1
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Kawagoe Y, Kinugawa Y, Matsumoto K, Ohno M, Kishimoto N, Kawai T, Okabe T. Effects of the chain length of nonaromatic epoxy resins on thermomechanical and optical properties: experiments, and ab initio and molecular dynamics simulations. Phys Chem Chem Phys 2024. [PMID: 39189417 DOI: 10.1039/d4cp02357a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Epoxy resin has been extensively used in the field of advanced electronic materials as an adhesive and encapsulant owing to its excellent material properties. However, recently, there has been a demand for further improvement in heat resistance, high transparency, environmental resistance, and enhanced handling properties for high-brightness light-emitting diodes. Conventional aromatic epoxy resins lack light resistance; therefore, a colorless and transparent epoxy resin without aromatic rings is desirable. In this study, tris(2,3-epoxypropyl) isocyanurate (TEPIC) was used as a nonaromatic epoxy resin, and three types of TEPIC with different side-chain lengths were prepared. The ultraviolet (UV)-visible absorption properties of TEPIC were evaluated using time-dependent density functional theory, and the practicality of the numerical prediction of light resistance was verified. TEPIC yields a UV absorbance spectrum with a lower intensity than those of conventional aromatic epoxy resins, suggesting that TEPIC is expected to have high light resistance. In addition, their thermomechanical properties and the influence of molecular structure were evaluated using both molecular dynamics (MD) simulations and experiments. The MD simulation and experimental results were in good agreement, indicating that the long side chains of TEPIC suppress triaxial deformation-induced failure and improve ductility instead of decreasing strength and stiffness. In addition, the longer side chains form a dense molecular structure with less free volume. These results indicate that numerical approaches can be used to predict various properties of epoxy resins and interpret them from the molecular structure. Accordingly, these approaches can be used to aid the material development process.
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Affiliation(s)
- Yoshiaki Kawagoe
- Department of Aerospace Engineering, Tohoku University, 6-6-01, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
| | - Yuuki Kinugawa
- Department of Aerospace Engineering, Tohoku University, 6-6-01, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
| | - Keigo Matsumoto
- Chemical Research Laboratories, Nissan Chemical Corporation, 10-1, Tsuboi-Nishi 2-chome, Funabashi, Chiba 274-8507, Japan
| | - Masashi Ohno
- Chemical Research Laboratories, Nissan Chemical Corporation, 10-1, Tsuboi-Nishi 2-chome, Funabashi, Chiba 274-8507, Japan
| | - Naoki Kishimoto
- Department of Chemistry, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Takahiko Kawai
- Research Center for Green X-Tech, Tohoku University, 468-1, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Tomonaga Okabe
- Department of Aerospace Engineering, Tohoku University, 6-6-01, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
- Department of Materials Science and Engineering, University of Washington, BOX 352120, Seattle, WA 98195-1750, USA
- Research Center for Structural Materials, Polymer Matrix Hybrid Composite Materials Group, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
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2
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Murakami T, Hayashi D, Kikuma Y, Yamaki K, Takayanagi T. Temperature effects on the branching dynamics in the model ambimodal (6 + 4)/(4 + 2) intramolecular cycloaddition reaction. J Comput Chem 2024. [PMID: 39166899 DOI: 10.1002/jcc.27484] [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: 04/16/2024] [Revised: 07/23/2024] [Accepted: 07/31/2024] [Indexed: 08/23/2024]
Abstract
C14H20 (tetradecapentaene) is a simple model system exhibiting post transition-state behavior, wherein both the (6 + 4) and (4 + 2) cycloaddition products are formed from one ambimocal transition state structure. We studied the bifurcation dynamics starting from the two ambimodal transition state structures, the chair-form and boat-form, using the quasi-classical trajectory, classical molecular dynamics, and ring-polymer molecular dynamics methods on the parameter-optimized semiempirical GFN2-xTB potential energy surface. It was found that the calculated branching fractions differ between the chair-form and boat-form due to the different nature in the IRC pathways. We also investigated the effects of temperature on bifurcation dynamics and found that, at higher temperatures, trajectories stay longer in the intermediate region of the potential energy surface.
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Affiliation(s)
- Tatsuhiro Murakami
- Department of Chemistry, Saitama University, Saitama, Japan
- Department of Materials & Life Sciences, Faculty of Science & Technology, Sophia University, Tokyo, Japan
| | - Daiki Hayashi
- Department of Chemistry, Saitama University, Saitama, Japan
| | - Yuya Kikuma
- Department of Chemistry, Saitama University, Saitama, Japan
| | - Keita Yamaki
- Department of Chemistry, Saitama University, Saitama, Japan
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3
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Ozeki M, Orito M, Ishikawa H. Observation of the Infrared-Induced Structural Change in the Microscopic Hydrogen Bond Network of Phenol-Methanol Cluster Cations in a Cold-Ion Trap. J Phys Chem A 2024; 128:5873-5882. [PMID: 38996183 DOI: 10.1021/acs.jpca.4c01998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
To gain insight into microscopic hydrogen bond networks, we measured ultraviolet photodissociation (UVPD) spectra of the phenol-methanol 1:3 cluster cation, [PhOH(MeOH)3]+ trapped in a variable temperature ion trap. At low temperatures, an isomer with a ring-type hydrogen bond structure dominates, whereas at higher temperatures the chain-type isomers become dominant due to the flexibility of their hydrogen bond structures. We also found a clear temperature dependence of the spectral features, such as band position and width. In addition to the above measurement, we observed the infrared (IR) induced isomerization of [PhOH(MeOH)3]+ to study the dynamical aspects of hydrogen bond networks. We succeeded in observing IR-induced isomerization from the ring to chain forms of [PhOH(MeOH)3]+ at low temperature. The isomerization was clearly identified as a change in the UVPD spectra. The time evolution of the UVPD spectra after IR excitation indicated that the IR-induced isomerization occurs within a nanosecond. The chain-type isomers produced by the IR-induced isomerization are then converted back to the ring-type form by collisions with cold He buffer gas in the trap. This backward isomerization proceeds with a time constant of 100 μs under our experimental conditions. In this study, we evaluated the temperatures of the chain isomers during the backward isomerization on the basis of the spectral features.
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Affiliation(s)
- Masayoshi Ozeki
- Department of Chemistry, School of Science, Kitasato University, Sagamihara 252-0373, Japan
| | - Masataka Orito
- Department of Chemistry, School of Science, Kitasato University, Sagamihara 252-0373, Japan
| | - Haruki Ishikawa
- Department of Chemistry, School of Science, Kitasato University, Sagamihara 252-0373, Japan
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4
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Joung JF, Fong MH, Roh J, Tu Z, Bradshaw J, Coley CW. Reproducing Reaction Mechanisms with Machine-Learning Models Trained on a Large-Scale Mechanistic Dataset. Angew Chem Int Ed Engl 2024:e202411296. [PMID: 38995205 DOI: 10.1002/anie.202411296] [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: 06/15/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/13/2024]
Abstract
Mechanistic understanding of organic reactions can facilitate reaction development, impurity prediction, and in principle, reaction discovery. While several machine learning models have sought to address the task of predicting reaction products, their extension to predicting reaction mechanisms has been impeded by the lack of a corresponding mechanistic dataset. In this study, we construct such a dataset by imputing intermediates between experimentally reported reactants and products using expert reaction templates and train several machine learning models on the resulting dataset of 5,184,184 elementary steps. We explore the performance and capabilities of these models, focusing on their ability to predict reaction pathways and recapitulate the roles of catalysts and reagents. Additionally, we demonstrate the potential of mechanistic models in predicting impurities, often overlooked by conventional models. We conclude by evaluating the generalizability of mechanistic models to new reaction types, revealing challenges related to dataset diversity, consecutive predictions, and violations of atom conservation.
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Affiliation(s)
- Joonyoung F Joung
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Mun Hong Fong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Jihye Roh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Zhengkai Tu
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - John Bradshaw
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Connor W Coley
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
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5
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Zhang D, Kishimoto N. Theoretical Analysis of Coordination Geometries in Transition Metal-Histidine Complexes Using Quantum Chemical Calculations. Molecules 2024; 29:3003. [PMID: 38998956 PMCID: PMC11243457 DOI: 10.3390/molecules29133003] [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: 05/14/2024] [Revised: 06/13/2024] [Accepted: 06/22/2024] [Indexed: 07/14/2024] Open
Abstract
A theoretical investigation utilizing density functional theory (DFT) calculations was conducted to explore the coordination complexes formed between histidine (His) ligands and various divalent transition metal ions (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, and Zn2+). Conformational exploration of the His ligand was initially performed to assess its stability upon coordination. Both 1:1 and 1:2 of metal-to-ligand complexes were scrutinized to elucidate their structural features and the relative stability of the complexes. This study examined the ability of His to act as a bidentate or tridentate coordinating ligand, along with the differences in coordination geometry when solvent effects were incorporated. The reduced density gradient (RDG) analysis and local electron attachment energy (LEAE) analysis were employed to elucidate the interaction planes and the nucleophilic and electrophilic properties. The electronic properties were analyzed through electrostatic potential (ESP) maps and natural population analysis (NPA) of atomic charge distributions. This computational study provides valuable insights into the diverse coordination modes of His and its interactions with divalent transition metal ions, contributing to a better understanding of the role of this amino acid ligand in the formation of transition metal complexes. The findings can aid in the design and construction of self-assembled structures involving His-metal coordination.
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Affiliation(s)
- Dapeng Zhang
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Naoki Kishimoto
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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6
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Zhang D, Kishimoto N. Quantum Chemical Investigation into the Structural Analysis and Calculated Raman Spectra of Amylose Modeled with Linked Glucose Molecules. Molecules 2024; 29:2842. [PMID: 38930907 PMCID: PMC11206574 DOI: 10.3390/molecules29122842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
This study presents a quantum chemical investigation into the structural analysis and calculated Raman spectra of modeled amylose with varying units of linked glucose molecules. We systematically examined the rotation of hydroxymethyl groups and intramolecular hydrogen bonds within these amylose models. Our study found that as the number of linked glucose units increases, the linear structure becomes more complex, resulting in curled, cyclic, or helical structures facilitated by establishing various intramolecular interactions. The hydroxymethyl groups were confirmed to form interactions with oxygen atoms and with hydroxymethyl and hydroxyl groups from adjacent rings in the molecular structures. We identified distinct peaks and selected specific bands applicable in various analytical contexts by comparing their calculated Raman spectra. Representative vibrational modes within selected regions were identified across the different lengths of amylose models, serving as characteristic signatures for linear and more coiled structural conformations. Our findings contribute to a deeper understanding of amylose structures and spectroscopic signatures, with implications for theoretical studies and potential applications. This work provides valuable reference points for the detailed assignment of Raman peaks of amylose structure, facilitating their application in broader research on carbohydrate structures and their associated spectroscopic properties.
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Affiliation(s)
| | - Naoki Kishimoto
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan;
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7
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Li J, Li Y, Wu B, Xie M, Hu Y. Proton Transfer Processes in 2-Butenenitrile Dimer Cation Studied by Mass-Selective Infrared Spectroscopy. J Phys Chem A 2024; 128:4694-4700. [PMID: 38833155 DOI: 10.1021/acs.jpca.4c01989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
2-Butenenitrile (2-Bu) is a recently discovered crucial interstellar molecule. Herein, an abnormal NH band was observed in the infrared spectrum of the 2-Bu dimer cation, suggestive of a proton transfer reaction within the cluster. Through a comprehensive theoretical analysis of the IR spectrum of (2-Bu)2+, we discovered not only the formation of a new C-N bond through the attachment of one 2-Bu to another but also the occurrence of a proton transfer reaction in the cluster. This proton was identified as originating from the methyl group of the attaching 2-Bu in the cluster based on the analysis of IR spectra of (2-Bu)+ and [2-Bu-acrylonitrile (AN)]+. Furthermore, the detailed reaction process of this ion-molecule reaction is examined with theoretical calculation. This finding contributes significantly to our deeper understanding of ion-molecule reactions in the gas phase and the formation of nitrogen-containing prebiotic molecules in the interstellar medium.
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Affiliation(s)
- Jingyu Li
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yujian Li
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Bingbing Wu
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Min Xie
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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8
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Murakami T, Takahashi S, Kikuma Y, Takayanagi T. Theoretical Study of the Thermal Rate Coefficients of the H 3+ + C 2H 4 Reaction: Dynamics Study on a Full-Dimensional Potential Energy Surface. Molecules 2024; 29:2789. [PMID: 38930853 PMCID: PMC11206701 DOI: 10.3390/molecules29122789] [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: 04/27/2024] [Revised: 06/08/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024] Open
Abstract
Ion-molecular reactions play a significant role in molecular evolution within the interstellar medium. In this study, the entrance channel reaction, H3+ + C2H4 → H2 + C2H5+, was investigated using classical molecular dynamic (classical MD) and ring polymer molecular dynamic (RPMD) simulation techniques. We developed an analytical potential energy surface function with a permutationally invariant polynomial basis, specifically employing the monomial symmetrized approach. Our dynamic simulations reproduced the rate coefficient of 300 K for H3+ + C2H4 → H2 + C2H5+, aligning reasonably well with the values in the kinetic database commonly utilized in astrochemistry. The thermal rate coefficients obtained using both the classical MD and RPMD techniques exhibited an increase from 100 K to 300 K as the temperature rose. Additionally, we analyzed the excess energy distribution of the C2H5+ fragment with respect to temperature to investigate the indirect reaction pathway of C2H5+ → H2 + C2H3+. This result suggests that the indirect reaction pathway of C2H5+ → H2 + C2H3+ holds minor significance, although the distribution highly depends on the collisional temperature.
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Affiliation(s)
- Tatsuhiro Murakami
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City 338-8570, Japan; (S.T.); (Y.K.)
- Department of Materials & Life Sciences, Faculty of Science & Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - Soma Takahashi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City 338-8570, Japan; (S.T.); (Y.K.)
| | - Yuya Kikuma
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City 338-8570, Japan; (S.T.); (Y.K.)
| | - Toshiyuki Takayanagi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City 338-8570, Japan; (S.T.); (Y.K.)
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9
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Xiong X, Hu Y. Infrared Spectroscopy of Neutral and Cationic Benzonitrile-Methanol Binary Clusters in Supersonic Jets. Molecules 2024; 29:2744. [PMID: 38930810 PMCID: PMC11206090 DOI: 10.3390/molecules29122744] [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: 05/10/2024] [Revised: 06/01/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
The formation of nitrogen-containing organic interstellar molecules is of great importance to reveal chemical processes and the origin of life on Earth. Benzonitrile (BN) is one of the simplest nitrogen-containing aromatic molecules in the interstellar medium (ISM) that has been detected in recent years. Methanol (CH3OH) exists widely in interstellar space with high reactivity. Herein, we measured the infrared (IR) spectra of neutral and cationic BN-CH3OH clusters by vacuum ultraviolet (VUV) photoionization combined with time-of-flight mass spectrometry. Combining IR spectra with the density functional theory calculations, we reveal that the BN-CH3OH intends to form a cyclic H-bonded structure in neutral clusters. However, after the ionization of BN-CH3OH clusters, proton-shared N···H···O and N···H···C structures are confirmed to form between BN and CH3OH, with the minor coexistence of H-bond and O-π structures. The formation of the proton-shared structure expands our knowledge of the evolution of the life-related nitrogen-containing molecules in the universe and provides a possible pathway to the further study of biorelevant aromatic organic macromolecules.
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Affiliation(s)
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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10
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Miyata T, Sato YK, Kawagoe Y, Shirasu K, Wang HF, Kumagai A, Kinoshita S, Mizukami M, Yoshida K, Huang HH, Okabe T, Hagita K, Mizoguchi T, Jinnai H. Effect of inorganic material surface chemistry on structures and fracture behaviours of epoxy resin. Nat Commun 2024; 15:1898. [PMID: 38459006 PMCID: PMC10923874 DOI: 10.1038/s41467-024-46138-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 02/15/2024] [Indexed: 03/10/2024] Open
Abstract
The mechanisms underlying the influence of the surface chemistry of inorganic materials on polymer structures and fracture behaviours near adhesive interfaces are not fully understood. This study demonstrates the first clear and direct evidence that molecular surface segregation and cross-linking of epoxy resin are driven by intermolecular forces at the inorganic surfaces alone, which can be linked directly to adhesive failure mechanisms. We prepare adhesive interfaces between epoxy resin and silicon substrates with varying surface chemistries (OH and H terminations) with a smoothness below 1 nm, which have different adhesive strengths by ~13 %. The epoxy resins within sub-nanometre distance from the surfaces with different chemistries exhibit distinct amine-to-epoxy ratios, cross-linked network structures, and adhesion energies. The OH- and H-terminated interfaces exhibit cohesive failure and interfacial delamination, respectively. The substrate surface chemistry impacts the cross-linked structures of the epoxy resins within several nanometres of the interfaces and the adsorption structures of molecules at the interfaces, which result in different fracture behaviours and adhesive strengths.
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Affiliation(s)
- Tomohiro Miyata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Yohei K Sato
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Yoshiaki Kawagoe
- Department of Aerospace Engineering, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan.
| | - Keiichi Shirasu
- Department of Finemechanics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan.
| | - Hsiao-Fang Wang
- Department of Chemical and Materials Engineering, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 320317, Taiwan
| | - Akemi Kumagai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Sora Kinoshita
- Department of Applied Chemistry, Graduate School of Engineering, Tohoku University, 6-6-07 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Masashi Mizukami
- New Industry Creation Hatchery Center, Tohoku University, Sendai, Miyagi, 980-0845, Japan
| | - Kaname Yoshida
- Nanostructures Research Laboratory, Japan Fine Ceramics Center, Nagoya, Aichi, 456-8587, Japan
| | - Hsin-Hui Huang
- Nanostructures Research Laboratory, Japan Fine Ceramics Center, Nagoya, Aichi, 456-8587, Japan
| | - Tomonaga Okabe
- Department of Aerospace Engineering, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
- Research Center for Structural Materials, Polymer Matrix Hybrid Composite Materials Group, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki, 305-0047, Japan
- Department of Materials Science and Engineering, University of Washington, BOX 352120, Seattle, WA, 98195, USA
| | - Katsumi Hagita
- Department of Applied Physics, National Defense Academy, Yokosuka, Kanagawa, 239-0811, Japan
| | - Teruyasu Mizoguchi
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
| | - Hiroshi Jinnai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
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11
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Kawagoe Y, Kikugawa G, Shirasu K, Kinugawa Y, Okabe T. Dissipative Particle Dynamics Simulation for Reaction-Induced Phase Separation of Thermoset/Thermoplastic Blends. J Phys Chem B 2024; 128:2018-2027. [PMID: 38373192 PMCID: PMC10911110 DOI: 10.1021/acs.jpcb.3c07756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 02/21/2024]
Abstract
Reaction-induced phase separation occurs during the curing reaction when a thermoplastic resin is dissolved in a thermoset resin, which enables toughening of the thermoset resin. As resin properties vary significantly depending on the morphology of the phase-separated structure, controlling the morphology formation is of critical importance. Reaction-induced phase separation is a phenomenon that ranges from the chemical reaction scale to the mesoscale dynamics of polymer molecules. In this study, we performed curing simulations using dissipative particle dynamics (DPD) coupled with a reaction model to reproduce reaction-induced phase separation. The curing reaction properties of the thermoset resin were determined by ab initio quantum chemical calculations, and the DPD parameters were determined by all-atom molecular dynamics simulations. This enabled mesoscopic simulations, including reactions that reflect the intrinsic material properties. The effects of the thermoplastic resin concentration, molecular weight, and curing conditions on the phase-separation morphology were evaluated, and the cure shrinkage and stiffness of each cured resin were confirmed to be consistent with the experimental trends. Furthermore, the local strain field under tensile deformation was visualized, and the inhomogeneous strain field caused by the phase-separated structures of two resins with different stiffnesses was revealed. These results can aid in understanding the toughening properties of thermoplastic additives at the molecular level.
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Affiliation(s)
- Yoshiaki Kawagoe
- Department
of Aerospace Engineering, Tohoku University, 6-6-01, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Gota Kikugawa
- Institute
of Fluid Science, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Keiichi Shirasu
- Department
of Finemechanics, Tohoku University, 6-6-01, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yuuki Kinugawa
- Department
of Aerospace Engineering, Tohoku University, 6-6-01, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Tomonaga Okabe
- Department
of Aerospace Engineering, Tohoku University, 6-6-01, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
- Department
of Materials Science and Engineering, University
of Washington, P.O. Box 352120, Seattle, Washington 98195-1750, United States
- Research
Center for Structural Materials, Polymer Matrix Hybrid Composite Materials
Group, National Institute for Materials
Science, 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
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12
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Zhang Y, Xu C, Lan Z. Automated Exploration of Reaction Networks and Mechanisms Based on Metadynamics Nanoreactor Simulations. J Chem Theory Comput 2023. [PMID: 38031422 DOI: 10.1021/acs.jctc.3c00752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
We developed an automated approach to construct a complex reaction network and explore the reaction mechanisms for numerous reactant molecules by integrating several theoretical approaches. Nanoreactor-type molecular dynamics was used to generate possible chemical reactions, in which the metadynamics was used to overcome the reaction barriers, and the semiempirical GFN2-xTB method was used to reduce the computational cost. Reaction events were identified from trajectories using the hidden Markov model based on the evolution of the molecular connectivity. This provided the starting points for further transition-state searches at the electronic structure levels of density functional theory to obtain the reaction mechanism. Finally, the entire reaction network containing multiple pathways was built. The feasibility and efficiency of the automated construction of the reaction network were investigated using the HCHO and NH3 biomolecular reaction and the reaction network for a multispecies system comprising dozens of HCN and H2O molecules. The results indicated that the proposed approach provides a valuable and effective tool for the automated exploration of the reaction networks.
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Affiliation(s)
- Yutai Zhang
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Chao Xu
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Zhenggang Lan
- Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety and MOE Key Laboratory of Environmental Theoretical Chemistry, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
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13
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Zhang D, Kishimoto N, Miyake R. Quantum Chemical Calculations of Flexible Tripeptide-Ni(II) Ion-Mediated Supramolecular Fragments and Comparative Analysis of Tripeptide Complexes with Various Metal(II) Ions. J Phys Chem A 2023; 127:9733-9742. [PMID: 37947796 DOI: 10.1021/acs.jpca.3c05277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
An automated conformational search method was employed to efficiently determine the stable conformers and weak hydrogen bonds of a flexible tripeptide coordinated with a solitary metal(II) ion in an aqueous environment. Quantum chemical calculations were performed to investigate the tendency of octahedral coordination formation between different metal(II) ions and various coordination models (ammonia molecule, chelate molecule, and flexible tripeptide). The octahedral coordination was analyzed by decomposing it into tridentate, bidentate, and monodentate coordination model complexes to assess their formation propensities and conformational properties. Additionally, population analysis, including electrostatic potential mapping and natural population analysis, was performed to identify the unique properties of the Ni(II) ion in forming octahedral coordination in crystals and to explore the potential of other metal(II) ions for self-assembling novel coordination configurations in peptide-metal compounds. Two common hydrogen bonding interactions were examined by using artificial forces to facilitate dissociation or reinforcement.
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Affiliation(s)
- Dapeng Zhang
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Naoki Kishimoto
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Ryosuke Miyake
- Department of Chemistry and Biochemistry, Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
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14
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Murakami T, Matsumoto N, Fujihara T, Takayanagi T. Possible Roles of Transition Metal Cations in the Formation of Interstellar Benzene via Catalytic Acetylene Cyclotrimerization. Molecules 2023; 28:7454. [PMID: 37959873 PMCID: PMC10649463 DOI: 10.3390/molecules28217454] [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: 10/12/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous interstellar molecules. However, the formation mechanisms of PAHs and even the simplest cyclic aromatic hydrocarbon, benzene, are not yet fully understood. Recently, we reported the statistical and dynamical properties in the reaction mechanism of Fe+-catalyzed acetylene cyclotrimerization, whereby three acetylene molecules are directly converted to benzene. In this study, we extended our previous work and explored the possible role of the complex of other 3d transition metal cations, TM+ (TM = Sc, Ti, Mn, Co, and Ni), as a catalyst in acetylene cyclotrimerization. Potential energy profiles for bare TM+-catalyst (TM = Sc and Ti), for TM+NC--catalyst (TM = Sc, Ti, Mn, Co, and Ni), and for TM+-(H2O)8-catalyst (TM = Sc and Ti) systems were obtained using quantum chemistry calculations, including the density functional theory levels. The calculation results show that the scandium and titanium cations act as efficient catalysts in acetylene cyclotrimerization and that reactants, which contain an isolated acetylene and (C2H2)2 bound to a bare (ligated) TM cation (TM = Sc and Ti), can be converted into a benzene-metal-cation product complex without an entrance barrier. We found that the number of electrons in the 3d orbitals of the transition metal cation significantly contributes to the catalytic efficiency in the acetylene cyclotrimerization process. On-the-fly Born-Oppenheimer molecular dynamics (BOMD) simulations of the Ti+-NC- and Ti+-(H2O)8 complexes were also performed to comprehensively understand the nuclear dynamics of the reactions. The computational results suggest that interstellar benzene can be produced via acetylene cyclotrimerization reactions catalyzed by transition metal cation complexes.
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Affiliation(s)
- Tatsuhiro Murakami
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City 338-8570, Japan; (N.M.); (T.F.)
- Department of Materials & Life Sciences, Faculty of Science & Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - Naoki Matsumoto
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City 338-8570, Japan; (N.M.); (T.F.)
| | - Takashi Fujihara
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City 338-8570, Japan; (N.M.); (T.F.)
- Comprehensive Analysis Center for Science, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City 338-8570, Japan
| | - Toshiyuki Takayanagi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City 338-8570, Japan; (N.M.); (T.F.)
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15
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Chen X, Wei C, Xie M, Hu Y. Single-Photon Ionization Induced New Covalent Bond Formation in Acrylonitrile(AN)-Pyrrole(Py) Clusters. J Phys Chem A 2023; 127:8272-8279. [PMID: 37769120 DOI: 10.1021/acs.jpca.3c02481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
The formation of nitrogen-containing organic compounds is crucial for understanding chemical evolution and the origin of life in the interstellar medium (ISM). In this study, we explore whether acrylonitrile (AN) and pyrrole (Py) can form new nitrogen-containing compounds after single-photon ionization in their gaseous clusters by vacuum ultraviolet (VUV)-infrared (IR) spectroscopy and theoretical calculations. The results show that a strong linear H-bond is formed in neutral AN-Py, while cyclic or bicyclic H-bonded networks are formed in the neutral AN-Py2 cluster. It is found that the structure containing a new C-C covalent bond between two moieties in (AN-Py)+ is formed besides the formation of H-bonded structures after AN-Py is ionized by VUV light. In (AN-Py2)+ cluster cations, new C-C or C-N covalent bonds tend to be formed between two Py, with (Py)2+ as the core in the cluster. The results reveal that new covalent bonds are more likely to be formed between two Py species when AN and Py are present in the cationic clusters. These results provide spectroscopic evidence of the formation of new nitrogen-containing organic compounds from AN and Py induced by VUV, which are helpful for our understanding of the formation of diverse prebiotic molecules in interstellar space.
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Affiliation(s)
- Xujian Chen
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Chengcheng Wei
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Min Xie
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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16
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Li G, Li Z, Gao L, Chen S, Wang G, Li S. Combined molecular dynamics and coordinate driving method for automatically searching complicated reaction pathways. Phys Chem Chem Phys 2023; 25:23696-23707. [PMID: 37610711 DOI: 10.1039/d3cp02443a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The combined molecular dynamics and coordinate driving (MD/CD) method is updated and generalized in this work to broaden its applications in automatically searching reaction pathways for complicated reactions. In this updated version, MD simulations are performed with the GFN's family of methods to systematically sample conformers for almost any systems with atomic numbers Z ≤ 86. The improved CD procedure is greatly accelerated by applying a pre-screening stage at the semiempirical GFN2-xTB level. An automatic module based on the Marcus theory and its improved version (the Wolynes theory) is designed to include single electron transfer (SET) processes into reaction pathways. The capabilities of this method are demonstrated by exploring the most possible reaction pathways of three experimentally reported reactions: the organophosphine-catalyzed trans phosphinoboration, the Fe(II) complex-mediated C(sp2)-H borylation reaction, and the SET-triggered deaminative radical cross-coupling reaction. Comprehensive reaction networks are obtained for all three reactions with reasonable computational costs. Detailed mechanisms for these reactions can account for the reported experimental facts.
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Affiliation(s)
- Guoao Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| | - Zhenxing Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| | - Liuzhou Gao
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| | - Shengda Chen
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| | - Guoqiang Wang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
| | - Shuhua Li
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, New Cornerstone Science Laboratory, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.
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17
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Sato H, Nakano M. Concertedness and Activation Energy Control by Distal Methyl Group during Ring Contraction/Expansion in Scalarane-Type Sesterterpenoid Biosynthesis. Chemistry 2023; 29:e202203076. [PMID: 36411271 DOI: 10.1002/chem.202203076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022]
Abstract
Salmahyritisol A, similan A, and hippospongide A, which are scalarane-type sesterterpenoids, feature 6/6/5/7/5 pentacyclic skeletons. Although their biosyntheses have been previously proposed to involve a unique skeletal rearrangement reaction, the detailed reaction mechanism remains unclear as none of the corresponding biosynthetic enzymes for this reaction have been reported. Herein, this skeletal rearrangement reaction was investigated using computational techniques, which revealed the following four key features: (i) the distal 24-Me substituent controls both the concertedness and activation energy of this transformation, (ii) enzymes are not responsible for the observed regioselectivity of C12-C20 bond formation, (iii) stereoselectivity is enzyme-regulated, and (iv) protonation is a key step in this skeletal rearrangement process. These new findings provide insight into the C-ring-contraction and D-ring-expansion mechanisms in scalarane-type sesterterpenoid biosyntheses.
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Affiliation(s)
- Hajime Sato
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Moe Nakano
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
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18
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Murakami T, Matsumoto N, Takayanagi T, Fujihara T. The importance of nuclear dynamics in reaction mechanisms of acetylene cyclotrimerization catalyzed by Fe+-compounds. J Organomet Chem 2023. [DOI: 10.1016/j.jorganchem.2023.122643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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19
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Nakao A, Harabuchi Y, Maeda S, Tsuda K. Exploring the Quantum Chemical Energy Landscape with GNN-Guided Artificial Force. J Chem Theory Comput 2023; 19:713-717. [PMID: 36689311 PMCID: PMC9933424 DOI: 10.1021/acs.jctc.2c01061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Artificial force has been proven useful to get over energy barriers and quickly search a large portion of the energy landscape. This work proposes a method based on graph neural networks to optimize the choice of transformation patterns to examine and accelerate energy landscape exploration. In open search from glutathione, the search efficiency was largely improved in comparison to random selection. We also applied transfer learning from glutathione to tuftsin, resulting in further efficiency gains.
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Affiliation(s)
- Atsuyuki Nakao
- Graduate
School of Frontier Sciences, The University
of Tokyo, Kashiwa277-8561, Japan
| | - Yu Harabuchi
- Institute
for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo001-0021, Japan,JST
ERATO Maeda Artificial Intelligence for Chemical Reaction Design and
Discovery Project, Sapporo060-0810, Japan,Department
of Chemistry, Faculty of Science, Hokkaido
University, Sapporo060-0810, Japan
| | - Satoshi Maeda
- Institute
for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo001-0021, Japan,JST
ERATO Maeda Artificial Intelligence for Chemical Reaction Design and
Discovery Project, Sapporo060-0810, Japan,Department
of Chemistry, Faculty of Science, Hokkaido
University, Sapporo060-0810, Japan
| | - Koji Tsuda
- Graduate
School of Frontier Sciences, The University
of Tokyo, Kashiwa277-8561, Japan,RIKEN
Center for Advanced Intelligence Project, Tokyo103-0027, Japan,Research
and Services Division of Materials Data and Integrated System, National Institute for Materials Science, Tsukuba305-0047, Japan,
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20
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Mita T, Takano H, Hayashi H, Kanna W, Harabuchi Y, Houk KN, Maeda S. Prediction of High-Yielding Single-Step or Cascade Pericyclic Reactions for the Synthesis of Complex Synthetic Targets. J Am Chem Soc 2022; 144:22985-23000. [PMID: 36451276 DOI: 10.1021/jacs.2c09830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Pericyclic reactions, which involve cyclic concerted transition states without ionic or radical intermediates, have been extensively studied since their definition in the 1960s, and the famous Woodward-Hoffmann rules predict their stereoselectivity and chemoselectivity. Here, we describe the application of a fully automated reaction-path search method, that is, the artificial force induced reaction (AFIR), to trace an input compound back to reasonable starting materials through thermally allowed pericyclic reactions via product-based quantum-chemistry-aided retrosynthetic analysis (QCaRA) without using any a priori experimental knowledge. All categories of pericyclic reactions, including cycloadditions, ene reactions, group-transfer, cheletropic, electrocyclic, and sigmatropic reactions, were successfully traced back via concerted reaction pathways, and starting materials were computationally obtained with the correct stereochemistry. Furthermore, AFIR was used to predict whether the identified reaction pathway can be expected to occur in good yield relative to other possible reactions of the identified starting material. In order to showcase its practical utility, this state-of-the-art technology was also applied to the retrosynthetic analysis of a natural product with a relatively high number of atoms (52 atoms: endiandric acid C methyl ester), which was first synthesized by Nicolaou in 1982 and provided the corresponding starting polyenes with the correct stereospecificity via three pericyclic reaction cascades (one Diels-Alder reaction as well as 6π and 8π electrocyclic reactions). Moreover, not only systems that obey the Woodward-Hoffmann rules but also systems that violate these rules, such as those recently calculated by Houk, can be retrosynthesized accurately.
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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 in Chemical Reaction Design and Discovery Project, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Hideaki Takano
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan.,JST, ERATO Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Hiroki Hayashi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan.,JST, ERATO Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Wataru Kanna
- Department of Chemistry, Faculty of Science, Hokkaido University, 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 in Chemical Reaction Design and Discovery Project, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.,Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - K N Houk
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan.,JST, ERATO Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.,Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.,Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS), Tsukuba, Ibaraki 305-0044, Japan
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21
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Murakami T, Iida R, Hashimoto Y, Takahashi Y, Takahashi S, Takayanagi T. Ring-Polymer Molecular Dynamics and Kinetics for the H – + C 2H 2 → H 2 + C 2H – Reaction Using the Full-Dimensional Potential Energy Surface. J Phys Chem A 2022; 126:9244-9258. [DOI: 10.1021/acs.jpca.2c05851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tatsuhiro Murakami
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama338-8570, Japan
- Department of Materials & Life Sciences, Faculty of Science & Technology, Sophia University, 7-1 Kioicho, Chiyoda-ku, Tokyo102-8554, Japan
| | - Ryusei Iida
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama338-8570, Japan
| | - Yu Hashimoto
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama338-8570, Japan
| | - Yukinobu Takahashi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama338-8570, Japan
| | - Soma Takahashi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama338-8570, Japan
| | - Toshiyuki Takayanagi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama338-8570, Japan
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22
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Ismail I, Chantreau Majerus R, Habershon S. Graph-Driven Reaction Discovery: Progress, Challenges, and Future Opportunities. J Phys Chem A 2022; 126:7051-7069. [PMID: 36190262 PMCID: PMC9574932 DOI: 10.1021/acs.jpca.2c06408] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/22/2022] [Indexed: 11/29/2022]
Abstract
Graph-based descriptors, such as bond-order matrices and adjacency matrices, offer a simple and compact way of categorizing molecular structures; furthermore, such descriptors can be readily used to catalog chemical reactions (i.e., bond-making and -breaking). As such, a number of graph-based methodologies have been developed with the goal of automating the process of generating chemical reaction network models describing the possible mechanistic chemistry in a given set of reactant species. Here, we outline the evolution of these graph-based reaction discovery schemes, with particular emphasis on more recent methods incorporating graph-based methods with semiempirical and ab initio electronic structure calculations, minimum-energy path refinements, and transition state searches. Using representative examples from homogeneous catalysis and interstellar chemistry, we highlight how these schemes increasingly act as "virtual reaction vessels" for interrogating mechanistic questions. Finally, we highlight where challenges remain, including issues of chemical accuracy and calculation speeds, as well as the inherent challenge of dealing with the vast size of accessible chemical reaction space.
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Affiliation(s)
- Idil Ismail
- Department of Chemistry, University
of Warwick, CoventryCV4 7AL, United Kingdom
| | | | - Scott Habershon
- Department of Chemistry, University
of Warwick, CoventryCV4 7AL, United Kingdom
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23
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Ebisawa S, Tsutsumi T, Taketsugu T. Extension of Natural Reaction Orbital Approach to Multiconfigurational Wavefunctions. J Chem Phys 2022; 157:084118. [DOI: 10.1063/5.0098230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Recently, we proposed a new orbital analysis method, natural reaction orbital (NRO), which automatically extracts orbital pairs that characterize electron transfer in reaction processes by singular value decomposition (SVD) of the first-order orbital response matrix to the nuclear coordinate displacements (S. Ebisawa, M. Hasebe, T. Tsutsumi, T. Tsuneda, and T. Taketsugu, Phys. Chem. Chem. Phys. 24, 3532 (2022)). NRO analysis along the intrinsic reaction coordinate (IRC) for several typical chemical reactions demonstrated that electron transfer occurs mainly in the vicinity of transition states and in regions where the energy profile along the IRC shows shoulder features, allowing the reaction mechanism to be explained in terms of electron motion. However, its application has been limited to single configuration theories such as Hartree-Fock theory and density functional theory (DFT). In this work, the concept of NRO is extended to multiconfigurational wavefunctions and formulated as the multiconfiguration NRO (MC-NRO). The MC-NRO method is applicable to various types of electronic structure theories, including multiconfigurational theory and linear response theory, and is expected to be a practical tool for extracting the qualitative essence of a broad range of chemical reactions, including covalent bond dissociation and chemical reactions in electronically excited states. In this paper, we calculate the IRC for five basic chemical reaction processes at the level of the complete active space self-consistent field (CASSCF) theory and discuss the electron transfer by performing MC-NRO analysis along each IRC. Finally, issues and future prospects of the MC-NRO method are discussed.
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24
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Borysenko IO, Okovytyy SI, Leszczynski J. Probability of reaction pathways of amine with epoxides in the reagent ratio of 1:1 and 1:2. Struct Chem 2022. [DOI: 10.1007/s11224-022-01979-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Ismail I, Robertson C, Habershon S. Successes and challenges in using machine-learned activation energies in kinetic simulations. J Chem Phys 2022; 157:014109. [DOI: 10.1063/5.0096027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The prediction of the thermodynamic and kinetic properties of chemical reactions is increasingly being addressed by machine-learning (ML) methods such as artificial neural networks (ANNs). While a number of recent studies have reported success in predicting chemical reaction activation energies, less attention has focused on how the accuracy of ML predictions filter through to predictions of macroscopic observables. Here, we consider the impact of the uncertainty associated with ML prediction of activation energies on observable properties of chemical reaction networks, as given by microkinetics simulations based on ML-predicted reaction rates. After training an ANN to predict activation energies given standard molecular descriptors for reactants and products alone, we performed microkinetics simulations of three different prototypical reaction networks: formamide decomposition, aldol reactions and decomposition of 3-hydroperoxypropanal. We find that the kinetic modelling predictions can be in excellent agreement with corresponding simulations performed with ab initio calculations, but this is dependent on the inherent energetic landscape of the networks. We use these simulations to suggest some guidelines for when ML-based activation energies can be reliable, and when one should take more care in applications to kinetics modelling.
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Affiliation(s)
| | | | - Scott Habershon
- Department of Chemistry, University of Warwick, United Kingdom
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26
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Sun X, Xie M, Qiu W, Wei C, Chen X, Hu Y. Spectroscopic evidence of S∴N and S∴O hemibonds in heterodimer cations. Phys Chem Chem Phys 2022; 24:19354-19361. [PMID: 35686608 DOI: 10.1039/d2cp00904h] [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
Computational and condensed phase experimental evidence for the existence of S∴N and S∴O hemibonded structures has been reported previously, but no gas phase experimental evidence has been reported. To experimentally explore the existence of the S∴N and S∴O hemibonds in the gas phase, we recorded the infrared photodissociation action spectra of four cationic clusters: [CH3SH-NH3]+, [CH3SCH3-NH3]+, [CH3SCH3-H2O]+, and [CH3OCH3-H2O]+. Combined with the calculation results, it is found that the S∴N hemibonded structure is competitive with the S⋯HN H-bonded structure, though only the latter structure is actually observed in [CH3SH-NH3]+. The spectral and theoretical results show that hemibonds can form between the second- (oxygen or nitrogen) and the third-period elements (sulfur) in the heterodimer clusters of [CH3SCH3-NH3]+ and [CH3SCH3-H2O]+. However, the S∴N and S∴O hemibonded structures are found competitive with the C⋯HN and CH⋯O H-bonded structures, respectively, and both the structures coexist. On the other hand, the O∴O hemibonded structure is much less stable than other hydrogen bonded (H-bonded) structures in [CH3OCH3-H2O]+, and it shows no clear contribution to the observed spectrum. This study provides direct spectroscopic evidence for the existence of S∴N and S∴O hemibonds in the gas phase and their competition with the H-bonds, which may be also fundamentally important in biological processes.
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Affiliation(s)
- Xiaonan Sun
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
| | - Min Xie
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
| | - Wei Qiu
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
| | - Chengcheng Wei
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
| | - Xujian Chen
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
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27
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Uchida K, Uematsu I, Iwamoto T, Kwon E, Yoshida S, Kato R, Fukui H. Structural Estimation and Hazard Evaluation of Potentially Explosive Residual Silanes Generated in Semiconductor Manufacturing Processes. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.1c05007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kenya Uchida
- Corporate Manufacturing Engineering Center, Toshiba Corporation, 33 Shin-Isogo-Cho Isogo-ku, Yokohama 235-0017, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Ikuo Uematsu
- Strategic Planning Division, Toshiba Corporation, 1-1-1 Shibaura, Minato-ku, Tokyo 105-8001, Japan
| | - Takeaki Iwamoto
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
- Research and Analytical Center for Giant Molecules, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Eunsang Kwon
- Research and Analytical Center for Giant Molecules, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Shinichiro Yoshida
- Research and Analytical Center for Giant Molecules, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Ryu Kato
- Yokkaichi Plant, Kioxia Corporation, 800 Yamanoisshiki-cho, Yokkaichi 512-8550, Japan
| | - Hiroyuki Fukui
- Yokkaichi Plant, Kioxia Corporation, 800 Yamanoisshiki-cho, Yokkaichi 512-8550, Japan
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28
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Two-state reactivity in the acetylene cyclotrimerization reaction catalyzed by a single atomic transition-metal ion: The case for V+ and Fe+. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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29
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Sakamoto K, Sato H, Uchiyama M. DFT Study on the Biosynthesis of Asperterpenol and Preasperterpenoid Sesterterpenoids: Exclusion of Secondary Carbocation Intermediates and Origin of Structural Diversification. J Org Chem 2022; 87:6432-6437. [PMID: 35467870 DOI: 10.1021/acs.joc.2c00291] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biosynthetic pathway to asperterpenol, a sesterterpenoid featuring a 6/6/8/5 tetracyclic ring system, was proposed to involve three secondary (2°) carbocation intermediates (B, D, and I), but it remains controversial whether or not these are viable. Further, the proposed 11/6/5 tricyclic intermediate C has the same "ChemDraw" structure as an intermediate in the biosynthesis of preasperterpenoid, which has a very different 5/7/(3)6/5 pentacyclic skeleton. Here, we present a detailed scrutiny of the asperterpenol/preasperterpenoid biosynthetic pathways based on comprehensive DFT calculations.
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Affiliation(s)
- Kyoka Sakamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hajime Sato
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Research Initiative for Supra-Materials (RISM), Shinshu University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
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30
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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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31
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Ito T, Maeda S, Harabuchi Y. Kinetic Analysis of a Reaction Path Network Including Ambimodal Transition States: A Case Study of an Intramolecular Diels-Alder Reaction. J Chem Theory Comput 2022; 18:1663-1671. [PMID: 35099971 DOI: 10.1021/acs.jctc.1c01297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study proposes a methodology for the kinetic analysis of a reaction path network including ambimodal transition states (TSs), through which an ensemble of trajectories bifurcates to multiple minima in a phenomenon called dynamical bifurcation. The proposed methodology consists of three techniques: an automated reaction path search to construct a reaction path network including ambimodal TSs, an ab initio molecular dynamics simulation to evaluate the branching ratio, and the definition of rate constants incorporating this ratio. Applying the procedure to a Diels-Alder reaction, it was found that the inclusion of dynamical bifurcations is necessary to explain the experimental reaction yield of a byproduct. In addition, it was verified that the products take 1013 s to reach thermal equilibrium and that the experimental selectivity is determined by the dynamical bifurcations.
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Affiliation(s)
- Takuma Ito
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan.,Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO) Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Sapporo 060-0810, Japan
| | - Yu Harabuchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan.,Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO) Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Sapporo 060-0810, Japan
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32
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Saito T, Shimizu Y, Araki Y, Ohgami Y, Kitazawa Y, Nishii Y. From Enantioenriched Donor‐Acceptor Cyclopropylcarbinols to Axially Chiral Arylnaphthalenes through Aryldihydronaphthalenes: Central‐to‐Axial Chirality Exchange. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Taichi Saito
- Department of Applied Chemistry, Faculty of Textile Science and Technology Shinshu University Tokida 3-15-1 Ueda Nagano 386–8567 Japan
| | - Yuka Shimizu
- Department of Applied Chemistry, Faculty of Textile Science and Technology Shinshu University Tokida 3-15-1 Ueda Nagano 386–8567 Japan
| | - Yusuke Araki
- Department of Applied Chemistry, Faculty of Textile Science and Technology Shinshu University Tokida 3-15-1 Ueda Nagano 386–8567 Japan
| | - Yoshino Ohgami
- Department of Applied Chemistry, Faculty of Textile Science and Technology Shinshu University Tokida 3-15-1 Ueda Nagano 386–8567 Japan
| | - Yu Kitazawa
- Department of Applied Chemistry, Faculty of Textile Science and Technology Shinshu University Tokida 3-15-1 Ueda Nagano 386–8567 Japan
| | - Yoshinori Nishii
- Department of Applied Chemistry, Faculty of Textile Science and Technology Shinshu University Tokida 3-15-1 Ueda Nagano 386–8567 Japan
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33
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Saito K, Hashimoto Y, Takayanagi T. Ring-Polymer Molecular Dynamics Calculations of Thermal Rate Coefficients and Branching Ratios for the Interstellar H 3+ + CO → H 2 + HCO +/HOC + Reaction and Its Deuterated Analogue. J Phys Chem A 2021; 125:10750-10756. [PMID: 34918514 DOI: 10.1021/acs.jpca.1c09160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reaction between H3+ and CO is important in understanding the H3+ destruction mechanism in the interstellar medium. In this work, thermal rate coefficients for the H3+ + CO and D3+ + CO reactions are calculated using ring-polymer molecular dynamics (RPMD) on a high-level machine-learning potential energy surface. The RPMD results agree well with the classical molecular dynamics results, where nuclear quantum effects are completely ignored, whereas the agreement between the RPMD results and the previous quasi-classical trajectory is good only at low temperatures. The calculated [HCO+]/[HOC+] product branching ratios decrease as the temperature increases, and the product branching is exclusively determined by the initial collisional orientation, which governs the formation of an ion-dipole complex, H3+···CO or H3+···OC, that dissociates into H2 + HCO+ or H2 + HOC+, respectively, via a direct mechanism. However, the contribution of the indirect mechanism via the rearrangement between H3+···CO and H3+···OC increases as the temperature increases, although its absolute fraction is small.
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Affiliation(s)
- Kohei Saito
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Yu Hashimoto
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama 338-8570, Japan
| | - Toshiyuki Takayanagi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama 338-8570, Japan
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34
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Maehara S, Kobayashi M, Kuwada M, Choshi T, Inoue H, Hieda Y, Nishiyama T, Hata T. In vitro and in silico studies of potential coronavirus-specific 3C-like protease inhibitors. Chem Pharm Bull (Tokyo) 2021; 70:195-198. [PMID: 34955489 DOI: 10.1248/cpb.c21-01002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We investigated similar compounds to ebselen and tideglusib, which exhibit strong activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), using MACCS keys. Four candidate compounds were identified. One of them, phenyl-benzothiazol-3-one, showed coronavirus-specific 3C-like (3CL) protease inhibitory activity. The results indicated that a similarity score above 0.81 is a good indicator of activity for ebselen-and-tideglusib-like compounds. Subsequently, we simulated the ring-cleavage Michael reaction of ebselen at the Se center, which is responsible for its 3CL protease inhibitory activity, and determined the activation free energy of the reaction. The results showed that reaction simulation is a useful tool for estimating the activity of inhibitory compounds that undergo Michael addition reactions with the relevant cysteine S atom of 3CL proteases.
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Affiliation(s)
- Shoji Maehara
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Manami Kobayashi
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Mari Kuwada
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Tominari Choshi
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Hirohumi Inoue
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Yuzou Hieda
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Takashi Nishiyama
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
| | - Toshiyuki Hata
- Faculty of Pharmacy and Pharmaceutical Sciences, Fukuyama University
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35
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Sato H, Takagi T, Miyamoto K, Uchiyama M. Theoretical Study on the Mechanism of Spirocyclization in Spiroviolene Biosynthesis. Chem Pharm Bull (Tokyo) 2021; 69:1034-1038. [PMID: 34602572 DOI: 10.1248/cpb.c21-00536] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Spiroviolene is a spirocyclic triquinane diterpene produced by Streptomyces violens. Recently, a biosynthetic pathway that includes secondary carbocation intermediates and a complicated concerted skeletal rearrangement was proposed for spiroviolene, based upon careful labeling experiments. On the basis of density functional theory (DFT) calculations, we propose a revised pathway for spiroviolene biosynthesis, involving a multistep carbocation cascade that bypasses the formation of unstable secondary carbocations by breaking the adjacent C-C bond to form a more stable tertiary carbocation (IM3) and by Wagner-Meerwein 1,2-methyl rearrangement (IM7).
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Affiliation(s)
- Hajime Sato
- Graduate School of Pharmaceutical Sciences, The University of Tokyo.,Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi
| | - Taisei Takagi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | | | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo.,Research Initiative for Supra-Materials (RISM), Shinshu University
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36
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Sato H, Li BX, Takagi T, Wang C, Miyamoto K, Uchiyama M. DFT Study on the Biosynthesis of Verrucosane Diterpenoids and Mangicol Sesterterpenoids: Involvement of Secondary-Carbocation-Free Reaction Cascades. JACS AU 2021; 1:1231-1239. [PMID: 34467361 PMCID: PMC8397367 DOI: 10.1021/jacsau.1c00178] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Indexed: 05/03/2023]
Abstract
Some experimental observations indicate that a sequential formation of secondary (2°) carbocations might be involved in some biosynthetic pathways, including those of verrucosane-type diterpenoids and mangicol-type sesterterpenoids, but it remains controversial whether or not such 2° cations are viable intermediates. Here, we performed comprehensive density functional theory calculations of these biosynthetic pathways. The results do not support previously proposed pathways/mechanisms: in particular, we find that none of the putative 2° carbocation intermediates is involved in either of the biosynthetic pathways. In verrucosane biosynthesis, the proposed 2° carbocations (II and IV) in the early stage are bypassed by the formation of the adjacent 3° carbocations and by unusual skeletal rearrangement reactions, and in the later stage, the putative 2° carbocation intermediates (VI, VII, and VIII) are not present as the proposed forms but as nonclassical structures between homoallyl and cyclopropylcarbinyl cations. In the mangicol biosynthesis, one of the two proposed 2° carbocations (X) is bypassed by a C-C bond-breaking reaction to generate a 3° carbocation with a C=C bond, while the other (XI) is bypassed by a strong hyperconjugative interaction leading to a nonclassical carbocation. We propose new biosynthetic pathways/mechanisms for the verrucosane-type diterpenoids and mangicol-type sesterterpenoids. These pathways are in good agreement with the findings of previous biosynthetic studies, including isotope-labeling experiments and byproducts analysis, and moreover can account for the biosynthesis of related terpenes.
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Affiliation(s)
- Hajime Sato
- Interdisciplinary
Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Bi-Xiao Li
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Taisei Takagi
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Chao Wang
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazunori Miyamoto
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masanobu Uchiyama
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Research
Initiative for Supra-Materials, Shinshu
University, 3-15-1 Tokida,
Ueda, Nagano 386-8567, Japan
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37
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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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38
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Kawagoe Y, Kikugawa G, Shirasu K, Okabe T. Thermoset resin curing simulation using quantum-chemical reaction path calculation and dissipative particle dynamics. SOFT MATTER 2021; 17:6707-6717. [PMID: 34169305 DOI: 10.1039/d1sm00600b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Thermoset resin, which is commonly used as a matrix in carbon-fiber-reinforced plastic, requires curing procedures. We propose a curing simulation technique involving a dissipative particle dynamics (DPD) simulation, which can simulate a larger system and longer time period than those of conventional all-atom molecular dynamics (AA-MD) simulations. The proposed curing DPD simulation can represent the thermoset resin exothermic reaction process precisely by considering each reactivity according to the reaction types calculated via quantum-chemical reaction path calculations. The cure reaction process given by the curing DPD simulation agrees well with that given by a conventional curing AA-MD simulation, but with run-time and computational-resource reductions of 1/480 and 1/10 times, respectively. We also conduct reverse mapping, through which the AA-MD system can be reconstructed from the DPD system, to evaluate the structural and thermomechanical properties. The X-ray diffraction pattern and thermomechanical properties of the reconstructed system agree well with those of the systems derived from the curing AA-MD simulation and experimental setup. Therefore, a cured-resin AA-MD system can be obtained from a curing DPD simulation at an extremely low computational cost, and the thermomechanical properties can be evaluated precisely using this system. The proposed curing simulation technique can be applied in high-throughput screening for better materials properties and in large system calculations.
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Affiliation(s)
- Yoshiaki Kawagoe
- Department of Aerospace Engineering, Tohoku University, Sendai 980-8579, Japan.
| | - Gota Kikugawa
- Institute of Fluid Science, Tohoku University, Sendai 980-8577, Japan.
| | - Keiichi Shirasu
- Department of Aerospace Engineering, Tohoku University, Sendai 980-8579, Japan.
| | - Tomonaga Okabe
- Department of Aerospace Engineering, Tohoku University, Sendai 980-8579, Japan. and Department of Materials Science and Engineering, University of Washington, Seattle, Washington, USA
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39
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Otomo T, Suzuki H, Iida R, Takayanagi T. SN1 reaction mechanisms of tert-butyl chloride in aqueous solution: What can be learned from reaction path search calculations and trajectory calculations for small hydrated clusters? COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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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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41
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Mitchell I, Qiu L, Lamb LD, Ding F. High Temperature Accelerated Stone-Wales Transformation and the Threshold Temperature of IPR-C 60 Formation. J Phys Chem A 2021; 125:4548-4557. [PMID: 34032443 DOI: 10.1021/acs.jpca.1c02151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Stone-Wales bond rotation isomerization of nonicosahedral C60 (C2v-C60) into isolated-pentagon rule following icosahedral C60 (Ih-C60 or IPR-C60) is a limiting step in the synthesis of Ih-C60. However, extensive previous studies indicate that the potential energy barrier of the Stone-Wales bond rotation is between 6 and 8 eV, extremely high to allow for bond rotation at the temperatures used to produce fullerenes conventionally. This is also despite data indicating a possible fullerene road mechanism that necessitates low-temperature annealing. However, these previous investigations often have limiting factors, such as using the harmonic approximation to determine free energies at high temperatures or considering only the reverse Ih-C60 to C2v-C60 transition as a basis. Indeed, when the difference in energy between Ih-C60 and C2v-C60 is accounted for, this barrier is generally reduced by ∼1.5 eV. Thus, utilizing the recently developed density functional tight binding metadynamics (DFTB-MTD) interface, the effects of temperature on the bond rotation in the conversion of C2v-C60 to Ih-C60 have been investigated. We found that Stone-Wales bond rotations are complex processes with both in-plane and out-of-plane transition states, and which transition path dominates depends on temperature. Our results clearly show that at temperatures of 2000 K, the free energy for a C2v-C60 to Ih-C60 transition is only ∼4.21 eV and further reduces to ∼3.77 eV at 3000 K. This translates to transition times of ∼971 μs at 2000 K and ∼34 ns at 3000 K, indicating that defect healing is a fast process at temperatures typical of arc jet or laser ablation experiments. Conversely, below ∼2000 K, bond rotation becomes prohibitively slow, putting a lower threshold limit on the temperature of fullerene formation and subsequent annealing.
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Affiliation(s)
- Izaac Mitchell
- Center for Multidimensional Carbon Materials, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,School of Materials Science and Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Lu Qiu
- Center for Multidimensional Carbon Materials, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,School of Materials Science and Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Lowell D Lamb
- Broadcom Inc., 1320 Ridder Park Drive, San Jose, California 95131, United States
| | - Feng Ding
- Center for Multidimensional Carbon Materials, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,School of Materials Science and Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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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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43
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Takayanagi T. Application of Reaction Path Search Calculations to Potential Energy Surface Fits. J Phys Chem A 2021; 125:3994-4002. [PMID: 33915053 DOI: 10.1021/acs.jpca.1c01512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There has been significant progress in recent years in the use of machine learning techniques to model high-dimensional reactive potential energy surfaces using large-scale data obtained from ab initio electronic structure calculations. In these methods, the strategy used to gather data becomes a key issue as the molecular size increases. In this work, we examine the applicability of the reaction path search algorithm implemented in the Global Reaction Route Mapping (GRRM) code as a data-gathering approach. The electronic energies and gradients sampled by using the GRRM calculation are directly used in potential energy surface fitting to a permutationally invariant polynomial function. This simple approach was applied to the HNS and HCNO reaction systems, and we found that the fitted potential energy surfaces reasonably reproduce the features of the electronic structure calculations used in the GRRM calculations. This suggests that the GRRM sampling scheme can be used to construct an initial potential energy surface.
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Affiliation(s)
- Toshiyuki Takayanagi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Saitama City, Saitama 338-8570, Japan
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Zhang Y, Xie M, Sun F, Zhang Z, Nie W, Sun X, Hu Y. Proton Transfer in Nitromethane-Ammonia Clusters under VUV Single-Photon Ionization Explored by Infrared Spectroscopy and Theoretical Calculations. J Phys Chem A 2021; 125:3279-3287. [PMID: 33878869 DOI: 10.1021/acs.jpca.1c00255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
It is known that the acidity and reactivity of the CH bond can be enhanced after ionization. Also, this property plays a pivotal role in proton transfer reaction and in the formation of new molecules. Herein, infrared spectroscopy and high-precision quantum chemical calculations are used to study the neutral and cationic clusters of nitromethane-ammonia (CH3NO2-NH3). It is found that in the neutral cluster, CH3NO2 and NH3 are mainly bonded by three intermolecular hydrogen bonds, in which electrostatic contribution plays a major role. After vacuum ultraviolet (VUV) single-photon ionization of CH3NO2-NH3, the positive charge redistributes from the ionized nitrogen atom of NH3 to the CH3NO2 molecule immediately. Then, the proton of CH3NO2 transfers to NH3 to form a proton-transferred type structure CH2NO2-NH4+, without any effective energy barrier, due to the positive hyperconjugation of cationic nitromethane. A closed loop of positive charge transfer takes place in the CH3NO2-NH3 cluster after VUV ionization. The present work demonstrates that both the proton transfer reaction and charge transfer process have occurred in the ionized CH3NO2-NH3 cluster. Moreover, it is found that the proton transfer reaction is a result of the highly acidic CH bond caused by hyperconjugation between the σ (CH) bond and π orbital.
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Affiliation(s)
- Yu Zhang
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Min Xie
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Fufei Sun
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Zhaoli Zhang
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Wuyi Nie
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Xiaonan Sun
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Yongjun Hu
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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Sun F, Xie M, Zhang Y, Song W, Sun X, Hu Y. Spectroscopic evidence of the C-N covalent bond formed between two interstellar molecules (ISM): acrylonitrile and ammonia. Phys Chem Chem Phys 2021; 23:9672-9678. [PMID: 33616131 DOI: 10.1039/d0cp06274j] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Acrylonitrile (AN) and ammonia (NH3) are two important nitrogen-containing interstellar molecules in outer space, especially on Titan. Herein, we measured infrared (IR) spectra of neutral and cationic AN-NH3 complexes by VUV single-photon ionization combined with time-of-flight mass spectrometry. On combining IR spectra with the theoretical calculations, we found that the molecules prefer to form a single-ring cyclic H-bonded structure in the neutral AN-NH3 and (AN)2-NH3 clusters. However, after ionization of AN-NH3 and (AN)2-NH3 clusters, a new C-N-covalent bond is confirmed to form directly between AN and NH3, without any energy barrier in the cationic complexes. Moreover, in the ionized (AN)2-NH3 cluster, the covalent C-N bond prefers to form between AN and NH3 rather than the two AN groups. These results provide spectroscopic evidence of AN forming a new molecule with NH3, induced by VUV radiation. The formation of the new C-N bond broadens our knowledge on the evolution of the prebiotic nitrogen-containing molecules in space.
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Affiliation(s)
- Fufei Sun
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, China.
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Abstract
As more data are introduced in the building of models of chemical reactivity, the mechanistic component can be reduced until 'big data' applications are reached. These methods no longer depend on underlying mechanistic hypotheses, potentially learning them implicitly through extensive data training. Reactivity models often focus on reaction barriers, but can also be trained to directly predict lab-relevant properties, such as yields or conditions. Calculations with a quantum-mechanical component are still preferred for quantitative predictions of reactivity. Although big data applications tend to be more qualitative, they have the advantage to be broadly applied to different kinds of reactions. There is a continuum of methods in between these extremes, such as methods that use quantum-derived data or descriptors in machine learning models. Here, we present an overview of the recent machine learning applications in the field of chemical reactivity from a mechanistic perspective. Starting with a summary of how reactivity questions are addressed by quantum-mechanical methods, we discuss methods that augment or replace quantum-based modelling with faster alternatives relying on machine learning.
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Odagiri N, Shirasu K, Kawagoe Y, Kikugawa G, Oya Y, Kishimoto N, Ohuchi FS, Okabe T. Amine/epoxy stoichiometric ratio dependence of crosslinked structure and ductility in
amine‐cured
epoxy thermosetting resins. J Appl Polym Sci 2021. [DOI: 10.1002/app.50542] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nobuyuki Odagiri
- Technology Collaboration Toray Composite Materials America, Inc Tacoma Washington USA
| | - Keiichi Shirasu
- Department of Aerospace Engineering Tohoku University Sendai Japan
| | - Yoshiaki Kawagoe
- Department of Aerospace Engineering Tohoku University Sendai Japan
| | - Gota Kikugawa
- Institute of Fluid Science Tohoku University Sendai Japan
| | - Yutaka Oya
- Department of Physics Tohoku University Sendai Japan
| | | | - Fumio S. Ohuchi
- Department of Materials Science and Engineering University of Washington Seattle Washington USA
- Organization for International Initiatives Tohoku University Sendai Japan
| | - Tomonaga Okabe
- Department of Aerospace Engineering Tohoku University Sendai Japan
- Department of Materials Science and Engineering University of Washington Seattle Washington USA
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Ohno K, Kishimoto N, Iwamoto T, Satoh H, Watanabe H. High performance global exploration of isomers and isomerization channels on quantum chemical potential energy surface of H 5 C 2 NO 2. J Comput Chem 2021; 42:192-204. [PMID: 33146910 DOI: 10.1002/jcc.26446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 11/07/2022]
Abstract
High performance global exploration of isomers and isomerization channels on the quantum chemical potential energy surface (PES) is performed for H5 C2 NO2 by using the scaled hypersphere search-anharmonic downward distortion following (SHS-ADDF) method. A multi-node operation, NeoGRRM, has achieved high performance exploration calculations for the large system by submitting SHS-ADDF sub-jobs into many cores in parallel and unifying the results of sub-jobs into the total lists of the main-job. Global exploration of equilibrium (EQ) and transition-state structures at the level of B3LYP/6-31G(d) gave 3210 EQs and 23278 TSs. Nine compounds were found in the low energy regions of 0-100 kJ/mol; the lowest energy compound is N-methylcarbamic acid, the second is methyl carbamate, and the third is glycine (the most fundamental amino acid). Interconversion pathways between the conformers of each of the low energy compounds were surveyed. Isomerization channels around glycine were explored in detail. The lowest energy barriers around some of the EQs turned to be negative after zero-point energy corrections. This indicates that those structures cannot exist as independent structures because they spontaneously collapse into more stable structures. The global PES search showed various interesting dissociating channels which indicate synthon reaction pathways in the reverse directions.
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Affiliation(s)
- Koichi Ohno
- Institute for Quantum Chemical Exploration, Tokyo, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Naoki Kishimoto
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Takeaki Iwamoto
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Hiroko Satoh
- Institute for Quantum Chemical Exploration, Tokyo, Japan.,Department of Chemistry, University of Zurich, Zurich, Switzerland.,Research Organization of Information and Systems (ROIS), Tokyo, Japan
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Ebisawa S, Tsutsumi T, Taketsugu T. Geometric analysis of anharmonic downward distortion following paths. J Comput Chem 2021; 42:27-39. [PMID: 33098122 DOI: 10.1002/jcc.26430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/16/2020] [Accepted: 09/27/2020] [Indexed: 11/07/2022]
Abstract
A mathematical aspect of the anharmonic downward distortion following (ADDF) path is discussed. The ADDF method is utilized as an automated reaction path search method, which can explore transition state geometries on a potential energy surface from a potential minimum. We show that the maximum number of the ADD stationary paths intersecting the potential minimum is 2f + 1 - 2, where f denotes the degree of freedom of the system. We also show that the bifurcation of the ADD stationary path is essential to detect all the transition states connected from a given minimum. The ADDF computation is demonstrated for a H2 O molecule in which pitchfork bifurcation is observed.
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Affiliation(s)
- Shuichi Ebisawa
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Takuro Tsutsumi
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
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50
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Borysenko IO, Sviatenko LK, Okovytyy SI, Leszczynski J. Efficient approach for exploring the multiple-channel bimolecular interactions of conformationally flexible reagents. Epoxide ring opening reaction. Struct Chem 2020. [DOI: 10.1007/s11224-020-01663-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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