Structure and bonding of sulfur- containing molecules and complexes Theoretical and experimental x-ray absorption, vibrational spectroscopic and crystallographic studies Emiliana Damian Risberg Department of Physical, Inorganic and Structural Chemistry Stockholm University 2007 Doctoral dissertation 2007 Department of Physical, Inorganic and Structural Chemistry Stockholm University 106 91 Stockholm Sweden Cover: Illustrates the sulfur K-edge XANES spectrum calculated for sulfur dioxide and the molecular orbital corresponding to the first transition of antibonding π* character. Faculty opponent: Professor Tsun-Kong Sham University of Western Ontario Department of Chemistry London, Canada Evaluation committee: Professor Kersti Hermansson, Uppsala University Docent Stefan Carlson, Lund University Docent Andreas Fischer, Royal Institute of Technology Substitute: Professor Gunnar Svensson, Stockholm University © Emiliana Damian Risberg, Stockholm 2007 ISBN (978-91-7155-423-9) Printed in Sweden by Printcenter, US-AB, City 2007 Distributor: Division of Structural Chemistry To Robert and my family, THE MORE ACCURATE THE CALCULATIONS BECOME, THE MORE THE CONCEPTS TEND TO VANISH INTO THIN AIR. -- R.S. MULLIKEN, J.C.P. 43,S2(1965) Abstract Synchrotron-based spectroscopic techniques enable investigations of the many important biological and environmental functions of the ubiquitous element sulfur. In this thesis the methods for interpreting sulfur K-edge X- ray absorption near edge structure (XANES) spectra are developed and ap- plied for analyses of functional sulfur groups. The influence of coordination, pH, hydrogen bonding, etc., on the sulfur 1s electronic excitations is evalu- ated by transition potential density functional theory. Analyses have been performed of reduced sulfur compounds in marine-archaeological wood from historical shipwrecks, including the Vasa, Stockholm, Sweden and the Mary Rose, Portsmouth, U.K.. The accumulation of sulfur as thiols in lignin- rich parts of the wood on the seabed is also a probable pathway in the natural sulfur cycle for how reduced sulfur enters fossil fuels via humic matter in anaerobic marine sediments. Sulfur K-edge XANES spectra for several bio- chemical model compounds and for coexisting isomeric sulfur species in cysteine and sulfite(IV) aqueous solutions have been analyzed with the aid of theoretical calculations. Cysteine derivatives are important for biochemi- cal detoxification, and mercury(II) cysteine complexes in solution have been structurally characterized by means of Extended X-ray Absorption Fine Structure (EXAFS), Raman and 199Hg NMR spectroscopy. Lanthanoid(III) ions were found to coordinate eight dimethyl sulfoxide oxygen atoms in a distorted square antiprism in the solid state and in solution, by combining crystallography, EXAFS, XANES and vibrational spectroscopy. The mean M-O bond distances for the disordered crystal structures are in good agree- ment with those from the lattice-independent EXAFS studies. The different sulfur K-edge XANES spectra for the dimethyl sulfoxide ligands in the hex- asolvated complexes of the trivalent group 13 metal ions, Tl(III), In(III), Ga(III) and Al(III), were interpreted by theoretical calculations. v Abbreviations DFT Density Functional Theory dmso Dimethyl Sulfoxide (in chemical formulae) DMSO Dimethyl Sulfoxide, (CH3)2SO EDS Energy Dispersive Spectroscopy ESCA Electron Spectroscopy for Chemical Analysis EXAFS Extended X-ray Absorption Fine Structure FT Fourier Transform KS Kohn-Sham density functional method HF Hartree-Fock approximation IP Ionization Potential IR Infrared LUMO Lowest Unoccupied Molecular Orbital - Mesylate Methanesulfonate, CH3SO3 MO Molecular Orbital NEXAFS Near-Edge X-ray Absorption Fine Structure NMR Nuclear Magnetic Resonance SCF Self Consistent Field SEM Scanning Electron Microscopy SSRL Stanford Synchrotron Radiation Laboratory SXM Scanning X-ray Spectromicroscopy TP Transition Potential - Triflate Trifluoromethanesulfonate, CF3SO3 - Trichlate Trichloromethanesulfonate, CCl3SO3 XAFS X-ray Absorption Fine Structure XANES X-ray Absorption Near Edge Structure XAS X-ray Absorption Spectroscopy XPS X-ray Photoelectron Spectroscopy vi List of publications This thesis is based on the results presented in the following papers which will be referred to by their Roman numerals in the text (reproduced by per- mission from Inorganic Chemistry, Acta Crystallographica, Physica Scripta and Proceedings of the National Academy of Sciences, U. S. A.): I. Analyses of sulfur and iron in marine-archaeological wood M. Sandström, Y. Fors, F. Jalilehvand, E. Damian and U. Gelius In Proceedings of the 9th ICOM Group on Wet Organic Archaeological Materials Conference, Copenhagen 2004; Eds. P. Hoffmann, J. A. Spriggs, T. Grant, C. Cook and A. Recht, Available in the German Maritime Museum (http://www.dsm.de/Pubs/woam.htm), Bremerhaven, 2005, p. 181-199. II. Sulfur K-edge X-ray Absorption Spectra for Dimethyl Sulfoxide in the Solvated Thallium(III), Indium(III), Gallium(III) and Alumi- num(III) Ions E. Damian, F. Jalilehvand, A. Abbasi, L.G.M. Pettersson and M. Sandström Phys. Scrip., T115, 2005, 1077-1079 III. Sulfur accumulation in the timbers of King Henry VIII's warship Mary Rose: a pathway in the sulfur cycle of conservation concern M. Sandström, F. Jalilehvand, E. Damian, Y. Fors, U. Gelius, M. Jones and Murielle Salomé Proc. Nat. Acad. Sci., USA (PNAS), 102, 2005, 14165–14170 IV. Mercury(II) Cysteine Complexes in Alkaline Aqueous Solution F. Jalilehvand, B. O. Leung, M. Izadifard and E. Damian Inorg. Chem., 45, 2006, 66-73 V. Sodium trichloromethanesulfonate monohydrate E. Damian, L. Eriksson and M. Sandström Acta Cryst., C62, 2006, m419-420 VI. Sulfur X-ray absorption and vibrational spectroscopic study of sul- fite, sulfur dioxide and sulfonate solutions, and of the substituted sul- - fonate ions X3CSO3 (X = H, Cl, F) E. Damian, L. Eriksson, J. Mink, L. G. M. Pettersson, M. Yu. Skripkin, M. Sandström Submitted to Inorganic Chemistry vii VII. Theoretical and experimental sulfur K-edge X-ray absorption spec- troscopic (XANES) study of cysteine, cystine, methionine and methion- ine sulfoxide E. Damian, F. Jalilehvand, B. Leung, L.G.M. Pettersson and M. Sandström In manuscript VIII. Crystallographic and Vibrational Spectroscopic Studies of Oc- takis(dimethyl sulfoxide)lanthanoid(III) Iodides A. Abbasi, E. Damian Risberg, L. Eriksson, J. Mink, I. Persson, M. Sandström, Y. V. Sidorov, M. Yu. Skripkin and A.-S. Ullström Submitted to Inorganic Chemistry IX. X-Ray Absorption Fine Structure Spectroscopic Studies of Octakis(dimethyl sulfoxide)lanthanoid(III) Complexes in Solution and in the Solid Iodides I. Persson, E. Damian Risberg, P. D’Angelo, S. Panfilis, M. Sandström and A. Abbasi Submitted to Inorganic Chemistry Additional paper that was not included in this thesis: The sulphur threat to marine archaeological artefacts: acid and iron removal from the Vasa M. Sandström, F. Jalilehvand, I. Persson, Y. Fors, E. Damian, U. Gelius, I. Hall-Roth, L. Dal, V.L. Richards and I. Godfrey Conservation Science 2002, Chapter 13, Archetype Press, 2003, Ch. 13, pp. 79-87. viii Table of contents 1 INTRODUCTION……………………………………….……………..…………...1 1.1 The Hard Soft Acid Base Principle (HSAB)..………………….………..3 1.2 Solvents…..…….………………………..……………….……………………….4 1.2.1 Water (H2O)……..………………..………………………………...….………..4 1.2.2 Dimethyl sulfoxide (CH3)2SO…………….…………………………………..4 2 EXPERIMENTAL SECTION…………………………..………………….….6 2.1 Methods……..………………………………………………………………….….6 2.1.1 X-ray absorption spectroscopy (XAS)…….…………….……………..6 2.1.2 X-ray Photoelectron Spectroscopy (XPS)….………………………...9 2.1.3 Vibrational spectroscopy…………………………………………...…...11 2.1.3.1 Infrared (IR) absorption………….…………..………...……….…11 2.1.3.2 Raman scattering…………………………………………...……...12 2.1.4 Force constant and bond strength……………...…………….……...13 2.1.5 Normal Coordinate Analysis…………………………...…..…………..14 2.2 Data collection……………………………………….…………………..…….16 2.2.1.1 XANES measurements………………………………………...……..16 2.2.1.2 Experimental setup.…………………………………………………...16 2.2.2 XPS measurements…………………………………………………...…17 2.2.3 IR and Raman measurements……………………………..……...…..19 3 THEORETICAL BACKGROUND………………...…………...………...20 3.1 Density Functional Theory (DFT) vs. Hartree-Fock (HF) approach…………….…………………………………………….…………...….….20 3.2 StoBe-deMon DFT calculations of XANES spectra……………..….22 4 RESULTS AND DISCUSSION………………….……………………......26 4.1 DMSO solvated metal ions…………………………………………….......26 4.1.1 Crystal structure of octakis(dmso)lanthanoid(III) iodides……………………………………………….....…………………………..26 3+ 4.1.2 EXAFS studies of [M(dmso)8] complexes in solution and in the solid state……………………………………….....………………….……….…..29 3+ 4.1.3 Vibrational spectroscopy on [M(dmso)8] complexes…………...33 4.1.4 XANES spectroscopy on dimethyl sulfoxide solvates…………....36 4.2 The sulfite system – sulfonate and derivates……………………......44 4.2.1 Crystal structures of sodium trichloromethanesulfonate monohydrate and deuterated cesium sulfonate…………………...……...44 4.2.2 XANES spectroscopy and DFT calculations…………..…………...45 4.2.2.1 Sulfite system……………………………………………….……….45 - - 4.2.2.2 Sulfonate (HSO3 ) and substituted (X3CSO3 ) sulfonates…52 ix 4.2.3 Vibrational spectroscopy and normal coordinate analysis……...57 4.2.3.1 Assignment of vibrational frequencies……………...….……...57 4.2.3.2 Force field analysis…………….…….………………………..…...58 4.3 Biologically relevant compounds………..…………...….…….…...…...61 4.3.1 XANES spectroscopy and DFT calculations on cysteine, cystine, methionine and methionine