1
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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. [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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2
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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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3
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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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4
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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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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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6
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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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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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8
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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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9
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Yasumura S, Saita K, Miyakage T, Nagai K, Kon K, Toyao T, Maeno Z, Taketsugu T, Shimizu KI. Designing main-group catalysts for low-temperature methane combustion by ozone. Nat Commun 2023; 14:3926. [PMID: 37400448 DOI: 10.1038/s41467-023-39541-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 06/16/2023] [Indexed: 07/05/2023] Open
Abstract
The catalytic combustion of methane at a low temperature is becoming increasingly key to controlling unburned CH4 emissions from natural gas vehicles and power plants, although the low activity of benchmark platinum-group-metal catalysts hinders its broad application. Based on automated reaction route mapping, we explore main-group elements catalysts containing Si and Al for low-temperature CH4 combustion with ozone. Computational screening of the active site predicts that strong Brønsted acid sites are promising for methane combustion. We experimentally demonstrate that catalysts containing strong Bronsted acid sites exhibit improved CH4 conversion at 250 °C, correlating with the theoretical predictions. The main-group catalyst (proton-type beta zeolite) delivered a reaction rate that is 442 times higher than that of a benchmark catalyst (5 wt% Pd-loaded Al2O3) at 190 °C and exhibits higher tolerance to steam and SO2. Our strategy demonstrates the rational design of earth-abundant catalysts based on automated reaction route mapping.
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Affiliation(s)
- Shunsaku Yasumura
- Institute for Catalysis, Hokkaido University, N-21 W-10, Sapporo, Hokkaido, 001-0021, Japan
| | - Kenichiro Saita
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| | - Takumi Miyakage
- Institute for Catalysis, Hokkaido University, N-21 W-10, Sapporo, Hokkaido, 001-0021, Japan
| | - Ken Nagai
- Institute for Catalysis, Hokkaido University, N-21 W-10, Sapporo, Hokkaido, 001-0021, Japan
| | - Kenichi Kon
- Institute for Catalysis, Hokkaido University, N-21 W-10, Sapporo, Hokkaido, 001-0021, Japan
| | - Takashi Toyao
- Institute for Catalysis, Hokkaido University, N-21 W-10, Sapporo, Hokkaido, 001-0021, Japan
| | - Zen Maeno
- School of Advanced Engineering, Kogakuin University, Tokyo, 192-0015, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Hokkaido, 001-0021, Japan
| | - Ken-Ichi Shimizu
- Institute for Catalysis, Hokkaido University, N-21 W-10, Sapporo, Hokkaido, 001-0021, Japan.
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Yasumura S, Kato T, Toyao T, Maeno Z, Shimizu KI. An automated reaction route mapping for the reaction of NO and active species on Ag 4 clusters in zeolites. Phys Chem Chem Phys 2023; 25:8524-8531. [PMID: 36883572 DOI: 10.1039/d2cp04761f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
A computational investigation of the catalytic reaction on multinuclear sites is very challenging. Here, using an automated reaction route mapping method, the single-component artificial force induced reaction (SC-AFIR) algorithm, the catalytic reaction of NO and OH/OOH species over the Ag42+ cluster in a zeolite is investigated. The results of the reaction route mapping for H2 + O2 reveal that OH and OOH species are formed over the Ag42+ cluster via an activation barrier lower than that of OH formation from H2O dissociation. Then, reaction route mapping is performed to examine the reactivity of the OH and OOH species with NO molecules over the Ag42+ cluster, resulting in the facile reaction path of HONO formation. With the aid of the automated reaction route mapping, the promotion effect of H2 addition on the SCR reaction was computationally proposed (boosting the formation of OH and OOH species). In addition, the present study emphasizes that automated reaction route mapping is a powerful tool to elucidate the complicated reaction pathway on multi-nuclear clusters.
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Affiliation(s)
- Shunsaku Yasumura
- Institute for Catalysis, Hokkaido University, N-21, W-10, Sapporo, 001-0021, Japan.
| | - Taisetsu Kato
- Institute for Catalysis, Hokkaido University, N-21, W-10, Sapporo, 001-0021, Japan.
| | - Takashi Toyao
- Institute for Catalysis, Hokkaido University, N-21, W-10, Sapporo, 001-0021, Japan.
| | - Zen Maeno
- School of Advanced Engineering, Kogakuin University, Tokyo, 192-0015, Japan
| | - Ken-Ichi Shimizu
- Institute for Catalysis, Hokkaido University, N-21, W-10, Sapporo, 001-0021, Japan.
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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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Mikhaylov OA, Gridnev ID. Global Search for Stable C 4H 5NO Compounds-Guinness Molecules and Stability Islands. Molecules 2023; 28:molecules28020728. [PMID: 36677787 PMCID: PMC9860754 DOI: 10.3390/molecules28020728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023] Open
Abstract
Global reaction route mapping (GRRM) analysis for compounds with the formula C4H5NO allowed for the detection of the corresponding "Guinness molecules" 000 and 001, as well as around 150 other stable minima of the same composition. The results suggest that compounds of similar functionality form a kind of "Stability Island" with their free energies of formation falling within s relatively limited range.
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Mitsuta Y, Asada T, Shigeta Y. Calculation of the permeability coefficients of small molecules through lipid bilayers by free-energy reaction network analysis following the explicit treatment of the internal conformation of the solute. Phys Chem Chem Phys 2022; 24:26070-26082. [PMID: 36268802 DOI: 10.1039/d2cp03678a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Biomembrane permeation represents a major barrier to pharmacokinetics. During preclinical drug discovery, the coefficients of the permeation of molecules through lipid bilayers account for a valuable property of such molecules. Therefore, the control of the permeation of molecules through lipid bilayers is an essential factor in drug design, and the estimation of the permeation phenomena is a crucial study in pharmacy. Thus, there are many published studies on the theoretical estimations of permeation coefficients. Here, we propose a molecular dynamics (MD) simulation method for estimating the permeation of small molecules through lipid bilayers based on the free-energy reaction network (FERN) analysis. In this method, the collective variables (CVs) of the free energy calculations explicitly include the conformational changes in the rotational bonds of the solute molecules. The advantages of the present method over the other method are that it is possible to estimate reaction pathways and their reaction rates, i.e., permeation coefficients or passage times, in multidimensional space spanned by CVs though conventional methods such as the umbrella sampling method and target MDs often dealt with a few degrees of freedom. To demonstrate the efficacy of our method, we calculate the coefficients of the permeation of three small aromatic peptides, namely N-acetylphenylalanineamide (Ac-Phe-NH2 or NAFA), N-acetyltyrosineamide (Ac-Tyr-NH2 or NAYA), and N-acetyltryptophanamide (Ac-Trp-NH2 or NATA), through a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid bilayer. In these cases we adopted one CV for the permeation direction and four CVs for the internal rotational coordinates. The results reveal that the permeation coefficients of NAFA, NAYA, and NATA are 1.7 × 10-2, 0.51 × 10-4, and 5.7 × 10-4 cm s-1, respectively. Compared with the experimental data, our simulation results followed the same trend, i.e., NAFA > NATA > NAYA. By analyzing the structures of metastable points of the solute molecules, our simulation result reveals that the aforementioned trend is caused by the differences in stability among their rotamers. Furthermore, we evaluate the statistical fluctuation of the rotamers, and the time scale of flipping the side chain reveals that the structures rigidify as the ligand moves deeper into the membrane.
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Affiliation(s)
- Yuki Mitsuta
- Department of Chemistry, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan.
- RIMED, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan
| | - Toshio Asada
- Department of Chemistry, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan.
- RIMED, Osaka Prefecture University, 1-1, Gakuen-cho, Sakai, Osaka, 599-8531, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
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14
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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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15
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Guo X, Fang L, Xu Y, Duan W, Rinke P, Todorović M, Chen X. Molecular Conformer Search with Low-Energy Latent Space. J Chem Theory Comput 2022; 18:4574-4585. [PMID: 35696366 PMCID: PMC9281398 DOI: 10.1021/acs.jctc.2c00290] [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: 11/30/2022]
Abstract
![]()
Identifying low-energy
conformers with quantum mechanical accuracy
for molecules with many degrees of freedom is challenging. In this
work, we use the molecular dihedral angles as features and explore
the possibility of performing molecular conformer search in a latent
space with a generative model named variational auto-encoder (VAE).
We bias the VAE towards low-energy molecular configurations to generate
more informative data. In this way, we can effectively build a reliable
energy model for the low-energy potential energy surface. After the
energy model has been built, we extract local-minimum conformations
and refine them with structure optimization. We have tested and benchmarked
our low-energy latent-space (LOLS) structure search method on organic
molecules with 5–9 searching dimensions. Our results agree
with previous studies.
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Affiliation(s)
- Xiaomi Guo
- State Key Laboratory of Low Dimensional Quantum Physics and Department of Physics, Tsinghua University, Beijing 100084, China.,Department of Applied Physics, Aalto University, Espoo 00076, Finland
| | - Lincan Fang
- Department of Applied Physics, Aalto University, Espoo 00076, Finland
| | - Yong Xu
- State Key Laboratory of Low Dimensional Quantum Physics and Department of Physics, Tsinghua University, Beijing 100084, China.,Frontier Science Center for Quantum Information, Beijing 100084, China.,RIKEN Center for Emergent Matter Science (CEMS), Wako, Saitama 351-0198, Japan
| | - Wenhui Duan
- State Key Laboratory of Low Dimensional Quantum Physics and Department of Physics, Tsinghua University, Beijing 100084, China.,Frontier Science Center for Quantum Information, Beijing 100084, China.,Institute for Advanced Study, Tsinghua University, Beijing 100084, China
| | - Patrick Rinke
- Department of Applied Physics, Aalto University, Espoo 00076, Finland
| | - Milica Todorović
- Department of Mechanical and Materials Engineering, University of Turku, FI-20014 Turku, Finland
| | - Xi Chen
- Department of Applied Physics, Aalto University, Espoo 00076, Finland
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16
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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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17
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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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18
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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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19
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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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20
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Buelna-García CE, Castillo-Quevedo C, Quiroz-Castillo JM, Paredes-Sotelo E, Cortez-Valadez M, Martin-del-Campo-Solis MF, López-Luke T, Utrilla-Vázquez M, Mendoza-Wilson AM, Rodríguez-Kessler PL, Vazquez-Espinal A, Pan S, de Leon-Flores A, Mis-May JR, Rodríguez-Domínguez AR, Martínez-Guajardo G, Cabellos JL. Relative Populations and IR Spectra of Cu38 Cluster at Finite Temperature Based on DFT and Statistical Thermodynamics Calculations. Front Chem 2022; 10:841964. [PMID: 35300385 PMCID: PMC8921525 DOI: 10.3389/fchem.2022.841964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
The relative populations of Cu38 isomers depend to a great extent on the temperature. Density functional theory and nanothermodynamics can be combined to compute the geometrical optimization of isomers and their spectroscopic properties in an approximate manner. In this article, we investigate entropy-driven isomer distributions of Cu38 clusters and the effect of temperature on their IR spectra. An extensive, systematic global search is performed on the potential and free energy surfaces of Cu38 using a two-stage strategy to identify the lowest-energy structure and its low-energy neighbors. The effects of temperature on the populations and IR spectra are considered via Boltzmann factors. The computed IR spectrum of each isomer is multiplied by its corresponding Boltzmann weight at finite temperature. Then, they are summed together to produce a final temperature-dependent, Boltzmann-weighted spectrum. Our results show that the disordered structure dominates at high temperatures and the overall Boltzmann-weighted spectrum is composed of a mixture of spectra from several individual isomers.
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Affiliation(s)
- Carlos Emiliano Buelna-García
- Departamento de Investigación en Polímeros y Materiales, Universidad de Sonora, Hermosillo, Mexico
- Organización Científica y Tecnológica del Desierto, Hermosillo, Mexico
| | - Cesar Castillo-Quevedo
- Departamento de Fundamentos del Conocimiento, Centro Universitario del Norte, Universidad de Guadalajara, Colotlán, Mexico
| | | | - Edgar Paredes-Sotelo
- Departamento de Investigación en Polímeros y Materiales, Universidad de Sonora, Hermosillo, Mexico
| | - Manuel Cortez-Valadez
- CONACYT-Departamento de Investigación en Física, Universidad de Sonora, Hermosillo, Mexico
| | | | - Tzarara López-Luke
- Instituto de Investigación en Metalurgia y Materiales, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, Mexico
| | | | | | - Peter L. Rodríguez-Kessler
- Laboratorio de Química Inorgánica y Materiales Moleculares, Facultad de Ingeniería, Universidad Autonoma de Chile, Santiago, Chile
| | - Alejandro Vazquez-Espinal
- Comput. Theor. Chem. Group Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago, Chile
| | - Sudip Pan
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Aned de Leon-Flores
- Departamento de Ciencias Químico Biologicas, Universidad de Sonora, Hermosillo, Mexico
| | | | | | - Gerardo Martínez-Guajardo
- Unidad Académica de Ciencias Químicas, Área de Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
- *Correspondence: Gerardo Martinez-Guajardo, ; Jose Luis Cabellos,
| | - Jose Luis Cabellos
- Universidad Politécnica de Tapachula, Tapachula, Mexico
- *Correspondence: Gerardo Martinez-Guajardo, ; Jose Luis Cabellos,
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21
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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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22
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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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23
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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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24
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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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25
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Kim J, Gu GH, Noh J, Kim S, Gim S, Choi J, Jung Y. Predicting potentially hazardous chemical reactions using an explainable neural network. Chem Sci 2021; 12:11028-11037. [PMID: 34522300 PMCID: PMC8386654 DOI: 10.1039/d1sc01049b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/12/2021] [Indexed: 11/21/2022] Open
Abstract
Predicting potentially dangerous chemical reactions is a critical task for laboratory safety. However, a traditional experimental investigation of reaction conditions for possible hazardous or explosive byproducts entails substantial time and cost, for which machine learning prediction could accelerate the process and help detailed experimental investigations. Several machine learning models have been developed which allow the prediction of major chemical reaction products with reasonable accuracy. However, these methods may not present sufficiently high accuracy for the prediction of hazardous products which particularly requires a low false negative result for laboratory safety in order not to miss any dangerous reactions. In this work, we propose an explainable artificial intelligence model that can predict the formation of hazardous reaction products in a binary classification fashion. The reactant molecules are transformed into substructure-encoded fingerprints and then fed into a convolutional neural network to make the binary decision of the chemical reaction. The proposed model shows a false negative rate of 0.09, which can be compared with 0.47-0.66 using the existing main product prediction models. To provide explanations for what substructures of the given reactant molecules are important to make a decision for target hazardous product formation, we apply an input attribution method, layer-wise relevance propagation, which computes the contributions of individual inputs per input data. The computed attributions indeed match some of the existing chemical intuitions and mechanisms, and also offer a way to analyze possible data-imbalance issues of the current predictions based on relatively small positive datasets. We expect that the proposed hazardous product prediction model will be complementary to existing main product prediction models and experimental investigations.
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Affiliation(s)
- Juhwan Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
| | - Geun Ho Gu
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
| | - Juhwan Noh
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
| | - Seongun Kim
- Graduate School of Artificial Intelligence KAIST Daejeon: 291 Daehak-ro, N24, Yuseong-gu Daejeon 34141 Republic of Korea
| | - Suji Gim
- Environment & Safety Research Center, Samsung Electronics Co. 1, Samsungjeonja-ro Hwasung-si Gyeonggi-do Republic of Korea
| | - Jaesik Choi
- Graduate School of Artificial Intelligence KAIST Daejeon: 291 Daehak-ro, N24, Yuseong-gu Daejeon 34141 Republic of Korea
| | - Yousung Jung
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea
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26
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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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27
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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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28
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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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29
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Mechanistic insights into entropy-driven 1,2-type Friedel-Crafts reaction with conformationally flexible guanidine-bisthiourea bifunctional organocatalysts. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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30
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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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31
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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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32
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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: 5] [Impact Index Per Article: 1.7] [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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33
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Srivastava R. Application of Optimization Algorithms in Clusters. Front Chem 2021; 9:637286. [PMID: 33777900 PMCID: PMC7994592 DOI: 10.3389/fchem.2021.637286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/21/2021] [Indexed: 12/23/2022] Open
Abstract
The structural characterization of clusters or nanoparticles is essential to rationalize their size and composition-dependent properties. As experiments alone could not provide complete picture of cluster structures, so independent theoretical investigations are needed to find out a detail description of the geometric arrangement and corresponding properties of the clusters. The potential energy surfaces (PES) are explored to find several minima with an ultimate goal of locating the global minima (GM) for the clusters. Optimization algorithms, such as genetic algorithm (GA), basin hopping method and its variants, self-consistent basin-to-deformed-basin mapping, heuristic algorithm combined with the surface and interior operators (HA-SIO), fast annealing evolutionary algorithm (FAEA), random tunneling algorithm (RTA), and dynamic lattice searching (DLS) have been developed to solve the geometrical isomers in pure elemental clusters. Various model or empirical potentials (EPs) as Lennard-Jones (LJ), Born-Mayer, Gupta, Sutton-Chen, and Murrell-Mottram potentials are used to describe the bonding in different type of clusters. Due to existence of a large number of homotops in nanoalloys, genetic algorithm, basin-hopping algorithm, modified adaptive immune optimization algorithm (AIOA), evolutionary algorithm (EA), kick method and Knowledge Led Master Code (KLMC) are also used. In this review the optimization algorithms, computational techniques and accuracy of results obtained by using these mechanisms for different types of clusters will be discussed.
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34
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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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35
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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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36
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Exploration of Free Energy Surface and Thermal Effects on Relative Population and Infrared Spectrum of the Be 6B 11- Flux-Ional Cluster. MATERIALS 2020; 14:ma14010112. [PMID: 33383889 PMCID: PMC7796227 DOI: 10.3390/ma14010112] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 02/06/2023]
Abstract
The starting point to understanding cluster properties is the putative global minimum and all the nearby local energy minima; however, locating them is computationally expensive and difficult. The relative populations and spectroscopic properties that are a function of temperature can be approximately computed by employing statistical thermodynamics. Here, we investigate entropy-driven isomers distribution on Be6B11− clusters and the effect of temperature on their infrared spectroscopy and relative populations. We identify the vibration modes possessed by the cluster that significantly contribute to the zero-point energy. A couple of steps are considered for computing the temperature-dependent relative population: First, using a genetic algorithm coupled to density functional theory, we performed an extensive and systematic exploration of the potential/free energy surface of Be6B11− clusters to locate the putative global minimum and elucidate the low-energy structures. Second, the relative populations’ temperature effects are determined by considering the thermodynamic properties and Boltzmann factors. The temperature-dependent relative populations show that the entropies and temperature are essential for determining the global minimum. We compute the temperature-dependent total infrared spectra employing the Boltzmann factor weighted sums of each isomer’s infrared spectrum and find that at finite temperature, the total infrared spectrum is composed of an admixture of infrared spectra that corresponds to the spectra of the lowest-energy structure and its isomers located at higher energies. The methodology and results describe the thermal effects in the relative population and the infrared spectra.
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37
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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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38
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Watanabe K, Takagi M, Watanabe A, Murata S, Takita R. Cu(I)/sucrose-catalyzed hydroxylation of arenes in water: the dual role of sucrose. Org Biomol Chem 2020; 18:7827-7831. [PMID: 32990294 DOI: 10.1039/d0ob01683g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A protocol for the hydroxylation of aryl halides catalyzed by copper(i) and sucrose in neat water has been developed. The dual role of sucrose, the reaction pathway, and the high selectivity for hydroxylation were investigated using a combination of experimental and theoretical techniques.
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Affiliation(s)
- Kohei Watanabe
- One-stop Sharing Facility Center for Future Drug Discoveries, Graduate School of Pharmaceutical Sciences, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, Japan.
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39
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Uchida M, Shimizu T, Shibutani R, Matsumoto Y, Ishikawa H. A comprehensive infrared spectroscopic and theoretical study on phenol-ethyldimethylsilane dihydrogen-bonded clusters in the S 0 and S 1 states. J Chem Phys 2020; 153:104305. [PMID: 32933300 DOI: 10.1063/5.0019755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To investigate microscopic characters of Si-H⋯H-O type dihydrogen bonds, we observed OH and SiH stretch bands in both the S0 and S1 states of phenol-ethyldimethylsilane (PhOH-EDMS) clusters by infrared (IR)-ultraviolet (UV) and UV-IR double resonance spectroscopies. Density functional theory (DFT) calculations and energy decomposition analysis were also performed. Structures of two isomers identified were unambiguously determined through the analysis of IR spectra and DFT calculations. To discuss the strength of dihydrogen bond in various systems, we performed theoretical calculations on clusters of EDMS with several acidic molecules in addition to PhOH. It was revealed that charge-transfer interaction energies from a bonding σ orbital of SiH bond to an anti-bonding σ* orbital of OH bond well reflect strengths of dihydrogen bonds. Additionally, it was found that the red shift of SiH stretch frequencies can be used as a crude measure of the strength of dihydrogen bonds. Relationship between the red shifts of OH/SiH stretch frequencies and various electrostatic components of the interaction energy was examined. In the S1 state, large increases in red shifts were observed for both the OH and SiH stretch frequencies. Since the EDMS moiety is not associated with the electronic excitation in a cluster, the strength of dihydrogen bonds in the S1 and S0 states was able to be directly compared based on the red shifts of the SiH stretch bands. A significant increase in the red shift of SiH stretch frequency indicates a strengthening of the dihydrogen bonds during the electronic excitation of the PhOH moiety.
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Affiliation(s)
- Masaaki Uchida
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
| | - Takutoshi Shimizu
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
| | - Ryo Shibutani
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
| | - Yoshiteru Matsumoto
- Department of Chemistry, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Haruki Ishikawa
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
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40
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Watanabe K, Kawashima Y, Mukai C, Takagi T, Suwa Y, Tian YS, Kawashita N. A Comparison between the Cycloadditions of Allenyl- and Vinyl-Cyclopentanes Using Density Functional Theory and GRRM Program. Chem Pharm Bull (Tokyo) 2020; 68:737-741. [DOI: 10.1248/cpb.c20-00144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Kazuki Watanabe
- Graduate School of Pharmaceutical Sciences, Osaka University
| | | | - Chisato Mukai
- Organization of Frontier Science and Innovation, Kanazawa University
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Yukinori Suwa
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Yu-Shi Tian
- Graduate School of Pharmaceutical Sciences, Osaka University
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41
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Water Radical Cations in the Gas Phase: Methods and Mechanisms of Formation, Structure and Chemical Properties. Molecules 2020; 25:molecules25153490. [PMID: 32751962 PMCID: PMC7435662 DOI: 10.3390/molecules25153490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/02/2022] Open
Abstract
Water radical cations, (H2O)n+•, are of great research interest in both fundamental and applied sciences. Fundamental studies of water radical reactions are important to better understand the mechanisms of natural processes, such as proton transfer in aqueous solutions, the formation of hydrogen bonds and DNA damage, as well as for the discovery of new gas-phase reactions and products. In applied science, the interest in water radicals is prompted by their potential in radiobiology and as a source of primary ions for selective and sensitive chemical ionization. However, in contrast to protonated water clusters, (H2O)nH+, which are relatively easy to generate and isolate in experiments, the generation and isolation of radical water clusters, (H2O)n+•, is tremendously difficult due to their ultra-high reactivity. This review focuses on the current knowledge and unknowns regarding (H2O)n+• species, including the methods and mechanisms of their formation, structure and chemical properties.
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42
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Midoro Y, Kodaya Y, Oki T, Mukai A, Yamakado H, Ohno K. Conformation Search of Glycine by Applying the Scaled Hypersphere Search Method to Discrete Atoms in the Molecule. CHEM LETT 2020. [DOI: 10.1246/cl.200239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yuuki Midoro
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Yoshitomo Kodaya
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Takuto Oki
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Akira Mukai
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Hideo Yamakado
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Koichi Ohno
- Institute for Quantum Chemical Exploration, 1-9-36 Konan, Minato-ku, Tokyo 108-0075, Japan
- Graduate School of Science, Tohoku University, 6-3 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
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43
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Mitsuta Y, Shigeta Y. Analytical Method Using a Scaled Hypersphere Search for High-Dimensional Metadynamics Simulations. J Chem Theory Comput 2020; 16:3869-3878. [PMID: 32384233 DOI: 10.1021/acs.jctc.0c00010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Metadynamics (MTD) is one of the most effective methods for calculating the free energy surface and finding rare events. Nevertheless, numerous studies using MTD have been carried out using 3D or lower dimensional collective variables (CVs), as higher dimensional CVs require costly computational resources and the obtained results are too complex to understand the important events. The latter issue can be conveniently solved by utilizing the free energy reaction network (FERN), which is a graph structure consisting of edges of minimum free energy paths (MFEPs), nodes of equation (EQ) points, and transition state (TS) points. In the present article, a new method for exploring FERNs on high-dimensional CVs using MTD and the scaled hypersphere search (SHS) method is described. A test calculation based on the MTD-SHS simulation of met-enkephalin in explicit water with 7 CVs was conducted. As a result, 889 EQ points and 1805 TS points were found. The MTD-SHS approach can find MFEPs exhaustively; therefore, the FERNs can be estimated without any a priori knowledge of the EQ and TS points.
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Affiliation(s)
- Yuki Mitsuta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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44
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Uchida M, Shimizu T, Matsumoto Y, Ishikawa H. An effective Hamiltonian analysis of a Franck-Condon-like pattern in the IR spectra of phenol-alkylsilane dihydrogen-bonded clusters in the S 1 state. J Chem Phys 2020; 152:194306. [PMID: 33687225 DOI: 10.1063/5.0005259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Infrared (IR) spectra in a region of the OH stretch band of phenol (PhOH)-ethyldimethylsilane (EDMS), phenol (PhOH)-triethylsilane (TES), and phenol (PhOH)-t-butyldimethylsilane (BDMS) dihydrogen-bonded clusters in the S1 state were observed. All of the species exhibited unconventional band patterns in which many combination bands appeared with comparable intensities to those of allowed bands. Such a behavior is sometimes called a Franck-Condon-like pattern. In the case of the PhOH-BDMS, one intermolecular vibrational mode is involved in this behavior. The observed IR spectra were well reproduced based on the concept of the Franck-Condon-like behavior. As an alternative treatment, we analyzed the band patterns on the concept of intensity borrowing due to the vibrational anharmonic interaction. The analysis was based on an effective Hamiltonian involving an anharmonic interaction between the OH stretch and intermolecular vibrational modes. Two treatments provided the same results. Thus, it was confirmed that the Franck-Condon-like behavior originates from vibrational anharmonic interactions. In the cases of the PhOH-EDMS and PhOH-TES, we carried out a two-dimensional Franck-Condon and an effective Hamiltonian analysis to interpret the Franck-Condon-like patterns. We examined vibrational wave functions obtained by the latter analysis. Shapes of the wave functions suggest that a recombination of the intermolecular vibrational modes occurs during the excitation of OH stretch mode in these clusters, which is a similar behavior to the Duschinsky effect in the electronic transition.
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Affiliation(s)
- Masaaki Uchida
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
| | - Takutoshi Shimizu
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
| | - Yoshiteru Matsumoto
- Department of Chemistry, Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Haruki Ishikawa
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Japan
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45
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Sato H, Yamazaki M, Uchiyama M. DFT Study on the Biosynthesis of Preasperterpenoid A: Role of Secondary Carbocations in the Carbocation Cascade. Chem Pharm Bull (Tokyo) 2020; 68:487-490. [PMID: 32378547 DOI: 10.1248/cpb.c20-00037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Preasperterpenoid A, featuring a 5/7/(3)6/5 pentacyclic structure, is a C25 sesterterpenoid produced by Penicillium verruculosum. The results of density functional calculations on putative biosynthetic carbocation cyclization/rearrangements leading to preasperterpenoid A revealed a highly concerted four-step cyclization mechanism. Interestingly, two secondary carbocation structures were obtained as minima, but appeared almost as shoulders in the energy profile, and may represent essentially transient structures during the highly concerted reaction.
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Affiliation(s)
- Hajime Sato
- Graduate School of Pharmaceutical Sciences, Chiba University.,Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Masanobu Uchiyama
- Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN.,Graduate School of Pharmaceutical Sciences, The University of Tokyo.,Research Initiative for Supra-Materials (RISM), Shinshu University
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46
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Quantum chemical exploration of polymerized forms of polycyclic aromatic hydrocarbons: D6h tetramer and polymer of coronene. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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47
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Saito K, Watabe Y, Fujihara T, Takayanagi T, Hasegawa JY. Spin-inversion mechanisms in O 2 binding to a model heme complex revisited by density function theory calculations. J Comput Chem 2020; 41:1130-1138. [PMID: 32020659 DOI: 10.1002/jcc.26159] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/12/2020] [Accepted: 01/16/2020] [Indexed: 01/10/2023]
Abstract
Spin-inversion mechanisms in O2 binding to a model heme complex, consisting of Fe(II)-porphyrin and imidazole, were investigated using density-functional theory calculations. First, we applied the recently proposed mixed-spin Hamiltonian method to locate spin-inversion structures between different total spin multiplicities. Nine spin-inversion structures were successfully optimized for the singlet-triplet, singlet-quintet, triplet-quintet, and quintet-septet spin-inversion processes. We found that the singlet-triplet spin-inversion points are located around the potential energy surface region at short Fe-O distances, whereas the singlet-quintet and quintet-septet spin-inversion points are located at longer Fe-O distances. This suggests that both narrow and broad crossing models play roles in O2 binding to the Fe-porphyrin complex. To further understand spin-inversion mechanisms, we performed on-the-fly Born-Oppenheimer molecular dynamics calculations. The reaction coordinates, which are correlated to the spin-inversion dynamics between different spin multiplicities, are also discussed.
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Affiliation(s)
- Kohei Saito
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Yuya Watabe
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Takashi Fujihara
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Toshiyuki Takayanagi
- Department of Chemistry, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Jun-Ya Hasegawa
- Instituteof Catalysis, Hokkaido University, Kita 21, Nishi 10, Kita-ku, Sapporo, Hokkaido, 001-0021, Japan
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48
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Matsuda Y, Hirano Y, Mizutani S, Sakai D, Fujii A, Maeda S, Ohno K. Migrations and Catalytic Action of Water Molecules in the Ionized Formamide-(H 2O) 2 Cluster. J Phys Chem A 2020; 124:2802-2807. [PMID: 32187496 DOI: 10.1021/acs.jpca.0c00637] [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
Isomerization dynamics involving the migrations, proton transfer reaction, and catalytic actions of water molecules upon vertical ionization of the formamide (FA)-(H2O)2 cluster is investigated by the infrared spectroscopy and theoretical reaction path search calculation. The infrared spectroscopic result indicates the [FA-(H2O)2]+ cation has the hydrogen-bonded structure of the enol isomer cation of formamide and the water dimer. This structure is formed by proton transfer from the CH bond to the carbonyl group through the catalytic action of the water molecules. The isomerization paths involving this enolization in ionized FA-(H2O)2 are explored by using the anharmonic downward distortion following method. We found multiple enolization paths which accompany proton exchanges among the formamide moiety and water molecules through the catalytic actions of the water molecules.
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Affiliation(s)
- Yoshiyuki Matsuda
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Yutaro Hirano
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Shinichi Mizutani
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Daichi Sakai
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Asuka Fujii
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, 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.,National Institute for Materials Science (NIMS) Research and Services Division of Materials Data and Integrated System (MaDIS) Tsukuba, 305-0044, Japan
| | - Koichi Ohno
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8578, Japan.,Institute for Quantum Chemical Exploration, 13F Area Shinagawa, Konan 1-9-36, Minato-ku, Tokyo, 108-0075, Japan
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49
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Miwa Y, Kurachi J, Sugino Y, Udagawa T, Kutsumizu S. Toward strong self-healing polyisoprene elastomers with dynamic ionic crosslinks. SOFT MATTER 2020; 16:3384-3394. [PMID: 32073111 DOI: 10.1039/d0sm00058b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
To compromise high mechanical strength and efficient self-healing capability in an elastomer with dynamic crosslinks, optimization of the molecular structure is crucial in addition to the tuning of the dynamic properties of the crosslinks. Herein, we studied the effects of molecular weight, content of carboxy groups, and neutralization level of ionically crosslinked polyisoprene (PI) elastomers on their morphology, network rearrangement behavior, and self-healing and mechanical properties. In this PI elastomer, nanosized sphere-shaped ionic aggregates are formed by both neutralized and non-neutralized carboxy groups that act as stickers. The number density of the ionic aggregates that act as physical crosslinks increased with increase in the stickers' concentration, although the size of the ionic aggregates was independent of the molecular weight and the stickers' concentration. The ionic network was dynamically rearranged by the stickers' hopping between the ionic aggregates, and the rearrangement was accelerated by decreasing the neutralization level. We found that the 2Rg of the PI must be significantly larger than the average distance between the ionic aggregates to obtain a mechanically strong PI elastomer. We also found that further increase in the molecular weight is effective to enhance the dimensional stability of the elastomer. However, this approach reduced the elastomer's self-healing rate at the same time because the diffusion and randomization of the polymer chains between the damaged faces were reduced. In this work, we clearly demonstrated the principle in the optimization of the molecular structure for the ionically crosslinked PI elastomers to tune the mechanical and autonomous self-healing properties.
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Affiliation(s)
- Yohei Miwa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido, Gifu 501-1193, Japan and PRESTO, Japan Science and Technology Agency, Japan
| | - Junosuke Kurachi
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido, Gifu 501-1193, Japan
| | - Yusuke Sugino
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido, Gifu 501-1193, Japan
| | - Taro Udagawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido, Gifu 501-1193, Japan
| | - Shoichi Kutsumizu
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido, Gifu 501-1193, Japan
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50
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Zhang Z, Nie W, Sun F, Zhang Y, Xie M, Hu Y. Conformational Landscapes and Infrared Spectra of Gas-phase Interstellar Molecular Clusters [(C 3H 3N)(CH 3OH) n, n = 1-4]. J Phys Chem A 2020; 124:2398-2407. [PMID: 32149507 DOI: 10.1021/acs.jpca.9b11387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acrylonitrile (A) is one of the important interstellar molecules, which is considered closely related to the origin of life. And methanol (M) is one of the commonly used solvents, which is also found in outer space. Herein, we obtained the infrared (IR) spectra of size-selected AMn (n = 1-4) clusters in supersonic jet by monitoring their fragments of H+AMn-1 (n = 1-4) with vacuum ultraviolet single-photon soft ionization/IR-depletion technique. IR spectra of AMn (n = 1-4) clusters were recorded in the CH and OH vibration bands in the range of 2700-3800 cm-1. Spectra of AMn (n = 1-4) clusters are similar in the CH stretching regions, while those show significant variations in the OH stretching regions with the increase of methanol molecules. Calculated IR spectra, which were predicted with the B3LYP-D3(BJ)/aug-cc-pVDZ method, were employed to compare with the experimental results. For AM, AM2, and AM3, the structures with the methanol cyclic hydrogen bonded with [N1-C4(H6)] of acrylonitrile are more stable than the other H-bonded structures. For the most stable structures of AM4, however, the results show that the acrylonitrile is binding to a H-bonded ring formed by OH groups of four methanol molecules. The AM, AM2, and AM3 conformers with the single ring on the C1 side of acrylonitrile, such as C1-AM-a, C1-AM2-a, and C1-AM3-a, are dominant in the gas phase, while the C2-AM4-a conformer with the H-bonded ring formed by the OH groups on the C2 side of acrylonitrile is more stable than that of CM4-A-a in our experimental conditions (>130 K). These findings may provide valuable insight into the microsolvation process of the interstellar molecules and other biomolecules in gas phase.
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Affiliation(s)
- Zhaoli Zhang
- MOE & Guangdong Province Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
| | - Wuyi Nie
- MOE & Guangdong Province Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
| | - Fufei Sun
- MOE & Guangdong Province Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
| | - Yu Zhang
- MOE & Guangdong Province Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
| | - Min Xie
- MOE & Guangdong Province Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
| | - Yongjun Hu
- MOE & Guangdong Province Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou 510631, P. R. China
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