Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Structure and bonding of sulfur-containing molecules and complexes
Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

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 applied for analyses of functional sulfur groups. The influence of coordination, pH, hydrogen bonding, etc., on the sulfur 1s electronic excitations is evaluated 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 biochemical 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 biochemical 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 agreement with those from the lattice-independent EXAFS studies. The different sulfur K-edge XANES spectra for the dimethyl sulfoxide ligands in the hexasolvated complexes of the trivalent group 13 metal ions, Tl(III), In(III), Ga(III) and Al(III), were interpreted by theoretical calculations.

Place, publisher, year, edition, pages
Stockholm: Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi , 2007. , p. 105
Keyword [en]
Sulfur species, x-ray absorption and vibrational spectroscopy, TP-DFT calculations
National Category
Chemical Sciences
Research subject
Structural Chemistry
Identifiers
URN: urn:nbn:se:su:diva-6843ISBN: 978-91-7155-423-9 (print)OAI: oai:DiVA.org:su-6843DiVA, id: diva2:197189
Public defence
2007-06-05, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 10:00 (English)
Opponent
Supervisors
Available from: 2007-05-15 Created: 2007-05-04 Last updated: 2010-01-15Bibliographically approved
List of papers
1. Analyses of sulfur and iron in marine-archaeological wood
Open this publication in new window or tab >>Analyses of sulfur and iron in marine-archaeological wood
Show others...
2005 (English)In: Proceedings of the 9th ICOM Group on Wet Organic Archaeological Materials Conference: Copenhagen 2004 / [ed] Per Hoffmann, Bremerhaven: International Council of Museums, Committee for Conservation, Working Group on Wet Organic Archaeological Materials , 2005, p. 181-199Conference paper, Published paper (Other academic)
Place, publisher, year, edition, pages
Bremerhaven: International Council of Museums, Committee for Conservation, Working Group on Wet Organic Archaeological Materials, 2005
National Category
Natural Sciences
Identifiers
urn:nbn:se:su:diva-24298 (URN)3-89757-308-3 (ISBN)
Available from: 2007-05-15 Created: 2007-05-04 Last updated: 2011-01-11Bibliographically approved
2. Sulfur K-edge X-ray Absorption Spectra for Dimethyl Sulfoxide in the Solvated Thallium(III), Indium(III), Gallium(III) and Aluminum(III) Ions
Open this publication in new window or tab >>Sulfur K-edge X-ray Absorption Spectra for Dimethyl Sulfoxide in the Solvated Thallium(III), Indium(III), Gallium(III) and Aluminum(III) Ions
Show others...
2005 In: Physica Scripta, Vol. T115, p. 1077-1079Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-24299 (URN)
Note
Part of urn:nbn:se:su:diva-6843Available from: 2007-05-15 Created: 2007-05-04Bibliographically approved
3. Sulfur Accumulation in the Timbers of King Henry VIII’s Warship Mary Rose: A Pathway in the Sulfur Cycle of Conservation Concern
Open this publication in new window or tab >>Sulfur Accumulation in the Timbers of King Henry VIII’s Warship Mary Rose: A Pathway in the Sulfur Cycle of Conservation Concern
Show others...
2005 (English)In: Proceedings of the National Academy of Sciences of the United States of America, PNAS, ISSN 0027-8424, Vol. 102, no 40, p. 14165-14170Article in journal (Refereed) Published
Abstract [en]

In marine-archaeological oak timbers of the Mary Rose large amounts of reduced sulfur compounds abound in lignin-rich parts such as the middle lamella between the cell walls, mostly as thiols and disulfides, whereas iron sulfides and elemental sulfur occur in separate particles. Synchrotron-based x-ray microspectroscopy was used to reveal this environmentally significant accumulation of organosulfur compounds in waterlogged wood. The total concentration of sulfur in reduced forms is ≈1 mass % throughout the timbers, whereas iron fluctuates up to several mass %. Conservation methods are being developed aiming to control acid-forming oxidation processes by removing the reactive iron sulfides and stabilizing the organosulfur compounds.

Identifiers
urn:nbn:se:su:diva-25011 (URN)10.1073/pnas.0504490102 (DOI)
Note
Part of urn:nbn:se:su:diva-7627Available from: 2008-05-13 Created: 2008-05-09 Last updated: 2010-01-15Bibliographically approved
4. Mercury(II) Cysteine Complexes in Alkaline Aqueous Solution
Open this publication in new window or tab >>Mercury(II) Cysteine Complexes in Alkaline Aqueous Solution
2006 In: Inorganic Chemistry, Vol. 45, no 1, p. 66 -73Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-24301 (URN)
Note
Part of urn:nbn:se:su:diva-6843Available from: 2007-05-15 Created: 2007-05-04Bibliographically approved
5. Sodium trichloromethanesulfonate monohydrate
Open this publication in new window or tab >>Sodium trichloromethanesulfonate monohydrate
2006 In: Acta Crystallographica, Vol. C62, p. m419-m420Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-24302 (URN)
Note
Part of urn:nbn:se:su:diva-6843Available from: 2007-05-15 Created: 2007-05-04Bibliographically approved
6. Sulfur X-ray absorption and vibrational spectroscopic study of sulfite, sulfur dioxide and sulfonate solutions, and of the substituted sulfonate ions X3CSO3- (X = H, Cl, F)
Open this publication in new window or tab >>Sulfur X-ray absorption and vibrational spectroscopic study of sulfite, sulfur dioxide and sulfonate solutions, and of the substituted sulfonate ions X3CSO3- (X = H, Cl, F)
Show others...
2007 (English)In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 46, no 20, p. 8332-8348Article in journal (Refereed) Published
Abstract [en]

Sulfur K-edge X-ray absorption near-edge structure (XANES) spectra have been recorded and the S(1s) electron excitations evaluated by means of density functional theory−transition potential (DFT−TP) calculations to provide insight into the coordination, bonding, and electronic structure. The XANES spectra for the various species in sulfur dioxide and aqueous sodium sulfite solutions show considerable differences at different pH values in the environmentally important sulfite(IV) system. In strongly acidic (pH < 1) aqueous sulfite solution the XANES spectra confirm that the hydrated sulfur dioxide molecule, SO2(aq), dominates. The theoretical spectra are consistent with an OSO angle of 119° in gas phase and acetonitrile solution, while in aqueous solution hydrogen bonding reduces the angle to 116°. The hydration affects the XANES spectra also for the sulfite ion, SO32-. At intermediate pH (4) the two coordination isomers, the sulfonate (HSO3-) and hydrogen sulfite (SO3H-) ions with the hydrogen atom coordinated to sulfur and oxygen, respectively, could be distinguished with the ratio HSO3-:SO3H- about 0.28:0.72 at 298 K. The relative amount of HSO3- increased with increasing temperature in the investigated range from 275 to 343 K. XANES spectra of sulfonate, methanesulfonate, trichloromethanesulfonate, and trifluoromethanesulfonate compounds, all with closely similar S−O bond distances in tetrahedral configuration around the sulfur atom, were interpreted by DFT−TP computations. The energy of their main electronic transition from the sulfur K-shell is about 2478 eV. The additional absorption features are similar when a hydrogen atom or an electron-donating methyl group is bonded to the −SO3 group. Significant changes occur for the electronegative trichloromethyl (Cl3C−) and trifluoromethyl (F3C−) groups, which strongly affect the distribution especially of the π electrons around the sulfur atom. The S−D bond distance 1.38(2) Å was obtained for the deuterated sulfonate (DSO3-) ion by Rietveld analysis of neutron powder diffraction data of CsDSO3. Raman and infrared absorption spectra of the CsHSO3, CsDSO3, H3CSO3Na, and Cl3CSO3Na·H2O compounds and Raman spectra of the sulfite solutions have been interpreted by normal coordinate calculations. The C−S stretching force constant for the trichloromethanesulfonate ion obtains an anomalously low value due to steric repulsion between the Cl3C− and −SO3 groups. The S−O stretching force constants were correlated with corresponding S−O bond distances for several oxosulfur species.

National Category
Inorganic Chemistry
Identifiers
urn:nbn:se:su:diva-24303 (URN)10.1021/ic062440i (DOI)000249698700033 ()
Available from: 2007-05-15 Created: 2007-05-04 Last updated: 2017-12-13Bibliographically approved
7. Theoretical and experimental sulfur K-edge X-ray absorption spectroscopic (XANES) study of cysteine, cystine, methionine and methionine sulfoxide
Open this publication in new window or tab >>Theoretical and experimental sulfur K-edge X-ray absorption spectroscopic (XANES) study of cysteine, cystine, methionine and methionine sulfoxide
Show others...
2009 (English)In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 18, p. 3542-3558Article in journal (Refereed) Published
Abstract [en]

The experimental sulfur K-edge x-ray absorption near edge structure (XANES) spectra of the amino acids cysteine, homocysteine, penicillamine, methionine, the oxidation products methionine sulfoxide and the disulfide cystine, have been analyzed by transition potential DFT calculations. The absolute energies and intensities of the main pre-edge sulfur 1s electron transitions have been computed to determine the character of the receiving low energy unoccupied molecular orbitals (MO), and to investigate the influence of external interactions, especially by introducing water molecules hydrogen bonded to the ionic species present in different pH ranges. When the thiol group deprotonates for the three amino acids cysteine, homocysteine and penicillamine the energy of the main transition, to an MO with antibonding σ*(S-H) character, reduces by ~1.1 eV and the receiving MO obtains σ*(S-C) character. The energy shifts due to hydrogen bonding were in most cases found to be relatively small, although the transition intensities could vary significantly due to the changes induced in the molecular charge distribution, thereby affecting the shapes of the spectral features. For the cysteine and penicillamine zwitterions deconvolution of the experimental spectra allowed the microscopic acid dissociation constants to be extracted separately for the thiol and the protonated amine groups, pKaT = 8.5 ± 0.1 and 8.2 ± 0.1, and pKaN = 8.9 ± 0.1 and 8.8 ± 0.1, respectively, in both cases with the thiol group the more acidic. Coordination of cysteine to nickel(II) or mercury(II) introduced a new low energy transition involving metal ion orbitals in the receiving LUMO. The small experimentally observed energy differences between the similar main absorption features of the cysteine and methionine zwitterions, 0.2-0.3 eV in comparable surrounding, as well as a minor difference in their intensity ratio, are reflected in the calculated transitions. The S K-edge XANES spectrum of the disulfide cystine displays a characteristic double peak with the lower energy transition (2469.9 eV) into the antibonding σ*(S-S) MO. The second peak, at 2471.5 eV in aqueous solution, contains several transitions into MO:s with σ*(S-C) character involving also charge transfer to the water molecules hydrating the protonated amine groups (NH3+) of cystine. The experimental energy difference between the two peaks increases by 0.2 eV for solid cystine, while no such increase occurs for the –S-S- bond between the cysteine residues in the oxidized disulfide of glutathione, where the amine groups are engaged in peptide bonds. This study shows that externally induced changes in the intramolecular bonding, e.g. by coordination, conformation geometry or hydrogen bonding, can significantly influence the S K-edge spectra, and emphasizes the importance of a similar chemical surrounding of the model compounds for standard spectra of sulfur functional groups, used to deconvolute composite experimental spectra.

Identifiers
urn:nbn:se:su:diva-24304 (URN)
Note
Part of urn:nbn:se:su:diva-6843Available from: 2007-05-15 Created: 2007-05-04 Last updated: 2017-12-13Bibliographically approved
8. Crystallographic and Vibrational Spectroscopic Studies of Octakis(dimethyl sulfoxide)lanthanoid(III) Iodides
Open this publication in new window or tab >>Crystallographic and Vibrational Spectroscopic Studies of Octakis(dimethyl sulfoxide)lanthanoid(III) Iodides
Show others...
2007 (English)In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 46, no 19, p. 7731-7741Article in journal (Refereed) Published
Abstract [en]

The octakis(DMSO) (DMSO = dimethylsulfoxide) neodymium(III), samarium(III), gadolinium(III), dysprosium(III), erbium(III), and lutetium(III) iodides crystallize in the monoclinic space group P21/n (No. 14) with Z = 4, while the octakis(DMSO) iodides of the larger lanthanum(III), cerium(III), and praseodymium(III) ions crystallize in the orthorhombic space group Pbca (No. 61), Z = 8. In all [Ln(OS(Me2)8]I3 compounds the lanthanoid(III) ions coordinate eight DMSO oxygen atoms in a distorted square antiprism. Up to three of the DMSO ligands were found to be disordered and were described by two alternative configurations related by a twist around the metal−oxygen (Ln−O) bond. To resolve the atomic positions and achieve reliable Ln−O bond distances, complete semirigid DMSO molecules with restrained geometry and partial occupancy were refined for the alternative sites. This disorder model was also applied on previously collected data for the monoclinic octakis(DMSO)yttrium(III) iodide. At ambient temperature, the eight Ln−O bond distances are distributed over a range of about 0.1 Å. The average value increases from Ln−O 2.30, 2.34, 2.34, 2.36, 2.38, 2.40 to 2.43 Å (Ln = Lu, Er, Y, Dy, Gd, Sm, and Nd) for the monoclinic [Ln(OSMe2)8]I3 structures, and from 2.44, 2.47 to 2.49 Å (Ln = Pr, Ce, and La) for the orthorhombic structures, respectively. The average of the La−O and Nd−O bond distances remained unchanged at 100 K, 2.49 and 2.43 Å, respectively. Despite longer bond distances and larger Ln−O−S angles, the cell volumes are smaller for the orthorhombic structures (Ln = Pr, Ce, and La) than for the monoclinic structure with Ln = Nd, showing a more efficient packing arrangement. Raman and IR absorption spectra for the [Ln(OS(CH3)2)8]I3 (Ln = La, Ce, Pr, Nd, Gd, Tb, Dy, Er, Lu, and Y) compounds, also deuterated for La and Y, have been recorded and analyzed by means of normal coordinate methods. The force constants for the Ln−O and S−O stretching modes in the complexes increase with decreasing Ln−O bond distance and show increasing polarization of the bonds for the smaller and heavier lanthanoid(III) ions.

National Category
Inorganic Chemistry
Identifiers
urn:nbn:se:su:diva-24305 (URN)10.1021/ic7006588 (DOI)000249371500015 ()
Note
Part of urn:nbn:se:su:diva-6843Available from: 2007-05-15 Created: 2007-05-04 Last updated: 2017-12-13Bibliographically approved
9. X-Ray Absorption Fine Structure Spectroscopic Studies of Octakis(dimethyl sulfoxide)lanthanoid(III) Complexes in Solution and in the Solid Iodides
Open this publication in new window or tab >>X-Ray Absorption Fine Structure Spectroscopic Studies of Octakis(dimethyl sulfoxide)lanthanoid(III) Complexes in Solution and in the Solid Iodides
Show others...
2007 (English)In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 46, no 19, p. 7742-7748Article in journal (Refereed) Published
Abstract [en]

Octakis(DMSO)lanthanoid(III) iodides (DMSO = dimethylsulfoxide), [Ln(OS(CH3)2)8]I3, of most lanthanoid(III) ions in the series from La to Lu have been studied in the solid state and in DMSO solution by extended X-ray absorption fine structure (EXAFS) spectroscopy. L3-edge and also some K-edge spectra were recorded, which provided mean Ln−O bond distances for the octakis(DMSO)lanthanoid(III) complexes. The agreement with the average of the Ln−O bond distances obtained in a separate study by X-ray crystallography was quite satisfactory. The crystalline octakis(DMSO)lanthanoid(III) iodide salts have a fairly broad distribution of Ln−O bond distances, ca. 0.1 Å, with a few disordered DMSO ligands. Their EXAFS spectra are in excellent agreement with those obtained for the solvated lanthanoid(III) ions in DMSO solution, both of which show slightly asymmetric distributions of the Ln−O bond distances. Hence, all lanthanoid(III) ions are present as octakis(DMSO)lanthanoid(III) complexes in DMSO solution, with the mean Ln−O distances centered at 2.50 (La), 2.45 (Pr), 2.43 (Nd), 2.41 (Sm), 2.40 (Eu), 2.39 (Gd), 2.37 (Tb), 2.36 (Dy), 2.34 (Ho), 2.33 (Er), 2.31 (Tm), and 2.29 Å (Lu). This decrease in the Ln−O bond distances is larger than expected from the previously established ionic radii for octa-coordination. This indicates increasing polarization of the LnIII−O(DMSO) bonds with increasing atomic number. However, the S(1s) electron transition energies in the sulfur K-edge X-ray absorption near-edge structure (XANES) spectra, probing the unoccupied molecular orbitals of lowest energy of the DMSO ligands for the [Ln(OS(CH3)2)8]3+ complexes, change only insignificantly from Ln = La to Lu. This indicates that there is no appreciable change in the σ-contribution to the S−O bond, probably due to a corresponding increase in the contribution from the sulfur lone pair to the bonding.

Place, publisher, year, edition, pages
American Chemical Society, 2007
National Category
Inorganic Chemistry
Identifiers
urn:nbn:se:su:diva-24306 (URN)10.1021/ic700659u (DOI)000249371500016 ()
Note
Part of urn:nbn:se:su:diva-6843Available from: 2007-05-15 Created: 2007-05-04 Last updated: 2017-12-13Bibliographically approved

Open Access in DiVA

fulltext(4200 kB)9189 downloads
File information
File name FULLTEXT01.pdfFile size 4200 kBChecksum SHA-1
6d721b675c384537ddd9352fe1a422610d59ca7b5e3b07397fc7133f25f003b7a8dd3e2f
Type fulltextMimetype application/pdf

By organisation
Department of Physical, Inorganic and Structural Chemistry
Chemical Sciences

Search outside of DiVA

GoogleGoogle Scholar
Total: 9189 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

isbn
urn-nbn

Altmetric score

isbn
urn-nbn
Total: 989 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf