A study of low-energy ion induced radiolysis of thiol-containing amino acid cysteine in the solid and aqueous solution states

The radiolysis of cysteine under plasma discharge and irradiation of low-energy Ion beam was investigated. The damage of cysteine in aqueous solution under discharge was assessed via the acid ninhydrin reagent and the yield of cystine produced from the reaction was analyzed by FTIR In addition, the generation of hydrogen sulfide was also identified The destruction of solid cysteine under low-energy ion beam irradiation was estimated via monitoring IR bands of different functional groups (-SH, -NH3, -COO-) of cysteine. and the production of cystine from ion-irradiated solid cysteine after dissolution in water was also verified These results may help us to understand the inactivation of sulphydryl enzymes under direct and indirect interaction with the low-energy ion irradiation (C) 2010 Elsevier B V All rights reserved.

Crystal packing motifs of oligothiophenes end-capped with N-containing aryls

Oligothiophenes (OThs) end-capped with 3-quinolyl or pyridyl with nitrogen atom at meta-, ortho- or para-position were synthesized. The single-crystal structures of the resulting molecules, i.e., o-PyTh4, m-PyTh4, p-PyTh4, QuTh2, and QuTh3, were successfully determined by single-crystal X-ray analysis. Pyridyl end-capped OThs; o-PyTh4, m-PyTh4, and p-PyTh4, adopt the different herringbone packing arrangement in crystals depending on the position of the nitrogen atom because of the presence of weak C-H center dot center dot center dot N hydrogen bonds. The p-PyTh4 molecules are linked each other along the long axis of the molecules to form the extended chains by C-H center dot center dot center dot N dimer synthon. For m-PyTh4, the C-H center dot center dot center dot N interactions two-dimensionally extend through C-H center dot center dot center dot N trimer synthon.

Formation of [Ru(bpy)(3)](2+)-containing microstructures induced by electrostatic assembly and their application in solid-state detection of electrochemiluminescence

Tris(2,2'-bipyridine)ruthenium(II) ((Ru(bpy)(3)](2+)) is one of the most extensively studied and used electrochemiluminescent (ECL) compounds owing to its superior properties, which include high sensitivity and stability under moderate conditions in aqueous solution. In this paper we present a simple method for the preparation of [Ru(bpy)(3)](2+)-containing microstructures based on electrostatic assembly The formation of such micro-structures occurs in a single process by direct mixing of aqueous solutions of [Ru(bpy)(3)]Cl-2 and K-3[Fe(CN)(6)] at room temperature. The electrostatic interactions between [Ru(bpy)(3)]Cl-2 cations and [Fe(CN)(6)](3-) anions cause them to assemble into the resulting microstructures. Both the molar ratio and concentration of reactants were found to have strong influences on the formation of these microstructures. Most importantly, the resulting [Ru(bpy)(3)](2+)- containing microstructures exhibit excellent ECL behavior and, therefore, hold great promise for solid-state ECL detection in capillary electrophoresis (CE) or CE microchips.

Electrochemiluminescent detection based on solid-phase extraction at tris(2,2 '-bipyridyl)ruthenium(II)-modified ceramic carbon electrode

A sensitive electrochemiluminescent detection scheme by solid-phase extraction at Ru(bpy)(3)(2+)-modified ceramic carbon electrodes (CCEs) was developed. The as-prepared Ru(bpy)(3)(2+)-modified CCEs show much better long-term stability than other Nafion-based Ru(bpy)(3)(2+)-modified electrodes and enjoy the inherent advantages of CCEs. The log-log calibration plot for dioxopromethazine is linear from 1.0 x 10(-9) to 1.0 x 10(-4) mol L-1 using the new detection scheme. The detection limit is 6.6 x 10(-10) mol L-1 at a signal-to-noise ratio of 3. The new scheme improves the sensitivity by similar to 3 orders of magnitude, which is the most sensitive Ru(bpy)(3)(2+) ECL method. The scheme allows the detection of dioxopromethazine in a urine sample within 3 min. Since Ru(bpy)(3)(2+) ECL is a powerful technique for determination of numerous amine-containing substances, the new detection scheme holds great promise in measurement of free concentrations, investigation of protein-drug interactions and DNA-drug interactions, pharmaceutical analysis, and so on.

From dissymmetrical mononuclear entities to centrosymmetrical heterotrinuclear complex with 2D supramolecular structure: synthesis, characterization, crystal structure, and magnetic properties

A new centrosymmetrical heterotrinuclear complex, {[Cu(oxbe)](2)Co(H2O)(2)}.2DMF.DMA with 2D supramolecular structure, has been obtained by the self-assembly of a dissymmetrical building block [Cu(oxbe)](-) with bivalent metal ion Co2+, where H(3)oxbe is dissymmetrical ligand N-benzoato-N'-(2-aminoethyl)oxamido, DMF = dimethylformamide, DMA = dimethylamine. Its structure was determined by single crystal X-ray analysis. The molecular structure is centrosymmetrical with the cobalt atom lying on an inversion center. Through the hydrogen bonds and d-pi stacking interactions, a 2D supramolecular structure is formed. This study exemplifies a new method for the assembly of supramolecular structure using a dissymmetrical brick. Magnetic susceptibility measurements (5-300 K) indicate that the central cobalt and terminal copper metal ions are antiferromagnetically coupled with J = -23.1 cm(-1).

Temperature dependence of the distribution of the first passage time: Results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G

More than 22 000 folding kinetic simulations were performed to study the temperature dependence of the distribution of first passage time (FPT) for the folding of an all-atom Go-like model of the second beta-hairpin fragment of protein G. We find that the mean FPT (MFPT) for folding has a U (or V)-shaped dependence on the temperature with a minimum at a characteristic optimal folding temperature T-opt*. The optimal folding temperature T-opt* is located between the thermodynamic folding transition temperature and the solidification temperature based on the Lindemann criterion for the solid. Both the T-opt* and the MFPT decrease when the energy bias gap against nonnative contacts increases. The high-order moments are nearly constant when the temperature is higher than T-opt* and start to diverge when the temperature is lower than T-opt*. The distribution of FPT is close to a log-normal-like distribution at T* greater than or equal to T-opt*. At even lower temperatures, the distribution starts to develop long power-law-like tails, indicating the non-self-averaging intermittent behavior of the folding dynamics. It is demonstrated that the distribution of FPT can also be calculated reliably from the derivative of the fraction not folded (or fraction folded), a measurable quantity by routine ensemble-averaged experimental techniques at dilute protein concentrations.

The multicolour three-photon resonant ionization spectrum studies in uranium atom

The multicolour three-photon resonant ionization spectra of U-238 were measured by using the pulsed dye lasers system synchronously pumped by a frequency doubled Nd:YAG-laser 532 nm output(operated at 10 Hz),a device for atomic beam of U, time-of-flight mass spectrometer and boxcar integrator. The dye laser pulses have a 6 ns duration. Beams from the dye lasers, which have the same polarization direction and are focused by lenses, entered an interaction chamber through opposite windows on a common axis and spatialy overlapped the U atomic beam. The optical pulse from dye laser DL2 was delayed to arrive at the interaction region 8 ns after the pulse from dye laser DL1; in the same way,the pulse from DL3 was delayed 8 ns after from DL2. The atomic beam device was made from stainless steel. We generated the U vapor by heating solid U in a graphite crucible by e-type electron -field on first excited states were studied in uranium atom. The question how to determine single-colour, two-colour and three-colour three-photon resonant ionization peak in the three-colour three-photon resonant ionization spectra diagram were solved.

Miscibility and specific interactions in poly(beta-hydroxybutyrate-co-beta-hydroxyvalerate) and poly(P-vinylphenol) blends

The blends of poly(beta-hydroxybutyrate-co-beta-hydroxyvalerate) (P(HB-co-HV)/poly(p-vinylphenol)(PVPh) were investigated by differential scanning calorimetry (DSC), Fourier transform IR (FT-IR) spectroscopy and high-resolution solid-state C-13 NMR techniques. Single glass transition temperatures existing in the whole composition range indicates that these blends are miscible. The presence of hydrogen bonding between the hydroxyl of PVPh and carbonyl of P(HB-co-HV), shown by FT-IR spectra, is the origin of the miscibility. Furthermore, results obtained by high-resolution solid-state C-13 NMR give more information about the structure of the blends. (C) 1998 Elsevier Science Ltd. All rights reserved.

Compatibility and specific interactions in poly(beta-hydroxybutyrate) and poly(p-vinylphenol) blends

The miscibility and specific interactions in poly (beta-hydroxybutyrate) (PHB)/poly(p-vinylphenol) (PVPh) blends were studied by differential scanning calorimetry(DSC) , fourier transform infrared(FTIR) spectrometer and high resolution solid state C-13 NMR, A single composition-dependent glass transition temperatures were obtained by DSC which indicate the blends of PHB/PVPh were miscible in the melt state, The experimental glass transition temperatures were fitted quite well with those obtained from Couchman-Karasz equation. The FTIR study shows that the strong intermolecular hydrogen bonding exists in blends of PHB with strong proton acceptor and PVPh with strong proton donor and is the origin of its compatibility. The CPMAS C-13 NMR spectra also show that the strong hydrogen bonding exists in PHB/PVPh blends. From the T-1 rho(H) relaxation time it follows that the blends of PHB/PVPh(40/60, 20/80) studied are completely homogeneous on the scale of about 3.2 nm.

INTERACTIONS OF THIAMINE WITH ANIONS - STRUCTURE OF THIAMINE DITHIOCYANATE

The crystal structure analysis of {3-[(4-amino-2-methyl-5-pyrimidinyl)methyl]-5-(2-hydroxyethyl)-4-methylthiazol}ium dithiocyanate reveals that there are two types of anion bridges between the two aromatic rings of the same thiamine which adopts the usual F conformation, one of which involves a contact between H(C2) on the thiazolium ring and the hydroxy O atom from a neighbouring molecule. The crystal packing shows a novel triple helical structure formed by strongly hydrogen-bonded thiamine-SCN- molecular chains.

Study of adsorption of methylene blue and new methylene blue in liquid-solid interface by slab optical waveguide spectroscopy

A slab optical waveguide (SOWG) has been used for study of adsorption of both methylene blue (MB) and new methylene blue (NMB) in liquid-solid interface. Adsorption characteristics of MB and NMB on both bare SOWG and silanized SOWG by octadecyltrichlorosilane (ODS) were compared. Effect of pH on adsorption on MB and NMB was investigated. Binding rate constant analysis showed that both MB and NMB on bare SOWG demonstrates larger association constants than those on ODS-SOWG. Interactions of NIB and NMB on bare SOWG and ODS-SOWG were analyzed by molecular mechanics calculation method. The binding energy change was in the following order: ENMB-bare > EMB-bare > ENMB-ODS > EMB-ODS. (c) 2004 Elsevier B.V. All rights reserved.

Crystal engineering: exploiting variation of sulfur oxidation for the control of the solid state structure of organosulfur compounds

This thesis is focused on the design and synthesis of a diverse range of novel organosulfur compounds (sulfides, sulfoxides and sulfones), with the objective of studying their solid state properties and thereby developing an understanding of how the molecular structure of the compounds impacts upon their solid state crystalline structure. In particular, robust intermolecular interactions which determine the overall structure were investigated. These synthons were then exploited in the development of a molecular switch. Chapter One provides a brief overview of crystal engineering, the key hydrogen bonding interactions utilized in this work and also a general insight into “molecular machines” reported in the literature of relevance to this work. Chapter Two outlines the design and synthetic strategies for the development of two scaffolds suitable for incorporation of terminal alkynes, organosulfur and ether functionalities, in order to investigate the robustness and predictability of the S=O•••H-C≡C- and S=O•••H-C(α) supramolecular synthons. Crystal structures and a detailed analysis of the hydrogen bond interactions observed in these compounds are included in this chapter. Also the biological activities of four novel tertiary amines are discussed. Chapter Three focuses on the design and synthesis of diphenylacetylene compounds bearing amide and sulfur functionalities, and the exploitation of the N-H•••O=S interactions to develop a “molecular switch”. The crystal structures, hydrogen bonding patterns observed, NMR variable temperature studies and computer modelling studies are discussed in detail. Chapter Four provides the overall conclusions from chapter two and chapter three and also gives an indication of how the results of this work may be developed in the future. Chapter Five contains the full experimental details and spectral characterisation of all novel compounds synthesised in this project, while details of the NCI (National Cancer Institute) biological test results are included in the appendix.

Dynamic fluid-structure interactions using finite volume unstructured mesh procedures

A three-dimensional finite volume, unstructured mesh (FV-UM) method for dynamic fluid–structure interaction (DFSI) is described. Fluid structure interaction, as applied to flexible structures, has wide application in diverse areas such as flutter in aircraft, wind response of buildings, flows in elastic pipes and blood vessels. It involves the coupling of fluid flow and structural mechanics, two fields that are conventionally modelled using two dissimilar methods, thus a single comprehensive computational model of both phenomena is a considerable challenge. Until recently work in this area focused on one phenomenon and represented the behaviour of the other more simply. More recently, strategies for solving the full coupling between the fluid and solid mechanics behaviour have been developed. A key contribution has been made by Farhat et al. [Int. J. Numer. Meth. Fluids 21 (1995) 807] employing FV-UM methods for solving the Euler flow equations and a conventional finite element method for the elastic solid mechanics and the spring based mesh procedure of Batina [AIAA paper 0115, 1989] for mesh movement. In this paper, we describe an approach which broadly exploits the three field strategy described by Farhat for fluid flow, structural dynamics and mesh movement but, in the context of DFSI, contains a number of novel features: a single mesh covering the entire domain, a Navier–Stokes flow, a single FV-UM discretisation approach for both the flow and solid mechanics procedures, an implicit predictor–corrector version of the Newmark algorithm, a single code embedding the whole strategy.

Vibrational spectroscopic studies of the structure of di-amino acid peptides. Part II: cyclo(L-Asp-L-Asp) in the solid state and in aqueous solution

Solid-state protonated and N,O-deuterated Fourier transform infrared (IR) and Raman scattering spectra together with the protonated and deuterated Raman spectra in aqueous solution of the cyclic di-amino acid peptide cyclo(L-Asp-L-Asp) are reported. Vibrational band assignments have been made on the basis of comparisons with previously cited literature values for diketopiperazine (DKP) derivatives and normal coordinate analyses for both the protonated and deuterated species based upon DFT calculations at the B3-LYP/cc-pVDZ level of the isolated molecule in the gas phase. The calculated minimum energy structure for cyclo(L-Asp-L-Asp), assuming C-2 symmetry, predicts a boat conformation for the DKP ring with both the two L-aspartyl side chains being folded slightly above the ring. The C=O stretching vibrations have been assigned for the side-chain carboxylic acid group (e.g. at 1693 and 1670 cm(-1) in the Raman spectrum) and the cis amide I bands (e.g. at 1660 cm(-1) in the Raman spectrum). The presence of two bands for the carboxylic acid C=O stretching modes in the solid-state Raman spectrum can be accounted for by factor group splitting of the two nonequivalent molecules in a crystallographic unit cell. The cis amide II band is observed at 1489 cm(-1) in the solid-state Raman spectrum, which is in agreement with results for cyclic di-amino acid peptide molecules examined previously in the solid state, where the DKP ring adopts a boat conformation. Additionally, it also appears that as the molecular mass of the substituent on the C-alpha atom is increased, the amide II band wavenumber decreases to below 1500 cm(-1); this may be a consequence of increased strain on the DKP ring. The cis amide II Raman band is characterized by its relatively small deuterium shift (29 cm(-1)), which indicates that this band has a smaller N-H bending contribution than the trans amide II vibrational band observed for linear peptides.

IR/Raman spectroscopy and DFT calculations of cyclic di-amino acid peptides. Part III: comparison of solid state and solution structures of cyclo(L-Ser-L-Ser)

B3-LYP/cc-pVDZ calculations of the gas-phase structure and vibrational spectra of the isolated molecule cyclo(L-Ser-L-Ser), a cyclic di-amino acid peptide (CDAP), were carried out by assuming C-2 symmetry. It is predicted that the minimum-energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L-Beryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol(-1)) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X-ray crystallographic structure of cyclo(L-Ser-L-Ser), shows that the DKP ring displays a near-planar conformation, with both the two L-Beryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier-transform infrared (FT-IR) spectra of solid state and aqueous solution samples of cyclo(L-Ser-L-Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid-state samples show characteristic amide I vibrations which are split (Raman:1661 and 1687 cm(-1), IR:1666 and 1680 cm(-1)), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of ~ 30 cm(-1), which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm(-1). The occurrence of this cis amide II mode at a wavenumber above 1500 cm(-1) concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C-alpha atoms, and is also indicative of a relatively unstrained DKP ring.