| 1. |
- Baev, Alexander, et al.
(författare)
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Theoretical Simulations of clamping levels in optical power limiting
- 2006
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207 .- 1520-5215. ; 110:42, s. 20912-20916
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Tidskriftsartikel (refereegranskat)abstract
- Multiphysics modeling, combining quantum mechanical and classical wave mechanical theories, of clamping levels has been performed for a platinum(II) organic compound in a sol-gel glass matrix. A clamping level of 2.5 mu J is found for a pulse duration of 10 ns. The excited-state absorption in the triplet manifold is shown to be crucial for clamping to occur.
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| 2. |
- Malysheva, Lyuba, et al.
(författare)
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Molecular Orientation in Helical and All-Trans Oligo(ethylene glycol)-Terminated Assemblies on Gold: Results of ab Initio Modeling
- 2005
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215 .- 1520-6106 .- 1520-5207. ; 109:34, s. 7788-7796
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Tidskriftsartikel (refereegranskat)abstract
- The structural properties of self-assembled monolayers (SAMs) of oligo(ethylene glycol) (OEG)-terminated and amide-containing alkanethiols (HS(CH2)15CONH(CH2CH2O)6H and related molecules with shorter alkyl or OEG portions) on gold are addressed. Optimized geometry of the molecular constituents, characteristic vibration frequencies, and transition dipole moments are obtained using density-functional theory methods with gradient corrections. These data are used to simulate IR reflection-absorption (RA) spectra associated with different OEG conformations. It is shown that the positions and relative intensities of all characteristic peaks in the fingerprint region are accurately reproduced by the model spectra within a narrow range of the tilt and rotation angles of the alkyl plane, which turns out to be nearly the same for the helical and all-trans OEG conformations. In contrast, the tilt of the OEG axis changes considerably under conformational transition from helical to all-trans OEG. By means of ab initio modeling, we also clarify other details of the molecular structure and orientation, including lateral hydrogen bonding, the latter of which is readily possessed by the SAMs in focus. These results are crucial for understanding phase and folding characteristics of OEG SAMs and other complex molecular assemblies. They are also expected to contribute to an improved understanding of the interaction with water, ions, and ultimately biological macromolecules.
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| 3. |
- Abbas, Zareen, 1962, et al.
(författare)
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Monte Carlo Simulations of Salt Solutions: Exploring the Validity of Primitive Models
- 2009
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 113:17, s. 5905-5916
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Tidskriftsartikel (refereegranskat)abstract
- An extensive series of Monte Carlo (MC) simulations were performed in order to explore the validity of simple primitive models of electrolyte solutions and in particular the effect of ion size asymmetry on the bulk thermodynamic properties of real salt solutions. Ionic activity and osmotic coefficients were calculated for 1:1, 2:1, and 3:1 electrolytes by using the unrestricted primitive model (UPM); i.e., ions are considered as charged hard spheres of different sizes dissolved in a dielectric continuum. Mean ionic activity and osmotic coefficients calculated by the MC simulations were fitted simultaneously to the experimental data by adjusting only the cation radius while keeping the anion radius fixed at its crystallographic value. Ionic radii were further optimized by systematically varying the cation and anion radii at a fixed sum of ionic radii. The success of this approach is found to be highly salt specific. For example, experimental data (mean ionic activity and osmotic coefficients) of salts which are usually considered as dissociated such as HCl, HBr, LiCl, LiBr, LiClO4, and KOH were successfully fitted up to 1.9, 2.5, 1.9, 3, 2.5, and 4.5 M concentrations, respectively. In the case of partially dissociated salts such as NaCl, the successful fits were only obtained in a more restricted concentration range. Consistent sets of the best fitted cation radii were obtained for acids, alkali, and alkaline earth halides. A list of recommended ionic radii is also provided. The reliability of the optimized ionic radii was further tested in simulations of the osmotic coefficients of LiCl−NaCl−KCl salt mixtures. A very good agreement between the simulated and experimental data was obtained up to ionic strength of 4.5 M.
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| 4. |
- Abdurrokhman, Iqbaal, 1991, et al.
(författare)
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Protic Ionic Liquids Based on the Alkyl-Imidazolium Cation: Effect of the Alkyl Chain Length on Structure and Dynamics
- 2019
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 123:18, s. 4044-4054
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Tidskriftsartikel (refereegranskat)abstract
- Protic ionic liquids are known to form extended hydrogen-bonded networks that can lead to properties different from those encountered in the aprotic analogous liquids, in particular with respect to the structure and transport behavior. In this context, the present paper focuses on a wide series of 1-alkyl-imidazolium bis(trifluoromethylsulfonyl)imide ionic liquids, [HC n Im][TFSI], with the alkyl chain length (n) on the imidazolium cation varying from ethyl (n = 2) to dodecyl (n = 12). A combination of several methods, such as vibrational spectroscopy, wide-angle X-ray scattering (WAXS), broadband dielectric spectroscopy, and 1 H NMR spectroscopy, is used to understand the correlation between local cation-anion coordination, nature of nanosegregation, and transport properties. The results indicate the propensity of the -NH site on the cation to form stronger H-bonds with the anion as the alkyl chain length increases. In addition, the position and width of the scattering peak q 1 (or the pre-peak), resolved by WAXS and due to the nanosegregation of the polar from the nonpolar domains, are clearly dependent on the alkyl chain length. However, we find no evidence from pulsed-field gradient NMR of a proton motion decoupled from molecular diffusion, hypothesized to be facilitated by the longer N-H bonds localized in the segregated ionic domains. Finally, for all protic ionic liquids investigated, the ionic conductivity displays a Vogel-Fulcher-Tammann dependence on inverse temperature, with an activation energy E a that also depends on the alkyl chain length, although not strictly linearly.
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| 5. |
- Acebes, S., et al.
(författare)
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Mapping the Long-Range Electron Transfer Route in Ligninolytic Peroxidases
- 2017
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 121:16, s. 3946-3954
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Tidskriftsartikel (refereegranskat)abstract
- Combining a computational analysis with site-directed mutagenesis, we have studied the long-range electron transfer pathway in versatile and lignin peroxidases, two enzymes of biotechnological interest that play a key role for fungal degradation of the bulky lignin molecule in plant biomass. The in silico study established two possible electron transfer routes starting at the surface tryptophan residue previously identified as responsible for oxidation of the bulky lignin polymer. Moreover, in both enzymes, a second buried tryptophan residue appears as a top electron transfer carrier, indicating the prevalence of one pathway. Site-directed mutagenesis of versatile peroxidase (from Pleurotus eryngii) allowed us to corroborate the computational analysis and the role played by the buried tryptophan (Trp244) and a neighbor phenylalanine residue (Phe198), together with the surface tryptophan, in the electron transfer. These three aromatic residues are highly conserved in all the sequences analyzed (up to a total of 169). The importance of the surface (Trp171) and buried (Trp251) tryptophan residues in lignin peroxidase has been also confirmed by directed mutagenesis of the Phanerochaete chrysosporium enzyme. Overall, the combined procedure identifies analogous electron transfer pathways in the long-range oxidation mechanism for both ligninolytic peroxidases, constituting a good example of how computational analysis avoids making extensive trial-error mutagenic experiments.
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| 6. |
- Acke, Filip, 1968, et al.
(författare)
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Role of adsorbed surface oxygen in the adsorption of NO on alkaline earth oxides and Pt-promoted CaO surfaces
- 1999
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Ingår i: Journal of Physical Chemistry B Materials. - : American Chemical Society (ACS). - 1089-5647 .- 1520-6106 .- 1520-5207. ; 103:6, s. 972-978
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Tidskriftsartikel (refereegranskat)abstract
- Adsorbed surface oxygens are formed on CaO, SrO, and BaO during exposure to N2O, and their presence is shown to affect the room-temperature NO adsorption. Information about the adsorbed intermediates is contained in the desorption products and in the desorption temperatures during the subsequent heating ramp in Ar. The presence of adsorbed oxygen species increases the total amount of adsorbed NO for CaO and BaO substrates, whereas for SrO the adsorbed intermediate is stabilized. Two NO desorption peaks are found for CaO and SrO, one at low and one at high temperature. The former is assigned to adsorbed NO, whereas the latter is assigned to adsorbed -NO2 and/or -NO3 species. NO adsorption as -NO2 and/or -NO3 species finds evidence in the corresponding O2 desorption. Only one NO desorption peak is found for BaO. This NO desorption peak disappears in the absence of preadsorbed surface oxygens. O2 desorption is observed, even in the absence of any preadsorbed surface oxygens, for CaO and SrO substrates. This suggests NO bond dissociation upon NO adsorption. The effect of the promotion of CaO by Pt has also been investigated. The respective desorption profiles are similar to those for the unpromoted CaO with preadsorbed surface oxygens, although the amounts are significantly increased.
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| 7. |
- Acke, Filip, et al.
(författare)
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Study of the reduction and reoxidation of a CaO surface
- 1997
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Ingår i: J Phys Chem B. - 1520-5207 .- 1520-6106. ; 101:33, s. 6484-
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Tidskriftsartikel (refereegranskat)abstract
- The reduction of NO with CO and H2 is shown to comprise two basic reactions: a surface oxygen abstraction by the reducing agent and a reoxidation of the surface by NO. The former reaction step has been demonstrated by transient CO2 formation during CO exposure of oxidized CaO surfaces, while the latter was demonstrated by N2 and/or N2O transient formation during NO exposure of a prereduced CaO surface. It was shown that at low temperatures (between room temperature and 500 °C) both N2 and N2O were formed, but at temperatures above 500 °C only N2 was observed. The activation energies of the respective steps have been determined using temperature-programmed reaction experiments. The activation energy of the surface oxygen abstraction was determined to be 25 kcal/mol and is similar to the apparent activation energy of the overall reaction. The activation energy of the NO bond breakage was determined to be maximum 10 kcal/mol as measured by N2O formation. The importance of an N2O2- or N2O22- intermediate in the formation of N2O will be discussed, and the importance of N2O decomposition in forming N2 at temperatures above 500 °C will be compared with a N surface diffusion mechanism.
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| 8. |
- Adebahr, J, et al.
(författare)
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Ion and solvent dynamics in gel electrolytes based on ethylene oxide grafted acrylate polymers
- 2002
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106 .- 1089-5647. ; 106:47, s. 12119-12123
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Tidskriftsartikel (refereegranskat)abstract
- Multinuclear pulsed field gradient NMR measurements and theological viscosity measurements were performed on three series of polymer gel electrolytes. The gels were based on a lithium salt electrolyte swollen into a copolymer matrix comprising an acrylate backbone and ethylene oxide side chains. In each series the side chains differed in length and number, but the acrylate-to-ethylene oxide ratio was kept constant. It was found that the self-diffusion coefficient of the cations was much lower than that of the anions, and that it decreased rapidly when the side chains got longer. In contrast, the self-diffusion coefficient of the anions was found to be independent of chain length. In the gel electrolytes, the diffusion coefficients of the solvent molecules are relatively constant despite an increased viscosity with increasing length of the side chains. However, in saltfree gels made for comparison, the diffusion coefficients of the solvent molecules decreased with, increasing length of the side chains, which is consistent with an increased viscosity.
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| 9. |
- Agrell, H. G., et al.
(författare)
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Conductivity studies of nanostructured TiO2 films permeated with electrolyte
- 2004
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 108:33, s. 12388-12396
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Tidskriftsartikel (refereegranskat)abstract
- Charge transport in nanostructured TiO2 films permeated with an electrolyte was studied, using temperature-dependent conductivity and electron accumulation measurements. Two regions for charge transport were distinguished from the relationship between conductivity and electron concentration. In the first region (similar to1-20 electrons per TiO2 particle), the effective electron mobility is dependent on the electron concentration and values between 7 x 10(-4) and 78 x 10(-4) cm(2) V-1 s(-1) were determined. The activation energy of the mobility was similar to0.3 eV. The charge transport can be described with a trapping/detrapping model that involves localized band-gap states. In the second region (> 20 electrons per TiO2 particle), the effective electron mobility is independent of electron concentration and values of similar to150 x 10(-4) cm(2) V-1 s(-1) are calculated. The activation energy of mobility is in the range of 0-0.15 eV, depending on the electrolyte. Transport of electrons in the conduction band seems to be the most applicable model.
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| 10. |
- Agzenai, Y, et al.
(författare)
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In Situ X-ray Polymerization: From Swollen Lamellae to Polymer-Surfactant Complexes
- 2014
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 118:4, s. 1159-1167
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Tidskriftsartikel (refereegranskat)abstract
- The influence of the monomer diallyldimethylammonium chloride (D) on the lamellar liquid crystal formed by the anionic surfactant aerosol OT (AOT) and water is investigated, determining the lamellar spacings by SAXS and the quadrupolar splittings by deuterium NMR, as a function of the D or AOT concentrations. The cationic monomer D induces a destabilization of the AOT lamellar structure such that, at a critical concentration higher than 5 wt %, macroscopic phase separation takes place. When the monomer, which is dissolved in the AOT lamellae, is polymerized in situ by X-ray initiation, a new collapsed lamellar phase appears, corresponding to the complexation of the surfactant with the resulting polymer. A theoretical model is employed to analyze the variation of the interactions between the AOT bilayers and the stability of the lamellar structure.
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| 11. |
- Ahadi, Aylin, et al.
(författare)
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Three-Dimensional Simulation of Nanoindentation Response of Viral Capsids. Shape and Size Effects
- 2009
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 113:11, s. 3370-3378
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Tidskriftsartikel (refereegranskat)abstract
- The nanoindentation response of empty viral capsids is modeled using three-dimensional finite element analysis. Simulation with two different geometries, spherical and icosahedral, is performed using the finite element code Abaqus. The capsids are modeled as nonlinear Hookean elastic, and both small and large deformation analysis is performed. The Young's modulus is determined by calibrating the force-indentation curve to data from atomic force microscopy (AFM) experiments. Force-indentation curves for three different viral capsids are directly compared to experimental data. Predictions are made for two additional viral capsids. The results from the simulation showed a good agreement with AFM data. The paper demonstrates that over the entire range of virus sizes (or Foppl-von Karman numbers) spherical and icosahedral models yield different force responses. In particular, it is shown that capsids with dominantly spherical shape (for low Foppl-von Karman numbers) exhibit nearly linear relationship between force and indentation, which has been experimentally observed on the viral shell studies so far. However, we predict that capsids with significant faceting (for large Foppl-von Karman numbers) and thus more pronounced icosahedral shape will exhibit rather nonlinear deformation behavior.
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| 12. |
- Ai, Yue-Jie, 1982-, et al.
(författare)
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Repair of DNA Dewar Photoproduct to (6-4) photoproduct in (6-4) Photolyase
- 2011
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 115:37, s. 10976-10982
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Tidskriftsartikel (refereegranskat)abstract
- Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.
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| 13. |
- Ai, Yue-Jie, et al.
(författare)
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Theoretical Studies on Photoisomerizations of (6-4) and Dewar Photolesions in DNA
- 2010
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:44, s. 14096-14102
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Tidskriftsartikel (refereegranskat)abstract
- The (6-4) photoproduct ((6-4) PP) is one of the main lesions in UV-induced DNA damage. The (6-4) PP and its valence isomer Dewar photoproduct (Dewar PP) can have a great threat of mutation and cancer but gained much less attention to date. In this study, with density functional theory (DFT) and the complete active space self-consistent field (CASSCF) methods, the photoisomerization processes between the (6-4) PP and the Dewar PP in the gas phase, the aqueous solution, and the photolyase have been carefully examined. Noticeably, the solvent effect is treated with the CASPT2//CASSCF/Amber (QM/MM) method. Our calculations show that the conical intersection (Cl) points play a crucial role in the photoisomerization reaction between the (6-4) PP and the Dewar PP in the gas and the aqueous solution. The ultrafast internal conversion between the S-2 ((1)pi pi*) and the So states via a distorted intersection point is found to be responsible for the formation of the Dewar PP lesion at 313 nm, as observed experimentally. For the reversed isomeric process, two channels involving the "dark" excited states have been identified. In addition to the above passages, in the photolyase, a new electron-injection isomerization process as an efficient way for the photorepair of the Dewar PP is revealed.
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| 14. |
- Aidas, Kestutis, et al.
(författare)
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Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics
- 2013
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 117:7, s. 2069-2080
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Tidskriftsartikel (refereegranskat)abstract
- Attempting to unravel mechanisms in optical probing of proteins, we have performed pilot calculations of two cationic chromophores-acridine yellow and proflavin-located at different binding sites within human serum albumin, including the two primary drug binding sites as well as a heme binding site. The computational scheme adopted involves classical molecular dynamics simulations of the ligands bound to the protein and subsequent linear response polarizable embedding density functional theory calculations of the excitation energies. A polarizable embedding potential consisting of point charges fitted to reproduce the electrostatic potential and isotropic atomic polarizabilities computed individually for every residue of the protein was used in the linear response calculations. Comparing the calculated aqueous solution-to-protein shifts of maximum absorption energies to available experimental data, we concluded that the cationic proflavin chromophore is likely not to bind albumin at its drug binding site I nor at its heme binding site. Although agreement with experimental data could only be obtained in qualitative terms, our results clearly indicate that the difference in optical response of the two probes is due to deprotonation, and not, as earlier suggested, to different binding sites. The ramifications of this finding for design of molecular probes targeting albumin or other proteins is briefly discussed.
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| 15. |
- Ainalem, Marie-Louise, et al.
(författare)
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On the Ability of PAMAM Dendrimers and Dendrimer/DNA Aggregates To Penetrate POPC Model Biomembranes
- 2010
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:21, s. 7229-7244
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Tidskriftsartikel (refereegranskat)abstract
- Poly(amido amine) (PAMAM) dendrimers have previously been shown, as cationic condensing agents of DNA, to have high potential for nonviral gene delivery. This study addresses two key issues for gene delivery: the interaction of the biomembrane with (i) the condensing agent (the cationic PAMAM dendrimer) and (ii) the corresponding dendrimer/DNA aggregate. Using in situ null ellipsometry and neutron reflection, parallel experiments were carried out involving dendrimers or generations 2 (G2), 4 (G4), and 6 (G6). The study demonstrates that free dendrimers of all three generations were able to traverse supported palmitoyloleoylphosphatidylcholine (POPC) bilayers deposited on silica surfaces. The model biomembranes were elevated front the solid surfaces upon dendrimer penetration, which offers a promising new way to generate more realistic model biomembranes where the contact with the supporting surface is reduced and where aqueous cavities are present beneath the bilayer. The largest dendrimer (GO) induced partial bilayer destruction directly upon penetration, whereas the smaller dendrimers (G2 and G4) leave the bilayer intact, so we propose that lower generation dendrimers have greater potential as transfection mediators. In addition to the experimental observations, coarse-grained simulations on the interaction between generation 3 (03) dendrimers and POPC bilayers were performed in the absence and presence of a bilayer-supporting negatively charged surface that emulates the support. The simulations demonstrate that G3 is transported across free-standing POPC bilayers by direct penetration and not by endocytosis. The penetrability was, however, reduced in the presence of a surface, indicating that the membrane transport observed experimentally was not driven solely by the surface. The experimental reflection techniques were also applied to dendrimer/DNA aggregates of charge ratio = 0.5, and while G2/DNA and G4/DNA aggregates interact with POPC bilayers. G6/DNA displays no such interaction. These results indicate that, in contrast to free dendrimer molecules, dendrimer/DNA aggregates of low charge ratios are not able to traverse a membrane by direct penetration.
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| 16. |
- Akhtar, Sultan, et al.
(författare)
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Real-Space Transmission Electron Microscopy Investigations of Attachment of Functionalized Magnetic Nanoparticles to DNA-Coils Acting as a Biosensor
- 2010
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:41, s. 13255-13262
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Tidskriftsartikel (refereegranskat)abstract
- The present work provides the first real-space analysis of nanobead-DNA coil interactions. Immobilization of oligonucleotide-functionalized magnetic nanobeads in rolling circle amplified DNA-coils was studied by complex magnetization measurements and transmission electron microscopy (TEM), and a statistical analysis of the number of beads hybridized to the DNA-coils was performed. The average number of beads per DNAcoil using the results from both methods was found to be around 6 and slightly above 2 for samples with 40 and 130 nm beads, respectively. The TEM analysis supported an earlier hypothesis that 40 nm beads are preferably immobilized in the interior of DNA-coils whereas 130 nm beads, to a larger extent, are immobilized closer to the exterior of the coils. The methodology demonstrated in the present work should open up new possibilities for characterization of interactions of a large variety of functionalized nanoparticles with macromolecules, useful for gaining more fundamental understanding of such interactions as well as for optimizing a number of biosensor applications.
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| 17. |
- Akinchina, Anna, et al.
(författare)
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Monte Carlo simulations of polyion-macroion complexes. 2. Polyion length and charge density dependence
- 2003
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 107:32, s. 8011-8021
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Tidskriftsartikel (refereegranskat)abstract
- The complexation between a polyion and an oppositely charged spherical macroion in the framework of the primitive model has been studied by the use of Monte Carlo simulations. The polyion length, linear charge density, and bare persistence length are varied systematically, while the properties of the macroion are kept constant. The polyion charge to macroion charge ratio is varied between 1/4 and 4. The structure of the complex is investigated by direct visualization; polyion bead complexation probability; loop, tail, and train characteristics; degree of overcharging; and tail joint probability functions. The strongest complexes are observed for flexible chains, where the polyion is folded around the macroion. In the case of fully flexible chains, a transition from a collapsed state to a fluctuating two-tail state and eventually to a one-tail state are observed as the chain length is increased. As the stiffness is increased, several complex structures, such as multiloop, single-loop, and solenoid arrangements, and finally a structure involving only a single contact between the polyion and the macroion occur. In particular, for long and highly charged polyions, a transition from the one-tail state to a two-tail state appears as the chain stiffness is increased. A discussion with recent theories and other simulation studies is also provided.
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| 18. |
- Akke, Mikael, et al.
(författare)
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NMR Studies of Aromatic Ring Flips to Probe Conformational Fluctuations in Proteins
- 2023
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 127:3, s. 591-599
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Forskningsöversikt (refereegranskat)abstract
- Aromatic residues form a significant part of the protein core, where they make tight interactions with multiple surrounding side chains. Despite the dense packing of internal side chains, the aromatic rings of phenylalanine and tyrosine residues undergo 180° rotations, or flips, which are mediated by transient and large-scale “breathing” motions that generate sufficient void volume around the aromatic ring. Forty years after the seminal work by Wagner and Wüthrich, NMR studies of aromatic ring flips are now undergoing a renaissance as a powerful means of probing fundamental dynamic properties of proteins. Recent developments of improved NMR methods and isotope labeling schemes have enabled a number of advances in addressing the mechanisms and energetics of aromatic ring flips. The nature of the transition states associated with ring flips can be described by thermodynamic activation parameters, including the activation enthalpy, activation entropy, activation volume, and also the isothermal volume compressibility of activation. Consequently, it is of great interest to study how ring flip rate constants and activation parameters might vary with protein structure and external conditions like temperature and pressure. The field is beginning to gather such data for aromatic residues in a variety of environments, ranging from surface exposed to buried. In the future, the combination of solution and solid-state NMR spectroscopy together with molecular dynamics simulations and other computational approaches is likely to provide detailed information about the coupled dynamics of aromatic rings and neighboring residues. In this Perspective, we highlight recent developments and provide an outlook toward the future.
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| 19. |
- Al-Manasir, Nodar, et al.
(författare)
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Effects of Temperature and pH on the Contraction and Aggregation of Microgels in Aqueous Suspensions
- 2009
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 113:32, s. 11115-11123
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Tidskriftsartikel (refereegranskat)abstract
- Chemically cross-linked poly(N-isopropylacrylamide) (PNIPAM) microgels and PNIPAM with different amounts of acrylic acid groups (PNIPAM-co-PAA) were synthesized and the temperature-induced aggregation behaviors of aqueous suspensions of these microgels were investigated mainly with the aid of dynamic light scattering (DLS) and turbidimetry. The DLS results show that the particles at all conditions shrink at temperatures up to approximately the lower critical solution temperature (LCST), but the relative contraction effect is larger for the microgels without acid groups or for microgels with added anionic surfactant (SDS). A significant depression of the cloud point is found in suspensions of PNIPAM with very low concentrations of SDS. The compression of the microgels cannot be traced from the turbidity results, but rather the values of the turbidity increase in this temperature interval. This phenomenon is discussed in the framework of a theoretical model. At temperatures above LCST, the size of the microgels without attached charged groups in a very dilute suspension is unaffected by temperature, while the charged particles (pH 7 and 11) continue to collapse with increasing temperature over the entire domain. In this temperature range, low-charged particles of higher concentration and particles containing acrylic acid groups at low pH (pH 2) aggregate, and macroscopic phase separation is approached at higher temperatures. This study demonstrates how the stabilization of microgels can be affected by factors such as polymer concentration, addition of ionic surfactant to particles without charged acid groups, amount of charged groups in the polymer, and pH.
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| 20. |
- Al-Tikriti, Yassir, et al.
(författare)
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Drug-Eluting Polyacrylate Microgels : Loading and Release of Amitriptyline
- 2020
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Ingår i: Journal of Physical Chemistry B. - : AMER CHEMICAL SOC. - 1520-6106 .- 1520-5207. ; 124:11, s. 2289-2304
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Tidskriftsartikel (refereegranskat)abstract
- We investigated the loading of an amphiphilic drug, amitriptyline hydrochloride (AMT), onto sodium polyacrylate hydrogels at low ionic strength and its release at high ionic strength. The purpose was to show how the self-assembling properties of the drug and the swelling of the gel network influenced the loading/release mechanisms and kinetics, important for the development of improved controlled-release systems for parenteral administration of amphiphilic drugs. Equilibrium studies showed that single microgels (similar to 100 mu m) in a large solution volume underwent a discrete transition between swollen and dense states at a critical drug concentration in the solution. For single macrogels in a small solution volume, the transition progressed gradually with increasing amount of added drug, with swollen and dense phases coexisting in the same gel; in a suspension of microgels, swollen and collapsed particles coexisted. Time-resolved micropipette-assisted microscopy studies showed that drug self-assemblies accumulated in a dense shell enclosing the swollen core during loading and that a dense core was surrounded by a swollen shell during release. The time evolution of the radius of single microgels was determined as functions of liquid flow rate, network size, and AMT concentration in the solution. Mass transport of AMT in the surrounding liquid, and in the dense shell, influenced the deswelling rate during loading. Mass transport in the swollen shell controlled the swelling rate during release. A steady-state kinetic model taking into account drug self-assembly, core-shell phase separation, and microgel volume changes was developed and found to be in semiquantitative agreement with the experimental loading and release data.
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| 21. |
- Alarcon, H., et al.
(författare)
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Dye-sensitized solar cells based on nanocrystalline TiO2 films surface treated with Al3+ ions : Photovoltage and electron transport studies
- 2005
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 109:39, s. 18483-18490
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Tidskriftsartikel (refereegranskat)abstract
- Nanocrystalline TiO2 films, surface modified with Al3+, were manufactured by depositing a TiO2 suspension containing small amounts of aluminum nitrate or aluminum chloride onto conducting glass substrates, followed by drying, compression, and finally heating to 530 degrees C. Electrodes prepared with TiO2 nanoparticles coated with less than 0.3 wt % aluminum oxide with respect to TiO2 improved the efficiency of the dye sensitized solar cell. This amount corresponds to less than a monolayer of aluminum oxide. Thus, the Al ions terminate the TiO2 surface rather than form a distinct aluminum oxide layer. The aluminum ion surface treatment affects the solar cell in different ways: the potential of the conduction band is shifted, the electron lifetime is increased, and the electron transport is slower when aluminum ions are present between interconnected TiO2 particles.
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| 22. |
- Alavi, Fatemeh Sadat, et al.
(författare)
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QM/MM Study of the Conversion of Oxophlorin into Verdoheme by Heme Oxygenase
- 2017
-
Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 121:51, s. 11427-11436
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Tidskriftsartikel (refereegranskat)abstract
- Heme oxygenase is an enzyme that degrades heme, thereby recycling iron in most organisms, including humans. Pervious density functional theory (DFT) calculations have suggested that iron(III) hydroxyheme, an intermediate generated in the first step of heme degradation by heme oxygenase, is converted to iron(III) superoxo oxophlorin in the presence of dioxygen. In this article, we have studied the detailed mechanism of conversion of iron(III) superoxo oxophlorin to verdoheme by using combined quantum mechanics and molecular mechanics (QM/MM) calculations. The calculations employed the B3LYP method and the def2-QZVP basis set, considering dispersion effects with the DFT-D3 approach, obtaining accurate energies with large QM regions of almost 1000 atoms. The reaction was found to be exothermic by -35 kcal/mol, with a rate-determining barrier of 19 kcal/mol in the doublet state. The protein environment and especially water in the enzyme pocket significantly affects the reaction by decreasing the reaction activation energies and changing the structures by providing strategic hydrogen bonds.
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| 23. |
- Albèr, Cathrine, et al.
(författare)
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Hydration of Hyaluronan : Effects on Structural and Thermodynamic Properties
- 2015
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 119:11, s. 4211-4219
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Tidskriftsartikel (refereegranskat)abstract
- Hyaluronan (HA) is a frequently occurring biopolymer with a large variety of functions in nature. During the past 60 years, there have been numerous reports on structural and dynamic behavior of HA in water. Nevertheless, studies covering a wider concentration range are still lacking. In this work, we use isothermal scanning sorption calorimetry for the first time to investigate hydration-induced transitions in HA (sodium hyaluronate, 17 kDa). From this method, we obtain the sorption isotherm and the enthalpy and the entropy of hydration. Thermotropic events are evaluated by differential scanning calorimetry (DSC), and structure analysis is performed with X-ray scattering (SWAXS) and light and scanning electron microscopy. During isothermal hydration, HA exhibits a glass transition, followed by crystallization and subsequent dissolution of HA crystals and formation of a one-phase solution. Structural analysis reveals that the crystal may be indexed on an orthorhombic unit cell with space group P212121. Crystallization of HA was found to occur either through endothermic or exothermic processes, depending on the temperature and water content. We propose a mechanism of crystallization that explains this phenomenon based on the interplay between the hydrophobic effect and strengthening of hydrogen bonds during formation of crystals. The combined results were used to construct a binary phase diagram for the HA–water system.
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| 24. |
- Ali, Ehesan, et al.
(författare)
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Influence of Solute-Solvent Hydrogen Bonding on Intramolecular Magnetic Exchange Interaction in Aminoxyl Diradicals : A QM/MM Broken-Symmetry DFT Study
- 2009
-
Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 113:16, s. 5545-5548
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Tidskriftsartikel (refereegranskat)abstract
- We have investigated the effect of nitroxide radical-water hydrogen bonding (NO center dot center dot center dot center dot H2O) on the intramolecular magnetic exchange interaction (J) for biologically relevant aminoxyl diradicals. We adopt a combination of broken-symmetry density functional theory and the quantum mechanics/molecular mechanics (QM/MM) approach. We find that the presence of hydrogen bonding reorients the radical spin density on -NO center dot. This phenomenon reduces the effective distance between the two interacting localized spin centers that eventually increases the intramolecular magnetic exchange interaction. We have also investigated the functional variation of the magnetic exchange interaction, using various GGA (BLYP, PBE, HCTH407), meta-GGA (TPSS, VXSC), and hybrid (O3LYP, B3LYP, B3P86, B3PW91, and PBE0) functionals.
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| 25. |
- Ali, Md. Ehesan, et al.
(författare)
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Electronic Structure, Spin-States, and Spin-Crossover Reaction of Heme-Related Fe-Porphyrins : A Theoretical Perspective
- 2012
-
Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 116:20, s. 5849-5859
-
Tidskriftsartikel (refereegranskat)abstract
- The electronic structures, spin-states, and geometrical parameters of tetra-, penta-, and hexa-coordinated iron-porphyrins are investigated applying density functional theory (DFT) based calculations, utilizing the plane-wave pseudopotential as well as localized basis set approaches. The splitting of the spin multiplet energies are investigated applying various functionals including recently developed hybrid meta-GGA (M06 family) functionals. Almost all of the hybrid functionals accurately reproduce the experimental ground state spins of the investigated Fe-porphyrins. However, the energetic ordering of the spin-states and the energies between them are still an issue. The widely used B3LYP provides consistent results for all chosen systems. The GGA+U functionals are found to be equally competent. After assessing the performance of various functionals in spin-state calculations, the potential energy surfaces of the oxygen binding process by heme is investigated. This reveals a "double spin-crossover" feature for the lowest energy reaction path that is consistent with previous CASPT2 calculations but predicting a lowest energy singlet state. The calculations have hence captured the spin-crossover as well as spin-flip processes. These are driven by the intra-atomic orbital polarization on the central metal atom due to the atomic and orbitals rearrangements. The nature of the chemical bonding and a molecular orbital analysis are also performed for the geometrically simple but electronic structurally complicated system tetra-coordinated planar Fe porphyrin in comparison to the penta-coordinated systems. This analysis explains the observed paradoxical appearance of certain peaks in the local density of states (DOS).
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| 26. |
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| 27. |
- Almgren, Mats, et al.
(författare)
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Contrast Variation SANS Investigation of Composition Distributions in Mixed Surfactant Micelles
- 2007
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 111:25, s. 7133-7141
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Tidskriftsartikel (refereegranskat)abstract
- Small angle neutron scattering measurements have been performed on three systems (HFDeP-d5-C (N-1(1,1,2,2-tetrahydroperfluorodecanoyl)pyridinium-d5 chloride)/C16PC in 63 mM NaCl; HFDeP-d5-C/C12PC in 200 mM NaCl, and as an example of an ideally mixed system, SDS/SDS-d25 in 200 mM NaCl) contg. micelles formed in a binary mixt. of surfactants, in order to investigate the compn. distribution of the mixed micelles. The exptl. data were collected varying the contrast between the av. scattering length d. of micelles and aq. solvent by changing the H2O/D2O ratio. Anal. of data includes a model-independent approach-the indirect Fourier transformation method and direct modeling-simultaneous fit at all contrasts by the scattering from micelles of equal size and shape with compn. distribution and an effective interaction. It has earlier been shown (Almgren, M.; Garamus, V. M. J. Phys. Chem. B 2005, 109, 11348) that for micelles of equal size, independent of the compn., and with negligible intermicellar interactions, the scattered intensity at zero angle varies quadratically with the contrast, with the min. intensity at the nominal match point proportional to s2, the variance of the micelle compn. distribution. Within the regular soln. framework, the compn. distribution and its variance are uniquely defined by the value of the interaction parameter and the micelle aggregation no. At 25 DegC, the first system gave s = 0.37, corresponding to a broad, bimodal compn. distribution, the second s = 0.22, a broad distribution with a shallow min. at the midpoint. For SDS/SDS-d25, we found s = 0.006 +- 0.030, which is a smaller value than that of the binominal compn. distribution expected for an ideally mixed system.
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| 28. |
- Alster, Jan, et al.
(författare)
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2D Spectroscopy Study of Water-Soluble Chlorophyll-Binding Protein from Lepidium virginicum
- 2014
-
Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 118:13, s. 3524-3531
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Tidskriftsartikel (refereegranskat)abstract
- Water-soluble chlorophyll-binding proteins (WSCPs) are interesting model systems for the study of pigment-pigment and pigment-protein interactions. While class IIa WSCP has been extensively studied by spectroscopic and theoretical methods, a comprehensive spectroscopic study of class IIb WSCP was lacking so far despite the fact that its structure was determined by X-ray crystallography. In this paper, results of two-dimensional electronic spectroscopy applied to the class IIb WSCP from Lepidium virginicum are presented. Global analysis of 2D data allowed determination of energy levels and excitation energy transfer pathways in the system. Some additional pathways, not present in class IIa WSCP, were observed. The data were interpreted in terms of a model comprising two interacting chlorophyll dimers. In addition, oscillatory signals were observed and identified as coherent beatings of vibrational origin.
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| 29. |
- Amira, S., et al.
(författare)
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Car-Parrinello molecular dynamics simulation of Fe3+(aq)
- 2005
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 109:29, s. 14235-14242
-
Tidskriftsartikel (refereegranskat)abstract
- The optimized geometry and energetic properties of Fe(D2O)(n)(3+) clusters, with n = 4 and 6, have been studied with density-functional theory calculations and the BLYP functional, and the hydration of a single Fell ion in a periodic box with 32 water molecules at room temperature has been studied with Car-Parrinello molecular dynamics and the same functional. We have compared the results from the CPMD simulation with classical MD simulations, using a flexible SPC-based water model and the same number of water molecules, to evaluate the relative strengths and weaknesses of the two MD methods. The classical MD simulations and the CPMD simulations both give Fe-water distances in good agreement with experiment, but for the intramolecular vibrations, the classical MD yields considerably better absolute frequencies and ion-induced frequency shifts. On the other hand, the CPMD method performs considerably better than the classical MD in describing the intramolecular geometry of the water molecule in the first hydration shell and the average first shell(...)second shell hydrogen-bond distance. Differences between the two methods are also found with respect to the second-shell water orientations. The effect of the small box size (32 vs 512 water molecules) was evaluated by comparing results from classical simulations using different box sizes; non-negligible effects are found for the ion-water distance and the tilt angles of the water molecules in the second hydration shell and for the O-D stretching vibrational frequencies of the water molecules in the first hydration shell.
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| 30. |
- Amira, S., et al.
(författare)
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Molecular dynamics simulation of Fe2+(aq) and Fe3+(aq)
- 2004
-
Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 108:1, s. 496-502
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Tidskriftsartikel (refereegranskat)abstract
- Molecular dynamics simulations of single-ion Fe2+(aq) and Fe3+(aq) solutions have been performed with two rigid-water models (SPC and SPC/E) and a newly constructed SPC-based flexible-water model (SPC+CCL). The SPC+CCL water model in combination with effective Fe2+ and Fe3+ ion-water potentials manages to reproduce many experimental structural and dynamical properties of the solutions. Special attention is given to the large ion-induced frequency shifts of the OH stretching bands, which are also well reproduced by the SPC+CCL model.
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| 31. |
- Andersen, A., et al.
(författare)
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Oscillating Bubble SHG on Surface Elastic and Surface Viscoelastic Systems : New Insights in the Dynamics of Adsorption Layers
- 2006
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 110:37, s. 18466-18472
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Tidskriftsartikel (refereegranskat)abstract
- Surface rheology governs a great variety of interfacial phenomena such as foams or emulsions and plays a dominant role in several technological processes such as high-speed coating. Its major difference with bulk rheology resides in the high compressibility of the surface phase, which is the direct consequence of the molecular exchange between adsorbed and dissolved species. In analogy to bulk rheology, a complex surface dilational modulus, ε, which captures surface tension changes upon defined area changes of the surface layer, can be defined. The module ε is complex, and the molecular interpretation of the dissipative process that gives rise to the imaginary part of the module is subject to some controversy. In this contribution, we used the oscillating bubble technique to study the surface dilational modulus in the mid-frequency range. The dynamic state of the surface layer was monitored by a pressure sensor and by surface second-harmonic generation (SHG). The pressure sensor measures the real and imaginary part of the modulus while SHG monitors independently the surface composition under dynamic conditions. The experiment allows the assessment of the contribution of the compositional term to the surface dilational modulus ε. Two aqueous surfactant solutions have been characterized: a surface elastic and a surface viscoelastic solution. The elastic surface layer can be described within the framework of the extended Lucassen−van den Tempel Hansen model. The change in surface concentration is in phase with the relative area change of the surface layer, which is in strong contrast with the results obtained from the surface viscoelastic solution. Here, surface tension, area change, and surface composition are phase-shifted, providing evidence for a nonequilibrium state within the surface phase. The data are used to assess existing surface rheology models.
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| 32. |
- Andersson, C. David, 1978-, et al.
(författare)
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Influence of Enantiomeric Inhibitors on the Dynamics of Acetylcholinesterase Measured by Elastic Incoherent Neutron Scattering
- 2018
-
Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 122:36, s. 8516-8525
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Tidskriftsartikel (refereegranskat)abstract
- The enzyme acetylcholinesterase (AChE) is essential in humans and animals because it catalyzes the breakdown of the nerve-signaling substance acetylcholine. Small molecules that inhibit the function of AChE are important for their use as drugs in the, for example, symptomatic treatment of Alzheimer's disease. New and improved inhibitors are warranted, mainly because of severe side effects of current drugs. In the present study, we have investigated if and how two enantiomeric inhibitors of AChE influence the overall dynamics of noncovalent complexes, using elastic incoherent neutron scattering. A fruitful combination of univariate models, including a newly developed non-Gaussian model for atomic fluctuations, and multivariate methods (principal component analysis and discriminant analysis) was crucial to analyze the fine details of the data. The study revealed a small but clear increase in the dynamics of the inhibited enzyme compared to that of the noninhibited enzyme and contributed to the fundamental knowledge of the mechanisms of AChE-inhibitor binding valuable for the future development of inhibitors.
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| 33. |
- Andersson, C. David, 1978-, et al.
(författare)
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Physical Mechanisms Governing Substituent Effects on Arene-Arene Interactions in a Protein Milieu
- 2020
-
Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 124:30, s. 6529-6539
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Tidskriftsartikel (refereegranskat)abstract
- Arene-arene interactions play important roles in protein-ligand complex formation. Here, we investigate the characteristics of arene-arene interactions between small organic molecules and aromatic amino acids in protein interiors. The study is based on X-ray crystallographic data and quantum mechanical calculations using the enzyme acetylcholinesterase and selected inhibitory ligands as a model system. It is shown that the arene substituents of the inhibitors dictate the strength of the interaction and the geometry of the resulting complexes. Importantly, the calculated interaction energies correlate well with the measured inhibitor potency. Non-hydrogen substituents strengthened all interaction types in the protein milieu, in keeping with results for benzene dimer model systems. The interaction energies were dispersion-dominated, but substituents that induced local dipole moments increased the electrostatic contribution and thus yielded more strongly bound complexes. These findings provide fundamental insights into the physical mechanisms governing arene-arene interactions in the protein milieu and thus into molecular recognition between proteins and small molecules.
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| 34. |
- Andersson, Johanna, 1983, et al.
(författare)
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Stereoselectivity for DNA Threading Intercalation of Short Binuclear Ruthenium Complexes
- 2011
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 115:49, s. 14768-14775
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Tidskriftsartikel (refereegranskat)abstract
- Threading intercalation is an unusual DNA binding mode with significantly slower association and dissociation rates compared with classical intercalation. The latter has been shown to correlate well with cytotoxicity, and therefore, threading intercalating compounds are of great interest in the search for new DNA binding drugs. Thus, there is a need for better understanding of the mechanisms behind this type of binding. In this work, we have investigated the threading intercalation ability, of the four stereoisomers of the AT-specific binuclear ruthenium complex [mu-dppzip(phen)(4)Ru(2)](4+) using different spectroscopic techniques. This complex contains an unsymmetrical bridging ligand consisting of a dipyridophenazine and an imidazophenanthroline ring system, in which the photophysical properties of the Ru-dipyridophenazine complex moiety make it possible to distinguish the intercalating part from the nonintercalating part We have found that Delta geometry around the ruthenium on the intercalating dipyridophenazine moiety and Lambda geometry on the nonintercalating imidazophenanthroline moiety is the optimal configuration for threading intercalation Of this complex and that the chirality on the ruthenium of the nonintercalating half dominates the stereospecificity in the threaded state. This is the cause of the reversed enantioselectivity compared with the parent threading intercalating complex [mu-bidppz(phen)(4)Ru(2)](4+), in which the enantioselectivity is controlled by the chirality on the intercalating half. The differences in the interactions with DNA between the two, complexes are most likely due to the fact that [mu-dppzip(phen)(4)Ru(2)](4+) has a slightly shorter bridging ligand than the parent complex.
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| 35. |
- Andersson, Martin, et al.
(författare)
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Fundamental, binary combination, and overtone modes in methoxy adsorbed on Cu(100): Infrared spectroscopy and ab initio calculations
- 2002
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 106:20, s. 5200-5211
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Tidskriftsartikel (refereegranskat)abstract
- Using surface infrared absorption spectroscopy, we have measured and assigned the vibrational spectra of six different methoxy isotopotners adsorbed on a Cu(100) surface in great detail. The assignments are based on ab initio calculations of the vibrational mode frequencies of all six isotopomers for a methoxy-Cu-5 complex. By combining different IR detectors and optical filters, we observe many, previously undetected, weak spectral features, which we can assign as various binary overtone and combination modes. On the basis of these binary modes conclusions on the intramolecular anharmonic coupling in the adsorbate can be drawn.
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| 36. |
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| 37. |
- Andersson, Martin, et al.
(författare)
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Phase Behavior of Salt-Free Polyelectrolyte Gel-Surfactant Systems
- 2017
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Ingår i: Journal of Physical Chemistry B. - : AMER CHEMICAL SOC. - 1520-6106 .- 1520-5207. ; 121:24, s. 6064-6080
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Tidskriftsartikel (refereegranskat)abstract
- Ionic surfactants tend to collapse the outer parts of polyelectrolyte gels, forming shells that can be used to encapsulate other species including protein and peptide drugs. In this paper, the aqueous phase behavior of covalently cross-linked polyacrylate networks containing sodium ions and dodecyltrimethylammonium ions as counterions is investigated by means of swelling isotherms, dye staining, small-angle X-ray scattering, and confocal Raman spectroscopy. The equilibrium state is approached by letting the networks absorb pure water. With an increasing fraction of surfactant ions, the state of the water-saturated gels is found to change from being swollen and monophasic, via multiphasic states, to collapsed and monophasic. The multiphasic gels have a swollen, micelle-lean core surrounded by a collapsed, micelle- rich shell, or a collapsed phase forming a spheroidal inner shell separating two micelle-lean parts. It is shown that the transition between monophasic and core-shell states can be induced by variation of the osmotic pressure and variation of the charge of the micelles by forming mixed micelles with the nonionic surfactant octaethyleneglycol monododecylether. The experimental data are compared with theoretical predictions of a model derived earlier. In the calculations, the collapsed shell is assumed to be homogeneous, an approximation introduced here and shown to be excellent for a wide range of compositions. The theoretical results highlight the electrostatic and hydrophobic driving forces behind phase separation.
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| 38. |
- Andersson, M, et al.
(författare)
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Preparation of nanosize anatase and rutile TiO2 by hydrothermal treatment of microemulsions and their activity for photocatalytic wet oxidation of phenol
- 2002
-
Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 106:41, s. 10674-10679
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Tidskriftsartikel (refereegranskat)abstract
- Titanium dioxide (TiO2) nanoparticles of both anatase and rutile phases were synthesized by hydrothermal treatment of microemulsions, and their photocatalytic activity for wet oxidation of phenol was studied. The only difference between the two syntheses used was that different acids were added to the microemulsions, making direct comparison of the catalytic activity of the two polymorphs possible. If hydrochloric acid was used, the rutile structure formed, and if nitric acid was used, anatase formed. The phase stability of the microemulsion was studied and according to conductivity and turbidity measurements the idea of a direct template effect could be discarded during the hydrothermal treatment. However, an initial size-templating phenomenon is possible during the mixing step. The particles, which were in the size range of a few nanometers were characterized with N-2-adsorption; XRD, SEM, and XPS. The activity of the two polymorphs for the photocatalytic oxidation of phenol in water was examined. It was shown that the rutile phase initially decomposed phenol much faster and follows a first-order process reasonably well (k = 4 x 10(-5) s(-1)). The photodecomposition process using the anatase phase led, however, to a much more rapid overall degradation following an initial slower rate of phenol oxidation. The results indicate that the observed difference of the photodecomposition process for the two TiO2 phases is due to the formation of different intermediates.
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| 39. |
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| 40. |
- Andersson, Ove, et al.
(författare)
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A Second Glass Transition in Pressure Collapsed Type II Clathrate Hydrates
- 2018
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 122:15, s. 4376-4384
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Tidskriftsartikel (refereegranskat)abstract
- Type II clathrate hydrates (CHs) M-17 H2O, with M = tetrahydrofuran (THF) or 1,3-dioxolane, are known to collapse, or amorphize, on pressurization to similar to 1.3 GPa in the temperature range 77-140 K. On heating at 1 GPa, these pressure-amorphized CH states show a weak, stretched sigmoid-shaped, heat-capacity increase because of a glass transition. Here we use thermal conductivity and heat capacity measurements to show that also type II CH with M = cyclobutanone (CB) collapses on isothermal pressurization and undergoes a similar, weak, glass transition upon heating at 1 GPa. Furthermore, we reveal for both THF CH and CB CH a second, much more pronounced, glass transition at temperatures above the thermally weak glass transition on heating in the 0.2-0.7 GPa range. This result suggests the general occurrence of two glass transitions in water-rich (94 mol %) pressure-collapsed CHs. Because of a large increase in dielectric permittivity concurrently as the weak heat capacity increase, the first glass transition must be due to kinetic unfreezing of water molecules. The thermal features of the second glass transition, measured on isobaric temperature cycling, are typical of a glass liquid glass transition, which suggests that pressure-amorphized CHs transform reversibly to liquids.
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| 41. |
- Andersson, Ove, et al.
(författare)
-
Thermal Conductivity and Heat Capacity of Dianin's Clathrates under Pressure
- 2001
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 106:1, s. 192-196
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Tidskriftsartikel (refereegranskat)abstract
- The thermal conductivities, λ, and heat capacities of polycrystalline Dianin’s compound and its CCl4 and ethanol clathrates have been investigated in the temperature range 40-300 K for pressures up to 1 GPa. All high-pressure results for λ show typical crystal-like behavior, whereas previous atmospheric pressure results for single crystals as well as recent results on polycrystalline samples show glasslike behavior. The change from glasslike to crystal-like dependence might be caused by a frequency shift of localized vibrations on pressurization, moving the localized vibrations outside the frequency range of the dominant heat carriers and reducing thermal resistance due to resonance scattering.
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| 42. |
- Andersson, Ove, et al.
(författare)
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Transitions in pressure collapsed clathrate hydrates
- 2015
-
Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 119:9, s. 3846-3853
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Tidskriftsartikel (refereegranskat)abstract
- Type II clathrate hydrates (CHs), or ice clathrates, are inclusion compounds in which a hydrogen-bonded cage-like structure of H2O accommodates molecules of suitable size, known as guest molecules. CHs have similar local geometrical arrangements of the hydrogen-bonded water network as ice and both are known to collapse to amorphous states on isothermal pressurization at temperatures below about 140 K. Moreover, the collapsed CH states undergo a glass, or glass-like, transition at 140 K on heating at 1 GPa, which is identical to that of collapsed ice, or high density amorphous ice. Here we use thermal conductivity and dielectric measurements to study the transition behavior of two type II CHs with tetrahydrofuran and 1,3 dioxolane, respectively, as guest molecules. After their collapsed states have been heated to well above the glass transition at 1 GPa, we find transitions corresponding to the high to low density amorphous ice transition of ice with only slightly shifted temperature-pressure (T-p) coordinates compared to those of pure water. Thus, collapsed CHs show the same transition behaviors as cold water, which provide the basis for the model that explains the unusual temperature and pressure behaviors of waters properties in terms of two distinct types of liquid water. Collapsed CHs are, however, more stable than collapsed ice and can therefore be studied in a wider T-p interval. The results suggest sluggish homogenizing and phase separation processes, which affect the transition behaviors of collapsed CHs.
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| 43. |
- Andreev, Georgy, et al.
(författare)
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Colabind : A Cloud-Based Approach for Prediction of Binding Sites Using Coarse-Grained Simulations with Molecular Probes
- 2024
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 128:13, s. 3211-3219
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Tidskriftsartikel (refereegranskat)abstract
- Binding site prediction is a crucial step in understanding protein-ligand and protein-protein interactions (PPIs) with broad implications in drug discovery and bioinformatics. This study introduces Colabind, a robust, versatile, and user-friendly cloud-based approach that employs coarse-grained molecular dynamics simulations in the presence of molecular probes, mimicking fragments of drug-like compounds. Our method has demonstrated high effectiveness when validated across a diverse range of biological targets spanning various protein classes, successfully identifying orthosteric binding sites, as well as known druggable allosteric or PPI sites, in both experimentally determined and AI-predicted protein structures, consistently placing them among the top-ranked sites. Furthermore, we suggest that careful inspection of the identified regions with a high affinity for specific probes can provide valuable insights for the development of pharmacophore hypotheses. The approach is available at https://github.com/porekhov/CG_probeMD
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| 44. |
- Andreu, Rafael, et al.
(författare)
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Direct electron transfer kinetics in horseradish peroxidase electrocatalysis
- 2007
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 111:2, s. 469-477
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Tidskriftsartikel (refereegranskat)abstract
- The study of direct electron transfer between enzymes and electrodes is frequently hampered by the small fraction of adsorbed proteins that remains electrochemically active. Here, we outline a strategy to overcome this limitation, which is based on a hierarchical analysis of steady-state electrocatalytic currents and the adoption of the "binary activity" hypothesis. The procedure is illustrated by studying the electrocatalytic response of horseradish peroxidase (HRP) adsorbed on graphite electrodes as a function of substrate (hydrogen peroxide) concentration, electrode potential, and solution pH. Individual contributions of the rates of substrate/enzyme reaction and of the electrode/enzyme electron exchange to the observed catalytic currents were disentangled by taking advantage of their distinct dependence on substrate concentration and electrode potential. In the absence of nonturnover currents, adoption of the "binary activity" hypothesis provided values of the standard electron-transfer rate constant for reduction of HRP Compound II that are similar to those reported previously for reduction of cytochrome c peroxidase Compound II. The variation of the catalytic currents with applied potential was analyzed in terms of the non-adiabatic Marcus-DOS electron transfer theory. The availability of a broad potential window, where catalytic currents could be recorded, facilitates an accurate determination of both the reorganization energy and the maximum electron-transfer rate for HRP Compound II reduction. The variation of these two kinetic parameters with solution pH provides some indication of the nature and location of the acid/base groups that control the electronic exchange between enzyme and electrode.
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| 45. |
- Angelescu, Daniel, et al.
(författare)
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Packaging of a flexible polyelectrolyte inside a viral capsid: Effect of salt concentration and salt valence
- 2007
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 111:29, s. 8477-8485
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Tidskriftsartikel (refereegranskat)abstract
- The effect of salt on the location and structure of a flexible polyelectrolyte confined inside a viral capsid and the Donnan equilibrium of the salt across the capsid have been examined using a coarse-grained model solved by Monte Carlo simulations. The polyelectrolyte was represented by a linear jointed chain of charged beads, and the capsid was represented by a spherical shell with embedded charges. At low salt concentration, the polyelectrolyte was strongly adsorbed onto the inner capsid surface, whereas at high salt concentration it was located preferentially in the central part of the capsid. Under the condition of equal Debye screening length, the electrostatic screening increased as the valence of the polyelectrolyte counterion was increased. The distribution of the small cations and anions was unequal across the capsid. An excess of polyelectrolyte counterions occurred inside the capsid, and the excess increased with the salt concentration. A simplified representation of the small ions through the use of the screened Coulomb potential provided only a qualitatively correct picture; the electrostatic screening originating from the small ions was exaggerated.
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| 46. |
- Angelico, R, et al.
(författare)
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Deuterium NMR study of slow relaxation dynamics in a polymerlike micelles system after flow-induced orientation
- 2003
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 107:38, s. 10325-10328
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Tidskriftsartikel (refereegranskat)abstract
- We present a first time-resolved deuterium NMR study on wormlike micelles under shear. For the investigation, a micellar system made of soybean phosphatidylcholine (lecithin), D2O, and cyclohexane was studied in the concentrated regime, in the vicinity of the isotropic/nematic transition but positioned in the equilibrium isotropic phase. The D2O dispersed in the micellar core was used as a probe to study the relaxation of a shearing-induced nematic phase back to the isotropic liquid state, after cessation of shear. The whole process was followed through time-resolved deuterium spectra and was characterized by a continuous decrease of the measured quadrupolar splitting, proportional to the nematic order parameter.
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| 47. |
- Angelico, R, et al.
(författare)
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Relaxation of shear-aligned wormlike micelles
- 2002
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 106:10, s. 2426-2428
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- We report on the first time-resolved small-angle neutron scattering (SANS) study of the structural relaxation from a shear-induced aligned state back to the isotropic state in a system of giant wormlike reverse micelles. The micelles are formed by lecithin and small amounts of water in cyclohexane. A liquid sample with the micellar volume fraction phi = 0.3 was exposed to a steady shear of (gamma) over dot = 10 s(-1) in a Couette shear cell. This was sufficient to transform the whole sample into an aligned state with the polymer-like micelles preferentially oriented parallel to the velocity direction. After cessation of shear, the sample relaxes back to the equilibrium liquid phase. By time-resolved SANS we could follow the relaxation process, which is characterized by a continuous decrease of the order parameter.
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| 48. |
- Angenendt, Knut, 1982, et al.
(författare)
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Ionic Liquid Based Lithium Battery Electrolytes: Charge Carriers and Interactions Derived by Density Functional Theory Calculations
- 2011
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 115:24, s. 7808-7813
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Tidskriftsartikel (refereegranskat)abstract
- The solvation of lithium salts in ionic liquids (ILs) leads to the creation of a lithium ion carrying species quite different from those found in traditional nonaqueous lithium battery electrolytes. The most striking differences are that these species are composed only of ions and in general negatively charged. In many IL-based electrolytes, the dominant species are triplets, and the charge, stability, and size of the triplets have a large impact on the total ion conductivity, the lithium ion mobility, and also the lithium ion delivery at the electrode. As an inherent advantage, the triplets can be altered by selecting lithium salts and ionic liquids with different anions. Thus, within certain limits, the lithium ion carrying species can even be tailored toward distinct important properties for battery application. Here, we show by DFT calculations that the resulting charge carrying species from combinations of ionic liquids and lithium salts and also some resulting electrolyte properties can be predicted.
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| 49. |
- Angles d'Ortoli, Thibault, et al.
(författare)
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Temperature Dependence of Hydroxymethyl Group Rotamer Populations in Cellooligomers
- 2015
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 119:30, s. 9559-9570
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Tidskriftsartikel (refereegranskat)abstract
- Empirical force fields for computer simulations of carbohydrates are often implicitly assumed to be valid also at temperatures different from room temperature for which they were optimited: Herein, the temperature dependence of the hydroxymethyl group rotamer populations in short oligogaccharides is invegtigated using Molecular dynamics simulations and NMR spectroscopy. Two oligosaccharides, methyl beta-cellobioside and beta-cellotetraose were simulated using three different carbohydrate force fields (CHARMM C35, GLYCAM06, and GROMOS 56A(carbo)) in combination with different water models (SPC, SPC/E, and TIP3P) using replica exchange molecular dynamics simulations. For comparison, hydroxymethyl group rotamer populations were investigated for methyl beta-cellobioside and cellopentaose based- on measured NMR (3)J(H5,H6) coupling constants, in the latter case by using a chemical shift selective NMR-filter. Molecular dynamics simulations in combination with NMR spectroscopy show that the temperature dependence of the hydroxymethyl rotamer population in these short cellooligomers, in the range 263-344 K, generally becomes exaggerated in simulations when compared to experimental data, but also that it is dependent on simulation conditions, and most notably properties of the water model.
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| 50. |
- Antonsson, Jakob, et al.
(författare)
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Modeling Colloidal Particle Aggregation Using Cluster Aggregation with Multiple Particle Interactions
- 2024
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Ingår i: Journal of Physical Chemistry B. - 1520-6106 .- 1520-5207. ; 128:18, s. 4513-4524
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we investigate the aggregation dynamics of colloidal silica by generating simulated structures and comparing them to experimental data gathered through scanning transmission electron microscopy (STEM). More specifically, diffusion-limited cluster aggregation and reaction-limited cluster aggregation models with different functions for the probability of particles sticking upon contact were used. Aside from using a constant sticking probability, the sticking probability was allowed to depend on the masses of the colliding clusters and on the number of particles close to the collision between clusters. The different models of the sticking probability were evaluated based on the goodness-of-fit of spatial summary statistics. Furthermore, the models were compared to the experimental data by calculating the structures’ fractal dimension and mass transport properties from simulations of flow and diffusion. The sticking probability, depending on the interaction with multiple particles close to the collision site, led to structures most similar to the STEM data.
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