Temperature and pressure dependence of the Raman active modes of vibration of α-quartz

The Raman spectra of a single crystal of natural quartz have been very carefully investigated as a function of temperature (range 77–300 K), and as a function of hydrostatic pressure (atmospheric up to 10 kbar). The temperature results shows that cooling the quartz increases the vibrational frequencies with corresponding reductions in linewidth, and that the 206 cm⁻¹, vibrational mode (the soft mode) is very strongly temperature dependent. The pressure dependent Raman data has been used to calculate the mode Gruneisen parameters γ_i, for the three strongest vibrational modes; these are 3.63, 0.64 and 1.55 for the 206, 464 and 128 cm⁻¹ lines, respectively.     

LiO Raman Bands of 6Li2CO3 and 7Li2CO3

The Raman spectra of polycrystalline ⁶Li₂CO₃ have been recorded in the frequency region from 600 to 300 cm⁻¹. Four very weak bands have been observed for each compound the isotopic frequency shifts are reported. The results have been compared with those from the i.r. spectra for the LiO₄ tetrahedra.     

BH−4 isolated in RbI: Internal and external modes of vibration as function of temperature and pressure as studied by Raman and i.r. spectroscopy

Previously unreported bands in the i.r. spectra of BH⁻₄ isolated in Rbl are interpreted in terms of summation bands of internal and external modes of vibration. Raman and far i.r. spectra of this system are reported for the first time. Reliable values for i.r. inactive internal modes ν₁ and ν₂ have been obtained and external modes due to torsional and translational motion have been identified. A gap-mode has also been found. The temperature and pressure dependence of these features have been measured spectroscopically.     

Two coordination modes of TCNE in the ruthenium amidinates: The first example providing experimental evidence for κ-N to η-C rearrangement

Reactions of Cp^∗Ru(κ²-N(R)C(R′)NR) (1a; R = ⁱPr, R′ = Me, 1b; R = ^tBu, R′ = Ph) with TCNE initially give dark green colored intermediary species, which are readily converted to brown colored “η²-C” coordination complexes, Cp^∗Ru(κ²-N(R)C(R′)NR)(η²-TCNE) (3a; R = ⁱPr, R′ = Me, 3b; R = ^tBu, R′ = Ph). These “η²-C” complexes are characterized by spectroscopy and crystallography. A stable ruthenium amidinate having a “κ¹-N”-coordinated TCNE, Cp^∗Ru(κ²-N(^tBu)C(Mes)N^tBu)(κ¹(N)-TCNE) (2c), is synthesized by treatment of Cp^∗Ru(κ²-N(^tBu)C(Mes)N^tBu) (1c) with TCNE, the structure of which is unequivocally confirmed by X-ray structure determination and the charge transfer nature is supported by ESR analysis. Close analogy in IR and UV-Vis spectroscopy of 2c with the dark green colored intermediary species formed from 1b suggests that this is “κ¹-N” ruthenium amidinate, which is rearranged to the “η²-C” complex 3b.     

A New Chemiluminescence Amplification Reaction for the Determination of HRP and Labelled HRP

A new chemiluminescence amplification reaction has been developed, which is on the coupling of the oxidation of Eosin by hydrogen peroxide under the catalysis of HRP at pH 3. 5 to the chemiluminescent reaction of luminol and hydrogen peroxide catalyzed by HRP at pH 10 to measure the activity of HRP and labelled-HRP. The detection limit of HRP is 10-10 g/mL. The lowest dilution ratio of HBsAb-HRP is 1 : 1. 8×102 and 1 : 106 for the direct method and coupled method respectively.     

Raman spectroscopic evidence for the inclusion of decanoate ion in trimethyl-β-cyclodextrin

A method for calibrating Raman intensities of diluted aqueous solutions, based on the integrated intensity of the OH stretching bands of liquid water as an external intensity standard, is described and used to obtain a difference spectrum that reveals intensity changes mainly due to the intermolecular interaction between two solutes. The method is applied to trimethyl-β-cyclodextrin in sodium decanoate aqueous solutions. The difference between the interaction spectra above and below the critical micellar concentration of sodium decanoate, in the CH stretching region between 2700 and 3100 cm⁻¹, shows an intensity increase of the CH stretching bands for trimethyl-β-cyclodextrin above the critical micellar concentration of sodium decanoate, whereas β-cyclodextrin is relatively insensitive to the presence of decanoate ion micelles in aqueous solution.     

Self-induced pressure shift and temperature dependence measurements of CO2 at 2.05μm with a tunable diode laser spectrometer

By using a high resolution tunable diode laser absorption spectrometer combined with a cryogenically cooled optical multi-pass cell, we have measured the self-induced pressure shift coefficients for 8 transitions in the R branch of the (20(0)1)(III)←(00(0)0)(I) band of carbon dioxide around 2.05μm. This spectral region is of particular interest for the monitoring of atmospheric CO(2) with Differential Absorption Lidars (DiAL). The measurement of these shift coefficients was realized at five different temperatures ranging from 218 to 292K in order to determine their temperature dependence. The results are thoroughly compared to previous values reported in the literature for the (20(0)1)(III)←(00(0)0)(I) band of CO(2). The temperature dependence of the self-induced pressure shifts are reported experimentally for the first time for this specific CO(2) band.     

Raman and infrared study of external and internal vibrational modes of the NO−3 ion isolated in rubidium halides

The vibrational spectra of the NO⁻₃ ion isolated within RbCl, RbBr and RbI has been investigated at various temperatures between 77 and 300 K, by means of i.r. and Raman techniques.At room temperature, the i.r. and Raman activities of the NO⁻₃ internal modes suggest that the NO⁻₃-occupied sites have D₃ symmetry. However at low temperature C_3ν symmetry is suggested.One localized mode has been observed for each system, close to the top of the optic branch of each lattice. They appear at 119, 145 and 166 cm⁻¹ for RbI, RbBr and RbCl respectively. In addition, one gap mode (low density of state mode), centred at 111 cm⁻, has been observed in the uncertain “gap” region between the acoustic and the optic branches of the lattice vibrations of RbCl.     

The configurational dependence of binding free energies: A Poisson–Boltzmann study of Neuraminidase inhibitors

The linear finite difference Poisson-Boltzmann (FDPB) equation is applied to the calculation of the electrostatic binding free energies of a group of inhibitors to the Neuraminidase enzyme. An ensemble of enzyme-inhibitor complex conformations was generated using Monte Carlo simulations and the electrostatic binding free energies of subtly different configurations of the enzyme-inhibitor complexes were calculated. It was seen that the binding free energies calculated using FDPB depend strongly on the configuration of the complex taken from the ensemble. This configurational dependence was investigated in detail in the electrostatic hydration free energies of the inhibitors. Differences in hydration energies of up to 7 kcal mol^–1 were obtained for root mean square (RMS) structural deviations of only 0.5 Å. To verify the result, the grid size and parameter dependence of the calculated hydration free energies were systematically investigated. This showed that the absolute hydration free energies calculated using the FDPB equation were very sensitive to the values of key parameters, but that the configurational dependence of the free energies was independent of the parameters chosen. Thus just as molecular mechanics energies are very sensitive to configuration, and single-structure values are not typically used to score binding free energies, single FDPB energies should be treated with the same caution.     

Raman intensities of the lattice modes of KH1−xDxF2 as the order parameter for phase transition

In this work, the Raman intensities of the librational mode of the bifluoride ion and the translational mode of the K⁺ ion are considered as the order parameters for the phase transition of KH_1−xD_xF₂ since group theoretical consideration shows that the Raman active translational and librational modes in the low temperature phase will be inactive in the high temperature phase if the latter is of symmetry group O or higher. The measured Raman intensities are correlated with the temperature from 163°C to 196°C to elucidate the exponent β which relates the Raman intensity to the temperature close to T_c through (T^c-T)^β for various deuteration compositions. The β value of KHF₂ is very close to that predicted by the Ising model of three-dimensional space with a one-dimensional order parameter, suggesting that the nearest-neighbour interaction of the translational modes can play a very important role for the phase transition. Experiments also show that the phase transition temperature is slightly isotope composition dependent.     

Carboxylation and decarboxylation of active site Lys 84 controls the activity of OXA-24 β-lactamase of Acinetobacter baumannii: Raman crystallographic and solution evidence

The class D β-lactamases are characterized by the presence of a carboxylated lysine in the active site that participates in catalysis. Found in Acinetobacter baumannii, OXA-24 is a class D carbapenem hydrolyzing enzyme that exhibits resistance to most available β-lactamase inhibitors. In this study, the reaction between a 6-alkylidiene penam sulfone inhibitor, SA-1-204, in single crystals of OXA-24 is followed by Raman microscopy. Details of its reaction with SA-1-204 provide insight into the enzyme's mode of action and help define the mechanism of inhibition. When the crystal is maintained in HEPES buffer, the reaction is fast, shorter than the time scale of the Raman experiment. However, when the crystal holding solution contains 28% PEG 2000, the reaction is slower and can be recorded by Raman microscopy in real time; the inhibitor's Raman bands quickly disappear, transient features are seen due to an early intermediate, and, at approximately 2-11 min, new bands appear that are assigned to the late intermediate species. At about 50 min, bands due to all intermediates are replaced by Raman signals of the unreacted inhibitor. The new population remains unchanged indicating (i) that the OXA-24 is no longer active and (ii) that the decarboxylation of Lys84 occurred during the first reaction cycle. Using absorbance spectroscopy, a one-cycle reaction could be carried out in aqueous solution producing inactive OXA-24 as assayed by the chromogenic substrate nitrocefin. However, activity could be restored by reacting aqueous OXA-24 with a large excess of NaHCO(3), which recarboxylates Lys84. In contrast, the addition of NaHCO(3) was not successful in reactivating OXA-24 in the crystalline state; this is ascribed to the inability to create a concentration of NaHCO(3) in large excess over the OXA-24 that is present in the crystal. The finding that inhibitor compounds can inactivate a class D enzyme by promoting decarboxylation of an active site lysine suggests a novel function that could be exploited in inhibitor design.     

Multicomponent CoMgONaZSM-5 catalyst for hydrocarbon synthesis from CO + H2 mixtures containing CO2 and/or N2

The catalyst under study was prepared by kneading a physical mixture of precipitated cobalt hydroxycarbonate, magnesia and NaZSM-5 with water as a binder. This mixture was pretreated by drying at 120 °C or by calcination at 450 °C. Adsorption measurements revealed that NaZSM-5 was not affected by the solid state reaction with cobalt component and magnesia. When the catalyst was reduced, the metallic phase originated from different precursors depending on the thermal pretreatment. The composition of the unreduced part of the oxidic cobalt was also affected; after reduction, the surface of the dried sample contained both Co(II) and Co(III) in the ratio of 1.8 to 1.0, while that of the calcined sample consisted mostly of Co(III). Carbon monoxide was adsorbed in several forms, but only the most weakly bonded form desorbed without decomposition. Pretreatment by calcination caused a shift in the optimum synthesis temperature and a very marked decrease in the C₅⁺ fraction yield compared with the dried sample. The addition of nitrogen to the syngas caused an increase in the liquid hydrocarbon selectivity, while carbon dioxide, especially at higher concentrations, decreased the hydrocarbon yield substantially. The effect of reaction pressure depended on the feed gas composition.     

Raman spectrum and secondary structure of the phage λ operator site OL1: evidence for multiple nucleoside conformations in an aqueous B-form DNA

The laser Raman spectrum of O_L1 has been obtained in the region 600–850 cm⁻¹ and the data have been interpreted in terms of different nucleoside conformations within the 17 base pair operator site. The O_L1 sequence, which is one of the tightest binding sites for the cI and Cro repressors of bacteriophage λ, displays several Raman conformation markers indicative of more than one backbone geometry for the same double-stranded DNA helix. Specific assignments for the Raman conformation markers are suggested by analogy with spectra of DNA single crystals and DNA fibers of known structure. Two Raman bands diagnostic of B-DNA backbone geometry are observed at 825 ± 3 and 838 ± 3 cm⁻¹, and may be due, respectively, to inequivalent conformations of GC and AT pairs. In addition, a weak band at 706 cm⁻¹ and a shoulder near 807 cm⁻¹ are consistent with a minor contribution from residues which assume the A-DNA backbone geometry or a structurally related configuration. The complex bandshape in the 650–700 cm⁻¹ interval, which is resolved into four peaks by Fourier deconvolution, is also consistent with the presence of multiple nucleoside conformers in O_L1 in physiological conditions.     

The origin of the shift in the CO vibration of chemisorbed CO: Cluster model studies for CO / Cu(100)

Two major contributions to the shift of the CO stretch vibrational frequency between free CO and chemisorbed CO/Cu(100) are identified. The overlap and consequent repulsion between the CO and metal orbitals leads to an increase in the frequency. The metal charge donation and dative bonding to CO 2π^* leads to a decrease.     

Assessing protein–ligand binding modes with computational tools: the case of PDE4B

In a first step in the discovery of novel potent inhibitor structures for the PDE4B family with limited side effects, we present a protocol to rank newly designed molecules through the estimation of their IC\(_{50}\) values. Our protocol is based on reproducing the linear relationship between the logarithm of experimental IC\(_{50}\) values [\(\log\)(IC\(_{50}\))] and their calculated binding free energies (\(\Delta G_\mathrm{binding}\)). From 13 known PDE4B inhibitors, we show here that (1) binding free energies obtained after a docking process by AutoDock are not accurate enough to reproduce this linear relationship; (2) MM-GB/SA post-processing of molecular dynamics (MD) trajectories of the top ranked AutoDock pose improves the linear relationship; (3) by taking into account all representative structures obtained by AutoDock and by averaging MM-GB/SA computations on a series of 40 independent MD trajectories, a linear relationship between \(\log\)(IC\(_{50}\)) and the lowest \(\Delta G_\mathrm{binding}\) is achieved with \(R^2=0.944\).     

High pressure phase behavior and modeling of CO2–propyl acrylate and CO2–propyl methacrylate systems

High pressure phase behavior are obtained for CO₂–propyl acrylate system at 40, 60, 80, 100 and 120 °C and pressure up to 161 bar and for CO₂–propyl methacrylate systems at 40, 60, 80, 100 and 120 °C and pressure up to 166 bar. The solubility of propyl acrylate and propyl methacrylate for the CO₂–propyl acrylate and CO₂–propyl methacrylate systems increases as the temperature increases at constant pressure. The CO₂–propyl acrylate and CO₂–propyl methacrylate systems have continuous critical mixture curves that exhibit maximums in pressure at temperatures between the critical temperatures of CO₂ and propyl acrylate or propyl methacrylate. The CO₂–propyl acrylate and CO₂–propyl methacrylate systems exhibit type-I phase behavior with a continuous mixture critical curve.The experimental results for CO₂–propyl acrylate and CO₂–propyl methacrylate systems are modeled using both the statistical associating fluid theory (SAFT) and Peng–Robinson equations of state. A good fit of the data are obtained with SAFT using two adjustable parameters for CO₂–propyl acrylate and CO₂–propyl methacrylate systems and Peng–Robinson equation using one and two adjustable parameter for CO₂–propyl acrylate and CO₂–propyl methacrylate system.     

Isomorphism of HTNaCaAsO4 and HTAgCaAsO4: New structural data and vibrational study

The new compound AgCaAsO₄ forms two crystalline solid phases; the high temperature phase is isomorphous with the high temperature phase of NaCaAsO₄ and with Na₂CrO₄. We show on the basis of salient features of the vibrational spectrum that the monovalent cations Na or Ag are located on the C_2ν symmetry sites in the Na₂CrO₄ structure, and how the cationic substitution NaAg produces as a consequence an increase of the covalency. The detailed study of the IR and Raman spectra evidences weak vibrational interactions between the two tetrahedral groups in the same primitive unit cell and leads to a realistic assignment of the observed frequencies. Subsequently, we are led to propose a partly different model for the na₂CrO₄ structure.     

FT Raman spectroscopic study of the diimide hydrogenation of cis-polybutadiene: Some evidence of cis—trans isomerization

The diimide hydrogenation of cis-polybutadiene is studied. p-Toluenesulfonylhydrazide is used to fully and partially hydrogenate cis-polybutadiene. The microstructure and hydrogenation of the samples obtained are subsequently studied by FT Raman spectroscopy. Cis—trans isomerization is found to take place during the reaction. A mechanism of isomerization and hydrogenation is also proposed.     

Infrared studies in the ν1 of ONCI: CO laser line coincidences and pressure broadening data

46 Spectral quasi-coincidences between CO laser lines and ClNO absorption lines are given. The ONCl ν₁ spectra have been obtained using a Fourier transform spectrometer. In four cases the discrepancies between the frequencies are smaller than the Doppler width. Pressure broadening parameters resulting from collisional perturbations by Ar for two rotational transitions in the ν₁ band of ONCl have been measured using a diode laser spectrometer.     

Identification of [PtCl2(phen)] binding modes in amyloid-β peptide and the mechanism of aggregation inhibition

Platinum phenanthroline complexes inhibit amyloid-β (Aβ) aggregation and reduce Aβ-caused neurotoxicity [Proc. Natl. Acad. Sci., 2008, 105, 6813-6818]. In this study, we investigated the interactions of Aβ(1-16) with [PtCl(2)(phen)] (phen=1,10-phenanthroline) using HPLC, ESI-MS, and NMR spectroscopy , and characterized the identity of products using tandem mass spectrometry. Results indicated that the phenanthroline ligand could induce noncovalent interactions between Aβ peptide and platinum complexes, leading to rapid Aβ platination. Multiple products were generated in the reaction, in which His6/His14 chelation was preferentially formed. Coordination of Asp7, His13, and Lys16 was also detected in other products. The majority of products were monoplatinated adducts with binding of the {Pt(phen)} scaffold, which impeded intermolecular interactions between Aβ peptides. Moreover, noncovalent interactions were confirmed by the interaction between Aβ peptide and [Pt(phen)(2)]Cl(2). The synergistic roles of the phen ligand and platinum(II) atom in the inhibition of Aβ aggregation are discussed.