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Ferrer M, Elguero J, Alkorta I, Azofra LM. Understanding the coupling of non-metallic heteroatoms to CO 2 from a Conceptual DFT perspective. J Mol Model 2024; 30:201. [PMID: 38853233 PMCID: PMC11162977 DOI: 10.1007/s00894-024-05992-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/23/2024] [Indexed: 06/11/2024]
Abstract
CONTEXT A Conceptual DFT (CDFT) study has been carry out to analyse the coupling reactions of the simplest amine (CH3NH2), alcohol (CH3OH), and thiol (CH3SH) compounds with CO2 to form the corresponding adducts CH3NHCO2H, CH3OCO2H, and CH3SCO2H. The reaction mechanism takes place in a single step comprising two chemical events: nucleophilic attack of the non-metallic heteroatoms to CO2 followed by hydrogen atom transfer (HAT). According to our calculations, the participation of an additional nucleophilic molecule as HAT assistant entails important decreases in activation electronic energies. In such cases, the formation of a six-membered ring in the transition state (TS) reduces the angular stress with respect to the non-assisted paths, characterised by four-membered ring TSs. Through the analysis of the energy and reaction force profiles along the intrinsic reaction coordinate (IRC), the ratio of structural reorganisation and electronic rearrangement for both activation and relaxation energies has been computed. In addition, the analysis of the electronic chemical potential and reaction electronic flux profiles confirms that the highest electronic activity as well as their changes take place in the TS region. Finally, the distortion/interaction model using an energy decomposition scheme based on the electron density along the reaction coordinate has been carried out and the relative energy gradient (REG) method has been applied to identify the most important components associated to the barriers. METHODS The theoretical calculation were performed with Gaussian-16 scientific program. The B3LYP-D3(BJ)/aug-cc-pVDZ level was used for optimization of the minima and TSs. IRC calculations has also been carried out connecting the TS with the associated minima. Conceptual-DFT (CDFT) calculations have been carried out with the Eyringpy program and in-house code. The distortion/interaction model along the reaction coordinate have used the decomposition scheme of Mandado et al. and the analysis of the importance of each components have been done with the relative energy gradient (REG) method.
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Affiliation(s)
- Maxime Ferrer
- Instituto de Química Médica, CSIC, Juan de La Cierva,3, 28006, Madrid, Spain
- PhD Program in Theoretical Chemistry and Computational Modelling, Doctoral School, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - José Elguero
- Instituto de Química Médica, CSIC, Juan de La Cierva,3, 28006, Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de La Cierva,3, 28006, Madrid, Spain.
| | - Luis Miguel Azofra
- Instituto de Estudios Ambientales y Recursos Naturales (iUNAT), Universidad de Las Palmas de Gran Canaria (ULPGC), Campus de Tafira, 35017, Las Palmas de Gran Canaria, Spain.
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2
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Orio M, Pantazis DA. Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research. Chem Commun (Camb) 2021; 57:3952-3974. [DOI: 10.1039/d1cc00705j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Overview of the rich and diverse contributions of quantum chemistry to understanding the structure and function of the biological archetypes for solar fuel research, photosystem II and hydrogenases.
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Affiliation(s)
- Maylis Orio
- Aix-Marseille Université
- CNRS
- iSm2
- Marseille
- France
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für Kohlenforschung
- Kaiser-Wilhelm-Platz 1
- 45470 Mülheim an der Ruhr
- Germany
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3
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Affiliation(s)
- Per E. M. Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Rong-Zhen Liao
- Key Laboratory for Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Media, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 430074 Wuhan, People’s Republic of China
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4
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Azofra LM, Elguero J, Alkorta I. A Conceptual DFT Study of Phosphonate Dimers: Dianions Supported by H-Bonds. J Phys Chem A 2020; 124:2207-2214. [DOI: 10.1021/acs.jpca.9b10681] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Luis Miguel Azofra
- CIDIA-FEAM (Unidad Asociada al Consejo Superior de Investigaciones Científicas, CSIC, avalada por el Instituto de Ciencia de Materiales de Sevilla, Universidad de Sevilla), Instituto de Estudios Ambientales y Recursos Naturales (i-UNAT), Universidad de Las Palmas de Gran Canaria (ULPGC), Campus de Tafira, 35017, Las Palmas de Gran Canaria, Spain
- Departamento de Química, Universidad de Las Palmas de Gran Canaria (ULPGC), Campus de Tafira, 35017, Las Palmas de Gran Canaria, Spain
| | - José Elguero
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain
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Drosou M, Kamatsos F, Mitsopoulou CA. Recent advances in the mechanisms of the hydrogen evolution reaction by non-innocent sulfur-coordinating metal complexes. Inorg Chem Front 2020. [DOI: 10.1039/c9qi01113g] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review comments on the homogeneous HER mechanisms for catalysts carrying S-non-innocent ligands in the light of experimental and computational data.
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Affiliation(s)
- Maria Drosou
- Inorganic Chemistry Laboratory
- Department of Chemistry
- National and Kapodistrian University of Athens
- Panepistimiopolis
- Greece
| | - Fotios Kamatsos
- Inorganic Chemistry Laboratory
- Department of Chemistry
- National and Kapodistrian University of Athens
- Panepistimiopolis
- Greece
| | - Christiana A. Mitsopoulou
- Inorganic Chemistry Laboratory
- Department of Chemistry
- National and Kapodistrian University of Athens
- Panepistimiopolis
- Greece
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6
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Ilina Y, Lorent C, Katz S, Jeoung J, Shima S, Horch M, Zebger I, Dobbek H. X‐ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling by [NiFe] Hydrogenases. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yulia Ilina
- Institut für Biologie, Strukturbiologie/BiochemieHumboldt-Universität zu Berlin Philippstraße 13 10115 Berlin Germany
| | - Christian Lorent
- Institut für ChemieTechnische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Sagie Katz
- Institut für ChemieTechnische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Jae‐Hun Jeoung
- Institut für Biologie, Strukturbiologie/BiochemieHumboldt-Universität zu Berlin Philippstraße 13 10115 Berlin Germany
| | - Seigo Shima
- Max-Planck-Institut für Terrestrische Mikrobiologie Karl-von-Frisch-Str. 10 35043 Marburg Germany
| | - Marius Horch
- Institut für ChemieTechnische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
- Department of Chemistry and York Biomedical Research InstituteUniversity of York Heslington York YO10 5DD UK
| | - Ingo Zebger
- Institut für ChemieTechnische Universität Berlin Straße des 17. Juni 135 10623 Berlin Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/BiochemieHumboldt-Universität zu Berlin Philippstraße 13 10115 Berlin Germany
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Ilina Y, Lorent C, Katz S, Jeoung JH, Shima S, Horch M, Zebger I, Dobbek H. X-ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling by [NiFe] Hydrogenases. Angew Chem Int Ed Engl 2019; 58:18710-18714. [PMID: 31591784 PMCID: PMC6916344 DOI: 10.1002/anie.201908258] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Indexed: 11/23/2022]
Abstract
[NiFe] hydrogenases are complex model enzymes for the reversible cleavage of dihydrogen (H2). However, structural determinants of efficient H2 binding to their [NiFe] active site are not properly understood. Here, we present crystallographic and vibrational‐spectroscopic insights into the unexplored structure of the H2‐binding [NiFe] intermediate. Using an F420‐reducing [NiFe]‐hydrogenase from Methanosarcina barkeri as a model enzyme, we show that the protein backbone provides a strained chelating scaffold that tunes the [NiFe] active site for efficient H2 binding and conversion. The protein matrix also directs H2 diffusion to the [NiFe] site via two gas channels and allows the distribution of electrons between functional protomers through a subunit‐bridging FeS cluster. Our findings emphasize the relevance of an atypical Ni coordination, thereby providing a blueprint for the design of bio‐inspired H2‐conversion catalysts.
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Affiliation(s)
- Yulia Ilina
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Philippstraße 13, 10115, Berlin, Germany
| | - Christian Lorent
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Jae-Hun Jeoung
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Philippstraße 13, 10115, Berlin, Germany
| | - Seigo Shima
- Max-Planck-Institut für Terrestrische Mikrobiologie, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Marius Horch
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.,Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK
| | - Ingo Zebger
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Philippstraße 13, 10115, Berlin, Germany
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Qiu S, Li Q, Xu Y, Shen S, Sun C. Learning from nature: Understanding hydrogenase enzyme using computational approach. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Siyao Qiu
- Science & Technology Innovation Institute Dongguan University of Technology Dongguan China
| | - Qinye Li
- School of Chemical Engineering Monash University Clayton Victoria Australia
| | - Yongjun Xu
- Science & Technology Innovation Institute Dongguan University of Technology Dongguan China
| | - Shaohua Shen
- International Research Center for Renewable Energy, State Key Laboratory of Multiphase Flow in Power Engineering Xi'an Jiaotong University Shaanxi China
| | - Chenghua Sun
- Department of Chemistry and Biotechnology, and Center for Translational Atomaterials Swinburne University of Technology Hawthorn Victoria Australia
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9
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New insights into Fe–H$$_{2}$$ and Fe–H$$^{-}$$ bonding of a [NiFe] hydrogenase mimic: a local vibrational mode study. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2463-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Qiu S, Azofra LM, Macfarlane DR, Sun C. Hydrogen Evolution in [NiFe] Hydrogenases: A Case of Heterolytic Approach between Proton and Hydride. Inorg Chem 2019; 58:2979-2986. [DOI: 10.1021/acs.inorgchem.8b02812] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Siyao Qiu
- Science & Technology Innovation Institute, Dongguan University of Technology, Dongguan 523808, China
- School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia
| | - Luis Miguel Azofra
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Douglas R. Macfarlane
- School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Electromaterials Science (ACES), School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia
| | - Chenghua Sun
- Science & Technology Innovation Institute, Dongguan University of Technology, Dongguan 523808, China
- Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
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11
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Qiu S, Azofra LM, MacFarlane DR, Sun C. Hydrogen bonding effect between active site and protein environment on catalysis performance in H 2-producing [NiFe] hydrogenases. Phys Chem Chem Phys 2018; 20:6735-6743. [PMID: 29457815 DOI: 10.1039/c7cp07685a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction between the active site and the surrounding protein environment plays a fundamental role in the hydrogen evolution reaction (HER) in [NiFe] hydrogenases. Our density functional theory (DFT) findings demonstrate that the reaction Gibbs free energy required for the rate determining step decreases by 7.1 kcal mol-1 when the surrounding protein environment is taken into account, which is chiefly due to free energy decreases for the two H+/e- addition steps (the so-called Ni-SIa to I1, and Ni-C to Ni-R), being the largest thermodynamic impediments of the whole reaction. The variety of hydrogen bonds (H-bonds) between the amino acids and the active site is hypothesised to be the main reason for such stability: H-bonds not only work as electrostatic attractive forces that influence the charge redistribution, but more importantly, they act as an electron 'pull' taking electrons from the active site towards the amino acids. Moreover, the electron 'pull' effect through H-bonds via the S- in cysteine residues shows a larger influence on the energy profile than that via the CN- ligands on Fe.
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Affiliation(s)
- Siyao Qiu
- School of Chemistry, Faculty of Science, Monash University, Clayton, VIC 3800, Australia.
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12
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Li Q, Qiu S, He L, Zhang X, Sun C. Impact of H-termination on the nitrogen reduction reaction of molybdenum carbide as an electrochemical catalyst. Phys Chem Chem Phys 2018; 20:23338-23343. [DOI: 10.1039/c8cp04474k] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
H-Terminals can remarkably affect the performance of catalysts in nitrogen reduction.
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Affiliation(s)
- Qinye Li
- School of Chemical Engineering
- Monash University
- Clayton
- VIC 3800
- Australia
| | - Siyao Qiu
- Science & Technology Innovation Institute
- Dongguan University of Technology
- Dongguan
- China
| | - Lizhong He
- School of Chemical Engineering
- Monash University
- Clayton
- VIC 3800
- Australia
| | - Xiwang Zhang
- School of Chemical Engineering
- Monash University
- Clayton
- VIC 3800
- Australia
| | - Chenghua Sun
- Science & Technology Innovation Institute
- Dongguan University of Technology
- Dongguan
- China
- Department of Chemistry and Biotechnology
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13
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Qiu S, Azofra LM, MacFarlane DR, Sun C. Unraveling the Role of Ligands in the Hydrogen Evolution Mechanism Catalyzed by [NiFe] Hydrogenases. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01359] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Siyao Qiu
- School
of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Luis Miguel Azofra
- School
of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
- ARC
Centre of Excellence for Electromaterials Science (ACES), School of
Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Douglas R. MacFarlane
- School
of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
- ARC
Centre of Excellence for Electromaterials Science (ACES), School of
Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
| | - Chenghua Sun
- School
of Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
- ARC
Centre of Excellence for Electromaterials Science (ACES), School of
Chemistry, Faculty of Science, Monash University, Clayton, Victoria 3800, Australia
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