| 1. |
- Han, Guangye, et al.
(author)
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Hydration of the oxygen-evolving complex of photosystem II probed in the dark-stable S1 state using proton NMR dispersion profiles
- 2014
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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; :16, s. 11924-11935
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Journal article (peer-reviewed)abstract
- The hydration of the oxygen-evolving complex (OEC) was characterized in the dark stable S1 state of photosystem II using water R1(ω) NMR dispersion (NMRD) profiles. The R1(ω) NMRD profiles were recorded over a frequency range from 0.01 MHz to 40 MHz for both intact and Mn-depleted photosystem II core complexes from Thermosynechococcus vulcanus (T. vulcanus). The intact-minus-(Mn)-depleted difference NMRD profiles show a characteristic dispersion from approximately 0.03 MHz to 1 MHz, which is interpreted on the basis of the Solomon-Bloembergen-Morgan (SBM) and the slow motion theories as being due to a paramagnetic enhanced relaxation (PRE) of water protons. Both theories are qualitatively consistent with the ST = 1, g = 4.9 paramagnetic state previously described for the S1 state of the OEC; however, an alternative explanation involving the loss of a separate class of long-lived internal waters due to the Mn-depletion procedure can presently not be ruled out. Using a point-dipole approximation the PRE-NMRD effect can be described as being caused by 1-2 water molecules that are located about 10 Å away from the spin center of the Mn4CaO5 cluster in the OEC. The application of the SBM theory to the dispersion observed for PSII in the S1 state is questionable, because the parameters extracted do not fulfil the presupposed perturbation criterion. In contrast, the slow motion theory gives a consistent picture indicating that the water molecules are in fast chemical exchange with the bulk (τw < 1 μs). The modulation of the zero-field splitting (ZFS) interaction suggests a (restricted) reorientation/structural equilibrium of the Mn4CaO5 cluster with a characteristic time constant of τZFS = 0.6-0.9 μs.
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| 2. |
- Huang, Yang, 1985-, et al.
(author)
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The water R1(ω) NMRD profiles of a hydrated protein from molecular dynamics simulation
- 2013
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In: Physical Chemistry, Chemical Physics - PCCP. - : RSC Publishing. - 1463-9076 .- 1463-9084. ; 15:33, s. 14089-14097
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Journal article (peer-reviewed)abstract
- The hydration of a protein, peroxiredoxin 5, is obtained from a molecular dynamics simulation and compared with the picture of hydration which is obtained by analysing the water proton R1 NMRD profiles using a generally accepted relaxation model [K. Venu, V.P. Denisov and B. Halle, J. Am. Chem. Soc. 119,3122(1997)]. The discrepancy between the hydration pictures derived from the water R1(ω 0)-NMRD profiles and MD is relevant in a discussion of the factors behind the stretched NMRD profile, the distribution of orientationalorder parameters and residence times of buried water used in the NMRD model.
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| 3. |
- Jonsson, Sofi, 1984-, et al.
(author)
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Mercury methylation rates for geochemically relevant HgII species in sediments
- 2012
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In: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 46:21, s. 11653-11659
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Journal article (peer-reviewed)abstract
- Monomethylmercury (MeHg) in fish from freshwater, estuarine and marine environments are a major global environmental issue. Mercury levels in biota are mainly controlled by the methylation of inorganic mercuric mercury (HgII) to MeHg in water, sediments and soils. There is, however, a knowledge gap concerning the mechanisms and rates of methylation of specific geochemical HgII species. Such information is crucial for a better understanding of variations in MeHg concentrations among ecosystems and, in particular, for predicting the outcome of currently proposed measures to mitigate mercury emissions and reduce MeHg concentrations in fish. To fill this knowledge gap we propose an experimental approach using HgII isotope tracers, with defined and geochemically important adsorbed and solid HgII forms in sediments, to study MeHg formation. We report HgII methylation rate constants, km, in estuarine sediments which span over two orders of magnitude depending on chemical form of added tracer: metacinnabar (β-201HgS(s)) < cinnabar (α-199HgS(s)) < HgII reacted with mackinawite (≡FeS-202HgII) < HgII bonded to natural organic matter (NOM-196HgII) < a typical aqueous tracer (198Hg(NO3)2(aq)). We conclude that a combination of thermodynamic and kinetic effects of HgII solid-phase dissolution and surface desorption control the HgII methylation rate in sediments and causes the large observed differences in km-values. The selection of relevant solid-phase and surface adsorbed HgII tracers will therefore be crucial to achieving biogeochemically accurate estimates of ambient HgII methylation rates.
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| 4. |
- Lindgren, Matteus, 1980-, et al.
(author)
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A combined molecular dynamic simulation and Urea 14N NMR relaxation study of the Urea - lysozyme system
- 2010
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In: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy. - : Elsevier. - 1386-1425 .- 1873-3557. ; 75:3, s. 953-9
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Journal article (peer-reviewed)abstract
- Urea in the lysozyme solvation shell has been studied by utilizing a combination of urea , water NMR relaxation experiments and a molecular dynamics simulation of the urea–lysozyme system. Samples with lysozyme in the native fold in water as well as in 3 M urea have been studied, as well as denatured lysozyme in a 8.5 M urea solvent. The spin relaxation rates of the samples with folded protein show a clear field dependence, which is consistent with a few urea molecules having long residence times on the protein surface and preferentially located in pockets and grooves on the protein. By combining the 3 M urea NMR relaxation data and data from the MD simulation, a full parameter set of the relaxation model is found which can successfully predict the experimental relaxation rates of the 3 M urea sample. However, in the parameter fitting it is evident that the rotational dynamics of urea in the MD simulation is slightly too fast to be consistent with the NMR relaxation rates, perhaps a result of the fast dynamics of the TIP3P water model. The relaxation rates of urea in the proximity of the unfolded lysozyme lack field dependence, which can be interpreted as a loss of pockets and grooves on the denatured protein. The extracted model parameters from the 3 M sample are adjusted and tested on a simple model of the unfolded protein sample and are seen to be in agreement with the relaxation rates. It is shown that the combination of NMR relaxation and MD simulations can be used to create a microscopic picture of the solvent at the protein interface, which can be used for example in the study of chemical denaturation.
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| 5. |
- Wennerström, Håkan, et al.
(author)
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The Stern-Gerlach experiment and the effects of spin relaxation
- 2012
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In: Physical Chemistry, Chemical Physics - PCCP. - : RSC Publishing. - 1463-9076 .- 1463-9084. ; 14, s. 1677-1684
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Journal article (peer-reviewed)abstract
- The classical Stern-Gerlach experiment is analyzed with an emphasis on the spin dynamics. The central question asked is whether there occurs a relaxation of the spin angular momentum during the time the particle passes through the Stern-Gerlach magnet. We examine in particular the transverse relaxation, involving angular momentum exchange between the spin of the particles and the spins of the magnet. A method is presented describing relaxation effects at an individual particle level. This leads to a stochastic equation of motion for the spins. This is coupled to a classical equation of motion for the particle translation. The experimental situation is then modeled through simulations of individual trajectories using two sets of parameter choices and three different sets of initial conditions. The two main conclusions are: (A) if the coupling between the magnet and the spin is solely described by the Zeeman interaction with the average magnetic field the simulations show a clear disagreement with the experimental observation of Stern and Gerlach. (B) If one, on the other hand, also allows for a T(2) relaxation time shorter than the passage time one can obtain a practically quantitative agreement with the experimental observations. These conclusions are at variance with the standard textbook explanation of the Stern-Gerlach experiment.
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| 6. |
- Westlund, Per-Olof, 1952-, et al.
(author)
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Electron spin relaxation at low field
- 2010
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In: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 12:1, s. 201-206
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Journal article (peer-reviewed)abstract
- The low field ESR lineshape and the electron spin-lattice relaxation correlation function are calculated using the stochastic Liouville theory for an effective electron spin quantum number S = 1. When an axially symmetric permanent zero field splitting provides the dominant relaxation mechanism, and when it is much larger than the rotational diffusion constant, it is shown that both electron spin correlation functions S(0)S(t) (n = 0,1) are characterized by the same relaxation time tau(S) = (4D(R))(-1). This confirms the conjectures made by Schaefle and Sharp, J. Chem. Phys., 2004, 121, 5287 and by Fries and Belorizky, J. Chem. Phys., 2005, 123, 124510, based on numerical results using a different formalism. The stochastic Liouville approach also gives the paramagnetically enhanced nuclear spin relaxation time constants, T(1) and T(2), and the ESR lineshape function I(omega). In particular, the L-band (B(0) = 0.035 T) ESR spectrum of a low symmetry Ni(ii)-complex with a cylindrical ZFS tensor is shown to be detectable at sufficiently slowly reorientation of the complex. The analysis shows that the L-band spectrum becomes similar to the zero-field spectrum with a electron spin relaxation time tau(S) = (4D(R))(-1).
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