Stretching Modes (stretching + mode)

Distribution by Scientific Domains

Kinds of Stretching Modes

  • symmetric stretching mode


  • Selected Abstracts


    Crystal structures and spectroscopic characterization of chiral and racemic 4-phenyl-1,3-oxazolidin-2-one

    CRYSTAL RESEARCH AND TECHNOLOGY, Issue 4 2004
    S. Kitoh
    Abstract Crystal structures of (R)- and (rac)-4-phenyl-1,3-oxazolidin-2-one (4-POO) have been determined by X-ray diffraction and characterized by the solid state 13C NMR and IR spectra. Molecular geometries and intermolecular interactions in (R)- and (rac)-4-POO crystals are very similar to each other; 4-POO molecules are linked via the N-H,O intermolecular hydrogen bonds to form the chained structure. Chemical shifts of the solid state 13C NMR spectra are very similar to each other, whereas the 1H spin-lattice relaxation times (T1H) value for (R)-4-POO is five times as large as that for (rac)-4-POO, reflecting the more restricted mobility of the (R)-4-POO chain. Although both crystals contain an unique molecule in the asymmetric unit, a doublet feature is observed for the C=O stretching mode in the IR spectra of (R)- and (rac)-4-POO crystals. The frequency gap of the C=O bands are correlated with the strength of the dipole-dipole interactions between the neighboring C=O groups. 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim [source]


    The Influence of UV Irradiation on Ketonic Defect Emission in Fluorene-Based Copolymers,

    ADVANCED FUNCTIONAL MATERIALS, Issue 17 2008
    Horst Scheiber
    Abstract The influence of UV irradiation in inert atmosphere on the emission spectrum of fluorenone containing poly[9,9-bis(2-ethyl)hexylfluorene] (PF2/6) has been investigated by means of optical absorption, photoluminescence (PL) and Fourier transform infrared (FTIR) spectroscopy. It is shown that a substantial reduction of green emission arising from ketonic defect sites can be achieved by irradiation of thin films with UV light. This is found to be accompanied by partial cross-linking of the films. FTIR measurements show no reduction of the C=O stretching mode upon irradiation, and, moreover, the degree of cross-linking does not scale with the relative fluorenone content (0.1, 0.5, and 5%). Therefore, the reduced emission intensity in the green spectral region is rather associated with the occurrence of interruptions in the polymer backbone, which reduce the effective conjugation length and subsequently inhibit the energy transfer onto the ketonic defect sites. The found results enabled us to build organic light emitting devices (OLEDs) that can be structured by selective illumination of the emitting layer with an intense UV light source. This method allows for the fabrication of rather efficient (2000,cd,m,2 at 7,V) two-color OLEDs. [source]


    Hydrogen bonding interaction between 1,4-dioxane and water

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2010
    Ajay Chaudhari
    Abstract This work reports an interaction of 1,4-dioxane with one, two, and three water molecules using the density functional theory method at B3LYP/6-311++G* level. Different conformers were studied and the most stable conformer of 1,4-dioxane-(water)n (n = 1,3) complex has total energies ,384.1964038, ,460.6570694, and ,537.1032381 hartrees with one, two, and three water molecules, respectively. Corresponding binding energy (BE) for these three most stable structures is 6.23, 16.73, and 18.11 kcal/mol. The hydrogen bonding results in red shift in OO stretching and CC stretching modes of 1,4-dioxane for the most stable conformer of 1,4-dioxane with one, two, and three water molecules whereas there was a blue shift in CO symmetric stretching and CO asymmetric stretching modes of 1,4-dioxane. The hydrogen bonding results in large red shift in bending mode of water and large blue shift in symmetric stretching and asymmetric stretching mode of water. 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source]


    Infrared spectra of water molecule encapsulated inside fullerene studied by instantaneous vibrational analysis,

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2009
    Kiyoshi Yagi
    Abstract Instantaneous vibrational analysis (IVA) is proposed for computing the infrared spectrum of dynamically fluctuating system, and applied to a water molecule encapsulated into fullerene (H2O@C60). A molecular dynamics simulation is first carried out to generate an ensemble of configurations averaging the rotational and translational motion of H2O inside fullerene. At each configuration, instantaneous vibrational frequencies of the water molecule are computed by the vibrational configuration interaction method, which are then employed to construct the line-shape of the spectrum. The vibrational spectrum in the OH stretching region is computed at a temperature of 10 and 100 K based on a direct potential energy surface incorporating the electronic structure theory. It is found that the vibrational frequency of the symmetric stretching mode is blue-shifted compared to that of isolated water, whereas that of the asymmetric stretching mode exhibits no shift in average. The relation between IVA and instantaneous normal mode analysis is presented, and their performances are compared. 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source]


    Interfacial structure of poly(methyl methacrylate)/TiO2 nanocomposites prepared through photocatalytic polymerization

    JOURNAL OF APPLIED POLYMER SCIENCE, Issue 6 2008
    Jiao Wang
    Abstract Poly(methyl methacrylate)/TiO2 nanocomposites have been prepared by the polymerization with photoexcited TiO2 nanoparticles as initiator. To reveal the interfacial structure, the composites obtained are investigated by FTIR and XPS analysis. The bound PMMA displays triply split IR bands attributed to the carbonyl stretching mode, meanwhile great changes also occur in the IR range closely related to the conformation of PMMA. Based on the area of the nonassociated and associated PMMA carbonyl stretching peaks in the FTIR spectrum, it is calculated out that the bound PMMA is constituted of 70% repeating units in nonassociated state and 30% units associated to TiO2 inorganic nanoparticles. Moreover, XPS analysis show that Ti2p doublet of the composites shift to lower binding energy by 1.0 eV, indicating the interaction between Ti atoms of TiO2 and oxygen atoms of PMMA. According to the observation that the interaction involves both carboxyl and carbonyl groups of PMMA, a bidentate complex is approved. In addition, compared with the extracted PMMA, certain backbone chains of bound PMMA have to change their rotational conformations from gauche to trans so as to bond to the surface active centers at TiO2 nanoparticles. 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008 [source]


    Spectroscopic investigations and computational study of 2-[acetyl(4-bromophenyl)carbamoyl]-4-chlorophenyl acetate

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 6 2010
    C. Yohannan Panicker
    Abstract The Fourier transform Raman (FT-Raman) and Fourier transform infrared (FT-IR) spectra of 2-[acetyl(4-bromophenyl)carbamoyl]-4-chlorophenyl acetate were studied. The vibrational wavenumbers were examined theoretically using the Gaussian03 set of quantum chemistry codes, and the normal modes were assigned by potential energy distribution (PED) calculations. The simultaneous Raman and infrared (IR) activations of the CO stretching mode in the carbamoyl moiety show a charge transfer interaction through a ,-conjugated path. From the optimized structure, it is clear that the hydrogen bonding decreases the double bond character of the CO bond and increases the double bond character of the CN bonds. The first hyperpolarizability and predicted IR intensities are reported. The calculated first hyperpolarizability is comparable with the reported values of similar structures, which makes this compound an attractive object for future studies of nonlinear optics. Optimized geometrical parameters of the compound are in agreement with similar reported structures. Copyright 2009 John Wiley & Sons, Ltd. [source]


    Raman spectroscopic study of the phosphate mineral churchite-(Y) YPO42H2O

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 2 2010
    Ray L. Frost
    Abstract Raman spectroscopy has been used to study the rare-earth mineral churchite-(Y) of formula (Y,REE)(PO4) 2H2O, where rare-earth element (REE) is a rare-earth element. The mineral contains yttrium and, depending on the locality, a range of rare-earth metals. The Raman spectra of two churchite-(Y) mineral samples from Jchymov and Medv,dn in the Czech Republic were compared with the Raman spectra of churchite-(Y) downloaded from the RRUFF data base. The Raman spectra of churchite-(Y) are characterized by an intense sharp band at 975 cm,1 assigned to the ,1 (PO43,) symmetric stretching mode. A lower intensity band observed at around 1065 cm,1 is attributed to the ,3 (PO43,) antisymmetric stretching mode. The (PO43,) bending modes are observed at 497 cm,1 (,2) and 563 cm,1 (,4). Some small differences in the band positions between the four churchite-(Y) samples from four different localities were found. These differences may be ascribed to the different compositions of the churchite-(Y) minerals. Copyright 2009 John Wiley & Sons, Ltd. [source]


    Raman spectroscopic study of the magnesium-carbonate minerals,artinite and dypingite

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 8 2009
    Ray L. Frost
    Abstract Magnesium minerals are important in the understanding of the concept of geosequestration. The two hydrated hydroxy magnesium-carbonate minerals artinite and dypingite were studied by Raman spectroscopy. Intense bands are observed at 1092 cm,1 for artinite and at 1120 cm,1 for dypingite, attributed ,1 symmetric stretching mode of CO32,. The ,3 antisymmetric stretching vibrations of CO32, are extremely weak and are observed at 1412 and 1465 cm,1 for artinite and at 1366, 1447 and 1524 cm,1 for dypingite. Very weak Raman bands at 790 cm,1 for artinite and 800 cm,1 for dypingite are assigned to the CO32,,2 out-of-plane bend. The Raman band at 700 cm,1 of artinite and at 725 and 760 cm,1 of dypingite are ascribed to CO32,,2 in-plane bending mode. The Raman spectrum of artinite in the OH stretching region is characterised by two sets of bands: (1) an intense band at 3593 cm,1 assigned to the MgOH stretching vibrations and (2) the broad profile of overlapping bands at 3030 and 3229 cm,1 attributed to water stretching vibrations. X-ray diffraction studies show that the minerals are disordered. This is reflected in the difficulty of obtaining Raman spectra of reasonable quality, and explains why the Raman spectra of these minerals have not been previously or sufficiently described. Copyright 2008 John Wiley & Sons, Ltd. [source]


    Coadsorption of trimethyl phosphine and thiocyanate on colloidal silver: a SERS study combined with theoretical calculations

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 4 2009
    Gengshen Hu
    Abstract The adsorption of trimethyl phosphine (TMP) on colloidal silver has been investigated by means of surface-enhanced Raman scattering spectroscopy (SERS). On the basis of surface selection rules, it is deduced from the SERS results that TMP adsorbs on silver surface via its P atom. The electron donor effect of TMP can be sensitively probed by the coadsorbed SCN,. The Raman wavenumber of ,CN of the adsorbed SCN, shifts to lower wavenumbers when TMP is coadsorbed with SCN, and the red shift of C,N stretching wavenumber is found to increase with increasing surface coverage of TMP. This could be explained in terms of the electron donor effect of TMP. Density functional theory (DFT) calculations further confirm the experimental results that the charge transfer is from TMP to silver surface rather than reversely. Natural bond orbital (NBO) analysis indicates that the red shift of C,N stretching mode is due the increase of electronic populations of ,* orbital of C,N bond induced by coadsorbed TMP, consequently the C,N bond is weakened, and the ,CN shifts to lower wavenumbers. An NBO analysis also indicates that the conjugated effect between S atom and C,N bond could easily make the charge transfer from silver surface to C,N bond. Copyright 2008 John Wiley & Sons, Ltd. [source]


    Density functional study on the structural conformations and intramolecular charge transfer from the vibrational spectra of the anticancer drug combretastatin-A2

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 4 2009
    L. Padmaja
    Abstract Combretastatin-A2 (CA2), a potential anticancer drug in advanced preclinical development, is extracted from the medicinal plant Combretum caffrum. The NIR-FT Raman and FT-IR spectral studies of the molecule were carried out and ab initio calculations performed at the B3LYP/6-31G(d) level to derive the equilibrium geometry as well as the vibrational wavenumbers and intensities of the spectral bands. The vibrational analysis showed that the molecule has a similar geometry as that of cis-stilbene, and has undergone steric repulsion resulting in twisting of the phenyl ring with respect to the ethylenic plane. Vibrational analysis was used to investigate the lowering of the stretching modes, and enhancement of infrared band intensities of the C,H stretching modes of Me2 may be attributed to the electronic effects caused by back-donation and induction from the oxygen atom. Analysis of phenyl ring modes shows that the CA2 stretching mode 8 and the aromatic C,H in-plane bending mode are equally active as strong bands in both IR and Raman spectra, which can be interpreted as the evidence of intramolecular charge transfer (ICT) between the OH and OCH3groups via conjugated ring path and is responsible for bioactivity of the molecule. Copyright 2008 John Wiley & Sons, Ltd. [source]


    Raman spectroscopic study of the uranyl selenite mineral marthozite Cu[(UO2)3(SeO3)2O2]8H2O

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 10 2008
    Ray L. Frost
    Abstract The mineral marthozite, a uranyl selenite, has been characterised by Raman spectroscopy at 298 K. The bands at 812 and 797 cm,1 were assigned to the symmetric stretching modes of the (UO2)2+ and (SeO3)2, units, respectively. These values gave the calculated UO bond lengths in uranyl of 1.799 and/or 1.814 . Average UO bond length in uranyl is 1.795 , inferred from the X-ray single crystal structure analysis of marthozite by Cooper and Hawthorne. The broad band at 869 cm,1 was assigned to the ,3 antisymmetric stretching mode of the (UO2)2+ (calculated UO bond length 1.808 ). The band at 739 cm,1 was attributed to the ,3 antisymmetric stretching vibration of the (SeO3)2, units. The ,4 and the ,2 vibrational modes of the (SeO3)2, units were observed at 424 and 473 cm,1. Bands observed at 257, and 199 and 139 cm,1 were assigned to OUO bending vibrations and lattice vibrations, respectively. OHO hydrogen bond lengths were inferred using Libowiztky's empirical relation. The infrared spectrum of marthozite was studied for complementation. Copyright 2008 John Wiley & Sons, Ltd. [source]


    Thermo-Raman spectroscopy of synthetic nesquehonite , implication for the geosequestration of greenhouse gases

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 9 2008
    Matthew C. Hales
    Abstract Pure nesquehonite (MgCO33H2O)/Mg(HCO3)(OH)2H2O was synthesised and characterised by a combination of thermo-Raman spectroscopy and thermogravimetry with evolved gas analysis. Thermo-Raman spectroscopy shows an intense band at 1098 cm,1, which shifts to 1105 cm,1 at 450 C, assigned to the ,1CO32, symmetric stretching mode. Two bands at 1419 and 1509 cm,1 assigned to the ,3 antisymmetric stretching mode shift to 1434 and 1504 cm,1 at 175 C. Two new peaks at 1385 and 1405 cm,1 observed at temperatures higher than 175 C are assigned to the antisymmetric stretching modes of the (HCO3), units. Throughout all the thermo-Raman spectra, a band at 3550 cm,1 is attributed to the stretching vibration of OH units. Raman bands at 3124, 3295 and 3423 cm,1 are assigned to water stretching vibrations. The intensity of these bands is lost by 175 C. The Raman spectra were in harmony with the thermal analysis data. This research has defined the thermal stability of one of the hydrous carbonates, namely nesquehonite. Thermo-Raman spectroscopy enables the thermal stability of the mineral nesquehonite to be defined, and, further, the changes in the formula of nesquehonite with temperature change can be defined. Indeed, Raman spectroscopy enables the formula of nesquehonite to be better defined as Mg(OH)(HCO3)2H2O. Copyright 2008 John Wiley & Sons, Ltd. [source]


    Concentration dependent Raman and IR study on salicylaldehyde in binary mixtures

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 12 2007
    A. Anis Fathima
    Abstract A vibrational spectroscopic study of binary mixtures of salicylaldehyde (SA) in three different solvents (polar and nonpolar) is presented. The vibrational modes ,(CO), hydroxyl stretching mode (COH) and aldehydic (CH) stretching vibration were analyzed. Changes in wavenumber position and full width half maximum have been explained for neat as well as binary mixtures with different volume fractions of the reference system, SA, in terms of inter- and intramolecular hydrogen bonding. The IR spectra of these mixtures have also been taken and compared with the Raman data. The spectral changes have been well explained using the concentration fluctuation model and solute,solvent interaction. Copyright 2007 John Wiley & Sons, Ltd. [source]


    DNA tertiary structure and changes in DNA supercoiling upon interaction with ethidium bromide and gyrase monitored by UV resonance Raman spectroscopy

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 10 2007
    U. Neugebauer
    Abstract The tertiary structure of DNA is important for many of its biological functions. In this work supercoiled and relaxed forms of purified plasmid DNA pBR322 in dilute aqueous solutions are investigated by means of UVRR spectroscopy to assess changes in B-DNA conformation. Spectral variation in the CO and exocyclic NH2 vibration above 1600 cm,1 indicate changes in hydrogen bonding. A minor shift of the CN stretching mode of adenosine and guanosine at 1487 cm,1 supports these findings. Changes in ribose conformation are visible in the spectral region 1320,1360 cm,1 by vibrational coupling of the ribose pucker to the vibrations of the purine and pyrimidine bases. The intercalating phenanthridinium drug ethidium bromide is known to reduce the negative supercoiling of DNA. This change in DNA topology is reflected in variations of the UVRR marker bands of DNA identified above. Principal component analysis helped to extract the features of interest from the complex spectra of the intercalation complex. Within the bacterial cells the change in DNA topology is achieved by the action of topoisomerases. In this work, the DNA-binding subunit GyrA of the enzyme gyrase was extracted from E. coli and applied to relaxed and supercoiled pBR322. The observed changes in the vibrational signature of the relaxed DNA in the presence of GyrA indicate a change of topology towards the supercoiled form. With already supercoiled DNA no further change in DNA topology is observed. Copyright 2007 John Wiley & Sons, Ltd. [source]


    Spectroscopic and computational studies on self-assembly complexes of bis(pyrrol-2- ylmethyleneamine) ligands linked by alkyl spacers with Cu(II)

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 5 2007
    Wei Li
    Abstract Bis(pyrrol-2-ylmethyleneamine) ligands and their mononuclear monomeric and dinuclear dimeric self-assembly complexes with Cu(II) were investigated by means of IR and Raman spectroscopies and density functional theory. The ground-state geometries were calculated by using the BeckeLeeYangParr composite exchange-correlation functional (B3LYP) and a combined basis set (LanL2DZ for Cu; 6,31G(d) for C, H, N), and they were compared with the single-crystal X-ray diffraction (XRD) structures. The DFT-calculated CuN bond lengths are generally higher by 0.001,0.040 than those determined through XRD. The vibrational spectra were also calculated at the same level of theory for the optimized geometries. The calculated wavenumbers were scaled by a uniform scaling factor and compared with the experimental fundamentals. The predicted spectra are in good agreement with the experimental ones with the deviations generally less than 30 cm,1. In comparison with the spectra of the ligands, the coordination effect shifts the ,(CN) wavenumber by about 50 cm,1 toward a lower value. Because of the weak intermolecular CHCu hydrogen bond, the CuN stretching mode is shifted toward a lower wavenumber. Copyright 2006 John Wiley & Sons, Ltd. [source]


    A Raman spectroscopic study of the uranyl selenite mineral haynesite

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 8 2006
    Ray L. Frost
    Abstract The mineral haynesite, a uranyl selenite, has been characterised by Raman spectroscopy at 298 and 77 K. Two bands at 811.5 and 800.2 cm,1 are assigned to the symmetric stretching modes of the (UO2)2+ and (SeO3)2, units respectively. These values give calculated UO bond lengths of 1.799 and/or 1.801 . The broad band at 861.8 cm,1 is assigned to the ,3 antisymmetric stretching mode of the (UO2)2+ (calculated UO bond length 1.813 ). Additional bands are observed in the 77 K spectrum. In the spectroscopy of selenite compounds, the position of the antisymmetric stretching vibration occurs at lower wavenumbers than the symmetric stretching mode and thus the band at 740.5 cm,1 is attributed to the ,3 antisymmetric stretching vibration of the (SeO3)2, units. The ,4 and the ,2 vibrational modes of the (SeO3)2, units are observed at 418.5 and 472.1 cm,1. Bands observed at 278.3, 257.3 and 218.8 cm,1 are assigned to OUO bending vibrations. Copyright 2006 John Wiley & Sons, Ltd. [source]


    Raman and IR spectral studies of D -phenylglycinium perchlorate

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 9 2002
    S. Ramaswamy
    The Raman and infrared spectra of D -phenylglycinium perchlorate were recorded at room temperature. Tentative vibrational assignments of the observed wavenumbers were made by comparison with the vibrational wavenumbers of glycine, phenylalanine and other similar compounds. Anions were found to coordinate through hydrogen bonding interactions to other ligands in the crystal, affecting the Td symmetry and thereby causing the degeneracies of several modes to be removed. The extensive intermolecular hydrogen bonding in the crystal leads to a shift of bands due to the stretching and bending modes of various functional groups. The broadening and appearance of multiple bands for the carbonyl stretching mode due to the resonance interaction is also discussed. Copyright 2002 John Wiley & Sons, Ltd. [source]


    Computed vibrational wavenumbers in ammonium fluoride crystals

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 12 2001
    A. Alavi
    The vibrational wavenumbers of crystalline ammonium fluoride were calculated using the density functional method. The results support the experimental conclusions that the symmetric stretching mode in NH4F lies at a higher wavenumber than the asymmetric stretch, that these wavenumbers are reversed in ND4F and that the librational wavenumbers lie at ,560 cm,1. Copyright 2001 John Wiley & Sons, Ltd. [source]


    Raman spectroscopy of descloizite and mottramite at 298 and 77 K

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 11 2001
    Ray L. Frost
    The Raman spectra of the isomorphous series descloizite [PbZn(VO4)(OH)] and mottramite [PbCu(VO4) (OH)] were obtained at 298 and 77 K. The Raman band at 844 cm,1, assigned to the ,1 symmetric (VO4,) stretching mode for descloizite, is shifted to 814 cm,1 for mottramite. The ,3 mode of descloizite is observed as a single band at 777 cm,1 but this mode is more complex for mottramite with three bands observed in the 77 K spectrum at 811, 785 and 767 cm,1. The bending mode (,2) is observed at 437 cm,1 for descloizite and at 426 cm,1 for mottramite. The ,3 region is complex for both minerals and this is attributed to symmetry reduction of the vanadate unit from Td to Cs. Collecting Raman spectra at 77 K allowed better band separation with observation of additional bands ascribed to the removal of degeneracy. Copyright 2001 John Wiley & Sons, Ltd. [source]


    Drug-induced corneal hydration changes monitored in vivo by non-invasive confocal Raman spectroscopy

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 9 2001
    Roel J. Erckens
    It is well established that the state of corneal hydration plays a crucial role in maintaining optimal vision. Therefore, any knowledge that can be obtained non-invasively about the status of corneal hydration could be of significant clinical value. A novel confocal Raman spectroscopic technique was used to monitor non-invasively drug-induced hydration changes in the rabbit cornea. The spectroscopic technique enables one to monitor the changes in water content of the cornea while the confocal probing reduces interference of signals from adjacent tissues and allows for measurement of corneal hydration at various depths. The corneal hydration is altered by applying a dehydrating agent (Muro 128) topically on the cornea. To determine the corneal hydration status, the OH/CH ratio between the Raman intensity of the water OH mode at 3390 cm,1 and the protein CH stretching mode at 2945 cm,1 is calculated. In the middle of the corneal stroma after 10 min, Muro 128 -treated corneas show an average decrease of about 30% in the OH/CH ratio (1.27 0.13) compared with the untreated corneas (1.76 0.09). In this in vivo model it is possible to monitor the hydration status of the living cornea using the Raman spectroscopic technique. Copyright 2001 John Wiley & Sons, Ltd. [source]


    Sub-5-fs Real-time Spectroscopy of Transition States in Bacteriorhodopsin During Retinal Isomerization,

    PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 2 2007
    Takayoshi Kobayashi
    By using a sub-5-fs visible laser pulse, we have made the first observation of the vibrational spectra of the transition state during trans-cis isomerization in the retinal chromophore of bacteriorhodopsin (bRS68). No instant isomerization of the retinal occurs in spite of electron promotion from the bonding ,-orbital to the anti-bonding ,*-orbital. The difference between the in-plane and out-of-plane vibrational frequencies (about 1150,1250 and 900,1000 cm,1, respectively) is reduced during the first time period. The vibrational spectra after this period became very broad and weak and are ascribed to a "silent state." The silent state lasts for 700,900 fs until the chromophore isomerizes to the cis -C13=C14 conformation. The frequency of the C=C stretching mode was modulated by the torsion mode of the C13=C14 double bond with a period of 200 fs. The modulation was clearly observed for four to five periods. Using the empirical equation for the relation between bond length and stretching frequency, we determined the transitional C=C bond length with about 0.01 accuracy during the torsion motion around the double bond with 1-fs time resolution. [source]


    Ultrafast coherent vibronic oscillations in regioregular poly(3-alkylthiophene)

    PHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue S1 2009
    Katsuichi Kanemoto
    Abstract Ultrafast degenerate four-wave mixing (DFWM) signals of the regioregular (RR) poly(3-hexylthiophene) (P3HT) film have been investigated by the experiments using sub-20 fs pulses generated from a noncollinear optical parametric amplifier (NOPA) system. Strong DFWM signals were observed owing to a large third-order nonlinear susceptibility ,(3) of the RR-P3HT film. The time profile of the DFWM signals exhibits clear coherent oscillation on a decaying signal. The oscillation turn out to be caused by the C=C stretching mode that gives strong Raman signal. The time profile of the DFWM signal is simulated by a numerical calculation. The result of simulation reveals that decay constants of electronic population and of vibronic oscillation are 200 fs and 210 fs, respectively. This is the first determination of the decay constants for the RR-P3HT film. The obtained result demonstrates that the ,(3) signal of the RR-P3HT film decays very rapidly. ( 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]


    Thickness-Dependent Structural Evolutions and Growth Models in Relation to Carrier Transport Properties in Polycrystalline Pentacene Thin Films,

    ADVANCED FUNCTIONAL MATERIALS, Issue 17 2007
    H.-L. Cheng
    Abstract Thickness-dependent crystal structure, surface morphology, surface energy, and molecular structure and microstructure of a series of polycrystalline pentacene films with different film thickness ranging from several monolayers to the several hundred nanometers have been investigated using X-ray diffraction (XRD), atomic force microscopy (AFM), contact angle meter, and Raman spectroscopy. XRD studies indicate that thin film polymorphs transformation behaviours are from the orthorhombic phase to the thin-film phase and then to the triclinic bulk phase as measured by the increased tilt angle (,tilt) of the pentacene molecule from the c- axis toward the a- axis. We propose a growth model that rationalizes the ,tilt increased along with increasing film thickness in terms of grain size and surface energy varying with film growth using AFM combined with contact angle measurements. The vibrational characterizations of pentacene molecules in different thickness films were investigated by Raman spectroscopy compared to density functional theory calculations of an isolated molecule. In combination with XRD and AFM the method enables us to distinguish the molecular microstructures in different thin film polymorphs. We proposed a methodology to probe the microscopic parameters determining the carrier transport properties based on Davydov splitting and the characteristics of aromatic C,C stretching modes in Raman spectra. When compared to the triclinic bulk phase at a high thickness, we suggest that the first few monolayer structures located at the dielectric surface could have inferior carrier transport properties due to weak intermolecular interactions, large molecular relaxation energy, and more grain boundaries. [source]


    Hydrogen bonding interaction between 1,4-dioxane and water

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2010
    Ajay Chaudhari
    Abstract This work reports an interaction of 1,4-dioxane with one, two, and three water molecules using the density functional theory method at B3LYP/6-311++G* level. Different conformers were studied and the most stable conformer of 1,4-dioxane-(water)n (n = 1,3) complex has total energies ,384.1964038, ,460.6570694, and ,537.1032381 hartrees with one, two, and three water molecules, respectively. Corresponding binding energy (BE) for these three most stable structures is 6.23, 16.73, and 18.11 kcal/mol. The hydrogen bonding results in red shift in OO stretching and CC stretching modes of 1,4-dioxane for the most stable conformer of 1,4-dioxane with one, two, and three water molecules whereas there was a blue shift in CO symmetric stretching and CO asymmetric stretching modes of 1,4-dioxane. The hydrogen bonding results in large red shift in bending mode of water and large blue shift in symmetric stretching and asymmetric stretching mode of water. 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source]


    Detection of Sublethal Thermal Injury in Salmonella enterica Serotype Typhimurium and Listeria monocytogenes Using Fourier Transform Infrared (FT-IR) Spectroscopy (4000 to 600 cm,1)

    JOURNAL OF FOOD SCIENCE, Issue 2 2008
    H.M. Al-Qadiri
    ABSTRACT:, Fourier transform infrared (FT-IR) spectroscopy (4000 to 600 cm,1) was utilized to detect sublethally heat-injured microorganisms: Salmonella enterica serotype Typhimurium ATCC 14028, a Gram-negative bacterium, and Listeria monocytogenes ATCC 19113, a Gram-positive bacterium. A range of heat treatments (N= 2) at 60 C were evaluated: 0D (control), 2D, 4D, 6D, and 8D using a D60 C (S. enterica serotype Typhimurium ATCC 14028 = 0.30 min, L. monocytogenes ATCC 19113 = 0.43 min). The mechanism of cell injury appeared to be different for Gram-negative and Gram-positive microbes as observed from differences in the 2nd derivative transformations and loadings plot of bacterial spectra following heat treatment. The loadings for PC1 and PC2 confirmed that the amide I and amide II bands were the major contribution to spectral variation, with relatively small contributions from C-H deformations, the antisymmetric P==O stretching modes of the phosphodiester nucleic acid backbone, and the C-O-C stretching modes of polysaccharides. Using soft independent modeling of class analogy (SIMCA), the extent of injury could be predicted correctly at least 83% of the time. Partial least squares (PLS) calibration analysis was constructed using 5 latent variables for predicting the bacterial counts for survivors of the different heat treatments and yielded a high correlation coefficient (R= 0.97 [S. enterica serotype Typhimurium] and 0.98 [L. monocytogenes]) and a standard error of prediction (SEP= 0.51 [S. enterica serotype Typhimurium] and 0.39 log10 CFU/mL [L. monocytogenes]), indicating that the degree of heat injury could be predicted. [source]


    Raman spectroscopic study of the uranyl mineral pseudojohannite Cu6.5[(UO2)4O4(SO4)2]2(OH)525H2O

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 12 2009
    Ray L. Frost
    Abstract Raman spectra of pseudojohannite were studied and related to the structure of the mineral. Observed bands were assigned to the stretching and bending vibrations of (UO2)2+ and (SO4)2, units and of water molecules. The published formula of pseudojohannite is Cu6.5(UO2)8[O8](OH)5[(SO4)4]25H2O. Raman bands at 805 and 810 cm,1 are assigned to (UO2)2+ stretching modes. The Raman bands at 1017 and 1100 cm,1 are assigned to the (SO4)2, symmetric and antisymmetric stretching vibrations. The three Raman bands at 423, 465 and 496 cm,1 are assigned to the (SO4)2,,2 bending modes. The bands at 210 and 279 cm,1 are assigned to the doubly degenerate ,2 bending vibration of the (UO2)2+ units. UO bond lengths in uranyl and OHO hydrogen bond lengths were calculated from the Raman and infrared spectra. Copyright 2009 John Wiley & Sons, Ltd. [source]


    Density functional study on the structural conformations and intramolecular charge transfer from the vibrational spectra of the anticancer drug combretastatin-A2

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 4 2009
    L. Padmaja
    Abstract Combretastatin-A2 (CA2), a potential anticancer drug in advanced preclinical development, is extracted from the medicinal plant Combretum caffrum. The NIR-FT Raman and FT-IR spectral studies of the molecule were carried out and ab initio calculations performed at the B3LYP/6-31G(d) level to derive the equilibrium geometry as well as the vibrational wavenumbers and intensities of the spectral bands. The vibrational analysis showed that the molecule has a similar geometry as that of cis-stilbene, and has undergone steric repulsion resulting in twisting of the phenyl ring with respect to the ethylenic plane. Vibrational analysis was used to investigate the lowering of the stretching modes, and enhancement of infrared band intensities of the C,H stretching modes of Me2 may be attributed to the electronic effects caused by back-donation and induction from the oxygen atom. Analysis of phenyl ring modes shows that the CA2 stretching mode 8 and the aromatic C,H in-plane bending mode are equally active as strong bands in both IR and Raman spectra, which can be interpreted as the evidence of intramolecular charge transfer (ICT) between the OH and OCH3groups via conjugated ring path and is responsible for bioactivity of the molecule. Copyright 2008 John Wiley & Sons, Ltd. [source]


    Structural conformations and electronic interactions of the natural product, oroxylin: a vibrational spectroscopic study

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 12 2008
    Jose P. Abraham
    Abstract 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 H13O12C6C5, H14O10C4C5, H13O12C6C5 and H14O10C4C5 is found to be most stable. The optimized geometry reveals that the dihedral angle , 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 (H29H18 = 2.198 ). 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 O10H14 and O12H13 stretching modes, which is justified by DFT results. Copyright 2008 John Wiley & Sons, Ltd. [source]


    Raman spectroscopic study of the uranyl selenite mineral marthozite Cu[(UO2)3(SeO3)2O2]8H2O

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 10 2008
    Ray L. Frost
    Abstract The mineral marthozite, a uranyl selenite, has been characterised by Raman spectroscopy at 298 K. The bands at 812 and 797 cm,1 were assigned to the symmetric stretching modes of the (UO2)2+ and (SeO3)2, units, respectively. These values gave the calculated UO bond lengths in uranyl of 1.799 and/or 1.814 . Average UO bond length in uranyl is 1.795 , inferred from the X-ray single crystal structure analysis of marthozite by Cooper and Hawthorne. The broad band at 869 cm,1 was assigned to the ,3 antisymmetric stretching mode of the (UO2)2+ (calculated UO bond length 1.808 ). The band at 739 cm,1 was attributed to the ,3 antisymmetric stretching vibration of the (SeO3)2, units. The ,4 and the ,2 vibrational modes of the (SeO3)2, units were observed at 424 and 473 cm,1. Bands observed at 257, and 199 and 139 cm,1 were assigned to OUO bending vibrations and lattice vibrations, respectively. OHO hydrogen bond lengths were inferred using Libowiztky's empirical relation. The infrared spectrum of marthozite was studied for complementation. Copyright 2008 John Wiley & Sons, Ltd. [source]


    Thermo-Raman spectroscopy of synthetic nesquehonite , implication for the geosequestration of greenhouse gases

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 9 2008
    Matthew C. Hales
    Abstract Pure nesquehonite (MgCO33H2O)/Mg(HCO3)(OH)2H2O was synthesised and characterised by a combination of thermo-Raman spectroscopy and thermogravimetry with evolved gas analysis. Thermo-Raman spectroscopy shows an intense band at 1098 cm,1, which shifts to 1105 cm,1 at 450 C, assigned to the ,1CO32, symmetric stretching mode. Two bands at 1419 and 1509 cm,1 assigned to the ,3 antisymmetric stretching mode shift to 1434 and 1504 cm,1 at 175 C. Two new peaks at 1385 and 1405 cm,1 observed at temperatures higher than 175 C are assigned to the antisymmetric stretching modes of the (HCO3), units. Throughout all the thermo-Raman spectra, a band at 3550 cm,1 is attributed to the stretching vibration of OH units. Raman bands at 3124, 3295 and 3423 cm,1 are assigned to water stretching vibrations. The intensity of these bands is lost by 175 C. The Raman spectra were in harmony with the thermal analysis data. This research has defined the thermal stability of one of the hydrous carbonates, namely nesquehonite. Thermo-Raman spectroscopy enables the thermal stability of the mineral nesquehonite to be defined, and, further, the changes in the formula of nesquehonite with temperature change can be defined. Indeed, Raman spectroscopy enables the formula of nesquehonite to be better defined as Mg(OH)(HCO3)2H2O. Copyright 2008 John Wiley & Sons, Ltd. [source]