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1.
J Mater Res ; 39(1): 150-164, 2024.
Article in English | MEDLINE | ID: mdl-38223565

ABSTRACT

A new integrated deposition system taking advantage of magnetron sputtering and electron cyclotron-plasma enhanced chemical vapour deposition (IMS ECR-PECVD) is presented that mitigates the drawbacks of each fabrication system. This tailor-made system provides users with highly homogeneous and pure thin films with less undesired hydrogen and well-controlled rare-earth concentration compared to existing methods of rare-earth doping, such as metalorganic powders, sputtering, and ion implantation. We established the first comprehensive report on the deposition parameters of argon flow and sputtering power to achieve desired rare-earth concentrations in a wide composition range of terbium (Tb) doped-silicon oxide (Tb:SiOx) matrices including silicon-rich (x < 2), oxygen-rich (x > 2), and stoichiometric silicon oxide (x = 2). The deposition parameters to fabricate crystalline structure (Tb2Si2O7) in oxygen-rich samples are reported where Tb ions are optically active. IMS ECR-PECVD pushes the solubility limit of the rare-earth dopant in silicon films to 17 at.% for the desired future nanophotonic devices. Supplementary Information: The online version contains supplementary material available at 10.1557/s43578-023-01207-2.

2.
Phys Chem Chem Phys ; 24(22): 13690-13697, 2022 Jun 08.
Article in English | MEDLINE | ID: mdl-35611965

ABSTRACT

Inclusion complexes of naphthalene (NP) with cyclodextrins (CD) have been investigated so far using non-NMR techniques resulting in inconsistent data. Here, the first application of high-field NMR spectroscopy in combination with a precise analysis of the results has allowed us to determine accurately the stoichiometry of complexes and their association constants. Titration measurements have been performed by 1H NMR spectroscopy in D2O at a magnetic field B0 of 18.8 T. NP and αCD form a 1 : 2 complex in which a single NP molecule is closed in a capsule made up of two αCD macrocycles. NP and ßCD build coexisting 2 : 1 and 2 : 2 complexes with large binding constants. Larger γCD host molecules form essentially similar complexes with NP as the ßCD but corresponding binding constants are smaller.


Subject(s)
Cyclodextrins , Cyclodextrins/chemistry , Magnetic Resonance Imaging , Magnetic Resonance Spectroscopy , Naphthalenes
3.
J Forensic Sci ; 67(2): 775-785, 2022 Mar.
Article in English | MEDLINE | ID: mdl-34766629

ABSTRACT

The Polish TU 154M plane, Polish Air Force Flight 101, had crashed near Smolensk on 10th of April 2010. The crash was investigated by The Interstate Aviation Committee, whose conclusions were questioned by a number of Polish scientists. The cause of the crash still appears to be incompletely documented and requires additional evidence. In this paper, investigations of a solid material eluted from a piece of cloth of one of the victims of the crash are described. High resolution mass spectrometry was applied to analyze the soot left after controlled ethylene oxide (EO) explosions, performed under different conditions. These included electric ignition of EO vapors in a large volume steel container, and explosions of glass tubes filled with liquid EO, stimulated by thermally initiated explosions of pentaerythritol tetranitrate (PETN). One of these explosions was conducted in the vessel used for the electric ignition of EO and the other in a hermetically locked, small volume container. It was shown that the soot comprises a set of C2 H4 O homopolymers and copolymers whose characteristic MS patterns are condition-dependent. The MS spectrum of the postcrash sample referred to above reveals a number of polymers that are also present in the soot obtained in PETN-initiated ethylene oxide explosions. It can be concluded that the piece of cloth was subjected to an EO explosion initiated by an explosion of energetic material, possibly PETN. Similar control experiments with ethylene glycol (EG) showed that the polymers identified in the investigated postcrash sample could not originate from exploding EG.


Subject(s)
Ethylene Oxide , Pentaerythritol Tetranitrate , Ethylene Oxide/analysis , Mass Spectrometry/methods , Pentaerythritol Tetranitrate/analysis , Pentaerythritol Tetranitrate/chemistry , Poland , Soot/analysis
4.
IUBMB Life ; 72(6): 1250-1261, 2020 06.
Article in English | MEDLINE | ID: mdl-32364671

ABSTRACT

A series of halogenated derivatives of natural flavonoids: baicalein and chrysin were designed and investigated as possible ligands for the catalytic subunit of tumor-associated human kinase CK2. Thermal shift assay method, in silico modeling, and high-performance liquid chromatography-derived hydrophobicity together with IC50 values determined in biochemical assay were used to explain the ligand affinity to the catalytic subunit of human protein kinase CK2. Obtained results revealed that substitution of baicalein and chrysin with halogen atom increases their binding affinity to hCK2α, and for 8-chlorochrysin the observed effect is even stronger than for the reference CK2 inhibitor-4,5,6,7-tetrabromo-1H-benzotriazole. The cytotoxic activities of the baicalein and chrysin derivatives in the in vitro model have been evaluated for MV4-11 (human biphenotypic B myelomonocytic leukemia), A549 (human lung adenocarcinoma), LoVo (human colon cancer), and MCF-7 (human breast cancer) as well as on the nontumorigenic human breast epithelial MCF-10A cell lines. Among the baicalein derivatives, the strongest cytotoxic effect was observed for 8-bromobaicalein, which exhibited the highest activity against breast cancer cell line MCF-7 (IC50 10 ± 3 µM). In the chrysin series, the strongest cytotoxic effect was observed for unsubstituted chrysin, which exhibited the highest activity against leukemic cell line MV4-11 (IC50 10 ± 4 µM).


Subject(s)
Casein Kinase II/antagonists & inhibitors , Flavanones/chemistry , Flavonoids/chemistry , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/pharmacology , Antineoplastic Agents/chemistry , Antineoplastic Agents/metabolism , Antineoplastic Agents/pharmacology , Casein Kinase II/chemistry , Casein Kinase II/metabolism , Cell Line, Tumor , Drug Screening Assays, Antitumor , Flavanones/metabolism , Flavanones/pharmacology , Flavonoids/metabolism , Flavonoids/pharmacology , Halogenation , Humans , Magnetic Resonance Spectroscopy , Models, Molecular , Protein Kinase Inhibitors/metabolism , Structure-Activity Relationship
5.
Phys Chem Chem Phys ; 21(13): 6925-6934, 2019 Mar 27.
Article in English | MEDLINE | ID: mdl-30865207

ABSTRACT

Complex formation between quinine and natural cyclodextrins (CD) was studied using NMR spectroscopy. The strongest association was observed for complexes of neutral quinine molecules with ßCD. Association constants for monocationic quinine were one order of magnitude smaller, while dicationic quinine did not bind to CDs. The distribution of complexation-induced shifts and ROESY spectra revealed bimodal quinine binding in complexes formed with ßCD and γCD. Complex formation resulted in a decrease of the vicinal coupling constant between H2 and H9 protons owing to the rotation about the C2-C9 bond and in consequence in mutual reorientation of two main constituents of quinine: quinoline and quinuclidine. DFT calculations allowed establishing that H2 and H9 protons are antiperiplanar in the prevailing quinine conformer(s) in aqueous solution. Conformers with synclinal H2 and H9 protons participated in quinine complexation with CDs.

6.
Steroids ; 143: 49-52, 2019 03.
Article in English | MEDLINE | ID: mdl-30582942

ABSTRACT

The application of 3D NMR experiments and DFT calculations enabled the structure investigation of C-17 epimer of 3-(25-hydroxycholest-5-enyl) acetate is presented. The H-17 and H-20 protons features the same values of 1H chemical shift, what causes that the structure elucidation require additional resolution enabled by 3D NMR experiments. The NMR experiments and theoretical calculations allowed for: the resonance assignment (3D COSY-HMBC and 3D TOCSY-HSQC techniques), the prediction of spatial structure (3D NOESY-HSQC and 3D ROESY-HSQC experiments), and the precise measurement of heteronuclear coupling constants (3D HSQC-TOCSY spectra with E.COSY-type multiplets).


Subject(s)
Hydroxycholesterols/chemistry , Magnetic Resonance Spectroscopy , Models, Molecular , Molecular Conformation , Stereoisomerism
7.
Chirality ; 29(11): 747-758, 2017 Nov.
Article in English | MEDLINE | ID: mdl-28877407

ABSTRACT

Gibbs energies of complex formation between enantiomers of bicyclic terpenoid, fenchone, and naturally occurring cyclodextrins, ßCD and γCD, were determined by means of 13 C and 1 H nuclear magnetic resonance (NMR) titration data. These results were compared with the corresponding data obtained previously for the diastereomeric fenchone/αCD complexes. The size of the inner cavity of host molecules significantly influences stoichiometry, association constants, and enantiomeric differentiation of the studied complexes. These complementary data allow us to discuss qualitatively the influence of the host size on the guest-host interactions. A method of the simultaneous use of titration data collected for several resonances of different isotopes in the determination of association constants was worked out and thoroughly analyzed. Comparison of the results of global data analyses with weighted means of individual ones revealed that both these approaches are equally trustworthy.


Subject(s)
Cyclodextrins/chemistry , Norbornanes/chemistry , Camphanes , Magnetic Resonance Spectroscopy , Stereoisomerism , Thermodynamics
8.
Plant Cell ; 29(7): 1709-1725, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28655749

ABSTRACT

Plants accumulate a family of hydrophobic polymers known as polyprenols, yet how they are synthesized, where they reside in the cell, and what role they serve is largely unknown. Using Arabidopsis thaliana as a model, we present evidence for the involvement of a plastidial cis-prenyltransferase (AtCPT7) in polyprenol synthesis. Gene inactivation and RNAi-mediated knockdown of AtCPT7 eliminated leaf polyprenols, while its overexpression increased their content. Complementation tests in the polyprenol-deficient yeast ∆rer2 mutant and enzyme assays with recombinant AtCPT7 confirmed that the enzyme synthesizes polyprenols of ∼55 carbons in length using geranylgeranyl diphosphate (GGPP) and isopentenyl diphosphate as substrates. Immunodetection and in vivo localization of AtCPT7 fluorescent protein fusions showed that AtCPT7 resides in the stroma of mesophyll chloroplasts. The enzymatic products of AtCPT7 accumulate in thylakoid membranes, and in their absence, thylakoids adopt an increasingly "fluid membrane" state. Chlorophyll fluorescence measurements from the leaves of polyprenol-deficient plants revealed impaired photosystem II operating efficiency, and their thylakoids exhibited a decreased rate of electron transport. These results establish that (1) plastidial AtCPT7 extends the length of GGPP to ∼55 carbons, which then accumulate in thylakoid membranes; and (2) these polyprenols influence photosynthetic performance through their modulation of thylakoid membrane dynamics.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/physiology , Photosynthesis/physiology , Plastids/metabolism , Transferases/metabolism , Arabidopsis Proteins/genetics , Dimethylallyltranstransferase/genetics , Dimethylallyltranstransferase/metabolism , Genetic Complementation Test , Plant Leaves/genetics , Plant Leaves/metabolism , Plants, Genetically Modified , Polyisoprenyl Phosphates/metabolism , RNA Interference , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Substrate Specificity , Thylakoids/metabolism , Transferases/genetics
9.
Plant Physiol ; 174(2): 857-874, 2017 Jun.
Article in English | MEDLINE | ID: mdl-28385729

ABSTRACT

The cooperation of the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways, operating in parallel in plants to generate isoprenoid precursors, has been studied extensively. Elucidation of the isoprenoid metabolic pathways is indispensable for the rational design of plant and microbial systems for the production of industrially valuable terpenoids. Here, we describe a new method, based on numerical modeling of mass spectra of metabolically labeled dolichols (Dols), designed to quantitatively follow the cooperation of MVA and MEP reprogrammed upon osmotic stress (sorbitol treatment) in Arabidopsis (Arabidopsis thaliana). The contribution of the MEP pathway increased significantly (reaching 100%) exclusively for the dominating Dols, while for long-chain Dols, the relative input of the MEP and MVA pathways remained unchanged, suggesting divergent sites of synthesis for dominating and long-chain Dols. The analysis of numerically modeled Dol mass spectra is a novel method to follow modulation of the concomitant activity of isoprenoid-generating pathways in plant cells; additionally, it suggests an exchange of isoprenoid intermediates between plastids and peroxisomes.


Subject(s)
Arabidopsis/metabolism , Dolichols/chemistry , Models, Theoretical , Spectrometry, Mass, Electrospray Ionization/methods , Terpenes/metabolism , Carbon Isotopes , Chromatography, Gas/methods , Dolichols/metabolism , Erythritol/analogs & derivatives , Erythritol/metabolism , Isotope Labeling/methods , Metabolic Networks and Pathways , Mevalonic Acid/analogs & derivatives , Mevalonic Acid/chemistry , Mevalonic Acid/metabolism , Osmotic Pressure , Phytosterols/biosynthesis , Sorbitol/metabolism , Sugar Phosphates/metabolism , Xylulose/analogs & derivatives , Xylulose/chemistry
10.
BMC Neurol ; 16(1): 134, 2016 Aug 11.
Article in English | MEDLINE | ID: mdl-27516084

ABSTRACT

BACKGROUND: Comprehensive epidemiologic data for multiple sclerosis (MS) in Poland are limited. The aim of this cross-sectional population-based study was to determine the incidence and prevalence of MS in the Swietokrzyskie Region (central Poland). METHODS: This study identified MS cases every year between 1 January 2010 and 31 December 2014. The study area population on the prevalence day (December 31, 2014) was 1,263,176 (646,506 women and 616,670 men). A total of 1462 patients with a clinically definite diagnosis of MS according to McDonald's criteria (2005), recorded in the Polish Multiple Sclerosis Registry, were considered for estimation of crude, age- and sex-specific prevalence, and incidence. RESULTS: The overall crude prevalence rate of confirmed MS patients was 115.7/100,000 (95 % confidence interval (CI), 111.2-121.4). A significantly higher prevalence was recorded in females (159.6/100,000; 95 % CI, 151.1-165.3) than in males (69.7/100,000; 95 % CI, 62.4-77.3) (P < 0.001). Age-adjusted rates for the Polish and European Standard Population were 109.8/100,000 (95 % CI, 105.4-114.8) and 106.6/100,000 (95 % CI, 101.1-111.2), respectively. The female/male ratio was 2.4. The mean annual incidence was 4.2/100,000 (95 % CI. 3.7-4.4). CONCLUSION: The incidence and prevalence of MS in the Swietokrzyskie region confirm that central Poland is a high risk area for MS. Compared with previous epidemiologic studies from Poland, the prevalence of MS has increased during recent years.


Subject(s)
Multiple Sclerosis/epidemiology , Adolescent , Adult , Aged , Cross-Sectional Studies , Female , Humans , Incidence , Male , Middle Aged , Poland/epidemiology , Prevalence
11.
Biochim Biophys Acta ; 1851(10): 1296-303, 2015 Oct.
Article in English | MEDLINE | ID: mdl-26143379

ABSTRACT

Dolichols are, among others, obligatory cofactors of protein glycosylation in eukaryotic cells. It is well known that yeast cells accumulate a family of dolichols with Dol-15/16 dominating while upon certain physiological conditions a second family with Dol-21 dominating is noted. In this report we identified the presence of additional short-chain length polyprenols - all-trans Pren-7 in three yeast strains (SS328, BY4741 and L5366), Pren-7 was accompanied by traces of putative Pren-6 and -8. Moreover, in two of these strains a single polyprenol mainly-cis-Pren-11 was synthesized at the stationary phase of growth. Identity of polyprenols was confirmed by HR-HPLC/MS, NMR and metabolic labeling. Additionally, simvastatin inhibited their biosynthesis.


Subject(s)
Saccharomyces cerevisiae/metabolism , Terpenes/metabolism , Saccharomyces cerevisiae/genetics
12.
J Org Chem ; 80(8): 3982-97, 2015 Apr 17.
Article in English | MEDLINE | ID: mdl-25816092

ABSTRACT

To broaden the scope of existing methods based on (19)F nucleotide labeling, we developed a new method for the synthesis of fluorophosphate (oligo)nucleotide analogues containing an O to F substitution at the terminal position of the (oligo)phosphate moiety and evaluated them as tools for (19)F NMR studies. Using three efficient and comprehensive synthetic approaches based on phosphorimidazolide chemistry and tetra-n-butylammonium fluoride, fluoromonophosphate, or fluorophosphate imidazolide as fluorine sources, we prepared over 30 fluorophosphate-containing nucleotides, varying in nucleobase type (A, G, C, U, m(7)G), phosphate chain length (from mono to tetra), and presence of additional phosphate modifications (thio, borano, imido, methylene). Using fluorophosphate imidazolide as fluorophosphorylating reagent for 5'-phosphorylated oligos we also synthesized oligonucleotide 5'-(2-fluorodiphosphates), which are potentially useful as (19)F NMR hybridization probes. The compounds were characterized by (19)F NMR and evaluated as (19)F NMR molecular probes. We found that fluorophosphate nucleotide analogues can be used to monitor activity of enzymes with various specificities and metal ion requirements, including human DcpS enzyme, a therapeutic target for spinal muscular atrophy. The compounds can also serve as reporter ligands for protein binding studies, as exemplified by studying interaction of fluorophosphate mRNA cap analogues with eukaryotic translation initiation factor (eIF4E).


Subject(s)
Endoribonucleases/chemistry , Eukaryotic Initiation Factor-4E/chemistry , Fluorides/chemical synthesis , Fluorine Radioisotopes/chemistry , Nucleotides/chemical synthesis , Oligonucleotides/chemical synthesis , Phosphates/chemical synthesis , Quaternary Ammonium Compounds/chemistry , RNA, Messenger/chemistry , Spin Labels/chemical synthesis , Endoribonucleases/pharmacology , Fluorides/chemistry , Humans , Magnetic Resonance Spectroscopy , Muscular Atrophy, Spinal/enzymology , Muscular Atrophy, Spinal/metabolism , Nucleotides/chemistry , Oligonucleotides/chemistry , Phosphates/chemistry , Protein Binding , RNA, Messenger/chemical synthesis
13.
Nanotechnology ; 26(8): 085203, 2015 Feb 27.
Article in English | MEDLINE | ID: mdl-25656362

ABSTRACT

Amorphous sub-nanometre Tb-doped SiOxNy/SiO2 superlattices were fabricated by means of alternating deposition of 0.7 nm thick Tb-doped SiOxNy layers and of 0.9 nm thick SiO2 barrier layers in an electron-cyclotron-resonance plasma enhanced chemical vapour deposition system with in situ Tb-doping capability. High resolution transmission electron microscopy images showed a well-preserved superlattice morphology after annealing at a high temperature of 1000 °C. In addition, transparent indium tin oxide (ITO) electrodes were deposited by electron beam evaporation using a shadow mask approach to allow for the optoelectronic characterization of superlattices. Tb(3+) luminescent spectral features were obtained using three different excitation sources: UV laser excitation (photoluminescence (PL)), under a bias voltage (electroluminescence (EL)) and under a highly energetic electron beam (cathodoluminescence (CL)). All techniques displayed Tb(3+) inner transitions belonging to (5)D4 levels except for the CL spectrum, in which (5)D3 transition levels were also observed. Two competing mechanisms were proposed to explain the spectral differences observed between PL (or EL) and CL excitation: the population rate of the (5)D3 state and the non-radiative relaxation rate of the (5)D3-(5)D4 transition due to a resonant OH-mode. Moreover, the large number of interfaces (trapping sites) that electrons have to get through was identified as the main reason for observing a bulk-limited charge transport mechanism governed by Poole-Frenkel conduction in the J-V characteristic. Finally, a linear EL-J dependence was measured, with independent spectral shape and an EL onset voltage as low as 6.7 V. These amorphous sub-nanometre superlattices are meant to provide low-cost solutions in different areas including sensing, photovoltaics or photonics.

14.
Biochim Biophys Acta ; 1841(7): 977-86, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24747199

ABSTRACT

2,3-Oxidosqualene is an intermediate in cholesterol biosynthesis and 2,3:22,23-dioxidosqualene act as the substrate for an alternative pathway that produces 24(S),25-epoxycholesterol which effects cholesterol homeostasis. In light of our previous findings concerning the biological effects of certain epoxidated all-trans-polyisoprenes, the effects of squalene carrying epoxy moieties on the second and third isoprene residues were investigated here. In cultures of HepG2 cells both monoepoxides of squalene and one of their hydrolytic products inhibited cholesterol synthesis and stimulated the synthesis of coenzyme Q (CoQ). Upon prolonged treatment the cholesterol content of these cells and its labeling with [(3)H]mevalonate were reduced, while the amount and labeling of CoQ increased. Injection of the squalene monoepoxides into mice once daily for 6days elevated the level of CoQ in their blood, but did not change the cholesterol level. The same effects were observed upon treatment of apoE-deficient mice and diabetic GK-rats. This treatment increased the hepatic level of CoQ10 in mice, but the amount of CoQ9, which is the major form, was unaffected. The presence of the active compounds in the blood was supported by the finding that cholesterol synthesis in the white blood cells was inhibited. Since the ratio of CoQ9/CoQ10 varies depending on the experimental conditions, the cells were titrated with substrate and inhibitors, leading to the conclusion that the intracellular isopentenyl-PP pool is a regulator of this ratio. Our present findings indicate that oxidosqualenes may be useful for stimulating both the synthesis and level of CoQ both in vitro and in vivo.


Subject(s)
Cholesterol/analogs & derivatives , Cholesterol/biosynthesis , Hemiterpenes/metabolism , Organophosphorus Compounds/metabolism , Squalene/analogs & derivatives , Ubiquinone/analogs & derivatives , Animals , Bridged Bicyclo Compounds, Heterocyclic/pharmacology , Diabetes Mellitus, Experimental/drug therapy , Diabetes Mellitus, Experimental/metabolism , Diabetes Mellitus, Experimental/pathology , Etidronic Acid/analogs & derivatives , Etidronic Acid/pharmacology , Hep G2 Cells , Humans , Lovastatin/pharmacology , Male , Mevalonic Acid/pharmacology , Mice , Mice, Inbred C57BL , Mice, Knockout , Rats , Rats, Wistar , Risedronic Acid , Squalene/metabolism , Squalene/pharmacology , Tricarboxylic Acids/pharmacology , Ubiquinone/biosynthesis
15.
Nanoscale Res Lett ; 8(1): 98, 2013 Feb 22.
Article in English | MEDLINE | ID: mdl-23433189

ABSTRACT

Silicon nanocrystals embedded in a silicon-rich silicon oxide matrix doped with Er3+ ions have been fabricated by electron cyclotron resonance plasma-enhanced chemical vapor deposition. Indirect excitation of erbium photoluminescence via silicon nanocrystals has been investigated. Temperature quenching of the photoluminescence originating from the silicon nanocrystals and the erbium ions has been observed. Activation energies of the thermally activated quenching process were estimated for different excitation wavelengths. The temperature quenching mechanism of the emission is discussed. Also, the origin of visible emission and kinetic properties of Er-related emission have been discussed in details.

16.
J Mol Graph Model ; 32: 67-74, 2012 Feb.
Article in English | MEDLINE | ID: mdl-22079210

ABSTRACT

Two variants of NMR-based conformational analyses of flexible peptides are compared using two examples meeting the formula Tyr-D-Daa-Phe-Daa-NH2 (Daa=diamino acid): 1 combining D-Dab² (α,γ-diaminobutyryl) with Lys4, and 2 -D-Dap² (α,ß-diaminopropionyl) with Orn4. The ω-amino groups of D-Daa² and Daa4 are coupled with C=O into the urea, restraining 1 and 2 with 16- and 14-membered rings and leading to potent and impotent µ/δ opioid peptides, respectively. To the current task, we took from an earlier work (Filip et al, J. Pept. Sci. 11 (2005) 347-352) the NMR NOE- and J-data in H2O/D2O; and the selection of the ensembles of 1 and 2, 822 and 788 conformational families, respectively, obtained by using the EDMC/ECEPP3 method. Here, we generated ensembles of 1 and 2 using AMBER molecular dynamics in explicit water to eventually selected 686 and 761 conformers for 1 and 2, respectively. We did numbers of fits for both types of the conformational ensembles of 1 and 2 to their NOE- and J-data using a common method i.e. maximum entropy approach (Groth et al, J. Biomol. NMR 15 (1999) 315-330). Both types of the well structurally diversified ensembles fit to quite different equilibria in regressions to common experimental NOE- and J-restraints using maximum entropy principle, which is a disappointing message. Intriguing is startlingly small standard deviation in J-couplings: σ(JNHαH) ≈ 0.01 Hz for LES-MD/AMBER ensemble, contrary to σ(JNHαH) = 0.8 - 1.1 Hz for the EDMC/ECEPP ensemble, over the wide range of entropy, i.e. relatively insensitive to it. A similar feature is not the case when comparing σ(NOE) in both methods. Hence, at minute entropy contributions, it follows that J does or does not transpose "overfitted" into the final σ(J) in the AMBER or ECEPP ensemble, respectively. Could this be an effect of softness of the AMBER flexible-valence force field compared to ECEPP rigid-geometry, and its effect on ensemble sampling? We do not know an answer.


Subject(s)
Peptides/chemistry , Water/chemistry , Computer Simulation , Entropy , Models, Molecular , Molecular Dynamics Simulation , Nuclear Magnetic Resonance, Biomolecular/methods , Protein Conformation
17.
Chemistry ; 17(46): 12981-93, 2011 Nov 11.
Article in English | MEDLINE | ID: mdl-21956694

ABSTRACT

A study concerning the effect of using a fluorinated aromatic solvent as the medium for olefin metathesis reactions catalysed by ruthenium complexes bearing N-heterocyclic carbene ligands is presented. The use of fluorinated aromatic hydrocarbons (FAH) as solvents for olefin metathesis reactions catalysed by standard commercially available ruthenium pre-catalysts allows substantially higher yields of the desired products to be obtained, especially in the case of demanding polyfunctional molecules, including natural and biologically active compounds. Interactions between the FAH and the second-generation ruthenium catalysts, which apparently improve the efficiency of the olefin metathesis transformation, have been studied by X-ray structure analysis and computations, as well as by carrying out a number of metathesis experiments. The optimisation of reaction conditions by using an FAH can be regarded as a complementary approach for the design of new improved ruthenium catalysts. Fluorinated aromatic solvents are an attractive alternative medium for promoting challenging olefin metathesis reactions.


Subject(s)
Alkenes/chemistry , Hydrocarbons, Fluorinated/chemistry , Methane/analogs & derivatives , Organometallic Compounds/chemistry , Ruthenium/chemistry , Catalysis , Methane/chemistry , Models, Molecular , Molecular Structure
18.
Nanoscale Res Lett ; 6(1): 168, 2011 Feb 23.
Article in English | MEDLINE | ID: mdl-21711680

ABSTRACT

Silicon nanoclusters (Si-ncs) embedded in silicon nitride films have been studied to determine the effects that deposition and processing parameters have on their growth, luminescent properties, and electronic structure. Luminescence was observed from Si-ncs formed in silicon-rich silicon nitride films with a broad range of compositions and grown using three different types of chemical vapour deposition systems. Photoluminescence (PL) experiments revealed broad, tunable emissions with peaks ranging from the near-infrared across the full visible spectrum. The emission energy was highly dependent on the film composition and changed only slightly with annealing temperature and time, which primarily affected the emission intensity. The PL spectra from films annealed for duration of times ranging from 2 s to 2 h at 600 and 800°C indicated a fast initial formation and growth of nanoclusters in the first few seconds of annealing followed by a slow, but steady growth as annealing time was further increased. X-ray absorption near edge structure at the Si K- and L3,2-edges exhibited composition-dependent phase separation and structural re-ordering of the Si-ncs and silicon nitride host matrix under different post-deposition annealing conditions and generally supported the trends observed in the PL spectra.

19.
Acta Biochim Pol ; 58(2): 225-30, 2011.
Article in English | MEDLINE | ID: mdl-21584287

ABSTRACT

Six hybrid N-ureidoethylamides of octapeptides in which an N-terminal cyclic structure related to enkephalin was elongated by a C-terminal fragment of deltorphin were synthesized on MBHA resin. The synthetic procedure involved deprotection of Boc groups with HCl/dioxane and cleavage of the peptide resin with 45 % TFA in DCM. d-Lys and d-Orn were incorporated in position 2, and Lys, Orn, Dab, or Dap in position 5. The side chains of the dibasic amino function were protected with the Fmoc group. This protection was removed by treatment with 55 % piperidine in DMF, and cyclization was achieved by treatment with bis-(4-nitrophenyl)carbonate. Using various combinations of dibasic amino acids, peptides containing a 17-, 18-, 19- or 20-membered ring structure were obtained. The peptides were tested in the guinea-pig ileum (GPI) and mouse vas deferens (MVD) assays. Diverse opioid activities were observed, depending on the size of the ring. Extension of the enkephalin sequence at the C-terminus by a deltorphin fragment resulted in a change of receptor selectivity in favor of the δ receptor. The conformational propensities of selected peptides were determined using the EDMC method in conjunction with data derived from NMR experiments carried out in water. This approach allowed proper examination of the dynamical behavior of these small peptides. The results were compared with those obtained earlier with corresponding N-(ureidoethyl)pentapeptide amides.


Subject(s)
Enkephalins/chemical synthesis , Oligopeptides/chemical synthesis , Peptides, Cyclic/chemical synthesis , Animals , Enkephalins/chemistry , Enkephalins/pharmacology , Guinea Pigs , Ileum/drug effects , In Vitro Techniques , Male , Mice , Models, Molecular , Nuclear Magnetic Resonance, Biomolecular , Oligopeptides/chemistry , Oligopeptides/pharmacology , Peptides, Cyclic/chemistry , Peptides, Cyclic/pharmacology , Protein Conformation , Vas Deferens/drug effects
20.
Inorg Chem ; 50(1): 72-85, 2011 Jan 03.
Article in English | MEDLINE | ID: mdl-21141850

ABSTRACT

Glutathione disulfide (GSSG), a long disregarded redox partner of glutathione (GSH), is thought to participate in intracellular zinc homeostasis. We performed a concerted potentiometric and NMR spectroscopic study of protonation and Zn(II) binding properties of GSSG ((γECG)(2)) and a series of its nine analogs with C-terminal modifications, tripeptide disulfides: (γECS)(2), (γECE)(2), (γECG-NH(2))(2), (γECG-OEt)(2), and (γEcG)(2); dipeptide disulfides, (γEC)(2) and (γEC-OEt)(2); and mixed disulfides, γECG-γEC and γECG-γEC-OEt. The acid-base and Zn(II) complexation properties in this group of compounds are strictly correlated to average C-terminal electrostatic charges. In particular, it was demonstrated that GSSG assumes a bent (head-to-tail) conformation in solution at neutral pH, which is controlled by electrostatic attraction between the protonated γ-amino groups of the Glu residue and the deprotonated C-terminal Gly carboxylates. This interaction modulates the ability of GSSG to coordinate Zn(II), both indirectly, by affecting the basicities of the amino groups, and directly, through the participation of the Gly carboxylates in the outer coordination sphere of the Zn(II) ion. A specific coiled structure of the major [Zn-GSSG](2-) complex is additionally stabilized by the formation of hydrogen bonds between glycinyl carboxylates and two Zn(II)-coordinated water molecules. The elevated stability of Zn(II)-GSSG complexes was demonstrated by competition with FluoZin-3, a fluorescent sensor with high Zn(II) affinity, commonly used in in vitro and in vivo studies. The potential biological functions and reactivity of GSSG complexes of Zn(II) ions are discussed.


Subject(s)
Glutathione Disulfide , Oligopeptides , Zinc , Fluorometry , Glutathione Disulfide/analogs & derivatives , Hydrogen Bonding , Hydrogen-Ion Concentration , Magnetic Resonance Spectroscopy , Molecular Conformation , Oligopeptides/chemistry , Polycyclic Compounds/analysis , Polycyclic Compounds/metabolism , Potentiometry , Protein Stability , Thermodynamics , Water/chemistry , Zinc/chemistry , Zinc/metabolism
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