Raman Spectroscopy: Current Research Articles
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On this page considered biochemistry journals:
Journal of Raman Spectroscopy - published by
Wiley-Interscience -
Current research articles of the mentioned
journals:
Raman scattering of L-tryptophan enhanced by surface plasmon of silver nanoparticles: vibrational assignment and structural determination
Vibrational bands of L-tryptophan which was adsorbed on Ag nanoparticles ([sim]10 nm in diameter) have been investigated in the spectral range of 200-1700 cm-1 using surface-enhanced Raman scattering (SERS) spectroscopy. Compared with the normal Raman scattering (NRS) of L-tryptophan in either 0.5 M aqueous solution (NRS-AS) or solid powder (NRS-SP), the intensified signals by SERS have made the SERS investigation at a lower molecular concentration (5 × 10-4 M) possible. Ab initio calculations at the B3LYP/6-311G level have been carried out to predict the optimal structure and vibrational wavenumbers for the zwitterionic form of L-tryptophan. Facilitated with the theoretical prediction, the observed vibrational modes of L-tryptophan in the NRS-AS, NRS-SP, and SERS spectra have been analyzed. In the spectroscopic observations, there are no significant changes for the vibrational bands of the indole ring in either NRS-AS, NRS-SP, or SERS. In contrast, spectral intensities involving the vibrations of carboxylate and amino groups are weak in NRS-AS and NRS-SP, but strong in SERS. The intensity enhancement in the SERS spectrum can reach 103-104-fold magnification. On the basis of spectroscopic analysis, the carboxylate and amino groups of L-tryptophan are determined to be the preferential terminal groups to attach onto the surfaces of Ag nanoparticles in the SERS measurement. Copyright © 2008 John Wiley & Sons, Ltd.
Vibrational analysis of trans-stilbene in the excited singlet state by time-dependent density functional theory: calculations of the Raman, infrared, and fluorescence excitation spectra
Time-dependent density functional theory (TD-DFT), together with the analytic calculation of gradients and numerical calculation of the Hessian matrix, has been applied to calculate the Raman, infrared, and fluorescence excitation spectra of trans-stilbene (tSB) in the lowest excited singlet (S1) state. The TURBOMOLE program package has been used at the B3LYP/6-311 + + G(d,p) level, and the results obtained are found useful for analyzing a wide range of experimental results so far obtained by many authors. The advantage of TD-DFT over other methods in performing such calculations seems to lie in its capability of treating electron correlation more appropriately with computational resources currently available. Copyright © 2008 John Wiley & Sons, Ltd.
Surface-enhanced Raman scattering spectroscopy via gold nanostars
Anisotropic metallic nanoparticles (NPs) have unique optical properties, which lend them to applications such as surface-enhanced Raman scattering (SERS) spectroscopy. Star-shaped gold (Au) NPs were prepared in aqueous solutions by the seed-mediated growth method and tested for Raman enhancement using 2-mercaptopyridine (2-MPy) and crystal violet (CV) probing molecules. For both molecules, the SERS activity of the nanostars was notably stronger than that of the spherical Au NPs of similar size. The Raman enhancement factors (EFs) for 2-MPy on Au nanostars and nanorods are comparable and estimated as greater than 5 orders of magnitude. However, the enhancement for CV on nanostars was significantly higher than for nanorods, in particular at CV concentrations of 100 nM or lower. This article is a US Government work and is in the public domain in the USA. Published in 2008 by John Wiley & Sons, Ltd.
DFT simulations and Vibrational spectra of 4-chloro and 4-bromophenylboronic acid molecules
The experimental and theoretical vibrational spectra of 4-chloro- and 4-bromophenylboronic acids (abbreviated as 4Clpba and 4Brpba) were studied. The Fourier transform Raman and Fourier transform infrared (FTIR) spectra of 4Clpba and 4Brpba molecules were recorded in the solid phase. The structural and spectroscopic analyses of the molecules were made by using Hartree-Fock and density functional harmonic calculations. In both 4Clpba and 4Brpba only one form was most stable using B3LYP level with the 6-311 + + G(d,p) basis set. Selected experimental bands were assigned and characterized on the basis of the scaled theoretical wavenumbers by their total energy distribution (TED). Finally, geometric parameters as well as infrared (IR) and Raman bands were compared with the experimental data of the molecules. Copyright © 2008 John Wiley & Sons, Ltd.
Raman spectroscopic study of the tellurite mineral: sonoraite Fe3+Te4+O3(OH)·H2O
Tellurites may be subdivided according to formula and structure. Raman spectroscopy has been used to study sonoraite, an example of a tellurite with hydroxyl and water units in the mineral structure. The free tellurite ion will have C3v symmetry and four modes, 2A1 and 2E. An intense Raman band at 779 cm-1 is assigned to the [nu]1 (TeO3)2- symmetric stretching mode. A band at 666 cm-1 with a shoulder at 638 cm-1 is assigned to the [nu]3 (TeO3)2- antisymmetric stretching mode. Bands at 374 and 387 cm-1 and the two bands at 425 and 468 cm-1 are assigned to the (TeO3)2-[nu]2(A1) and (TeO3)2-[nu]4(E) bending modes, respectively. The sharp band at 3423 cm-1 assigned to the OH stretching vibration of the OH unit is superimposed upon a broader spectral profile with Raman bands at 3000, 3223, 3350 and 3450 cm-1 which are attributed to water stretching bands. The technique of Raman spectroscopy is excellent for the study of tellurite minerals. Copyright © 2008 John Wiley & Sons, Ltd.
Origin of the forbidden phonons in Raman scattering spectra of uranium-doped Ca2CuO3, a spin 1/2 chain system
The Raman scattering spectra of uranium-doped Ca2CuO3 were investigated. The small doping of uranium ([les]5%) in this one-dimensional spin 1/2 chain system induced three new first-order scattering bands and two new multiphonon bands in the structure of forbidden phonons. The first-order bands were found to agree well with the existing theoretical results from the ab initio and tight-binding calculation. Among them, the 470 and 665 cm-1 bands appeared as the basic wavenumbers of which the multiphonon overtones were composed. The grain size effect in this strongly anisotropic system was proposed not to originate from the classical phonon confinement but rather as a result of the segmentation of one-dimensional spin chains due to doping, which in turn allowed the new vibrational modes and implied the appearance of higher overtones in the scattering spectra. Copyright © 2008 John Wiley & Sons, Ltd.
Raman spectroscopic study of kuranakhite PbMn4+Te6+O6-a rare tellurate mineral
Tellurates are rare minerals as the tellurate anion is easily reduced to the tellurite ion. An example of a tellurate-containing mineral is kuranakhite. Two bands at 617 and 686 cm-1 are observed and assigned to the Te6+O6[nu]1 symmetric stretching mode. The observation of two bands suggests the non-equivalence of the Te6+O6 in the structure. The broad band centred at 743 cm-1 is attributed to the Te6+O6[nu]3 antisymmetric stretching mode. Sharp intense bands at 452 and 462 cm-1 are assigned to the Te6+O6[nu]4 bending mode. A comparison of the Raman spectra of kuranakhite with that of tellurate-containing minerals tlapallite and xocomecatlite is made in this article. Copyright © 2008 John Wiley & Sons, Ltd.
On the relative intensities of the Raman active fundamentals, r0 structural parameters, and pathway of chair-boat interconversion of cyclohexane and cyclohexane-d12
Raman spectra of liquid cyclohexane, C6H12, and deuterated cyclohexane, C6D12, were recorded with both parallel and perpendicular polarizations. The observed vibrational wavenumbers, depolarization ratios, and their intensities were measured and compared with the corresponding predicted values as well as the experimental values previously reported. The conformational energetics were obtained with the Møller-Plesset perturbation method to the second order [MP2(full)] as well as with density functional theory by the B3LYP method utilizing a variety of basis sets. The average ab initio predicted difference in energy between the more stable chair form (D3d) and the less stable twisted-boat form (D2) is 2213 cm-1 (26.47 kJ/mol), with a similar value of 2223 cm-1 (26.59 kJ/mol) from the density function theory calculations. By using two dihedral angles as variables, we calculated the chair-boat interconversion pathway for cyclohexane at the MP2(full)/6-31G(d) level. The harmonic force constants, Raman intensities, depolarization values, and the potential energy distribution were predicted from both MP2(full) and B3LYP calculations with the 6-31G(d) basis set and compared with the experimental values for the chair form when available. The 'adjusted' r0 structural parameters were obtained from MP2/6-311 + G(d,p) calculations and previously reported microwave rotational constants of five isotopomers of cyclohexane: i.e. 1,1-d2, 13C-1,1-d2, 1,1,2,2,3,3-d6, and d1 (equatorial and axial). The determined distances in Å are: r(CC) = 1.536(3), r(CH)ax = 1.098(1); r(CH)eq = 1.095(1); and the angles in degrees: [ang]CCHax = 108.8(3); [ang]CCHeq = 110.2(3); [ang]CCC = 111.1(3); and [ang]HCH = 107.6(3) with dihedral angle [ang]CCCC = 55.7(3). These values are compared with those previously reported and it is found that the difference in the r0 distances (0.003 Å) between the two CH values is much smaller than the difference (0.008 Å) previously reported for the rs values. Copyright © 2008 John Wiley & Sons, Ltd.
Binary mixture of p-methylbenzaldehyde with polar and nonpolar solvents
In this work, a combined theoretical and experimental study of binary mixture of liquid p-methylbenzaldehyde (PMBz) is reported using ab initio calculations as well as Raman and IR spectroscopies. The purpose of this study was twofold: firstly, to describe the interaction of PMBz in terms of bonding energies and preferred geometries; and secondly, to characterize the spectroscopic effects on the vibrational modes of PMBz in the binary mixture of different polar and nonpolar solvents. The three vibrational modes, namely, carbonyl stretching, [nu](C[bond]CH3) and aldehydic (C[bond]H) vibrations have been analyzed in all the three solvents in different concentrations. The dependence of Raman linewidth on the concentration of PMBz of these modes was also taken into account. By analyzing the peak position and linewidth of these modes, it is seen that the solute-solvent interaction is stronger in BuOH and 1,2 dichloroethane (DCE) because of the hydrogen-bonding interaction between these molecules. The formation of C[bond]H···O hydrogen bonds in liquid p-methylbenzaldehyde is also investigated by Gaussian fitting. The ab initio calculations suggest several possible dimer configurations. Copyright © 2008 John Wiley & Sons, Ltd.
Characterization of corrosion products formed on the surface of carbon steel by Raman spectroscopy
Corrosion of carbon steel in seashore salty soils containing 10, 20, and 34 wt% (saturated) water was investigated. The corrosion rate was measured and corrosion products were analyzed using Raman spectroscopy. It was found that carbon steel in the soil with 10 wt% water content had the largest corrosion rate and the corrosion was dominated by localized corrosion. The corrosion rate drops dramatically and turns to be general corrosion with increase of water content. The corrosion products in the soil with 20 and 34 wt% water content are mainly composed of [alpha]-FeOOH, while in the soil with 10 wt% water content, the products show a delaminated structure of two layers with the inner layer mainly consisting of [alpha]-FeOOH and the outer layer composed of Fe2O3 and Fe3O4. Copyright © 2008 John Wiley & Sons, Ltd.
Vibrational spectral studies on charge transfer and ionic hydrogen-bonding interactions of nonlinear optical material L-arginine nitrate hemihydrate
The near infrared Fourier-transform (NIR FT)-Raman and Fourier-transform infrared (FT-IR) spectroscopies supported by HF/6-31G(d) computations have been employed to derive equilibrium geometry, vibrational wavenumbers and the first hyperpolarizability of the nonlinear optical (NLO) material, L-arginine nitrate (LAN) hemihydrate. The reasonable NLO efficiency, predicted for the first time in this novel compound, has been confirmed by Kurtz-Perry powder second harmonic generation (SHG) experiments. The changes in the atomic charge distribution among different groups due to the presence of strong electronegative atoms and the shrinking of N[bond]O bonds of nitrate anion and C[bond]N bonds of guanidyl group have been analyzed. The splitting of the carboxylate stretching modes, blue shifting of methine vibrations and the electronic effects such as backdonation and induction on the methylene hydrogen atoms have also been examined in detail. The intense low wavenumber H-bond Raman vibrations due to electron-phonon coupling and nonbonded interactions in making the LAN molecule NLO active have been discussed based on the vibrational spectral features. The natural bond orbital (NBO) analysis and HF computations confirm the occurrence of strong intra- and intermolecular N[bond]H·O and O[bond]H·O ionic hydrogen bonding between charged species providing the noncentrosymmetric structure in the LAN crystal. Copyright © 2008 John Wiley & Sons, Ltd.
Confocal Raman imaging and atomic force microscopy of the surface reaction of NO2 and NaCl(100) under humidity
Polarized confocal Raman imaging combined with non-contact atomic force microscopy (AFM) was used to study the three-dimensional evolution of the NaCl(100) surface during its reaction with NO2 at low pressure as a function of relative humidity (RH) from 0% to nearly 80%. Sea salt particles containing NaCl as the main constituent are believed to be the major source of reactive tropospheric chlorine and nitrate fallouts. At an RH of 0%, the reaction of dry NO2 generates surface conversion to NaNO3 monolayer capping the NaCl(100) surface and releases NOCl. The subsequent exposure of this NaNO3 layer to RH below [sim]45% induces the formation of rare NaNO3 tetrahedral crystals less than 0.5 µm in size. The crystallization occurs through two-dimensional NO3- migration under the H2O monolayer regime. After another subsequent exposure to RH above 45% and below 75%, supermicrometric NaNO3 rhombohedral plates were obtained under the H2O multilayer regime. On the other hand, the simultaneous exposure of NaCl(100) to NO2 and H2O below [sim]45% RH rapidly generates numerous submicrometric NaNO3 tetrahedra on the NaCl(100) surface. The dramatic increase of NaNO3 production in the presence of water vapour is explained by the formation of HNO3 and its easy reaction with the NaCl(100) surface. For RH above 45% and below 75%, the tetrahedra evolve to rhombohedral plates of supermicrometric size. The exposure of NaCl(100) to NO2/H2O mixtures under RH above 75% induces the coexistence of both solid-state NaNO3 and dissolved NO3- in droplets. Copyright © 2008 John Wiley & Sons, Ltd.
Surface-enhanced Raman scattering study of L-tryptophan
Surface-enhanced Raman scattering (SERS) spectra of tryptophan (Trp) were obtained. A unique SERS spectrum of Trp, corresponding to the most stable conformation and orientation on the metal surface, is observed after a stabilization period. The Trp molecules interact with the surface through both the carboxylate and amino groups; the aliphatic moiety is close to the surface. The pyrrole ring of the indole moiety is farther from the surface than the benzene fragment. The observed spectra vary depending on both the preparation of the silver colloid and the aggregation time. The interpretation of the experimental results is supported by theoretical treatment of the molecule on the silver surface. Copyright © 2008 John Wiley & Sons, Ltd.
Deposition of Ag nanoparticles on porous anodic alumina for surface enhanced Raman scattering substrate
Ag nanoparticles were exclusively deposited inside the pores of the porous anodic alumina (PAA) template through the deposition cycle including the incubation and the subsequent reduction of Ag(NH3). Both the density and size of the produced Ag nanoparticles increased as the deposition cycle number increased. A field-emission scanning electron microscopeand an ultraviolet-visible spectrometer were applied, respectively, to study the morphology and the extinction spectra of the Ag nanoparticles. The optimum deposition number was found from the scanning electron microscope (SEM) analysis. Surface enhanced Raman scattering (SERS) spectra of p-aminothiophenol recorded on the Ag-PAA substrates prepared under increasing number of deposition cycles, manifested an enlarging trend of peak intensity. A point-by-point SERS mapping of p-aminothiophenol on the Ag-PAA substrate was acquired to characterise the homogeneity of the substrate. Copyright © 2008 John Wiley & Sons, Ltd.
Laser-induced phase changes in olivine FePO4: a warning on characterizing LiFePO4-based cathodes with Raman spectroscopy
Raman spectroscopy is an excellent technique for probing lithium intercalation reactions of many diverse lithium ion battery electrode materials. The technique is especially useful for probing LiFePO4-based cathodes because the intramolecular vibrational modes of the PO43- anions yield intense bands in the Raman spectrum, which are sensitive to the presence of Li+ ions. However, the high power lasers typically used in Raman spectroscopy can induce phase transitions in solid-state materials. These phase transitions may appear as changes in the spectroscopic data and could lead to erroneous conclusions concerning the delithiation mechanism of LiFePO4. Therefore, we examine the effect of exposing olivine FePO4 to a range of power settings of a 532-nm laser. Laser power settings higher than 1.3 W/mm2 are sufficient to destroy the FePO4 crystal structure and result in the formation of disordered FePO4. After the laser is turned off, the amorphous FePO4 compound crystallizes in the electrochemically inactive [alpha]-FePO4 phase. The present experimental results strongly suggest that the power setting of the excitation laser should be carefully controlled when using Raman spectroscopy to characterize fundamental lithium ion intercalation processes of olivine materials. In addition, Raman spectra of the amorphous intermediate might provide insight into the [alpha]-FePO4 to olivine FePO4 phase transition that is known to occur at temperatures higher than 450 °C. Copyright © 2008 John Wiley & Sons, Ltd.
UV resonance Raman spectroscopy probes the localization of tryptophan-containing antimicrobial peptides in lipid vesicles
In this work we employed UV resonance Raman spectroscopy with 229 nm excitation to study two tryptophan-containing antimicrobial peptides with a broad-spectrum activity against Gram-positive and Gram-negative bacteria: lactoferricin B (LfB, RRWQWRMKKLG) and pEM-2 (KKWRWWLKALAKK). UV resonance Raman spectra of both peptides are dominated by tryptophan bands. Raman spectra of LfB and pEM-2 in D2O and 2,2,2-trifluoro ethanol (TFE) have been measured and used to identify the hydrogen-bond strength marker bands W6 and W17. The tryptophan doublet, W7, at 1340 and 1360 cm-1 was used to detect an increase in the hydrophobicity of Trp environment in TFE. The spectra of LfB in complex with model cell membranes composed of zwitterionic dipalmitoylglycero-phosphocholine (DPPC) or anionic dipalmitoyglycero-phosphoglycerol (DPPG) lipid vesicles revealed a more hydrophobic Trp environment in DPPG, suggesting stronger interactions between the cationic peptide and anionic model cell membrane. Copyright © 2008 John Wiley & Sons, Ltd.
Investigation on microstructures of MnSix thin films by Raman spectroscopy
In this paper, Raman spectroscopy is used to study the microstructures of MnSix thin films annealed at different temperatures. Two phases of Mn silicides, MnSi1.73 and MnSi, are identified, and their Raman spectra are reported. Each phase of Mn silicides shows a set of three well-defined peaks at about 300 cm-1 in the spectrum, which could be used as fingerprints in identifying the formation of the Mn silicides. Compared with conventional X-ray diffraction method, Raman spectroscopy is found to be more sensitive to investigate the microstructures of Mn silicides, especially at the initial stage of formation of the Mn silicides. Copyright © 2008 John Wiley & Sons, Ltd.
Antioxidant phenolic esters with potential anticancer activity: solution equilibria studied by Raman spectroscopy
The solution Raman pattern of a series of structurally related hydroxycinnamic and hydroxybenzoicesters (caffeates and gallates) with potential antioxidant/anticancer activity was studied, for different biologically significant concentrations. The spectra were assigned with the help of theoretical calculations in the light of previously reported experimental data for these compounds in the solid state. Evidence of the formation of dimeric entities in solution, via (C)[double bond]O[single bond (dotted line)]H(O) and/or (C)[double bond]O[single bond (dotted line)]H(C) intermolecular hydrogen bonds, was obtained. The dimer-to-monomer equilibrium, which influences the antioxidant activity of this kind of systems, was monitored through Raman titration experiments. Copyright © 2008 John Wiley & Sons, Ltd.
Experimental study of the vibrational spectra of (CH3)3GeBr supported by DFT calculations
The infrared and Raman spectra of bromotrimethylgermane (BTMG) were recorded afresh to complete the assignment of its vibrational spectra. The vibrational spectrum of BTMG has been predicted from hybrid density functional theory calculations (B3LYP) with several basis sets. The resulting harmonic wavenumbers were scaled by Pulay's scaled quantum mechanical (SQM) and the wavenumber-linear scaling (WLS) methods to obtain accurate force fields which could aid in the vibrational assignment. Low-temperature infrared techniques together with Fourier self-deconvolution (FSD) on the Raman spectrum were used to improve the resolution of the spectra for the modes that could not be observed before. An SQM analysis was carried out to obtain the valence force constants and a set of scale factors that best reproduced the experimental data. Copyright © 2008 John Wiley & Sons, Ltd.
High-pressure Brillouin study of the elastic properties of rare-gas solid xenon at pressures up to 45 GPa
The pressure dependences of three adiabatic elastic constants, adiabatic bulk modulus, refractive index, and elastic anisotropy, as well as Cauchy deviation of fcc solid Xe have been determined up to 10 GPa at 296 K by high-pressure Brillouin scattering spectroscopy. The characteristics of elastic properties at high pressure of rare-gas solid Xe are investigated by comparison with the previous studies on Ne, Ar, and Kr. Above 10 GPa, the occurrence of splitting in the Brillouin signals and the direction dependence of acoustic velocities for solid Xe clearly show partial phase transformation to the hcp structure reported by the previous X-ray diffraction and Raman scattering studies. The shear elastic modulus in the hcp phase of solid Xe has also been estimated at pressures up to 45 GPa by using the pressure dependence of the Raman wavenumber shift for the E2g mode. Copyright © 2008 John Wiley & Sons, Ltd.
Molecular dynamics study of the vibrational pattern of ring structures in the Raman spectra of vitreous silica
Raman scattering spectra of silica glass models were studied by means of molecular dynamics computer simulation. The study principally aimed at the inspection of the assignment of the defect bands of the Raman spectra of a-SiO2 proposed by Galeener and co-workers (Galeener FL, Barrio RA, Martinez E, Elliott RJ. Phys. Rev. Lett. 1984; 53: 2429). The results of the study have shown that the D2 peak at 606 cm-1 can probably be related to the presence of three-membered rings in a-SiO2, whereas the D1 feature at 495 cm-1 correlates with the presence of both three- and four-membered rings, and can therefore, be used for structural characterisation of silica glasses only with care. Copyright © 2008 John Wiley & Sons, Ltd.
An analytical form for the Raman shift dependence on size of nanocrystals
An analytical form of the Raman shift dependence on the size of nanocrystals is presented. On the basis of the hard confinement model, this form describes the deviations from Raman shifts in infinite crystals as [Delta][omega] = [pi]2A[1 - exp(-[eta])]/12x2[eta]2, where [eta] = L/12ax and x = (A/[Gamma]0)1/2, L standing for the crystal size, [Gamma]0 for the intrinsic band linewidth, a for the lattice parameter and A for a suitable phonon curve parameter. It works in those cases where the average phonon curve shows a quadratic dependence on the phonon quasi-momentum in the range of interest. Copyright © 2008 John Wiley & Sons, Ltd.
Micro-Raman spectroscopic characterization of a tunable electrochromic device for application in smart windows
An asymmetric electrochromic (EC) device based on an active EC tungsten oxide-titanium oxide (WO3-TiO2) layer was constructed. The EC active layer consisted predominantly of monoclinic WO3 nanocrystallites with a minor additional component of hexagonal WO3 and amorphous TiO2. Detailed micro-Raman spectroscopic studies of the intercalation and deintercalation of lithium in the EC active layer of the EC device as a function of the applied voltage were performed. Three significant structural stages occur upon intercalating Li into the WO3-TiO2 layer when coloration potentials of 1.0, 1.5, 2.0, and 3.0 V are applied to the EC device. In the first stage (applied potential of 1.0 V), the m-Lix WO3 phase is retained. In the second stage, (applied potential of 1.5 and 2.0 V) the m-Lix WO3 transforms to a tetragonal phase. In the third stage, (applied potential of 3.0 V) the Raman spectrum exhibits no spectral bands, showing that Lix WO3 has attained the highest-symmetry cubic phase. This phase sequence is confirmed by the X-ray diffraction (XRD) measurement. These phase transitions can be reversed and, upon complete deintercalation, m-WO3 with traces of h-WO3 is recovered. Optical transmission studies were performed in conjunction with Raman and XRD studies. A shift of the optical transmittance peak position from 639 to 466 nm and reduction in the width of the transmittance curve with increasing applied potential opens up the possibility of smart window applications for the nanocrystalline WO3-based EC device. Copyright © 2008 John Wiley & Sons, Ltd.
Experimental and theoretical study of the structure and vibrational spectra of valpromide, C7H15CONH2
In this work, we present results of the conformational and vibrational properties of valpromide (Vpd), an amide with antiepileptic activity, studied by IR and Raman spectroscopy at 300 and 77 K, and 300 K, respectively. Experimental data are compared against ab initio calculations performed at B3LYP level with the inclusion of solvatation effects.Experimental results, reinforced by theoretical calculations, point out that Vpd has three conformers on the potential energy surface, with different structures that can be identified in the C[double bond]O and NH spectral regions. These conformers are defined by different angular arrays of the dihedral angles formed with the C[double bond]O, C[bond]N and C[lang][bond]H, C[bond]C of the aliphatic chain bonds.The existence of different conformations and structures are discussed on the basis of results derived from electronic localization function (ELF) and natural orbital bond (NBO) analysis. Copyright © 2008 John Wiley & Sons, Ltd.
Raman spectroscopic study of the selenite mineral: ahlfeldite, NiSeO3·2H2O
Raman spectroscopy has been used to study the selenite mineral ahlfeldite. A comparison is made with the Raman spectra of chalcomenite, cobaltomenite and clinochalcomenite. Selenite minerals are characterised by the position of the symmetric stretching mode which is observed at higher wavenumbers than the anti-symmetric stretching mode. The selenite ion has C3v symmetry and four modes, 2A1 and 2E. These modes are observed at 813, 472 cm-1 (A1) and 685, 710, 727 and 367 and 396 cm-1 (E). Bands assigned to the water stretching vibrations are observed for ahlfeldite at 3385 cm-1, for chalcomenite at 2953, 3184 and 3506 cm-1 and for clinochalcomenite at 2909, 3193 and 3507 cm-1. A comparison of the Raman spectra of chalcomenite, clinochalcomenite and cobaltomenite is made. The position of these bands enabled hydrogen bond distances in the selenite structure to be estimated. Hydrogen bond distances for ahlfeldite, chalcomenite and clinochalcomenite were determined to be similar. Copyright © 2008 John Wiley & Sons, Ltd.
Photoinduced electron transfer in glucose oxidase: a picosecond time-resolved ultraviolet resonance Raman study
Picosecond time-resolved ultraviolet resonance Raman (UVRR) spectroscopy has been applied to photoinduced electron transfer (ET) of glucose oxidase (GOD). In this study, we succeeded in directly observing changes in the aromatic amino acid residues in the photoinduced ET of GOD for the first time. UVRR spectra excited at 226 nm showed bands from Trp and Tyr residues. An intensity decrease of the Trp UVRR bands and the appearance of the UVRR bands attributable to Trp[bull]+ were observed in the time-resolved spectra. In the time-resolved UVRR spectra excited at 240 nm, the intensity decrease of the flavin adenine dinucleotide (FAD) bands was also observed on the same time scale. These results showed that the Trp residue(s) serves as an electron donor to excited-state FAD in the photoinduced ET of GOD. The comparison of the temporal changes of the Trp and FAD band intensities suggested that the ET from the Trp residue(s) to the FAD occurs with a time constant of [sim]1.5 ps. Copyright © 2008 John Wiley & Sons, Ltd.
Preparation and SERS study of triangular silver nanoparticle self-assembled films
We report a novel type of self-assembly of triangular silver nanoparticles onto a quartzose substrate with a monolayer of poly(diallyldimethylammonium chloride). Attractive electrostatic interactions between the negatively charged nanoparticles and the positively charged polyelectrolyte are responsible for the self-assembly. Surface morphology and optical properties of the triangular, silver nanoparticle self-assembly film were studied by atomic force microscopy (AFM) and ultraviolet-visible (UV-vis) spectroscopy, and then compared with those of the spherical silver nanoparticle self-assembly film. It was found from the AFM measurement that most of the spherical and triangular silver nanoparticles were assembled directly onto the substrate rather than aggregated to each other. The UV-vis spectrum of the triangular, silver nanoparticle self-assembled film is quite different from that of the colloid of silver nanoparticles. A peak at 697 nm assigned to the in-plane dipole plasmon resonance shows a blue shift by 55 nm after the triangular silver nanoparticles are immobilized onto the substrate. The triangular, silver nanoparticle self-assembly film can be used as a surface-enhanced Raman scattering (SERS) substrate, and Rhodamine 6G as a Raman probe to evaluate its enhancement ability. It was found that the enhancement ability of the triangular, silver nanoparticle film is remarkable but somewhat lower than that of the spherical silver nanoparticle film. The reason for this is discussed from the point of electromagnetic mechanism and chemical mechanism. Copyright © 2008 John Wiley & Sons, Ltd.
Micro-Raman spectroscopy and SEM/EDX applied to improve the zircon fission track method used for dating geological formations
The zircon mineral is widely studied in geochronology. In the case of the fission track method (FTM), the age is determined by the density of fission tracks at the zircon surface, which can be observed with an optical microscope after an appropriate chemical treatment (etching). The etching must be isotropic at the zircon grain surface to be used in the FTM, which leads those zircon grains whose etching is anisotropic to be discarded. The only reason for this discarding is the nonuniform morphology of the surface grain seen by optical microscopy, that is, no further physicochemical analysis is performed. In this work, combining micro-Raman and scanning electron microscopy (SEM) to study the etching anisotropy, it was shown that zircon grains that present at least one area at the surface where the density of fission track is uniform can be used in the FTM. The micro-Raman showed characteristic spectra of the standard zircon sample either from the areas where there are tracks or from where there are not. The only difference found was in the Raman bandwidths, which were broader for the areas with higher density of fission tracks. This suggests simply a decrease in the relative percentage of the crystalline/amorphous phases at these areas. The SEM/energy dispersive spectrometry (EDX) showed that there were no significant differences in the principal chemical composition at the areas with and without fission tracks. Copyright © 2008 John Wiley & Sons, Ltd.
Raman spectroscopic study of the tellurite minerals: graemite CuTeO3·H2O and teineite CuTeO3·2H2O
Tellurites may be subdivided according to formula and structure. There are five groups based upon the formulae (a) A(XO3), (b) A(XO3)·xH2O, (c) A2(XO3)3·xH2O, (d) A2(X2O5) and (e) A(X3O8). Raman spectroscopy has been used to study the tellurite minerals teineite and graemite; both contain water as an essential element of their stability. The tellurite ion should show a maximum of six bands. The free tellurite ion will have C3v symmetry and four modes, 2A1 and 2 E.Raman bands for teineite at 739 and 778 cm-1 and for graemite at 768 and 793 cm-1 are assigned to the [nu]1 (TeO3)2- symmetric stretching mode while bands at 667 and 701 cm-1 for teineite and 676 and 708 cm-1 for graemite are attributed to the [nu]3 (TeO3)2- antisymmetric stretching mode. The intense Raman band at 509 cm-1 for both teineite and graemite is assigned to the water librational mode. Raman bands for teineite at 318 and 347 cm-1 are assigned to the (TeO3)2-[nu]2(A1) bending mode and the two bands for teineite at 384 and 458 cm-1 may be assigned to the (TeO3)2-[nu]4(E) bending mode. Prominent Raman bands, observed at 2286, 2854, 3040 and 3495 cm-1, are attributed to OH stretching vibrations. The values for these OH stretching vibrations provide hydrogen bond distances of 2.550(6) Å (2341 cm-1), 2.610(3) Å (2796 cm-1) and 2.623(2) Å (2870 cm-1) which are comparatively short for secondary minerals. Copyright © 2008 John Wiley & Sons, Ltd.
Optical probing and imaging of live cells using SERS labels
During surface-enhanced Raman scattering (SERS), molecules exhibit a significant increase in their Raman signals when attached, or in very close vicinity, to gold or silver nanostructures. This effect is exploited as the basis of a new class of optical labels. Here we demonstrate robust and sensitive SERS labels as probes for imaging live cells. These hybrid labels consist of gold nanoparticles with Rose Bengal or Crystal Violet attached as reporter molecules. These new labels are stable and nontoxic, do not suffer from photobleaching, and can be excited at any excitation wavelength, even in the near infrared. SERS labels can be detected and imaged through the specific Raman signatures of the reporters. In addition, surface-enhanced Raman spectroscopy in the local optical fields of the gold nanoparticles also provides sensitive information on the immediate molecular environment of the label in the cell and allows imaging of the native constituents of the cell. This is demonstrated by images based on a characteristic Raman line of the reporter as well as by displaying lipids based on the SERS signal of the C[bond]H deformation/bending modes at [sim]1470 cm-1. Copyright © 2008 John Wiley & Sons, Ltd.
A study of the effect of JB particles on Saccharomyces cerevisiae (yeast) cells by Raman spectroscopy
The mechanism of interaction of particulate matter with living system is not completely understood. Evaluation of the effect of particulate Indian traditional medicine JB(JB) on Saccharomyces cerevisiae (yeast) cells is the major focus of the present study. In India, JB is considered as a rejuvenating medicine and used for the treatment of diseases such as diabetes and age-related eye diseases, as well as a health promoting tonic by the traditional practitioners. In presence of JB, higher growth has been observed at the late stationary growth phase of yeast. Ultra-structure analysis using transmission electron microscopy (TEM) has shown that JB-treated yeast cells have better morphology over control in the late stationary growth phase. In this investigation, cellular response from yeast cells after interaction with JB particles was measured using Raman spectroscopy. Raman spectroscopy - a noninvasive tool to distinguish between particle-treated and untreated cells - revealed that treatment with JB is able to slow the degradation of cellular components (e.g. DNA, proteins and lipids) with the aging of yeast cells. Copyright © 2008 John Wiley & Sons, Ltd.
Raman spectroscopic study of the uranyl tellurite mineral moctezumite PbUO2(TeO3)2
The uranyl tellurite mineral moctezumite, Pb(UO2)(TeO3)2, was studied by Raman spectroscopy and complemented with infrared spectroscopy. The presence of the stretching and bending vibrations of uranyl (UO2)2+ and tellurite (TeO3)2- ions was inferred, and the observed bands were assigned to uranyl and tellurite units vibrations. U[bond]O bond lengths calculated from the spectra with two empirical relations are close to those inferred from the X-ray single-crystal structure of moctezumite. Copyright © 2008 John Wiley & Sons, Ltd.
Raman spectroscopic study of the selenite mineral mandarinoite Fe2Se3O9·6H2O
Selenites and tellurites may be subdivided according to formula and structure. There are five groups, based upon the formulae (a) A(XO3), (b) A(XO3·) xH2O, (c) A2(XO3)3·xH2O, (d) A2(X2O5) and (e) A(X3O8). Of the selenites, molybdomenite is an example of type (a); chalcomenite, clinochalcomenite, cobaltomenite and ahlfeldite are minerals of type (b); mandarinoite Fe2Se3O9·6H2O is an example of type (c). Raman spectroscopy has been used to characterise the mineral mandarinoite. The intense, sharp band at 814 cm-1 is assigned to the symmetric stretching (Se3O9)6- units. Three Raman bands observed at 695, 723 and 744 cm-1 are attributed to the [nu]3 (Se3O9)6- anti-symmetric stretching modes. Raman bands at 355, 398 and 474 cm-1 are assigned to the [nu]4 and [nu]2 bending modes. Raman bands are observed at 2796, 2926, 3046, 3189 and 3507 cm-1 and are assigned to OH stretching vibrations. The observation of multiple OH stretching vibrations suggests the non-equivalence of water in the mandarinoite structure. The use of the Libowitzky empirical function provides hydrogen bond distances of 2.633(9) Å (2926 cm-1), 2.660(0) Å (3046 cm-1), 2.700(0) Å (3189 cm-1) and 2.905(3) Å (3507 cm-1). The sharp, intense band at 3507 cm-1 may be due to hydroxyl units. It is probable that some of the selenite units have been replaced by hydroxyl units. Copyright © 2008 John Wiley & Sons, Ltd.
Pressure-induced phase transitions in L-leucine crystal
Raman spectra of a crystal of L-leucine, an essential amino acid, were obtained for pressures between 0 and 6 GPa. The results show anomalies at three pressure values, one between 0 and 0.46 GPa, another between 0.8 and 1.46 GPa, and a third at P [sim] 3.6 GPa. The first two anomalies are characterized by the disappearance of lattice modes (which can indicate occurrence of phase transitions), the appearance of several internal modes, or the splitting of modes of high wavenumbers. The changes of internal modes are related to CH and CH3 unit motions as well as hydrogen bonds, as can be inferred from the behavior of bands associated with CO2- moieties. The third anomaly is a discrete change of the slopes of the wavenumber versus pressure plots for most modes observed. Further, decompression to ambient pressure generates the original Raman spectrum, showing that the pressure-induced anomalies undergone by L-leucine crystals are reversible. Copyright © 2008 John Wiley & Sons, Ltd.
Electron-phonon coupling and vibrational modes contributing to linear electro-optic effect of the efficient NLO chromophore 4-(N,N-dimethylamino)-N-methyl-4[prime]-toluene sulfonate (DAST) from their vibrational spectra
The optimized geometry and structural features of the most prospective electro-optic crystal 4-(N,N-dimethylamino)-N-methyl-4[prime]-toluene sulfonate (DAST), and the vibrational spectral investigations have been comprehensively described with the near infrared Fourier transform (NIR FT) Raman and Fourier transform infrared (FT-IR) spectra supported by the density functional theoretical (DFT) computations to elucidate the contribution of vibrational modes to the linear electro-optic (LEO) effect. Mulliken population analysis and natural bond orbital (NBO) analysis have also been carried out to analyze the effects of intramolecular charge transfer (ICT), intramolecular hydrogen bonding and hyperconjugative interactions on the geometries. The influence of CT interaction between the phenyl ring and the dimethylamino group of the nonlinear optical (NLO) chromophore on the endocyclic and exocyclic angles, and the electronic effects such as hyperconjugation and back-donation on the methyl hydrogen atoms have been examined. The concurrent intense activation of Raman and IR activities of the effective conjugation vibrational coordinate, which significantly contributes to the LEO effect resulting from the strong electron-phonon (e/ph) coupling, has been analyzed in detail. The effects of frontier orbitals, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO), transition of electron density (ED) transfer and the influence of planarity in the stilbazolium ring on the first hyperpolarizability are also discussed. Copyright © 2008 John Wiley & Sons, Ltd.
Raman spectroscopic study of the mineral guilleminite Ba(UO2)3(SeO3)2(OH)4·3H2O
The Raman spectrum of the mineral guilleminite Ba[(UO2)3O2(SeO3)2](H2O)3 was studied and complemented by the infrared spectrum of this mineral. Both spectra were interpreted and compared with the spectra of marthozite, larisaite, haynesite and piretite, all of which should have the same phosphuranylite anion sheet topology. The presence of symmetrically distinct water molecules and hydrogen bonds was inferred from the spectra. This is in agreement with the crystal structural analysis of guilleminite. U[bond]O bond lengths in uranyl and O[bond]H···O hydrogen bond lengths were calculated from the Raman and/or infrared spectra of guilleminite. Copyright © 2008 John Wiley & Sons, Ltd.
Raman spectroscopic study of the uranyl selenite mineral demesmaekerite Pb2Cu5(UO2)2(SeO3)6(OH)6·2H2O
The Raman spectrum of the uranyl selenite mineral demesmaekerite was studied, complemented by the infrared spectrum and tentatively interpreted. The observed bands were attributed to the stretching and bending vibrations of (UO2)2+, (SeO3)2- and OH groupings. U[bond]O bond lengths in uranyl and O[bond]H···O hydrogen bond lengths were calculated from Raman and/or infrared spectra and compared with published data. Copyright © 2008 John Wiley & Sons, Ltd.
In situ nucleation and growth of silver nanoparticles in membrane materials: a controllable roughened SERS substrate with high reproducibility
A controllable roughened silver surface with high surface-enhanced Raman scattering (SERS) activity and high reproducibility has been developed in this study. This silver surface was prepared by silver nucleation in polyelectrolyte multilayers (PEMs) and silver-enlarged growth. First, the small Ag nuclei were synthesized by NaBH4 in situ reduction of Ag ions on a surface of PEMs. Then the small Ag nuclei formed were effectively enlarged by using a mixture of commercially available reagents named Li Silver. The optical properties and morphologies of the silver substrates have been investigated by ultraviolet-visible (UV-vis) spectroscopy and atomic force microscopy (AFM). The UV-vis and AFM results revealed that the small Ag nuclei separately appeared on the PEMs after NaBH4 in situ reduction. The size of the enlarged Ag nanoparticles can be easily controlled with the immersing cycle in Li Silver. 4-Mercaptopyridine (4-MPY) and Rhodamine 6G (R6G) have been used as Raman probes to evaluate the properties of the new SERS substrates. It has been found that the enhancement factor of R6G reached [sim]109 after treatment in Li Silver. Reproducibility has been investigated using the SERS signal intensity at 1094 cm-1 of 4-MPY. Signals collected over multiple spots within the same substrate resulted in a relative standard deviation (RSD) of 6.38%, while an RSD of 10.33% was measured in signals collected from different substrates. Copyright © 2008 John Wiley & Sons, Ltd.
Surface-enhanced Raman scattering of protoberberine alkaloids
Quaternary protoberberine alkaloids are a class of natural dyes characterized by bright colors ranging from yellow to orange. As they present a strong fluorescence emission, their analysis by Raman spectroscopy is limited to specific techniques such as Fourier transform (FT)-Raman and spectral shift Raman techniques such as shifted subtracted Raman difference spectroscopy (SSRDS) and shifted excitation Raman difference spectroscopy (SERDS). In a previous article, we successfully used surface-enhanced Raman scattering (SERS) in the analysis of the alkaloid dye berberine in an ancient textile. The examination of the Raman and SERS spectra of berberine in combination with density functional theory (DFT) calculations indicated a flat adsorption geometry of the molecule on the Ag surface. In this article we extend that work to the study of related protoberberine alkaloids, palmatine, jatrorrhizine, and coptisine. The same adsorption geometry as in berberine was deduced. We found that the four alkaloids, although minimally different in their chemical structures, could be differentiated by the position of marker bands. Those bands are the most enhanced ones in the SERS spectra, which appear in the 700-800 cm-1 region. Copyright © 2008 John Wiley & Sons, Ltd.
Ultrafast vibrational dynamics and solvation complexes of methyl acetate in methanol studied by sub-picosecond infrared spectroscopy
The vibrational dynamics of the CO stretching mode of methyl acetate (MA) in methanol was studied by time-resolved infrared (IR) pump-probe spectroscopy. The vibrational energy relaxation (VER) process includes two components with time constants of 1.3 ± 0.1 and 4.0 ± 0.2 ps. These components result from the vibrational excitations of the hydrogen-bonding complex of MA with one methanol and the MA monomer, respectively. The difference in the VER time is explained by the increase of the vibrational density of states (VDOS) by the intermolecular hydrogen bond. The time constants and the decay-associated spectra are almost identical between the CH3OH and the CH3OD solutions. The vibrational modes localized in the intramolecular OH/OD bond of the solvent methanol have little effect on the vibrational dynamics of MA. Copyright © 2008 John Wiley & Sons, Ltd.
Investigation of an unnatural amino acid for use as a resonance Raman probe: detection limits and solvent and temperature dependence of the [nu]C[triple bond] N band of 4-cyanophenylalanine
The incorporation of unnatural amino acids into proteins that act as spectroscopic probes can be used to study protein structure and function. One such probe is 4-cyanophenylalanine (PheCN), the nitrile group of which has a stretching mode that occurs in a region of the vibrational spectrum that does not contain any modes from the usual components of proteins and whose wavenumber is sensitive to the polarity of its environment. In this work we evaluate the potential of UV resonance Raman spectroscopy for monitoring the sensitivity of the [nu]C[triple bond] N band of PheCN incorporated into proteins to the protein environment. Measurement of the Raman excitation profile of PheCN showed that considerable resonance enhancement of the Raman signal was obtained using UV excitation and the best signal-to-noise ratios were obtained with excitation wavelengths of 229 and 244 nm. The detection limit for PheCN in proteins was [sim]10 µM, approximately 100-fold lower than the concentrations used in infrared (IR) studies, which increases the potential applications of PheCN as a vibrational probe. The wavenumber of the PheCN [nu]C[triple bond] N band was strongly dependent on the polarity of its environment; when the solvent was changed from H2O to tetrahydrofuran (THF) it decreased by 8 cm-1. The presence of liposomes caused a similar though smaller decrease in [nu]C[triple bond]N for a peptide, mastoparan X, modified to contain PheCN. The selectivity and sensitivity of resonance Raman spectroscopy of PheCN mean that it can be a useful probe of intra- and intermolecular interactions in proteins and opens the door to its application in the study of protein dynamics using time-resolved resonance Raman spectroscopy. Copyright © 2008 John Wiley & Sons, Ltd.
Density functional theory calculations and vibrational spectra of 3,5 dichloro hydroxy benzaldehyde and 2,4 dichloro benzaldehyde
The solid-phase Fourier transform infrared (FT-IR) and FT-Raman spectra of 3,5 dichloro hydroxy benzaldehyde (DHB) and 2,4 dichloro benzaldehyde (DB) have been recorded in the regions 4000-400 and 4000-0 cm-1, respectively. Theoretical information on the optimized geometry, harmonic vibrational wavenumbers as well as infrared and Raman intensities were obtained by means of density functional theory (DFT) using standard B3LYP/6-31G** level. This information was used in the assignment of the various fundamentals. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. Copyright © 2008 John Wiley & Sons, Ltd.
The vibrational assignment of phenanthridine molecule based on normal coordinate analysis and DFT
A complete vibrational assignment of phenanthridine C13NH9 has been presented. The infrared (IR) and the Raman spectra of the molecule are analyzed with the help of theoretical prediction of the normal vibrational wavenumbers estimated from normal coordinate analysis (NCA) and density functional theory (DFT) calculations. A general valence force field (GVFF) including 31 parameters (13 diagonal and 18 off-diagonal) reproduces satisfactorily the in-plane vibrational signatures of the aforesaid molecule and as well as those for the other related hydrocarbons [phenanthrene and benzo(c)cinnoline]. The bivariate and multivariate data analysis reveals that calculated wavenumbers using GVFF are more accurate than the DFT result. However, DFT yields the relative Raman intensities, which are in good agreement with the experimental ones. The decomposition of the normal mode frequencies into those related to different internal coordinates is also discussed. Copyright © 2008 John Wiley & Sons, Ltd.
Vibrational spectroscopic studies and DFT calculations of 4-fluoro-N-(2-hydroxy-4-nitrophenyl)benzamide
Fourier transform infrared (FT-IR) and FT-Raman spectra of 4-fluoro-N-(2-hydroxy-4-nitrophenyl)benzamide were recorded and analyzed. The vibrational wavenumbers and corresponding vibrational assignments were examined theoretically using the Gaussian03 set of quantum chemistry codes. The red-shift of the NH-stretching wavenumber in the infrared (IR) spectrum from the computed wavenumber indicates the weakening of the NH bond resulting in proton transfer to the neighboring oxygen atom. The simultaneous IR and Raman activation of the C[double bond]O-stretching mode gives the charge transfer interaction through a [pi]-conjugated path. Copyright © 2008 John Wiley & Sons, Ltd.
Out-of-plane deformations of the heme group in different ferrocytochrome c proteins probed by resonance Raman spectroscopy
We measured the low-wavenumber polarized resonance Raman spectra of horse heart (hhc), chicken (chc) and yeastC102T (yc) ferrocytochromes c with Soret excitation. We examined the out-of-plane (oop) deformations of the heme groups by virtue of relative intensities and depolarization ratios of a variety of oop and in-plane (ip) Raman active bands. Analysis of relative Raman intensities shows differences in deviation from planarity of the heme groups of yeast, horse heart and chicken cytochromes c. The heme groups in cytochrome c proteins have been shown by normal coordinate static deformation (NSD) analysis from crystal structures to exhibit a dominant ruffling (B1u) deformation. As a consequence the B1u modes, [gamma]10 - [gamma]12, become resonance Raman active. We used normalized Raman intensity ratios and depolarization ratios of oop Raman active modes, whose intensities are attributable to specific nonplanar deformations, to estimate and compare their Franck-Condon-type and Jahn-Teller-type coupling magnitudes for horse heart, chicken and yeast ferrocytochrome c at neutral pH. These coupling magnitudes allow for a quantitative comparison of oop deformations between individual heme groups. Chicken ferrocytochrome was found to have the largest ruffling deformation of the three investigated proteins, followed by horse heart and yeast cytochrome c. The heme group of the former is slightly more ruffled than the corresponding active site of the latter, while saddling in both proteins is substantially larger than in chicken ferrocytochrome c. The Raman data are sensitive enough to allow a comparison of lesser deformations. Doming, which is a kinetic coordinate in many heme proteins, is largest in chicken and smallest in yeast cytochrome c. Waving is largest in yeast, followed by horse heart and chicken cytochrome c. Propellering deformations could be compared for chicken and horse heart cytochrome c and were found to be substantially larger in the latter. A comparison with heme deformations obtained from X-ray structures (for horse heart and yeast cytochrome c) and from molecular dynamics simulations (MDS) (performed for all three proteins) yields some agreement with the main ruffling and saddling deformations derived from the crystal structures, whereas the heme conformations produced by MDS seem to account better for smaller deformations like doming and propellering. The present study demonstrates the usefulness of resonance Raman spectroscopy for the analysis of nonplanar deformations in heme proteins. Copyright © 2008 John Wiley & Sons, Ltd.
Resonance Raman study of He+ ion implanted nanostructured ZnS
ZnS nanocrytsals of size [sim]2.5 nm were prepared by chemical precipitation technique. Pressed pellets of nanostructured ZnS were implanted with He+ ions at doses of 5 × 1014, 1 × 1015 and 5 × 1015 ions/cm2. Raman spectra of both unimplanted and He+ ion implanted samples were recorded with ultraviolet (UV) excitation. LO, 2LO, 2TO, (LO + TA) and (2TO - TA) modes of ZnS were observed in the resonance Raman spectra of the unimplanted nanostructured ZnS samples. In addition, a surface mode was observed at 294 cm-1. With the implantation of He+ ions, the 2TO mode disappeared and 2LO mode became prominent and this observation was attributed to the decrease in band gap of ZnS nanocrytsals due to ion implantation. The exciton-LO phonon coupling strength was determined from the intensity ratio of 2LO to LO modes and it was observed that the exciton-LO phonon coupling strength increases with increase in implantation dose. In the present work, we report for the first time the observation of 2TO mode in the resonance Raman spectrum of nanostructured ZnS and also the modification of exciton-LO phonon coupling strength of semiconductor nanoparticles by ion implantation. Copyright © 2008 John Wiley & Sons, Ltd.
Pseudopolymorphic transitions of niclosamide monitored by Raman spectroscopy
Niclosamide suffers pseudopolymorphic transformations when exposed to different ambient conditions, which can lead to changes in its bioavailability. In this study, the kinetics of the pseudopolymorphic transitions of niclosamide crystals are characterized. FT-Raman spectroscopy is used to quantify the anhydrate and hydrate forms of niclosamide crystals, mostly because of its high sensitivity to the strong intermolecular interactions present in these systems. The samples are exposed to well-characterized relative humidity (RH) conditions during different periods of time and both water diffusion and polymorphic changes are monitored from the corresponding changes observed in the vibrational spectra. Both hydration and dehydration were found to be single-step processes, with a half-life time of ca. 142 and 63 h, respectively, at 24 °C. Copyright © 2008 John Wiley & Sons, Ltd.
Structural conformations and electronic interactions of the natural product, oroxylin: a vibrational spectroscopic study
The oroxylin, 5,7-dihydroxy 6-methoxy flavone is a potent natural product extracted from 'Vitex peduncularis'. Density functional theory (DFT) at B3LYP/6-311G(d,p) level has been used to compute energies of different conformers of oroxylin to find out their stability, the optimized geometry of the most stable conformer and its vibrational spectrum. The conformer ORLN-1 with torsion angles 0, 180, 180 and 0 degrees, respectively, for H13[bond]O12[bond]C6[bond]C5, H14[bond]O10[bond]C4[bond]C5, H13[bond]O12[bond]C6[bond]C5 and H14[bond]O10[bond]C4[bond]C5 is found to be most stable. The optimized geometry reveals that the dihedral angle [phiv] between phenyl ring B and the chrome part of the molecule in - 19.21° is due to the repulsive force due to steric interaction between the ortho-hydrogen atom H29 of the B ring and H18 of the ring C (H29·H18 = 2.198 Å). A vibrational analysis based on the near-infrared Fourier transform(NIR-FT) Raman, Fourier transform-infrared (FT-IR) and the computed spectrum reveals that the methoxy group is influenced by the oxygen lone pair-aryl pz orbital by back donation. Hence the stretching and bending vibrational modes of the methoxy group possess the lowest wavenumber from the normal values of methyl group. The carbonyl stretching vibrations have been lowered due to conjugation and hydrogen bonding in the molecules. The intramolecular H-bonding and nonbonded intramolecular interactions shift the band position of O10[bond]H14 and O12[bond]H13 stretching modes, which is justified by DFT results. Copyright © 2008 John Wiley & Sons, Ltd.
Mechanisms of drug-DNA recognition distinguished by Raman spectroscopy, ,
The highly chromophoric drugs, ethidium bromide (EtBr), 9-aminoacridine (9AA) and proflavine (PF) (3,6-diaminoacridine) bind to DNA by insertion of a polycyclic aromatic ring between adjacent base pairs of the double helix. Despite similar intercalative mechanisms, these drugs exhibit distinct DNA affinities and produce characteristic mutagenic effects. Complexes of the intercalants with small nucleotide fragments have been investigated by various methods, including X-ray crystallography. However, the structural impact of drug intercalation on a DNA molecule of genetic consequence has not yet been reported. Here, we employ near-infrared laser excitation (752 nm) and a DNA target of genomic size to obtain and compare Raman spectra of complexes of EtBr, 9AA and PF with DNA. Raman signatures of solution complexes have been analyzed by difference methods to reveal the specific structural changes induced at the drug/DNA intercalation sites. Perturbation of the DNA backbone geometry, as reflected in the Raman marker diagnostic of the phosphodiester group (800-880 cm-1), ranges from disruption of the B-form duplex in favor of either the A-form duplex, or separated strands, or a combination of altered DNA backbone geometries. The acridine intercalants, PF and 9AA, also perturb hydrogen-bonding interactions between the paired bases of duplex DNA, although in distinct ways. Conversely, base pairing is relatively unperturbed by ethidium intercalation. The results are discussed in relation to frameshift mutagenic activities of the intercalating drugs. Copyright © 2008 John Wiley & Sons, Ltd.
Raman spectroscopic study of the tellurite minerals: emmonsite Fe23+Te34+O9·2H2O and zemannite Mg0.5[Zn2+Fe3+(TeO3)3]4.5H2O
Raman spectroscopy has been used to study zemannite Mg0.5[Zn2+Fe3+(TeO3)3]4.5H2O and emmonsite Fe23+Te34+O9·2H2O. Raman bands for zemannite and emmonsite, observed at 740 and 650 cm-1 and at 764 and 788 cm-1, respectively, are attributed to the [nu]1 (TeO3)2- symmetric stretching mode. The splitting of the symmetric stretching mode for emmonsite is in harmony with the results of X-ray crystallography which shows three non-equivalent TeO3 units in the crystal structure. Two bands at 658 and 688 cm-1 are assigned to [nu]3 (TeO3)2- anti-symmetric stretching modes. Raman bands observed at 372 and 408 cm-1 for zemannite and 397 and 414 cm-1 for emmonsite are attributed to the (TeO3)2-[nu]2(A1) bending mode. The two Raman bands at 400 and 440 cm-1 for emmonsite are ascribed to the [nu]4(E) bending modes, while the band at 326 cm-1 is due to the [nu]2(A1) bending vibration. Copyright © 2008 John Wiley & Sons, Ltd.
Raman spectroscopic study of the selenite minerals - chalcomenite CuSeO3·2H2O, clinochalcomenite and cobaltomenite
Raman spectroscopy has been used to study the dimorphous selenite minerals chalcomenite, cobaltomenite and clinochalcomenite. Selenite minerals are characterised by the position of the symmetric stretching mode that is observed at higher wavenumbers than the anti-symmetric stretching mode. The selenite ion has C3v symmetry and four modes, 2A1 and 2E. These modes are observed at 813, 472 cm-1 (A1) and 685, 710, 727 and 367 and 396 cm-1 (E). Bands assigned to the water stretching vibrations are observed for chalcomenite at 2953, 3184 and 3506 cm-1 and for clinochalcomenite at 2909, 3193 and 3507 cm-1. A comparison of the Raman spectra of chalcomenite, clinochalcomenite and cobaltomenite is made. The position of these bands enabled hydrogen bond distances in the selenite structure to be estimated. Hydrogen bond distances for chalcomenite and clinochalmenite were determined to be similar. Copyright © 2008 John Wiley & Sons, Ltd.
Nanomechanics of single silkworm and spider fibres: a Raman and micro-mechanical in situ study of the conformation change with stress
The combination of micro-Raman spectroscopy and an advanced universal fibre tester (UFT) made it possible to probe at the nanoscale (through monitoring the modification of chemical bonds) the change in conformation ([alpha]-helix, [beta]-sheet, etc.), macromolecular fibroin chain orientation and coupling during the application of stress, quantitatively. Different single fibres of silkworms (Bombyx mori, Gonometa rufobrunea, Gonometa postica) and a spider (Nephila madagascariensis) were tested in a dry environment and compared with the behaviour of keratin fibre. As observed previously for single keratin fibres, a direct relationship is observed between nano- and micro-mechanical tensile behaviour. The phase transition plateau, well defined for some pristine B. mori fibres, disappears in degummed fibres, which indicates a structural modification and increasing disorder with chemical treatments. Stress-controlled micro-Raman analysis shows that a few modes involving CH2 and/or amide groups of [beta]-conformation chains undergo a wavenumber softening during the elastic behaviour ([sim]0-3%), although most of the modes are not affected. A different behaviour is observed for modes associated with 'ordered' and 'disordered' [beta]-sheets and helical chains. Larger softening is observed for lattice modes with increasing stress/strain, as expected. Structural changes and relationships with mechanical behaviour are discussed. Copyright © 2008 John Wiley & Sons, Ltd.
Surface-enhanced Raman scattering on colloid gels originated from low molecular weight gelator
Surface-enhanced Raman scattering (SERS) on silver and gold colloid gels formed by a low molecular weight organic gelator, bis-(S-phenylalanine) oxalyl amide, was obtained. Strong Raman signals dominate in the SERS spectra of hydrogels containing silver nanoparticles prepared by citrate and borohydride reduction methods, whereas broad bands of low intensity are detected in the spectra of gold colloid gels. Resemblance between Raman spectrum of the crystalline substance and the SERS spectra of the silver nanoparticle-hydrogel composites implies the electromagnetic nature of the signal enhancement. A change in Raman intensity of the benzene and amide II bands caused by an increase in temperature and concentration indicates that the gelling molecules are strongly attached through the benzene moieties to the metal nanoparticles while participating in gel formation by intermolecular hydrogen bonding between the adjacent oxalyl amide groups. Transmission electron microscopy reveals a dense gel structure in the close vicinity of the enhancing metal particles for both silver colloid gels. Copyright © 2008 John Wiley & Sons, Ltd.
NIR-FT Raman, FT-IR and surface-enhanced Raman scattering spectra, with theoretical simulations on chloramphenicol
Chloramphenicol (CLM), originally derived from the bacterium Streptomyces venezuelae, is an inhibitor of bacterial ribosomal peptidyl transferase activity. The near infrared Fourier transform (NIR-FT) Raman, surface-enhanced Raman spectroscopy (SERS) and Fourier transform infrared (FT-IR) spectral analyses of CLM, a potential antibacterial drug for the treatment of typhoid fever, were carried out along with density functional computations. The vibrational spectral analysis reveals that the CH2 asymmetric and symmetric stretching modes are shifted to higher wavenumbers than the computed values, owing to the electronic effects resulting from induction of methylene group with the adjacent electronegative atom. The lowering of C[double bond]O stretching wavenumber is due to the presence of the strong electronegative atom, nitrogen, attached to the carbonyl carbon, causing large degree of molecular [pi]-electron delocalization and redistribution of electrons, which weakens the C[double bond]O bond. The absence of a C[bond]H stretching vibration and the observed C[bond]H out-of-plane bending modes suggest that the CLM molecule may be adsorbed in a flat orientation with respect to the silver surface. Copyright © 2008 John Wiley & Sons, Ltd.
Three-state model for femtosecond broadband stimulated Raman scattering
Stimulated Raman scattering (SRS) is analyzed with a three-state model. Using a diagrammatic density-matrix formalism, SRS by a pair of Raman pump and probe pulses, with observation along the probe direction, is described principally by eight terms. The eight terms can be grouped into four sets, which are labeled as SRS or IRS (inverse Raman scattering): SRS(I), SRS(II), IRS(I), and IRS(II). Specializing to the case of femtosecond SRS (FSRS) by a picosecond (ps) Raman pump pulse and a femtosecond (fs) probe pulse, the spectra for the four sets of terms under off-resonance and resonance conditions were calculated. The results obtained can explain the FSRS experimental observations from a (decaying) stationary vibrational state, such as (1) high wavenumber resolution (determined by the narrow bandwidth Raman pump pulse) and high time resolution (determined by the fs probe pulse), (2) Stokes gain vs anti-Stokes loss in off-resonance FSRS, and (3) dispersive lineshapes in resonance FSRS. Copyright © 2008 John Wiley & Sons, Ltd.
The utilization of silver salts of aromatic thiols as core materials of SERS-based molecular sensors
Silver salts of aromatic thiols are one class of organic-inorganic heterostructured materials, showing peculiar photoreaction characteristics. When an argon ion laser is exposed to silver benzenethiolate (AgBT), for instance, its Raman spectrum changes over time, eventually becoming the same as the surface-enhanced Raman scattering (SERS) spectrum of benzenethiol on a roughened Ag substrate. AgBT and its analogs can thus be used as a core material of molecular sensors operating via SERS; we demonstrate this specifically, by monitoring the SERS peaks of BT, in which biotinylated AgBT selectively recognizes streptavidin molecules down to concentrations of 10-11 g ml-1 (i.e. [sim]0.2 pM). Since numerous silver thiolates can be used as the core material, multiple bioassays are readily accomplished using the present methodology. Copyright © 2008 John Wiley & Sons, Ltd.
