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od 2020-09-20 |
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1. |
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Combination of SAXS and NMR techniques as a tool for the determination of peptide structure in solution: conformation of the 28-43 fragment of the B3 domain of immunoglobulin binding protein G from Streptococcus The biological activity of peptides is largely determined by their spatial structure in solution. Because of flexibility of these molecules, the NMR technique, commonly used to determine the solution structures, usually provides only the information of the local geometry of peptide chains. On the other hand, small-angle X-ray scattering (SAXS) gives interatomic distance distribution in the molecule, thereby defining the shape of a molecule. In this work we carried out a SAXS study of the 28-43 sequence fragment of the B3 domain of immunoglobulin binding protein G from Streptococcus, IG(28-43). We fitted the conformational ensembles obtained in our previous work by using the NMR-restrained molecular dynamics simulations to the distance distribution obtained from SAXS measurements. Only two clusters of conformations with shape bent in the middle out of 11, consistent with NMR data had nonzero statistical weights. Thus, SAXS and NMR provide complementary structural information and appear to be an excellent tool for peptide structure determination when combined.
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Journal of Physical Chemistry Letters, 1(20), 3128-3131, (2010) |
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2. |
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Studies of the structure and chemistry of SBA-15 organosilicas functionalized with amine, thiol, vinyl and phenyl groups SBA-15 organosilicas containing amine, thiol, vinyl and phenyl pendant groups were synthesized by co-condensation of tetraethoxysilane and appropriate alkoxysilanes in the presence of Pluronic P123 surfactant. The obtained materials have usually well-developed porous structure-values of specific surface area are in the range 820-950 m(2)/g. Sizes of the ordered mesopores are in the range 7.5-9.1 nm while the interconnecting pores are 2.3-3.1 nm in size. It was establish that size of the mesopores strongly depends even on small amounts of co-monomers co-condensing with tetraethoxysilane. Several instrumental techniques such as infrared spectroscopy, X-ray diffraction, nitrogen sorption measurements, elemental analysis, transmission electron microscopy. FT-IR photoacoustic spectroscopy (FT-IR/PAS) was used to determine chemical composition of the final materials and to monitor the efficiency of the template removal.
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Adsorption - Journal of the International Adsorption Society, 16(4-5), 457-463, (2010) |
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3. |
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DSC and EPR analysis of some radiation sterilized alkaloids The effect of ionising radiation on the physico-chemical properties of salts of three alkaloids has been studied: codeine phosphate (COD), papaverine hydrochloride (PAP) and pilocarpine hydrochloride (PIL). These compounds in the solid state were irradiated with an e-beam of the energy of 9.96 MeV to achieve doses ranging from 25 to 400 kGy, and then they were subjected to organoleptic analysis, thermal analysis (differential scanning calorimetry, DSC), electron resonance (EPR) spectroscopy, scanning electron microscopy observations and X-ray diffraction study. The most informative were the results provided by the EPR and DSC methods. The EPR spectra revealed the presence of long-lived radicals whose concentration was directly proportional to the dose of irradiation for all the compounds studied. (PIL 2.14 x 10(16) spin/g, COD 6.85 x 10(15) spin/g, PAP 2.50 x 10(14) spin/g-for the dose of 100 kGy). The DSC results revealed a decrease in the melting point by 5.9 A degrees C for COD and by 0.8 A degrees C for PIL after irradiation with 200 kGy, which is indicative of products of radiolysis, of which at least one is non-white, and changes the colour of the compounds. PAP, for which no decrease in the melting point and no colour change was observed and for which the concentration of free radicals was the lowest, was found to be most stable from among the compounds studied. It will probably be suitable for radiation sterilisation. The other two compounds COD and PIL show much lower radiochemical stability and should be subjected to more detailed examination to establish the mechanism of radiolysis and the possibility of radiation sterilisation. Our results have confirmed the earlier reports on high radiochemical stability of PAP, but do not confirm the resistance to ionising radiation of COD and PIL.
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Journal of Thermal Analysis and Calorimetry, 102(1), 261-267, (2010) |
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4. |
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Studies of intrawall porosity in the hexagonally ordered mesostructures of SBA-15 by small angle X-ray scattering and nitrogen adsorption Ordered mesoporous silicas (OMSs) such as SBA-15 (p6mm symmetry group) synthesized in the presence of block copolymers containing poly(ethylene oxide) blocks possess irregular complementary pores in the walls of ordered mesopores. The X-ray scattering caused by this complementary porosity contributes to the background of the SAXS patterns. This work shows the possibility of using the SAXS data for the study of intrawall channels interconnecting ordered cylinders in SBA-15. The proposed SAXS analysis was tested by using a series of SBA-15 samples obtained at different temperatures of hydrothermal treatment (from 60 to 180 degrees C). The structural modelling of the SAXS patterns recorded for a series of SBA-15 samples was performed by using the continuous density function (CDF) technique in combination with the derivative difference minimization (DDM) method of full-profile refinement. This method is well suited for extraction of the background curves from the SAXS patterns. The resulting smooth background curves were analyzed by the well-known method in the SAXS theory used for evaluation of heterogeneity distributions, which in this case characterize the intrawall complementary porosity. A relatively good agreement has been observed between the data obtained by SAXS and nitrogen adsorption analysis. The SAXS analysis is sufficiently sensitive for examination of heterogeneous microporosity in SBA-15 materials. The average diameter of intrawall pores for the SBA-15 sample obtained at 60 degrees C was only about 1.4 nm. However, this diameter increased with the increasing temperature of hydrothermal treatment; namely, it was 1.5, 1.8, 2.6, 2.6, 3.5 and 5.2 nm for the SBA-15 samples hydrothermally treated at 80, 100, 120, 140, 160 and 180 degrees C, respectively.
(C) 2009 Elsevier B.V. All rights reserved. |
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Applied Surface Science, 256(17), 5311-5315, (2010) |
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5. |
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NMR dispersion studies of poly(ethylene oxide)/sodium montmorillonite nanocomposites The frequency dependence of spin lattice relaxation times measured by means of Fast Field Cycling (FFC) Relaxometry and spin locking on and off-resonance NMR techniques were used to study the molecular dynamics of poly(ethylene oxide) polymer in the confined and bulk phases of PEO/MMT nanocomposite systems. The Rouse model, the renormalized Rouse formalism and the concept of reptation were applied to describe the polymer behavior in the samples studied. The polymer dynamics was found to depend on the molecular weight of the polymer intercalated in the clay structure. Analysis of the NMR T(1)(nu) profiles allowed discrimination of the molecular dynamics of polymer chains at different locations in the nanocomposite structure. Two components of the T(1) spin-lattice relaxation times were indicated for low molecular weight PEO polymers using the FFC method. The longer one was connected with the bulk polymer, whereas the shorter one was attributed to the intercalated polymer fraction. Analysis of the correlation times indicated that polymer confined in montmorillonite galleries is more rigid than that in the bulk phase. To determine the two phases of the polymer for the high molecular weights polymers, additional methods were applied: spin locking, off-resonance NMR techniques and inversion-recovery experiment at a static magnetic field.
(C) 2010 Elsevier B.V. All rights reserved. |
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Journal of Non-Crystalline Solids, 356(20-22), 945-951, (2010) |
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6. |
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The phase structure and molecular dynamics in poly(styrene-b-isoprene) diblock copolymer Molecular dynamics of polyisoprene, polystyrene and poly(styrene-b-isoprene) diblock copolymer has been studied by means of broadband dielectric and magnetic resonance spectroscopies. The measurements of dielectric permittivity as well as NMR second moment, spin-lattice relaxation times T(1) and T(1ρ), in wide range of temperature were performed. It was found that the copolymer exhibits all motions observed in the neat components i.e., three motions connected with polyisoprene blocks (segmental, normal-mode and methyl group rotation) and one (segmental) related to polystyrene blocks. The mutual interaction between polystyrene and polyisoprene chains leads to stiffening of polyisoprene blocks and loosening of polystyrene structure. The polyisoprene segmental and normal-mode motions were analyzed in terms of the Havriliak-Negami model and Vogel-Fulcher-Tamman (VFT) relation. Based on NMR spin-diffusion experiment the size of polystyrene domains in copolymer was evaluated and accounts to 9 nm.
(C) 2010 Elsevier B.V. All rights reserved. |
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Journal od Non-Crystalline Solids, 356(11-17), 582-588, (2010) |
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7. |
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Molecular dynamics in grafted polydimethylsiloxanes Rheological and dielectric behavior of linear PDMS and alkyl-modified PDMS melts has been studied. Molecular dynamics of linear PDMS, being a model of grafted polydimethylsiloxanes studied, has been examined carefully with particular attention paid to its ability to form the semicrystalline phase. Random incorporation of alkyl groups into PDMS chain has been shown to prevent the polymer crystallization. The glass transition temperature of the grafted PDMS changes proportionally to the modifier content. Both techniques allow characterization of the main alpha-relaxation, which is related to the glass transition and exhibits similar behavior in all systems. This relaxation is discussed in terms of the Vogel-Fulcher-Tammann-Hesse (VFTH) approach. The fragility of grafted PDMS materials was found to be higher as compared to the linear polymer. The analysis of the rheological data shows the existence of additional slow relaxation, which has been interpreted as the polymer chain motion.
(C) 2010 Elsevier B.V. All rights reserved. |
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Journal of Non-Crystalline Solids, 356(11-17), 669-675, (2010) |
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8. |
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Structural and spectroscopic studies of DMPC/cationic surfactant system Aqueous suspension of a mixture of 1,2-dimyrilstoyl-sn-glycero-3-phosphocholine (DMPC) and (dodecyloxymethyl)dodecydimethylammonium (DDMDDAC) has been investigated by Fourier transform infrared spectroscopy (FTIR), small angle scattering of synchrotron radiation (SAXS) and dielectric spectroscopy (DS). The introduction of surfactant to DMPC water solution probably induces formation of discoidal (bicellar) phase, as revealed by SAXS studies. The presence of the surfactant has been found to decrease the main phase transition temperature, i.e., from rippled gel to liquid crystalline phase, as indicated by the DS and FTIR results. The small steps in the real part of dielectric permittivity plot vs. temperature can be related to the: planar gel to rippled gel (L(beta') -> P(beta')) and rippled gel-liquid crystal (P(beta') -> L(alpha)) phase transitions, which is supported by the temperature dependencies of the symmetric and anti-symmetric CH(2) band frequencies from FTIR measurements.
(C) 2010 Elsevier B.V. All rights reserved. |
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Journal of Non-Crystalline Solids, 356(11-17), 747-753, (2010) |
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9. |
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Dynamic mechanical study of molecular dynamics in ethylene-norbornene copolymers Dynamic mechanical studies of Molecular dynamics have been performed for two ethylene-norbornene copolymers. The analysis of data indicates the existence of three relaxation processes: a primary (alpha) and two secondary (beta and gamma) ones. It was found that the secondary processes beta and gamma are connected with the local motions of ethylene and norbornene groups, respectively and that their rates follow the Arrhenius relation. Moreover, the beta process was recognized as the Johari-Goldstein process acting as the precursor of the cooperative structural alpha-relaxation. Contrary to gamma and beta processes, the motional rate of alpha-one follows the Vogel-Fulcher-Tammann equation indicating the cooperative nature of motions involved in this process. An increase in norbornene content in copolymer slows down the molecular dynamics of both norbornene fragments and whole chains, and in consequence shifts these relaxation Processes into higher temperatures. Using the Havriliak-Negami formalism the motional parameters for the processes mentioned above were estimated.
(C) 2009 Elsevier Ltd. All rights reserved. |
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Polymer, 51(4), 908-912, (2010) |
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10. |
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Low resolution structure of RAR1-GST-Tag fusion protein in solution RAR1 is a protein required for resistance mediated by many R genes and function upstream of signaling pathways leading to H(2)O(2) accumulation. The structure and conformation of RAR1-GST-Tag fusion protein from barley (Hordeum vulgare) in solution was studied by the small angle scattering of synchrotron radiation. It was found that the dimer of RAR1-GST-Tag protein is characterized in solution by radius of gyration R(G) = 6.19 nm and maximal intramolecular vector D(max) = 23 nm. On the basis of the small angle scattering of synchrotron radiation SAXS data two bead models obtained by ab initio modeling are proposed. Both models show elongated conformations. We also concluded that molecules of fusion protein form dimers in solution via interaction of GST domains.
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Acta Physica Polonica A, 117(2), 307-310, (2010) |
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11. |
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SAXS study of influence of gemini surfactant, 1,1'-(1,4-butanediyl)bis 3-cyclododecyloxymethylimidazolium di-chloride, on the fully hydrated DMPC The study has been performed on model systems of biological membranes obtained on the basis of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and cationic gemini surfactant derivative of 1,1'-(1,4-butane)bis 3-alkyloxymethylimidazolium chlorides with cyclic chains. The small angle X-ray scattering SAXS results implied a gradual disappearance (as a function of surfactant concentration) of the lamellar phase typical of DMPC and formation of unilamellar phase - probably a bicellar phase.
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Acta Physica Polonica A, 117(2), 311-314, (2010) |
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12. |
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Long-range ordering in lyotropic lamellar phase studied by high resolution MR diffusion-weighted imaging Diffusion-weighted magnetic resonance imaging (DW MRI) was applied to the lyotropic lamellar phase of the dodecylammonium chloride/water system (DDACl/H(2)O). In the course of employing a well-known medical imaging method, namely, diffusion tensor imaging (DTI), the system morphology was assessed accurately ill the most straightforward way by two-dimensional visualization of eigenvectors associated with planar distribution of effective diffusion tensors throughout the whole slice with 40 mu m in-plane resolution. Long-range order was observed in the Studied lamellar phase, and morphology was best described by a combination of three- and one-dimensional diffusion.
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The Journal of Physical Chemistry B, 114(1), 165-173, (2010) |
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13. |
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NMR imaging and cryoporometry of swelling clays Compacted bentonite clay is currently attracting attention as a promising “self-sealing” buffer material to build in-ground barriers for the encapsulation of radioactive waste. It is expected to fill up the space between waste canister and surrounding ground by swelling and thus delay flow and migration from the host rock to the canister. In environmental sciences, evaluation and understanding of the swelling properties of pre-compacted clay are of uttermost importance for designing such buffers. Major goal of present study was to provide, in a non-invasive manner, a quantitative measure of bentonite distribution in extended samples during different physical processes in an aqueous environment such as swelling, dissolution, and sedimentation on the time scale from minutes to years. The propagation of the swelling front during clay expansion depending on the geometry of the confining space was also studied. Magnetic resonance imaging and nuclear magnetic resonance spectroscopy were adapted and used as main experimental techniques. With this approach, spatially resolved movement of the clay/water interface as well as clay particle distributions in gel phase can be monitored [1]. Bulk samples with swelling in a vertical tube and in a horizontal channel were investigated and clay content distribution profiles in the concentration range over five orders of magnitude and with sub-millimetre spatial resolution were obtained. Expansion rates for bulk swelling and swelling in narrow slits were compared. For sodium-exchanged montmorillonite in contact with de-ionised water, we observed a remarkable acceleration of expansion as compared to that obtained in the bulk. To characterize the porosity of the clay a cryoporometric study [2] has been performed. Our results have important implications to waste repository designs and for the assessment of its long-term performance. Further research exploring clay-water interaction over a wide variety of clay composition and water ionic strength as well as investigating the effect of the confining geometry and material surface properties seem to be worth to pursue.
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Geophysical Research Abstracts, 12, EGU2010-15180, (2010) |
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(Pobrane: aktualizowanie) |
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Zaktualizowano: podstrony 2025-01-24 / bazę danych: 2025-02-04 by Webmaster: Zbigniew Fojud