| 1. |
- Fors, Yvonne, 1975, et al.
(författare)
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Sulfur and iron accumulation in three marine-archaeological shipwrecks in the Baltic Sea. The Ghost, the Crown and the Sword.
- 2014
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 4
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 2. |
- Fors, Yvonne, et al.
(författare)
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Sulfur and iron analyses of marine archaeological wood in shipwrecks from the Baltic Sea and Scandinavian waters
- 2012
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Ingår i: Journal of Archaeological Science. - : Elsevier BV. - 0305-4403 .- 1095-9238. ; 39:7, s. 2521-2532
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 3. |
- Mink, Janos, et al.
(författare)
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Vibrational Spectroscopic Studies of Molecules with Biochemical Interest : The Cysteine Zwitterion
- 2012
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Ingår i: Applied spectroscopy reviews (Softcover ed.). - : Informa UK Limited. - 0570-4928 .- 1520-569X. ; 47:6, s. 415-483
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Forskningsöversikt (refereegranskat)abstract
- 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.
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| 4. |
- Fors, Yvonne, et al.
(författare)
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Analytical Aspects of Waterlogged Wood in Historical Shipwrecks
- 2011
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Ingår i: Analytical Sciences. - : Springer Science and Business Media LLC. - 0910-6340 .- 1348-2246. ; 27:8, s. 785-792
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Forskningsöversikt (refereegranskat)abstract
- 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.
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| 5. |
- Sandström, Magnus, 1945-, et al.
(författare)
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Vibrational spectroscopic and theoretical studies of urea derivatives with biochemical interest: N,N’-dimethylurea, N,N,N’,N’-tetramethylurea and N,N’-dimethylpropyleneurea
- 2010
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Ingår i: Applied spectroscopy reviews (Softcover ed.). - : Taylor and Francis. - 0570-4928 .- 1520-569X. ; 45, s. 274-326
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 6. |
- Damian, Emiliana, et al.
(författare)
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Theoretical and experimental sulfur K-edge X-ray absorption spectroscopic (XANES) study of cysteine, cystine, methionine and methionine sulfoxide
- 2009
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Ingår i: Dalton Transactions. - 1477-9226 .- 1477-9234. ; 18, s. 3542-3558
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 7. |
- Risberg, Emiliana Damian, et al.
(författare)
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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 spectroscopy
- 2009
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Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; , s. 1328-1339
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 8. |
- Risberg, Emiliana Damian, et al.
(författare)
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Theoretical and Experimental Sulfur K-edge X-ray Absorption Spectroscopic Study of Cysteine, Cystine, Homocysteine, Penicillamine, Methionine and Methionine Sulfoxide
- 2009
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Ingår i: Dalton Transactions. - : Royal Society of Chemistry (RSC). - 1477-9226 .- 1477-9234. ; , s. 3542-3558
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 9. |
- Damian Risberg, Emiliana, et al.
(författare)
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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 spectroscopy
- 2008
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Ingår i: Dalton Transactions.
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 10. |
- Fors, Yvonne, et al.
(författare)
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Sulfur Accumulation in Pine Wood (Pinus sylvestris) Induced by Bacteria in Simulated Seabed Environment : Implications for Marine Archaeological Wood and Fossil Fuels
- 2008
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Ingår i: International Biodeterioration & Biodegradation. - 0964-8305 .- 1879-0208. ; :62, s. 336-347
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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