@article {ISI:000287150300002,
	title = {Electronic structure of S -nitrosothiols from sulfur K-edge X-ray absorption spectroscopy},
	journal = {Can. J. Chem.},
	volume = {89},
	number = {2},
	year = {2011},
	month = {feb},
	pages = {93{\textendash}97},
	abstract = {Sulfur K-edge X-ray absorption spectroscopy (S K-edge XAS) was applied to investigate the electronic structure of primary and tertiary S-nitrosothiols. Our experimental data, supported by density functional calculations, indicate that changes at C(alpha) affect the S-nitroso group through both inductive and direct orbital effects. Furthermore, our data are consistent with a weakening of the S-N bond in tertiary S-nitrosothiols as compared to their primary S-nitroso analogues. These results support existing computational models and suggest that the reactivity of S-nitrosothiols is not dominated by the electronics of the S-N bond.},
	keywords = {DFT, sulfur nitrosyls, XAS},
	issn = {0008-4042},
	doi = {10.1139/V10-083},
	url = {http://www.nrcresearchpress.com/doi/abs/10.1139/V10-083},
	author = {Martin-Diaconescu, Vlad and Perepichka, Inna and Bohle, D Scott and Kennepohl, Pierre}
}
@article {Delgado-Jaime2010a,
	title = {Blueprint XAS: a Matlab-based toolbox for the fitting and analysis of XAS spectra.},
	journal = {J. Syncr. Rad.},
	volume = {17},
	number = {1},
	year = {2010},
	month = {jan},
	pages = {132{\textendash}7},
	abstract = {Blueprint XAS is a new Matlab-based program developed to fit and analyse X-ray absorption spectroscopy (XAS) data, most specifically in the near-edge region of the spectrum. The program is based on a methodology that introduces a novel background model into the complete fit model and that is capable of generating any number of independent fits with minimal introduction of user bias [Delgado-Jaime \& Kennepohl (2010), J. Synchrotron Rad. 17, 119-128]. The functions and settings on the five panels of its graphical user interface are designed to suit the needs of near-edge XAS data analyzers. A batch function allows for the setting of multiple jobs to be run with Matlab in the background. A unique statistics panel allows the user to analyse a family of independent fits, to evaluate fit models and to draw statistically supported conclusions. The version introduced here (v0.2) is currently a toolbox for Matlab. Future stand-alone versions of the program will also incorporate several other new features to create a full package of tools for XAS data processing.},
	keywords = {ALGORITHMS, Computer-Assisted, Data Interpretation, METHODOLOGY, Numerical Analysis, Programming Languages, Software, Statistical, X-ray absorption spectroscopy, X-Ray Absorption Spectroscopy: methods, XAS},
	issn = {1600-5775},
	doi = {10.1107/S0909049509046561},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/20029122},
	author = {Delgado-Jaime, Mario Ulises and Mewis, Craig Philip and Kennepohl, Pierre}
}
@article {Delgado-Jaime2010,
	title = {Development and exploration of a new methodology for the fitting and analysis of XAS data.},
	journal = {Journal of synchrotron radiation},
	volume = {17},
	number = {1},
	year = {2010},
	month = {jan},
	pages = {119{\textendash}28},
	abstract = {A new data analysis methodology for X-ray absorption near-edge spectroscopy (XANES) is introduced and tested using several examples. The methodology has been implemented within the context of a new Matlab-based program discussed in a companion related article [Delgado-Jaime et al. (2010), J. Synchrotron Rad. 17, 132-137]. The approach makes use of a Monte Carlo search method to seek appropriate starting points for a fit model, allowing for the generation of a large number of independent fits with minimal user-induced bias. The applicability of this methodology is tested using various data sets on the Cl K-edge XAS data for tetragonal CuCl(4)(2-), a common reference compound used for calibration and covalency estimation in M-Cl bonds. A new background model function that effectively blends together background profiles with spectral features is an important component of the discussed methodology. The development of a robust evaluation function to fit multiple-edge data is discussed and the implications regarding standard approaches to data analysis are discussed and explored within these examples.},
	keywords = {ALGORITHMS, Computer-Assisted, Data Interpretation, METHODOLOGY, Numerical Analysis, Software, Software Design, Statistical, X-ray absorption spectroscopy, X-Ray Absorption Spectroscopy: methods, XAS},
	issn = {1600-5775},
	doi = {10.1107/S090904950904655X},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2816928\&tool=pmcentrez\&rendertype=abstract},
	author = {Delgado-Jaime, Mario Ulises and Kennepohl, Pierre}
}
@article {Martin-Diaconescu2009,
	title = {Effects of hyperconjugation on the electronic structure and photoreactivity of organic sulfonyl chlorides.},
	journal = {Inorg. Chem.},
	volume = {48},
	number = {3},
	year = {2009},
	month = {feb},
	pages = {1038{\textendash}44},
	publisher = {The University of British Columbia, Department of Chemistry, Vancouver, British Columbia V6T 1Z1.},
	abstract = {The electronic structure of organic sulfonyl compounds of the form RSO(2)G (G = -Cl, -OH, -CH(3)) is investigated to evaluate the effect of aryl R groups on photocleavage of the S-G bond. Sulfur K-edge X-ray absorption spectroscopy (XAS) provides a direct measure of the empty low-lying molecular orbitals in these complexes and, in combination with DFT calculations, a detailed description of the bonding in these compounds. The presence of an aryl group bound to the sulfonyl moiety has a significant impact on the spectroscopy and electronic structure of the site. The analysis suggests that the SCl(sigma*) orbital is significantly affected by mixing with the aryl pi* manifold. This mixing is dependent upon the nature of G and is most pronounced in the sulfonyl chlorides, where the energy of the SCl(sigma*) orbital is lowered by approximately 0.5 eV. The observed mixing is best described as excited-state hyperconjugation of the aryl pi system into the SCl(sigma*) orbital. The magnitude of the effect can be estimated directly from the S K-edge XAS spectra. These results are discussed in relation to the observed photochemistry of RSO(2)Cl, which is significantly enhanced when R = aryl as compared to alkyl substituents.},
	keywords = {DFT, ELECTRONS, models, MOLECULAR, molecular structure, Organic Chemicals, Organic Chemicals: chemistry, PHOTOCHEMISTRY, Spectrum Analysis, Sulfinic Acids, Sulfinic Acids: chemistry, sulfur redox, XAS},
	issn = {1520-510X},
	doi = {10.1021/ic801665f},
	url = {http://pubs.acs.org/doi/abs/10.1021/ic50073a047 http://www.ncbi.nlm.nih.gov/pubmed/19132932},
	author = {Martin-Diaconescu, Vlad and Kennepohl, Pierre}
}
@article {ISI:000270186500047,
	title = {Influence of oxygenation on the reactivity of ruthenium-thiolato bonds in arene anticancer complexes: insights from XAS and DFT.},
	journal = {J. Am. Chem. Soc.},
	volume = {131},
	number = {37},
	year = {2009},
	month = {sep},
	pages = {13355{\textendash}61},
	publisher = {American Chemical Society},
	abstract = {Thiolate ligand oxygenation is believed to activate cytotoxic half-sandwich [(eta(6)-arene)Ru(en)(SR)](+) complexes toward DNA binding. We have made detailed comparisons of the nature of the Ru-S bond in the parent thiolato complexes and mono- (sulfenato) and bis- (sulfinato) oxygenated species including the influence of substituents on the sulfur and arene. Sulfur K-edge XAS indicates that S(3p) donation into the Ru(4d) manifold depends strongly on the oxidation state of the sulfur atom, whereas Ru K-edge data suggest little change at the metal center. DFT results are in agreement with the experimental data and allow a more detailed analysis of the electronic contributions to the Ru-S bond. Overall, the total ligand charge donation to the metal center remains essentially unchanged upon ligand oxygenation, but the origin of the donation differs markedly. In sulfenato complexes, the terminal oxo group makes a large contribution to charge donation and even small electronic changes in the thiolato complexes are amplified upon ligand oxygenation, an observation which carries direct implications for the biological activity of this family of complexes. Details of Ru-S bonding in the mono-oxygenated complexes suggest that these should be most susceptible to ligand exchange, yet only if protonation of the terminal oxo group can occur. The potential consequences of these results for biological activation are discussed.},
	keywords = {Antineoplastic Agents, Antineoplastic Agents: chemical synthesis, Antineoplastic Agents: chemistry, Antineoplastic Agents: metabolism, AROMATIC, Aromatic: chemistry, DFT, DNA, DNA: metabolism, Drug Design, ELECTRONS, HYDROCARBONS, LIGANDS, metal-based drugs, models, MOLECULAR, Molecular Conformation, ORGANOMETALLIC COMPOUNDS, Organometallic Compounds: chemical synthesis, Organometallic Compounds: chemistry, Organometallic Compounds: metabolism, OXYGEN, Oxygen: chemistry, quantum theory, ruthenium, Ruthenium: chemistry, Spectrum Analysis, Sulfhydryl Compounds, Sulfhydryl Compounds: chemistry, X-Rays, XAS},
	issn = {1520-5126},
	doi = {10.1021/ja903405z},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19719101 http://dx.doi.org/10.1021/ja903405z},
	author = {Sriskandakumar, Thamayanthy and Petzold, Holm and Bruijnincx, Pieter C A and Habtemariam, Abraha and Sadler, Peter J and Kennepohl, Pierre}
}
@article {ISI:000264792600048,
	title = {Redox photochemistry of methionine by sulfur K-edge X-ray absorption spectroscopy: potential implications for cataract formation.},
	journal = {J. Am. Chem. Soc.},
	volume = {131},
	number = {10},
	year = {2009},
	month = {mar},
	pages = {3577{\textendash}82},
	abstract = {The photochemistry of methionine, methionine sulfoxide, and methionine sulfone have been investigated by using sulfur K-edge X-ray absorption spectroscopy to explore the redox photochemical processes under different conditions. Methionine is easily photooxidized to the sulfoxide and the sulfone in the presence of dioxygen. In the absence of oxidant, photoirradiation leads to the one-electron-oxidized cation radical with no further reaction, suggesting that an alternative mechanism for photooxidation of thioethers through direct oxidation is feasible. The photochemistry of methionine sulfoxide allows for independent oxidative and reductive processes. Photoreduction of the sulfoxide leads back to the parent thioether under both aerobic and anaerobic conditions. Photooxidation occurs only under aerobic conditions. In contrast, methionine sulfone is photochemically inert. These results provide new insights into potential photochemical processes that may lead to cataract formation.},
	keywords = {Cataract, Cataract: etiology, METHIONINE, Methionine: chemistry, Oxidation-Reduction, PHOTOCHEMISTRY, Spectrum Analysis, Spectrum Analysis: methods, sulfur redox, XAS},
	issn = {1520-5126},
	doi = {10.1021/ja806946r},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/19226173},
	author = {Karunakaran-Datt, Anusha and Kennepohl, Pierre}
}
@article {ISI:000254858100027,
	title = {Assignment of Pre-edge Features in the Ru K-edge X-ray Absorption Spectra of Organometallic Ruthenium Complexes.},
	journal = {Inorg. Chim. Acta},
	volume = {361},
	number = {4},
	year = {2008},
	pages = {1059},
	abstract = {The nature of the lowest energy bound-state transition in the Ru K-edge X-ray Absorption Spectra for a series of Grubbs-type ruthenium complexes was investigated. The pre-edge feature was unambiguously assigned as resulting from formally electric dipole forbidden Ru 4d<{\textendash}1s transitions. The intensities of these transitions are extremely sensitive to the ligand environment and the symmetry of the metal centre. In centrosymmetric complexes the pre-edge is very weak since it is limited by the weak electric quadrupole intensity mechanism. By contrast, upon breaking centrosymmetry, Ru 5p-4d mixing allows for introduction of electric dipole allowed character resulting in a dramatic increase in the pre-edge intensity. The information content of this approach is explored as it relates to complexes of importance in olefin metathesis and its relevance as a tool for the study of reactive intermediates.},
	keywords = {DFT, OLEFIN METATHESIS, XAS},
	issn = {0020-1693},
	doi = {10.1016/j.ica.2007.07.029},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2819416\&tool=pmcentrez\&rendertype=abstract},
	author = {Getty, Kendra and Delgado-Jaime, Mario Ulises and Kennepohl, Pierre}
}
@article {ISI:000254173600010,
	title = {N-heterocyclic carbene complexes of Rh: reaction with dioxygen without oxidation.},
	journal = {J. Am. Chem. Soc.},
	volume = {130},
	number = {12},
	year = {2008},
	month = {mar},
	pages = {3724{\textendash}5},
	abstract = {The reaction of oxygen with rhodium complexes containing N-heterocyclic carbenes was found to give dioxygen complexes with rare square planar geometries and unusually short O-O bond lengths. Analysis of the bonding in these complexes by Rh L-edge X-ray absorption spectroscopy (XAS), Raman spectroscopy, and DFT calculations provides evidence for a bonding model in which singlet oxygen is bound to a Rh(I) d8 metal complex, rather than the more common Rh(III) d6 peroxo species with octahedral geometry and O-O bond lengths in the 1.4-1.5 A range.},
	keywords = {chemical, DFT, dioxygen complexes, Heterocyclic Compounds, Heterocyclic Compounds: chemistry, METHANE, Methane: analogs \& derivatives, Methane: chemistry, models, MOLECULAR, molecular structure, ORGANOMETALLIC COMPOUNDS, Organometallic Compounds: chemical synthesis, Organometallic Compounds: chemistry, OXYGEN, Oxygen: chemistry, rhodium, Rhodium: chemistry, SPECTROMETRY, X-Ray Emission, X-Ray Emission: methods, XAS},
	issn = {1520-5126},
	doi = {10.1021/ja7108213},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18321109},
	author = {Praetorius, Jeremy M and Allen, Daryl P and Wang, Ruiyao and Webb, Jonathan D and Grein, Friedrich and Kennepohl, Pierre and Crudden, Cathleen M}
}
@article {ISI:000251974000023,
	title = {An electronic rationale for observed initiation rates in ruthenium-mediated olefin metathesis: charge donation in phosphine and N-heterocyclic carbene ligands.},
	journal = {J. Am. Chem. Soc.},
	volume = {129},
	number = {51},
	year = {2007},
	month = {dec},
	pages = {15774{\textendash}6},
	chapter = {15774},
	abstract = {Ru K-edge XAS data indicate that second generation ruthenium-based olefin metathesis precatalysts (L = N-heterocyclic carbene) possess a more electron-deficient metal center than in the corresponding first generation species (L = tricyclohexylphosphine). This surprising effect is also observed from DFT calculations and provides a simple rationale for the slow phosphine dissociation kinetics previously noted for second-generation metathesis precatalysts.},
	keywords = {ALKENES, Alkenes: chemistry, BOND, carbenes, CATALYSTS, CL, DFT, ELECTRONS, Heterocyclic Compounds, Heterocyclic Compounds: chemistry, HYDROCARBONS, Hydrocarbons: chemistry, KINETICS, LIGANDS, MECHANISM, METHANE, Methane: analogs \& derivatives, Methane: chemistry, MOIETY, NHC LIGANDS, OLEFIN METATHESIS, phosphines, Phosphines: chemistry, RAY-ABSORPTION SPECTROSCOPY, ruthenium, Ruthenium: chemistry, TRANSITION-METAL-COMPLEXES, XAS},
	isbn = {0002-7863},
	issn = {1520-5126},
	doi = {10.1021/ja0747674},
	url = {<Go to ISI>://000251974000023 http://www.ncbi.nlm.nih.gov/pubmed/18047332},
	author = {Getty, Kendra and Delgado-Jaime, Mario Ulises and Kennepohl, Pierre}
}
@article {ISI:000244896900002,
	title = {Sulfur K-edge XAS as a probe of sulfur-centered radical intermediates.},
	journal = {J. Am. Chem. Soc.},
	volume = {129},
	number = {11},
	year = {2007},
	month = {mar},
	pages = {3034{\textendash}5},
	abstract = {Sulfur K-edge XAS is used in the identification and characterization of sulfur based radicals obtained from UV irradiated glutathione. Ground state and time-dependent DFT calculations are used to identify thiyl (RS center dot) and perthiyl (RSS center dot) radical species.},
	keywords = {DFT, Free Radicals, Free Radicals: analysis, Free Radicals: chemistry, GLUTATHIONE, Glutathione: chemistry, Oxidation-Reduction, PHOTOCHEMISTRY, SPECTROMETRY, SPECTROPHOTOMETRY, Sulfhydryl Compounds, Sulfhydryl Compounds: chemistry, SULFUR, sulfur redox, Sulfur: chemistry, ULTRAVIOLET, X-Ray Emission, X-Ray Emission: methods, XAS},
	issn = {0002-7863},
	doi = {10.1021/ja0676760},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17319664},
	author = {Martin-Diaconescu, Vlad and Kennepohl, Pierre}
}
@article {ISI:000238269600054,
	title = {X-ray absorption methods for the determination of Ru{\textendash}Cl bond covalency in olefin metathesis catalysts: On the normalization of chlorine K-edges in ruthenium complexes},
	journal = {Inorg. Chim. Acta},
	volume = {359},
	number = {9},
	year = {2006},
	pages = {3042{\textendash}3047},
	abstract = {A systematic approach to quantitative analysis of Cl K-edge XAS spectra in ruthenium complexes is outlined and applied to ruthenium carbene complexes involved in olefin metathesis catalysis. This method is generally well-suited for probing ligand donor contributions into empty transition metal d orbitals, but overlap of the Ru L-2,L-3 edge makes this very difficult in these complexes. A method for removing the Ru L-2,L-3 edges from the Cl K-edge spectrum is developed and tested. The normalization procedure makes use of the well-separated Ru L-2 edge and an appropriate L-3/L-2 branching ratio to unambiguously remove contributions from these edges and allow for accurate normalization of the Cl K-edge spectrum. A generalized background subtraction that accounts for variability over the large energy range involved is also described. The methodology should be general for any similarly overlapping edges, as long as one component of the spin-orbit split metal (L- or M-) edge is unperturbed. The results of this study indicate a substantial difference in Ru-Cl bonding depending on the nature of the catalyst. (c) 2006 Elsevier B.V. All rights reserved.},
	keywords = {METHODOLOGY, OLEFIN METATHESIS, XAS},
	issn = {00201693},
	doi = {10.1016/j.ica.2005.12.058},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0020169306000260},
	author = {Delgado-Jaime, Mario Ulises and Conrad, Jay C and Fogg, Deryn E and Kennepohl, Pierre}
}
