101
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Guillet GL, Gordon JB, Di Francesco GN, Calkins MW, Čižmár E, Abboud KA, Meisel MW, García-Serres R, Murray LJ. A Family of Tri- and Dimetallic Pyridine Dicarboxamide Cryptates: Unusual O,N,O-Coordination and Facile Access to Secondary Coordination Sphere Hydrogen Bonding Interactions. Inorg Chem 2015; 54:2691-704. [DOI: 10.1021/ic502873d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Gary L. Guillet
- Center for Catalysis, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Jesse B. Gordon
- Center for Catalysis, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Gianna N. Di Francesco
- Center for Catalysis, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Matthew W. Calkins
- Department
of Physics and the National High Magnetic Field Laboratory, University of Florida, Gainesville, Florida 32611-8440, United States
| | - Erik Čižmár
- Institute
of Physics, Faculty of Science, P.J. Šafárik University, 04154 Košice, Slovakia
| | - Khalil A. Abboud
- Center for Catalysis, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Mark W. Meisel
- Department
of Physics and the National High Magnetic Field Laboratory, University of Florida, Gainesville, Florida 32611-8440, United States
| | - Ricardo García-Serres
- Laboratoire
de Chimie de Biologie des Métaux, UMR 5249, Université Joseph Fourier, Grenoble-1, CNRS-CEA, 17 Rue des Martyrs, 38054 Grenoble Cedex 9, France
| | - Leslie J. Murray
- Center for Catalysis, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
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102
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Chatterjee S, Sengupta K, Samanta S, Das PK, Dey A. Concerted Proton–Electron Transfer in Electrocatalytic O2 Reduction by Iron Porphyrin Complexes: Axial Ligands Tuning H/D Isotope Effect. Inorg Chem 2015; 54:2383-92. [DOI: 10.1021/ic5029959] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sudipta Chatterjee
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Kushal Sengupta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Subhra Samanta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Pradip Kumar Das
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Abhishek Dey
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
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103
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Wikström M, Sharma V, Kaila VRI, Hosler JP, Hummer G. New Perspectives on Proton Pumping in Cellular Respiration. Chem Rev 2015; 115:2196-221. [DOI: 10.1021/cr500448t] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mårten Wikström
- Institute
of Biotechnology, University of Helsinki, Biocenter 3 (Viikinkaari 1), PB
65, Helsinki 00014, Finland
| | - Vivek Sharma
- Department
of Physics, Tampere University of Technology, Korkeakoulunkatu 3, Tampere 33720, Finland
| | - Ville R. I. Kaila
- Department
Chemie, Technische Universität München, Lichtenbergstraße 4, D-85748 Garching, Germany
| | - Jonathan P. Hosler
- Department
of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi 39216, United States
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße
3, 60438 Frankfurt
am Main, Germany
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104
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Cardona T, Murray JW, Rutherford AW. Origin and Evolution of Water Oxidation before the Last Common Ancestor of the Cyanobacteria. Mol Biol Evol 2015; 32:1310-28. [PMID: 25657330 PMCID: PMC4408414 DOI: 10.1093/molbev/msv024] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster (Mn4CaO5) of Photosystem II. We show that D1 exists in several forms making well-defined clades, some of which could have evolved before the origin of water oxidation and presenting many atypical characteristics. The most ancient form is found in the genome of Gloeobacter kilaueensis JS-1 and this has a C-terminus with a higher sequence identity to D2 than to any other D1. Two other groups of early evolving D1 correspond to those expressed under prolonged far-red illumination and in darkness. These atypical D1 forms are characterized by a dramatically different Mn4CaO5 binding site and a Photosystem II containing such a site may assemble an unconventional metal cluster. The first D1 forms with a full set of ligands to the Mn4CaO5 cluster are grouped with D1 proteins expressed only under low oxygen concentrations and the latest evolving form is the dominant type of D1 found in all cyanobacteria and plastids. In addition, we show that the plastid ancestor had a D1 more similar to those in early branching Synechococcus. We suggest each one of these forms of D1 originated from transitional forms at different stages toward the innovation and optimization of water oxidation before the last common ancestor of all known cyanobacteria.
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Affiliation(s)
- Tanai Cardona
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - James W Murray
- Department of Life Sciences, Imperial College London, London, United Kingdom
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105
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Cheng GJ, Zhang X, Chung LW, Xu L, Wu YD. Computational organic chemistry: bridging theory and experiment in establishing the mechanisms of chemical reactions. J Am Chem Soc 2015; 137:1706-25. [PMID: 25568962 DOI: 10.1021/ja5112749] [Citation(s) in RCA: 234] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding the mechanisms of chemical reactions, especially catalysis, has been an important and active area of computational organic chemistry, and close collaborations between experimentalists and theorists represent a growing trend. This Perspective provides examples of such productive collaborations. The understanding of various reaction mechanisms and the insight gained from these studies are emphasized. The applications of various experimental techniques in elucidation of reaction details as well as the development of various computational techniques to meet the demand of emerging synthetic methods, e.g., C-H activation, organocatalysis, and single electron transfer, are presented along with some conventional developments of mechanistic aspects. Examples of applications are selected to demonstrate the advantages and limitations of these techniques. Some challenges in the mechanistic studies and predictions of reactions are also analyzed.
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Affiliation(s)
- Gui-Juan Cheng
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
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106
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Saucedo-Vázquez JP, Kroneck PMH, Sosa-Torres ME. The role of molecular oxygen in the iron(iii)-promoted oxidative dehydrogenation of amines. Dalton Trans 2015; 44:5510-9. [DOI: 10.1039/c4dt03606a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A mechanistic study is presented of the oxidative dehydrogenation of the iron(iii) complex [FeIIIL3]3+, 1, (L3 = 1,9-bis(2′-pyridyl)-5-[(ethoxy-2′′-pyridyl)methyl]-2,5,8-triazanonane) in ethanol in the presence of molecular oxygen.
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Affiliation(s)
- Juan Pablo Saucedo-Vázquez
- Departamento de Química Inorgánica y Nuclear
- Facultad de Química
- Universidad Nacional Autónoma de México
- Ciudad Universitaria
- México, D.F. 04510
| | | | - Martha Elena Sosa-Torres
- Departamento de Química Inorgánica y Nuclear
- Facultad de Química
- Universidad Nacional Autónoma de México
- Ciudad Universitaria
- México, D.F. 04510
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107
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Dance I. The pathway for serial proton supply to the active site of nitrogenase: enhanced density functional modeling of the Grotthuss mechanism. Dalton Trans 2015; 44:18167-86. [DOI: 10.1039/c5dt03223g] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proton translocation along a chain of eight waters to the active site of nitrogenase is described in detail, using density functional simulations with a 269 atom system that includes surrounding amino acids.
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Affiliation(s)
- Ian Dance
- School of Chemistry
- UNSW Australia
- Sydney 2052
- Australia
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108
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Cassimjee KE, Manta B, Himo F. A quantum chemical study of the ω-transaminase reaction mechanism. Org Biomol Chem 2015; 13:8453-64. [DOI: 10.1039/c5ob00690b] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The detailed half-transamination mechanism of Chromobacterium violaceum ω-transaminase is investigated by means of density functional theory calculations.
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Affiliation(s)
| | - Bianca Manta
- Department of Organic Chemistry
- Arrhenius Laboratory
- Stockholm University
- SE-106 91 Stockholm
- Sweden
| | - Fahmi Himo
- Department of Organic Chemistry
- Arrhenius Laboratory
- Stockholm University
- SE-106 91 Stockholm
- Sweden
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109
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How cytochrome c oxidase can pump four protons per oxygen molecule at high electrochemical gradient. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:364-376. [PMID: 25529353 DOI: 10.1016/j.bbabio.2014.12.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 11/18/2014] [Accepted: 12/10/2014] [Indexed: 12/12/2022]
Abstract
Experiments have shown that the A-family cytochrome c oxidases pump four protons per oxygen molecule, also at a high electrochemical gradient. This has been considered a puzzle, since two of the reduction potentials involved, Cu(II) and Fe(III), were estimated from experiments to be too low to afford proton pumping at a high gradient. The present quantum mechanical study (using hybrid density functional theory) suggests a solution to this puzzle. First, the calculations show that the charge compensated Cu(II) potential for CuB is actually much higher than estimated from experiment, of the same order as the reduction potentials for the tyrosyl radical and the ferryl group, which are also involved in the catalytic cycle. The reason for the discrepancy between theory and experiment is the very large uncertainty in the experimental observations used to estimate the equilibrium potentials, mainly caused by the lack of methods for direct determination of reduced CuB. Second, the calculations show that a high energy metastable state, labeled EH, is involved during catalytic turnover. The EH state mixes the low reduction potential of Fe(III) in heme a3 with another, higher potential, here suggested to be that of the tyrosyl radical, resulting in enough exergonicity to allow proton pumping at a high gradient. In contrast, the corresponding metastable oxidized state, OH, is not significantly higher in energy than the resting state, O. Finally, to secure the involvement of the high energy EH state it is suggested that only one proton is taken up via the K-channel during catalytic turnover.
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110
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Mechanism for O-O bond formation in a biomimetic tetranuclear manganese cluster--A density functional theory study. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 152:162-72. [PMID: 25534173 DOI: 10.1016/j.jphotobiol.2014.12.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 11/25/2014] [Accepted: 12/01/2014] [Indexed: 11/21/2022]
Abstract
Density functional theory calculations have been used to study the reaction mechanism of water oxidation catalyzed by a tetranuclear Mn-oxo cluster Mn4O4L6 (L=(C6H4)2PO4(-)). It is proposed that the O-O bond formation mechanism is different in the gas phase and in a water solution. In the gas phase, upon phosphate ligand dissociation triggered by light absorption, the O-O bond formation starting with both the Mn4(III,III,IV,IV) and Mn4(III,IV,IV,IV) oxidation states has to take place via direct coupling of two bridging oxo groups. The calculated barriers are 42.3 and 37.1 kcal/mol, respectively, and there is an endergonicity of more than 10 kcal/mol. Additional photons are needed to overcome these large barriers. In water solution, water binding to the two vacant sites of the Mn ions, again after phosphate dissociation triggered by light absorption, is thermodynamically and kinetically very favorable. The catalytic cycle is suggested to start from the Mn4(III,III,III,IV) oxidation state. The removal of three electrons and three protons leads to the formation of a Mn4(III,IV,IV,IV)-oxyl radical complex. The O-O bond formation then proceeds via a nucleophilic attack of water on the Mn(IV)-oxyl radical assisted by a Mn-bound hydroxide that abstracts a proton during the attack. This step was calculated to be rate-limiting with a total barrier of 29.2 kcal/mol. This is followed by proton-coupled electron transfer, O2 release, and water binding to start the next catalytic cycle.
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111
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Liao RZ, Siegbahn PEM. Which Oxidation State Leads to O–O Bond Formation in Cp*Ir(bpy)Cl-Catalyzed Water Oxidation, Ir(V), Ir(VI), or Ir(VII)? ACS Catal 2014. [DOI: 10.1021/cs501160x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Rong-Zhen Liao
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Per E. M. Siegbahn
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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112
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Silva PJ. With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase. PeerJ 2014; 2:e551. [PMID: 25237602 PMCID: PMC4157233 DOI: 10.7717/peerj.551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 08/09/2014] [Indexed: 11/20/2022] Open
Abstract
The addition of two electrons and two protons to the C17=C18 bond in protochlorophyllide is catalyzed by a light-dependent enzyme relying on NADPH as electron donor, and by a light-independent enzyme bearing a (Cys)3Asp-ligated [4Fe–4S] cluster which is reduced by cytoplasmic electron donors in an ATP-dependent manner and then functions as electron donor to protochlorophyllide. The precise sequence of events occurring at the C17=C18 bond has not, however, been determined experimentally in the dark-operating enzyme. In this paper, we present the computational investigation of the reaction mechanism of this enzyme at the B3LYP/6-311+G(d,p)//B3LYP/6-31G(d) level of theory. The reaction mechanism begins with single-electron reduction of the substrate by the (Cys)3Asp-ligated [4Fe–4S], yielding a negatively-charged intermediate. Depending on the rate of Fe–S cluster re-reduction, the reaction either proceeds through double protonation of the single-electron-reduced substrate, or by alternating proton/electron transfer. The computed reaction barriers suggest that Fe–S cluster re-reduction should be the rate-limiting stage of the process. Poisson–Boltzmann computations on the full enzyme–substrate complex, followed by Monte Carlo simulations of redox and protonation titrations revealed a hitherto unsuspected pH-dependence of the reaction potential of the Fe–S cluster. Furthermore, the computed distributions of protonation states of the His, Asp and Glu residues were used in conjuntion with single-point ONIOM computations to obtain, for the first time, the influence of all protonation states of an enzyme on the reaction it catalyzes. Despite exaggerating the ease of reduction of the substrate, these computations confirmed the broad features of the reaction mechanism obtained with the medium-sized models, and afforded valuable insights on the influence of the titratable amino acids on each reaction step. Additional comparisons of the energetic features of the reaction intermediates with those of common biochemical redox intermediates suggest a surprisingly simple explanation for the mechanistic differences between the dark-catalyzed and light-dependent enzyme reaction mechanisms.
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Affiliation(s)
- Pedro J Silva
- REQUIMTE, Faculdade de Ciências da Saúde, Universidade Fernando Pessoa , Rua Carlos da Maia, Porto , Portugal
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113
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Shakib FA, Hanna G. An analysis of model proton-coupled electron transfer reactions via the mixed quantum-classical Liouville approach. J Chem Phys 2014; 141:044122. [DOI: 10.1063/1.4890915] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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114
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Xie X, Bakker E. Photoelectric Conversion Based on Proton-Coupled Electron Transfer Reactions. J Am Chem Soc 2014; 136:7857-60. [DOI: 10.1021/ja503491k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xiaojiang Xie
- Department of Inorganic and
Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva, Switzerland
| | - Eric Bakker
- Department of Inorganic and
Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva, Switzerland
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115
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Nakamura S, Nagao R, Takahashi R, Noguchi T. Fourier transform infrared detection of a polarizable proton trapped between photooxidized tyrosine YZ and a coupled histidine in photosystem II: relevance to the proton transfer mechanism of water oxidation. Biochemistry 2014; 53:3131-44. [PMID: 24786306 DOI: 10.1021/bi500237y] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The redox-active tyrosine YZ (D1-Tyr161) in photosystem II (PSII) functions as an immediate electron acceptor of the Mn4Ca cluster, which is the catalytic center of photosynthetic water oxidation. YZ is also located in the hydrogen bond network that connects the Mn4Ca cluster to the lumen and hence is possibly related to the proton transfer process during water oxidation. To understand the role of YZ in the water oxidation mechanism, we have studied the hydrogen bonding interactions of YZ and its photooxidized neutral radical YZ(•) together with the interaction of the coupled His residue, D1-His190, using light-induced Fourier transform infrared (FTIR) difference spectroscopy. The YZ(•)-minus-YZ FTIR difference spectrum of Mn-depleted PSII core complexes exhibited a broad positive feature around 2800 cm(-1), which was absent in the corresponding spectrum of another redox-active tyrosine YD (D2-Tyr160). Analyses by (15)N and H/D substitutions, examination of the pH dependence, and density functional theory and quantum mechanics/molecular mechanics (QM/MM) calculations showed that this band arises from the N-H stretching vibration of the protonated cation of D1-His190 forming a charge-assisted strong hydrogen bond with YZ(•). This result provides strong evidence that the proton released from YZ upon its oxidation is trapped in D1-His190 and a positive charge remains on this His. The broad feature of the ~2800 cm(-1) band reflects a large proton polarizability in the hydrogen bond between YZ(•) and HisH(+). QM/MM calculations further showed that upon YZ oxidation the hydrogen bond network is rearranged and one water molecule moves toward D1-His190. From these data, a novel proton transfer mechanism via YZ(•)-HisH(+) is proposed, in which hopping of the polarizable proton of HisH(+) to this water triggers the transfer of the proton from substrate water to the luminal side. This proton transfer mechanism could be functional in the S2 → S3 transition, which requires proton release before electron transfer because of an excess positive charge on the Mn4Ca cluster.
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Affiliation(s)
- Shin Nakamura
- Division of Material Science, Graduate School of Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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116
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Hirao H, Thellamurege N, Zhang X. Applications of density functional theory to iron-containing molecules of bioinorganic interest. Front Chem 2014; 2:14. [PMID: 24809043 PMCID: PMC4010748 DOI: 10.3389/fchem.2014.00014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/10/2014] [Indexed: 12/29/2022] Open
Abstract
The past decades have seen an explosive growth in the application of density functional theory (DFT) methods to molecular systems that are of interest in a variety of scientific fields. Owing to its balanced accuracy and efficiency, DFT plays particularly useful roles in the theoretical investigation of large molecules. Even for biological molecules such as proteins, DFT finds application in the form of, e.g., hybrid quantum mechanics and molecular mechanics (QM/MM), in which DFT may be used as a QM method to describe a higher prioritized region in the system, while a MM force field may be used to describe remaining atoms. Iron-containing molecules are particularly important targets of DFT calculations. From the viewpoint of chemistry, this is mainly because iron is abundant on earth, iron plays powerful (and often enigmatic) roles in enzyme catalysis, and iron thus has the great potential for biomimetic catalysis of chemically difficult transformations. In this paper, we present a brief overview of several recent applications of DFT to iron-containing non-heme synthetic complexes, heme-type cytochrome P450 enzymes, and non-heme iron enzymes, all of which are of particular interest in the field of bioinorganic chemistry. Emphasis will be placed on our own work.
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Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological UniversitySingapore, Singapore
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117
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Le Goff A, Vénec D, Le Roy C, Pétillon FY, Schollhammer P, Talarmin J. Acid-Base Control of Hemilabile Proton-Responsive Protecting Devices in Dimolybdenum, Thiolate-Bridged Complexes. Inorg Chem 2014; 53:2200-10. [DOI: 10.1021/ic402873c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Alan Le Goff
- UMR CNRS 6521 ≪ Chimie,
Electrochimie Moléculaires et Chimie Analytique ≫ Université de Bretagne Occidentale, UFR Sciences et Techniques, CS 93837, 29238 Brest-Cedex
3, France
| | - David Vénec
- UMR CNRS 6521 ≪ Chimie,
Electrochimie Moléculaires et Chimie Analytique ≫ Université de Bretagne Occidentale, UFR Sciences et Techniques, CS 93837, 29238 Brest-Cedex
3, France
| | - Christine Le Roy
- UMR CNRS 6521 ≪ Chimie,
Electrochimie Moléculaires et Chimie Analytique ≫ Université de Bretagne Occidentale, UFR Sciences et Techniques, CS 93837, 29238 Brest-Cedex
3, France
| | - François Y. Pétillon
- UMR CNRS 6521 ≪ Chimie,
Electrochimie Moléculaires et Chimie Analytique ≫ Université de Bretagne Occidentale, UFR Sciences et Techniques, CS 93837, 29238 Brest-Cedex
3, France
| | - Philippe Schollhammer
- UMR CNRS 6521 ≪ Chimie,
Electrochimie Moléculaires et Chimie Analytique ≫ Université de Bretagne Occidentale, UFR Sciences et Techniques, CS 93837, 29238 Brest-Cedex
3, France
| | - Jean Talarmin
- UMR CNRS 6521 ≪ Chimie,
Electrochimie Moléculaires et Chimie Analytique ≫ Université de Bretagne Occidentale, UFR Sciences et Techniques, CS 93837, 29238 Brest-Cedex
3, France
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118
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 436] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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119
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Blomberg MRA, Siegbahn PEM. Proton pumping in cytochrome c oxidase: energetic requirements and the role of two proton channels. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1165-77. [PMID: 24418352 DOI: 10.1016/j.bbabio.2014.01.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 01/02/2014] [Accepted: 01/06/2014] [Indexed: 12/15/2022]
Abstract
Cytochrome c oxidase is a superfamily of membrane bound enzymes catalyzing the exergonic reduction of molecular oxygen to water, producing an electrochemical gradient across the membrane. The gradient is formed both by the electrogenic chemistry, taking electrons and protons from opposite sides of the membrane, and by proton pumping across the entire membrane. In the most efficient subfamily, the A-family of oxidases, one proton is pumped in each reduction step, which is surprising considering the fact that two of the reduction steps most likely are only weakly exergonic. Based on a combination of quantum chemical calculations and experimental information, it is here shown that from both a thermodynamic and a kinetic point of view, it should be possible to pump one proton per electron also with such an uneven distribution of the free energy release over the reduction steps, at least up to half the maximum gradient. A previously suggested pumping mechanism is developed further to suggest a reason for the use of two proton transfer channels in the A-family. Since the rate of proton transfer to the binuclear center through the D-channel is redox dependent, it might become too slow for the steps with low exergonicity. Therefore, a second channel, the K-channel, where the rate is redox-independent is needed. A redox-dependent leakage possibility is also suggested, which might be important for efficient energy conservation at a high gradient. A mechanism for the variation in proton pumping stoichiometry over the different subfamilies of cytochrome oxidase is also suggested. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Per E M Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
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120
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Kalva S, Azhagiya Singam ER, Rajapandian V, Saleena LM, Subramanian V. Discovery of potent inhibitor for matrix metalloproteinase-9 by pharmacophore based modeling and dynamics simulation studies. J Mol Graph Model 2014; 49:25-37. [PMID: 24473069 DOI: 10.1016/j.jmgm.2013.12.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 12/17/2013] [Accepted: 12/20/2013] [Indexed: 12/21/2022]
Abstract
Matrix metalloproteinase-9 (MMP-9) is an attractive target for anticancer therapy. In the present study ligand based pharmacophore modeling was performed to elucidate the structural elements for a diverse class of MMP-9 inhibitors. The pharmacophore model was validated through Güner-Henry (GH) scoring method. The final pharmacophore model consisted of three hydrogen bond acceptors (HBA), and two ring aromatic regions (RA). This model was utilized to screen the natural compound database to seek novel compounds as MMP-9 inhibitors. The identified hits were validated using molecular docking and molecular dynamics simulation studies. Finally, one compound named Hinokiflavone from Juniperus communis had high binding free energy of -26.54kJ/mol compared with the known inhibitors of MMP-9. Cytotoxicity for hinokiflavone was evaluated by MTT assay. Inhibition of MMP-9 in the presence of hinokiflavone was detected by gelatin zymography and gelatinolytic inhibition assay. Results revealed that the natural compounds derived based on the developed pharmacophore model would be useful for further design and development of MMP-9 inhibitors.
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Affiliation(s)
- Sukesh Kalva
- Department of Bioinformatics, SRM University, Kattankulathur, Kancheepuram District 603 203, India
| | - E R Azhagiya Singam
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V Rajapandian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - Lilly M Saleena
- Department of Bioinformatics, SRM University, Kattankulathur, Kancheepuram District 603 203, India.
| | - V Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India.
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121
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Linke K, Ho FM. Water in Photosystem II: Structural, functional and mechanistic considerations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:14-32. [DOI: 10.1016/j.bbabio.2013.08.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/08/2013] [Accepted: 08/13/2013] [Indexed: 12/30/2022]
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122
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Sun S, Li ZS, Chen SL. A dominant homolytic O-Cl bond cleavage with low-spin triplet-state Fe(IV)=O formed is revealed in the mechanism of heme-dependent chlorite dismutase. Dalton Trans 2013; 43:973-81. [PMID: 24162174 DOI: 10.1039/c3dt52171k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chlorite dismutase (Cld) is a heme-dependent enzyme that catalyzes the decomposition of toxic chlorite (ClO2(-)) into innocuous chloride and O2. In this paper, using the hybrid B3LYP density functional theory (DFT) method including dispersion interactions, the Cld reaction mechanism has been studied with a chemical model constructed on the X-ray crystal structure. The calculations indicate that the reaction proceeds along a stepwise pathway in the doublet state, i.e. a homolytic O-Cl bond cleavage of the substrate leading to an O-Fe(heme) species and a ClO˙ radical, followed by a rebinding O-O bond formation between them. The O-Fe(heme) species is demonstrated to be a low-spin triplet-state Fe(IV)=O diradicaloid. A low-spin singlet-state Fe(IV)=O is much less stable than the former, with an energy difference of 9.2 kcal mol(-1). The O-Cl bond cleavage is rate-limiting with a barrier of 10.6 kcal mol(-1), in good agreement with the experimental reaction rate of 2.0 × 10(5) s(-1). Furthermore, a heterolytic O-Cl bond dissociation in the initial step is shown to be unreachable, which ensures the high efficiency of the Cld enzyme by avoiding the generation of chlorate byproduct observed in the reactions of synthetic Fe porphyrins. Also, the pathways in the quartet and sextet states are unfavorable for the Cld reaction. The present results reveal a detailed mechanism III (defined in the text) including an interesting di-radical intermediate composed of a low-spin triplet-state Fe(IV)=O and a ClO˙ radical. Compared to a competitive heterolytic Cl-O cleavage in synthetic Fe porphyrins, the revelation of the domination of homolysis in Cld indicates not only the high efficiency of enzyme, but also the sensitivity of a heme and the significance of the enzymatic active-site surroundings (the His170 and Arg183 residues in the present case), which gives more insights into heme chemistry.
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Affiliation(s)
- Shuo Sun
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry, Beijing Institute of Technology, Beijing 100081, China.
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123
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Liao RZ, Li XC, Siegbahn PEM. Reaction Mechanism of Water Oxidation Catalyzed by Iron Tetraamido Macrocyclic Ligand Complexes - A DFT Study. Eur J Inorg Chem 2013. [DOI: 10.1002/ejic.201300710] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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124
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Gunner MR, Amin M, Zhu X, Lu J. Molecular mechanisms for generating transmembrane proton gradients. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:892-913. [PMID: 23507617 PMCID: PMC3714358 DOI: 10.1016/j.bbabio.2013.03.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/28/2013] [Accepted: 03/01/2013] [Indexed: 01/02/2023]
Abstract
Membrane proteins use the energy of light or high energy substrates to build a transmembrane proton gradient through a series of reactions leading to proton release into the lower pH compartment (P-side) and proton uptake from the higher pH compartment (N-side). This review considers how the proton affinity of the substrates, cofactors and amino acids are modified in four proteins to drive proton transfers. Bacterial reaction centers (RCs) and photosystem II (PSII) carry out redox chemistry with the species to be oxidized on the P-side while reduction occurs on the N-side of the membrane. Terminal redox cofactors are used which have pKas that are strongly dependent on their redox state, so that protons are lost on oxidation and gained on reduction. Bacteriorhodopsin is a true proton pump. Light activation triggers trans to cis isomerization of a bound retinal. Strong electrostatic interactions within clusters of amino acids are modified by the conformational changes initiated by retinal motion leading to changes in proton affinity, driving transmembrane proton transfer. Cytochrome c oxidase (CcO) catalyzes the reduction of O2 to water. The protons needed for chemistry are bound from the N-side. The reduction chemistry also drives proton pumping from N- to P-side. Overall, in CcO the uptake of 4 electrons to reduce O2 transports 8 charges across the membrane, with each reduction fully coupled to removal of two protons from the N-side, the delivery of one for chemistry and transport of the other to the P-side.
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Affiliation(s)
- M R Gunner
- Department of Physics, City College of New York, New York, NY 10031, USA.
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125
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Blomberg MR, Siegbahn PE. Why is the reduction of NO in cytochrome c dependent nitric oxide reductase (cNOR) not electrogenic? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:826-33. [DOI: 10.1016/j.bbabio.2013.04.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 03/27/2013] [Accepted: 04/13/2013] [Indexed: 11/29/2022]
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126
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Li Y, Zhong W, Qian G, Xiao Z, Liu X. Using polyethyleneimine (PEI) as a scaffold to construct mimicking systems of [FeFe]-hydrogenase: preparation, characterization of PEI-based materials, and their catalysis on proton reduction. Appl Organomet Chem 2013. [DOI: 10.1002/aoc.2979] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yao Li
- Department of Chemistry; Nanchang University; Nanchang; 330031; China
| | - Wei Zhong
- College of Biological, Chemical Sciences and Engineering; Jiaxing University; Jiaxing; 314001; China
| | - Guifen Qian
- Department of Chemistry; Nanchang University; Nanchang; 330031; China
| | - Zhiyin Xiao
- College of Biological, Chemical Sciences and Engineering; Jiaxing University; Jiaxing; 314001; China
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127
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Why is the molybdenum-substituted tungsten-dependent formaldehyde ferredoxin oxidoreductase not active? A quantum chemical study. J Biol Inorg Chem 2013; 18:175-181. [PMID: 23183892 DOI: 10.1007/s00775-012-0961-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 11/13/2012] [Indexed: 01/12/2023]
Abstract
Formaldehyde ferredoxin oxidoreductase is a tungsten-dependent enzyme that catalyzes the oxidative degradation of formaldehyde to formic acid. The molybdenum ion can be incorporated into the active site to displace the tungsten ion, but is without activity. Density functional calculations have been employed to understand the incapacitation of the enzyme caused by molybdenum substitution. The calculations show that the enzyme with molybdenum (Mo-FOR) has higher redox potential than that with tungsten, which makes the formation of the Mo(VI)=O complex endothermic by 14 kcal/mol. Following our previously suggested mechanism for this enzyme, the formaldehyde substrate oxidation was also investigated for Mo-FOR using the same quantum-mechanics-only model, except for the displacement of tungsten by molybdenum. The calculations demonstrate that formaldehyde oxidation occurs via a sequential two-step mechanism. Similarly to the tungsten-catalyzed reaction, the Mo(VI)=O species performs the nucleophilic attack on the formaldehyde carbon, followed by proton transfer in concert with two-electron reduction of the metal center. The first step is rate-limiting, with a total barrier of 28.2 kcal/mol. The higher barrier is mainly due to the large energy penalty for the formation of the Mo(VI)=O species.
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128
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Latifi R, Sainna MA, Rybak-Akimova EV, de Visser SP. Does Hydrogen-Bonding Donation to Manganese(IV)-Oxo and Iron(IV)-Oxo Oxidants Affect the Oxygen-Atom Transfer Ability? A Computational Study. Chemistry 2013; 19:4058-68. [DOI: 10.1002/chem.201202811] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Revised: 11/16/2012] [Indexed: 12/21/2022]
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129
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Bikas R, Hosseini-Monfared H, Zoppellaro G, Herchel R, Tucek J, Owczarzak AM, Kubicki M, Zboril R. Synthesis, structure, magnetic properties and theoretical calculations of methoxy bridged dinuclear iron(iii) complex with hydrazone based O,N,N-donor ligand. Dalton Trans 2013; 42:2803-12. [DOI: 10.1039/c2dt31751f] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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130
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Recent Progress in Density Functional Methodology for Biomolecular Modeling. STRUCTURE AND BONDING 2013. [DOI: 10.1007/978-3-642-32750-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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131
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Liu Y, Mukherjee A, Nahumi N, Ozbil M, Brown D, Angeles-Boza AM, Dooley DM, Prabhakar R, Roth JP. Experimental and Computational Evidence of Metal-O2 Activation and Rate-Limiting Proton-Coupled Electron Transfer in a Copper Amine Oxidase. J Phys Chem B 2012; 117:218-29. [DOI: 10.1021/jp3121484] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yi Liu
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - Arnab Mukherjee
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - Nadav Nahumi
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - Mehmet Ozbil
- Department of Chemistry, University of Miami, 1301 Memorial Drive,
Coral Gables, Florida 33146, United States
| | - Doreen Brown
- Department of Chemistry
and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Alfredo M. Angeles-Boza
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
| | - David M. Dooley
- Department of Chemistry
and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive,
Coral Gables, Florida 33146, United States
| | - Justine P. Roth
- Department of Chemistry, Johns Hopkins University, 3400 North
Charles Street, Baltimore, Maryland 21218, United States
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132
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Efremenko I, Neumann R. Computational insight into the initial steps of the Mars-van Krevelen mechanism: electron transfer and surface defects in the reduction of polyoxometalates. J Am Chem Soc 2012; 134:20669-80. [PMID: 23210519 DOI: 10.1021/ja308625q] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metal oxides as a rule oxidize and oxygenate substrates via the Mars-van Krevelen mechanism. A well-defined α-Keggin polyoxometalate, H(5)PV(2)Mo(10)O(40), can be viewed as an analogue of discrete structure that reacts via the Mars-van Krevelen mechanism both in solution and in the gas phase. Guided by previous experimental observations, we have studied the key intermediates on the reaction pathways of its reduction by various compounds using high-level DFT calculations. These redox reactions of polyoxometalates require protons, and thus such complexes were explicitly considered. First, the energetics of outer-sphere proton and electron transfer as well as coupled proton and electron transfer were calculated for seven substrates. This was followed by identification of possible key intermediates on the subsequent reaction pathways that feature displacement of the metal atom from the Keggin structure and coordinatively unsaturated sites on the H(5)PV(2)Mo(10)O(40) surface. Such metal defects are favored at vanadium sites. For strong reducing agents the initial outer-sphere electron transfer, alone or possibly coupled with proton transfer, facilitates formation of metal defects. Subsequent coordination allows for formation of reactive ensembles on the catalyst surface, for which the selective oxygen-transfer step becomes feasible. Weak reducing agents do not facilitate defect formation by outer-sphere electron and/or proton transfers, and thus formation of metal defect structures prior to the substrate activation is suggested as an initial step. Calculated geometries and energies of metal defect structures support experimentally observed intermediates and demonstrate the complex nature of the Mars-van Krevelen mechanism.
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Affiliation(s)
- Irena Efremenko
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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133
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Vijaya Sundar J, Subramanian V. Mechanistic Studies on the pH-Controllable Hydrogenation of NAD+ by H2 and Generation of H2 from NADH by a Water-Soluble Biomimetic Iridium Complex. Organometallics 2012. [DOI: 10.1021/om300812k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. Vijaya Sundar
- Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai 600 020, India
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134
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Cembran A, Provorse MR, Wang C, Wu W, Gao J. The Third Dimension of a More O'Ferrall-Jencks Diagram for Hydrogen Atom Transfer in the Isoelectronic Hydrogen Exchange Reactions of (PhX)(2)H(•) with X = O, NH, and CH(2). J Chem Theory Comput 2012; 8:4347-4358. [PMID: 23226989 PMCID: PMC3516191 DOI: 10.1021/ct3004595] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A critical element in theoretical characterization of the mechanism of proton-coupled electron transfer (PCET) reactions, including hydrogen atom transfer (HAT), is the formulation of the electron and proton localized diabatic states, based on which a More O'Ferrall-Jencks diagram can be represented to determine the step-wise and concerted nature of the reaction. Although the More O'Ferrall-Jencks diabatic states have often been used empirically to develop theoretical models for PCET reactions, the potential energy surfaces for these states have never been determined directly based on first principles calculations using electronic structure theory. The difficulty is due to a lack of practical method to constrain electron and proton localized diabatic states in wave function or density functional theory calculations. Employing a multistate density functional theory (MSDFT), in which the electron and proton localized diabatic configurations are constructed through block-localization of Kohn-Sham orbitals, we show that distinction between concerted proton-electron transfer (CPET) and HAT, which are not distinguishable experimentally from phenomenological kinetic data, can be made by examining the third dimension of a More O'Ferrall-Jencks diagram that includes both the ground and excited state potential surfaces. In addition, we formulate a pair of effective two-state valence bond models to represent the CPET and HAT mechanisms. We found that the lower energy of the CPET and HAT effective diabatic states at the intersection point can be used as an energetic criterion to distinguish the two mechanisms. In the isoelectronic series of hydrogen exchange reaction in (PhX)(2)H(•), where X = O, NH, and CH(2), there is a continuous transition from a CPET mechanism for the phenoxy radical-phenol pair to a HAT process for benzyl radical and toluene, while the reaction between PhNH(2) and PhNH(•) has a mechanism intermediate of CPET and HAT. The electronically nonadiabatic nature of the CPET mechanism in the phenol system can be attributed to the overlap interactions between the ground and excited state surfaces, resulting in roughly orthogonal minimum energy paths on the adiabatic ground and excited state potential energy surfaces. On the other hand, the minimum energy path on the adiabatic ground state for the HAT mechanism coincides with that on the excited state, producing a large electronic coupling that separates the two surfaces by more than 120 kcal/mol.
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Affiliation(s)
- Alessandro Cembran
- Department of Chemistry, Digital Technology Center and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
| | - Makenzie R. Provorse
- Department of Chemistry, Digital Technology Center and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
| | - Changwei Wang
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Jiali Gao
- Department of Chemistry, Digital Technology Center and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
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135
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Zinglé C, Kuntz L, Tritsch D, Grosdemange-Billiard C, Rohmer M. Modifications around the hydroxamic acid chelating group of fosmidomycin, an inhibitor of the metalloenzyme 1-deoxyxylulose 5-phosphate reductoisomerase (DXR). Bioorg Med Chem Lett 2012; 22:6563-7. [DOI: 10.1016/j.bmcl.2012.09.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 09/04/2012] [Accepted: 09/06/2012] [Indexed: 11/30/2022]
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136
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Schrauben JN, Cattaneo M, Day TC, Tenderholt AL, Mayer JM. Multiple-site concerted proton-electron transfer reactions of hydrogen-bonded phenols are nonadiabatic and well described by semiclassical Marcus theory. J Am Chem Soc 2012; 134:16635-45. [PMID: 22974135 PMCID: PMC3476473 DOI: 10.1021/ja305668h] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Photo-oxidations of hydrogen-bonded phenols using excited-state polyarenes are described to derive fundamental understanding of multiple-site concerted proton-electron transfer reactions (MS-CPET). Experiments have examined phenol bases having -CPh(2)NH(2), -Py, and -CH(2)Py groups ortho to the phenol hydroxyl group and tert-butyl groups in the 4,6-positions for stability (HOAr-NH(2), HOAr-Py, and HOAr-CH(2)Py, respectively; Py = pyridyl; Ph = phenyl). The photo-oxidations proceed by intramolecular proton transfer from the phenol to the pendent base concerted with electron transfer to the excited polyarene. For comparison, 2,4,6-(t)Bu(3)C(6)H(2)OH, a phenol without a pendent base and tert-butyl groups in the 2,4,6-positions, has also been examined. Many of these bimolecular reactions are fast, with rate constants near the diffusion limit. Combining the photochemical k(CPET) values with those from prior thermal stopped-flow kinetic studies gives data sets for the oxidations of HOAr-NH(2) and HOAr-CH(2)Py that span over 10(7) in k(CPET) and nearly 0.9 eV in driving force (ΔG(o)'). Plots of log(k(CPET)) vs ΔG(o)', including both excited-state anthracenes and ground state aminium radical cations, define a single Marcus parabola in each case. These two data sets are thus well described by semiclassical Marcus theory, providing a strong validation of the use of this theory for MS-CPET. The parabolas give λ(CPET) ≅ 1.15-1.2 eV and H(ab) ≅ 20-30 cm(-1). These experiments represent the most direct measurements of H(ab) for MS-CPET reactions to date. Although rate constants are available only up to the diffusion limit, the parabolas clearly peak well below the adiabatic limit of ca. 6 × 10(12) s(-1). Thus, this is a very clear demonstration that the reactions are nonadiabatic. The nonadiabatic character slows the reactions by a factor of ~45. Results for the oxidation of HOAr-Py, in which the phenol and base are conjugated, and for oxidation of 2,4,6-(t)Bu(3)C(6)H(2)OH, which lacks a base, show that both have substantially lower λ and larger pre-exponential terms. The implications of these results for MS-CPET reactions are discussed.
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Affiliation(s)
| | | | - Thomas C. Day
- Department of Chemistry, University of Washington, Seattle WA 98195
| | | | - James M. Mayer
- Department of Chemistry, University of Washington, Seattle WA 98195
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137
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Oxygen and hydrogen peroxide reduction by 1,2-diferrocenylethane at a liquid/liquid interface. J Electroanal Chem (Lausanne) 2012. [DOI: 10.1016/j.jelechem.2012.04.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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138
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Cirera J, Paesani F. Theoretical Prediction of Spin-Crossover Temperatures in Ligand-Driven Light-Induced Spin Change Systems. Inorg Chem 2012; 51:8194-201. [DOI: 10.1021/ic300750c] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jordi Cirera
- Department of Chemistry and Biochemistry, University
of California, San Diego, 9500 Gilman Drive, La Jolla, California
92093-0314, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University
of California, San Diego, 9500 Gilman Drive, La Jolla, California
92093-0314, United States
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139
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Blomberg MRA, Siegbahn PEM. Mechanism for N2O Generation in Bacterial Nitric Oxide Reductase: A Quantum Chemical Study. Biochemistry 2012; 51:5173-86. [DOI: 10.1021/bi300496e] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Margareta R. A. Blomberg
- Department of Physics, AlbaNova university
center,
and Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Per E. M. Siegbahn
- Department of Physics, AlbaNova university
center,
and Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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140
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Theoretical investigation of astacin proteolysis. J Inorg Biochem 2012; 111:70-9. [DOI: 10.1016/j.jinorgbio.2012.02.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 11/06/2011] [Accepted: 02/07/2012] [Indexed: 11/19/2022]
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141
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Petruk AA, Bartesaghi S, Trujillo M, Estrin DA, Murgida D, Kalyanaraman B, Marti MA, Radi R. Molecular basis of intramolecular electron transfer in proteins during radical-mediated oxidations: computer simulation studies in model tyrosine-cysteine peptides in solution. Arch Biochem Biophys 2012; 525:82-91. [PMID: 22640642 DOI: 10.1016/j.abb.2012.05.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 05/05/2012] [Accepted: 05/20/2012] [Indexed: 11/15/2022]
Abstract
Experimental studies in hemeproteins and model Tyr/Cys-containing peptides exposed to oxidizing and nitrating species suggest that intramolecular electron transfer (IET) between tyrosyl radicals (Tyr-O(·)) and Cys residues controls oxidative modification yields. The molecular basis of this IET process is not sufficiently understood with structural atomic detail. Herein, we analyzed using molecular dynamics and quantum mechanics-based computational calculations, mechanistic possibilities for the radical transfer reaction in Tyr/Cys-containing peptides in solution and correlated them with existing experimental data. Our results support that Tyr-O(·) to Cys radical transfer is mediated by an acid/base equilibrium that involves deprotonation of Cys to form the thiolate, followed by a likely rate-limiting transfer process to yield cysteinyl radical and a Tyr phenolate; proton uptake by Tyr completes the reaction. Both, the pKa values of the Tyr phenol and Cys thiol groups and the energetic and kinetics of the reversible IET are revealed as key physico-chemical factors. The proposed mechanism constitutes a case of sequential, acid/base equilibrium-dependent and solvent-mediated, proton-coupled electron transfer and explains the dependency of oxidative yields in Tyr/Cys peptides as a function of the number of alanine spacers. These findings contribute to explain oxidative modifications in proteins that contain sequence and/or spatially close Tyr-Cys residues.
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Affiliation(s)
- Ariel A Petruk
- Instituto Superior de Investigaciones Biológicas (CONICET-UNT), Chacabuco 461, S.M. de Tucumán, Tucumán, T4000CAN, Argentina
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142
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Bingöl B, Durrell AC, Keller GE, Palmer JH, Grubbs RH, Gray HB. Electron transfer triggered by optical excitation of phenothiazine-tris(meta-phenylene-ethynylene)-(tricarbonyl)(bpy)(py)rhenium(I). J Phys Chem B 2012; 117:4177-82. [PMID: 22533820 DOI: 10.1021/jp3010053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have investigated excited-state electron transfer in a donor-bridge-acceptor complex containing phenothiazine (PTZ) linked via tris(meta-phenylene-ethynylene) to a tricarbonyl(bipyridine)(pyridine)Re(I) unit. Time-resolved luminescence experiments reveal two excited-state (*Re) decay regimes, a multiexponential component with a mean lifetime of 2.7 ns and a longer monoexponential component of 530 ns in dichloromethane solution. The faster decay is attributed to PTZ → *Re electron transfer in a C-shaped PTZ-bridge-Re conformer (PTZ-Re ≈ 7.5 Å). We assign the longer lifetime, which is virtually identical to that of free *Re, to an extended conformer (PTZ-Re > 20 Å). The observed biexponential *Re decay requires that interconversion of PTZ-bridge-Re conformers be slower than 10(6) s(-1).
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Affiliation(s)
- Bahar Bingöl
- The Arnold and Mabel Beckman Laboratory of Chemical Synthesis, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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143
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Chen SL, Blomberg MRA, Siegbahn PEM. How Is Methane Formed and Oxidized Reversibly When Catalyzed by Ni-Containing Methyl-Coenzyme M Reductase? Chemistry 2012; 18:6309-15. [DOI: 10.1002/chem.201200274] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Indexed: 11/07/2022]
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144
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He Y, Chen S, Liu Y, Liang Y, Xiang J, Wu D, Zhou F. Coordination of Bi3+ to metal-free metallothionein: spectroscopy and density functional calculation of structure, coordination, and electronic excitations. J Inorg Biochem 2012; 113:9-14. [PMID: 22687489 DOI: 10.1016/j.jinorgbio.2012.02.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 02/15/2012] [Accepted: 02/15/2012] [Indexed: 11/24/2022]
Abstract
Understanding the structure of mammal Bi-containing metallothionein-2 (Bi-MT2) is of great physiological significance due to the importance of Bi-MT2 in alleviating adverse effect of anti-cancer drugs. A unique feature of rabbit liver Bi-MT2 is the metal-oxygen bond (BiO), which is absent in well-characterized Zn-MT2 and Cd-MT2. However, the ligand contributing to the BiO bonding in Bi-MT2 remains unidentified. In this study, the coordination of Bi(3+) to rabbit liver metal-free metallothionein was investigated using both experimental and theoretical methods. UV-visible and circular dichroism spectra indicate that Bi-MT2 has a different secondary structure from those of Zn-MT2 and Cd-MT2. Three possible Bi(3+) coordination structures in Bi(7)-MT2 and relative binding free energies were calculated using the density functional theory. Absorption spectra corresponding to these coordination structures were evaluated by time-dependent density functional theory. Our computation results are consistent with the UV-vis spectroscopic data and strongly suggest that the carboxyl group in the aspartic acid residues contributes to the BiO bond formation.
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Affiliation(s)
- Yonghui He
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
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145
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Peljo P, Murtomäki L, Kallio T, Xu HJ, Meyer M, Gros CP, Barbe JM, Girault HH, Laasonen K, Kontturi K. Biomimetic Oxygen Reduction by Cofacial Porphyrins at a Liquid–Liquid Interface. J Am Chem Soc 2012; 134:5974-84. [DOI: 10.1021/ja3004914] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pekka Peljo
- Department of Chemistry, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Lasse Murtomäki
- Department of Chemistry, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Tanja Kallio
- Department of Chemistry, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Hai-Jun Xu
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), UMR CNRS 6302, 9 avenue A. Savary, BP 47870, 21078 Dijon Cedex,
France
| | - Michel Meyer
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), UMR CNRS 6302, 9 avenue A. Savary, BP 47870, 21078 Dijon Cedex,
France
| | - Claude P. Gros
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), UMR CNRS 6302, 9 avenue A. Savary, BP 47870, 21078 Dijon Cedex,
France
| | - Jean-Michel Barbe
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), UMR CNRS 6302, 9 avenue A. Savary, BP 47870, 21078 Dijon Cedex,
France
| | - Hubert H. Girault
- Laboratoire d’Electrochimie
Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 6, CH-1015 Lausanne, Switzerland
| | - Kari Laasonen
- Department of Chemistry, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Kyösti Kontturi
- Department of Chemistry, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
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146
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Conductivity by Electron Pairs. Chem Phys 2012. [DOI: 10.1201/b11524-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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147
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Markle TF, Tenderholt AL, Mayer JM. Probing quantum and dynamic effects in concerted proton-electron transfer reactions of phenol-base compounds. J Phys Chem B 2012; 116:571-84. [PMID: 22148459 PMCID: PMC3974916 DOI: 10.1021/jp2091736] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The oxidation of three phenols, which contain an intramolecular hydrogen bond to a pendent pyridine or amine group, has been shown, in a previous experimental study, to undergo concerted proton-electron transfer (CPET). In this reaction, the electron is transferred to an outer-sphere oxidant, and the proton is transferred from the oxygen to nitrogen atom. In the present study, this reaction is studied computationally using a version of Hammes-Schiffer's multistate continuum theory where CPET is formulated as a transmission frequency between neutral and cation vibrational-electronic states. The neutral and cation proton vibrational wave functions are computed from one-dimensional potential energy surfaces (PESs) for the transferring proton in a fixed heavy atom framework. The overlap integrals for these neutral/cation wave functions, considering several initial (i.e., neutral) and final (i.e., cation) vibrational states, are used to evaluate the relative rates of oxidation. The analysis is extended to heavy atom configurations with various proton donor-acceptor (i.e., O-N) distances to assess the importance of heavy atom "gating". Such changes in d(ON) dramatically affect the nature of the proton PESs and wave functions. Surprisingly, the most reactive configurations have similar donor-acceptor distances despite the large (~0.2 Å) differences in the optimized structures. These theoretical results qualitatively reproduce the experimental faster reactivity of the reaction of the pyridyl derivative 1 versus the CH(2)-pyridyl 2, but the computed factor of 5 is smaller than the experimental 10(2). The amine derivative is calculated to react similarly to 1, which does not agree with the experiments, likely due to some of the simplifying assumptions made in applying the theory. The computed kinetic isotope effects (KIEs) and their temperature dependence are in agreement with experimental results.
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Affiliation(s)
| | - Adam L. Tenderholt
- Department of Chemistry, University of Washington, Box 351700 Seattle, WA 98195-1700
| | - James M. Mayer
- Department of Chemistry, University of Washington, Box 351700 Seattle, WA 98195-1700
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148
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Okamura M, Yoshida M, Kuga R, Sakai K, Kondo M, Masaoka S. A mononuclear ruthenium complex showing multiple proton-coupled electron transfer toward multi-electron transfer reactions. Dalton Trans 2012; 41:13081-9. [DOI: 10.1039/c2dt30773a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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149
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Klimacek M, Brunsteiner M, Nidetzky B. Dynamic mechanism of proton transfer in mannitol 2-dehydrogenase from Pseudomonas fluorescens: mobile GLU292 controls proton relay through a water channel that connects the active site with bulk solvent. J Biol Chem 2011; 287:6655-67. [PMID: 22194597 PMCID: PMC3307286 DOI: 10.1074/jbc.m111.289223] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The active site of mannitol 2-dehydrogenase from Pseudomonas fluorescens (PfM2DH) is connected with bulk solvent through a narrow protein channel that shows structural resemblance to proton channels utilized by redox-driven proton pumps. A key element of the PfM2DH channel is the "mobile" Glu(292), which was seen crystallographically to adopt distinct positions up and down the channel. It was suggested that the "down → up" conformational change of Glu(292) could play a proton relay function in enzymatic catalysis, through direct proton shuttling by the Glu or because the channel is opened for water molecules forming a chain along which the protons flow. We report evidence from site-directed mutagenesis (Glu(292) → Ala) substantiated by data from molecular dynamics simulations that support a role for Glu(292) as a gate in a water chain (von Grotthuss-type) mechanism of proton translocation. Occupancy of the up and down position of Glu(292) is influenced by the bonding and charge state of the catalytic acid base Lys(295), suggesting that channel opening/closing motions of the Glu are synchronized to the reaction progress. Removal of gatekeeper control in the E292A mutant resulted in a selective, up to 120-fold slowing down of microscopic steps immediately preceding catalytic oxidation of mannitol, consistent with the notion that formation of the productive enzyme-NAD(+)-mannitol complex is promoted by a corresponding position change of Glu(292), which at physiological pH is associated with obligatory deprotonation of Lys(295) to solvent. These results underscore the important role of conformational dynamics in the proton transfer steps of alcohol dehydrogenase catalysis.
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Affiliation(s)
- Mario Klimacek
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, A-8010 Graz, Austria
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150
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Riccardi D, Zhu X, Goyal P, Yang S, Hou G, Cui Q. Toward molecular models of proton pumping: Challenges, methods and relevant applications. Sci China Chem 2011. [DOI: 10.1007/s11426-011-4458-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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