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

Title: Characterizing the Intermediates Compound I and II in the Cytochrome P450 Catalytic Cycle with Nonlinear X‐ray Spectroscopy: A Simulation Study

Journal Article · · ChemPhysChem

Abstract Cytochrome P450 enzymes are an important family of biocatalysts that oxidize chemically inert CH bonds. There are many unresolved questions regarding the catalytic reaction intermediates, in particular P450 Compound I (Cpd‐I) and II (Cpd‐II). By using simple molecular models, we simulate various X‐ray spectroscopy signals, including X‐ray absorption near‐edge structure (XANES), resonant inelastic X‐ray scattering (RIXS), and stimulated X‐ray Raman spectroscopy (SXRS) of the low‐ and high‐spin states of Cpd‐I and II. Characteristic peak patterns are presented and connected to the corresponding electronic structures. These X‐ray spectroscopy techniques are complementary to more conventional infrared and optical spectroscopy and they help to elucidate the evolving electronic structures of transient species along the reaction path.

Sponsoring Organization:
USDOE
Grant/Contract Number:
DE‐FG02‐04ER15571
OSTI ID:
1400919
Journal Information:
ChemPhysChem, Journal Name: ChemPhysChem Vol. 16 Journal Issue: 9; ISSN 1439-4235
Publisher:
Wiley Blackwell (John Wiley & Sons)Copyright Statement
Country of Publication:
Germany
Language:
English
Citation Metrics:
Cited by: 4 works
Citation information provided by
Web of Science

References (92)

Preparation and Reactivity of Oxoiron(IV) Porphyrins journal October 1994
Three-dimensional attosecond resonant stimulated X-ray Raman spectroscopy of electronic excitations in core-ionized glycine journal January 2014
Hydrogen Atom Abstraction and Hydride Transfer Reactions by Iron(IV)-Oxo Porphyrins journal September 2008
Kinetic Characterization of Compound I Formation in the Thermostable Cytochrome P450 CYP119 journal January 2002
Spectroscopic characterization of cytochrome P450 Compound I journal March 2011
Multiplet effects in X-ray spectroscopy journal January 2005
Spectra and Kinetic Studies of the Compound I Derivative of Cytochrome P450 119 journal October 2008
Free-Electron Laser Design for Four-Wave Mixing Experiments with Soft-X-Ray Pulses journal July 2014
Probing valence electronic wave-packet dynamics by all x-ray stimulated Raman spectroscopy: A simulation study journal July 2007
Cytochromes P450: Roles in Diseases journal April 2013
Double-core excitations in formamide can be probed by X-ray double-quantum-coherence spectroscopy journal April 2013
Linear-Response and Real-Time Time-Dependent Density Functional Theory Studies of Core-Level Near-Edge X-Ray Absorption journal August 2012
Ab initio effective core potentials for molecular calculations. Potentials for K to Au including the outermost core orbitals journal January 1985
Über die Streuung von Strahlung durch Atome journal February 1925
Substrate Modulation of the Properties and Reactivity of the Oxy-Ferrous and Hydroperoxo-Ferric Intermediates of Cytochrome P450cam As Shown by Cryoreduction-EPR/ENDOR Spectroscopy journal February 2005
Resonant Inelastic X-ray Scattering on Ferrous and Ferric Bis-imidazole Porphyrin and Cytochrome c : Nature and Role of the Axial Methionine–Fe Bond journal December 2014
Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen journal January 1989
X-ray absorption spectroscopic characterization of a cytochrome P450 compound II derivative journal January 2008
Metal–Ligand Covalency of Iron Complexes from High-Resolution Resonant Inelastic X-ray Scattering journal October 2013
Two-dimensional stimulated resonance Raman spectroscopy of molecules with broadband x-ray pulses journal May 2012
Catalytic Mechanism of Cytochrome P450 for 5′-Hydroxylation of Nicotine: Fundamental Reaction Pathways and Stereoselectivity journal May 2011
Time-dependent density functional theory calculations of the spectroscopy of core electrons journal January 2010
C-H bond activation in heme proteins: the role of thiolate ligation in cytochrome P450 journal February 2009
Cytochrome P450: The Active Oxidant and Its Spectrum journal April 2010
Sequential Electron-Transfer and Proton-Transfer Pathways in Hydride-Transfer Reactions from Dihydronicotinamide Adenine Dinucleotide Analogues to Non-heme Oxoiron(IV) Complexes and p -Chloranil. Detection of Radical Cations of NADH Analogues in Acid-Promoted Hydride-Transfer Reactions journal November 2008
Hydrogen Atom Abstraction and Hydride Transfer Reactions by Iron(IV)-Oxo Porphyrins journal September 2008
On the status of ferryl protonation journal April 2006
Stimulated X-ray emission for materials science journal August 2013
Cytochrome P450 and Chemical Toxicology journal January 2008
Structure and Chemistry of Cytochrome P450 journal June 2005
One oxidant, many pathways: a theoretical perspective of monooxygenation mechanisms by cytochrome P450 enzymes journal July 2004
Time-Dependent Density Functional Theory Study of the X-ray Absorption Spectroscopy of Acetylene, Ethylene, and Benzene on Si(100) journal January 2007
Recent advances on ultrafast X-ray spectroscopy in the chemical sciences journal January 2014
Time dependent density functional theory of core electrons excitations journal May 2003
Human cytochromes P450 in health and disease journal February 2013
The Catalytic Pathway of Cytochrome P450cam at Atomic Resolution journal March 2000
Evidence for Basic Ferryls in Cytochromes P450 journal September 2006
Electronic Structure of Compound I in Human Isoforms of Cytochrome P450 from QM/MM Modeling journal September 2005
Self‐consistent molecular orbital methods. XXIII. A polarization‐type basis set for second‐row elements journal October 1982
Core and valence excitations in resonant X-ray spectroscopy using restricted excitation window time-dependent density functional theory journal November 2012
NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations journal September 2010
Reaction of Ferric Cytochrome P450cam with Peracids: KINETIC CHARACTERIZATION OF INTERMEDIATES ON THE REACTION PATHWAY journal March 2005
Fe L-Edge X-ray Absorption Spectra of Fe(II) Polypyridyl Spin Crossover Complexes from Time-Dependent Density Functional Theory journal December 2013
Cytochrome P450 enzymes: Central players in cardiovascular health and disease journal November 2006
Reactivity of Compound II: Electronic Structure Analysis of Methane Hydroxylation by Oxoiron(IV) Porphyrin Complexes journal September 2012
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
Density‐functional thermochemistry. III. The role of exact exchange journal April 1993
First Direct Evidence for Stereospecific Olefin Epoxidation and Alkane Hydroxylation by an Oxoiron(IV) Porphyrin Complex journal December 2003
Time-dependent density functional calculations of ligand K-edge X-ray absorption spectra journal March 2008
The Elusive Oxidant Species of Cytochrome P450 Enzymes:  Characterization by Combined Quantum Mechanical/Molecular Mechanical (QM/MM) Calculations journal July 2002
Evidence for Two Ferryl Species in Chloroperoxidase Compound II journal May 2006
Resonant X-ray Raman scattering journal May 1999
Simulating Ru L 3 -Edge X-ray Absorption Spectroscopy with Time-Dependent Density Functional Theory: Model Complexes and Electron Localization in Mixed-Valence Metal Dimers journal May 2013
Amplified X-Ray Emission from Core-Ionized Diatomic Molecules journal January 2013
Generation of oxoiron(IV) tetramesitylporphyrin π-cation radical complexes by m-CPBA oxidation of ferric tetramesitylporphyrin derivatives in butyronitrile at −78 °C. Evidence for the formation of six-coordinate oxoiron(IV) tetramesitylporphyrin π-cation radical complexes FeIV=O(tmp)X (X=Cl−, Br−), by Mössbauer and X-ray absorption spectroscopy journal January 2000
Hydrocarbon Hydroxylation by Cytochrome P450 Enzymes journal February 2010
Understanding excitation energy transfer in metalloporphyrin heterodimers with different linkers, bonding structures, and geometries through stimulated X-ray Raman spectroscopy journal March 2014
Quantum Mechanical/Molecular Mechanical Investigation of the Mechanism of C−H Hydroxylation of Camphor by Cytochrome P450 c am :  Theory Supports a Two-State Rebound Mechanism journal March 2004
Bethe–Salpeter treatment of X-ray absorption including core-hole multiplet effects journal June 2005
Medium Polarization and Hydrogen Bonding Effects on Compound I of Cytochrome P450:  What Kind of a Radical Is It Really? journal December 2000
Application of Badger's Rule to Heme and Non-Heme Iron−Oxygen Bonds:  An Examination of Ferryl Protonation States journal February 2006
Correlated ab Initio Electronic Structure Calculations for Large Molecules journal April 1999
Multidimensional x-ray spectroscopy of valence and core excitations in cysteine journal April 2013
Theoretical study of N-dealkylation of N-cyclopropyl-N-methylaniline catalyzed by cytochrome P450: insight into the origin of the regioselectivity journal January 2009
Watching energy transfer in metalloporphyrin heterodimers using stimulated X-ray Raman spectroscopy journal September 2013
Monitoring Long-Range Electron Transfer Pathways in Proteins by Stimulated Attosecond Broadband X-ray Raman Spectroscopy journal October 2014
Experimental Demonstration of Femtosecond Two-Color X-Ray Free-Electron Lasers journal March 2013
Recent density functional theory model calculations of drug metabolism by cytochrome P450 journal June 2012
Time-dependent density functional theory within the Tamm–Dancoff approximation journal December 1999
What is the Active Species of Cytochrome P450 during Camphor Hydroxylation? QM/MM Studies of Different Electronic States of Compound I and of Reduced and Oxidized Iron−Oxo Intermediates journal July 2007
Evidence for Compound I Formation in the Reaction of Cytochrome-P450cam with m-Chloroperbenzoic Acid journal June 1994
Cryotrapped Reaction Intermediates of Cytochrome P450 Studied by Radiolytic Reduction with Phosphorus-32 journal January 2001
Resonance Raman spectroscopy of chloroperoxidase compound II provides direct evidence for the existence of an iron(IV)-hydroxide journal August 2006
Structural characterization of horseradish peroxidase using EXAFS spectroscopy. Evidence for Fe = O ligation in compounds I and II journal November 1986
X-ray absorption spectroscopy of chloroperoxidase compound I: Insight into the reactive intermediate of P450 chemistry journal November 2005
The Experimentally Elusive Oxidant of Cytochrome P450: A Theoretical “Trapping” Defining More Closely the “Real” Species journal November 2001
Theoretical Perspective on the Structure and Mechanism of Cytochrome P450 Enzymes journal June 2005
Reactive Intermediates in Cytochrome P450 Catalysis journal April 2013
Multidimensional Attosecond Resonant X-Ray Spectroscopy of Molecules: Lessons from the Optical Regime journal April 2013
Kinetics of Oxidation of Benzphetamine by Compounds I of Cytochrome P450 2B4 and Its Mutants journal March 2009
Modeling Near-Edge Fine Structure X-ray Spectra of the Manganese Catalytic Site for Water Oxidation in Photosystem II journal October 2012
Simulation and visualization of attosecond stimulated x-ray Raman spectroscopy signals in trans -N-methylacetamide at the nitrogen and oxygen K-edges journal March 2011
Photochemical Processes Revealed by X-ray Transient Absorption Spectroscopy journal November 2013
The mystery of cytochrome P450 Compound I journal January 2011
Spin equilibrium and O2-binding kinetics of Mycobacterium tuberculosis CYP51 with mutations in the histidine–threonine dyad journal July 2014
Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields journal November 1994
Cytochrome P450 pharmacogenetics and cancer journal March 2006
Cytochrome P450 Compound I: Capture, Characterization, and C-H Bond Activation Kinetics journal November 2010
Oxoiron(IV) in Chloroperoxidase Compound II Is Basic: Implications for P450 Chemistry journal June 2004
Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study journal February 2007
P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations journal February 2010
Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules journal March 1972

Similar Records

Functional and structural insight into the flexibility of cytochrome P450 reductases from Sorghum bicolor and its implications for lignin composition
Journal Article · Fri Apr 01 00:00:00 EDT 2022 · Journal of Biological Chemistry · OSTI ID:1400919

Synthetic Model Complex of the Key Intermediate in Cytochrome P450 Nitric Oxide Reductase
Journal Article · Wed Jan 09 00:00:00 EST 2019 · Inorganic Chemistry · OSTI ID:1400919

A High‐Throughput Mass Spectrometric Enzyme Activity Assay Enabling the Discovery of Cytochrome P450 Biocatalysts
Journal Article · Wed May 29 00:00:00 EDT 2019 · Angewandte Chemie (International Edition) · OSTI ID:1400919

Related Subjects