| 1. |
- Fredriksson, Andreas, et al.
(författare)
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Comparison between in situ total internal reflection vibrational spectroscopy of an adsorbed collector and spectra calculated by ab initio density functional theory methods
- 2007
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 111:26, s. 9299-9304
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Tidskriftsartikel (refereegranskat)abstract
- In this investigation, adsorbed heptyl xanthate on a Ge(111) surface was studied, as well as the free heptyl xanthate molecule, by means of first-principle density functional theory calculations. The modeled results were compared with the in situ total internal reflection vibrational spectroscopy spectra of heptyl xanthate adsorbed on a germanium internal reflection element and the transmission infrared spectrum of a heptyl xanthate ion in aqueous solution. The assignments of the vibrational frequencies were done for the adsorbed xanthate. The region between 1150 and 1000 cm(-1) seems suitable for discussing differences between an adsorbed xanthate and its corresponding ion. The modeled spectra for both the adsorbed xanthate and the xanthate ion are in good agreement with the experimentally retrieved spectra. This investigation shows the strength of using DFT calculations in the interpretation of absorption bands from molecules adsorbed at surfaces in situ.
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| 2. |
- Gurmu, Daniel, et al.
(författare)
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The crystal structure of the protein YhaK from Escherichia coli reveals a new subclass of redox sensitive enterobacterial bicupins
- 2009
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Ingår i: Proteins. - : Wiley. - 0887-3585 .- 1097-0134. ; 74:1, s. 18-31
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Tidskriftsartikel (refereegranskat)abstract
- YhaK is a protein of unknown function found in low abundance in the cytosol of Escherichia coli. DNA array studies have revealed that YhaK is strongly up-regulated by nitroso-glutathione (GSNO) and also displays a 12-fold increase in expression during biofilm growth of E. coli 83972 and VR50 in human urine. We have determined the YhaK crystal structure and demonstrated that in vitro YhaK is a good marker for monitoring oxidative stresses in E. coli. The YhaK protein structure shows a bicupin fold where the two cupin domains are crosslinked with one intramolecular disulfide bond (Cys10 to Cys204). We found that the third cysteine in YhaK, Cys122, is oxidized to a sulfenic acid. Two chloride ions are found in the structure, one close to the reactive Cys122, and the other on a hydrophobic surface close to a symmetry-related molecule. There are major structural differences at the N-terminus of YhaK compared with similar structures that also display the bicupin fold (YhhW and hPirin). YhaK showed no quercetinase and peroxidase activity. However, reduced YhaK was very sensitive to reactive oxygen species (ROS). The complete, functional E. coli glutaredoxin or thioredoxin systems protected YhaK from oxidation. E. coli thioredoxin reductase and NADPH produced ROS and caused oxidation and oligomerization of reduced YhaK. Taken together, we propose that YhaK is the first of a new sub-class of bicupins that lack the canonical cupin metal-binding residues of pirins and may be involved in chloride binding and/or sensing of oxidative stress in enterobacteria.
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| 3. |
- Hellström, Pär, et al.
(författare)
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A theoretical and experimental study of vibrational properties of alkyl xanthates
- 2006
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Ingår i: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy. - : Elsevier BV. - 1386-1425 .- 1873-3557. ; 65:3-4, s. 887-895
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Tidskriftsartikel (refereegranskat)abstract
- Geometrical structure and vibrational modes of potassium and sodium ethyl/heptyl xanthates were studied, using both theoretical and experimental methods. Both Hartree-Fock and density functional theory were used. The experimental method used was infrared absorption spectroscopy (FTIR). Our work showed that vibrational frequencies calculated with density functional theory, using the local density approximation, are in very good agreement with experiments. The results were not improved by using the more sophisticated and computationally demanding B3LYP functional.
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| 4. |
- Hellström, Pär, et al.
(författare)
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An ab initio study of ethyl xanthate adsorbed on Ge(111) surfaces
- 2007
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 111:45, s. 16920-16926
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Tidskriftsartikel (refereegranskat)abstract
- The interaction between adsorbed ethyl xanthate on a clean Ge(111) surface and a hydroxylated surface was studied, using first-principle density functional theory. Geometrically optimized structures are presented and discussed. Results suggest a bidentate bridging conformation on a clean Ge(111) surface, whereas a monodentate bonding is preferred when the surface is saturated by hydrogen atoms. Then the interaction with a hydroxylated surface was considered. The lowest energy configuration was obtained when xanthate binds with one sulfur to the surface and with the other to an OH group adsorbed on the surface. A marker for this configuration was found in the vibrational spectra at 3200 cm-1. Vibrational frequencies down to 250 cm-1 were calculated and assigned to vibrational modes and presented together with the calculated infrared spectra. The tilt angle of the hydrocarbon chain was also investigated.
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| 5. |
- Hellström, Pär, et al.
(författare)
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Study of potassium O,O′-dibutyldithiophosphate combining DFT, 31P CP/MAS NMR and infrared spectroscopy
- 2008
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 112:46, s. 11777-11783
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Tidskriftsartikel (refereegranskat)abstract
- Dithiophosphates are used in many different industrial applications. To explain their functions and properties in these applications, a fundamental understanding on a molecular level is needed. Potassium O,O′-Dibutyldithiophosphate and its anion have been investigated by means of a combination of DFT and 31P CP/MAS NMR and infrared spectroscopy. Several low-energy conformations were studied by DFT. Three different conformations with significantly different torsion angles of the O-C bond relative to the O-P-O plane were selected for further studies of infrared frequencies and 31P NMR chemical-shift tensors. A good agreement between theoretical and experimental results was obtained, especially when the IR spectra or 31P chemical shift tensor parameters of all three conformations were added, indicating that, because of the low energy difference between the conformations, the molecules are rapidly fluctuating between them.
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