| 1. |
- Åman, Ken, et al.
(författare)
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Structure and dynamics of interfacial water in an L-alpha phase lipid bilayer from molecular dynamics simulations
- 2003
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Ingår i: Biophysical Journal. - 0006-3495 .- 1542-0086. ; 84, s. 102-15
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Tidskriftsartikel (refereegranskat)abstract
- Based on molecular dynamics simulations, an analysis of structure and dynamics is performed on interfacial water at a liquid crystalline dipalmitoylphosphatidycholine/water system. Water properties relevant for understanding NMR relaxation are emphasized. The first and second rank orientational order parameters of the water O-H bonds were calculated, where the second rank order parameter is in agreement with experimental determined quadrupolar splittings. Also, two different interfacial water regions (bound water regions) are revealed with respect to different signs of the second rank order parameter. The water reorientation correlation function reveals a mixture of fast and slow decaying parts. The fast (ps) part of the correlation function is due to local anisotropic water reorientation whereas the much slower part is due to more complicated processes including lateral diffusion along the interface and chemical exchange between free and bound water molecules. The 100-ns-long molecular dynamics simulation at constant pressure (1 atm) and at a temperature of 50degreesC of 64 lipid molecules and 64 x 23 water molecules lack a slow water reorientation correlation component in the ns time scale. The (H2O)-H-2 powder spectrum of the dipalmitoylphosphatidycholine/water system is narrow and consequently, the NMR relaxation time T-2 is too short compared to experimental results.
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| 2. |
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| 3. |
- Edman, Peter, et al.
(författare)
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On determining intramolecular distances from donor–donor energy migration (DDEM) within bifluorophoric macromolecules
- 2000
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Ingår i: PHYSICAL CHEMISTRY CHEMICAL PHYSICS. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 2, s. 1789-94
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Tidskriftsartikel (refereegranskat)abstract
- Recently a model based on donor–donor energy migration (DDEM) was developed for examining structure–function properties of biomacromolecules such as proteins (J. Chem. Soc., Faraday Trans., 1996, 92, 1563). Unlike the extended Förster theory (EFT; J. Chem. Phys., 1996, 105, 10896) the DDEM model is straightforward to apply in the analyses of fluorescence depolarisation experiments, as obtained by the time-correlated single photon counting (TCSPC) technique. In order to test the validity of the DDEM model, the EFT was used to create synthetic depolarisation data. These mimic true TCSPC experiments and cover a wide range of physical conditions, which are difficult to arrange for in real experiments with model systems. In particular, the relative rate of DDEM () and the rotation correlation time () of the donor molecules was examined. The DDEM rates obtained from the analyses were compared to the true rates. From these results the relative error of the intramolecular distances were calculated. For values 1<12<25, the DDEM model is slightly overestimating the distances. Typically, the distances determined with the DDEM model are overestimated by 5–10%.
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| 4. |
- Håkansson, Pär, et al.
(författare)
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A direct simulation of EPR slow-motion spectra of spin labelled phospholipids in liquid crystalline bilayers based on a molecular dynamics simulation of the lipid dynamics
- 2001
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : RSC Publishing. - 1463-9076 .- 1463-9084. ; 3:23, s. 5311-5319
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Tidskriftsartikel (refereegranskat)abstract
- EPR line shapes can be calculated from the stochastic Liouville equation assuming a stochastic model for the reorientation of the spin probe. Here we use instead and for the first time a detailed molecular dynamics (MD) simulation to generate the stochastic input to the Langevin form of the Liouville equation. A 0.1 μs MD simulation at T = 50°C of a small lipid bilayer formed by 64 dipalmitoylphosphatidylcholine (DPPC) molecules at the water content of 23 water molecules per lipid was used. In addition, a 10 ns simulation of a 16 times larger system consisting of 32 DPPC molecules with a nitroxide spin moiety attached at the sixth position of the sn2 chain and 992 ordinary DPPC molecules, was used to investigate the extent of the perturbation caused by the spin probe. Order parameters, reorientational dynamics and the EPR FID curve were calculated for spin probe molecules and ordinary DPPC molecules. The timescale of the electron spin relaxation for a spin-moiety attached at the sixth carbon position of a DPPC lipid molecule is 11.9 × 107 rad s−1 and for an unperturbed DPPC molecule it is 3.5 × 107 rad s−1.
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| 5. |
- Håkansson, Pär, et al.
(författare)
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Extended Förster theory for determining intraprotein distances : 1. The K2-dynamics and fluorophore reorientation
- 2004
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 108:44, s. 17243-17250
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Tidskriftsartikel (refereegranskat)abstract
- A detailed analysis of the previously developed (J. Chem. Phys. 1996, 105, 10896) extended Förster theory (EFT) is presented for analyzing electronic energy migration within pairs of donors (D). Synthetic data that mimics experimental time-correlated single photon counting data were generated and re-analyzed. To cover a wide dynamic range and various orientational restrictions, the rates of reorientation, as well as the orientational configurations of the interacting D-groups were varied. In general DD distances are recovered within an error limit of 5%, while the errors in orientational configurations are usually larger. The Maier−Saupe and cone potentials were used to generate an immense variety of orientational trajectories. The results obtained exhibit no significant dependence on the choice of potential function used for generating EFT data. Present work demonstrates how to overcome the classical “κ2-problem” and the frequently applied approximation of κ2 = 2/3 in the data analyses. This study also outlines the procedure for analyzing fluorescence depolarization data obtained for proteins, which are specifically labeled with D-groups. The EFT presented here brings the analyses of DDEM data to the same level of molecular detail as in ESR- and NMR-spectroscopy.
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| 6. |
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| 7. |
- Håkansson, P, et al.
(författare)
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Itô diffusions on hypersurfaces with application to the Schwarz-P surface and nuclear magnetic resonance theory
- 2002
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Ingår i: The Journal of Chemical Physics. ; 117:19, s. 8634-43
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Tidskriftsartikel (refereegranskat)abstract
- This work presents a new Brownian dynamics simulation method of translational diffusion on curved surfaces. This new method introduce any implicit defined surface into the stochastic differential equation describing Brownian motion on that surface. The surface curvature will thus enter the force term (A) in the stochastic differential equation dXt = A(Xt)dt + B(Xt)dWt describing an Itô process. We apply the method calculating time correlation functions relevant in nuclear magnetic resonance (NMR) relaxation and translational diffusion studies of cubic phases of lyotropic systems. In particularly we study some bicontinuous cubic liquid crystalline phases which can be described as triply periodic minimal surfaces. The curvature dependent spin relaxation of the Schwarz-P minimal surface is calculated. A comparison of relaxation is made with the more complex topology of the Neovius surface which is another minimal surface in the same space group, and with parallel displacement of the minimal surface which thus results in a nonminimal surface. The curvature dependent relaxation effects are determined by calculating the translational diffusion modulated time-correlation function which determine the relaxation rates of a quadrupole nuclei residing in the water–lipid interface. The results demonstrates that spin relaxation data can provide quantitative information about micro-structure of biocontinuous cubic phases and that it is sensitive to the topology of the surface and to parallel displacement of the model surface. Consequently, spin relaxation may be used as a complement to x-ray diffraction in order to discriminate between different microstructures. It is concluded that fast and accurate computer simulations experiments is needed to be able to interpret NMR relaxation experiments on curved surfaces. © 2002 American Institute of Physics.
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| 8. |
- Håkansson, Pär, et al.
(författare)
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Nuclear magnetic relaxation study of the microstructure of a bicontinuous cubic phase
- 2004
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - Cambridge : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; :6, s. 4321-4329
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Tidskriftsartikel (refereegranskat)abstract
- A NMR relaxation and NMR translational diffusion study is performed on a bicontinuous cubic phase of the dodecyltrimethylammonium chloride/2H2O system with low water content. It is demonstrated how NMR relaxation measurements are combined with structural investigations of X-ray and NMR molecular diffusion measurements to create a consistent picture of the mesoscopic structure of the cubic phase. The 14N, spin-lattice (R1) and spin-spin relaxation rates (R2), were measured for the surfactant at two different field strengths and at four temperatures. The water and the surfactant translational diffusion coefficients were measured by NMR field gradient technique. The experimental spin relaxation rates, and translation diffusion coefficients were interpreted in a model based on a Brownian dynamics (BD) simulation of translational diffusion along curved interfaces (P. Håkansson, L. Persson and P.-O. Westlund, J. Chem. Phys., 2002,117(19), 8634-8643, ). The model surfaces used in our BD relaxation model are also frequently used in interpretations of X-ray crystallography and in free energy calculations on bicontinuous phases. One of our BD-models was able to quantify the influence of the water/lipid interface on the NMR relaxation and diffusion data. Together with X-ray data, a consistent picture of the microstructure for this system was obtained.
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| 9. |
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| 10. |
- Kruk, Danuta, et al.
(författare)
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Nuclear and electron spin relaxation in paramagnetic complexes in solution: Effects of the quantum nature of molecular vibrations
- 2004
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Ingår i: The Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 121:5, s. 2215-27
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Tidskriftsartikel (refereegranskat)abstract
- A model of the paramagnetic relaxation enhancement is developed in terms of electron-spin relaxation caused by the zero-field splitting (ZFS) fluctuating in time due to a coupling between the electron-spin variables and quantum vibrations. The ZFS interaction provides a coupling between the electron-spin variables and vibrational degrees of freedom, and is represented as a Taylor series expansion in a set of vibrational modes (normal coordinates). A two-level harmonic oscillator subsystem is assumed, and the electron-spin relaxation associated with T2V and T1V vibrational relaxation is considered. The description of vibrationally induced electron-spin dynamics is incorporated into the calculations of the paramagnetic relaxation enhancement by the Solomon–Bloembergen–Morgan approach as well as in the framework of the general slow-motion theory. The theoretical predictions are compared with the experimental paramagnetic relaxation enhancement values for the Ni(H2O) complex in aqueous solution. The parameters required by the model are obtained from quantum chemical and molecular dynamics studies. Comparison is made between the current model and its recently published classical counterpart.
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