions. We demonstrate the approach via electrodynamics-Langevin dynamics simulations of six electrodynamically-bound nanoparticles in an incident laser beam. The reaction coordinate we discover is in excellent accord with a rigorous committor analysis, and the identified mechanism for structural isomerization is in very good agreement with the experimental observations. The PCA-HLDA approach to data-driven discovery of reaction coordinates can aid in understanding and eventually controlling non-conservative and overdamped systems including optical and active matter systems.
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Affiliation(s)
- Shiqi Chen
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- James Franck Institute, University of Chicago, Chicago, IL, USA
| | - Curtis W Peterson
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- James Franck Institute, University of Chicago, Chicago, IL, USA
| | - John A Parker
- James Franck Institute, University of Chicago, Chicago, IL, USA
- Department of Physics, University of Chicago, Chicago, IL, USA
| | - Stuart A Rice
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- James Franck Institute, University of Chicago, Chicago, IL, USA
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA.
| | - Norbert F Scherer
- Department of Chemistry, University of Chicago, Chicago, IL, USA.
- James Franck Institute, University of Chicago, Chicago, IL, USA.
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75
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Maeda S, Harabuchi Y. Exploring paths of chemical transformations in molecular and periodic systems: An approach utilizing force. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1538] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI‐ICReDD), Hokkaido University Sapporo Hokkaido Japan
- Department of Chemistry, Faculty of Science Hokkaido University Sapporo Hokkaido Japan
- JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project Sapporo Hokkaido Japan
- National Institute for Materials Science (NIMS) Research and Services Division of Materials Data and Integrated System (MaDIS) Tsukuba Ibaraki Japan
| | - Yu Harabuchi
- Institute for Chemical Reaction Design and Discovery (WPI‐ICReDD), Hokkaido University Sapporo Hokkaido Japan
- Department of Chemistry, Faculty of Science Hokkaido University Sapporo Hokkaido Japan
- JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project Sapporo Hokkaido Japan
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76
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Pieri E, Lahana D, Chang AM, Aldaz CR, Thompson KC, Martínez TJ. The non-adiabatic nanoreactor: towards the automated discovery of photochemistry. Chem Sci 2021; 12:7294-7307. [PMID: 34163820 PMCID: PMC8171323 DOI: 10.1039/d1sc00775k] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The ab initio nanoreactor has previously been introduced to automate reaction discovery for ground state chemistry. In this work, we present the nonadiabatic nanoreactor, an analogous framework for excited state reaction discovery. We automate the study of nonadiabatic decay mechanisms of molecules by probing the intersection seam between adiabatic electronic states with hyper-real metadynamics, sampling the branching plane for relevant conical intersections, and performing seam-constrained path searches. We illustrate the effectiveness of the nonadiabatic nanoreactor by applying it to benzene, a molecule with rich photochemistry and a wide array of photochemical products. Our study confirms the existence of several types of S0/S1 and S1/S2 conical intersections which mediate access to a variety of ground state stationary points. We elucidate the connections between conical intersection energy/topography and the resulting photoproduct distribution, which changes smoothly along seam space segments. The exploration is performed with minimal user input, and the protocol requires no previous knowledge of the photochemical behavior of a target molecule. We demonstrate that the nonadiabatic nanoreactor is a valuable tool for the automated exploration of photochemical reactions and their mechanisms.
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Affiliation(s)
- Elisa Pieri
- 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
| | - Dean Lahana
- 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
| | - Cody R Aldaz
- 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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77
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Gong S, Wang Y, Tian Y, Wang L, Liu G. Rapid enthalpy prediction of transition states using molecular graph convolutional network. AIChE J 2021. [DOI: 10.1002/aic.17269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Siyuan Gong
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology Tianjin University Tianjin China
| | - Yutong Wang
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology Tianjin University Tianjin China
| | - Yajie Tian
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology Tianjin University Tianjin China
- Henan Engineering Research Center of Resource and Energy Recovery from Waste, College of Chemistry and Chemical Engineering Henan University Kaifeng China
| | - Li Wang
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin China
| | - Guozhu Liu
- Key Laboratory for Green Chemical Technology of Ministry of Education, School of Chemical Engineering and Technology Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin University Tianjin China
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78
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Stuyver T, Shaik S. Promotion Energy Analysis Predicts Reaction Modes: Nucleophilic and Electrophilic Aromatic Substitution Reactions. J Am Chem Soc 2021; 143:4367-4378. [PMID: 33689334 DOI: 10.1021/jacs.1c00307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
To develop an approach to pre-emptively predict the existence of major reaction modes associated with a chemical system, based on exclusive consideration of reactant properties, we build herein on the valence bond perspective of chemical reactivity. In this perspective, elementary chemical reactions are conceptualized as crossovers between individual diabatic/semilocalized states. As demonstrated, the spacings between the main diabatic states in the reactant geometries-the so-called promotion energies-contain predictive information about which types of crossings are likely to occur on a potential energy surface, facilitating the identification of potential transition states and products. As an added bonus, promotion energy analysis provides direct insight into the impact of environmental effects, e.g., the presence of (polar) solvents and/or (local) electric fields, on a mechanistic landscape. We illustrate the usefulness of our approach by focusing on model nucleophilic and electrophilic aromatic substitution reactions. Overall, we envision our analysis to be useful not only as a tool for conceptualizing individual mechanistic landscapes but also as a facilitator of systematic reaction-network exploration efforts. Because the emerging VB descriptors are computationally inexpensive (and can alternatively be inferred through machine learning), they could be evaluated on-the-fly as part of an exploration algorithm. The so-predicted reaction modes could subsequently be examined in detail through computationally more-demanding methods.
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Affiliation(s)
- Thijs Stuyver
- Institute of Chemistry, The Hebrew University, Jerusalem 91904, Israel
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University, Jerusalem 91904, Israel
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79
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Robertson C, Hyland R, Lacey AJD, Havens S, Habershon S. Identifying Barrierless Mechanisms for Benzene Formation in the Interstellar Medium Using Permutationally Invariant Reaction Discovery. J Chem Theory Comput 2021; 17:2307-2322. [DOI: 10.1021/acs.jctc.1c00046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Ross Hyland
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Andrew J. D. Lacey
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Sebastian Havens
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Scott Habershon
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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80
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Fornari RP, Silva P. Molecular modeling of organic redox‐active battery materials. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Rocco Peter Fornari
- Department of Energy Conversion and Storage Technical University of Denmark Copenhagen Denmark
| | - Piotr Silva
- Department of Energy Conversion and Storage Technical University of Denmark Copenhagen Denmark
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81
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Young TA, Silcock JJ, Sterling AJ, Duarte F. autodE: Automated Calculation of Reaction Energy Profiles— Application to Organic and Organometallic Reactions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tom A. Young
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Joseph J. Silcock
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Alistair J. Sterling
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Fernanda Duarte
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
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82
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Palenik MC. Initial estimate for minimum energy pathways and transition states using velocities in internal coordinates. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2020.111046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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83
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Gimadiev T, Nugmanov R, Batyrshin D, Madzhidov T, Maeda S, Sidorov P, Varnek A. Combined Graph/Relational Database Management System for Calculated Chemical Reaction Pathway Data. J Chem Inf Model 2021; 61:554-559. [PMID: 33502186 DOI: 10.1021/acs.jcim.0c01280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Presently, quantum chemical calculations are widely used to generate extensive data sets for machine learning applications; however, generally, these sets only include information on equilibrium structures and some close conformers. Exploration of potential energy surfaces provides important information on ground and transition states, but analysis of such data is complicated due to the number of possible reaction pathways. Here, we present RePathDB, a database system for managing 3D structural data for both ground and transition states resulting from quantum chemical calculations. Our tool allows one to store, assemble, and analyze reaction pathway data. It combines relational database CGR DB for handling compounds and reactions as molecular graphs with a graph database architecture for pathway analysis by graph algorithms. Original condensed graph of reaction technology is used to store any chemical reaction as a single graph.
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Affiliation(s)
- Timur Gimadiev
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, 001-0021 Sapporo, Japan
| | - Ramil Nugmanov
- Laboratory of Chemoinformatics and Molecular Modeling, Butlerov Institute of Chemistry, Kazan Federal University, 18, Kremlyovskaya str., 420008 Kazan, Russia
| | - Dinar Batyrshin
- Laboratory of Chemoinformatics and Molecular Modeling, Butlerov Institute of Chemistry, Kazan Federal University, 18, Kremlyovskaya str., 420008 Kazan, Russia
| | - Timur Madzhidov
- Laboratory of Chemoinformatics and Molecular Modeling, Butlerov Institute of Chemistry, Kazan Federal University, 18, Kremlyovskaya str., 420008 Kazan, Russia
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, 001-0021 Sapporo, Japan
| | - Pavel Sidorov
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, 001-0021 Sapporo, Japan
| | - Alexandre Varnek
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, 001-0021 Sapporo, Japan.,Laboratory of Chemoinformatics, UMR 7140 CNRS, University of Strasbourg, 4, Blaise Pascal str., 67081 Strasbourg, France
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84
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Abstract
The design of heterogeneous catalysts relies on understanding the fundamental surface kinetics that controls catalyst performance, and microkinetic modeling is a tool that can help the researcher in streamlining the process of catalyst design. Microkinetic modeling is used to identify critical reaction intermediates and rate-determining elementary reactions, thereby providing vital information for designing an improved catalyst. In this review, we summarize general procedures for developing microkinetic models using reaction kinetics parameters obtained from experimental data, theoretical correlations, and quantum chemical calculations. We examine the methods required to ensure the thermodynamic consistency of the microkinetic model. We describe procedures required for parameter adjustments to account for the heterogeneity of the catalyst and the inherent errors in parameter estimation. We discuss the analysis of microkinetic models to determine the rate-determining reactions using the degree of rate control and reversibility of each elementary reaction. We introduce incorporation of Brønsted-Evans-Polanyi relations and scaling relations in microkinetic models and the effects of these relations on catalytic performance and formation of volcano curves are discussed. We review the analysis of reaction schemes in terms of the maximum rate of elementary reactions, and we outline a procedure to identify kinetically significant transition states and adsorbed intermediates. We explore the application of generalized rate expressions for the prediction of optimal binding energies of important surface intermediates and to estimate the extent of potential rate improvement. We also explore the application of microkinetic modeling in homogeneous catalysis, electro-catalysis, and transient reaction kinetics. We conclude by highlighting the challenges and opportunities in the application of microkinetic modeling for catalyst design.
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Affiliation(s)
- Ali Hussain Motagamwala
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - James A Dumesic
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
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85
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Thakkar A, Johansson S, Jorner K, Buttar D, Reymond JL, Engkvist O. Artificial intelligence and automation in computer aided synthesis planning. REACT CHEM ENG 2021. [DOI: 10.1039/d0re00340a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this perspective we deal with questions pertaining to the development of synthesis planning technologies over the course of recent years.
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Affiliation(s)
- Amol Thakkar
- Hit Discovery
- Discovery Sciences
- R&D
- AstraZeneca
- Gothenburg
| | | | - Kjell Jorner
- Early Chemical Development
- Pharmaceutical Sciences
- R&D
- AstraZeneca
- Macclesfield
| | - David Buttar
- Early Chemical Development
- Pharmaceutical Sciences
- R&D
- AstraZeneca
- Macclesfield
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry
- University of Bern
- 3012 Bern
- Switzerland
| | - Ola Engkvist
- Hit Discovery
- Discovery Sciences
- R&D
- AstraZeneca
- Gothenburg
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86
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Young TA, Silcock JJ, Sterling AJ, Duarte F. autodE: Automated Calculation of Reaction Energy Profiles— Application to Organic and Organometallic Reactions. Angew Chem Int Ed Engl 2020; 60:4266-4274. [DOI: 10.1002/anie.202011941] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Indexed: 01/18/2023]
Affiliation(s)
- Tom A. Young
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Joseph J. Silcock
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Alistair J. Sterling
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Fernanda Duarte
- Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
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87
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Stocker S, Csányi G, Reuter K, Margraf JT. Machine learning in chemical reaction space. Nat Commun 2020; 11:5505. [PMID: 33127879 PMCID: PMC7603480 DOI: 10.1038/s41467-020-19267-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/01/2020] [Indexed: 12/29/2022] Open
Abstract
Chemical compound space refers to the vast set of all possible chemical compounds, estimated to contain 1060 molecules. While intractable as a whole, modern machine learning (ML) is increasingly capable of accurately predicting molecular properties in important subsets. Here, we therefore engage in the ML-driven study of even larger reaction space. Central to chemistry as a science of transformations, this space contains all possible chemical reactions. As an important basis for 'reactive' ML, we establish a first-principles database (Rad-6) containing closed and open-shell organic molecules, along with an associated database of chemical reaction energies (Rad-6-RE). We show that the special topology of reaction spaces, with central hub molecules involved in multiple reactions, requires a modification of existing compound space ML-concepts. Showcased by the application to methane combustion, we demonstrate that the learned reaction energies offer a non-empirical route to rationally extract reduced reaction networks for detailed microkinetic analyses.
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Affiliation(s)
- Sina Stocker
- Chair of Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Garching, Germany
| | - Gábor Csányi
- Engineering Laboratory, University of Cambridge, Cambridge, CB2 1PZ, UK
| | - Karsten Reuter
- Chair of Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Garching, Germany
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, Germany
| | - Johannes T Margraf
- Chair of Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Garching, Germany.
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88
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Pattanaik L, Ingraham JB, Grambow CA, Green WH. Generating transition states of isomerization reactions with deep learning. Phys Chem Chem Phys 2020; 22:23618-23626. [PMID: 33112304 DOI: 10.1039/d0cp04670a] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Lack of quality data and difficulty generating these data hinder quantitative understanding of reaction kinetics. Specifically, conventional methods to generate transition state structures are deficient in speed, accuracy, or scope. We describe a novel method to generate three-dimensional transition state structures for isomerization reactions using reactant and product geometries. Our approach relies on a graph neural network to predict the transition state distance matrix and a least squares optimization to reconstruct the coordinates based on which entries of the distance matrix the model perceives to be important. We feed the structures generated by our algorithm through a rigorous quantum mechanics workflow to ensure the predicted transition state corresponds to the ground truth reactant and product. In both generating viable geometries and predicting accurate transition states, our method achieves excellent results. We envision workflows like this, which combine neural networks and quantum chemistry calculations, will become the preferred methods for computing chemical reactions.
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Affiliation(s)
- Lagnajit Pattanaik
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - John B Ingraham
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Colin A Grambow
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - William H Green
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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89
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Savara A, Walker EA. CheKiPEUQ Intro 1: Bayesian Parameter Estimation Considering Uncertainty or Error from both Experiments and Theory**. ChemCatChem 2020. [DOI: 10.1002/cctc.202000953] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Aditya Savara
- Surface Chemistry and Catalysis group Oak Ridge National Laboratory 1 Bethel Valley Road Oak Ridge TN 37830 USA
| | - Eric A. Walker
- Institute for Computational and Data Sciences Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 USA
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90
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Mancini G, Fusè M, Lazzari F, Chandramouli B, Barone V. Unsupervised search of low-lying conformers with spectroscopic accuracy: A two-step algorithm rooted into the island model evolutionary algorithm. J Chem Phys 2020; 153:124110. [DOI: 10.1063/5.0018314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Marco Fusè
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Federico Lazzari
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy
| | | | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy
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91
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Lam YH, Abramov Y, Ananthula RS, Elward JM, Hilden LR, Nilsson Lill SO, Norrby PO, Ramirez A, Sherer EC, Mustakis J, Tanoury GJ. Applications of Quantum Chemistry in Pharmaceutical Process Development: Current State and Opportunities. Org Process Res Dev 2020. [DOI: 10.1021/acs.oprd.0c00222] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yu-hong Lam
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yuriy Abramov
- Pfizer Worldwide Research & Development, Groton, Connecticut 06340, United States
| | - Ravi S. Ananthula
- Small Molecule Design and Development, Eli Lilly and Company, Bangalore 560103, India
| | - Jennifer M. Elward
- Molecular Design, Data and Computational Sciences, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Lori R. Hilden
- Small Molecule Design and Development, Eli Lilly and Company, Indianapolis, Indiana 46221, United States
| | - Sten O. Nilsson Lill
- Early Product Development and Manufacturing, Pharmaceutical Sciences, R&D, AstraZeneca Gothenburg, Mölndal 431 50, Sweden
| | - Per-Ola Norrby
- Data Science & Modelling, Pharmaceutical Sciences, R&D, AstraZeneca Gothenburg, Mölndal 431 50 Sweden
| | - Antonio Ramirez
- Chemical and Synthetic Development, Bristol-Myers Squibb Company, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Edward C. Sherer
- Computational and Structural Chemistry, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Jason Mustakis
- Pfizer Worldwide Research & Development, Groton, Connecticut 06340, United States
| | - Gerald J. Tanoury
- Process Chemistry, Vertex Pharmaceuticals, 50 Northern Avenue, Boston, Massachusetts 02210, United States
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92
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Coley CW, Eyke NS, Jensen KF. Autonomous Discovery in the Chemical Sciences Part I: Progress. Angew Chem Int Ed Engl 2020; 59:22858-22893. [DOI: 10.1002/anie.201909987] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Connor W. Coley
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Natalie S. Eyke
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Klavs F. Jensen
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
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93
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Coley CW, Eyke NS, Jensen KF. Autonome Entdeckung in den chemischen Wissenschaften, Teil I: Fortschritt. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201909987] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Connor W. Coley
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Natalie S. Eyke
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Klavs F. Jensen
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA
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94
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Mita T, Harabuchi Y, Maeda S. Discovery of a synthesis method for a difluoroglycine derivative based on a path generated by quantum chemical calculations. Chem Sci 2020; 11:7569-7577. [PMID: 34094133 PMCID: PMC8159455 DOI: 10.1039/d0sc02089c] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The systematic exploration of synthetic pathways to afford a desired product through quantum chemical calculations remains a considerable challenge. In 2013, Maeda et al. introduced 'quantum chemistry aided retrosynthetic analysis' (QCaRA), which uses quantum chemical calculations to search systematically for the decomposition paths of a target product and proposes a synthesis method. However, until now, no new reactions suggested by QCaRA have been reported to lead to experimental discoveries. Using a difluoroglycine derivative as a target, this study investigated the ability of QCaRA to suggest various synthetic paths to the target without relying on previous data or the knowledge and experience of chemists. Furthermore, experimental verification of the most promising path chosen by an organic chemist among the predicted paths led to the discovery of a synthesis method for a difluoroglycine derivative. We emphasize that the purpose of this study is not to propose a fully automated workflow. Therefore, the extent of the hands-on expertise of chemists required during the verification process was also evaluated. These insights are expected to advance the applicability of QCaRA to the discovery of viable experimental synthetic routes.
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Affiliation(s)
- 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 for Chemical Reaction Design and Discovery Project Kita 10 Nishi 8, Kita-ku Sapporo Hokkaido 060-0810 Japan
| | - 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 for 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.,JST, PRESTO 4-1-8 Honcho Kawaguchi Saitama 332-0012 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 for 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) Tsukuba Ibaraki 305-0044 Japan
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95
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Sumiya Y, Maeda S. Rate Constant Matrix Contraction Method for Systematic Analysis of Reaction Path Networks. CHEM LETT 2020. [DOI: 10.1246/cl.200092] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yosuke Sumiya
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
- National Institute for Materials Science (NIMS), Research and Services Division of Materials Data and Integrated System (MaDIS), Tsukuba, Ibaraki 305-0044, Japan
- JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
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96
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Abstract
Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various algorithmic advances have shown that such structural screenings must and can be automated and routinely carried out. This will replace the standard approach of manually studying a selected and restricted number of molecular structures for a chemical mechanism. The complexity of the task has led to many different approaches. However, all of them address the same general target, namely to produce a complete atomistic picture of the kinetics of a chemical process. It is the purpose of this overview to categorize the problems that should be targeted and to identify the principal components and challenges of automated exploration machines so that the various existing approaches and future developments can be compared based on well-defined conceptual principles.
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Affiliation(s)
- Jan P. Unsleber
- Laboratory for Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Markus Reiher
- Laboratory for Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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97
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Quapp W, Bofill JM. Some Mathematical Reasoning on the Artificial Force Induced Reaction Method. J Comput Chem 2020; 41:629-634. [PMID: 31792984 DOI: 10.1002/jcc.26115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 11/07/2022]
Abstract
There are works of the Maeda-Morokuma group, which propose the artificial force induced reaction (AFIR) method (Maeda et al., J. Comput. Chem. 2014, 35, 166 and 2018, 39, 233). We study this important method from a theoretical point of view. The understanding of the proposers does not use the barrier breakdown point of the AFIR parameter, which usually is half of the reaction path between the minimum and the transition state which is searched for. Based on a comparison with the theory of Newton trajectories, we could better understand the method. It allows us to follow along some reaction pathways from minimum to saddle point, or vice versa. We discuss some well-known two-dimensional test surfaces where we calculate full AFIR pathways. If one has special AFIR curves at hand, one can also study the behavior of the ansatz. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
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Affiliation(s)
- Wolfgang Quapp
- Leipzig University, Mathematisches Institut, Universität Leipzig, PF 100920, D-04009, Leipzig, Germany
| | - Josep Maria Bofill
- Universitat de Barcelona, Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, and Institut de Química Teòrica i Computacional, Universitat de Barcelona, (IQTCUB), Martí i Franquès, 1, 08028, Barcelona, Spain
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98
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Grimmel SA, Reiher M. The electrostatic potential as a descriptor for the protonation propensity in automated exploration of reaction mechanisms. Faraday Discuss 2020; 220:443-463. [PMID: 31528869 DOI: 10.1039/c9fd00061e] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We discuss the possibility of exploiting local minima of the molecular electrostatic potential for locating protonation sites in molecules in a fully automated manner. We implement and apply this concept to exploring the mechanism of proton reduction catalyzed by a hydrogenase model complex [Orthaber et al., Dalton Trans., 2014, 43, 4537]. A large number of distinct structures arising already in the early stages of the hydrogen evolution mechanism demonstrates the need for reliable, automated algorithms for the thorough analysis of catalytic processes.
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Affiliation(s)
- Stephanie A Grimmel
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.
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99
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Computer-aided molecular and processes design based on quantum chemistry: current status and future prospects. Curr Opin Chem Eng 2020. [DOI: 10.1016/j.coche.2019.11.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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100
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Kurilovich AA, Alexander CT, Pazhetnov EM, Stevenson KJ. Active learning-based framework for optimal reaction mechanism selection from microkinetic modeling: a case study of electrocatalytic oxygen reduction reaction on carbon nanotubes. Phys Chem Chem Phys 2020; 22:4581-4591. [PMID: 32048660 DOI: 10.1039/c9cp06190h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The elucidation of complex electrochemical reaction mechanisms requires advanced models with many intermediate reaction steps, which are governed by a large number of parameters like reaction rate constants and charge transfer coefficients. Overcomplicated models introduce high uncertainty in the choice of the parameters and cannot be used to obtain meaningful insights on the reaction pathway. We describe a new framework of optimal reaction mechanism selection based on the mean-field microkinetic modeling approach (MF-MKM) and adaptive sampling of model parameters. The optimal model is selected to provide both the accurate fitting of experimental data within the experimental error and low uncertainty of model parameters choice. Generally, this approach can be applied for any complex heterogeneous electrochemical reaction. We use the "2e-" electrocatalytic oxygen reduction reaction (ORR) on carbon nanotubes (CNTs) as a representative example of a sufficiently complex reaction. Rotating disk electrode (RDE) experimental data for both ORR in O2-saturated 0.1 M KOH solution and hydrogen peroxide oxidation/reduction reaction (HPRR/HPOR) in Ar-purged 0.1 M KOH solution with different HO2- concentrations were used to show the dependence of the model parameters uniqueness on the completeness of the experimental dataset. It is demonstrated that the optimal reaction mechanism for ORR on CNT and available experimental data consists of O2 adsorption step on the electrode surface and effective step of two-electron reduction to HO2- combined with its desorption from the electrode. The low uncertainty of estimated model parameters is provided only within the 2-step model being applied to the full available experimental dataset. The assessment of elementary step mechanisms on electro-catalytic materials including carbon-based electrodes requires more diverse experimental data and/or higher precision of experimental measurements to facilitate more precise microkinetic modeling of more complex reaction mechanisms.
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Affiliation(s)
- Aleksandr A Kurilovich
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Building 3, Moscow, 143026, Russian Federation.
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