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Miarzlou DA, Leisinger F, Joss D, Häussinger D, Seebeck FP. Structure of formylglycine-generating enzyme in complex with copper and a substrate reveals an acidic pocket for binding and activation of molecular oxygen. Chem Sci 2019; 10:7049-7058. [PMID: 31588272 PMCID: PMC6676471 DOI: 10.1039/c9sc01723b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/11/2019] [Indexed: 01/25/2023] Open
Abstract
The formylglycine generating enzyme (FGE) catalyzes oxidative conversion of specific peptidyl-cysteine residues to formylglycine. FGE mediates O2-activation and hydrogen-atom abstraction in an active site that contains Cu(i) coordinated to two cysteine residues. Similar coordination geometries are common among copper-sensing transcription factors and copper-chaperone but are unprecedented among copper-dependent oxidases. To examine the mechanism of this unusual catalyst we determined the 1.04 Å structure of FGE from Thermomonospora curvata in complex with copper and a cysteine-containing peptide substrate. This structure unveils a network of four crystallographic waters and two active site residues that form a highly acidic O2-binding pocket juxtaposed to the trigonal planar tris-cysteine coordinated Cu(i) center. Comparison with structures of FGE in complex with Ag(i) and Cd(ii) combined with evidence from NMR spectroscopy and kinetic observations highlight several structural changes that are induced by substrate binding and prime the enzyme for O2-binding and subsequent activation.
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Affiliation(s)
- Dzmitry A Miarzlou
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland . ; Tel: +41 612071143
| | - Florian Leisinger
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland . ; Tel: +41 612071143
| | - Daniel Joss
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland . ; Tel: +41 612071143
| | - Daniel Häussinger
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland . ; Tel: +41 612071143
| | - Florian P Seebeck
- Department of Chemistry , University of Basel , Mattenstrasse 24a , Basel 4002 , Switzerland . ; Tel: +41 612071143
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2
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Yin S, Bernstein ER. Fe-V sulfur clusters studied through photoelectron spectroscopy and density functional theory. Phys Chem Chem Phys 2018; 20:22610-22622. [PMID: 30123901 DOI: 10.1039/c8cp03157f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Iron-vanadium sulfur cluster anions are studied by photoelectron spectroscopy (PES) at 3.492 eV (355 nm) and 4.661 eV (266 nm) photon energies, and by density functional theory (DFT) calculations. The structural properties, relative energies of different structural isomers, and the calculated first vertical detachment energies (VDEs) of different structural isomers for cluster anions FeVS1-3- and FemVnSm+n- (m + n = 3, 4; m > 0, n > 0) are investigated at a BPW91/TZVP theory level. The experimental first VDEs for these Fe-V sulfur clusters are reported. The most probable ground state structures and spin multiplicities for these clusters are tentatively assigned by comparing their theoretical and experiment first VDE values. For FeVS1-3- clusters, their first VDEs are generally observed to increase with the number of sulfur atoms from 1.45 eV to 2.86 eV. The NBO/HOMOs of the ground state of FeVS1-3- clusters are localized in a p orbital on a S atom; the partial charge distribution on the NBO/HOMO localized site of each cluster anion is responsible for the trend of their first VDEs. A less negative localized charge distribution is correlated with a higher first VDE. Structure and steric effect differences for FemVnSm+n- (m + n = 3, m > 0, n > 0) clusters are suggested to be responsible for their different first VDEs and properties. Two types of structural isomers are identified for FemVnSm+n- (m + n = 4, m > 0, n > 0) clusters: a tower structure isomer and a cubic structure isomer. The first VDEs for tower like isomers are generally higher than those for cubic like isomers of FemVnSm+n- (m + n = 4, m > 0, n > 0) clusters. Their first VDEs are can be understood through: (1) NBO/HOMO distributions, (2) structures (steric effects), and (3) partial charge numbers on the NBO/HOMO's localized sites. EBEs for excited state transitions for all Fe-V sulfur clusters are calculated employing OVGF and TDDFT approaches at the TZVP level. The OVGF approach for these Fe/V/S cluster anions is better for the higher transition energies than the TDDTF approach. The experimental and theoretical results for these Fe/V/S cluster anions are compared with their related pure iron sulfur cluster anions. Properties of the NBO/HOMO are essential for understanding and estimating the different first VDEs for Fe/V/S, and comparing them to those of the pure Fe/S cluster anions.
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Affiliation(s)
- Shi Yin
- Department of Chemistry, NSF ERC for Extreme Ultraviolet Science and Technology, Colorado State University, Fort Collins, CO 80523, USA.
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3
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Yin S, Bernstein ER. Photoelectron spectroscopy and density functional theory studies of (FeS) mH - (m = 2-4) cluster anions: effects of the single hydrogen. Phys Chem Chem Phys 2017; 20:367-382. [PMID: 29210391 DOI: 10.1039/c7cp07012h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single hydrogen containing iron hydrosulfide cluster anions (FeS)mH- (m = 2-4) are studied by photoelectron spectroscopy (PES) at 3.492 eV (355 nm) and 4.661 eV (266 nm) photon energies, and by Density Functional Theory (DFT) calculations. The structural properties, relative energies of different spin states and isomers, and the first calculated vertical detachment energies (VDEs) of different spin states for these (FeS)mH- (m = 2-4) cluster anions are investigated at various reasonable theory levels. Two types of structural isomers are found for these (FeS)mH- (m = 2-4) clusters: (1) the single hydrogen atom bonds to a sulfur site (SH-type); and (2) the single hydrogen atom bonds to an iron site (FeH-type). Experimental and theoretical results suggest such available different SH- and FeH-type structural isomers should be considered when evaluating the properties and behavior of these single hydrogen containing iron sulfide clusters in real chemical and biological systems. Compared to their related, respective pure iron sulfur (FeS)m- clusters, the first VDE trend of the diverse type (FeS)mH0,1- (m = 1-4) clusters can be understood through (1) the different electron distribution properties of their highest singly occupied molecular orbital employing natural bond orbital analysis (NBO/HSOMO), and (2) the partial charge distribution on the NBO/HSOMO localized sites of each cluster anion. Generally, the properties of the NBO/HSOMOs play the principal role with regard to the physical and chemical properties of all the anions. The change of cluster VDE from low to high is associated with the change in nature of their NBO/HSOMO from a dipole bound and valence electron mixed character, to a valence p orbital on S, to a valence d orbital on Fe, and to a valence p orbital on Fe or an Fe-Fe delocalized valence bonding orbital. For clusters having the same properties for NBO/HSOMOs, the partial charge distributions at the NBO/HSOMO localized sites additionally affect their VDEs: a more negative or less positive localized charge distribution is correlated with a lower first VDE. The single hydrogen in these (FeS)mH- (m = 2-4) cluster anions is suggested to affect their first VDEs through the different structure types (SH- or FeH-), the nature of the NBO/HSOMOs at the local site, and the value of partial charge number at the local site of the NBO/HSOMO.
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Affiliation(s)
- Shi Yin
- Department of Chemistry, NSF ERC for Extreme Ultraviolet Science and Technology, Colorado State University, Fort Collins, CO 80523, USA.
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4
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Yin S, Bernstein ER. Photoelectron Spectroscopy and Density Functional Theory Studies of Iron Sulfur (FeS)m– (m = 2–8) Cluster Anions: Coexisting Multiple Spin States. J Phys Chem A 2017; 121:7362-7373. [DOI: 10.1021/acs.jpca.7b07676] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shi Yin
- Department of Chemistry,
NSF ERC for Extreme Ultraviolet Science and Technology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Elliot R. Bernstein
- Department of Chemistry,
NSF ERC for Extreme Ultraviolet Science and Technology, Colorado State University, Fort Collins, Colorado 80523, United States
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5
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Yin S, Bernstein ER. Properties of iron sulfide, hydrosulfide, and mixed sulfide/hydrosulfide cluster anions through photoelectron spectroscopy and density functional theory calculations. J Chem Phys 2016; 145:154302. [DOI: 10.1063/1.4964651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Shi Yin
- Department of Chemistry, NSF ERC for Extreme Ultraviolet Science and Technology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Elliot R. Bernstein
- Department of Chemistry, NSF ERC for Extreme Ultraviolet Science and Technology, Colorado State University, Fort Collins, Colorado 80523, USA
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Harris TV, Szilagyi RK. Protein environmental effects on iron-sulfur clusters: A set of rules for constructing computational models for inner and outer coordination spheres. J Comput Chem 2016; 37:1681-96. [DOI: 10.1002/jcc.24384] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Travis V. Harris
- NAI Astrobiology Biogeocatalysis Research Center, Department of Chemistry and Biochemistry, Montana State University; Bozeman Montana 59717
| | - Robert K. Szilagyi
- NAI Astrobiology Biogeocatalysis Research Center, Department of Chemistry and Biochemistry, Montana State University; Bozeman Montana 59717
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Abdel-Azeim S, Jedidi A, Eppinger J, Cavallo L. Mechanistic insights into the reductive dehydroxylation pathway for the biosynthesis of isoprenoids promoted by the IspH enzyme. Chem Sci 2015; 6:5643-5651. [PMID: 28757951 PMCID: PMC5511988 DOI: 10.1039/c5sc01693b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/22/2015] [Indexed: 11/21/2022] Open
Abstract
Here, we report an integrated quantum mechanics/molecular mechanics (QM/MM) study of the bio-organometallic reaction pathway of the 2H+/2e- reduction of (E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate (HMBPP) into the so called universal terpenoid precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), promoted by the IspH enzyme. Our results support the viability of the bio-organometallic pathway through rotation of the OH group of HMBPP away from the [Fe4S4] cluster at the core of the catalytic site, to become engaged in a H-bond with Glu126. This rotation is synchronous with π-coordination of the C2[double bond, length as m-dash]C3 double bond of HMBPP to the apical Fe atom of the [Fe4S4] cluster. Dehydroxylation of HMBPP is triggered by a proton transfer from Glu126 to the OH group of HMBPP. The reaction pathway is completed by competitive proton transfer from the terminal phosphate group to the C2 or C4 atom of HMBPP.
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Affiliation(s)
- Safwat Abdel-Azeim
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
| | - Abdesslem Jedidi
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
| | - Jorg Eppinger
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
| | - Luigi Cavallo
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
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8
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Blachly PG, Sandala GM, Giammona DA, Bashford D, McCammon JA, Noodleman L. Broken-Symmetry DFT Computations for the Reaction Pathway of IspH, an Iron-Sulfur Enzyme in Pathogenic Bacteria. Inorg Chem 2015; 54:6439-61. [PMID: 26098647 PMCID: PMC4568833 DOI: 10.1021/acs.inorgchem.5b00751] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recently discovered methylerythritol phosphate (MEP) pathway provides new targets for the development of antibacterial and antimalarial drugs. In the final step of the MEP pathway, the [4Fe-4S] IspH protein catalyzes the 2e(-)/2H(+) reductive dehydroxylation of (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP) to afford the isoprenoid precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). Recent experiments have attempted to elucidate the IspH catalytic mechanism to drive inhibitor development. Two competing mechanisms have recently emerged, differentiated by their proposed HMBPP binding modes upon 1e(-) reduction of the [4Fe-4S] cluster: (1) a Birch reduction mechanism, in which HMBPP remains bound to the [4Fe-4S] cluster through its terminal C4-OH group (ROH-bound) until the -OH is cleaved as water; and (2) an organometallic mechanism, in which the C4-OH group rotates away from the [4Fe-4S] cluster, allowing the HMBPP olefin group to form a metallacycle complex with the apical iron (η(2)-bound). We perform broken-symmetry density functional theory computations to assess the energies and reduction potentials associated with the ROH- and η(2)-bound states implicated by these competing mechanisms. Reduction potentials obtained for ROH-bound states are more negative (-1.4 to -1.0 V) than what is typically expected of [4Fe-4S] ferredoxin proteins. Instead, we find that η(2)-bound states are lower in energy than ROH-bound states when the [4Fe-4S] cluster is 1e(-) reduced. Furthermore, η(2)-bound states can already be generated in the oxidized state, yielding reduction potentials of ca. -700 mV when electron addition occurs after rotation of the HMBPP C4-OH group. We demonstrate that such η(2)-bound states are kinetically accessible both when the IspH [4Fe-4S] cluster is oxidized and 1e(-) reduced. The energetically preferred pathway gives 1e(-) reduction of the cluster after substrate conformational change, generating the 1e(-) reduced intermediate proposed in the organometallic mechanism.
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Affiliation(s)
| | - Gregory M Sandala
- ‡Department of Chemistry and Biochemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
| | - Debra Ann Giammona
- §Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Donald Bashford
- §Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | | | - Louis Noodleman
- #Department of Integrative Structural and Computational Biology, CB213, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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9
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Blachly PG, Sandala GM, Giammona D, Liu T, Bashford D, McCammon JA, Noodleman L. Use of Broken-Symmetry Density Functional Theory To Characterize the IspH Oxidized State: Implications for IspH Mechanism and Inhibition. J Chem Theory Comput 2014; 10:3871-3884. [PMID: 25221444 PMCID: PMC4159220 DOI: 10.1021/ct5005214] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Indexed: 12/31/2022]
Abstract
With current therapies becoming less efficacious due to increased drug resistance, new inhibitors of both bacterial and malarial targets are desperately needed. The recently discovered methylerythritol phosphate (MEP) pathway for isoprenoid synthesis provides novel targets for the development of such drugs. Particular attention has focused on the IspH protein, the final enzyme in the MEP pathway, which uses its [4Fe-4S] cluster to catalyze the formation of the isoprenoid precursors IPP and DMAPP from HMBPP. IspH catalysis is achieved via a 2e-/2H+ reductive dehydroxylation of HMBPP; the mechanism by which catalysis is achieved, however, is highly controversial. The work presented herein provides the first step in assessing different routes to catalysis by using computational methods. By performing broken-symmetry density functional theory (BS-DFT) calculations that employ both the conductor-like screening solvation model (DFT/COSMO) and a finite-difference Poisson-Boltzmann self-consistent reaction field methodology (DFT/SCRF), we evaluate geometries, energies, and Mössbauer signatures of the different protonation states that may exist in the oxidized state of the IspH catalytic cycle. From DFT/SCRF computations performed on the oxidized state, we find a state where the substrate, HMBPP, coordinates the apical iron in the [4Fe-4S] cluster as an alcohol group (ROH) to be one of two, isoenergetic, lowest-energy states. In this state, the HMBPP pyrophosphate moiety and an adjacent glutamate residue (E126) are both fully deprotonated, making the active site highly anionic. Our findings that this low-energy state also matches the experimental geometry of the active site and that its computed isomer shifts agree with experiment validate the use of the DFT/SCRF method to assess relative energies along the IspH reaction pathway. Additional studies of IspH catalytic intermediates are currently being pursued.
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Affiliation(s)
- Patrick G. Blachly
- Department
of Chemistry and Biochemistry, University
of California San Diego, 9500 Gilman Drive, Mail Code 0365, La Jolla, California 92093-0365, United States
| | - Gregory M. Sandala
- Department
of Chemistry and Biochemistry, Mount Allison
University, 63C York
Street, Sackville, New Brunswick E4L 1G8, Canada
| | - Debra
Ann Giammona
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, 262
Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Tiqing Liu
- Skaggs School of Pharmacy and Pharmaceutical
Sciences, Howard Hughes Medical
Institute, and Department of Pharmacology, University
of California San Diego, La Jolla, California 92093-0365, United States
| | - Donald Bashford
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, 262
Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - J. Andrew McCammon
- Department
of Chemistry and Biochemistry, University
of California San Diego, 9500 Gilman Drive, Mail Code 0365, La Jolla, California 92093-0365, United States
- Skaggs School of Pharmacy and Pharmaceutical
Sciences, Howard Hughes Medical
Institute, and Department of Pharmacology, University
of California San Diego, La Jolla, California 92093-0365, United States
| | - Louis Noodleman
- Department
of Integrative Structural and Computational Biology, The Scripps Research Institute, TPC15, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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10
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Niu S, Huang DL, Dau PD, Liu HT, Wang LS, Ichiye T. Assessment of Quantum Mechanical Methods for Copper and Iron Complexes by Photoelectron Spectroscopy. J Chem Theory Comput 2014; 10:1283-1291. [PMID: 24803858 PMCID: PMC3958136 DOI: 10.1021/ct400842p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Indexed: 11/28/2022]
Abstract
![]()
Broken-symmetry
density functional theory (BS-DFT) calculations
are assessed for redox energetics [Cu(SCH3)2]1–/0, [Cu(NCS)2]1–/0, [FeCl4]1–/0, and [Fe(SCH3)4]1–/0 against vertical detachment
energies (VDE) from valence photoelectron spectroscopy (PES), as a
prelude to studies of metalloprotein analogs. The M06 and B3LYP hybrid
functionals give VDE that agree with the PES VDE for the Fe complexes,
but both underestimate it by ∼400 meV for the Cu complexes;
other hybrid functionals give VDEs that are an increasing function
of the amount of Hartree–Fock (HF) exchange and so cannot show
good agreement for both Cu and Fe complexes. Range-separated (RS)
functionals appear to give a better distribution of HF exchange since
the negative HOMO energy is approximately equal to the VDEs but also
give VDEs dependent on the amount of HF exchange, sometimes leading
to ground states with incorrect electron configurations; the LRC-ωPBEh functional reduced to 10% HF exchange at short-range
give somewhat better values for both, although still ∼150 meV
too low for the Cu complexes and ∼50 meV too high for the Fe
complexes. Overall, the results indicate that while HF exchange compensates
for self-interaction error in DFT calculations of both Cu and Fe complexes,
too much may lead to more sensitivity to nondynamical correlation
in the spin-polarized Fe complexes.
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Affiliation(s)
- Shuqiang Niu
- Department of Chemistry, Georgetown University , Washington, DC 20057, United States
| | - Dao-Ling Huang
- Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States
| | - Phuong D Dau
- Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States
| | - Hong-Tao Liu
- Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States
| | - Lai-Sheng Wang
- Department of Chemistry, Brown University , Providence, Rhode Island 02912, United States
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University , Washington, DC 20057, United States
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11
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Bergeler M, Stiebritz MT, Reiher M. Structure-Property Relationships of Fe4S4Clusters. Chempluschem 2013; 78:1082-1098. [DOI: 10.1002/cplu.201300186] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Indexed: 11/08/2022]
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12
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Perrin BS, Niu S, Ichiye T. Calculating standard reduction potentials of [4Fe-4S] proteins. J Comput Chem 2013; 34:576-82. [PMID: 23115132 PMCID: PMC3570669 DOI: 10.1002/jcc.23169] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 09/20/2012] [Accepted: 09/30/2012] [Indexed: 11/08/2022]
Abstract
The oxidation-reduction potentials of electron transfer proteins determine the driving forces for their electron transfer reactions. Although the type of redox site determines the intrinsic energy required to add or remove an electron, the electrostatic interaction energy between the redox site and its surrounding environment can greatly shift the redox potentials. Here, a method for calculating the reduction potential versus the standard hydrogen electrode, E°, of a metalloprotein using a combination of density functional theory and continuum electrostatics is presented. This work focuses on the methodology for the continuum electrostatics calculations, including various factors that may affect the accuracy. The calculations are demonstrated using crystal structures of six homologous HiPIPs, which give E° that are in excellent agreement with experimental results.
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Affiliation(s)
- Bradley Scott Perrin
- Department of Chemistry, Georgetown University, Box 571227, Washington, DC 20057-1227
| | - Shuqiang Niu
- Department of Chemistry, Georgetown University, Box 571227, Washington, DC 20057-1227
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Box 571227, Washington, DC 20057-1227
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Yin S, Wang Z, Bernstein ER. Formaldehyde and methanol formation from reaction of carbon monoxide and hydrogen on neutral Fe2S2 clusters in the gas phase. Phys Chem Chem Phys 2013; 15:4699-706. [DOI: 10.1039/c3cp50183c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Wilson TD, Yu Y, Lu Y. Understanding copper-thiolate containing electron transfer centers by incorporation of unnatural amino acids and the CuA center into the type 1 copper protein azurin. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.06.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Dau PD, Hruszkewycz DP, Huang DL, Chalkley MJ, Liu HT, Green JC, Hazari N, Wang LS. Photoelectron Spectroscopy of Palladium(I) Dimers with Bridging Allyl Ligands. Organometallics 2012. [DOI: 10.1021/om300956g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Phuong Diem Dau
- The Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Damian P. Hruszkewycz
- The Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut
06520, United States
| | - Dao-Ling Huang
- The Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Matthew J. Chalkley
- The Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut
06520, United States
| | - Hong-Tao Liu
- The Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Jennifer C. Green
- The
Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QR, U.K
| | - Nilay Hazari
- The Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut
06520, United States
| | - Lai-Sheng Wang
- The Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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16
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Feng YN, Xu FF, Chen RP, Wen N, Li ZH, Du SW. Preparation, structures and electrochemical property of diiron dithiolate complexes with hydrophilic N-donor ligands. J Organomet Chem 2012. [DOI: 10.1016/j.jorganchem.2012.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Luo Y, Niu S, Ichiye T. Understanding rubredoxin redox sites by density functional theory studies of analogues. J Phys Chem A 2012; 116:8918-24. [PMID: 22881577 DOI: 10.1021/jp3057509] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Determining the redox energetics of redox site analogues of metalloproteins is essential in unraveling the various contributions to electron transfer properties of these proteins. Since studies of the [4Fe-4S] analogues show that the energies are dependent on the ligand dihedral angles, broken symmetry density functional theory (BS-DFT) with the B3LYP functional and double-ζ basis sets calculations of optimized geometries and electron detachment energies of [1Fe] rubredoxin analogues are compared to crystal structures and gas-phase photoelectron spectroscopy data, respectively, for [Fe(SCH(3))(4)](0/1-/2-), [Fe(S(2)-o-xyl)(2)](0/1-/2-), and Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) in different conformations. In particular, the study of Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) is the only direct comparison of calculated and experimental gas phase detachment energies for the 1-/2- couple found in the rubredoxins. These results show that variations in the inner sphere energetics by up to ∼0.4 eV can be caused by differences in the ligand dihedral angles in either or both redox states. Moreover, these results indicate that the protein stabilizes the conformation that favors reduction. In addition, the free energies and reorganization energies of oxidation and reduction as well as electrostatic potential charges are calculated, which can be used as estimates in continuum electrostatic calculations of electron transfer properties of [1Fe] proteins.
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Affiliation(s)
- Yan Luo
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
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18
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Niu S, Ichiye T. Density functional theory calculations of redox properties of iron–sulphur protein analogues. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.582111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Perrin BS, Ichiye T. Fold versus sequence effects on the driving force for protein-mediated electron transfer. Proteins 2011; 78:2798-808. [PMID: 20635418 DOI: 10.1002/prot.22794] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Electron transport chains composed of electron transfer reactions mainly between proteins provide fast efficient flow of energy in a variety of metabolic pathways. Reduction potentials are essential characteristics of the proteins because they determine the driving forces for the electron transfers. As both polar and charged groups from the backbone and side chains define the electrostatic environment, both the fold and the sequence will contribute. However, although the role of a specific sequence may be determined by experimental mutagenesis studies of reduction potentials, understanding the role of the fold by experiment is much more difficult. Here, continuum electrostatics and density functional theory calculations are used to analyze reduction potentials in [4Fe-4S] proteins. A key feature is that multiple homologous proteins in three different folds are compared: six high potential iron-sulfur proteins, four bacterial ferredoxins, and four nitrogenase iron proteins. Calculated absolute reduction potentials are shown to be in quantitative agreement with electrochemical reduction potentials. Calculations further demonstrate that the contribution of the backbone is larger than that of the side chains and is consistent for homologous proteins but differs for nonhomologous proteins, indicating that the fold is the major protein factor determining the reduction potential, whereas the specific amino acid sequence tunes the reduction potential for a given fold. Moreover, the fold contribution is determined mainly by the proximity of the redox site to the protein surface and the orientation of the dipoles of backbone near the redox site.
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Affiliation(s)
- Bradley Scott Perrin
- Department of Chemistry, Georgetown University, Box 571227, Washington, District of Columbia 20057-1227, USA
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20
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Harris TV, Szilagyi RK. Nitrogenase structure and function relationships by density functional theory. Methods Mol Biol 2011; 766:267-291. [PMID: 21833874 DOI: 10.1007/978-1-61779-194-9_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Modern density functional theory has tremendous potential with matching popularity in metalloenzymology to reveal the unseen atomic and molecular details of structural data, spectroscopic measurements, and biochemical experiments by providing insights into unobservable structures and states, while also offering theoretical justifications for observed trends and differences. An often untapped potential of this theoretical approach is to bring together diverse experimental structural and reactivity information and allow for these to be critically evaluated at the same level. This is particularly applicable for the tantalizingly complex problem of the structure and molecular mechanism of biological nitrogen fixation. In this chapter we provide a review with extensive practical details of the compilation and evaluation of experimental data for an unbiased and systematic density functional theory analysis that can lead to remarkable new insights about the structure-function relationships of the iron-sulfur clusters of nitrogenase.
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Affiliation(s)
- Travis V Harris
- Department of Chemistry and Biochemistry, Astrobiology Biogeochemistry Research Center, Montana State University, Bozeman, MT 59717, USA.
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21
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Chen J, Vannucci AK, Mebi CA, Okumura N, Borowski SC, Swenson M, Lockett LT, Evans DH, Glass RS, Lichtenberger DL. Synthesis of Diiron Hydrogenase Mimics Bearing Hydroquinone and Related Ligands. Electrochemical and Computational Studies of the Mechanism of Hydrogen Production and the Role of O−H···S Hydrogen Bonding. Organometallics 2010. [DOI: 10.1021/om100396j] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jinzhu Chen
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721-0041
| | - Aaron K. Vannucci
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721-0041
| | - Charles A. Mebi
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721-0041
| | - Noriko Okumura
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721-0041
| | - Susan C. Borowski
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721-0041
| | - Matthew Swenson
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721-0041
| | - L. Tori Lockett
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721-0041
| | - Dennis H. Evans
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721-0041
| | - Richard S. Glass
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721-0041
| | - Dennis L. Lichtenberger
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721-0041
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Gámiz-Hernández AP, Galstyan AS, Knapp EW. Understanding Rubredoxin Redox Potentials: Role of H-Bonds on Model Complexes. J Chem Theory Comput 2009; 5:2898-908. [DOI: 10.1021/ct900328c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana Patricia Gámiz-Hernández
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Fabeckstrasse 36a, D-14195 Berlin, Germany
| | - Artur S. Galstyan
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Fabeckstrasse 36a, D-14195 Berlin, Germany
| | - Ernst-Walter Knapp
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Fabeckstrasse 36a, D-14195 Berlin, Germany
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23
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Niu S, Ichiye T. Probing ligand effects on the redox energies of [4Fe-4S] clusters using broken-symmetry density functional theory. J Phys Chem A 2009; 113:5671-6. [PMID: 19378988 DOI: 10.1021/jp809446q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A central issue in understanding redox properties of iron-sulfur proteins is determining the factors that tune the reduction potentials of the Fe-S clusters. Recently, Solomon and coworkers have shown that the Fe-S bond covalency of protein analogs measured by %L, the percent ligand character of the Fe 3d orbitals, from ligand K-edge X-ray absorption spectroscopy (XAS) correlates with the electrochemical redox potentials. Also, Wang and coworkers have measured electron detachment energies for iron-sulfur clusters without environmental perturbations by gas-phase photoelectron spectroscopy (PES). Here the correlations of the ligand character with redox energy and %L character are examined in [Fe(4)S(4)L(4)](2-) clusters with different ligands by broken symmetry density functional theory (BS-DFT) calculations using the B3LYP functional together with PES and XAS experimental results. These gas-phase studies assess ligand effects independently of environmental perturbations and thus provide essential information for computational studies of iron-sulfur proteins. The B3LYP oxidation energies agree well with PES data, and the %L character obtained from natural bond orbital analysis correlates with XAS values, although it systematically underestimates them because of basis set effects. The results show that stronger electron-donating terminal ligands increase %L(t), the percent ligand character from terminal ligands, but decrease %S(b), the percent ligand character from the bridging sulfurs. Because the oxidized orbital has significant Fe-L(t) antibonding character, the oxidation energy correlates well with %L(t). However, because the reduced orbital has varying contributions of both Fe-L(t) and Fe-S(b) antibonding character, the reduction energy does not correlate with either %L(t) or %S(b). Overall, BS-DFT calculations together with XAS and PES experiments can unravel the complex underlying factors in the redox energy and chemical bonding of the [4Fe-4S] clusters in iron-sulfur proteins.
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Affiliation(s)
- Shuqiang Niu
- Department of Chemistry, Georgetown University, Washington, DC 20057-1227, USA
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Abstract
The cleavage of [4Fe-4S]-type clusters is thought to be important in proteins such as Fe-S scaffold proteins and nitrogenase. However, most [4Fe-4S](2+) clusters in proteins have two antiferromagnetically coupled high-spin layers in which a minority spin is delocalized in each layer, thus forming a symmetric Fe(2.5+)-Fe(2.5+) pair, and how cleavage occurs between the irons is puzzling because of the shared electron. Previously, we proposed a novel mechanism for the fission of a [4Fe-4S] core into two [2Fe-2S] cores in which the minority spin localizes on one iron, thus breaking the symmetry and creating a transition state with two Fe(3+)-Fe(2+) pairs. Cleavage first through the weak Fe(2+)-S bonds lowers the activation energy. Here, we propose a test of this mechanism: break the symmetry of the cluster by changing the ligands to promote spin localization, which should enhance reactivity. The cleavage reactions for the homoligand [Fe(4)S(4)L(4)](2-) (L = SCH(3), Cl, H) and heteroligand [Fe(4)S(4)(SCH(3))(2)L(2)](2-) (L = Cl, H) clusters in the gas phase were examined via broken-symmetry density functional theory calculations. In the heteroligand clusters, the minority spin localized on the iron coordinated by the weaker electron-donor ligand, and the reaction energy and activation barrier of the cleavage were lowered, which is in accord with our proposed mechanism and consistent with photoelectron spectroscopy and collision-induced dissociation experiments. These studies suggest that proteins requiring facile fission of their [4Fe-4S] cluster in their biological function might have spin-localized [4Fe-4S] clusters.
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Affiliation(s)
- Shuqiang Niu
- Department of Chemistry, Georgetown University, Washington, D.C. 20057-1227, USA
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Niu S, Ichiye T. Insight into environmental effects on bonding and redox properties of [4Fe-4S] clusters in proteins. J Am Chem Soc 2009; 131:5724-5. [PMID: 19341280 DOI: 10.1021/ja900406j] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The large differences in redox potentials between the HiPIPs and ferredoxins are generally attributed to hydrogen bonds and electrostatic effects from the protein and solvent. Recent ligand K-edge X-ray absorption studies by Solomon and co-workers show that the Fe-S covalencies of [4Fe-4S] clusters in the two proteins differ considerably apparently because of hydrogen bonds from water, indicating electronic effects may be important. However, combined density function theory (DFT) and photoelectron spectroscopy studies by our group and Wang and co-workers indicate that hydrogen bonds tune the potential of [4Fe-4S] clusters by mainly electrostatics. The DFT studies here rationalize both results, namely that the observed change in the Fe-S covalency is due to differences in ligand conformation between the two proteins rather than hydrogen bonds. Moreover, the ligand conformation affects the calculated potentials by approximately 100 mV and, thus, is a heretofore unconsidered means of tuning the potential.
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Affiliation(s)
- Shuqiang Niu
- Department of Chemistry, Georgetown University, Washington, DC 20057-1227, USA
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26
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Niu S, Nichols JA, Ichiye T. Optimization of Spin-Unrestricted Density Functional Theory for Redox Properties of Rubredoxin Redox Site Analogues. J Chem Theory Comput 2009; 5:1361-1368. [PMID: 20161267 DOI: 10.1021/ct800357c] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum chemical calculations of metal clusters in proteins for redox studies require both computational feasibility as well as accuracies of at least ∼50 mV for redox energies but only ∼0.05 Å for bond lengths. Thus, optimization of spin-unrestricted density functional theory (DFT) methods, especially the hybrid generalized gradient approximation functionals, for energies while maintaining good geometries is essential. Here, different DFT functionals with effective core potential (ECP) and full core basis sets for [Fe(SCH(3))(4)](2-/1-) and [Fe(SCH(3))(3)](1-/0), which are analogs of the iron-sulfur protein rubredoxin, are investigated in comparison to experiment as well as other more computationally intensive electron correlation methods. In particular, redox energies are calibrated against gas-phase photoelectron spectroscopy data so no approximations for the environment are needed. B3LYP gives the best balance of accuracy in energy and geometry compared B97gga1 and BHandH and is better for energies than Møller-Plesset perturbation theory series (MP2, MP3, MP4SDQ) and comparable to coupled cluster [CCSD, CCSD(T)] methods. Of the full core basis sets tested, the 6-31G** basis sets give good geometries, and addition of diffuse functions to only the sulfur significantly improves the energies. Moreover, a basis set with an ECP on only the iron gives a less accurate but still reasonable geometries and energies.
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Affiliation(s)
- Shuqiang Niu
- Department of Chemistry, Georgetown University, Washington, DC 20057-1227
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27
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Krasilnikov PM, Knox PP, Rubin AB. Relaxation mechanism of molecular systems containing hydrogen bonds and free energy temperature dependence of reaction of charges recombination within Rhodobacter sphaeroides RC. Photochem Photobiol Sci 2009; 8:181-95. [PMID: 19247510 DOI: 10.1039/b811014j] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Wang XB, Wang LS. Development of a low-temperature photoelectron spectroscopy instrument using an electrospray ion source and a cryogenically controlled ion trap. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2008; 79:073108. [PMID: 18681692 DOI: 10.1063/1.2957610] [Citation(s) in RCA: 239] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The ability to control ion temperatures is critical for gas phase spectroscopy and has been a challenge in chemical physics. A low-temperature photoelectron spectroscopy instrument has been developed for the investigation of complex anions in the gas phase, including multiply charged anions, solvated species, and biological molecules. The new apparatus consists of an electrospray ionization source, a three dimensional (3D) Paul trap for ion accumulation and cooling, a time-of-flight mass spectrometer, and a magnetic-bottle photoelectron analyzer. A key feature of the new instrument is the capability to cool and tune ion temperatures from 10 to 350 K in the 3D Paul trap, which is attached to the cold head of a closed cycle helium refrigerator. Ion cooling is accomplished in the Paul trap via collisions with a background gas and has been demonstrated by observation of complete elimination of vibrational hot bands in photoelectron spectra of various anions ranging from small molecules to complex species. Further evidence of ion cooling is shown by the observation of H2-physisorbed anions at low temperatures. Cold anions result in better resolved photoelectron spectra due to the elimination of vibrational hot bands and yield more accurate energetic and spectroscopic information. Temperature-dependent studies are made possible for weakly bonded molecular and solvated clusters, allowing thermodynamic information to be obtained.
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Affiliation(s)
- Xue-Bin Wang
- Department of Physics, Washington State University, 2710 University Drive, Richland, Washington 99354, USA and Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, MS 8-88, P.O. Box 999, Richland, Washington 99352, USA
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Dey A, Green KN, Jenkins RM, Jeffrey SP, Darensbourg M, Hodgson KO, Hedman B, Solomon EI. S K-edge XAS and DFT calculations on square-planar NiII-thiolate complexes: effects of active and passive H-bonding. Inorg Chem 2007; 46:9655-60. [PMID: 17949080 DOI: 10.1021/ic7006292] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
S K-edge XAS for a low-spin NiII-thiolate complex shows a 0.2 eV shift to higher pre-edge energy but no change in Ni-S bond covalency upon H-bonding. This is different from the H-bonding effect we observed in high-spin FeIII-thiolate complexes where there is a significant decrease in Fe-S bond covalency but no change in energy due to H-bonding (Dey, A.; Okamura, T.-A.; Ueyama, N.; Hedman, B.; Hodgson, K. O.; Solomon, E. I. J. Am. Chem. Soc. 2005, 127, 12046-12053). These differences were analyzed using DFT calculations, and the results indicate that two different types of H-bonding interactions are possible in metal-thiolate systems. In the high-spin FeIII-thiolate case, the H-bonding involves a thiolate donor orbital which is also involved in bonding with the metal (active), while in the low-spin NiII-thiolate, the orbital involved in H-bonding is nonbonding with respect to the M-S bonding (passive). The contributions of active and passive H-bonds to the reduction potential and Lewis acid properties of a metal center are evaluated.
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Affiliation(s)
- Abhishek Dey
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Bönisch H, Schmidt CL, Bianco P, Ladenstein R. Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin: II. Introduction of an O–H···Sγ–Fe hydrogen bond increased the reduction potential by 65 mV. J Biol Inorg Chem 2007; 12:1163-71. [PMID: 17712580 DOI: 10.1007/s00775-007-0289-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Accepted: 08/01/2007] [Indexed: 10/22/2022]
Abstract
The effect of D-H...S(gamma)-Fe hydrogen bonding on the reduction potential of rubredoxin was investigated by the introduction of an O-H...S(gamma)-Fe hydrogen bond on the surface of Pyrococcus abyssi rubredoxin. The formation of a weak hydrogen bond between Ser44-O(gamma) and Cys42-S(gamma) in mutant W4L/R5S/A44S increased the reduction potential by 56 mV. When side effects of the mutation were taken into account, the contribution of the additional cluster hydrogen bond to the reduction potential was estimated to be +65 mV. The structural analysis was based on ultrahigh-resolution structures of oxidized P. abyssi rubredoxin W4L/R5S and W4L/R5S/A44S refined to 0.69 and 0.86 A, respectively.
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Affiliation(s)
- Heiko Bönisch
- Center of Biosciences, Karolinska Institutet, Hälsovägen 7-9, Huddinge, Sweden.
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31
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Waters T, Wang XB, Wang LS. Electrospray ionization photoelectron spectroscopy: Probing the electronic structure of inorganic metal complexes in the gas-phase. Coord Chem Rev 2007. [DOI: 10.1016/j.ccr.2006.04.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Woo HK, Lau KC, Wang XB, Wang LS. Observation of Cysteine Thiolate and-S···H−O Intermolecular Hydrogen Bond. J Phys Chem A 2006; 110:12603-6. [PMID: 17107110 DOI: 10.1021/jp0643799] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cysteine anion was produced in the gas phase by electrospray ionization and investigated by photoelectron spectroscopy at low temperature (70 K). The cysteine anion was found to exhibit the thiolate form [-SCH2CH(NH2)CO2H], rather than the expected carboxylate form [HSCH2CH(NH2)CO2-]. This observation was confirmed by two control experiments, that is, methyl cysteine [CH3SCH2CH(NH2)CO2-] and cysteine methyl ester [-SCH2CH(NH2)CO2CH3]. The electron binding energy of [-SCH2CH(NH2)CO2H] was measured to be about 0.7 eV blue-shifted relative to [-SCH2CH(NH2)CO2CH3] due to the formation of an intramolecular -S-...HO2C- hydrogen bond in the cysteine thiolate. Theoretical calculations at the CCSD(T)/6-311++G(2df,p) and B3LYP/6-311++G(2df,p) levels were carried out to estimate the strength of this intramolecular -S-...HO2C- hydrogen bond. Combining experimental measurements and theoretical calculations yielded an estimated value of 16.4 +/- 2.0 kcal/mol for the -S-...HO2C- intramolecular hydrogen-bond strength.
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Affiliation(s)
- Hin-Koon Woo
- Department of Physics, Washington State University, 2710 University Drive, Richland, Washington 99354, USA
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Glaser T, Liratzis I, Kataeva O, Fröhlich R, Piacenza M, Grimme S. Direct influence of hydrogen-bonding on the reduction potential of a CuII center. Chem Commun (Camb) 2006:1024-6. [PMID: 16491197 DOI: 10.1039/b517340j] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two hydrogen-bonds from geometrically constrained OH groups to coordinated oxygen donors shift the reduction potential of a Cu(II) complex by +270 mV as compared to the structurally analogous reference complex missing the OH groups.
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Affiliation(s)
- Thorsten Glaser
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany.
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Dey A, Okamura TA, Ueyama N, Hedman B, Hodgson KO, Solomon EI. Sulfur K-edge XAS and DFT calculations on P450 model complexes: effects of hydrogen bonding on electronic structure and redox potentials. J Am Chem Soc 2005; 127:12046-53. [PMID: 16117545 PMCID: PMC2880190 DOI: 10.1021/ja0519031] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen bonding (H-bonding) is generally thought to play an important role in tuning the electronic structure and reactivity of metal-sulfur sites in proteins. To develop a quantitative understanding of this effect, S K-edge X-ray absorption spectroscopy (XAS) has been employed to directly probe ligand-metal bond covalency, where it has been found that protein active sites are significantly less covalent than their related model complexes. Sulfur K-edge XAS data are reported here on a series of P450 model complexes with increasing H-bonding to the ligated thiolate from its substituent. The XAS spectroscopic results show a dramatic decrease in preedge intensity. DFT calculations reproduce these effects and show that the observed changes are in fact solely due to H-bonding and not from the inductive effect of the substituent on the thiolate. These calculations also indicate that the H-bonding interaction in these systems is mainly dipolar in nature. The -2.5 kcal/mol energy of the H-bonding interaction was small relative to the large change in ligand-metal bond covalency (30%) observed in the data. A bond decomposition analysis of the total energy is developed to correlate the preedge intensity change to the change in Fe-S bonding interaction on H-bonding. This effect is greater for the reduced than the oxidized state, leading to a 260 mV increase in the redox potential. A simple model shows that E degrees should vary approximately linearly with the covalency of the Fe-S bond in the oxidized state, which can be determined directly from S K-edge XAS.
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Affiliation(s)
- Abhishek Dey
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Taka-aki Okamura
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Norikazu Ueyama
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Britt Hedman
- Stanford Synchrotron Radiation Laboratory, Stanford University, SLAC, Menlo Park, 94025
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Stanford Synchrotron Radiation Laboratory, Stanford University, SLAC, Menlo Park, 94025
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Corresponding author:
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35
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Lewiński J, Bury W, Justyniak I. Significance of Intermolecular S···C(π) Interaction Involving M-S and -C=O Centers in Crystal Structures of Metal Thiolate Complexes. Eur J Inorg Chem 2005. [DOI: 10.1002/ejic.200500668] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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36
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Fu YJ, Yang X, Wang XB, Wang LS. Probing the Electronic Structure of [2Fe-2S] Clusters with Three Coordinate Iron Sites by Use of Photoelectron Spectroscopy. J Phys Chem A 2005; 109:1815-20. [PMID: 16833511 DOI: 10.1021/jp045177k] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Five series of [2Fe-2S] complexes, [Fe(2)S(2)Cl(2)(-)(x)(CN)(x)](-), [Fe(2)S(2)(SEt)(2)(-)(x)Cl(x)](-), [Fe(2)S(2)(SEt)(2)(-)(x)(CN)(x)](-), [Fe(2)S(2)Cl(2)(-)(x)(OAc)(x)](-) (OAc = acetate), and [Fe(2)S(2)(SEt)(2)(-)(x)(OPr)(x)](-) (OPr = propionate) (x = 0-2), were produced by collision-induced dissociation of the corresponding [4Fe-4S] complexes, and their electronic structures were studied by photoelectron spectroscopy. All the [2Fe-2S] complexes contain a [Fe(2)S(2)](+) core similar to that in reduced [2Fe] ferredoxins but with different coordination geometries. For the first three series, which only involve tricoordinated Fe sites, a linear relationship between the measured binding energies and the substitution number (x) was observed, revealing the independent ligand contributions to the total electron binding energies. The effect of the ligand increases in the order SEt --> Cl --> CN, conforming to their electron-withdrawing ability in the same order. The carboxylate ligands in the [Fe(2)S(2)Cl(2)(-)(x)(OAc)(x)](-) and [Fe(2)S(2)(SEt)(2)(-)(x)(OPr)(x)](-) complexes were observed to act as bidentate ligands, giving rise to tetracoordinated iron sites. This is different from their monodentate coordination behavior in the [4Fe-4S] cubane complexes, reflecting the high reactivity of the unsatisfied three-coordinate iron site in the [2Fe-2S] complexes. The [2Fe-2S] complexes with tetracoordinated iron sites exhibit lower electron binding energies, that is, higher reductive activity than the all tricoordinate planar clusters. The electronic structures of all the [2Fe-2S] complexes were shown to conform to the "inverted energy level scheme".
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Affiliation(s)
- You-Jun Fu
- W. R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
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