Quantifying similarity for spectra with a large number of overlapping transitions: Examples from soft X-ray spectroscopy

Elsevier BV - Tập 535 - 2020
Erik Erik, Mickaël G. Mickaël G., Meiyuan Meiyuan, Roland Roland, Marcus Marcus

Tài liệu tham khảo

Stephenson, 1980, Automated analysis of high-resolution nmr spectra. i. principles and computational strategy, J. Magn. Reson., 37, 395 Stephenson, 1980, Automated analysis of high-resolution nmr spectra. ii. Illustrative applications of the computer program davins, J. Magn. Reson, 37, 409 Lorant Bodis, 2007, A novel spectra similarity measure, Chemom. Intell. Lab. Syst., 85, 1, 10.1016/j.chemolab.2005.10.002 Debie, 2011, A confidence level algorithm for the determination of absolute configuration using vibrational circular dichroism or raman optical activity, Chem. Phys. Chem., 12, 1542, 10.1002/cphc.201100050 Bruhn, 2013, Specdis: quantifying the comparison of calculated and experimental electronic circular dichroism spectra, Chirality, 25, 243, 10.1002/chir.22138 Lawton, 1994, Application of the overlap integral in x-ray diffraction powder pattern recognition, Powder Diffr., 9, 124, 10.1017/S088571560001410X de Gelder, 2001, A generalized expression for the similarity of spectra: application to powder diffraction pattern classification, J. Comput. Chem, 22, 273, 10.1002/1096-987X(200102)22:3<273::AID-JCC1001>3.0.CO;2-0 Hageman, 2003, Powder pattern indexing using the weighted crosscorrelation and genetic algorithms, J. Comput. Chem, 24, 1043, 10.1002/jcc.10253 Pierloot, 2011, Transition metals compounds: outstanding challenges for multiconfigurational methods, Int. J. Quantum Chem, 111, 3291, 10.1002/qua.23029 Vogiatzis, 2018, Computational approach to molecular catalysis by 3d transition metals: challenges and opportunities, Chem. Rev., 119, 2453, 10.1021/acs.chemrev.8b00361 de Groot, 2005, Multiplet effects in X-ray spectroscopy, Coordin. Chem. Rev, 249, 31, 10.1016/j.ccr.2004.03.018 Hocking, 2006, Fe L-edge XAS studies of K4[Fe(CN)6] and K3[Fe(CN)6]: a direct probe of back-bonding, J. Am. Chem. Soc., 128, 10442, 10.1021/ja061802i Kowalska, 2017, 3-Edge X-ray absorption and X-ray magnetic circular dichroism studies of molecular iron complexes with relevance to the FeMoco and FeVco active sites of nitrogenase, Inorg. Chem., 56, 8147, 10.1021/acs.inorgchem.7b00852 Kubin, 2018, Probing the oxidation state of transition metal complexes: a case study on how charge and spin densities determine Mn L-edge X-ray absorption energies, Chem. Sci., 9, 6813, 10.1039/C8SC00550H Delcey, 2019, Efficient calculations of a large number of highly excited states for multiconfigurational wavefunctions, J. Comput. Chem., 40, 1789, 10.1002/jcc.25832 Wasinger, 2003, L-edge X-ray absorption spectroscopy of non-heme iron sites: experimental determination of differential orbital covalency, J. Am. Chem. Soc., 125, 12894, 10.1021/ja034634s Wernet, 2015, Orbital-specific mapping of the ligand exchange dynamics of Fe(CO)5 in solution, Nature, 520, 78, 10.1038/nature14296 Guo, 2019, Fingerprinting electronic structure of heme iron by ab initio modeling of metal l-edge x-ray absorption spectra, J. Chem. Theory Comput., 15, 477, 10.1021/acs.jctc.8b00658 Stener, 2003, Time dependent density functional theory of core electrons excitations, Chem. Phys. Lett., 373, 115, 10.1016/S0009-2614(03)00543-8 Hua, 2013, Fe l-edge x-ray absorption spectra of fe (ii) polypyridyl spin crossover complexes from time-dependent density functional theory, J. Phys. Chem. A, 117, 14075, 10.1021/jp408776p Stetina, 2019, Modeling l2, 3-edge x-ray absorption spectroscopy with linear response exact two-component relativistic time-dependent density functional theory, J. Chem. Phys., 150, 10.1063/1.5091807 Roemelt, 2013, A combined DFT and restricted open-shell configuration interaction method including spin-orbit coupling: application to transition metal L-edge X-ray absorption spectroscopy, J. Chem. Phys., 138, 10.1063/1.4804607 Klooster, 2012, Calculation of x-ray photoelectron spectra with the use of the normalized elimination of the small component method, Chem. Phys., 395, 122, 10.1016/j.chemphys.2011.05.009 Josefsson, 2012, Ab initio calculations of x-ray spectra: atomic multiplet and molecular orbital effects in a multiconfigurational scf approach to the l-edge spectra of transition metal complexes, J. Phys. Chem. Lett., 3, 3565, 10.1021/jz301479j Bokarev, 2013, State-dependent electron delocalization dynamics at the solute-solvent interface: soft-x-ray absorption spectroscopy and ab initio calculations, Phys. Rev. Lett., 111, 083002, 10.1103/PhysRevLett.111.083002 Pinjari, 2014, Restricted active space calculations of l-edge x-ray absorption spectra: from molecular orbitals to multiplet states, J. Chem. Phys., 141, 10.1063/1.4896373 Chantzis, 2018, Ab initio wave function-based determination of element specific shifts for the efficient calculation of x-ray absorption spectra of main group elements and first row transition metals, J. Chem. Theory Comput., 14, 3686, 10.1021/acs.jctc.8b00249 Lundberg, 2019, Multiconfigurational approach to x-ray spectroscopy of transition metal complexes, vol. 29, 185 Shaw, 1981, An introduction to the coherence function and its use in eeg signal analysis, J. Med. Eng. Technol., 5, 273, 10.3109/03091908109009362 Miguel, 1996, Eeg coherence or eeg correlation, Int. J. Psychophysiol., 23, 145, 10.1016/S0167-8760(96)00038-4 Karfunkel, 1993, Continuous similarity measure between nonoverlapping x-ray powder diagrams of different crystal modifications, J. Comput. Chem., 14, 1125, 10.1002/jcc.540141002 Thole, 1988, Branching ratio in x-ray absorption spectroscopy, Phys. Rev. B, 38, 3158, 10.1103/PhysRevB.38.3158 Pearson, 1984, Contributions to the mathematical theory of evolution, Philos. Trans. R. Soc. London, 185, 71 Adam, 2012, Disentangling gaussians, Commun. ACM, 55, 113, 10.1145/2076450.2076474 Malmqvist, 2002, The restricted active space (RAS) state interaction approach with spin-orbit coupling, Chem. Phys. Lett., 357, 230, 10.1016/S0009-2614(02)00498-0 Malmqvist, 2008, The restricted active space followed by second-order perturbation theory method: theory and application to the study of cuo2 and cu2o2 systems, J. Chem. Phys., 128, 10.1063/1.2920188 Kubin, 2018, Direct determination of absolute absorption cross sections at the L-edge of dilute Mn complexes in solution using a transmission flatjet, Inorg. Chem., 57, 5449, 10.1021/acs.inorgchem.8b00419 Galván, 2019, Openmolcas: from source code to insight, J.Chem. Theory Comput., 15, 5925, 10.1021/acs.jctc.9b00532 Pinjari, 2016, Cost and sensitivity of restricted active-space calculations of metal l-edge x-ray absorption spectra, J. Comput. Chem., 37, 477, 10.1002/jcc.24237 Roos, 2004, Main group atoms and dimers studied with a new relativistic ANO basis set, J. Phys. Chem. A, 108, 2851, 10.1021/jp031064+ Roos, 2005, New relativistic ANO basis sets for transition metal atoms, J. Phys. Chem. A, 109, 6575, 10.1021/jp0581126 Forsberg, 1997, Multiconfiguration perturbation theory with imaginary level shift, Chem. Phys. Lett., 274, 196, 10.1016/S0009-2614(97)00669-6 Ghigo, 2004, A modified definition of the zeroth-order Hamiltonian in multiconfigurational perturbation theory (CASPT2), Chem. Phys. Lett., 396, 142, 10.1016/j.cplett.2004.08.032 Vancoillie, 2010, Performance of caspt2 and dft for relative spin-state energetics of heme models, J. Chem. Theory. Comput., 6, 576, 10.1021/ct900567c Zobel, 2017, The ipea dilemma in caspt2, Chem. Sci., 8, 1482, 10.1039/C6SC03759C Engel, 2014, Chemical bonding in aqueous ferrocyanide: experimental and theoretical x-ray spectroscopic study, J. Phys. Chem. B, 118, 1555, 10.1021/jp411782y Kunnus, 2016, Viewing the valence electronic structure of ferric and ferrous hexacyanide in solution from the fe and cyanide perspectives, J. Phys. Chem. B, 120, 7182, 10.1021/acs.jpcb.6b04751 Guo, 2016, Molecular orbital simulations of metal 1s2p resonant inelastic x-ray scattering, J. Phys. Chem. A, 120, 5848, 10.1021/acs.jpca.6b05139 Bühl, 2006, Geometries of transition-metal complexes from density-functional theory, J. Chem. Theory Comput., 2, 1282, 10.1021/ct6001187 Mathew, 2018, High-throughput computational x-ray absorption spectroscopy, Sci. Data, 5, 10.1038/sdata.2018.151 Ghosh, 2019, Deep learning spectroscopy: neural networks for molecular excitation spectra, Adv. Sci., 6, 1801367, 10.1002/advs.201801367