Impact of finite‐temperature and condensed‐phase effects on theoretical X‐ray absorption spectra of transition metal complexes

The impact of condensed‐phase and finite‐temperature effects on the theoretical X‐ray absorption spectra of transition metal complexes is assessed. The former are included in terms of the all‐electron Gaussian and augmented plane‐wave approach, whereas the latter are taken into account by extensive ensemble averaging along second‐generation Car–Parrinello ab initio molecular dynamics trajectories. We find that employing the periodic boundary conditions and including finite‐temperature effects systematically improves the agreement between our simulated X‐ray absorption spectra and experimental measurements. © 2018 Wiley Periodicals, Inc.

[1]  Peter M W Gill,et al.  Self-consistent-field calculations of core excited states. , 2009, The Journal of chemical physics.

[2]  J. Nocedal.  Updating Quasi-Newton Matrices With Limited Storage , 1980 .

[3]  Matthias Krack,et al.  Efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics. , 2007, Physical review letters.

[4]  Marcella Iannuzzi,et al.  X-ray absorption spectra of hexagonal ice and liquid water by all-electron Gaussian and augmented plane wave calculations. , 2008, The Journal of chemical physics.

[5]  Giulia Galli,et al.  X-ray absorption spectra of water from first principles calculations. , 2006, Physical review letters.

[6]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[7]  Friedhelm Bechstedt,et al.  Many-Body Approach to Electronic Excitations: Concepts and Applications , 2016 .

[8]  Michele Parrinello,et al.  Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach , 2005, Comput. Phys. Commun..

[9]  Matthias Krack,et al.  Static and Dynamical Properties of Liquid Water from First Principles by a Novel Car-Parrinello-like Approach. , 2009, Journal of chemical theory and computation.

[10]  Matthias Bauer,et al.  X-ray spectroscopic verification of the active species in iron-catalyzed cross-coupling reactions. , 2013, Chemistry.

[11]  Matthias Bauer,et al.  HERFD-XAS and valence-to-core-XES: new tools to push the limits in research with hard X-rays? , 2014, Physical chemistry chemical physics : PCCP.

[12]  Stefan Goedecker,et al.  Efficient solution of Poisson's equation with free boundary conditions. , 2006, The Journal of chemical physics.

[13]  Kristina O. Kvashnina,et al.  Reflections on hard X-ray photon-in/photon-out spectroscopy for electronic structure studies , 2013 .

[14]  J. Janak,et al.  Proof that ? E /? n i =e in density-functional theory , 1978 .

[15]  Harry B. Gray,et al.  Copper coordination in blue proteins , 2000, JBIC Journal of Biological Inorganic Chemistry.

[16]  Uwe Bergmann,et al.  High resolution 1s core hole X-ray spectroscopy in 3d transition metal complexes—electronic and structural information , 2005 .

[17]  Alexander Hoffmann,et al.  Experimental and Theoretical High-Energy-Resolution X-ray Absorption Spectroscopy: Implications for the Investigation of the Entatic State. , 2016, Inorganic chemistry.

[18]  Yu Zhang,et al.  Simulating Valence-to-Core X-ray Emission Spectroscopy of Transition Metal Complexes with Time-Dependent Density Functional Theory. , 2015, Journal of chemical theory and computation.

[19]  Marcella Iannuzzi,et al.  Ground and excited state density functional calculations with the Gaussian and augmented-plane-wave method , 2005 .

[20]  Marcella Iannuzzi,et al.  Inner-shell spectroscopy by the Gaussian and augmented plane wave method. , 2007, Physical chemistry chemical physics : PCCP.

[21]  Harry B. Gray,et al.  Type Zero Copper Proteins , 2009, Nature chemistry.

[22]  Frank Neese,et al.  The protonation states of oxo-bridged Mn(IV) dimers resolved by experimental and computational Mn K pre-edge X-ray absorption spectroscopy. , 2013, Inorganic chemistry.

[23]  Helmut Bertagnolli,et al.  X‐Ray Absorption Spectroscopy of Amorphous Solids, Liquids, and Catalytic and Biochemical Systems—Capabilities and Limitations , 1994 .

[24]  Uwe Kolb,et al.  Investigation of the Formation Reaction and Structural Characterization of the „Platinum Grignard Reagent”︁ [Pt(MgCl)2(THF)x] by Extended X‐ray absorption fine structure (EXAFS) and Other methods , 1997 .

[25]  Frank Neese,et al.  Molybdenum L-Edge XAS Spectra of MoFe Nitrogenase , 2014, Zeitschrift fur anorganische und allgemeine Chemie.

[26]  Matthias Bauer,et al.  X-Ray absorption in homogeneous catalysis research: the iron-catalyzed Michael addition reaction by XAS, RIXS and multi-dimensional spectroscopy. , 2010, Physical chemistry chemical physics : PCCP.

[27]  Julia Stanek,et al.  Implications of Guanidine Substitution on Copper Complexes as Entatic‐State Models , 2016 .

[28]  Eric L. Shirley,et al.  AB INITIO INCLUSION OF ELECTRON-HOLE ATTRACTION : APPLICATION TO X-RAY ABSORPTION AND RESONANT INELASTIC X-RAY SCATTERING , 1998 .

[29]  H. H. Johann,et al.  Die Erzeugung lichtstarker Röntgenspektren mit Hilfe von Konkavkristallen , 1931 .

[30]  Mariana Rossi,et al.  Ab initio molecular dynamics , 2013 .

[31]  Nicholas A Besley,et al.  The effect of basis set and exchange-correlation functional on time-dependent density functional theory calculations within the Tamm-Dancoff approximation of the x-ray emission spectroscopy of transition metal complexes. , 2016, The Journal of chemical physics.

[32]  Michele Parrinello,et al.  A hybrid Gaussian and plane wave density functional scheme , 1997 .

[33]  Michele Parrinello,et al.  General and efficient algorithms for obtaining maximally localized Wannier functions , 2000 .

[34]  Hans Ågren,et al.  Calculations of near-edge x-ray-absorption spectra of gas-phase and chemisorbed molecules by means of density-functional and transition-potential theory , 1998 .

[35]  Peter C. Schmidt,et al.  Methods in physical chemistry , 2012 .

[36]  Peter Comba,et al.  Computation of structures and properties of transition metal compounds , 2009 .

[37]  Joost VandeVondele,et al.  Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases. , 2007, The Journal of chemical physics.

[38]  Frank Neese,et al.  Prediction of iron K-edge absorption spectra using time-dependent density functional theory. , 2008, The journal of physical chemistry. A.

[39]  Christoph R Jacob,et al.  High-resolution X-ray absorption spectroscopy of iron carbonyl complexes. , 2015, Physical chemistry chemical physics : PCCP.

[40]  Frank Neese,et al.  Prediction of high-valent iron K-edge absorption spectra by time-dependent density functional theory. , 2011, Dalton transactions.

[41]  Thomas Bredow,et al.  Consistent Gaussian basis sets of triple‐zeta valence with polarization quality for solid‐state calculations , 2013, J. Comput. Chem..

[42]  Frank Neese,et al.  Time-dependent density functional calculations of ligand K-edge X-ray absorption spectra , 2008 .

[43]  Teter,et al.  Separable dual-space Gaussian pseudopotentials. , 1996, Physical review. B, Condensed matter.

[44]  Roberto Car,et al.  Calculation of near-edge x-ray-absorption fine structure at finite temperatures: spectral signatures of hydrogen bond breaking in liquid water. , 2004, The Journal of chemical physics.

[45]  Matthias Krack,et al.  All-electron ab-initio molecular dynamics , 2000 .

[46]  M. Grabolle,et al.  Photosynthetic O2 Formation Tracked by Time-Resolved X-ray Experiments , 2005, Science.

[47]  Matthias Bauer,et al.  X‐Ray Absorption Spectroscopy – the Method and Its Applications , 2012 .

[48]  Anders Nilsson,et al.  X-ray absorption spectra of water within a plane-wave Car-Parrinello molecular dynamics framework. , 2004, The Journal of chemical physics.

[49]  Frank Rominger,et al.  Gold catalysis: in situ EXAFS study of homogeneous oxidative esterification. , 2010, Chemistry.

[50]  D. Rorabacher,et al.  Electron transfer by copper centers. , 2004, Chemical reviews.

[51]  A. Becke,et al.  Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.

[52]  Holger Dau,et al.  X-ray absorption spectroscopy to analyze nuclear geometry and electronic structure of biological metal centers—potential and questions examined with special focus on the tetra-nuclear manganese complex of oxygenic photosynthesis , 2003, Analytical and bioanalytical chemistry.

[53]  Michele Parrinello,et al.  The Gaussian and augmented-plane-wave density functional method for ab initio molecular dynamics simulations , 1999 .

[54]  Matthias Krack,et al.  Pseudopotentials for H to Kr optimized for gradient-corrected exchange-correlation functionals , 2005 .

[55]  Anders Nilsson,et al.  Half or full core hole in density functional theory X-ray absorption spectrum calculations of water? , 2005, Physical chemistry chemical physics : PCCP.