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  • 1. Abbasi, Alireza
    et al.
    Damian Risberg, Emiliana
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Eriksson, Lars
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Mink, Janos
    Persson, Ingmar
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Sidorov, Yurii V.
    Skripkin, Mikhail Yu.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Ullström, Ann-Sofi
    Crystallographic and Vibrational Spectroscopic Studies of Octakis(dimethyl sulfoxide)lanthanoid(III) Iodides2007Inngår i: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 46, nr 19, s. 7731-7741Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 2.
    Abbasi, Alireza
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Lindqvist-Reis, Patric
    Eriksson, Lars
    Sandström, Dick
    Lidin, Sven
    Persson, Ingmar
    Sandström, Magnus
    Highly hydrated cations: Deficiency, mobility and coordination of water in crystalline nonahydrated scandium(III), yttrium(III) and lanthanoid(III) trifluoromethanesulfonate2005Inngår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 11, nr 14, s. 4065-4077Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Trivalent lanthanide-like metal ions coordinate nine water oxygen atoms, which form a tricapped trigonal prism in a large number of crystalline hydrates. Water deficiency, randomly distributed over the capping positions, was found for the smallest metal ions in the isomorphous nonahydrated trifluoromethanesulfonates, [M(H2O)(n)]CF3SO3)(3), in which M=Sc-III, Lu-III, Yb-III, Tm-III or Er-III. The hydration number n increases (n=8.0(1), 8.4(1), 8.7(1), 8.8(1) and 8.96(5), respectively) with increasing ionic size. Deuterium (H-2) solid-state NMR spectroscopy revealed fast positional exchange between the coordinated capping and prism water molecules; this exchange started at temperatures higher than about 280 K for lutetium(m) and below 268 K for scandium(m). Similar positional exchange for the fully nonahydrated yttrium(m) and lanthanum(m) compounds started at higher temperatures, over about 330 and 360 K, respectively. An exchange mechanism is proposed that can exchange equatorial and capping water molecules within the restrictions of the crystal lattice, even for fully hydrated lanthanoid(III) ions. Phase transitions occurred for all the water-deficient compounds at; 185 K. The hydrated scandium(III) trifluoromethanesulfonate transforms reversibly (Delta H degrees= -0.80(1) kJ mol(-1) on cooling) to a trigonal unit cell that is almost nine times larger, with the scandium ion surrounded by seven fully occupied and two partly occupied oxygen atom positions in a distorted capped trigonal prism. The hydrogen bonding to the trifluoromethanesulfonate anions stabilises the trigonal prism of water ligands, even for the crowded hydration sphere of the smallest metal ions in the series. Implications for the Lewis acid catalytic activity of the hydrated scandium(III) and lanthanoid(III) trifluoromethanesulfonates for organic syntheses performed in aqueous media are discussed.

  • 3.
    Damian, E
    et al.
    Stockholms universitet.
    Eriksson, L
    Stockholms universitet.
    Sandström, M
    Stockholms universitet.
    Sodium trichloromethanesulfonate monohydrate2006Inngår i: Acta Crystallographica Section C-Crystal Structure Communications, Vol. 62, s. M419-M420Artikkel i tidsskrift (Fagfellevurdert)
  • 4.
    Damian, Emiliana
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Jalilehvand, Farideh
    Leung, Bonnie
    Pettersson, Lars G. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Theoretical and experimental sulfur K-edge X-ray absorption spectroscopic (XANES) study of cysteine, cystine, methionine and methionine sulfoxide2009Inngår i: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 18, s. 3542-3558Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 5.
    Damian Risberg, Emiliana
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Mink, János
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Abbasi, Alireza
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Skripkin, Mikhail Yu.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Hajba, Laszló
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Lindqvist-Reis, Patric
    Bencze, Éva
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Ambidentate dimethyl sulfoxide coordination in protonated dimethyl sulfoxide, (CH3)2SO-H+, and in dichlorobis(dimethyl sulfoxide) palladium(II) and platinum(II) solid solvates, by vibrational and sulfur K-edge X-ray absorption spectroscopy2008Inngår i: Dalton TransactionsArtikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The protonated dimethyl sulfoxide cation (CH3)2SO-H+ formed in concentrated hydrochloric acid displays a new low energy feature in its sulfur K-edge X-ray absorption near edge structure (XANES) spectrum. Density Functional Theory – Transition Potential (DFT-TP) calculations reveal that the energy of the transition S(1s)  LUMO, which has antibonding *(S-O) character, has decreased about 0.8 eV. Normal coordinate force field analyses of the vibrational spectra show that the SO stretching force constant of the oxygen-coordinated (CH3)2SO-H+ species has decreased to 3.73 N cm-1 from 4.72 N cm-1 in neat liquid dimethyl sulfoxide. The effects of sulfur coordination on the ambidentate dimethyl sulfoxide molecule were investigated for the trans-Pd((CH3)2SO)2Cl2 and cis-Pt((CH3)2SO)2Cl2 complexes with square planar coordination of the chlorine and sulfur atoms. The XANES spectra again showed shifts toward low energy of the transition S(1s)  LUMO, now with antibonding *(M-Cl, M-S) character, with a larger shift for M = Pt than Pd. DFT-TP calculations indicated that the differences between the XANES spectra of the geometrical isomers of the M((CH3)2SO)2Cl2 complexes are expected to be too small to allow experimental distinction. The vibrational spectra of the palladium(II) and platinum(II) complexes were recorded and complete assignments of the fundamentals were achieved. Even though the M-S bond distances are quite similar the high covalency especially of the Pt-S bonds induces significant increases in the S-O stretching force constants, 6.79 and 7.18 N cm-1, respectively.

  • 6.
    Fors, Y
    et al.
    Stockholms universitet.
    Sandström, M
    Stockholms universitet.
    Sulfur and iron in shipwrecks cause conservation concerns2006Inngår i: Chemical Society Reviews, Vol. 35, s. 399-415Artikkel i tidsskrift (Fagfellevurdert)
  • 7. Fors, Yvonne
    et al.
    Grudd, Håkan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för naturgeografi och kvartärgeologi (INK).
    Rindby, Anders
    Jalilehvand, Farideh
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Cato, Ingemar
    Bornmalm, Lennart
    Sulfur and iron accumulation in three marine-archaeological shipwrecks in the Baltic Sea: The Ghost, the Crown and the Sword2014Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 4, s. 4222-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Sulfur and iron concentrations in wood from three 17th century shipwrecks in the Baltic Sea, the Ghost wreck, the Crown and the Sword, were obtained by X-ray fluorescence (XRF) scanning. In near anaerobic environments symbiotic microorganisms degrade waterlogged wood, reduce sulfate and promote accumulation of low-valent sulfur compounds, as previously found for the famous wrecks of the Vasa and Mary Rose. Sulfur K-edge X-ray absorption near-edge structure (XANES) analyses of Ghost wreck wood show that organic thiols and disulfides dominate, together with elemental sulfur probably generated by sulfur-oxidizing Beggiatoa bacteria. Iron sulfides were not detected, consistent with the relatively low iron concentration in the wood. In a museum climate with high atmospheric humidity oxidation processes, especially of iron sulfides formed in the presence of corroding iron, may induce post-conservation wood degradation. Subject to more general confirmation by further analyses no severe conservation concerns are expected for the Ghost wreck wood.

  • 8.
    Fors, Yvonne
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Jalilehvand, Farideh
    Risberg, Emiliana Damian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Bjordal, Charlotte
    Phillips, Ebba
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Sulfur and iron analyses of marine archaeological wood in shipwrecks from the Baltic Sea and Scandinavian waters2012Inngår i: Journal of Archaeological Science, ISSN 0305-4403, E-ISSN 1095-9238, Vol. 39, nr 7, s. 2521-2532Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Analyses of marine archaeological wood from shipwrecks in the Baltic Sea area, Kronan, Riksnyckeln, Tattran, the Puck Bay Boat and the Ghost wreck, and at the Scandinavian West coast, the Gota wreck, Stora Sofia and the Viking shipwrecks of Skuldelev, show accumulation of sulfur compounds. The penetration profiles of sulfur and iron into the wood and the speciation of characteristic sulfur groups were evaluated by combining X-ray spectroscopic analyses, in particular S K-edge XANES (X-ray absorption near edge structure) and X-ray fluorescence, with ESCA and elemental analyses. The combined analyses support the hypothesis that hydrogen sulfide produced by sulfate-reducing bacteria reacts and accumulates at low iron concentration mainly as organically bound sulfur, which as in previous studies was found by X-ray spectro-microscopy to accumulate in lignin-rich parts of the wood cell walls. The presence of iron(II) ions from corroding iron promotes formation of pyrite and other iron(II) sulfides, which easily oxidise in aerobic conditions with high humidity. No significant differences in sulfur and iron accumulation were found in wood from shipwrecks in the east coast brackish water and the west coast seawater. Sediments from three wreck sites, the Gota wreck, Stora Sofia and Kronan, were analyzed to a depth of a few decimeters and showed especially at the Stora Sofia high sulfur concentrations, exceeding 3 mass%. S K-edge XANES analyses of the sediments showed mainly reduced forms of sulfur, in particular pyrite and iron(II) sulfides together with elemental sulfur.

  • 9.
    Fors, Yvonne
    et al.
    Stockholms universitet, Humanistiska fakulteten, Institutionen för arkeologi och antikens kultur.
    Jalilehvand, Farideh
    Department of Chemistry, University of Calgary.
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Analytical Aspects of Waterlogged Wood in Historical Shipwrecks2011Inngår i: Analytical Sciences, ISSN 0910-6340, E-ISSN 1348-2246, Vol. 27, nr 8, s. 785-792Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Conservation methods applied to historical shipwrecks increasingly rely on combining modern analytical techniques to obtain new insights for specially adapted conservation treatments. Crystalline salts formed on waterlogged wood are identified by powder X-ray diffraction while X-ray fluorescence measurements along wood cores show penetration profiles of contaminating elements. Dedicated synchrotron-based X-ray absorption spectroscopy, especially sulfur and iron K-edge XANES, allows speciation of the large amounts of detrimental sulfur and iron compounds that often are found accumulated within the hull timbers, while high resolution X-ray imaging shows the distribution within the wood microstructure. By fitting spectra of model compounds to high quality sulfur K-edge XANES spectra one can obtain the relative amounts of different types of functional sulfur groups. FT-IR, NMR, ESCA, MALDI-TOF mass spectrometry and size exclusion chromatography are other useful techniques to analyze the status of the wood and of the consolidation agent polyethylene glycol. Examples are given from analyses of famous artifacts.

  • 10.
    Fors, Yvonne
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Nilsson, Thomas
    Damian Risberg, Emiliana
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Torssander, Peter
    Sulfur Accumulation in Pine Wood (Pinus sylvestris) Induced by Bacteria in Simulated Seabed Environment: Implications for Marine Archaeological Wood and Fossil Fuels2008Inngår i: International Biodeterioration & Biodegradation, ISSN 0964-8305, E-ISSN 1879-0208, nr 62, s. 336-347Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Fresh pine wood blocks were submerged in sulfate and iron(II) containing media, inoculated with bacterial consortia isolated from seawater, aiming to simulate the seabed conditions of the Vasa shipwreck (1628). The consortia contained erosion (EB) and sulfate-reducing bacteria (SRB). Sulfur K-edge x-ray absorption near edge structure (XANES) spectroscopy and scanning x-ray spectromicroscopy images showed that organic sulfur, mainly thiols (R-SH), had accumulated in the lignin-rich middle lamella in EB-degraded parts of the wood. The sulfur content in the wood increased more than 10 times in two years. In another series with active inoculums from marine archaeological wood, the sulfur XANES spectra showed after four years anaerobic treatment considerable amounts also of inorganic iron sulfides, Fe1-xS, which oxidized at atmospheric exposure. A sediment sample from the Vasa’s seabed was also rich in iron sulfides, including pyrite FeS2. X-ray fluorescence mappings of sulfur and phosphorous distributions indicate that scavenging SRB penetration, producing hydrogen sulfide in situ, is restricted to EB-degraded parts of the wood structure. The sulfur isotope depletion of 34S from d34S = 21‰ in marine sulfate to d34S = 6‰ and 1.8‰ for fractions of reduced sulfur and sulfate separated from a Vasa wood sample, respectively, suggests bacterial transformation. A fuller understanding of the routes of sulfur accumulation, as reactive iron sulfides and as organic sulfur, has important implications for improving conservation methods of marine archaeological wood. Moreover, the biogenic accumulation of organically bound sulfur specifically in lignin-rich parts of waterlogged wood has wider geochemical significance for fossil fuels of marine origin, as lignin-rich humic matter is important for the diagenetic formation of kerogens from anoxic marine sediments.

  • 11.
    Fors, Yvonne
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Sulfur and Iron in Shipwrecks Create Conservation Concerns2006Inngår i: Chemical Society Reviews, ISSN 0306-0012, E-ISSN 1460-4744, Vol. 35, nr 5, s. 399-415Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Synchrotron-based sulfur X-ray absorption spectroscopy reveals considerable accumulation of organosulfur (e.g. thiols), pyrite and iron(II) sulfides in marine-archaeological wood preserved in seawater, e.g. for historical shipwrecks such as the Vasa and Mary Rose. In the museum, oxidation of the sulfur compounds in the presence of iron ions may cause severe acidity in the moist wood. This tutorial review discusses developments of conservation methods to remove acid and iron, and how to analyse and stabilise sulfur compounds in the wood.

  • 12. Mink, Janos
    et al.
    Hajba, Laszlo
    Mihaly, Judith
    Nemeth, Csaba
    Palmai, Marcell
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Vibrational Spectroscopic Studies of Molecules with Biochemical Interest: The Cysteine Zwitterion2012Inngår i: Applied spectroscopy reviews (Softcover ed.), ISSN 0570-4928, E-ISSN 1520-569X, Vol. 47, nr 6, s. 415-483Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    The L-cysteine zwitterions in the orthorhombic crystal structure and in aqueous solution, including the deuterated isotopologues HSCD2CH(NH3+)COO-, DSCH2CH(ND3+)COO-, and DSCD2CH(ND3+)COO-, have been studied by midinfrared, far-infrared, and Raman spectroscopy. Density functional theory (DFT) calculations were performed for an equilibrium molecular geometry of the cysteine zwitterion to obtain vibrational frequencies of fundamental modes, infrared (IR) and Raman intensities, and the depolarization ratio of the Raman bands and combined with normal coordinate force field analyses. The force field obtained for dissolved (in H2O and D2O) cysteine, based on the 4 x 36 experimental fundamental modes of the four isotopologues, was successfully transferred to the two conformers in the solid state. The experimentally observed multiple bands (generally doublets) of L-cysteine and its deuterated isotopologues in the solid state were interpreted based on the coexistence of two conformers in the unit cell. The calculated frequencies were used for full assignments of the fundamental IR and Raman vibrational transitions, including an attempt to interpret all low-frequency vibrations (below 400 cm(-1)) of the zwitterion also in the solid state. In particular, the hydrogen bonding effects on conformation, bond lengths, and force constants were studied, including those of the distorted NH3+ amino group. The -S-H and -S-D stretching vibrations were found to be local modes, not sensitive to deuterium substitution of the -CH2 and -NH3+ groups in the molecule or to the H(D)-S-C-C torsional angle. The two major -S-H or -S-D stretching bands observed in the solid state correspond to different S-H/D bond lengths and resulted in the force constants K-SH = 3.618 N.cm(-1) and 3.657 N.cm(-1) for the SH center dot center dot center dot S and SH center dot center dot center dot O hydrogen-bonded interactions. A remarkable result was that the S(H)center dot center dot center dot O interaction was weaker than the S(H)center dot center dot center dot S interaction in the solid state and even weaker in aqueous solution, K-SH = 3.715 N.cm(-1), possibly due to intramolecular interactions between the thiol and amino groups. A general correlation between the S-H/D bond length and vibrational frequency was developed, allowing the bond length to be estimated for sulfhydryl groups in, for example, proteins. The C-S stretching modes were fitted with different C-S stretching force constants, K-CS = 3.213 and 2.713 N.cm(-1), consistent with the different CS bond lengths for the two solid-state conformers.

  • 13.
    Mink, Janos
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Skripkin, Mikhail
    Hajba, L
    Németh, C
    Abbasi, Alireza
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Infrared and raman spectroscopic and theoretical studies of nonaaqua complexes of trivalent rare earth metal ions2005Inngår i: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, E-ISSN 1873-3557, Vol. 61, nr 7, s. 1639-1645Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Infrared (IR), far-infrared (far-IR) and Raman spectra have been recorded of the hydrated lanthanide(III) trifluoromethanesulfonates, [Ln(OH2)9](CF3SO3)3, (Ln = La, Pr, Nd, Sm, Gd, Tb, Dy, Ho, Er, Tm, Yb and Lu), and also for the deuterated [La(OD2)9](CF3SO3)3 compound. This has enabled complete assignments of all seven metal–oxygen stretching modes for the first time. Force constant calculations have been performed for an LnO93+ moiety, with a tricapped trigonal prismatic oxygen atom arrangement in D3h point group symmetry.

    The lanthanide contraction in reflected in continuously increasing trends for the averaged LnO stretching frequencies and force constants with increasing inverse of ionic radii. The stretching force constants increased from 0.81 to 1.16 Ncm−1 for the LnO6 prism in the series from La to Lu, while those for the capping LnO3 bonds increased from 0.49 to 0.65 Ncm−1. The LnO stretching force constants showed a smooth correlation with the LnO bond distances to the prism oxygen atoms, while the correlation to the LnO capping oxygen atoms has a different shape, reflecting the increased ligand–ligand repulsion with decreasing lanthanide ion size.

  • 14. Nilsson, Kersti B.
    et al.
    Maliarik, Mikhail
    Persson, Ingmar
    Fischer, Andreas
    Ullström, Ann-Sofi
    Eriksson, Lars
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Coordination Chemistry of Mercury(II) in Liquid and Aqueous Ammonia Solution and the Crystal Structure of Tetraamminemercury(II) Perchlorate2008Inngår i: Inorganic Chemistry, Vol. 47, s. 1953-1964Artikkel i tidsskrift (Fagfellevurdert)
  • 15. Nilsson, Kersti B.
    et al.
    Maliarik, Mikhail
    Persson, Ingmar
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Structure of solvated mercury(II) halides in liquid ammonia, triethyl phosphite and tri-n-butylphosphine solution2008Inngår i: Dalton Transactions, s. 2303-2313Artikkel i tidsskrift (Fagfellevurdert)
  • 16. Persson, Ingmar
    et al.
    Damian Risberg, Emiliana
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    D’Angelo, Paola
    De Panfilis, Simone
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Abbasi, Alireza
    X-Ray Absorption Fine Structure Spectroscopic Studies of Octakis(dimethyl sulfoxide)lanthanoid(III) Complexes in Solution and in the Solid Iodides2007Inngår i: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 46, nr 19, s. 7742-7748Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 17. Persson, Ingmar
    et al.
    D'Angelo, Paola
    De Panfilis, Simone
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Eriksson, Lars
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Hydration of Lanthanoid(III) ions in Aqueous Solution and Crystalline Hydrates Studied by EXAFS Spectroscopy and Crystallography: The Myth of the2008Inngår i: Chemistry - A European Journal, ISSN 0947-6539, Vol. 14, s. 3056-3066Artikkel i tidsskrift (Fagfellevurdert)
  • 18. Persson, Ingmar
    et al.
    Eriksson, Lars
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Lindqvist-Reis, Patric
    Persson, Per
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    An EXAFS Spectroscopic, Large Angle X-Ray Scattering and Crystallo¬graphic Study of the Hexahydrated and the Dimethyl Sulfoxide and Pyridine-1-Oxide Hexasolvated Mercury(II) Ions2008Inngår i: Chemistry, A European Journal, Vol. 14, s. 6687-6696Artikkel i tidsskrift (Annet (populærvitenskap, debatt, mm))
    Abstract [en]

    The structure of the solvated mercury(II) ion in aqueous and dimethyl sulfoxide solution has been studied by means of large angle X-ray scattering (LAXS) and EXAFS tech¬niques. The distribution of the Hg-O bond distances is unusually wide and asymmetric in both solvents. In aqueous solution hexahydrated [Hg(OH2)6]2+ ions in distorted octahedral configuration, with the centroid of the Hg-O bond distances at 2.38(1) Å, are surrounded by a diffuse second hydration sphere, with HgOII distances around a mean value of 4.20(2) Å. In dimethyl sulfoxide solution the six Hg-O and HgS distances of the hexasolvated Hg(OS(CH3)2)6]2+ complex are centered around 2.38(1) and 3.45(2) Å, respectively. The crystal structure of hexakis¬(pyridine-1-oxide)mercury(II) perchlorate has been re-determi¬ned at 100 K. The space group R implies six equal Hg-O bond distances of 2.3416(7) Å for the Hg(ONC5H5)62+ complex, as also for the hexaaquamercury(II) perchlorate and hexakis(dimethyl sulfoxide)mercury(II) trifluoro¬methanesulfonate compounds, according to previous crystallographic results. However, EXAFS results for those compounds in all cases reveal strongly asymmetric Hg-O bond distance distributions. Vibronic coupling of close valence states in a so-called Pseudo Jahn-Teller Effect probably induces the distorted configurations.

  • 19.
    Risberg, Emiliana, Damian
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Eriksson, Lars
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Mink, Janos
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Pettersson, Lars G. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Skripkin, Mikhail Yu.
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    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)2007Inngår i: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 46, nr 20, s. 8332-8348Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 20. Risberg, Emiliana Damian
    et al.
    Jalilehvand, Farideh
    Leung, Bonnie O.
    Pettersson, Lars G. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Fysikum.
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Theoretical and Experimental Sulfur K-edge X-ray Absorption Spectroscopic Study of Cysteine, Cystine, Homocysteine, Penicillamine, Methionine and Methionine Sulfoxide2009Inngår i: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, s. 3542-3558Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

      The experimental sulfur K-edge X-ray absorption near-edge structure (XANES) spectra of the amino acids cysteine, homocysteine, penicillamine, methionine, including 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 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 cysteine, homocysteine and penicillamine and also for the cysteine residue in glutathione 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 changes in transition energy 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, pKaS = 8.5 ± 0.1 and 8.2 ± 0.1, and pKaN = 8.9 ± 0.1 and 8.8 ± 0.1, respectively, with the thiol group in both cases being 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 intensities, 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 MOs with σ*(S–C) character involving also charge transfer to the water molecules hydrating the protonated amine groups (NH3+) of cystine. For solid cystine without hydrogen bonding the experimental energy difference between the two peaks is 0.2 eV larger, while no such increase occurs for the oxidized disulfide of glutathione, with a similar –S–S– bond between its cysteine residues as in cystine, because 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 when choosing the model compounds for standard spectra of sulfur functional groups, used to deconvolute composite experimental spectra.

  • 21. Risberg, Emiliana Damian
    et al.
    Mink, János
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Abbasi, Alireza
    Skripkin, Mikhail Yu.
    Hajba, Laszló
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Lindqvist-Reis, Patric
    Bencze, Éva
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Ambidentate coordination in hydrogen bonded dimethyl sulfoxide, (CH3)2SO H3O+, and in dichlorobis(dimethyl sulfoxide) palladium(II) and platinum(II) solid solvates, by vibrational and sulfur K-edge X-ray absorption spectroscopy2009Inngår i: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, s. 1328-1339Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

     

    The strongly hydrogen bonded species (CH3)2SOH3O+ formed in concentrated hydrochloric acid displays a new low energy feature in its sulfur K-edge X-ray absorption near edge structure (XANES) spectrum. Density Functional Theory-Transition Potential (DFT-TP) calculations reveal that the strong hydrogen bonding decreases the energy of the transition S(1s) → LUMO, which has antibonding σ*(S–O) character, with about 0.8 eV. Normal coordinate force field analyses of the vibrational spectra show that the SO stretching force constant decreases from 4.72 N cm−1 in neat liquid dimethyl sulfoxide to 3.73 N cm−1 for the hydrogen bonded (CH3)2SOH3O+ species. The effects of sulfur coordination on the ambidentate dimethyl sulfoxide molecule were investigated for the trans-Pd((CH3)2SO)2Cl2, trans-Pd((CD3)2SO)2Cl2 and cis-Pt((CH3)2SO)2Cl2 complexes with square planar coordination of the chlorine and sulfur atoms. The XANES spectra again showed shifts toward low energy for the transition S(1 s) → LUMO, now with antibonding σ*(M–Cl, M–S) character, with a larger shift for M = Pt than Pd. DFT-TP calculations indicated that the differences between the XANES spectra of the geometrical cis and trans isomers of the M((CH3)2SO)2Cl2 complexes are expected to be too small to allow experimental distinction. The vibrational spectra of the palladium(II) and platinum(II) complexes were recorded and complete assignments of the fundamentals were achieved. Even though the M–S bond distances are quite similar the high covalency especially of the Pt–S bonds induces significant increases in the S–O stretching force constants, 6.79 and 7.18 N cm−1, respectively.

  • 22.
    Sandström, Magnus
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Fors, Yvonne
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Jalilehvand, Farideh
    Damian, Emiliana
    Gelius, Ulrik
    Analyses of sulfur and iron in marine-archaeological wood2005Inngår i: 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, s. 181-199Konferansepaper (Annet vitenskapelig)
  • 23.
    Sandström, Magnus
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Fors, Yvonne
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Persson, Ingmar
    The Vasa’s New Battle: Sulfur, Acid and Iron2003Bok (Annet vitenskapelig)
  • 24.
    Sandström, Magnus
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Jalilehvand, Farideh
    Damian, Emiliana
    Fors, Yvonne
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Gelius, Ulrik
    Jones, Mark
    Salomé, Murielle
    Sulfur Accumulation in the Timbers of King Henry VIII’s Warship Mary Rose: A Pathway in the Sulfur Cycle of Conservation Concern2005Inngår i: Proceedings of the National Academy of Sciences of the United States of America, PNAS, ISSN 0027-8424, Vol. 102, nr 40, s. 14165-14170Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 25.
    Sandström, Magnus
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Jalilehvand, Farideh
    Persson, Ingmar
    Fors, Yvonne
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Damian, Emiliana
    Gelius, Ulrik
    Hall-Roth, Ingrid
    Dal, Lovisa
    Vicki, Richards
    Ian, Godfrey
    The sulfur threat to marine archaeological artefacts: acid and iron removal from the Vasa2003Inngår i: Conservation science 2002: papers from the conference held in Edinburgh, Scotland 22-24 May 2002, London: Archetype Publications , 2003, s. 79-87Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    An outbreak of acidity and sulphate salts was observed on the hull of the 17th-century Swedish warship Vasa, following humidity variations in the Vasa Museum during the rainy summer in 2000. Analyses of total sulphur in oak cores sampled from 16 locations showed, in the outermost 2 cm., mean concentrations betwen 0.2 and 6 mass percent. Synchrotron-based sulphur K-edge X-ray absorption spectroscopy revealed that a large amount of elemental sulphur in the moist wood was being oxidised to sulphuric acid, possibly catalysed by iron compounds, with the overall rate estimated to be about 100 kg sulphuric acid annually. Associated acid catalysed hydrolysis of the cellulose threatens the future preservation of the vessel. Results of tests of proposed new treatments using chelating agents to extract iron compounds from waterlogged wood and simultaneously neutralise acid are presented.

  • 26.
    Sandström, Magnus
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Mink, János
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Papai, Imre
    Chemical Research Center of the Hungarian Academy of Sciences, P.O. Box 77, H-1525, Budapest, Hungary.
    Skripkin, Mikhail
    Department of Chemistry, St. Petersburg State University, Universitetski pr., 26, 198504 St. Petersburg, Russia.
    Hajba, László
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Mihály, Judith
    Chemical Research Center of the Hungarian Academy of Sciences, Budapest.
    Neméth, Csaba
    Chemical Research Center of the Hungarian Academy of Sciences, Budapest.
    Vibrational spectroscopic and theoretical studies of urea derivatives with biochemical interest: N,N’-dimethylurea, N,N,N’,N’-tetramethylurea and N,N’-dimethylpropyleneurea2010Inngår i: Applied spectroscopy reviews (Softcover ed.), ISSN 0570-4928, E-ISSN 1520-569X, Vol. 45, s. 274-326Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Mid-infrared, far-infrared and Raman vibrational spectroscopic studies were combined with DFT calculations and normal coordinate force field analyses for N,N’-dimethylurea (DMU), N,N,N’,N’-tetramethylurea (TMU) and N,N'-dimethylpropyleneurea (DMPU, IUPAC name 1,3-dimethyltetrahydropyrimidin-2(1H)-one). The equilibrium molecular geometry of DMU (all three conformers), TMU and DMPU, and the frequencies, intensities and depolarization ratios of their fundamental IR and Raman vibrational transitions were obtained by DFT calculations. The vibrational spectra were fully analysed by normal coordinate methods as well. A starting force field for DMPU was obtained by adapting corresponding force constants for DMU and TMU, resulting after refinements in the stretching force constants: C=O (7.69, 7.30, 7.68 N×cm -1), C-N (5.16, 5.55, 5.05 N×cm -1) and C-Me (5.93, 4.00, 4.22 N×cm-1) for DMU, TMU and DMPU, respectively. The dominating conformer of liquid DMU was identified as trans-trans, strong intermolecular hydrogen bonding was verified in solid DMU, and weak dipole-dipole association was found in liquid TMU and in DMPU. Special attention was paid to analysing the methyl group frequencies, which revealed deviations from local C3v symmetry. A linear correlation was found between the CH stretching force constants and the inverse of the CH bond lengths (1/r2). The averaged NH stretching frequencies of gaseous, dissolved and solid urea and of DMU, with variations for hydrogen bonding of different strength, are linearly correlated to the NH stretching force constants. Characteristic skeletal vibrations were assigned for a broad variety of urea derivatives and also for pyrimidine derivatives, which all contain the N2C=O entity. The very strong IR bands of C=O stretching (1676 ± 40 cm-1) and asymmetric CN2 stretching (1478 ± 60 cm-1), and the very intense Raman feature of symmetric CN2 stretching or ring breathing (757 ± 80 cm-1), can be recognized as fingerprint bands also for the pyrimidine derivatives cytosine, thymine and uracil, which all are nucleobases in DNA and RNA nucleotides.

  • 27. Stepakova, Liubov V.
    et al.
    Skripkin, Mikhail Yu.
    Chernykh, Lyudmila V.
    Starova, Galina L.
    Hajba, Laszlo
    Mink, Janos
    Sandström, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi.
    Vibrational spectroscopic and force field studies of copper(II) chloride and bromide compounds, and crystal structure of KCuBr32008Inngår i: Journal of Raman Spectroscopy, ISSN 0377-0486, Vol. 39, s. 16-31Artikkel i tidsskrift (Fagfellevurdert)
1 - 27 of 27
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