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  • 1.
    Blochin, Dimri S.
    et al.
    Institute of Physics, Kazan (Volga Region) Federal University.
    Aganova, Oksana V.
    Institute of Physics, Kazan (Volga Region) Federal University.
    Yulmetov, Aidar R.
    Institute of Physics, Kazan (Volga Region) Federal University.
    Filippov, Andrei
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Sustainable Process Engineering.
    Gizatulin, Bulat L.
    Institute of Physics, Kazan (Volga Region) Federal University.
    Afonin, Sergii
    Karlsruhe Institute of Technology.
    Antzutkin, Oleg
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Sustainable Process Engineering.
    Klochkov, Vladimir V.
    Institute of Physics, Kazan (Volga Region) Federal University.
    Spatial structure of heptapeptide Glu-Ile-Leu-Asn-His-Met-Lys, a fragment of the HIV enhancer prostatic acid phosphatase, in aqueous and SDS micelle solutions2013In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 1033, p. 59-66Article in journal (Refereed)
    Abstract [en]

    Prostatic acid phosphatase (PAP) is a protein abundantly present in human seminal fluid. PAP plays important role in fertilization. Its 39-amino-acid fragment, PAP(248-286), is effective in enhancing infectivity of HIV virus. In this work, we determined the spatial structure in aqueous solution of a heptapeptide within the PAP fragment, containing amino acid residues 266-272 (Glu-Ile-Leu-Asn-His-Met-Lys). We also report the structure of the complex formed by this heptapeptide with sodium dodecyl sulfate micelles, a model of a biological membrane, as determined by 1H NMR spectroscopy and 2D NMR (TOCSY, HSQC-HECADE, NOESY) spectroscopy. Complex formation was confirmed by chemical shift alterations in the 1H NMR spectra of the heptapeptide, as well as by the signs and values of NOE effects. We also present a comparison of the spatial structure of Glu-Ile-Leu-Asn-His-Met-Lys in water and in complex with sodium dodecyl sulfate

  • 2.
    Blokhin, Dimitry S.
    et al.
    Institute of Physics, Kazan (Volga Region) Federal University.
    Fayzullina, Adeliya R.
    Chemistry Institute, Kazan Federal University.
    Filippov, Andrei
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    Karataeva, Farida Kh.
    Alexander Butlerov Institute of Chemistry, Kazan Federal University, Chemistry Institute, Kazan Federal University.
    Klochkov, Vladimir V.
    Institute of Physics, Kazan (Volga Region) Federal University.
    Spatial structure of fibrinopeptide B in water solution with DPC micelles by NMR spectroscopy2015In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 1102, p. 91-94Article in journal (Refereed)
    Abstract [en]

    Fibrinopeptide B (GluFib) is one of the factors of thrombosis. Normal blood protein soluble, fibrinogen (fibrinopeptide A and fibrinopeptide B), is transformed into the insoluble, fibrin, which in the form of filaments adheres to the vessel wall at the site of injury, forming a grid. However, the spatial structure of this peptide has not been established till now. In this article, GluFib peptide is investigated together with dodecylphosphocholine (DPC) micelles which were used for mimicking the environment of peptide in blood vessels. The spatial structure was obtained by applying 1D and 2D 1H-1H NMR spectroscopy (TOCSY, NOESY). It was shown that the fibrinopeptide B does not have a secondary structure but we can distinguish the fragment Gly 9 – Arg 14 with a good convergence (the backbone RMSD for the Gly9 – Arg14 is 0.18 ± 0.08 Å).

  • 3.
    Blokhin, Dimitry S.
    et al.
    Institute of Physics, Kazan (Volga Region) Federal University.
    Filippov, Andrei
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    Antzutkin, Oleg
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    Karataeva, Farida Kh.
    Alexander Butlerov Institute of Chemistry, Kazan Federal University.
    Klochkov, Vladimir V.
    Institute of Physics, Kazan (Volga Region) Federal University.
    Spatial structure of oligopeptide PAP(248-261), the N-terminal fragment of the HIV enhancer prostatic acid phosphatase peptide PAP(248-286), in aqueous and SDS micelle solutions2014In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 1070, p. 38-42Article in journal (Refereed)
    Abstract [en]

    Prostatic acid phosphatase (PAP) is an enzyme that facilitates infection of cells by HIV. Its peptide fragment PAP(248-286) forms amyloid fibrils known as SEVI, which enhance attachment of the virus by viral adhesion to the host cell prior to receptor-specific binding via reducing the electrostatic repulsion between the membranes of the virus and the target cell. The secondary structure of PAP(248-286) in aqueous and SDS solutions can be divided into an N-terminal disordered region, an -helical central part and an /310-helical C-terminal region (R.P.R. Nanga et al., JACS, 2009, 131, 17972). In this work, we used NMR spectroscopy to study the spatial structure of the isolated N-terminal fragment of PAP(248-286), PAP(248-261) (GIHKQKEKSRLQGG), in aqueous and SDS micelle solutions. Formation of a PAP(248-261)-SDS complex was confirmed by chemical shift alterations in the 1H NMR spectra of the peptide, as well as by the signs and values of Nuclear Overhauser Effect (NOE). In addition, the PAP(248-261) peptide does not form any specified secondary structure in either aqueous or SDS solutions.

  • 4.
    Ivanov, Alexander
    et al.
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Sustainable Process Engineering.
    Korneeva, Eugenia V.
    Far Eastern Branch of the Russian Academy of Sciences, 675000, Blagoveschensk, Amur Region.
    Lutsenko, Irina A.
    Far Eastern Branch of the Russian Academy of Sciences, 675000, Blagoveschensk, Amur Region.
    Gerasimenko, Andrey V.
    Institute of Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 690022, Vladivostok.
    Antzutkin, Oleg
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Sustainable Process Engineering.
    Larsson, Anna-Carin
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Sustainable Process Engineering.
    Sergienko, Valentin I.
    Institute of Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 690022, Vladivostok.
    A fixation mode of gold from solutions using heterogeneous reaction of cadmium dicyclohexyl dithiophosphate with H[AuCl4]. Structural and (13C, 31P) CP/MAS NMR studies and thermal behaviour of crystalline polymeric gold(I) dicyclohexyl dithiophosphate and bis(dicyclohexylthiophosphoryl) disulphide2013In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 1034, p. 152-161Article in journal (Refereed)
    Abstract [en]

    Two novel compounds: polynuclear catena-poly[bis(3-O,O’-di-cyclo-hexyldithiophosphato-S,S,S’)digold(I)] (Au–Au) (1) and crystalline bis(O,O’-di-cyclo-hexylthiophosphoryl)disulphide, (cyclo-C6H11O)2P(S)S–S(S)P(O-cyclo-C6H11) (2) were prepared using heterogeneous reaction between freshly precipitated binuclear cadmium(II) dithiophosphate (Dtph), [Cd2{S2P(O-cyclo-C6H11}4] and H[AuCl4] in 2 M hydrochloric acid. The isolated compounds 1 and 2 (the fixation mode of gold from the solution and the oxidised form of Dtph groups, respectively) have been studied by means of single-crystal X-ray diffraction, 13C and 31P cross-polarisation / magic-angle-spinning (CP/MAS) NMR spectroscopy and simultaneous thermal analysis (STA). Centrosymmetric binuclear molecule of 1, [Au2{S2P(O-cyclo-C6H11)2}2] comprises a pair of -bridging di-cyclo-hexyl Dtph ligands, linking two neighbouring gold atoms, and displays additional intramolecular aurophilic bond Au···Au. At the supramolecular level of structural self-organisation of complex 1, infinite polymeric zigzag chains arise due to pairs of the secondary bonds Au···S between neighbouring binuclear molecules. Centrosymmetric molecule of 2 displays two O,O-di-cyclo-hexythiophosphoryl fragments, which are connected by the chemical bond S(1)–S(1)a, and a planar zigzag array [S=P–S–S–P=S] passing through the central part of the molecule. To characterise additionally the Dtph groups in both compounds 1 and 2, chemical shift anisotropy (CSA) parameters (aniso and) were calculated from spinning sideband manifolds in experimental 31P MAS NMR spectra. The thermal behaviour of complex 1 was studied using simultaneous thermal analysis (a combination of TG and DSC) under an argon atmosphere. The thermal behaviour displays stepwise mass loss, comprising thermal decompositions of the organic and inorganic parts of 1 with gold(I) dithio-meta-phosphate and reduced metallic gold as the intermediate and the final products, respectively.

  • 5.
    Klug, Otto
    et al.
    Luleå tekniska universitet.
    Parlagh, G.
    Technical University of Budapest.
    Forsling, Willis
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Sustainable Process Engineering.
    Raman spectroscopy of aromatic acids adsorbed on oxidised aluminium foil1997In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 410, p. 183-188Article in journal (Refereed)
    Abstract [en]

    Adsorption of ortho- and para-phthalic acids on oxidised aluminium foil was investigated by Raman and surface-enhanced Raman spectroscopy (SERS). Without any treatment of the foil only a modified method of SERS provided spectroscopic evidence of the adsorption. However, by dissolving the metal aluminium from the Al2O3-Al-Al2O3 structure of the foil, the adsorption could be investigated by Raman spectroscopy without surface-enhanced conditions. The vibrational bands of the adsorbed species, obtained by both types of Raman spectroscopy, are compared to the solid-state spectra of the pure acids and their dipotassium salts. The band shifts suggest that the adsorbed species are essentially in the carboxylate form; however, the Raman and the SER spectra of the same species are not identical indicating a separate chemical reaction occurring at the surface upon depositing the sol. (C) 1997 Elsevier Science B.V.

  • 6. Larsson, Andreas
    et al.
    Cremer, Dieter
    Department of Theoretical Chemistry, Göteborg University.
    Theoretical verification and extension of the McKean relationship between bond lengths and stretching frequencies1999In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 485-486, p. 385-407Article in journal (Refereed)
    Abstract [en]

    Vibrational spectra contain explicit information on the electronic structure and the bonding situation of a molecule, which can be obtained by transforming the vibrational normal modes of a molecule into appropriate internal coordinate modes, which are localized in a fragment of the molecule and which are associated to that internal coordinate that describes the molecular fragment in question. It is shown that the adiabatic internal modes derived recently (Int. J. Quant. Chem., 67 (1998) 1) are the theoretical counterparts of McKean's isolated CH stretching modes (Chem. Soc. Rev., 7 (1978) 399). Adiabatic CH stretching frequencies obtained from experimental vibrational spectra can be used to determine CH bond lengths with high accuracy. Contrary to the concept of isolated stretching frequencies a generalization to any bond of a molecule is possible as is demonstrated for the CC stretching frequencies. While normal mode frequencies do not provide a basis to determine CC bond lengths and CC bond strengths, this is possible with the help of the adiabatic CC stretching frequencies. Measured vibrational spectra are used to describe different types of CC bonds in a quantitative way. For CH bonds, it is also shown that adiabatic stretching frequency leads to the definition of an ideal dissociation energy, which contrary to the experimentally determined dissociation energy is a direct measure of the bond strength. The difference between measured and ideal dissociation energies gives information on stabilization or destabilization of the radicals formed in a dissociation process

  • 7.
    Nagarajan, V.
    et al.
    School of Basic Sciences, Indian Institute of Technology Bhubaneswar.
    Pedireddia, V.R.
    School of Basic Sciences, Indian Institute of Technology Bhubaneswar.
    Shimpi, Manishkumar R.
    Luleå University of Technology, Department of Health Sciences, Medical Science.
    Hydrated and anhydrous molecular complexes of benzenepentacarboxylic acid and 4,4’-bipyridine2013In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 1050, p. 216-221Article in journal (Refereed)
    Abstract [en]

    Supramolecular assemblies of benzenepentacarboxylic acid (BPC) and 4,4’-bipyridine (bpy) as hepta- and di- hydrates in a 2:1 and 1:1 ratios of the respective co-crystal formers, as well as an anhydrous complex of 1:2 ratio have been reported. The three supramolecular complexes [(BPC-)2(bpy2+)(H2O)7], 1a, [(BPC-)(bpy+)(bpy)], 1b and [(BPC2-)(bpy2+)(H2O)2], 1c, were obtained by carrying out co-crystallization experiments at varied conditions. 1a and 1b were obtained at ambient and hydrothermal conditions, resepctively, while 1c also was obtained at hydrothermal conditions but only in the presence of Ni(NO3)2. All the molecular complexes were characterized by single-crystal X-ray diffraction method. Molecules in all the complexes are packed in the form of stacked layers with the realization of host-guest network in 1a and 1c along a crystallographic axis, wherein the host network is formed by BPC and water molecules through different types of hydrogen bonding patterns and bpy molecules remain as guests in the voids, while in 1b, a ladder type network is observed.

  • 8.
    Prajapati, Preeti
    et al.
    Physics Department, University of Lucknow.
    Pandey, Jaja
    Physics Department, University of Lucknow.
    Shimpi, Manishkumar
    Luleå University of Technology, Department of Health Sciences, Medical Science.
    Srivastava, Anubha
    Physics Department, University of Lucknow.
    Tandon, Poonam
    Physics Department, University of Lucknow.
    Velaga, Sitaram
    Luleå University of Technology, Department of Health Sciences, Medical Science.
    Sinha, Kirti
    Physics Department, University of Lucknow.
    Combined spectroscopic and quantum chemical studies of ezetimibe2016In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 1125, p. 193-203Article in journal (Refereed)
    Abstract [en]

    Ezetimibe (EZT) is a hypocholesterolemic agent used for the treatment of elevated blood cholesterol levels as it lowers the blood cholesterol by blocking the absorption of cholesterol in intestine. Study aims to combine experimental and computational methods to provide insights into the structural and vibrational spectroscopic properties of EZT which is important for explaining drug substance physical and biological properties. Computational study on molecular properties of ezetimibe is presented using density functional theory (DFT) with B3LYP functional and 6-311++G(d,p) basis set. A detailed vibrational assignment has been done for the observed IR and Raman spectra of EZT. In addition to the conformational study, hydrogen bonding and molecular docking studies have been also performed. For conformational studies, the double well potential energy curves have been plotted for the rotation around the six flexible bonds of the molecule. UV absorption spectrum was examined in methanol solvent and compared with calculated one in solvent environment (IEF-PCM) using TD-DFT/6-31G basis set. HOMO-LUMO energy gap of both the conformers have also been calculated in order to predict its chemical reactivity and stability. The stability of the molecule was also examined by means of natural bond analysis (NBO) analysis. To account for the chemical reactivity and site selectivity of the molecules, molecular electrostatic potential (MEPS) map has been plotted. The combination of experimental and calculated results provide an insight into the structural and vibrational spectroscopic properties of EZT. In order to give an insight for the biological activity of EZT, molecular docking of EZT with protein NPC1L1 has been done.

  • 9.
    Shimpi, Manishkumar
    et al.
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    Biswas, Sharmita Nandy
    Solid State and Supramolecular Structural Chemistry Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar.
    Sarkar, Sohini
    Solid State and Supramolecular Structural Chemistry Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar.
    Pedireddi, V.R.
    Solid State and Supramolecular Structural Chemistry Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar.
    Synthesis and Structural Evaluation of Five Coordination Complexes of Benzenepentacarboxylic Acid with Aza-donor Ligands2016In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 1114, p. 38-47Article in journal (Refereed)
    Abstract [en]

    Synthesis and structural features of five new coordination assemblies, [Co(bpyH)(H2O)5](BPCH)·(bpyH2)0.5·(H2O) (1a), [{Cu(H2O)3}·{Cu0.5(bpy)0.5(H2O)0.5}2(μ-BPCH)] (1b), [{Cd0.5(BPCH)}2·{Cd0.5(bpy)(H2O)2}2]·6(H2O) (1c), [Cu(BPCH2)(bpyeaH)].2(H2O) (1d) and [Cd2 (bpyea)0.5(oxalate)0.5(μ-BPC)(H2O)]·(bpyeaH2)·2(H2O) (1e), have been reported. All the assemblies were prepared by co-crystallization of benzenepentacarboxylic acid (BPCH5) either with 4,4′-bipyridine (bpy) or 1,2-bis(4-pyridyl)ethane (bpyea) in the presence of a transition metal ion (either Co(II), Cu(II) or Cd(II)) as the case may be. All the five compounds were synthesized by hydrothermal method and structures were determined by single crystal X-ray diffraction. All the obtained compounds, 1a-1e, exhibit distinct 3-D polymeric architectures either in the form of stacked layers or host-guest networks in which water molecules play a pivotal role providing additional stabilization by coordinate bonds as well as hydrogen bonds. Other non-covalent interactions such as C–H…π and π…π stacking also participate in the formation of exotic 3-D structures of these complexes.

  • 10.
    Usachev, Konstatin S.
    et al.
    Kazan (Volga Region) Federal University, Kazan.
    Filippov, Andrei
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    Khairutdinov, B.I.
    Kazan (Volga Region) Federal University, Kazan.
    Antzutkin, Oleg
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Chemical Engineering.
    Klochkov, V.V.
    Kazan (Volga Region) Federal University, Kazan.
    NMR structure of the Arctic mutation of the Alzheimer’s Aβ(1-40) peptide docked to SDS micelles2014In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 1076, p. 518-523Article in journal (Refereed)
    Abstract [en]

    The “Arctic” point mutation of the Alzheimeŕs amyloid β-peptide is a rare mutation leading to an early onset of Alzheimeŕs disease. The peptide may interact with neuronal membranes, where it can provide its toxic effects. We used 2D NMR spectroscopy to investigate the conformation of the “Arctic” mutant of Aβ1-40 Alzheimer’s amyloid peptide in sodium dodecyl sulfate micelle solutions, which are the type of amphiphilic structures mimicking some properties of biomembranes. The study showed that the Arctic mutant of Aβ1-40 interacts with the surface of SDS micelles mainly through the Leu17-Asn27 310-helical region, while the Ile31-Val40 region is buried in the hydrophobic interior of the micelle. In contrast, wild-type Aβ1-40 interacts with SDS micelles through the Lys16-Asp23 α-helical region and Gly29-Met35. Both the Arctic mutant and the wild-type Aβ1-40 peptides interactions with SDS micelles are hydrophobic in nature. Aβ peptides are thought to be capable of forming pores in biomembranes that can cause changes in neuronal and endothelial cell membrane permeability. It has also been shown that Aβ peptides containing the “Arctic” mutation are more neurotoxic and aggregate more readily than the wild-type Aβ peptides at physiological conditions. Here, we propose that the extension of the helical structure of Leu17-Asn27 and a high aliphaticity (neutrality) of the C-terminal region in the Arctic Aβ peptides are consistent with the idea that formation of ion-permeable pores by Aβ oligomers may be one of prevailing mechanisms of a larger neuronal toxicity of the Arctic Aβ compared to the wild-type Aβ peptides, independent of oxidative damage and lipid peroxidation.

  • 11.
    Usachev, K.S.
    et al.
    Kazan (Volga Region) Federal University, Kazan.
    Filippov, Andrei
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Sustainable Process Engineering.
    Filippova, E.A.
    Kazan (Volga Region) Federal University, Kazan.
    Antzutkin, Oleg
    Luleå University of Technology, Department of Civil, Environmental and Natural Resources Engineering, Sustainable Process Engineering.
    Klochkov, V.V.
    Kazan (Volga Region) Federal University, Kazan.
    Solution structures of Alzheimer’s amyloid Aβ13-23 peptide: NMR studies in solution and in SDS2013In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 1049, p. 436-440Article in journal (Refereed)
    Abstract [en]

    To be believed that interaction of amyloid peptides with the cellular membrane is one of the mechanisms for the neurotoxicity of Aβ. Therefore, structural studies of beta-amyloid in solution and in a “peptide - bio-membrane” complex are of intense interest. The aim of this study was to acquire a better understanding of the mechanism of “Aβ peptide-micelle surface” complex formation. Previous studies of Aβ peptides binding on the micelle surface show the presence of helical region between 15-24 residues and that fragment between 11-28 residues have a tendency to exit the hydrophobic environment of the micelle core and to bind to the micelle surface. In present paper we considered the fragment of Aβ from 13 to 23 residues and found that L17, F19 and F20 residues region play a great role in the process of binding of Aβ to the micelle surface.

  • 12.
    Velaga, Sitaram
    et al.
    Luleå University of Technology, Department of Health Sciences, Medical Science.
    Basavoju, Srinivas
    Luleå University of Technology, Department of Health Sciences, Medical Science.
    Boström, Dan
    Energy Technology and Thermal Process Chemistry, Umeå University.
    Norfloxacin saccharinate-saccharin dihydrate cocrystal: a new pharmaceutical cocrystal with an organic counter ion2008In: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 859, no 1-3, p. 150-153Article in journal (Refereed)
    Abstract [en]

    A novel pharmaceutical cocrystal was obtained with an organic counter ion. Norfloxacin saccharinate dihydrate and its cocrystal, norfloxacin saccharinate-saccharin dihydrate, were crystallized.

1 - 12 of 12
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