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K P S, Russelisaac Premakumari S, Cho KB, Lee A. Hydrosulfonylation of Alkynes for Stereodivergent Synthesis of Vinyl Sulfones: Synthetic Strategy and Mechanistic Insights. J Am Chem Soc 2024; 146:14816-14828. [PMID: 38752975 DOI: 10.1021/jacs.4c03372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Direct synthesis of thermodynamically less favorable (Z)-vinyl sulfones presents a notable challenge in organic synthesis. In addition, the development of a stereodivergent synthesis for (E)- and (Z)-vinyl sulfones is crucial but remains elusive. In this study, we present a hydrosulfonylation of aryl-substituted alkynes, achieving a stereodivergent synthesis of (E)- and (Z)-vinyl sulfones by leveraging both thermodynamic and kinetic controls. Notably, the synthesis of challenging (Z)-vinyl sulfones was achieved through a kinetically controlled process without the need for a catalyst. To synthesize (E)-vinyl sulfones, unconventional visible light-mediated isomerization was employed as a means of facilitating the transition to the thermodynamically favored form. The present study encompasses a comprehensive experimental and computational investigation, which provides valuable insights into the reaction mechanism. This investigation reveals two plausible isomerization pathways: a novel double spin-flip mechanism and a hydrogen atom transfer process in the presence of eosin Y. This study not only advances our understanding of isomerization mechanisms beyond conventional energy-transfer routes but also offers a robust and switchable strategy for synthesizing (E)- and (Z)-vinyl sulfones, thereby providing a versatile avenue for the creation of valuable compounds in the fields of organic synthesis and medicinal chemistry.
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Affiliation(s)
- Sujith K P
- Department of Chemistry and Research Institute of Physics and Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Steiny Russelisaac Premakumari
- Department of Chemistry and Research Institute of Physics and Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Kyung-Bin Cho
- Department of Chemistry and Research Institute of Physics and Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Anna Lee
- Department of Chemistry and Research Institute of Physics and Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
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2
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Dergachev ID, Dergachev VD, Rooein M, Mirzanejad A, Varganov SA. Predicting Kinetics and Dynamics of Spin-Dependent Processes. Acc Chem Res 2023; 56:856-866. [PMID: 36926853 DOI: 10.1021/acs.accounts.2c00843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
ConspectusPredicting mechanisms and rates of nonadiabatic spin-dependent processes including photoinduced intersystem crossings, thermally activated spin-forbidden reactions, and spin crossovers in metal centers is a very active field of research. These processes play critical roles in transition-metal-based and metalloenzymatic catalysis, molecular magnets, light-harvesting materials, organic light-emitting diodes, photosensitizers for photodynamic therapy, and many other applications. Therefore, accurate modeling of spin-dependent processes in complex systems and on different time scales is important for many problems in chemistry, biochemistry, and materials sciences.Nonadiabatic statistical theory (NAST) and nonadiabatic molecular dynamics (NAMD) are two complementary approaches to modeling the kinetics and dynamics of spin-dependent processes. NAST predicts the probabilities and rate constants of nonradiative transitions between electronic states with different spin multiplicities using molecular properties at only few critical points on the potential energy surfaces (PESs), including the reactant minimum and the minimum energy crossing point (MECP) between two spin states. This makes it possible to obtain molecular properties for NAST calculations using accurate but often computationally expensive electronic structure methods, which is critical for predicting the rate constants of spin-dependent processes. Alternatively, NAST can be used to study spin-dependent processes in very large complex molecular systems using less computationally expensive electronic structure methods. The nuclear quantum effects, such as zero-point vibrational energy, tunneling, and interference between reaction paths can be easily incorporated. However, the statistical and local nature of NAST makes it more suitable for large systems and slow kinetics. In contrast, NAMD explores entire PESs of interacting electronic states, making it ideal for modeling fast barrierless spin-dependent processes. Because the knowledge of large portions of PESs is often needed, the simulations require a very large number of electronic structure calculations, which limits the NAMD applicability to relatively small molecular systems and ultrafast kinetics.In this Account, we discuss our contribution to the development of the NAST and NAMD approaches for predicting the rates and mechanism of spin-dependent processes. First, we briefly describe our NAST and NAMD implementations. The NAST implementation is an extension of the transition state theory to the processes involving two crossing potential energy surfaces of different spin multiplicities. The NAMD approach includes the trajectory surface hopping (TSH) and ab initio multiple spawning (AIMS) methods. Second, we discuss several applications of NAST and NAMD to model spin-dependent processes in different systems. The NAST applicability to large complex systems is demonstrated by the studies of the spin-forbidden isomerization of the active sites of metal-sulfur proteins. Our implementation of the MECP search algorithm within the fully ab initio fragment molecular orbital method allows applying NAST to systems with thousands of atoms, such as the solvated protein rubredoxin. Applications of NAMD to ultrafast spin-dependent processes are represented by the generalized AIMS simulations utilizing the fast GPU-based TeraChem electronic structure program to gain insight into the complex photoexcited state relaxation in 2-cyclopentenone.
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Affiliation(s)
- Ilya D Dergachev
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
| | - Vsevolod D Dergachev
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
| | - Mitra Rooein
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
| | - Amir Mirzanejad
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
| | - Sergey A Varganov
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
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Mirzanejad A, Varganov SA. The role of the intermediate triplet state in iron-catalyzed multi-state C-H activation. Phys Chem Chem Phys 2022; 24:20721-20727. [PMID: 36018581 DOI: 10.1039/d2cp02733j] [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
Efficient activation and functionalization of the C-H bond under mild conditions are of a great interest in chemical synthesis. We investigate the previously proposed spin-accelerated activation of the C(sp2)-H bond by a Fe(II)-based catalyst to clarify the role of the intermediate triplet state in the reaction mechanism. High-level electronic structure calculations on a small model of a catalytic system utilizing the coupled cluster with the single, double, and perturbative triple excitations [CCSD(T)] are used to select the density functional for the full-size model. Our analysis indicates that the previously proposed two-state quintet-singlet reaction pathway is unlikely to be efficient due to a very weak spin-orbit coupling between these two spin states. We propose a more favorable multi-state quintet-triplet-singlet reaction pathway and discuss the importance of the intermediate triplet state. This triplet state facilitates a spin-accelerated reaction mechanism by strongly coupling to both quintet and singlet states. Our calculations show that the C-H bond activation through the proposed quintet-triplet-singlet reaction pathway is more thermodynamically favorable than the single-state quintet and two-state singlet-quintet mechanisms.
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Affiliation(s)
- Amir Mirzanejad
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV 89557-0216, USA.
| | - Sergey A Varganov
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV 89557-0216, USA.
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Mališ M, Vandaele E, Luber S. Spin-Orbit Couplings for Nonadiabatic Molecular Dynamics at the ΔSCF Level. J Chem Theory Comput 2022; 18:4082-4094. [PMID: 35666703 DOI: 10.1021/acs.jctc.1c01046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A procedure for the calculation of spin-orbit coupling (SOC) at the delta self-consistent field (ΔSCF) level of theory is presented. Singlet and triplet excited electronic states obtained with the ΔSCF method are expanded into a linear combination of singly excited Slater determinants composed of ground electronic state Kohn-Sham orbitals. This alleviates the nonorthogonality between excited and ground electronic states and introduces a framework, similar to the auxiliary wave function at the time-dependent density functional theory (TD-DFT) level, for the calculation of observables. The ΔSCF observables of the formaldehyde system were compared to reference TD-DFT values. Our procedure gives all components (energies, gradients, nonadiabatic couplings, and SOC terms) at the ΔSCF level of theory for conducting efficient, full-atomistic nonadiabatic molecular dynamics with intersystem crossing, particularly in condensed phase systems.
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Affiliation(s)
- Momir Mališ
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Eva Vandaele
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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NAST: Nonadiabatic Statistical Theory Package for Predicting Kinetics of Spin-Dependent Processes. Top Curr Chem (Cham) 2022; 380:15. [PMID: 35201520 DOI: 10.1007/s41061-022-00366-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/15/2022] [Indexed: 10/19/2022]
Abstract
We present a nonadiabatic statistical theory (NAST) package for predicting kinetics of spin-dependent processes, such as intersystem crossings, spin-forbidden unimolecular reactions, and spin crossovers. The NAST package can calculate the probabilities and rates of transitions between the electronic states of different spin multiplicities. Both the microcanonical (energy-dependent) and canonical (temperature-dependent) rate constants can be obtained. Quantum effects, including tunneling, zero-point vibrational energy, and reaction path interference, can be accounted for. In the limit of an adiabatic unimolecular reaction proceeding on a single electronic state, NAST reduces to the traditional transition state theory. Because NAST requires molecular properties at only a few points on potential energy surfaces, it can be applied to large molecular systems, used with accurate high-level electronic structure methods, and employed to study slow nonadiabatic processes. The essential NAST input data include the nuclear Hessian at the reactant minimum, as well as the nuclear Hessians, energy gradients, and spin-orbit coupling at the minimum energy crossing point (MECP) between two states. The additional computational tools included in the NAST package can be used to extract the required input data from the output files of electronic structure packages, calculate the effective Hessian at the MECP, and fit the reaction coordinate for more advanced NAST calculations. We describe the theory, its implementation, and three examples of application to different molecular systems.
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Treviño RE, Shafaat HS. Protein-based models offer mechanistic insight into complex nickel metalloenzymes. Curr Opin Chem Biol 2022; 67:102110. [PMID: 35101820 DOI: 10.1016/j.cbpa.2021.102110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/22/2021] [Accepted: 12/06/2021] [Indexed: 11/03/2022]
Abstract
There are ten nickel enzymes found across biological systems, each with a distinct active site and reactivity that spans reductive, oxidative, and redox-neutral processes. We focus on the reductive enzymes, which catalyze reactions that are highly germane to the modern-day climate crisis: [NiFe] hydrogenase, carbon monoxide dehydrogenase, acetyl coenzyme A synthase, and methyl coenzyme M reductase. The current mechanistic understanding of each enzyme system is reviewed along with existing knowledge gaps, which are addressed through the development of protein-derived models, as described here. This opinion is intended to highlight the advantages of using robust protein scaffolds for modeling multiscale contributions to reactivity and inspire the development of novel artificial metalloenzymes for other small molecule transformations.
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Affiliation(s)
- Regina E Treviño
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.
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7
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Farcaş AA, Bende A. Theoretical modeling of the singlet-triplet spin transition in different Ni(II)-diketo-pyrphyrin-based metal-ligand octahedral complexes. Phys Chem Chem Phys 2021; 23:4784-4795. [PMID: 33599640 DOI: 10.1039/d0cp05366j] [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
The structural stability, charge transfer effects and strength of the spin-orbit couplings in different Ni(ii)-ligand complexes have been studied at the DFT (B3LYP and CAM-B3LYP) and coupled cluster (DLPNO-CCSD(T)) levels of theory. Accordingly, two different, porphyrin- and diketo-pyrphyrin-based four-coordination macrocycles as planar ligands as well as pyridine (or pyrrole) and mesylate anion molecular groups as vertical ligands were considered in order to build metal-organic complexes with octahedral coordination configurations. For each molecular system, the identification of equilibrium geometries and the intersystem crossing (the minimum energy crossing) points between the potential energy surfaces of the singlet and triplet spin states is followed by computing the spin-orbit couplings between the two spin states. Structures, based on the diketo-pyrphyrin macrocycle as the planar ligand, show stronger six-coordination metal-organic complexes due to the extra electrostatic interaction between the positively charged central metal cation and the negatively charged vertical ligands. The results also show that the magnitude of the spin-orbit coupling is influenced by the atomic positions of deprotonations of the ligands, and implicitly the direction of the charge transfer between the ligand and the central metal ion.
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Affiliation(s)
- Alex-Adrian Farcaş
- Faculty of Physics, "Babeş-Bolyai" University, Mihail Kogalniceanu Street No. 1, Ro-400084 Cluj-Napoca, Romania
| | - Attila Bende
- Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, Donat Street, No. 67-103, Ro-400293 Cluj-Napoca, Romania.
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8
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Nelson TR, White AJ, Bjorgaard JA, Sifain AE, Zhang Y, Nebgen B, Fernandez-Alberti S, Mozyrsky D, Roitberg AE, Tretiak S. Non-adiabatic Excited-State Molecular Dynamics: Theory and Applications for Modeling Photophysics in Extended Molecular Materials. Chem Rev 2020; 120:2215-2287. [PMID: 32040312 DOI: 10.1021/acs.chemrev.9b00447] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Optically active molecular materials, such as organic conjugated polymers and biological systems, are characterized by strong coupling between electronic and vibrational degrees of freedom. Typically, simulations must go beyond the Born-Oppenheimer approximation to account for non-adiabatic coupling between excited states. Indeed, non-adiabatic dynamics is commonly associated with exciton dynamics and photophysics involving charge and energy transfer, as well as exciton dissociation and charge recombination. Understanding the photoinduced dynamics in such materials is vital to providing an accurate description of exciton formation, evolution, and decay. This interdisciplinary field has matured significantly over the past decades. Formulation of new theoretical frameworks, development of more efficient and accurate computational algorithms, and evolution of high-performance computer hardware has extended these simulations to very large molecular systems with hundreds of atoms, including numerous studies of organic semiconductors and biomolecules. In this Review, we will describe recent theoretical advances including treatment of electronic decoherence in surface-hopping methods, the role of solvent effects, trivial unavoided crossings, analysis of data based on transition densities, and efficient computational implementations of these numerical methods. We also emphasize newly developed semiclassical approaches, based on the Gaussian approximation, which retain phase and width information to account for significant decoherence and interference effects while maintaining the high efficiency of surface-hopping approaches. The above developments have been employed to successfully describe photophysics in a variety of molecular materials.
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Affiliation(s)
- Tammie R Nelson
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Alexander J White
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Josiah A Bjorgaard
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Andrew E Sifain
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States.,U.S. Army Research Laboratory , Aberdeen Proving Ground , Maryland 21005 , United States
| | - Yu Zhang
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Benjamin Nebgen
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | | | - Dmitry Mozyrsky
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Adrian E Roitberg
- Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - Sergei Tretiak
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
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9
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Kaliakin DS, Fedorov DG, Alexeev Y, Varganov SA. Locating Minimum Energy Crossings of Different Spin States Using the Fragment Molecular Orbital Method. J Chem Theory Comput 2019; 15:6074-6084. [DOI: 10.1021/acs.jctc.9b00641] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Danil S. Kaliakin
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
| | - Yuri Alexeev
- Computational Science Division and Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Sergey A. Varganov
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, Nevada 89557-0216, United States
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10
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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: 0.6] [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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11
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Fedorov DA, Lykhin AO, Varganov SA. Predicting Intersystem Crossing Rates with AIMS-DFT Molecular Dynamics. J Phys Chem A 2018. [PMID: 29533626 DOI: 10.1021/acs.jpca.8b00883] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dmitry A. Fedorov
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557-0216, United States
| | - Aleksandr O. Lykhin
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557-0216, United States
- Department of Chemistry, Siberian Federal University, 79 Svobodny Prospect, Krasnoyarsk, Krasnoyarsk krai, 660041, Russia
| | - Sergey A. Varganov
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557-0216, United States
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12
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Dong G, Ryde U, Aa. Jensen HJ, Hedegård ED. Exploration of H2 binding to the [NiFe]-hydrogenase active site with multiconfigurational density functional theory. Phys Chem Chem Phys 2018; 20:794-801. [DOI: 10.1039/c7cp06767d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The combination of density functional theory (DFT) with a multiconfigurational wave function is an efficient way to include dynamical correlation in calculations with multiconfiguration self-consistent field wave functions.
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Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
| | - Hans Jørgen Aa. Jensen
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- DK-5230 Odense M
- Denmark
| | - Erik D. Hedegård
- Department of Theoretical Chemistry
- Lund University
- Chemical Centre
- SE-221 00 Lund
- Sweden
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13
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Activation of acetonitrile by gas-phase uranium: bond structure analysis and spin–flip reaction mechanism. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2137-4] [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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14
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Quantum chemical approaches to [NiFe] hydrogenase. Essays Biochem 2017; 61:293-303. [PMID: 28487405 DOI: 10.1042/ebc20160079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 11/17/2022]
Abstract
The mechanism by which [NiFe] hydrogenase catalyses the oxidation of molecular hydrogen is a significant yet challenging topic in bioinorganic chemistry. With far-reaching applications in renewable energy and carbon mitigation, significant effort has been invested in the study of these complexes. In particular, computational approaches offer a unique perspective on how this enzyme functions at an electronic and atomistic level. In this article, we discuss state-of-the art quantum chemical methods and how they have helped deepen our comprehension of [NiFe] hydrogenase. We outline the key strategies that can be used to compute the (i) geometry, (ii) electronic structure, (iii) thermodynamics and (iv) kinetic properties associated with the enzymatic activity of [NiFe] hydrogenase and other bioinorganic complexes.
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15
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Dong G, Phung QM, Hallaert SD, Pierloot K, Ryde U. H2binding to the active site of [NiFe] hydrogenase studied by multiconfigurational and coupled-cluster methods. Phys Chem Chem Phys 2017; 19:10590-10601. [DOI: 10.1039/c7cp01331k] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
CCSD(T) and DMRG-CASPT2 calculations show that H2prefers to bind to Ni rather than to Fe in [NiFe] hydrogenase.
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Affiliation(s)
- Geng Dong
- Department of Theoretical Chemistry
- Lund University
- SE-221 00 Lund
- Sweden
| | - Quan Manh Phung
- Department of Chemistry
- University of Leuven
- B-3001 Leuven
- Belgium
| | | | | | - Ulf Ryde
- Department of Theoretical Chemistry
- Lund University
- SE-221 00 Lund
- Sweden
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16
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dePolo GE, Kaliakin DS, Varganov SA. Spin-Forbidden Transitions between Electronic States in the Active Site of Rubredoxin. J Phys Chem A 2016; 120:8691-8698. [DOI: 10.1021/acs.jpca.6b07717] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gwen E. dePolo
- Department of Chemistry, University of Nevada, Reno, 1664 North
Virginia Street, Reno, Nevada 89557-0216, United States
| | - Danil S. Kaliakin
- Department of Chemistry, University of Nevada, Reno, 1664 North
Virginia Street, Reno, Nevada 89557-0216, United States
| | - Sergey A. Varganov
- Department of Chemistry, University of Nevada, Reno, 1664 North
Virginia Street, Reno, Nevada 89557-0216, United States
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Schilter D, Camara JM, Huynh MT, Hammes-Schiffer S, Rauchfuss TB. Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides. Chem Rev 2016; 116:8693-749. [PMID: 27353631 PMCID: PMC5026416 DOI: 10.1021/acs.chemrev.6b00180] [Citation(s) in RCA: 397] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or Fe active sites. Synthetic modeling of the many H2ase states has provided insight into H2ase structure and mechanism, as well as afforded catalysts for the H2 energy vector. Particularly important are hydride-bearing states, with synthetic hydride analogues now known for each hydrogenase class. These hydrides are typically prepared by protonation of low-valent cores. Examples of FeFe and NiFe hydrides derived from H2 have also been prepared. Such chemistry is more developed than mimicry of the redox-inactive monoFe enzyme, although functional models of the latter are now emerging. Advances in physical and theoretical characterization of H2ase enzymes and synthetic models have proven key to the study of hydrides in particular, and will guide modeling efforts toward more robust and active species optimized for practical applications.
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Affiliation(s)
- David Schilter
- Center for Multidimensional Carbon Materials, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - James M. Camara
- Department of Chemistry, Yeshiva University, 500 West 185th Street, New York, New York 10033, United States
| | - Mioy T. Huynh
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Thomas B. Rauchfuss
- Department of Chemistry, University of Illinois at Urbana–Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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18
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Chambers GM, Rauchfuss TB, Arrigoni F, Zampella G. Effect of Pyramidalization of the M2(SR)2 Center: The Case of (C5H5)2Ni2(SR)2. Organometallics 2016. [DOI: 10.1021/acs.organomet.6b00068] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Geoffrey M. Chambers
- School of Chemical Sciences, University of Illinois, Urbana, Illinois 61801, United States
| | - Thomas B. Rauchfuss
- School of Chemical Sciences, University of Illinois, Urbana, Illinois 61801, United States
| | - Federica Arrigoni
- Department of Biotechnology
and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126-Milan, Italy
| | - Giuseppe Zampella
- Department of Biotechnology
and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126-Milan, Italy
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Vandemeulebroucke A, Aldag C, Stiebritz MT, Reiher M, Hilvert D. Kinetic Consequences of Introducing a Proximal Selenocysteine Ligand into Cytochrome P450cam. Biochemistry 2015; 54:6692-703. [DOI: 10.1021/acs.biochem.5b00939] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- An Vandemeulebroucke
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Caroline Aldag
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin T. Stiebritz
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Markus Reiher
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry and ‡Laboratory of
Physical Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
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