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Csizi KS, Steiner M, Reiher M. Nanoscale chemical reaction exploration with a quantum magnifying glass. Nat Commun 2024; 15:5320. [PMID: 38909029 PMCID: PMC11193806 DOI: 10.1038/s41467-024-49594-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 06/04/2024] [Indexed: 06/24/2024] Open
Abstract
Nanoscopic systems exhibit diverse molecular substructures by which they facilitate specific functions. Theoretical models of them, which aim at describing, understanding, and predicting these capabilities, are difficult to build. Viable quantum-classical hybrid models come with specific challenges regarding atomistic structure construction and quantum region selection. Moreover, if their dynamics are mapped onto a state-to-state mechanism such as a chemical reaction network, its exhaustive exploration will be impossible due to the combinatorial explosion of the reaction space. Here, we introduce a "quantum magnifying glass" that allows one to interactively manipulate nanoscale structures at the quantum level. The quantum magnifying glass seamlessly combines autonomous model parametrization, ultra-fast quantum mechanical calculations, and automated reaction exploration. It represents an approach to investigate complex reaction sequences in a physically consistent manner with unprecedented effortlessness in real time. We demonstrate these features for reactions in bio-macromolecules and metal-organic frameworks, diverse systems that highlight general applicability.
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Affiliation(s)
- Katja-Sophia Csizi
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Miguel Steiner
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- ETH Zurich, NCCR Catalysis, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Markus Reiher
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
- ETH Zurich, NCCR Catalysis, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland.
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2
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Sirianni D, Song X, Wairegi S, Wang EB, Mendoza-Gomez SA, Luxon A, Zimmerley M, Nussdorf A, Filatov M, Hoffmann R, Parish CA. Variations on the Bergman Cyclization Theme: Electrocyclizations of Ionic Penta-, Hepta-, and Octadiynes. J Am Chem Soc 2023; 145:21408-21418. [PMID: 37747784 PMCID: PMC10557144 DOI: 10.1021/jacs.3c06691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Indexed: 09/26/2023]
Abstract
The Bergman cyclization of (Z)-hexa-3-ene-1,5-diyne to form the aromatic diradical p-benzyne has garnered attention as a potential antitumor agent due to its relatively low cyclization barrier and the stability of the resulting diradical. Here, we present a theoretical investigation of several ionic extensions of the fundamental Bergman cyclization: electrocyclizations of the penta-1,4-diyne anion, hepta-1,6-diyne cation, and octa-1,7-diyne dication, leveraging the spin-flip formulation of the equation-of-motion coupled cluster theory with single and double substitutions (EOM-SF-CCSD). Though the penta-1,4-diyne anion exhibits a large cyclization barrier of +66 kcal mol-1, cyclization of both the hepta-1,6-diyne cation and octa-1,7-diyne dication along a previously unreported triplet pathway requires relatively low energy. We also identified the presence of significant aromaticity in the triplet diradical products of these two cationic cyclizations.
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Affiliation(s)
- Dominic
A. Sirianni
- Department
of Natural Sciences, Daemen University, Amherst, New York 14226, United States
- Department
of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | - Xinli Song
- Department
of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | - Salmika Wairegi
- Department
of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | - Evan B. Wang
- Department
of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | | | - Adam Luxon
- Department
of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | - Maxwell Zimmerley
- Department
of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | - Ariana Nussdorf
- Department
of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
| | - Michael Filatov
- Department
of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Roald Hoffmann
- Department
of Chemistry, Cornell University, Ithaca, New York 14853, United States
| | - Carol A. Parish
- Department
of Chemistry, University of Richmond, Richmond, Virginia 23173, United States
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3
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Yanagisawa D, Ishida S, Iwamoto T. Silacyclopropenylsilylene-NHC Complex: Synthesis by (1+2) Retro-cycloaddition, Dynamic Behavior in Solution, and Ring-expansion Reaction. CHEM LETT 2023. [DOI: 10.1246/cl.220528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- Daichi Yanagisawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Shintaro Ishida
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Takeaki Iwamoto
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan
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4
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Roy S, Anoop A. Insights into the Active Catalyst Formation from Dinuclear Palladium Acetate in Pd-Catalyzed Coupling Reactions: A DFT Study. J Phys Chem A 2022; 126:8562-8576. [DOI: 10.1021/acs.jpca.2c03762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Saikat Roy
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Anakuthil Anoop
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
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5
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Mitsuta Y, Asada T, Shigeta Y. Calculation of the permeability coefficients of small molecules through lipid bilayers by free-energy reaction network analysis following the explicit treatment of the internal conformation of the solute. Phys Chem Chem Phys 2022; 24:26070-26082. [PMID: 36268802 DOI: 10.1039/d2cp03678a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Biomembrane permeation represents a major barrier to pharmacokinetics. During preclinical drug discovery, the coefficients of the permeation of molecules through lipid bilayers account for a valuable property of such molecules. Therefore, the control of the permeation of molecules through lipid bilayers is an essential factor in drug design, and the estimation of the permeation phenomena is a crucial study in pharmacy. Thus, there are many published studies on the theoretical estimations of permeation coefficients. Here, we propose a molecular dynamics (MD) simulation method for estimating the permeation of small molecules through lipid bilayers based on the free-energy reaction network (FERN) analysis. In this method, the collective variables (CVs) of the free energy calculations explicitly include the conformational changes in the rotational bonds of the solute molecules. The advantages of the present method over the other method are that it is possible to estimate reaction pathways and their reaction rates, i.e., permeation coefficients or passage times, in multidimensional space spanned by CVs though conventional methods such as the umbrella sampling method and target MDs often dealt with a few degrees of freedom. To demonstrate the efficacy of our method, we calculate the coefficients of the permeation of three small aromatic peptides, namely N-acetylphenylalanineamide (Ac-Phe-NH2 or NAFA), N-acetyltyrosineamide (Ac-Tyr-NH2 or NAYA), and N-acetyltryptophanamide (Ac-Trp-NH2 or NATA), through a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid bilayer. In these cases we adopted one CV for the permeation direction and four CVs for the internal rotational coordinates. The results reveal that the permeation coefficients of NAFA, NAYA, and NATA are 1.7 × 10-2, 0.51 × 10-4, and 5.7 × 10-4 cm s-1, respectively. Compared with the experimental data, our simulation results followed the same trend, i.e., NAFA > NATA > NAYA. By analyzing the structures of metastable points of the solute molecules, our simulation result reveals that the aforementioned trend is caused by the differences in stability among their rotamers. Furthermore, we evaluate the statistical fluctuation of the rotamers, and the time scale of flipping the side chain reveals that the structures rigidify as the ligand moves deeper into the membrane.
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Affiliation(s)
- Yuki Mitsuta
- Department of Chemistry, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan.
- RIMED, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan
| | - Toshio Asada
- Department of Chemistry, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan.
- RIMED, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
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6
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Geiger J, Settels V, Deglmann P, Schäfer A, Bergeler M. Automated input structure generation for single-ended reaction path optimizations. J Comput Chem 2022; 43:1662-1674. [PMID: 35866245 DOI: 10.1002/jcc.26969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/05/2022]
Abstract
The exploration of a reaction network requires highly automated workflows to avoid error-prone and time-consuming manual steps. In this respect, a major bottleneck is the search for transition-state (TS) structures, which frequently fails and, therefore, makes (manual) revision necessary. In this work, we present a technique for obtaining suitable input structures for automated TS searches based on single-ended reaction path optimization algorithms, which makes subsequent TS searches via this method significantly more robust. First, possible input structures are generated based on the spatial alignment of the reactants. The appropriate orientation of reacting groups is achieved via stepwise rotations along selected torsional degrees of freedom. Second, a ranking of the obtained structures is performed according to selected geometric criteria. The main goals are to properly align the reactive atoms, to avoid hindrance within the reaction channel and to resolve steric clashes between the reactants. The developed procedure has been carefully tested on a variety of examples and provides suitable input structures for TS searches within seconds. The method is in daily use in an industrial setting.
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Affiliation(s)
- Julian Geiger
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Tarragona, Spain
| | | | | | | | - Maike Bergeler
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Tarragona, Spain
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7
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Suzuki K, Maeda S. Multistructural microiteration combined with QM/MM-ONIOM electrostatic embedding. Phys Chem Chem Phys 2022; 24:16762-16773. [PMID: 35775395 DOI: 10.1039/d2cp02270b] [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
Multistructural microiteration (MSM) is a method to take account of contributions of multiple surrounding structures in a geometrical optimization or reaction path calculation using the quantum mechanics/molecular mechanics (QM/MM) ONIOM method. In this study, we combined MSM with the electrostatic embedding (EE) scheme of the QM/MM-ONIOM method by extending its original formulation for mechanical embedding (ME). MSM-EE takes account of the polarization in the QM region induced by point charges assigned to atoms in the multiple surrounding structures, where the point charges are scaled by the weight factor of each surrounding structure determined through MSM. The performance of MSM-EE was compared with that of the other methods, i.e., ONIOM-ME, ONIOM-EE, and MSM-ME, by applying them to three chemical processes: (1) chorismate-to-prephenate transformation in aqueous solution, (2) the same transformation as (1) in an enzyme, and (3) hydroxylation in p-hydroxybenzoate hydroxylase. These numerical tests of MSM-EE yielded barriers and reaction energies close to experimental values with computational costs comparable to those of the other three methods.
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Affiliation(s)
- Kimichi Suzuki
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan. .,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Sapporo 060-0810, Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan. .,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Sapporo 060-0810, Japan.,Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS), Tsukuba 305-0044, Japan
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9
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Yu F, Zhou Z, Song J, Zhao Y. DFT and AFIR study on the copper(i)-catalyzed mechanism of 5-enamine-trisubstituted-1,2,3-triazole synthesis via C-N cross-coupling and the origin of ring-opening of 2 H-azirines. RSC Adv 2021; 11:2744-2755. [PMID: 35424213 PMCID: PMC8693862 DOI: 10.1039/d0ra07498e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/03/2020] [Indexed: 12/04/2022] Open
Abstract
Understanding the synthesis mechanism of substituted 1,2,3-triazoles is an important and state-of-the-art research area of contemporary copper(i)-catalyzed terminal alkyne and organic azide click reaction (CuAAC), which has invoked increasing close collaborations between experiment and theory including copper catalyzed interrupted click reaction. In this study, the mechanism of Cu(i)-catalyzed 5-enamine-functionalized fully substituted 1,2,3-triazole synthesis was rationalized via density functional theory (DFT) and multicomponent artificial force-induced reaction (MC-AFIR) methods. The reasonable reaction route consists of (a) di-copper catalyzed ring-opening of 2H-azirines, (b) alkyne hydrogen atom transfer, (c) [3 + 2] ring cycloaddition, and (d) C-N bond formation through reductive elimination. The MC-AFIR method was used for the systematic determination of transition states for the C/N-Cu bond formation, C-N bond coupling and crossing points between singlet and triplet states. Our survey on the prereactant complexes suggested that the dicopper-catalyzed 2H-azirine ring-opening and alkyne hydrogen activation are both thermodynamically feasible via a singlet/triplet crossing point. This explains why Et3N is critical for alkyne hydrogen transfer (HT) before the [3 + 2] cycloaddition reaction, and the C-N cross-coupling product instead of the click product (byproduct). Our DFT results indicate that the transmetalation process is the rate determination step along the triplet state potential energy surface. This study provides important mechanistic insights for the interrupted CuAAC reaction to form 5-enamine-fully-substituted-1,2,3-triazoles. Further insight prediction interprets that solvent and extra strong ligand coordination play a certain role in competitive reactions.
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Affiliation(s)
- Fan Yu
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University Hangzhou 310018 China
| | - Zhaoman Zhou
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University Hangzhou 310018 China
| | - Jiajia Song
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University Hangzhou 310018 China
| | - Yanying Zhao
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University Hangzhou 310018 China
- State Key Laboratory of Advanced Textiles Materials and Manufacture Technology, Ministry of Education, Zhejiang Sci-Tech University Hangzhou 310018 China
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Hirakawa F, Nakagawa H, Honda S, Ishida S, Iwamoto T. Trialkylphosphines Having a Bulky Phosphacyclopentane Backbone: Structural and Redox Properties Depending on the Exocyclic Alkyl Groups and EPR Observation of a Persistent Trialkylphosphine Radical Cation. J Org Chem 2020; 85:14634-14642. [PMID: 32700539 DOI: 10.1021/acs.joc.0c01393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bulky phosphines and their redox properties have received increased attention in the view of useful auxiliary ligands for transition metal catalysts and Lewis-base components of frustrated Lewis pairs for chemical transformations. Herein we report the synthesis, structure, and properties of a series of trialkylphosphines 2R (R = methyl, ethyl, isopropyl, tert-butyl, 1-adamantyl) that possess the bulky 2,2,5,5-tetrakis(trimethylsilyl)-1-phosphacyclopentane as a structural backbone. Among these phosphines, 2Ad, which contains an adamantyl moiety, has a very large buried volume (%Vbur) for a trialkylphosphine (62.0) and shows a quasi-reversible oxidative wave at a lower oxidation potential (-0.12 V in CH2Cl2, vs ferrocene/ferrocenium couple) by cyclic voltammetry. The reaction of 2Ad with AgPF6 afforded a cationic silver aquo complex [Ag(2Ad)(H2O)]+[PF6]-, whereas the reaction with NOSbF6 gave a persistent phosphine radical cation [2Ad]•+. Based on the EPR spectra and DFT studies, the spin and positive charge of [2Ad]•+ are localized on the phosphorus atom.
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Affiliation(s)
- Fumiya Hirakawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Hiroshi Nakagawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Shunya Honda
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Shintaro Ishida
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Takeaki Iwamoto
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
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11
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Otsuka M, Miyaguchi H. Evaluation of the possibility of binary synthesis of VX by theoretical calculation. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137808] [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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12
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Midoro Y, Kodaya Y, Oki T, Mukai A, Yamakado H, Ohno K. Conformation Search of Glycine by Applying the Scaled Hypersphere Search Method to Discrete Atoms in the Molecule. CHEM LETT 2020. [DOI: 10.1246/cl.200239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yuuki Midoro
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Yoshitomo Kodaya
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Takuto Oki
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Akira Mukai
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Hideo Yamakado
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Koichi Ohno
- Institute for Quantum Chemical Exploration, 1-9-36 Konan, Minato-ku, Tokyo 108-0075, Japan
- Graduate School of Science, Tohoku University, 6-3 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
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Mitsuta Y, Shigeta Y. Analytical Method Using a Scaled Hypersphere Search for High-Dimensional Metadynamics Simulations. J Chem Theory Comput 2020; 16:3869-3878. [PMID: 32384233 DOI: 10.1021/acs.jctc.0c00010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Metadynamics (MTD) is one of the most effective methods for calculating the free energy surface and finding rare events. Nevertheless, numerous studies using MTD have been carried out using 3D or lower dimensional collective variables (CVs), as higher dimensional CVs require costly computational resources and the obtained results are too complex to understand the important events. The latter issue can be conveniently solved by utilizing the free energy reaction network (FERN), which is a graph structure consisting of edges of minimum free energy paths (MFEPs), nodes of equation (EQ) points, and transition state (TS) points. In the present article, a new method for exploring FERNs on high-dimensional CVs using MTD and the scaled hypersphere search (SHS) method is described. A test calculation based on the MTD-SHS simulation of met-enkephalin in explicit water with 7 CVs was conducted. As a result, 889 EQ points and 1805 TS points were found. The MTD-SHS approach can find MFEPs exhaustively; therefore, the FERNs can be estimated without any a priori knowledge of the EQ and TS points.
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Affiliation(s)
- Yuki Mitsuta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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Otsuka M, Miyaguchi H, Uchiyama M. Analysis of degradation products of nitrogen mustards via hydrophilic interaction liquid chromatography-tandem mass spectrometry. J Chromatogr A 2019; 1602:199-205. [PMID: 31109745 DOI: 10.1016/j.chroma.2019.05.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 12/22/2022]
Abstract
A hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) method was developed for qualitative and quantitative analysis of ethanolamines (EAs), which are nitrogen mustard degradation products. With this method, the retention times of the highly hydrophilic EAs on the HILIC column were sufficient (retention times: methyl diethanolamine, 12.2 min; ethyl diethanolamine, 11.2 min; and triethanolamine, 9.5 min) and the EAs were analyzed more efficiently than with reported HILIC-MS/MS methods. The detection limits of methyl diethanolamine and ethyl diethanolamine in serum and urine using this approach were 15-20 ng/mL. The suitability of the method for real samples was evaluated via recovery tests involving urine and serum, and the method was validated. The MS/MS fragmentation of EAs was discussed based on density functional theory calculations.
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Affiliation(s)
- Mai Otsuka
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan; Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Hajime Miyaguchi
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan; Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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15
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Ishida S, Takiguchi M, Iwamoto T. Alkoxy(tetraaryl)silicates bearing 9,10-disilatriptycene skeleton. HETEROATOM CHEMISTRY 2018. [DOI: 10.1002/hc.21481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Shintaro Ishida
- Department of Chemistry; Graduate School of Science; Tohoku University; Sendai Japan
| | - Minori Takiguchi
- Department of Chemistry; Graduate School of Science; Tohoku University; Sendai Japan
| | - Takeaki Iwamoto
- Department of Chemistry; Graduate School of Science; Tohoku University; Sendai Japan
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16
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Yang M, Yang L, Wang G, Zhou Y, Xie D, Li S. Combined Molecular Dynamics and Coordinate Driving Method for Automatic Reaction Pathway Search of Reactions in Solution. J Chem Theory Comput 2018; 14:5787-5796. [DOI: 10.1021/acs.jctc.8b00799] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manyi Yang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People’s Republic of China
| | - Guoqiang Wang
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Yanzi Zhou
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Daiqian Xie
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, People’s Republic of China
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17
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Yokouchi Y, Ishida S, Iwamoto T. Facile Skeletal Rearrangement of Polycyclic Disilenes with Bicyclo[1.1.1]pentasilanyl Groups. Chemistry 2018; 24:11393-11401. [DOI: 10.1002/chem.201801517] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/19/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Yuki Yokouchi
- Department of Chemistry, Graduate School of Science; Tohoku University; Aoba-ku Sendai 980-8578 Japan
| | - Shintaro Ishida
- Department of Chemistry, Graduate School of Science; Tohoku University; Aoba-ku Sendai 980-8578 Japan
| | - Takeaki Iwamoto
- Department of Chemistry, Graduate School of Science; Tohoku University; Aoba-ku Sendai 980-8578 Japan
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18
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Ishida S, Tamura T, Iwamoto T. Dearomative cycloadditions of a silylene with pyrazine and quinoxaline. Dalton Trans 2018; 47:11317-11321. [DOI: 10.1039/c8dt02802h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The dearomative cycloaddition of a dialkylsilylene with pyrazine affords an eight-membered heterocyclic compound with a trans-cycloalkene moiety.
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Affiliation(s)
- Shintaro Ishida
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Tomofumi Tamura
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
| | - Takeaki Iwamoto
- Department of Chemistry
- Graduate School of Science
- Tohoku University
- Sendai 980-8578
- Japan
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19
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Maeda S, Harabuchi Y, Takagi M, Saita K, Suzuki K, Ichino T, Sumiya Y, Sugiyama K, Ono Y. Implementation and performance of the artificial force induced reaction method in the GRRM17 program. J Comput Chem 2017; 39:233-251. [PMID: 29135034 PMCID: PMC5765425 DOI: 10.1002/jcc.25106] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 12/20/2022]
Abstract
This article reports implementation and performance of the artificial force induced reaction (AFIR) method in the upcoming 2017 version of GRRM program (GRRM17). The AFIR method, which is one of automated reaction path search methods, induces geometrical deformations in a system by pushing or pulling fragments defined in the system by an artificial force. In GRRM17, three different algorithms, that is, multicomponent algorithm (MC-AFIR), single-component algorithm (SC-AFIR), and double-sphere algorithm (DS-AFIR), are available, where the MC-AFIR was the only algorithm which has been available in the previous 2014 version. The MC-AFIR does automated sampling of reaction pathways between two or more reactant molecules. The SC-AFIR performs automated generation of global or semiglobal reaction path network. The DS-AFIR finds a single path between given two structures. Exploration of minimum energy structures within the hypersurface in which two different electronic states degenerate, and an interface with the quantum mechanics/molecular mechanics method, are also described. A code termed SAFIRE will also be available, as a visualization software for complicated reaction path networks. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yu Harabuchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
| | - Makito Takagi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
| | - Kenichiro Saita
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kimichi Suzuki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, 606-8103, Japan
| | - Tomoya Ichino
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yosuke Sumiya
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
| | - Kanami Sugiyama
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-8628, Japan
| | - Yuriko Ono
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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20
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Bhoorasingh PL, Slakman BL, Seyedzadeh Khanshan F, Cain JY, West RH. Automated Transition State Theory Calculations for High-Throughput Kinetics. J Phys Chem A 2017; 121:6896-6904. [PMID: 28820268 DOI: 10.1021/acs.jpca.7b07361] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A scarcity of known chemical kinetic parameters leads to the use of many reaction rate estimates, which are not always sufficiently accurate, in the construction of detailed kinetic models. To reduce the reliance on these estimates and improve the accuracy of predictive kinetic models, we have developed a high-throughput, fully automated, reaction rate calculation method, AutoTST. The algorithm integrates automated saddle-point geometry search methods and a canonical transition state theory kinetics calculator. The automatically calculated reaction rates compare favorably to existing estimated rates. Comparison against high level theoretical calculations show the new automated method performs better than rate estimates when the estimate is made by a poor analogy. The method will improve by accounting for internal rotor contributions and by improving methods to determine molecular symmetry.
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Affiliation(s)
- Pierre L Bhoorasingh
- Department of Chemical Engineering, Northeastern University , Boston, Massachusetts 02115, United States
| | - Belinda L Slakman
- Department of Chemical Engineering, Northeastern University , Boston, Massachusetts 02115, United States
| | - Fariba Seyedzadeh Khanshan
- Department of Chemical Engineering, Northeastern University , Boston, Massachusetts 02115, United States
| | - Jason Y Cain
- Department of Chemical Engineering, Northeastern University , Boston, Massachusetts 02115, United States
| | - Richard H West
- Department of Chemical Engineering, Northeastern University , Boston, Massachusetts 02115, United States
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21
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Nandi S, McAnanama-Brereton SR, Waller MP, Anoop A. A tabu-search based strategy for modeling molecular aggregates and binary reactions. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.03.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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22
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Suzuki K, Morokuma K, Maeda S. Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems. J Comput Chem 2017. [PMID: 28643353 DOI: 10.1002/jcc.24857] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We propose a multistructural microiteration (MSM) method for geometry optimization and reaction path calculation in large systems. MSM is a simple extension of the geometrical microiteration technique. In conventional microiteration, the structure of the non-reaction-center (surrounding) part is optimized by fixing atoms in the reaction-center part before displacements of the reaction-center atoms. In this method, the surrounding part is described as the weighted sum of multiple surrounding structures that are independently optimized. Then, geometric displacements of the reaction-center atoms are performed in the mean field generated by the weighted sum of the surrounding parts. MSM was combined with the QM/MM-ONIOM method and applied to chemical reactions in aqueous solution or enzyme. In all three cases, MSM gave lower reaction energy profiles than the QM/MM-ONIOM-microiteration method over the entire reaction paths with comparable computational costs. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Kimichi Suzuki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, 606-8103, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, 606-8103, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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23
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Jafari M, Zimmerman PM. Reliable and efficient reaction path and transition state finding for surface reactions with the growing string method. J Comput Chem 2017; 38:645-658. [PMID: 28130776 DOI: 10.1002/jcc.24720] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/20/2016] [Accepted: 12/10/2016] [Indexed: 11/08/2022]
Abstract
The computational challenge of fast and reliable transition state and reaction path optimization requires new methodological strategies to maintain low cost, high accuracy, and systematic searching capabilities. The growing string method using internal coordinates has proven to be highly effective for the study of molecular, gas phase reactions, but difficulties in choosing a suitable coordinate system for periodic systems has prevented its use for surface chemistry. New developments are therefore needed, and presented herein, to handle surface reactions which include atoms with large coordination numbers that cannot be treated using standard internal coordinates. The double-ended and single-ended growing string methods are implemented using a hybrid coordinate system, then benchmarked for a test set of 43 elementary reactions occurring on surfaces. These results show that the growing string method is at least 45% faster than the widely used climbing image-nudged elastic band method, which also fails to converge in several of the test cases. Additionally, the surface growing string method has a unique single-ended search method which can move outward from an initial structure to find the intermediates, transition states, and reaction paths simultaneously. This powerful explorative feature of single ended-growing string method is demonstrated to uncover, for the first time, the mechanism for atomic layer deposition of TiN on Cu(111) surface. This reaction is found to proceed through multiple hydrogen-transfer and ligand-exchange events, while formation of H-bonds stabilizes intermediates of the reaction. Purging gaseous products out of the reaction environment is the driving force for these reactions. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Mina Jafari
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, Michigan, 48109
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, Michigan, 48109
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24
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Ohno K. Study of Potential Energy Surfaces towards Global Reaction Route Mapping. CHEM REC 2016; 16:2198-2218. [PMID: 27059804 DOI: 10.1002/tcr.201500284] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Indexed: 11/11/2022]
Abstract
The potential energy surface (PES) is just a theoretical construct based on the Born-Oppenheimer approximation, but it underlies various phenomena, including molecular vibrations, collisional ionizations, and chemical reactions. This account describes how a new idea for global reaction route mapping (GRRM), which had seemed to be impossible for chemical systems with more than three atoms, was born and has been developed during the course of the study of the PES. GRRM has pioneered new fields of chemistry. Furthermore, techniques for GRRM are still developing, and GRRM is further extending its application to various areas of chemistry and chemical physics.
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Affiliation(s)
- Koichi Ohno
- Institute for Quantum Chemical Exploration, Minato-ku, Tokyo, 108-0022, Japan.
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25
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Zhang Y, Xie P, He X, Han K. High-Efficiency Microiterative Optimization in QM/MM Simulations of Large Flexible Systems. J Chem Theory Comput 2016; 12:4632-43. [DOI: 10.1021/acs.jctc.6b00547] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Yan Zhang
- State Key Laboratory
of Molecular
Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
| | - Peng Xie
- State Key Laboratory
of Molecular
Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
| | - Xiaohu He
- State Key Laboratory
of Molecular
Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
| | - Keli Han
- State Key Laboratory
of Molecular
Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, China
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26
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Kearns FL, Hudson PS, Boresch S, Woodcock HL. Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis. Methods Enzymol 2016; 577:75-104. [PMID: 27498635 DOI: 10.1016/bs.mie.2016.05.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Enzyme activity is inherently linked to free energies of transition states, ligand binding, protonation/deprotonation, etc.; these free energies, and thus enzyme function, can be affected by residue mutations, allosterically induced conformational changes, and much more. Therefore, being able to predict free energies associated with enzymatic processes is critical to understanding and predicting their function. Free energy simulation (FES) has historically been a computational challenge as it requires both the accurate description of inter- and intramolecular interactions and adequate sampling of all relevant conformational degrees of freedom. The hybrid quantum mechanical molecular mechanical (QM/MM) framework is the current tool of choice when accurate computations of macromolecular systems are essential. Unfortunately, robust and efficient approaches that employ the high levels of computational theory needed to accurately describe many reactive processes (ie, ab initio, DFT), while also including explicit solvation effects and accounting for extensive conformational sampling are essentially nonexistent. In this chapter, we will give a brief overview of two recently developed methods that mitigate several major challenges associated with QM/MM FES: the QM non-Boltzmann Bennett's acceptance ratio method and the QM nonequilibrium work method. We will also describe usage of these methods to calculate free energies associated with (1) relative properties and (2) along reaction paths, using simple test cases with relevance to enzymes examples.
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Affiliation(s)
- F L Kearns
- University of South Florida, Tampa, FL, United States
| | - P S Hudson
- University of South Florida, Tampa, FL, United States
| | - S Boresch
- Faculty of Chemistry, University of Vienna, Vienna, Austria.
| | - H L Woodcock
- University of South Florida, Tampa, FL, United States.
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27
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 743] [Impact Index Per Article: 82.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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28
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Zimmerman PM. Single-ended transition state finding with the growing string method. J Comput Chem 2015; 36:601-11. [DOI: 10.1002/jcc.23833] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 12/14/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Paul M. Zimmerman
- Department of Chemistry; University of Michigan; 930 N. University Ave Ann Arbor Michigan 48109
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29
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Maeda S, Taketsugu T, Morokuma K, Ohno K. Anharmonic Downward Distortion Following for Automated Exploration of Quantum Chemical Potential Energy Surfaces. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20140189] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University
| | | | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University
| | - Koichi Ohno
- Graduate School of Science, Tohoku University
- Institute for Quantum Chemical Exploration
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30
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Motomatsu D, Ishida S, Ohno K, Iwamoto T. Isolable 2,3-Disila-1,3-butadiene from a Double Sila-Peterson Reaction. Chemistry 2014; 20:9424-30. [DOI: 10.1002/chem.201402868] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Indexed: 11/06/2022]
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31
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Zhang XJ, Shang C, Liu ZP. Double-Ended Surface Walking Method for Pathway Building and Transition State Location of Complex Reactions. J Chem Theory Comput 2013; 9:5745-53. [DOI: 10.1021/ct4008475] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Xiao-Jie Zhang
- Shanghai Key Laboratory of
Molecular Catalysis and Innovative Materials, Key Laboratory of Computational
Physical Science (Ministry of Education), Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Cheng Shang
- Shanghai Key Laboratory of
Molecular Catalysis and Innovative Materials, Key Laboratory of Computational
Physical Science (Ministry of Education), Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Zhi-Pan Liu
- Shanghai Key Laboratory of
Molecular Catalysis and Innovative Materials, Key Laboratory of Computational
Physical Science (Ministry of Education), Department of Chemistry, Fudan University, Shanghai 200433, China
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32
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Zimmerman P. Reliable Transition State Searches Integrated with the Growing String Method. J Chem Theory Comput 2013; 9:3043-50. [DOI: 10.1021/ct400319w] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paul Zimmerman
- Department of Chemistry, University
of Michigan, Ann
Arbor, Michigan 48109, United States
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33
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Zimmerman PM. Growing string method with interpolation and optimization in internal coordinates: Method and examples. J Chem Phys 2013; 138:184102. [DOI: 10.1063/1.4804162] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Zimmerman PM. Automated discovery of chemically reasonable elementary reaction steps. J Comput Chem 2013; 34:1385-92. [DOI: 10.1002/jcc.23271] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 01/15/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Paul M. Zimmerman
- Department of Chemistry; University of Michigan; Ann Arbor; Michigan; 48109
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35
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Lundberg M, Borowski T. Oxoferryl species in mononuclear non-heme iron enzymes: Biosynthesis, properties and reactivity from a theoretical perspective. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.03.047] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Maeda S, Ohno K, Morokuma K. Systematic exploration of the mechanism of chemical reactions: the global reaction route mapping (GRRM) strategy using the ADDF and AFIR methods. Phys Chem Chem Phys 2013; 15:3683-701. [DOI: 10.1039/c3cp44063j] [Citation(s) in RCA: 358] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Mallikarjun Sharada S, Zimmerman PM, Bell AT, Head-Gordon M. Automated Transition State Searches without Evaluating the Hessian. J Chem Theory Comput 2012; 8:5166-74. [PMID: 26593206 DOI: 10.1021/ct300659d] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate and speedy determination of transition structures (TSs) is essential for computational studies on reaction pathways, particularly when the process involves expensive electronic structure calculations. Many search algorithms require a good initial guess of the TS geometry, as well as a Hessian input that possesses a structure consistent with the desired saddle point. Among the double-ended interpolation methods for generation of the guess for the TS, the freezing string method (FSM) is proven to be far less expensive compared to its predecessor, the growing string method (GSM). In this paper, it is demonstrated that the efficiency of this technique can be improved further by replacing the conjugate gradient optimization step (FSM-CG) with a quasi-Newton line search coupled with a BFGS Hessian update (FSM-BFGS). A second crucial factor that affects the speed with which convergence to the TS is achieved is the quality and cost of the Hessian of the energy for the guessed TS. For electronic structure calculations, the cost of calculating an exact Hessian increases more rapidly with system size than the energy and gradient. Therefore, to sidestep calculation of the exact Hessian, an approximate Hessian is constructed, using the tangent direction and local curvature at the TS guess. It is demonstrated that the partitioned-rational function optimization algorithm for locating TSs with this approximate Hessian input performs at least as well as with an exact Hessian input in most test cases. The two techniques, FSM and approximate Hessian construction, therefore can significantly reduce costs associated with finding TSs.
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Affiliation(s)
- Shaama Mallikarjun Sharada
- Department of Chemical and Biomolecular Engineering and ‡Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - Paul M Zimmerman
- Department of Chemical and Biomolecular Engineering and ‡Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - Alexis T Bell
- Department of Chemical and Biomolecular Engineering and ‡Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Department of Chemical and Biomolecular Engineering and ‡Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
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38
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Exploring Multiple Potential Energy Surfaces: Photochemistry of Small Carbonyl Compounds. ACTA ACUST UNITED AC 2012. [DOI: 10.1155/2012/268124] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In theoretical studies of chemical reactions involving multiple potential energy surfaces (PESs) such as photochemical reactions, seams of intersection among the PESs often complicate the analysis. In this paper, we review our recipe for exploring multiple PESs by using an automated reaction path search method which has previously been applied to single PESs. Although any such methods for single PESs can be employed in the recipe, the global reaction route mapping (GRRM) method was employed in this study. By combining GRRM with the proposed recipe, all critical regions, that is, transition states, conical intersections, intersection seams, and local minima, associated with multiple PESs, can be explored automatically. As illustrative examples, applications to photochemistry of formaldehyde and acetone are described. In these examples as well as in recent applications to other systems, the present approach led to discovery of many unexpected nonadiabatic pathways, by which some complicated experimental data have been explained very clearly.
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39
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Maeda S, Abe E, Hatanaka M, Taketsugu T, Morokuma K. Exploring Potential Energy Surfaces of Large Systems with Artificial Force Induced Reaction Method in Combination with ONIOM and Microiteration. J Chem Theory Comput 2012; 8:5058-63. [DOI: 10.1021/ct300633e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Satoshi Maeda
- Department of Chemistry,
Faculty
of Science, Hokkaido University, Sapporo
060-0810, Japan
| | - Erika Abe
- Fukui Institute
for Fundamental
Chemistry, Kyoto University, Kyoto 606-8103,
Japan
| | - Miho Hatanaka
- Fukui Institute
for Fundamental
Chemistry, Kyoto University, Kyoto 606-8103,
Japan
| | - Tetsuya Taketsugu
- Department of Chemistry,
Faculty
of Science, Hokkaido University, Sapporo
060-0810, Japan
| | - Keiji Morokuma
- Fukui Institute
for Fundamental
Chemistry, Kyoto University, Kyoto 606-8103,
Japan
- Department of Chemistry
and Cherry
L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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40
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Kumar RM, Baskar P, Balamurugan K, Das S, Subramanian V. On the perturbation of the H-bonding interaction in ethylene glycol clusters upon hydration. J Phys Chem A 2012; 116:4239-47. [PMID: 22530594 DOI: 10.1021/jp300693r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ab initio and density functional methods have been employed to study the structure, stability, and spectral properties of various ethylene glycol (EG(m)) and ethylene glycol-water (EG(m)W(n)) (m = 1-3, n = 1-4) clusters. The effective fragment potential (EFP) approach was used to explore various possible EG(m)W(n) clusters. Calculated interaction energies of EG(m)W(n) clusters confirm that the hydrogen-bonding interaction between EG molecules is perturbed by the presence of water molecules and vice versa. Further, energy decomposition analysis shows that both electrostatic and polarization interactions predominantly contribute to the stability of these clusters. It was found from the same analysis that ethylene glycol-water interaction is predominant over the ethylene glycol-ethylene glycol and water-water interactions. Overall, the results clearly illustrate that the presence of water disrupts the ethylene glycol-ethylene glycol hydrogen bonds.
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Affiliation(s)
- R Mahesh Kumar
- Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai 600 020, India
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Behn A, Zimmerman PM, Bell AT, Head-Gordon M. Efficient exploration of reaction paths via a freezing string method. J Chem Phys 2011; 135:224108. [DOI: 10.1063/1.3664901] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Teramae H, Ishimoto T, Nagashima U. Mixing parameters for geometry optimization using the Hamiltonian algorithm. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1010-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Machado-Charry E, Béland LK, Caliste D, Genovese L, Deutsch T, Mousseau N, Pochet P. Optimized energy landscape exploration using the ab initio based activation-relaxation technique. J Chem Phys 2011; 135:034102. [DOI: 10.1063/1.3609924] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Chung LW, Hirao H, Li X, Morokuma K. The ONIOM method: its foundation and applications to metalloenzymes and photobiology. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.85] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Maeda S, Morokuma K. Finding Reaction Pathways of Type A + B → X: Toward Systematic Prediction of Reaction Mechanisms. J Chem Theory Comput 2011; 7:2335-45. [DOI: 10.1021/ct200290m] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Satoshi Maeda
- The Hakubi Center, Kyoto University, Kyoto 606-8302, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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Schlegel HB. Geometry optimization. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.34] [Citation(s) in RCA: 186] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Maeda S, Saito R, Morokuma K. Finding Minimum Structures on the Seam of Crossing in Reactions of Type A + B → X: Exploration of Nonadiabatic Ignition Pathways of Unsaturated Hydrocarbons. J Phys Chem Lett 2011; 2:852-857. [PMID: 26295618 DOI: 10.1021/jz200262m] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A new theoretical approach is proposed for finding automatically minimum structures on the seam of crossing (MSX) in reactions of type A + B → X, where the artificial-force-induced reaction (AFIR) method is combined with the seam model function (SMF) approach. Its application to reactions between triplet dioxygen and unsaturated hydrocarbons provided many MSX structures. In addition to known ignition pathways, we discovered a pathway through a new type of MSX in the reaction of dioxygen with aromatic hydrocarbons; for benzene, this new pathway requires a lower energy than those of three known ignition pathways and is likely to be the most important. This demonstrates that the AFIR-SMF approach has the ability to discover unknown/unexpected MSX structures without prejudice for presumed pathways or mechanisms.
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Affiliation(s)
- Satoshi Maeda
- †The Hakubi Center, Kyoto University, Kyoto 606-8302, Japan
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Ryo Saito
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
- §Faculty of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
- ⊥Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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Iwamoto T, Ohnishi N, Gui Z, Ishida S, Isobe H, Maeda S, Ohno K, Kira M. Synthesis and structure of stable base-free dialkylsilanimines. NEW J CHEM 2010. [DOI: 10.1039/c0nj00121j] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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