skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: How Accurately Can Extended X-ray Absorption Spectra Be Predicted from First Principles? Implications for Modeling the Oxygen-Evolving Complex in Photosystem II

Journal Article · · Journal of the American Chemical Society
DOI:https://doi.org/10.1021/jacs.5b00783· OSTI ID:1249121
; ; ; ; ; ; ; ; ; ; ; ; ;

Research Organization:
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Sponsoring Organization:
USDOE
DOE Contract Number:
AC52-07NA27344
OSTI ID:
1249121
Report Number(s):
LLNL-JRNL-651665
Journal Information:
Journal of the American Chemical Society, Vol. 137, Issue 40; ISSN 0002-7863
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English

References (70)

The molybdenum site of nitrogenase. Preliminary structural evidence from x-ray absorption spectroscopy journal May 1978
State of manganese in the photosynthetic apparatus. 1. Extended x-ray absorption fine structure studies on chloroplasts and di-.mu.-oxo-bridged dimanganese model compounds journal September 1981
An Fe2IVO2 Diamond Core Structure for the Key Intermediate Q of Methane Monooxygenase journal January 1997
EXAFS Characterization of the Intermediate X Generated During the Assembly of the Escherichia coli Ribonucleotide Reductase R2 Diferric Tyrosyl Radical Cofactor journal February 1998
X-ray absorption spectroscopy of chloroperoxidase compound I: Insight into the reactive intermediate of P450 chemistry journal November 2005
On the status of ferryl protonation journal April 2006
Nature of the Intermediate Formed in the Reduction of O 2 to H 2 O at the Trinuclear Copper Cluster Active Site in Native Laccase journal May 2002
On the structure of the manganese complex of photosystem II: extended-range EXAFS data and specific atomic-resolution models for four S-states journal October 2007
The Manganese Complex of Oxygenic Photosynthesis Conversion of FiveCoordinated MnIII to SixCoordinated MnIV in the S2S3 Transition is Implied by XANES Simulations journal January 2005
Structural Changes of the Oxygen-evolving Complex in Photosystem II during the Catalytic Cycle journal June 2013
Structural models of the manganese complex of photosystem II and mechanistic implications journal January 2012
Structural and Oxidation State Changes of the Photosystem II Manganese Complex in Four Transitions of the Water Oxidation Cycle (S 0 → S 1 , S 1 → S 2 , S 2 → S 3 , and S 3,4 → S 0 ) Characterized by X-ray Absorption Spectroscopy at 20 K and Room Temperature † journal February 2005
Structure and Orientation of the Mn 4 Ca Cluster in Plant Photosystem II Membranes Studied by Polarized Range-extended X-ray Absorption Spectroscopy journal December 2006
Where Water Is Oxidized to Dioxygen: Structure of the Photosynthetic Mn4Ca Cluster journal November 2006
Mn 4 Ca Cluster in Photosynthesis: Where and How Water is Oxidized to Dioxygen journal March 2014
Simulation of the isotropic EXAFS spectra for the S 2 and S 3 structures of the oxygen evolving complex in photosystem II journal March 2015
Theoretical EXAFS studies of a model of the oxygen-evolving complex of photosystem II obtained with the quantum cluster approach journal May 2012
S 1 -State Model of the O 2 -Evolving Complex of Photosystem II journal July 2011
A Model of the Oxygen-Evolving Center of Photosystem II Predicted by Structural Refinement Based on EXAFS Simulations journal May 2008
Structure of the Oxygen Evolving Complex of Photosystem II at Room Temperature journal February 2015
EXAFS structure refinement supplemented by computational chemistry journal December 2006
Accurate metal-site structures in proteins obtained by combining experimental data and quantum chemistry journal January 2007
Ab initio theory and calculations of X-ray spectra journal July 2009
Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses journal November 2014
Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å journal April 2011
Water oxidation mechanism in photosystem II, including oxidations, proton release pathways, O―O bond formation and O2 release journal August 2013
Quantum Mechanics/Molecular Mechanics Study of the Catalytic Cycle of Water Splitting in Photosystem II journal March 2008
Structure of the oxygen-evolving complex of photosystem II: information on the S2 state through quantum chemical calculation of its magnetic properties journal January 2009
Theoretical modelling of biomolecular systems I. Large-scale QM/MM calculations of hydrogen-bonding networks of the oxygen evolving complex of photosystem II journal August 2014
Large-Scale QM/MM Calculations of Hydrogen Bonding Networks for Proton Transfer and Water Inlet Channels for Water Oxidation—Theoretical System Models of the Oxygen-Evolving Complex of Photosystem II book January 2015
Origin of the Zero-Field Splitting in Mononuclear Octahedral Dihalide Mn II Complexes:  An Investigation by Multifrequency High-Field Electron Paramagnetic Resonance and Density Functional Theory journal June 2007
Structural Characterization and Electronic Properties Determination by High-Field and High-Frequency EPR of a Series of Five-Coordinated Mn(II) Complexes journal October 2004
High-Spin Chloro Mononuclear Mn III Complexes: A Multifrequency High-Field EPR Study journal February 2005
Redox-Induced μ-Acetato and μ-Oxo Core Interconversions in Dinuclear Manganese Tris(2-methylpyridyl)amine (tpa) Complexes: Isolation and Characterization of [Mn2III(μ-O)(μ-O2CCH3)(tpa)2]3+ journal July 2007
Synthesis and characterization of the binuclear mixed valence complex di-μ-oxobis[tris(2-methyl-pyridyl)amine] dimanganese(III, IV) dithionate heptahydrate, [(tpa)MnO]2(S2O6)3/2·7H2O journal January 1988
Mononuclear Mn III and Mn IV Bis-terpyridine Complexes: Electrochemical Formation and Spectroscopic Characterizations journal April 2009
An Unusual Stable Mononuclear Mn III Bis-terpyridine Complex Exhibiting Jahn-Teller Compression: Electrochemical Synthesis, Physical Characterisation and Theoretical Study journal December 2008
Molecular and Electronic Structures of Mononuclear Iron Complexes Using Strongly Electron-Donating Ligands and their Oxidized Forms journal June 2008
Relativistic calculations of spin-dependent x-ray-absorption spectra journal July 1997
Parameter-free calculations of X-ray spectra with FEFF9 journal January 2010
A weak antiferromagnetic interaction between manganese(2+) centers through a TCNQ column: crystal structures and magnetic properties of [MnII(tpa)(TCNQ)(CH3OH)](TCNQ)2.cntdot.CH3CN, [MnII(tpa)(.mu.-O2CCH3)]2(TCNQ)2.cntdot.2CH3CN, and [MnII(tpa)(NCS)2].cntdot.CH3CN (tpa = tris(2-pyridylmethyl)amine) journal December 1993
Aerobic Catechol Oxidation Catalyzed by a Bis(μ-oxo)dimanganese(III,III) Complex via a Manganese(II)−Semiquinonate Complex journal May 2005
Carboxylate Ligands Drastically Enhance the Rates of Oxo Exchange and Hydrogen Peroxide Disproportionation by Oxo Manganese Compounds of Potential Biological Significance journal March 2008
The ORCA program system: The ORCA program system journal June 2011
Multiple-scattering x-ray-absorption fine-structure Debye-Waller factor calculations journal January 1999
Characterization of a Genuine Iron(V)−Nitrido Species by Nuclear Resonant Vibrational Spectroscopy Coupled to Density Functional Calculations journal September 2007
Manganese K-Edge X-Ray Absorption Spectroscopy as a Probe of the Metal–Ligand Interactions in Coordination Compounds journal December 2011
Density-functional exchange-energy approximation with correct asymptotic behavior journal September 1988
Density-functional approximation for the correlation energy of the inhomogeneous electron gas journal June 1986
Relativistic regular two‐component Hamiltonians journal September 1993
Molecular density functional calculations in the regular relativistic approximation: Method, application to coinage metal diatomics, hydrides, fluorides and chlorides, and comparison with first-order relativistic calculations journal July 1998
All-Electron Scalar Relativistic Basis Sets for Third-Row Transition Metal Atoms journal May 2008
All-electron basis sets for heavy elements: All-electron basis sets for heavy elements journal July 2014
Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy journal January 2005
Semiempirical GGA-type density functional constructed with a long-range dispersion correction journal January 2006
Accurate description of van der Waals complexes by density functional theory including empirical corrections journal January 2004
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu journal April 2010
An Energetic Comparison of Different Models for the Oxygen Evolving Complex of Photosystem II journal December 2009
Rapid Loss of Structural Motifs in the Manganese Complex of Oxygenic Photosynthesis by X-ray Irradiation at 10–300 K journal December 2005
Oxygen-Evolving Mn Cluster in Photosystem II: The Protonation Pattern and Oxidation State in the High-Resolution Crystal Structure journal April 2012
Harmonic vibrational frequencies: Scale factors for pure, hybrid, hybrid meta, and double-hybrid functionals in conjunction with correlation consistent basis sets journal May 2011
Spectroscopic and Theoretical Investigations of Vibrational Frequencies in Binary Unsaturated Transition-Metal Carbonyl Cations, Neutrals, and Anions journal July 2001
Theoretical Evaluation of Structural Models of the S 2 State in the Oxygen Evolving Complex of Photosystem II: Protonation States and Magnetic Interactions journal December 2011
Two Interconvertible Structures that Explain the Spectroscopic Properties of the Oxygen-Evolving Complex of Photosystem II in the S 2 State journal August 2012
Analysis of the Radiation-Damage-Free X-ray Structure of Photosystem II in Light of EXAFS and QM/MM Data journal February 2015
Metal oxidation states in biological water splitting journal January 2015
On the guiding principles for lucid understanding of the damage-free S1 structure of the CaMn4O5 cluster in the oxygen evolving complex of photosystem II journal May 2015
Reproducible radiation-damage processes in proteins irradiated by intense x-ray pulses journal February 2015
A close look at dose: Toward L-edge XAS spectral uniformity, dose quantification and prediction of metal ion photoreduction journal January 2015
Biological Water Oxidation journal March 2013

Cited By (1)

Non-patchy strategy for inter-atomic distances from Extended X-ray Absorption Fine Structure journal February 2017

Linked Research (1)

Similar Records

How Accurately Can Extended X-ray Absorption Spectra Be Predicted from First Principles? Implications for Modeling the Oxygen-Evolving Complex in Photosystem II
Journal Article · Wed Sep 09 00:00:00 EDT 2015 · Journal of the American Chemical Society · OSTI ID:1249121
+11 more
The O 2 -Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data
Journal Article · Wed Dec 21 00:00:00 EST 2016 · Accounts of Chemical Research · OSTI ID:1249121
Comparison of the manganese oxygen-evolving complex in photosystem II of spinach and Synechococcus sp. with multinuclear manganese model compounds by X-ray absorption spectroscopy
Journal Article · Wed Jun 15 00:00:00 EDT 1994 · Journal of the American Chemical Society; (United States) · OSTI ID:1249121
+3 more

Related Subjects

37 INORGANIC
ORGANIC
PHYSICAL AND ANALYTICAL CHEMISTRY