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Sample records for fluorescence spectra vibrational

  1. Vibrational spectra study of fluorescent dendrimers built from the cyclotriphosphazene core with terminal dansyl and carbamate groups

    Science.gov (United States)

    Furer, V. L.; Vandyukova, I. I.; Vandyukov, A. E.; Fuchs, S.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

    2011-08-01

    The FTIR and FT Raman spectra of the "Janus"-type dendrimers, possessing five carbamate groups on one side and five fluorescent dansyl derivatives on the other side, with amide G1 and hydrazone G2 central linkages were studied. These surface-block dendrimers are obtained by the coupling of two different dendrons. The FTIR and FT-Raman spectra of the zero generation dendrons, built from the hexafunctional cyclotriphosphazene core, with five dansyl terminal groups and one carbamate G0 v and one oxybenzaldehyde function G0v have been recorded. The structural optimization and normal mode analysis were performed for dendron G0v on the basis of the density functional theory (DFT). The calculated geometrical parameters and harmonic vibrational frequencies are predicted in a good agreement with the experimental data. It was found that dendron molecule G0v has a concave lens structure with planar -O-C6H4-CHdbnd O fragments and slightly non-planar cyclotriphosphazene core. The experimental IR and Raman spectra of dendron G0v were interpreted by means of potential energy distributions. Relying on DFT calculations a complete vibrational assignment is proposed. The strong band 1597 cm -1 show marked changes of the optical density in dependence of substituents in the aromatic ring. The frequencies of ν(N-H) bands in the IR spectra reveal the presence of the different types of H-bonds in the dendrimers.

  2. Vibrational spectra of ordered perovskites

    NARCIS (Netherlands)

    Corsmit, A.F.; Hoefdraad, H.E.; Blasse, G.

    1972-01-01

    The vibrational spectra of the molecular M6+O6 (M = Mo, Te, W) group in ordered perovskites of the type Ba2M2+M6+O6 are reported. These groups have symmetry Oh, whereas their site symmetry is also Oh. An assignment of the internal vibrations is presented.

  3. The crystal structure and vibrational spectra of two molecules emitting dual fluorescence: 4-(1H-Pyrrol-1-yl)benzonitrile (PBN) and 5-cyano-2-(1pyrrolyl)-pyridine (CPP)

    Energy Technology Data Exchange (ETDEWEB)

    Schweke, D.; Abramov, S. [Department of Physical Chemistry and the Farkas Center for Light Induced Processes, Hebrew University of Jerusalem, Jerusalem (Israel); Haas, Y. [Department of Physical Chemistry and the Farkas Center for Light Induced Processes, Hebrew University of Jerusalem, Jerusalem (Israel)], E-mail: yehuda@chem.ch.huji.ac.il

    2007-05-21

    Crystal structures and vibrational spectra are reported for the two title molecules which exhibit dual fluorescence due to the existence of a low lying charge transfer excited state. The data show that in the ground state PBN is twisted whereas CPP is planar, and the crystal structures are quite different. The experimental spectra are in very good agreement with quantum mechanical calculations, which also predict considerable differences between the vibrational spectra of CPP in the ground state and in the charge transfer excited state.

  4. Interpretation of Nitroindolinospirobenzothiopyran Vibrational Spectra

    Science.gov (United States)

    Gladkov, L. L.; Khamchukov, Yu. D.; Lyubimov, A. V.

    2016-05-01

    The structures of four possible stereoisomers of the closed form of photochromic nitroindolinospirobenzothiopyran (NISTP) {1',3'-dihydro-1',3',3'-trimethyl-6-nitrospiro[2H-1-benzothiopyran-2,2'-(2H)-indoline]} were determined by the DFT method. The geometry of the most stable isomer was defined. Nitro-substitution changes mainly the lengths of bonds formed by S and N with spiro-atom Cs. According to the calculations, the CsS bond changes most and lengthens by 0.019 Å. It is shown that the S atom has large displacement amplitudes in normal modes assigned to Raman lines at 230, 285, 360, and 575 cm-1 and weak IR bands at 467 and 577 cm-1. Oscillations involving the nitro group are very active in Raman and IR spectra. Their frequencies are slightly lower than similar frequencies of nitrobenzene and nitroindolinospirobenzopyran, indicating a higher degree of vibrational coupling of the NO2 group with the NISTP molecular skeleton.

  5. Molecular Dynamics and Picosecond Vibrational Spectra.

    Science.gov (United States)

    1980-07-01

    and Identify by block number) molecular dynamics picosecond infra-red spectra crmputer simulation vibrational spectra array processor linear rcsponse...that for molecular dynamics theoretical computation is now long enough, to significantly overlap. This overlap of theory and experiment can, at least...to discover these microscopic atomic trajectories, i.e. the molecular dynamics of solution processes, we must be able to both theoretically compute

  6. Vibrational Spectra of a Mechanosensitive Channel

    NARCIS (Netherlands)

    Liang, Chungwen; Louhivuori, Martti; Marrink, Siewert J.; Jansen, Thomas L.C.; Knoester, Jasper

    2013-01-01

    We report the simulated vibrational spectra of a mechanosensitive membrane channel in different gating states. Our results show that while linear absorption is insensitive to structural differences, linear dichroism and sum-frequency generation spectroscopies are sensitive to the orientation of the

  7. [Vibrational spectra of Corallium elatius].

    Science.gov (United States)

    Fan, Lu-wei; Zhang, Yan; Hu, Yang

    2013-09-01

    Corallium elatius, which has unique color distribution characteristic, is the most important species of Taiwan precious corals. EPMA, XRD, FTIR and Laser Raman detective methods were used to study the chemical, mineral composition and spectra characteristics of Corallium elatius. The result of EPMA, XRD and FTIR shows the high-Mg calcite mineral componentand the stable minor chemical constituents of the samples. Meanwhile, the cell parameter indicates the lattice distortion and the preferred orientation of calcite grain caused by organic matter. The red part of the samples shows a different Raman spectrum from that of the white part, located at 1517/1128 cm(-1) and 1296/1016 cm(-1). Raman scattering measurement reveals the relationship between the organic matter and color.

  8. Synthesis and Fluorescence Spectra of Triazolylcoumarin Fluorescent Dyes

    Institute of Scientific and Technical Information of China (English)

    PENG Xian-fu; LI Hong-qi

    2009-01-01

    Much attention is devoted to fluorescent dyes especially those with potential in versatile applications. Reactions under "click" conditions between nonfluorescent 3 - azidocoumarins and terminal alkynes produced 3 -(1, 2, 3- triazol- 1 - yl)cournarins, a novel type of fluorescent dyes with intense fluorescence. The structures of the new coumarins were characterized by 1H NMR, MS, and IR spectra. Fluorescence spectra measurement demonstrated excellent fluorescence performance of the triazolylcoumarins and this click reaction is a promising candidate for bioconjugation and bioimaging applications since both azide and alkynes are quite inert to biological systems.

  9. Algebraic Hamiltonian for Vibrational Spectra of Stibine

    Institute of Scientific and Technical Information of China (English)

    HOU Xi-Wen

    2004-01-01

    @@ An algebraic Hamiltonian, which in a limit can be reduced to an extended local mode model by Law and Duncan,is proposed to describe both stretching and bending vibrational energy levels of polyatomic molecules, where Fermi resonances between the stretches and the bends are considered. The Hamiltonian is used to study the vibrational spectra of stibine (SbH3). A comparison with the extended local mode model is made. Results of fitting the experimental data show that the algebraic Hamiltonian reproduces the observed values better than the extended local mode model.

  10. Multivariate analysis of endometrial tissue fluorescence spectra

    Science.gov (United States)

    Vaitkuviene, Aurelija; Auksorius, E.; Fuchs, D.; Gavriushin, V.

    2002-10-01

    Background and Objective: The detailed multivariate analysis of endometrial tissue fluorescence spectra was done. Spectra underlying features and classification algorithm were analyzed. An effort has been made to determine the importance of neopterin component in endometrial premalignization. Study Design/Materials and Methods: Biomedical tissue fluorescence was measured by excitation with the Nd YAG laser third harmonic. Multivariate analysis techniques were used to analyze fluorescence spectra. Biomedical optics group at Vilnius University analyzed the neopterin substance supplied by the Institute of Medical Chemistry and Biochemistry of Innsbruck University. Results: Seven statistically significant spectral compounds were found. The classification algorithm classifying samples to histopathological categories was developed and resulted in sensitivity of 80% and specificity 93% for malignant vs. hyperplastic and normal. Conclusions: Fluorescence spectra could be classified with high accuracy. Spectral variation underlying features can be extracted. Neopterin component might play an important role in endometrial hyperplasia development.

  11. Vibrational spectra study on quinolones antibiotics

    Science.gov (United States)

    Wang, Yu; Yu, Ke; Wang, Sihuan

    2006-09-01

    In order to be able to fully understand and easily identify the quilonoles, we collected IR and Raman spectra of six quinolones, and attempted to assign the attribution of the observed frequencies and their association with specific modes of vibration. According to the structure, the compounds were divided into the groups, and the similarities and differences were further studied by comparing. The result of the study shows that the frequency and intensity are comparable to the corresponding structure. The spectra not only have the commonness but also the individualities.

  12. [Vibrational spectra of Hetian nephrite from Xinjiang].

    Science.gov (United States)

    Zhang, Yong-wang; Liu, Yan; Liu, Tao-tao; Muhetaer, Zari; Liu, Yuan-qing

    2012-02-01

    In previous studies, EMPA, PIXE and others were employed to study the chemical compositions of nephrite separately without a systematical measurement. In the present study, XRF, XRD, IR and LR were used together to examine chemical and spectra characteristics of white, green and black nephrite from Hetian, Xinjiang. XRD results indicate that all nephrite samples consist of tremolite. Then IR spectra of nephrite samples suggest that the M-OH stretching vibration bands show that the M1 and M3 sites are not only occupied by Mg2+ and Fe2+, but also by Fe3+, which is consistent with the chemical compositions of these samples. This information might be useful to understanding the variety of nephrite. Their Raman spectra are almost the same, while some differences exist because of different content of FeO/Fe2O3.

  13. Universality of Vibrational Spectra of Globular Proteins

    CERN Document Server

    Na, Hyuntae; ben-Avraham, Daniel

    2015-01-01

    It is shown that the density of modes of the vibrational spectrum of globular proteins is universal, i.e., regardless of the protein in question it closely follows one universal curve. The present study, including 135 proteins analyzed with a full atomic empirical potential (CHARMM22) and using the full complement of all atoms Cartesian degrees of freedom, goes far beyond confirming previous claims of universality, finding that universality holds even in the high-frequency range (300- 4000 1/cm), where peaks and turns in the density of states are faithfully reproduced from one protein to the next. We also characterize fluctuations of the spectral density from the average, paving the way to a meaningful discussion of rare, unusual spectra and the structural reasons for the deviations in such "outlier" proteins. Since the method used for the derivation of the vibrational modes (potential energy formulation, set of degrees of freedom employed, etc.) has a dramatic effect on the spectral density, another signific...

  14. Vibrational spectra of corticosteroid hormones in the terahertz range

    Science.gov (United States)

    Cherkasova, O. P.; Nazarov, M. M.; Sapozhnikov, D. A.; Man'kova, A. A.; Fedulova, E. V.; Volodin, V. A.; Minaeva, V. A.; Minaev, B. F.; Baryshnikov, G. V.

    2010-11-01

    The terahertz time-domain and Raman spectra of corticosteroid hormones in the region of low-frequency infrared vibrations have been measured. On the ground of quantum chemical calculations of the frequencies and normal modes the assignments of vibrational bands in the THz-spectra are performed.

  15. Vibrational spectra, normal coordinate treatment and simulation of the vibrational spectra of piperazine glyoxime and its Co(III) complex

    Science.gov (United States)

    Özpozan, T.; Küçükusta, D.; Büyükmumcu, Z.

    2003-12-01

    Newly synthesized Co(III) complexes of piperazine glyoxime (PGO) are examined from the vibrational spectroscopy point of view. A complete interpretation of the vibrational spectra of both the ligand and the complex has been carried out on the basis of normal coordinate analysis. A valence force field has been developed for both of the compounds. The vibrational spectra of the compounds are simulated by a visual basic program prepared to run on an MS Excel data sheet.

  16. Molecular vibrations the theory of infrared and Raman vibrational spectra

    CERN Document Server

    Wilson, E Bright; Cross, Paul C

    1980-01-01

    Pedagogical classic and essential reference focuses on mathematics of detailed vibrational analyses of polyatomic molecules, advancing from application of wave mechanics to potential functions and methods of solving secular determinant.

  17. Vibrational Spectra and Quantum Calculations of Ethylbenzene

    Institute of Scientific and Technical Information of China (English)

    Jian Wang; Xue-jun Qiu; Yan-mei Wang; Song Zhang; Bing Zhang

    2012-01-01

    Normal vibrations of ethylbenzene in the first excited state have been studied using resonant two-photon ionization spectroscopy.The band origin of ethylbenzene of S1←S0 transition appeared at 37586 cm-1.A vibrational spectrum of 2000 cm-1 above the band origin in the first excited state has been obtained.Several chain torsions and normal vibrations are obtained in the spectrum.The energies of the first excited state are calculated by the time-dependent density function theory and configuration interaction singles (CIS) methods with various basis sets.The optimized structures and vibrational frequencies of the S0 and S1 states are calculated using Hartree-Fock and CIS methods with 6-311++G(2d,2p) basis set.The calculated geometric structures in the S0 and S1 states are gauche conformations that the symmetric plane of ethyl group is perpendicular to the ring plane.All the observed spectral bands have been successfully assigned with the help of our calculations.

  18. Mirror symmetry and vibrational structure in optical spectra of chlorophyll a.

    Science.gov (United States)

    Rätsep, Margus; Linnanto, Juha; Freiberg, Arvi

    2009-05-21

    The absorption and fluorescence emission spectra of chlorophyll a in different organic solvents where the central Mg atom is either penta- or hexacoordinated have been studied using conventional and selective spectroscopy methods at ambient and cryogenic temperatures. A breakdown of the basic model mirror-symmetry rule in relation to the lowest-energy Q(y) transitions was observed due to Franck-Condon and Hertzberg-Teller interactions. Detailed vibrational structure in the ground electronic state, virtually independent of the Mg coordination state, was revealed by hole-burning fluorescence line-narrowing technique. The total Huang-Rhys factor associated with the linear vibronic coupling strength of the solvent collective vibrations and the local chlorophyll a intramolecular vibrations is equal to 0.53+/-0.07 in fluorescence and to 0.39+/-0.05 in absorption. The electron-phonon coupling part was also found to depend on the excitation wavelength within the inhomogeneously broadened absorption origin band, its average value being S(ph) approximately = 0.38. All these numbers qualify for the weak vibronic coupling. A comparison of the conjugate Q(y) absorption and fluorescence emission spectra as well as the temperature dependence of the absorption spectra allowed unambiguous locating of the still controversial Q(x) absorption band position for penta- and hexacoordinated chlorophyll a species. The basic experimental findings have been qualitatively supported by semiempirical quantum chemical calculations.

  19. Vibrational spectra of molecular fluids in nanopores

    Science.gov (United States)

    Arakcheev, V. G.; Morozov, V. B.

    2012-12-01

    Coherent anti-Stokes Raman spectroscopy (CARS) is applied for quantitative analysis of carbon dioxide phase composition in pores of nanoporous glass samples at nearcritical temperatures. Measurements of the 1388 1/cm Q-branch were made in a wide pressure range corresponding to coexistence of gas (gas-like), adsorbed and condensed phases within pores. At temperatures several degrees below the critical value, CARS spectra behavior is easy to interpret in terms of thermodynamic model of surface adsorption and capillary condensation. It allows estimating mass fractions of different phase components. Moreover, spectra measured at near critical temperatures 30.5 and 33°C have pronounced inhomogeneous shapes and indicate the presence of condensed phase in the volume of pores. The effect obviously reflects the fluid behaviour near the critical point in nanopores. Pores with smaller radii are filled with condensed phase at lower pressures. The analysis of the CARS spectra is informative for quantitative evaluation of phase composition in nanopores.

  20. Theoretical prediction on vibrational spectra of [Ar…Ar-H]+

    Institute of Scientific and Technical Information of China (English)

    LI; Wei(李巍); ZHAO; Xinsheng(赵新生)

    2003-01-01

    Centrosymmetric linear [Ar-H-Ar]+ and asymmetric linear [Ar…Ar-H]+ are two stable configurations of [Ar2H]+. Based on the global potential energy surface of [Ar2H]+ provided by our group recently, we calculated the vibrational spectra of [Ar…Ar-H]+ with total angular momentum J = 0 by time-dependent quantum mechanical method, and the influence of quantum tunneling effect on vibrational spectra was found. With the help of the observation on the eigenstate functions and the modified potential energy surface, assignments were made to the spectra. The strong coupling between the excited bending mode of [Ar-H-Ar]+ and the vibrational states of [Ar…Ar-H]+ was discussed.

  1. Vibrational Spectra of N-Butyryl-Homoserine Lactone

    DEFF Research Database (Denmark)

    Bak, Jimmy; Spanget-Larsen, Jens

    in the solid state, and in liquid CCl4 solution. Quantum chemical calculations are performed in order to support the assignment of the measured vibrational bands and explain intermolecular interactions and solvent effects. The resulting designation of the reported spectral bands of C4-HSL lactone demonstrates...... spectra that resembles the measured one was possible. Here we report for the first time the key vibrational band of the monomer form....

  2. Vibrational spectra of pilocarpine hydrochloride crystals

    Energy Technology Data Exchange (ETDEWEB)

    Bento, R.R.F. [Universidade Federal de Mato Grosso (UFMT), Cuiaba, MT (Brazil). Inst. de Fisica; Freire, P.T.C. [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil). Dept. de Fisica]. E-mail: tarso@fisica.ufc.br; Teixeira, A.M.R.; Silva, J.H. [Universidade Regional do Cariri, Crato, CE (Brazil). Dept. Ciencias Fisicas e Biologicas; Lima Junior, J.A. [Universidade Estadual do Ceara (UECE), Limoeiro do Norte, CE (Brazil); Oliveira, M.C.F. de; Andrade-Neto, M. [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil). Dept. de Quimica Organica e Inorganica; Romero, N.R. [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil). Dept. de Farmacia; Pontes, F.M. [Universidade Estadual Paulista, Bauru, SP (Brazil). Faculdade de Ciencias

    2009-03-15

    Pilocarpine is a natural substance with potential application in the treatment of several diseases. In this work Fourier Transform (FT)-Raman spectrum and the Fourier Transform infra red (FT-IR) spectrum of pilocarpine hydrochloride C{sub 11} H{sub 17} N{sub 2} O{sup +}{sub 2} .Cl{sup -1} were investigated at 300 K. Vibrational wavenumber and wave vector have been predicted using density functional theory (B3LYP) calculations with the 6-31 G(d,p) basis set. A comparison with experiment allowed to assign most of the normal modes of the crystal. (author)

  3. Body vibrational spectra of metal flute models

    Science.gov (United States)

    Hurtgen, Clare M.; Lawson, Dewey T.

    2002-11-01

    For years, flutists have argued over the tonal advantages of using different precious metals for their instruments. Occasionally, scientists have entered the fray and attempted to offer an objective point of view based on experimental measurements. However, their research often involved actual instruments and performers, ignoring variations in wall thickness, craftsmanship, and human consistency. These experiments have been conducted using a variety of methods; all have concluded that wall material has no effect on tone. This paper approaches the question using simple tubular models, excited by a wind source through a fipple mouthpiece. The amplitude and phase of the harmonic components of the body vibrational signal were measured with a stereo cartridge. Results demonstrated the existence of complex patterns of wall vibrations in the vicinity of a tone hole lattice, at frequencies that match significant harmonics of the air column. Additionally, the tube wall was found to expand in a nonuniform or ''elliptical'' manner due to the asymmetry of the tone holes. While this method is somewhat removed from direct musical applications, it can provide an objective, quantitative basis for assessing the source of differences among flutes. [Work financed by two Undergraduate Research Support grants from Duke University.

  4. Fluorescence spectra of atomic ensembles in a magneto-optical trap as an optical lattice

    CERN Document Server

    Yoon, Seokchan; Kang, Sungsam; Kim, Wook-Rae; Kim, Jung-Ryul; An, Kyungwon

    2015-01-01

    We present a study on characteristics of a magneto-optical trap (MOT) as an optical lattice. Fluorescence spectra of atoms trapped in a MOT with a passively phase-stabilized beam configuration have been measured by means of the photon-counting heterodyne spectroscopy. We observe a narrow Rayleigh peak and well-resolved Raman sidebands in the fluorescence spectra which clearly show that the MOT itself behaves as a three-dimensional optical lattice. Optical-lattice-like properties of the phase-stabilized MOT such as vibrational frequencies and lineshapes of Rayleigh peak and Raman sidebands are investigated systematically for various trap conditions.

  5. Electronic and vibrational circular dichroism spectra of (R)-(-)-apomorphine

    Energy Technology Data Exchange (ETDEWEB)

    Abbate, Sergio, E-mail: abbate@med.unibs.it [Dipartimento di Scienze Biomediche e Biotecnologie, Universita di Brescia, Viale Europa 11, 25123 Brescia (Italy); CNISM, Consorzio Interuniversitario Scienze Fisiche della Materia, Via della Vasca Navale 84, 00146 Roma (Italy); Longhi, Giovanna; Lebon, France [Dipartimento di Scienze Biomediche e Biotecnologie, Universita di Brescia, Viale Europa 11, 25123 Brescia (Italy); CNISM, Consorzio Interuniversitario Scienze Fisiche della Materia, Via della Vasca Navale 84, 00146 Roma (Italy); Tommasini, Matteo [Dipartimento di Chimica, Materiali e Ingegneria Chimica ' G. Natta' , Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Consorzio Interuniversitario per la Scienza e Tecnologia dei Materiali (INSTM), Unita di Ricerca del Politecnico di Milano (Dip. CMIC), Piazza Leonardo da Vinci 32, 20133 Milano (Italy)

    2012-09-11

    Highlights: Black-Right-Pointing-Pointer ECD and VCD Spectra of (R)-(-)-apomorphine measured in various solvents. Black-Right-Pointing-Pointer DFT calculations allow to study the protonation state and conformations. Black-Right-Pointing-Pointer Contributions from catechol OH vibrations to the VCD spectra is studied. -- Abstract: Apomorphine is a chiral drug molecule; notwithstanding its extraordinary importance, little attention has been paid to the characterization of its chiroptical properties. Here we report on its electronic circular dichroism (ECD) spectra, recorded in methanol and water, and vibrational circular dichroism (VCD) in methanol and dimethyl sulfoxide (DMSO) solutions. Density functional theory (DFT) calculations have allowed us to interpret the spectra and to evaluate the role of possible conformations, charge-states and interactions with counter ions.

  6. Calculation of ground vibration spectra from heavy military vehicles

    Science.gov (United States)

    Krylov, V. V.; Pickup, S.; McNuff, J.

    2010-07-01

    The demand for reliable autonomous systems capable to detect and identify heavy military vehicles becomes an important issue for UN peacekeeping forces in the current delicate political climate. A promising method of detection and identification is the one using the information extracted from ground vibration spectra generated by heavy military vehicles, often termed as their seismic signatures. This paper presents the results of the theoretical investigation of ground vibration spectra generated by heavy military vehicles, such as tanks and armed personnel carriers. A simple quarter car model is considered to identify the resulting dynamic forces applied from a vehicle to the ground. Then the obtained analytical expressions for vehicle dynamic forces are used for calculations of generated ground vibrations, predominantly Rayleigh surface waves, using Green's function method. A comparison of the obtained theoretical results with the published experimental data shows that analytical techniques based on the simplified quarter car vehicle model are capable of producing ground vibration spectra of heavy military vehicles that reproduce basic properties of experimental spectra.

  7. Vibrational Spectra of the Azabenzenes Revisited: Anharmonic Force Fields

    CERN Document Server

    Boese, A D; Martin, Jan M.L.

    2003-01-01

    Anharmonic force fields and vibrational spectra of the azabenzene series (pyridine, pyridazine, pyrimidine, pyrazine, s-triazine, 1,2,3-triazine, 1,2,4-triazine and s-tetrazine) and benzene are obtained using density functional theory (DFT) with the B97-1 exchange-correlation functional and a triple-zeta plus double polarization (TZ2P) basis set. Overall, the fundamental frequencies computed by second-order rovibrational perturbation theory are in excellent agreement with experiment. The resolution of the presently calculated anharmonic spectra is such that they represent an extremely useful tool for the assignment and interpretation of the experimental spectra, especially where resonances are involved.

  8. Analytic calculations of anharmonic infrared and Raman vibrational spectra.

    Science.gov (United States)

    Cornaton, Yann; Ringholm, Magnus; Louant, Orian; Ruud, Kenneth

    2016-02-07

    Using a recently developed recursive scheme for the calculation of high-order geometric derivatives of frequency-dependent molecular properties [Ringholm et al., J. Comp. Chem., 2014, 35, 622], we present the first analytic calculations of anharmonic infrared (IR) and Raman spectra including anharmonicity both in the vibrational frequencies and in the IR and Raman intensities. In the case of anharmonic corrections to the Raman intensities, this involves the calculation of fifth-order energy derivatives-that is, the third-order geometric derivatives of the frequency-dependent polarizability. The approach is applicable to both Hartree-Fock and Kohn-Sham density functional theory. Using generalized vibrational perturbation theory to second order, we have calculated the anharmonic infrared and Raman spectra of the non- and partially deuterated isotopomers of nitromethane, where the inclusion of anharmonic effects introduces combination and overtone bands that are observed in the experimental spectra. For the major features of the spectra, the inclusion of anharmonicities in the calculation of the vibrational frequencies is more important than anharmonic effects in the calculated infrared and Raman intensities. Using methanimine as a trial system, we demonstrate that the analytic approach avoids errors in the calculated spectra that may arise if numerical differentiation schemes are used.

  9. Vibrational spectra and DFT calculations of sonderianin diterpene

    Science.gov (United States)

    Oliveira, I. M. M.; Santos, H. S.; Sena, D. M.; Cruz, B. G.; Teixeira, A. M. R.; Freire, P. T. C.; Braz-Filho, R.; Sousa, J. W.; Albuquerque, M. R. J. R.; Bandeira, P. N.; Bernardino, A. C. S. S.; Gusmão, G. O. M.; Bento, R. R. F.

    2015-11-01

    In the present study, the natural product sonderianin diterpene (C21H26O4), a diterpenoid isolated from Croton blanchetianus, with potential application in the drug industry, was characterized by nuclear magnetic resonance, infrared and Raman spectroscopy. Vibrational spectra were supported by Density Functional Theory calculations. Infrared and Raman spectra of sonderianin were recorded at ambient temperature in the regions from 400 cm-1 to 3600 cm-1 and from 40 cm-1 to 3500 cm-1, respectively. DFT calculations with the hybrid functional B3LYP and the basis set 6-31 G(d,p) were performed with the purpose of obtaining information on the structural and vibrational properties of this organic compound. A comparison with experimental spectra allowed us to assign all of the normal modes of the crystal. The assignment of the normal modes was carried out by means of potential energy distribution.

  10. Quantitative analysis for nonlinear fluorescent spectra based on edges matching

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A novel spectra-edge-matching approach is proposed for the quantitative analysis of the nonlinear fluorescence spectra of the air impurities excited by a femtosecond laser.The fluorescence spectra are first denoised and compressed,both by wavelet transform,and several peak groups are then picked from each spectrum according to a threshold of intensity and are used to extract the spectral features through principal component analysis.It is indicated that the first two principle components actually cover up to 98% of the total information and are sufficient for the final concentration analysis.The analysis reveals a monotone relationship between the spectra intensity and the concentration of the air impurities,suggesting that the femtosecond laser induced fluorescence spectroscopy along with the proposed spectra analysis method can become a powerful tool for monitoring environmental pollutants.

  11. Structure and Vibrational Spectra of Slags Produced from Radioactive Waste

    Science.gov (United States)

    Malinina, G. A.; Stefanovsky, S. V.

    2014-05-01

    The structure of the anionic motif of aluminosilicate and aluminoborosilicate glasses containing simulated slags from a solid radioactive waste incinerator was studied by IR and Raman spectroscopy. Spectra of melted slag were consistent with Si-O tetrahedra with various numbers of bridging O ions and Al-O tetrahedra embedded in the Si-O network in the slag vitreous and crystalline phases (nepheline, nagelschmidtite). Vibrations of doubly and triply bound Si-O tetrahedra and Al-O tetrahedra embedded between them were mainly responsible for the spectra as the content of sodium disilicate fl ux and the glass fraction in the materials increased. Addition of sodium tetraborate fl ux caused the appearance of B-O vibrations of predominantly three-coordinate B and a tendency toward chemical differentiation preceding phase separation.

  12. NONLINEARLY VIBRATIONAL ENERGY-SPECTRA OF MOLECULAR CRYSTALS

    Institute of Scientific and Technical Information of China (English)

    PANG XIAO-FENG; CHEN XIANG-RONG

    2000-01-01

    The nonlinear quantum vibrational energy spectra of amide-I in the molecular crystals acetanilide are calculatedby using the discrete nonlinear Schrodinger equation appropriate to this kind of crystals. The numerical results obtainedby this method are in good agreement with the experimental values. Meanwhile, the energy levels at high excited stateshave also been obtained for the acetanilide, which is helpful in researching the Raman scattering and infrared absorptionproperties of the this kind of crystals.

  13. Analyzing of LED-induced Blood Fluorescent Spectra

    Institute of Scientific and Technical Information of China (English)

    高淑梅; 骆晓森; 兰秀风; 刘莹; 陆健; 倪晓武

    2002-01-01

    The visible fluorescence spectra of healthy mice blood cells have been measured by light emitting diode (LED) excitation at about 570 nm (Δλ1/2≈32 nm ) in vitro. It is found that the spectral profiles of mouse blood, erythrocyte and hemoglobin are similar. The physical mechanism for LED-induced blood cells fluorescence spectra is analyzed. The development of low intensity laser or light irradiating blood therapy in vivo and in vitro may be guided by the understanding of blood fluorescence characteristics.

  14. Vibrational spectra of berberine and their interpretation by means of DFT quantum-mechanical calculations

    CERN Document Server

    Bashmakova, N; Zhurakivsky, R; Hovorun, D; Yashchuk, V

    2011-01-01

    Experimental vibrational spectra (Raman and infrared absorption) of berberine are obtained at room temperature. The vibrational spectra of berberine are calculated by the DFT method at the B3LYP/6-311++G(d,p) level. Based on the correlation between experimental and calculated data, the vibrational spectrum is interpreted in the frequency range of 800-1700 cm-1 in detail. The experimental and calculated spectra of intramolecular vibrations are found to correlate closely

  15. Electronic and vibrational spectra of some rare earth trifluoromethanesulfonates crystals

    Science.gov (United States)

    Paul, P.; Ghosh, M.; Neogy, D.; Mallick, P. K.

    2011-01-01

    The Raman and infrared spectra of some rare earth (dysprosium and terbium) trifluoromethanesulfonates crystals have been analyzed. Different vibrational frequencies of trifluoromethanesulfonate ions (CF 3SO 3-) are identified and assigned to different vibrations of the SO 3 and CF 3 groups. Electronic transitions of R 3+ ions (R = Dy, Tb) in these salts have been assigned to transitions from the ground to different energy levels of the ground multiplet. The electronic energy levels of the rare earth ions are also determined theoretically with the help of single electron crystal field theory. They are found to yield results not only in good agreement with the observed spectral data but also in good conformity with those obtained previously from magnetic measurements.

  16. Discrimination of phytoplankton classes using characteristic spectra of 3D fluorescence spectra.

    Science.gov (United States)

    Zhang, Qian-Qian; Lei, Shu-He; Wang, Xiu-Lin; Wang, Lei; Zhu, Chen-Jian

    2006-02-01

    The discrimination of phytoplankton classes using the characteristic fluorescence spectra extracted from three-dimensional fluorescence spectra was investigated. Single species cultures of 11 phytoplankton species, representing 5 major phytoplankton divisions, were used. The 3D fluorescence spectra of the cultures grown at different temperatures (20 and 15 degrees C) and illumination intensities (140, 80 and 30 microM m(-2) s(-1)) were measured and their feature extraction methods were explored. Ordering Rayleigh and Raman scattering data as zero, the obtained excitation-emission matrices were processed by both singular value decomposition (SVD) and trilinear decomposition methods. The resulting first principal component can be regarded as the characteristic spectrum of the original 3D fluorescence spectrum. The analysis shows that such characteristic spectra have a discriminatory capability. At different temperatures, the characteristic spectra of Isochrysis galbana, Platymonas helgolanidica and Skeletonema costatuma have high degrees of similarity to their own species samples, while the spectra similarities of Alexandrium tamarense, Prorocentrum dentatum, Pseudo-nitzschia pungens, Chaetoceros curvisetus, Ch. Debilis, Ch. Didymus and Synechococcus sp. are not as significant as the other three species. C. curvisetus, Ch. Debilis and Ch. Didymus, belonging to genus Chaetoceros, have identical spectra and cannot be discriminated at all. Regarding all six diatom species as one class, the average discriminant error rate is below 9%. It is worth mentioning that the diatom class can be distinguished from A. tamarense and P. dentatum, which belong to Dinophyta.

  17. Discrimination of phytoplankton classes using characteristic spectra of 3D fluorescence spectra

    Science.gov (United States)

    Zhang, Qian-Qian; Lei, Shu-He; Wang, Xiu-Lin; Wang, Lei; Zhu, Chen-Jian

    2006-02-01

    The discrimination of phytoplankton classes using the characteristic fluorescence spectra extracted from three-dimensional fluorescence spectra was investigated. Single species cultures of 11 phytoplankton species, representing 5 major phytoplankton divisions, were used. The 3D fluorescence spectra of the cultures grown at different temperatures (20 and 15 °C) and illumination intensities (140, 80 and 30 μM m -2 s -1) were measured and their feature extraction methods were explored. Ordering Rayleigh and Raman scattering data as zero, the obtained excitation-emission matrices were processed by both singular value decomposition (SVD) and trilinear decomposition methods. The resulting first principal component can be regarded as the characteristic spectrum of the original 3D fluorescence spectrum. The analysis shows that such characteristic spectra have a discriminatory capability. At different temperatures, the characteristic spectra of Isochrysis galbana, Platymonas helgolanidica and Skeletonema costatuma have high degrees of similarity to their own species samples, while the spectra similarities of Alexandrium tamarense, Prorocentrum dentatum, Pseudo-nitzschia pungens, Chaetoceros curvisetus, Ch. Debilis, Ch. Didymus and Synechococcus sp. are not as significant as the other three species. C. curvisetus, Ch. Debilis and Ch. Didymus, belonging to genus Chaetoceros, have identical spectra and cannot be discriminated at all. Regarding all six diatom species as one class, the average discriminant error rate is below 9%. It is worth mentioning that the diatom class can be distinguished from A. tamarense and P. dentatum, which belong to Dinophyta.

  18. Absorption and fluorescence spectra of poly(p-phenylenevinylene) (PPV) oligomers: an ab initio simulation.

    Science.gov (United States)

    Cardozo, Thiago M; Aquino, Adélia J A; Barbatti, Mario; Borges, Itamar; Lischka, Hans

    2015-03-05

    The absorption and fluorescence spectra of poly(p-phenylenevinylene) (PPV) oligomers with up to seven repeat units were theoretically investigated using the algebraic diagrammatic construction method to second order, ADC(2), combined with the resolution-of-the-identity (RI) approach. The ground and first excited state geometries of the oligomers were fully optimized. Vertical excitation energies and oscillator strengths of the first four transitions were computed. The vibrational broadening of the absorption and fluorescence spectra was studied using a semiclassical nuclear ensemble method. After correcting for basis set and solvent effects, we achieved a balanced description of the absorption and fluorescence spectra by means of the ADC(2) approach. This fact is documented by the computed Stokes shift along the PPV series, which is in good agreement with the experimental values. The experimentally observed band width of the UV absorption and fluorescence spectra is well reproduced by the present simulations showing that the nuclear ensemble generated should be well suitable for consecutive surface hopping dynamics simulations.

  19. Vibrational spectra of solid solution series with ordered perovskite structure

    NARCIS (Netherlands)

    Blasse, G.

    1975-01-01

    I.R. and Raman spectra are reported for the following three systems: Ba2CaMo1−xTexO6, Ba2−xSrxMgWO6 and Ba2Ca1−xMgxWO6. In the first series the internal vibrations of the M6+O6 octahedra do not influence each other. The intensity of ν1 (MoO6) is five times that of ν1 (TeO6). In the second system the

  20. Vibrational spectra of 3,5-dimethylpyrazole and deuterated derivatives.

    Science.gov (United States)

    Orza, J M; García, M V; Alkorta, I; Elguero, J

    2000-07-01

    The infrared (IR) and Raman spectra of 3,5-dimethylpyrazole have been recorded in the vapor, liquid (melt and solution) and solid states. Two deuterated derivatives, C5H7N-ND and C5D7N-NH, were also studied in solid state and in solutions. Instrumental resolution was relatively low, 2.0 cm(-1) in the IR and approximately 2.7 cm(-1) in the Raman spectra. The solids are made of cyclic hydrogen-bonded trimers. These trimers, present also in chloroform and acetone solutions, give rise to characteristic high absorption IR spectra in the 3200-2500 cm(-1) region, related to Fermi resonance involving nu(NH) vibrations. Bands from trimers are not present in water solutions but these solutions show spectral features similar in several ways to those of the trimer, attributable to solvent-bonded complexes. Evidence of H-bonding interactions with the other solvents is also visible in the high-frequency region. The two very intense bands in the Raman spectra of the solids appearing at 115 and 82 cm(-1) in the parent compound are also connected with a trimer formation. To interpret the experimental data, ab initio computations of the harmonic vibrational frequencies and IR and Raman intensities were carried out using the Gaussian 94 program package after full optimization at the RHF/6-31G* level for the three monomeric compounds as well as for three models of the trimer, with C3h, C3 and C1 symmetry. The combined use of experiments and computations allow a firm assignment of most of the observed bands for all the systems. In general, the agreement between theory and experiment is very good, with the exception of the IR and Raman intensities of some transitions. Particularly noticeable is the failure of the theoretical calculation in accounting for the high intensity of the Raman bands of the solid about 115 and 82 cm(-1).

  1. Fluorescence Spectra Studies on the Interaction between Lanthanides and Calmodulin

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    The conformation of Calmodulin(CaM) induced by lanthanides has been examined using fluorescence methods.With the addition of lanthanide (Ln3+), the intrinsic fluorescence intensity of CaM without calcium ions (Apo-CaM) first increases and then decreases.Ln3+ causes the decrease of intrinsic fluorescence intensity of calcium saturated CaM (Ca2+4-CaM) only at high concentrations.At low concentrations, Ln3+ results not only in the enhancement of fluorescence intensity of Apo-CaM, but also in a blue shift of the maximum emission wavelengh of dansyl labeled calmodulin(Apo-D-CaM).The molecular mechanism of the interaction between Ln3+ and CaM has been discussed in the light of the fluorescence spectra.

  2. Vibrational spectra and force constants of symmetric tops

    Science.gov (United States)

    Lattanzi, F.; di Lauro, C.; Bürger, H.; Eujen, R.; Schulz, P.; Cradock, S.

    The infrared spectra of the monoisotopic species H3 74Ge 79Br and H3 74Ge 81Br in the 750-1000 cm-1 region covering the vibrations v2, v5 and v3 + v6 have been recorded with a resolution of 0·04 cm-1 and rotationally analysed. In addition, information concerning the hot band (v3 + v5) - v3 has been obtained and data on v6 and (v3 + v6) - v3 have been used. Fermi resonance between v5 and v3 + v6 has been established with |W356| = 4·4067(7)/4·3055(8) cm-1 (79/81Br) and the Coriolis x, y resonance linking v2 with v5 has been evaluated. Sets of vibration-rotation parameters for the three bands have been determined by least squares calculations, σ(J, K) = 9·4/9·5 × 10-3 cm-1. The vibrational frequencies are v20 = 831·825(1)/831·796(1), v50 = 872·612(1)/872·601(1) and (v3 + v6)0 = 882·551(3)/880·647(4) cm-1.

  3. Lifetime-vibrational interference effects in resonantly excited x-ray emission spectra of CO

    Energy Technology Data Exchange (ETDEWEB)

    Skytt, P.; Glans, P.; Gunnelin, K. [Uppsala Univ. (Sweden)] [and others

    1997-04-01

    The parity selection rule for resonant X-ray emission as demonstrated for O{sub 2} and N{sub 2} can be seen as an effect of interference between coherently excited degenerate localized core states. One system where the core state degeneracy is not exact but somewhat lifted was previously studied at ALS, namely the resonant X-ray emission of amino-substituted benzene (aniline). It was shown that the X-ray fluorescence spectrum resulting from excitation of the C1s at the site of the {open_quotes}aminocarbon{close_quotes} could be described in a picture separating the excitation and the emission processes, whereas the spectrum corresponding to the quasi-degenerate carbons could not. Thus, in this case it was necessary to take interference effects between the quasi-degenerate intermediate core excited states into account in order to obtain agreement between calculations and experiment. The different vibrational levels of core excited states in molecules have energy splittings which are of the same order of magnitude as the natural lifetime broadening of core excitations in the soft X-ray range. Therefore, lifetime-vibrational interference effects are likely to appear and influence the band shapes in resonant X-ray emission spectra. Lifetime-vibrational interference has been studied in non-resonant X-ray emission, and in Auger spectra. In this report the authors discuss results of selectively excited soft X-ray fluorescence spectra of molecules, where they focus on lifetime-interference effects appearing in the band shapes.

  4. [Study on fluorescence spectra of Chinese rice wine].

    Science.gov (United States)

    Liu, Zhou-yi; Zhu, Tuo; Gu, En-dong; Liu, Ying; Song, Chun-yuan

    2008-10-01

    Chinese rice wine has a history of more than 5000 years, only in China, hich is called "Nation Wine", and Shao Xing Chinese rice wine is a representative of it. The fluorescence spectra of 3 kinds of Shao Xing Chinese rice wine with different storage age induced by suitable UV-light were obtained in the present paper through experiment. The authors compared and analyzed them comprehensively by using three dimensional contour and two dimensional fluorescence technique, and found that their best induced light was all in the vicinity of 370 nm. The peak wavelength of 3 year storage age wine was 504 nm, while 488 nm and 505 nm were for 5 and 8 year storage age wine respectively. The emitted fluorescence existed in 400 to 680 nm, which had wide peak. More over, the emitting mechanism of Shao Xing Chinese rice wine was discussed. The authors also have explained the similarity and difference of fluorescence spectra among the 3 kinds of wine. The reason for wide fluorescence peak was also analyzed. This investigation contributes to the study of the characteristic, year detection and food safety of Chinese rice wine.

  5. Rotational spectra of HCCCN in some excited vibrational states

    Science.gov (United States)

    Yamada, Koichi M. T.; Creswell, R. A.

    1986-04-01

    The rotational spectra have been measured up to 220 GHz for HCCCN in excited vibrational states up to about 1000 cm -1; the states of ( v4, v5, v6, v7) = (0, 0, 0, 1), (0, 0, 0, 2), (0, 0, 0, 3), (0, 0, 0, 4), (0, 0, 1, 0), (0, 0, 1, 1), (0, 0, 1, 2), (0, 0, 2, 0), (0, 1, 0, 0), (0, 1, 0, 1), (1, 0, 0, 0), and (1, 0, 0, 1). Accurate molecular constants have been determined using an effective Hamiltonian newly proposed by K. M. T. Yamada, F. W. Birss, and M. R. Aliev ( J. Mol. Spectrosc.112, 347-356 (1985). By analyzing the anharmonic resonances, the unperturbed rotational constants for the v4 = 1 and for the v5 = 1 states were obtained as 4537.958(15) and 4550.6218(35) MHz, respectively.

  6. Temperature-dependent THz vibrational spectra of clenbuterol hydrochloride

    Science.gov (United States)

    Yang, YuPing; Lei, XiangYun; Yue, Ai; Zhang, Zhenwei

    2013-04-01

    Using the high-resolution Terahertz Time-domain spectroscopy (THz-TDS) and the standard sample pellet technique, the far-infrared vibrational spectra of clenbuterol hydrochloride (CH), a β 2-adrenergic agonist for decreasing fat deposition and enhancing protein accretion, were measured in temperature range of 77-295 K. Between 0.2 and 3.6 THz (6.6-120.0 cm-1), seven highly resolved spectral features, strong line-narrowing and a frequency blue-shift were observed with cooling. However, ractopamine hydrochloride, with some structural and pharmacological similarities to clenbuterol hydrochloride, showed no spectral features, indicating high sensitivity and strong specificity of THz-TDS. These results could be used for the rapid and nondestructive CH residual detection in food safety control.

  7. Conformational study of neutral histamine monomer and their vibrational spectra

    Science.gov (United States)

    Mukherjee, V.; Yadav, T.

    2016-08-01

    Molecular modeling and potential energy scanning of histamine molecule, which is an important neurotransmitter, with respect to the dihedral angle of methylamine side chain have done which prefer three different conformers of histamine monomer. We have calculated molecular structures and vibrational spectra with IR and Raman intensities of these conformers using Density Functional Theory (DFT) with the exchange functional B3LYP incorporated with the basis set 6-31 ++G(d,p) and Hartree-Fock (HF) with the same basis set. We have also employed normal coordinate analysis (NCA) to scale the theoretical frequencies and to calculate potential energy distributions (PEDs) for the conspicuous assignments. Normal modes assignments of some of the vibrational frequencies of all the three conformers are in good agreement with the earlier reported experimental frequencies of histamine whereas others have modified. The standard deviations between the theoretical and experimental frequencies fall in the region 13-20 cm- 1 for the three conformers. NBO analyses of histamine conformers were also performed. The net charge transfers from ethylamine side chain to the imidazole ring. The intensive interactions between bonding and anti-bonding orbitals are found in imidazole ring. The HOMO-LUMO energy gap is nearly 5.50 eV.

  8. The harmonic force field and vibrational spectra of pyrrole

    Science.gov (United States)

    Xie, Yaoming; Fan, Kangnian; Boggs, James E.

    The complete harmonic vibrational force field of pyrrole has been calculated by the ab initio gradient method at the Hartree-Fock level using the 4-21 basis set. The force field was then scaled with a set of six factors transferred from benzene, and the vibrational spectrum of pyrrole was calculated. This a priori prediction, made with no reference to observations on pyrrole, agreed with the known experimental fundamental frequencies with a mean deviation of 12 cm-1 for in-plane modes and 20 cm-1 for out-of-plane modes except for the NH wagging and NH stretch. A new set of ten scale factors was next obtained by direct fitting of the computed force field to the observed pyrrole spectrum, producing the best force field obtainable by combined use of the theoretical and experimental information. This force field reproduced the entire pyrrole spectrum with mean deviations of 4·2 cm-1 (in-plane) and 5·9 cm-1 (out-of-plane). The spectra of three deuterated forms of pyrrole were also computed. Infrared absorption intensities were calculated and proved very useful in examining assignments of the two ring torsional modes and the CH stretching modes.

  9. Vibrational spectra, electronic and quantum mechanical investigations on ciprofloxacin

    Science.gov (United States)

    Rajalakshmi, K.; Gunasekaran, S.; Kumaresan, S.

    2014-07-01

    The Fourier transform infrared and FT-Raman spectra of ciprofloxacin have been recorded in region 4,000-400 and 4,000-100 cm-1, respectively. A complete assignment and analysis of fundamental vibrational modes of the molecule have been carried out. The observed fundamental modes have been compared with harmonic vibrational frequencies computed using density functional theory calculations by employing B3LYP functional at 6-31 G ( d, p) level. The most stable geometry of compound under investigation has been determined from potential energy scan. The first-order hyperpolarizability ( β o ) and other related properties ( μ, α o ) of ciprofloxacin have been calculated using this theory on a finite field approach. UV-vis spectrum of the compound has been recorded and electronic properties, such as highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies have been calculated with B3LYP/6-31 G ( d, p) level. These calculated energies show that charge transfer occurs within molecule. The other molecular properties like molecular electrostatic potential, Mulliken population analysis and thermodynamic properties of title compound have also been calculated.

  10. Interpretation of fluorescence correlation spectra of biopolymer solutions.

    Science.gov (United States)

    Phillies, George D J

    2016-05-01

    Fluorescence correlation spectroscopy (FCS) is regularly used to study diffusion in non-dilute "crowded" biopolymer solutions, including the interior of living cells. For fluorophores in dilute solution, the relationship between the FCS spectrum G(t) and the diffusion coefficient D is well-established. However, the dilute-solution relationship between G(t) and D has sometimes been used to interpret FCS spectra of fluorophores in non-dilute solutions. Unfortunately, the relationship used to interpret FCS spectra in dilute solutions relies on an assumption that is not always correct in non-dilute solutions. This paper obtains the correct form for interpreting FCS spectra of non-dilute solutions, writing G(t) in terms of the statistical properties of the fluorophore motions. Approaches for applying this form are discussed.

  11. [Vibrational spectra of Caesious nephrite from Qinghai Province].

    Science.gov (United States)

    Chen, Quan-li; Xu, Ya-lan; Ai, Su-jie; He, An-qi; Yin, Zuo-wei

    2014-08-01

    Qinghai caesious nephrite is discovered in the 1990s in the Golmud area of Qinghai Province. The conventional gemological testing methods, electron microprobe, infrared absorption spectroscopy and Raman spectroscopy were used in this study to analyze the chemical composition and infrared spectra characteristics of the caesious nephrite, selected from the jade mine of Xiaozhaohuo river in Golmud area. The results show that, the gemological physical properties of the Qinghai caesious nephrite are similar to other origin nephrite. Electron microprobe analysis indicates that the MgO, CaO and SiO2 are the major and stable composition for the caesious nephrite. The content of MgO and CaO are 18. 572%-23.603% and 12.333%-12.807% respectively. Moreover, the content of SiO2 is 56.799%-59.926%. In addition, it also contains a higher content of FeOr(Wt%: 1.924%-8.699%) and an amount of Al2O3, TiO2 and Na2O. Infrared absorption and Raman spectra show that the Qinghai caesious nephrite has a characteristic spectral features of tremolite indicating it is mainly composed of tremolite. The different frequency of the infrared absorption bands is due to the difference of Mg--Fe2+ isomorphous substitutionand Fe2+ content of the caesious nephrite. Comprehensive analysis of chemical composition and vibrational spectroscopy indicate that the color of dark gray blue for the Qinghai nephrite is mainly related to its high content of FeOr, and the Fe is a main coloring element.

  12. Tautomerism of 4-hydrazinoquinazolines: vibrational spectra and computational study

    Directory of Open Access Journals (Sweden)

    Tetiana Yu. Sergeieva

    2014-03-01

    Full Text Available The tautomerism of 4-hydrazinoquinazoline and its derivatives was investigated. Geometry and thermodynamic parameters were computed theoretically using Gaussian 03 software. All calculations were performed at the MP2 level of theory using the standard 6-31G(d basis. Energetics and relative stabilities of tautomers were compared and analyzed in a gas phase. The effect of solvents (1,4-dioxane, acetic acid, ethanol and water on the tautomeric equlibria was evaluated using PCM. It was determined that solvents induced slight changes in the relative stability. In all cases 4-hydrazinoquinazoline exists predominantly as the amino form. The variation of dipole moments was studied. The anharmonic vibrational wavenumbers for unsubstituted 4-hydrazinoquinazoline were calculated at MP2/6-31G(d level and compared with experimental data. The modes of IR spectra were assigned. The calculated herein wavenumbers and intensities of amino form are in good agreement with those observed experimentally.      

  13. Practical use of corrected fluorescence excitation and emission spectra of fluorescent proteins in Förster Resonance Energy Transfer (FRET) studies

    NARCIS (Netherlands)

    Hink, M.A.; Visser, N.V.; Borst, J.W.; Hoek, van A.; Visser, A.J.W.G.

    2003-01-01

    Corrected fluorescence excitation and emission spectra have been obtained from several enhanced variants of the green fluorescent protein (EGFP) isolated from the jellyfish Aequorea victoria, blue fluorescence protein (EBFP), cyan fluorescent protein (ECFP), EGFP and yellow fluorescent protein (EYFP

  14. Practical use of corrected fluorescence excitation and emission spectra of fluorescent proteins in Förster Resonance Energy Transfer (FRET) studies

    NARCIS (Netherlands)

    Hink, M.A.; Visser, N.V.; Borst, J.W.; Hoek, van A.; Visser, A.J.W.G.

    2003-01-01

    Corrected fluorescence excitation and emission spectra have been obtained from several enhanced variants of the green fluorescent protein (EGFP) isolated from the jellyfish Aequorea victoria, blue fluorescence protein (EBFP), cyan fluorescent protein (ECFP), EGFP and yellow fluorescent protein

  15. A study of aliphatic amino acids using simulated vibrational circular dichroism and Raman optical activity spectra

    CERN Document Server

    Ganesan, Aravindhan; Wang, Feng

    2013-01-01

    Vibrational optical activity (VOA) spectra, such as vibrational circular dichroism (VCD) and Raman optical activity (ROA) spectra, of aliphatic amino acids are simulated using density functional theory (DFT) methods in both gas phase (neutral form) and solution (zwitterionic form), together with their respective infrared (IR) and Raman spectra of the amino acids. The DFT models, which are validated by excellent agreements with the available experimental Raman and ROA spectra of alanine in solution, are employed to study other aliphatic amino acids. The inferred (IR) intensive region (below 2000 cm-1) reveals the signature of alkyl side chains, whereas the Raman intensive region (above 3000 cm-1) contains the information of the functional groups in the amino acids. Furthermore, the chiral carbons of the amino acids (except for glycine) dominate the VCD and ROA spectra in the gas phase, but the methyl group vibrations produce stronger VCD and ROA signals in solution. The C-H related asymmetric vibrations domina...

  16. Vibrational spectra of (BaF2)n (n=1-6) clusters

    Science.gov (United States)

    Pandey, Ratnesh K.; Waters, Kevin; Nigam, Sandeep; Pandey, Ravindra; Pandey, Avinash C.

    2016-05-01

    The vibrational properties of alkaline-earth metal fluoride clusters (BaF2)n (n=1-6) are investigated in the framework of density functional theory. The calculated Raman and Infrared (IR) spectra reveals shift in Raman and IR peak position towards lower frequency region with the increase in the cluster size. Further the calculated spectra have been compared with the experimental vibrational spectra of bulk BaF2 crystal. Even though the smaller size cluster lacks translational symmetry, the structural and vibrational characteristic of (BaF2)5-6 are nearer to bulk counterpart.

  17. Theoretical structure and vibrational spectra of ciprofloxacin: Density functional theory study

    Science.gov (United States)

    Yang, Yue; Gao, Hongwei

    2013-02-01

    The molecular structure and vibrational spectra of ciprofloxacin(1-cyclopropyl-6-fluoro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid) have been calculated using the different density functional theory (DFT) methods and various basis sets. This paper examines the comparative performance of different DFT methods at various basis sets in predicting molecular and vibrational spectra of ciprofloxacin. The calculation results show that SVWN/LANL2DZ level and SVWN/6-31G level offer the highest certainty to predict the structure and vibrational spectra of ciprofloxacin, respectively.

  18. Vibrational spectra, ab initio calculations and vibrational assignments of 3-butyn-1-ol

    Science.gov (United States)

    Nielsen, Claus J.; Horn, Anne; Klaeboe, Peter; Guirgis, Gamil A.

    2008-08-01

    The infrared spectra of 3-butyn-1-ol, HC tbnd CCH 2CH 2OH, have been recorded as a vapour in the range 3600-50 cm -1 and as a liquid between 3600 and 400 cm -1. Additional spectra of the alcohol isolated in an argon matrix at ca. 5 K were obtained and spectra were recorded after annealing to various temperatures between 10 and 35 K. Raman spectra of the liquid were recorded at room temperature and at various temperatures between 295 and 143 K. Spectra of an amorphous solid were recorded at 78 K. In spite of several attempts and many different annealing temperatures, the sample crystallized neither in the IR nor in the Raman cryostats. In the variable temperature Raman spectra, some bands of the liquid changed in relative intensity and were interpreted in terms of conformational equilibria between two of the five possible conformers. Complete assignments were made for all the bands of the most stable conformer gg, in which the OH group is approaching the triple bond, forming an intramolecular hydrogen bond. From various bands assigned to a second conformer aa, in which OH is oriented anti to the sbnd C tbnd C sbnd bond, or a third conformer ag, the conformational enthalpy difference was found to be Δ confH( ag-gg) = 0.9 kJ mol -1 in the liquid. The two highest energy conformers g'g and ag were not detected. Quantum-chemical calculations have been carried out at the MP2 and B3LYP levels with a variety of basis sets. The calculations revealed that gg was the low energy conformer and CBS-QB3 calculations suggested the gg conformer was more stable by 5.4 and 4.2 kJ mol -1 relative to ag and aa, respectively, in the vapour. Vibrational wavenumbers and infrared and Raman band intensities for the three low energy conformers are reported from B3LYP/cc-pVTZ calculations.

  19. Laser-Excited Fluorescence Spectra of Strontium Monoiodide.

    Science.gov (United States)

    Bernard; Effantin; d'incan; Topouzkhanian; Wannous

    1999-05-01

    Fluorescence spectra of strontium monoiodide excited by Ar++ and Kr+ laser lines have been analyzed by Fourier transform spectrometry. Rotational levels have been populated either directly or after collisional relaxation: (i) in D2Sigma+ (v = 0, 1) by ultraviolet lines of Ar++, inducing numerous fluorescence transitions ending in the levels v = 0-3 of the strongly interacting A2Pi and B2Sigma+ states, (ii) in A2Pi3/2 (v = 0-4) by Kr+ line at 676.44 nm, de-exciting into transitions to X2Sigma+ (v = 0-6). Deperturbed constants for A2Pi and B2Sigma+ states and A approximately B interaction parameter are calculated from the numerical treatment of D2Sigma+ (v = 0, 1) --> A2Pi (v = 0-3) approximately B2Sigma+ (v = 0-3) transitions. Rotational constants for D2Sigma+ (v = 0, 1) are obtained for the first time. The wavenumbers of some 670 fluorescence lines are cataloged. Copyright 1999 Academic Press.

  20. Fermi resonance-algebraic model for molecular vibrational spectra

    Institute of Scientific and Technical Information of China (English)

    侯喜文; 董世海; 谢汨; 马中骐

    1999-01-01

    A Fermi resonance-algebraic model is proposed for molecular vibrations, where a U(2) algebra is used for describing the vibrations of each bond, and Fermi resonances between stretching and bending modes are taken into account. The model for a bent molecule XY2 and a molecule XY3 is successfully applied to fitting the recently observed vibrational spectrum of the water molecule and arsine (AsH3), respectively, and the results are compared with those of other models. Calculations show that algebraic approaches can be used as an effective method to describe molecular vibrations with small standard deviations.

  1. [Study on the characters of phytoplankton chlorophyll fluorescence excitation spectra based on fourth-derivative].

    Science.gov (United States)

    Lu, Lu; Su, Rong-Guo; Wang, Xiu-Lin; Zhu, Chen-Jian

    2007-11-01

    Chlorophyll fluorescence excitation spectra of six phytoplankton species, belonging to Bacillariophyta and Dinophyta, were dealt by fourth-derivative analysis with the Matlab program. The results show that between 350 nm and 550 nm six fluorescence peaks were found in the fourth-derivative spectra, which are representatives of non-pigments, chlorophylls and carotenoides respectively. The method makes Bacillariophyta and Dinophyta more distinguishable when the fourth-derivative spectra are compared with the chlorophyll fluorescence excitation spectra. It can be used not only to discriminate the two groups of algaes, but also to reduce the effect of noise. The fluorescence peaks in the fourth-derivative spectra are proved to be stable.

  2. Studies on the full vibrational energy spectra for some electronic states of diatomic molecular ions XY+

    Institute of Scientific and Technical Information of China (English)

    LIU Yi-ding; SUN Wei-guo; REN Wei-yi

    2006-01-01

    The first accurate studies on the vibrational spectroscopic constants and the corresponding full vibrational energy spectra of some electronic states of diatomic molecular ions XY+ were performed using algebraic method(AM).The AM is applied on the X1Σ+ state of BeH+,the X2Σ+ state of CO+ , the X21-Π state of F2+ the A2Πu state of O2+ and theX2Σ+g Li2+.The results show that AM can generate accurate vibrational spectroscopic constants as well as accurate full vibrational energy spectra by using some accurate experimental vibrational energies,and that the AM vibrational energies are better than other theoretical data.

  3. Structure and vibrational spectra of a model of a-Si:H with periodic boundary conditions

    Energy Technology Data Exchange (ETDEWEB)

    Winer, K.; Wooten, F.

    1983-08-01

    A ball-and -stick model of a-Si:H with periodic boundary conditions has been constructed. A computer replica of the structure has been relaxed and the density, radial distribution function and vibrational spectra calculated.

  4. Fluorescence and FTIR Spectra Analysis of Trans-A2B2-Substituted Di- and Tetra-Phenyl Porphyrins

    Directory of Open Access Journals (Sweden)

    Chantal Andraud

    2010-08-01

    Full Text Available A series of asymmetrically substituted free-base di- and tetra-phenylporphyrins and the associated Zn-phenylporphyrins were synthesized and studied by X-ray diffraction, NMR, infrared, electronic absorption spectra, as well as fluorescence emission spectroscopy, along with theoretical simulations of the electronic and vibration structures. The synthesis selectively afforded trans-A2B2 porphyrins, without scrambling observed, where the AA and BB were taken as donor- and acceptor-substituted phenyl groups. The combined results point to similar properties to symmetrically substituted porphyrins reported in the literature. The differences in FTIR and fluorescence were analyzed by means of detailed density functional theory (DFT calculations. The X-ray diffraction analysis for single crystals of zinc-containing porphyrins revealed small deviations from planarity for the porphyrin core in perfect agreement with the DFT optimized structures. All calculated vibrational modes (2162 modes for all six compounds studied were found and fully characterized and assigned to the observed FTIR spectra. The most intense IR bands are discussed in connection with the generic similarity and differences of calculated normal modes. Absorption spectra of all compounds in the UV and visible regions show the typical ethio type feature of meso-tetraarylporphyrins with a very intense Soret band and weak Q bands of decreasing intensity. In diphenyl derivatives, the presence of only two phenyl rings causes a pronounced hypsochromic shift of all bands in the absorption spectra. Time-dependent DFT calculations revealed some peculiarities in the electronic excited states structure and connected them with vibronic bands in the absorption and fluorescence spectra from associated vibrational sublevels.

  5. Investigation of fluorescence spectra disturbances influencing the classification performance of fluorescently labeled plastic flakes

    Science.gov (United States)

    Fomin, Petr; Brunner, Siegfried; Kargel, Christian

    2013-04-01

    The recycling of plastic products becomes increasingly attractive not only from an environmental point of view, but also economically. For recycled (engineering) plastic products with the highest possible quality, plastic sorting technologies must provide clean and virtually mono-fractional compositions from a mixture of many different types of (shredded) plastics. In order to put this high quality sorting into practice, the labeling of virgin plastics with specific fluorescent markers at very low concentrations (ppm level or less) during their manufacturing process is proposed. The emitted fluorescence spectra represent "optical fingerprints" - each being unique for a particular plastic - which we use for plastic identification and classification purposes. In this study we quantify the classification performance using our prototype measurement system and 15 different plastic types when various influence factors most relevant in practice cause disturbances of the fluorescence spectra emitted from the labeled plastics. The results of these investigations help optimize the development and incorporation of appropriate fluorescent markers as well as the classification algorithms and overall measurement system in order to achieve the lowest possible classification error rates.

  6. Calculating vibrational spectra without determining excited eigenstates: Solving the complex linear equations of damped response theory for vibrational configuration interaction and vibrational coupled cluster states.

    Science.gov (United States)

    Godtliebsen, Ian H; Christiansen, Ove

    2015-10-07

    It is demonstrated how vibrational IR and Raman spectra can be calculated from damped response functions using anharmonic vibrational wave function calculations, without determining the potentially very many eigenstates of the system. We present an implementation for vibrational configuration interaction and vibrational coupled cluster, and describe how the complex equations can be solved using iterative techniques employing only real trial vectors and real matrix-vector transformations. Using this algorithm, arbitrary frequency intervals can be scanned independent of the number of excited states. Sample calculations are presented for the IR-spectrum of water, Raman spectra of pyridine and a pyridine-silver complex, as well as for the infra-red spectrum of oxazole, and vibrational corrections to the polarizability of formaldehyde.

  7. Vibrational spectra of nickel metalloporphyrins: An algebraic approach

    Indian Academy of Sciences (India)

    Srinivasa Rao Karumuri; Joydeep Choudhury; Nirmal Kumar Sarkar; Ramendu Bhattacharjee

    2009-03-01

    One of the most interesting areas of current research in molecular physics is the study of the vibrationally excitated states of medium and large molecules. In view of the considerable amount of experimental activity in this area, one needs theoretical models within which to interpret experimental data. Using Lie algebraic method, the vibrational energy levels of nickel metalloporphyrins like Ni(OEP), Ni porphyrin and Ni(TPP) are calculated for 16 vibrational modes. The algebraic Hamiltonian $$H = E_{0} + \\sum_{i=1}^{n} A_{i}C_{i} + \\sum_{i < j} A_{ij}C_{ij} + \\sum_{i < j}^{n} _{ij}M_{ij}$,$$ where , and are the algebraic parameters which vary from molecule to molecule and , and are algebraic operators. The vibrational energy levels are calculated using algebraic model Hamiltonian and the results are compared with the experimental values. The results obtained by this model are very accurate.

  8. Vibrational relaxation beyond the linear damping limit in two-dimensional optical spectra of molecular aggregates

    Science.gov (United States)

    Perlík, Václav; Šanda, František

    2017-08-01

    We present a computational model for the spectra of molecular aggregates with signatures of vibronic progression. Vibronic dynamics is implemented by coupling the dynamics of Frenkel excitons with underdamped vibrations. Vibrational dynamics includes linear damping resulting in the exponential decay and quadratic damping inducing subexponential or power law relaxation and increasing vibrational decoherence as demonstrated on lineshapes of the absorption spectrum. Simulations of the third-order coherent response account for bath reorganization during excitonic transport, which allows us to study the line-shape evolution of cross peaks of 2D spectra.

  9. Density functional theory study of vibrational spectra, and assignment of fundamental modes of dacarbazine

    Indian Academy of Sciences (India)

    S Gunasekaran; S Kumaresan; R Arunbalaji; G Anand; S Srinivasan

    2008-05-01

    The FTIR and FT Raman spectra of dacarbazine were recorded in the regions 4000-400 and 3500-100 cm-1, respectively. The optimized geometry, wavenumber, polarizability and several thermodynamic properties of dacarbazine were studied using ab initio Hartree-Fock, MP2 and DFT methods. A complete vibrational assignment aided by the theoretical harmonic wavenumber analysis was proposed. The calculated harmonic vibrational frequencies were compared with experimental FTIR and FT Raman spectra. Based on the comparison between calculated and experimental results and the comparison with related molecules, assignments of fundamental vibrational modes were made. The X-ray geometry and experimental frequencies were compared with the results of theoretical calculations.

  10. Vibrational techniques applied to photosynthesis: Resonance Raman and fluorescence line-narrowing.

    Science.gov (United States)

    Gall, Andrew; Pascal, Andrew A; Robert, Bruno

    2015-01-01

    Resonance Raman spectroscopy may yield precise information on the conformation of, and the interactions assumed by, the chromophores involved in the first steps of the photosynthetic process. Selectivity is achieved via resonance with the absorption transition of the chromophore of interest. Fluorescence line-narrowing spectroscopy is a complementary technique, in that it provides the same level of information (structure, conformation, interactions), but in this case for the emitting pigment(s) only (whether isolated or in an ensemble of interacting chromophores). The selectivity provided by these vibrational techniques allows for the analysis of pigment molecules not only when they are isolated in solvents, but also when embedded in soluble or membrane proteins and even, as shown recently, in vivo. They can be used, for instance, to relate the electronic properties of these pigment molecules to their structure and/or the physical properties of their environment. These techniques are even able to follow subtle changes in chromophore conformation associated with regulatory processes. After a short introduction to the physical principles that govern resonance Raman and fluorescence line-narrowing spectroscopies, the information content of the vibrational spectra of chlorophyll and carotenoid molecules is described in this article, together with the experiments which helped in determining which structural parameter(s) each vibrational band is sensitive to. A selection of applications is then presented, in order to illustrate how these techniques have been used in the field of photosynthesis, and what type of information has been obtained. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

  11. DFT studies of the vibrational spectra of salicylic acid and related compounds

    Science.gov (United States)

    Compounds that exhibit intra- and intermolecular hydrogen bonds can have infrared and Raman spectra that show evidences of these hydrogen bonds. In modeling the vibrational spectra of such compounds, the addition of explicit hydrogen bonding species (e.g. solvent molecules) can often improve agreeme...

  12. Vibrational spectra and structural considerations of compounds NaLnTiO4

    NARCIS (Netherlands)

    Blasse, G.; Heuvel, G.P.M. van den

    1974-01-01

    The Raman and infrared spectra of compounds NaLnTiO4 (Ln = lanthanide, including yttrium) are reported and discussed. Their most striking feature is a strong band in both spectra at about 900 cm−1. This band is ascribed to a vibration localized in the Ti---O bond directed towards the Na---O layers.

  13. Vibrational spectra, NMR and theoretical studies of the enantiomers and rotamers of alpha-cypermethrin

    Science.gov (United States)

    Jubert, Alicia H.; Alegre, María L.; Diez, Reinaldo Pis; Pomilio, Alicia B.; Szewczuk, Víctor D.

    2007-04-01

    NMR, infrared and Raman vibrational spectra of alpha-cypermethrin have been measured at room temperature. Infrared spectra were also recorded to low temperature. The spectra were analyzed by means of ab initio calculations. The conformational space of both enantiomers and some rotamers A, B and C of alpha-cypermethrin has been scanned using molecular dynamics and complemented with functional density calculations that optimize the geometry of the lowest-energy conformers of each species as obtained in the simulations. The vibrational frequencies and the 1H and 13C NMR chemical shifts were assigned using functional density calculations. The molecular electrostatic potential maps were obtained and analyzed.

  14. CO2 laser photoacoustic spectra and vibrational modes of heroin, morphine and narcotine

    Indian Academy of Sciences (India)

    R L Prasad; S N Thakur; G C Bhar

    2002-09-01

    Heroin, morphine and narcotine are very large molecules having 50, 40 and 53 atoms respectively. Moderately high resolution photoacoustic (PA) spectra have been recorded in 9.6 m and 10.6 m regions of CO2 laser. It is very difficult to assign the modes of vibrations for PA bands by comparison with conventional low resolution IR spectra. The ab initio quantum chemical calculations were used for determining the molecular geometries and normal mode frequencies of vibrations of these molecules for assignments of PA spectra.

  15. Vibrational spectra of the two hydrates of strontium oxalate.

    Science.gov (United States)

    D'Antonio, Maria C; Torres, María M; Palacios, Daniel; González-Baró, Ana C; Baran, Enrique J

    2015-02-25

    The infrared and Raman spectra of the two hydrates of strontium oxalate, SrC2O4⋅H2O and SrC2O4⋅2H2O, were recorded and discussed on the basis of their structural peculiarities and in comparison with the spectra of the related calcium oxalates and other previously investigated metallic oxalates.

  16. Calculating vibrational spectra using modified Shepard interpolated potential energy surfaces.

    Science.gov (United States)

    Evenhuis, Christian R; Manthe, Uwe

    2008-07-14

    A potential energy interpolation approach based on modified Shepard interpolation and specifically designed for calculation of vibrational states is presented. The importance of the choice of coordinates for the rate of convergence is demonstrated. Studying the vibrational states of the water molecule as a test case, a coordinate system comprised of inverse bond distances and trigonometric functions of the bond angle is found to be particularly efficient. Different sampling schemes used to locate the reference points in the modified Shepard interpolation are investigated. A final scheme is recommended, which allows the construction of potential energy surfaces to sub-wave-number accuracy.

  17. Electron-Vibration Structure of Absorption Spectra of Resazurine

    Directory of Open Access Journals (Sweden)

    T.N. Sakun

    2011-01-01

    Full Text Available In the work the experimental and theoretical investigation of the spectral characteristics of a resazurin molecule are carried out. Comparison of results of experimental and theoretical researches has allowed showing, that the spectrum of absorption in the visible region is formed by quantum transitions between electronic states of the molecule, and also by the electron-vibration interaction. In the work the method of reception of theoretical results with the control of molecule symmetry is offered. It has allowed to receive the completely coordinated theoretical and experimental results both by position and by size of the extinction factor and to find out the nature of all quantum transitions and oscillatory frequencies. It is shown, that strips of absorption in the visible region of the spectrum are formed at participation of the totally symmetrical vibrations of the molecule among which the greatest participation stand out vibrations with frequencies in the region of 478 cm – 1, 1467 cm – 1, and also by group of oscillatory frequencies in the region of 1800-2000 cm – 1 which were less than found theoretically for the basic state of the molecule because the degree of loosening of the bonds that responsible for specified vibrations, increases at excitation of the molecule.

  18. Fluorescence action spectra of algae and bean leaves at room and at liquid nitrogen temperatures

    NARCIS (Netherlands)

    Goedheer, J.C.

    1965-01-01

    Fluorescence action spectra were determined, both at room temperature and at liquid nitrogen temperature, with various blue-green, red and green algae, and greening bean leaves. The action spectra of algae were established with samples of low light absorption as well as dense samples. Fluorescence

  19. Vibrational absorption spectra from vibrational coupled cluster damped linear response functions calculated using an asymmetric Lanczos algorithm

    DEFF Research Database (Denmark)

    Thomsen, Bo; Hansen, Mikkel Bo; Seidler, Peter

    2012-01-01

    We report the theory and implementation of vibrational coupled cluster (VCC) damped response functions. From the imaginary part of the damped VCC response function the absorption as function of frequency can be obtained, requiring formally the solution of the now complex VCC response equations...... with results from the recently reported [P. Seidler, M. B. Hansen, W. Györffy, D. Toffoli, and O. Christiansen, J. Chem. Phys. 132, 164105 (2010)] vibrational configuration interaction damped response function calculated using a symmetric Lanczos algorithm. Calculations of IR spectra of oxazole, cyclopropene...

  20. Probing symmetry and symmetry breaking in resonant soft-x-ray fluorescence spectra of molecules

    Energy Technology Data Exchange (ETDEWEB)

    Glans, P.; Gunnelin, K.; Guo, J. [Uppsala Univ. (Sweden)] [and others

    1997-04-01

    Conventional non-resonant soft X-ray emission brings about information about electronic structure through its symmetry and polarization selectivity, the character of which is governed by simple dipole rules. For centro-symmetric molecules with the emitting atom at the inversion center these rules lead to selective emission through the required parity change. For the more common classes of molecules which have lower symmetry or for systems with degenerate core orbitals (delocalized over identical sites), it is merely the local symmetry selectivity that provides a probe of the local atomic orbital contribution to the molecular orbital. For instance, in X-ray spectra of first row species the intensities essentially map the p-density at each particular atomic site, and, in a molecular orbital picture, the contribution of the local p-type atomic orbitals in the LCAO description of the molecular orbitals. The situation is different for resonant X-ray fluorescence spectra. Here strict parity and symmetry selectivity gives rise to a strong frequency dependence for all molecules with an element of symmetry. In addition to symmetry selectivity the strong frequency dependence of resonant X-ray emission is caused by the interplay between the shape of a narrow X-ray excitation energy function and the lifetime and vibrational broadenings of the resonantly excited core states. This interplay leads to various observable effects, such as linear dispersion, resonance narrowing and emission line (Stokes) doubling. Also from the point of view of polarization selectivity, the resonantly excited X-ray spectra are much more informative than the corresponding non-resonant spectra. Examples are presented for nitrogen, oxygen, and carbon dioxide molecules.

  1. Laser-induced fluorescence and optical reflection spectra of Japanese natural dyes on silk

    OpenAIRE

    Miyoshi, Tadaki; Matsuda, Yasunori

    1987-01-01

    Fluorescence spectra under nitrogen-laser excitation were measured for silk cloth dyed with Japanese natural dyes. An identification of the dyes on silk was carried out using a laser-induced fluorescence (LIF) technique since dyed cloth has a characteristic fluorescence spectra. Moreover, it is possible to identify dyes on faded cloth and on cloth prepared by a combination dyeing using two kinds of dyes. The LIF technique can identify dyes on cloth which is difficult to identify using the ref...

  2. Calculation of Vibrational Energy-Spectra of α-Helical Protein Molecules and Its Properties

    Institute of Scientific and Technical Information of China (English)

    PANG XiaoFeng; CHEN XiangRong

    2002-01-01

    The quantum vibrational energy-spectra of amide-Is in alpha-protein molecules are calculated by using the discretely nonlinear Schrodinger equation and physical parameters appropriate to the systems on the basis of theory of bio-energy transport. The numerical results for the energy-spectra are basically consistent with the experimental values obtained by the infrared absorption and Raman scattering and emission-spectra of infrared lights of person's hand-fingers. Utilizing the energy-spectra we explain the laser-Raman spectrum from metabolically active E. Coli. and give some features of the infrared absorption of the protein molecules.

  3. Multiphoton fluorescence spectra and lifetimes of biliverdins and their protein-associated complex

    Science.gov (United States)

    Huang, Chin-Jie; Wu, Cheng-Ham; Liu, Tzu-Ming

    2012-03-01

    To investigate whether endogenous biliverdins can serve as a fluorescence metabolic marker in cancer diagnosis, we measured their multiphoton fluorescence spectra and lifetimes with femtosecond Cr:forsterite laser. Excited at 1230nm, the two-photon fluorescence of biliverdins peaks around 670nm. The corresponding lifetime (catabolism in human cells or tissues.

  4. PGOPHER: A program for simulating rotational, vibrational and electronic spectra

    Science.gov (United States)

    Western, Colin M.

    2017-01-01

    The PGOPHER program is a general purpose program for simulating and fitting molecular spectra, particularly the rotational structure. The current version can handle linear molecules, symmetric tops and asymmetric tops and many possible transitions, both allowed and forbidden, including multiphoton and Raman spectra in addition to the common electric dipole absorptions. Many different interactions can be included in the calculation, including those arising from electron and nuclear spin, and external electric and magnetic fields. Multiple states and interactions between them can also be accounted for, limited only by available memory. Fitting of experimental data can be to line positions (in many common formats), intensities or band contours and the parameters determined can be level populations as well as rotational constants. PGOPHER is provided with a powerful and flexible graphical user interface to simplify many of the tasks required in simulating, understanding and fitting molecular spectra, including Fortrat diagrams and energy level plots in addition to overlaying experimental and simulated spectra. The program is open source, and can be compiled with open source tools. This paper provides a formal description of the operation of version 9.1.

  5. Vibronic phenomena and exciton–vibrational interference in two-dimensional spectra of molecular aggregates

    Energy Technology Data Exchange (ETDEWEB)

    Butkus, Vytautas; Valkunas, Leonas [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius (Lithuania); Center for Physical Sciences and Technology, Gostauto 9, 01108 Vilnius (Lithuania); Abramavicius, Darius, E-mail: darius.abramavicius@ff.vu.lt [Department of Theoretical Physics, Faculty of Physics, Vilnius University, Sauletekio 9-III, 10222 Vilnius (Lithuania)

    2014-01-21

    A general theory of electronic excitations in aggregates of molecules coupled to intramolecular vibrations and the harmonic environment is developed for simulation of the third-order nonlinear spectroscopy signals. It is applied in studies of the time-resolved two-dimensional coherent spectra of four characteristic model systems: weakly/strongly vibronically coupled molecular dimers interacting with high/low frequency intramolecular vibrations. The results allow us to (i) classify and define the typical spectroscopic features of vibronically coupled molecules, (ii) separate the cases, when the long-lived quantum coherences due to vibrational lifetime borrowing should be expected, (iii) define when the complete exciton–vibrational mixing occurs, and (iv) when separation of excitonic and vibrational coherences is possible.

  6. Ab initio and DFT studies on vibrational spectra of some halides of group IIIB elements

    Science.gov (United States)

    Zhang, Yu; Zhao, Jianying; Tang, Guodong; Zhu, Longgen

    2005-11-01

    The vibrational spectra of some group IIIB elements halides MX 3 and their dimmers, M 2X 6 (M = Sc(III), Y(III), La(III); X = F, Cl, Br, I), have been systematically investigated by ab initio restricted Hartree-Fock (RHF) and density functional B3LYP methods with LanL2DZ and SDD basis sets. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational frequencies, calculated by two methods with different basis sets, are compared to each other. The effect of the methods and the basis sets used on the calculated vibrational frequencies are discussed. Some vibrational frequencies of these complexes are also predicted.

  7. A Theoretical Study on the Vibrational Spectra of PAH Molecules with Aliphatic Sidegroups

    CERN Document Server

    Sadjadi, SeyedAbdolreza; Kwok, Sun

    2015-01-01

    The role of aliphatic side groups on the formation of astronomical unidentified infrared emission (UIE) features is investigated by applying the density functional theory (DFT) to a series of molecules with mixed aliphatic-aromatic structures. The effects of introducing various aliphatic groups to a fixed polycyclic aromatic hydrocarbon (PAH) core (ovalene) are studied. Simulated spectra for each molecule are produced by applying a Drude profile at $T$=500 K while the molecule is kept at its electronic ground state. The vibrational normal modes are classified using a semi-quantitative method. This allows us to separate the aromatic and aliphatic vibrations and therefore provide clues to what types of vibrations are responsible for the emissions bands at different wavelengths. We find that many of the UIE bands are not pure aromatic vibrational bands but may represent coupled vibrational modes. The effects of aliphatic groups on the formation of the 8 $\\mu$m plateau are qua ntitatively determined. The vibratio...

  8. Vibrationally resolved ¹Lb (¹A')↔S0 (¹A') electronic spectra of benzimidazole and indene: Influence of Duschinsky and Herzberg-Teller effects on weak dipole-allowed transitions.

    Science.gov (United States)

    Yang, Pan; Pang, Min; Li, Ming; Shen, Wei; He, Rongxing

    2015-12-05

    Geometrical optimizations of the ground and first excited states of benzimidazole and indene were performed using the density functional theory (DFT) and its time-dependent extension methods (TD-DFT), respectively. Their vibrationally resolved (1)Lb ((1)A')↔S0 ((1)A') absorption and fluorescence spectra were simulated within the Franck-Condon approximation including the Herzberg-Teller (HT) and Duschinsky effects. Calculated results revealed that, with the HT and Duschinsky effects getting involved, the simulated weak (1)Lb ((1)A')↔S0 ((1)A') electronic spectra of the two molecules excellently reproduce the experimental findings. Based on the experimental data and other theoretical results, we tentatively assigned most of the vibrational normal modes which emerged in the experimental spectra of the two molecules. The present theoretical insights are expected to help us understand the nature of electronic transitions in the vibrationally resolved absorption and fluorescence spectra of benzimidazole and its analogues.

  9. Structure and vibrational spectra of L-alanine L-alaninium picrate monohydrate

    Science.gov (United States)

    Ghazaryan, V. V.; Fleck, M.; Petrosyan, A. M.

    2012-05-01

    Preparation, crystal and molecular structure as well as vibrational spectra of the crystal L-alanine L-alaninium picrate monohydrate are described. The title crystal is monoclinic, space group P21. The asymmetric unit contains one dimeric (L-Ala⋯L-Ala+) cation, one picrate anion and a water molecule. The O⋯O distance in the dimeric cation is equal to 2.553(2) Å. The IR and Raman spectra are interpreted based on the structure.

  10. Study on fluorescence spectra of molecular association of acetic acid-water

    Institute of Scientific and Technical Information of China (English)

    Caiqin Han; Ying Liu; Yang Yang; Xiaowu Ni; Jian Lu; Xiaosen Luo

    2009-01-01

    Fluorescence spectra of acetic acid-water solution excited by ultraviolet (UV) light are studied, and the relationship between fluorescence spectra and molecular association of acetic acid is discussed. The results indicate that when the exciting light wavelength is longer than 246 nm, there are two fluorescence peaks located at 305 and 334 nm, respectively. By measuring the excitation spectra, the optimal wavelengths of the two fluorescence peaks are obtained, which are 258 and 284 nm, respectively. Fluorescence spectra of acetic acid-water solution change with concentrations, which is primarily attributed to changes of molecular association of acetic acid in aqueous solution. Through theoretical analysis, three variations of molecular association have been obtained in acetic acid-water solution, which are the hydrated monomers, the linear dimers, and the water separated dimers. This research can provide references to studies of molecular association of acetic acid-water, especially studies of hydrogen bonds.

  11. Vibrational analysis of various irotopes of L-alanyl-L-alanine in aqueous solution: Vibrational Absorption (VA), Vibrational Circular Dichroism (VCD), Raman and Raman Optical Activity (ROA) Spectra

    DEFF Research Database (Denmark)

    Jalkanen, Karl J.; Nieminen, R.M.; Knapp-Mohammady, M.

    2003-01-01

    In a recent work (Knapp-Mohammady, M.; Jalkanen, K. J.; Nardi, F.; Wade, R. C.; Suhai, S. Chem Phys 1999, 240, 63-77) the structures of the zwitterionic species Of L-alanyI-L-alanine (LALA) in aqueous solution using a combination of molecular mechanics (MM) and density functional theory (DFT) have...... been reported. Subsequently, the vibrational absorption (VA) and vibrational circular dichroism (VCD) and the Raman and Raman Optical Activity (ROA) spectra have been reported. In this work an analysis of the aqueous solution VA, VCD, Raman, and ROA spectra for various isotopomers of LALA are reported...... pattern could be reproduced with the DIFT atomic axial tensors calculated for the LALA plus explicit water molecules. The continuum treatment of the solvent for the calculation of these tensors appeirs to be a secondary effect. The ROA spectra are not well reproduced due to the failure to take...

  12. Study on fluorescence spectra of thiamine, riboflavin and pyridoxine

    Science.gov (United States)

    Yang, Hui; Xiao, Xue; Zhao, Xuesong; Hu, Lan; Lv, Caofang; Yin, Zhangkun

    2016-01-01

    This paper presents the intrinsic fluorescence characteristics of vitamin B1, B2 and B6 measured with 3D fluorescence Spectrophotometer. Three strong fluorescence areas of vitamin B2 locate at λex/λem=270/525nm, 370/525nm and 450/525nm, one fluorescence areas of vitamin B1 locates at λex/λem=370/460nm, two fluorescence areas of vitamin B6 locate at λex/λem=250/370nm and 325/370nm were found. The influence of pH of solution to the fluorescence profile was also discussed. Using the PARAFAC algorithm, 10 vitamin B1, B2 and B6 mixed solutions were successfully decomposed, and the emission profiles, excitation profiles, central wavelengths and the concentration of the three components were retrieved precisely through about 5 iteration times.

  13. Lattice vibration frequencies in Raman spectra of manganese and rhenium decacarbonyls

    Energy Technology Data Exchange (ETDEWEB)

    Volkov, V.E.; Danilov, I.Yu.; Zhidkov, L.L.; Kovalev, Yu.G.; Ioganson, A.A. (AN SSSR, Krasnoyarsk. Inst. Khimii i Khimicheskoj Tekhnologii)

    1983-06-01

    Raman spectra (RS) in the 170-10 cm/sup -1/ region of Mn/sub 2/(CO)/sub 10/, Re/sub 2/(CO)/sub 10/ polycrystal samples and their mixed crystals with different component percentage were obtained in the 296-123 K range. Investigations at low temperatures enabled to obtain most complete spectra in the given region. The spectra were separated to intramolecular and lattice ones on the basis of both comparing the spectra of pure components with those of mixed crystals, and studying the temperature behaviour of frequencies in the spectra. It was established that frequencies, placed below 60 cm/sup -1/ as well as in the region of 130-150 cm/sup -1/ in the spectra of manganese- and rhenium decacarbonyls are determined by the lattice vibrations of molecules in crystals.

  14. Vibrational spectra of copper polysilicate, CuSiO3

    OpenAIRE

    2009-01-01

    This is a representation of the first Raman and IR / FIR spectra for orthorhombic copper polysilicate, CuSiO3, measured at room temperature on polycrystalline samples and a comparison of the optical phonons with those observed for the spin-Peierls compound CuGeO3. CuSiO3 represents a further example of a quasi-one-dimensional spin = 1/2 antiferromagnetic Heisenberg chain system. A mode assignment for the silicate is given. From the analysis of the Davydov doublets a reduced intralayer- to-int...

  15. Calculation of the vibrational spectra of α-rdx using the grimme DFT potential

    Science.gov (United States)

    Perger, Warren; Slough, William J.; Valenzano, Loredana; Flurchick, K. M.

    2012-03-01

    The density-functional theory (DFT) potential by Grimme has been proposed for describing longrange dispersion corrections. This potential has been implemented into the CRYSTAL09 program and used to calculate the vibrational spectra in α-RDX at equilibrium. The frequencies and intensities are reported and compared with prior theory and experiment where possible.

  16. Vibrational wave packet induced oscillations in two-dimensional electronic spectra. II. Theory

    CERN Document Server

    Mancal, Tomas; Milota, Franz; Lukes, Vladimir; Kauffmann, Harald F; Sperling, Jaroslaw

    2010-01-01

    We present a theory of vibrational modulation of two-dimensional coherent Fourier transformed electronic spectra. Based on an expansion of the system's energy gap correlation function in terms of Huang-Rhys factors, we explain the time-dependent oscillatory behavior of the absorptive and dispersive parts of two-dimensional spectra of a two-level electronic system, weakly coupled to intramolecular vibrational modes. The theory predicts oscillations in the relative amplitudes of the rephasing and non-rephasing parts of the two-dimensional spectra, and enables to analyze time dependent two-dimensional spectra in terms of simple elementary components whose line-shapes are dictated by the interaction of the system with the solvent only. The theory is applicable to both low and high energy (with respect to solvent induced line broadening) vibrations. The results of this paper enable to qualitatively explain experimental observations on low energy vibrations presented in the preceding paper [A. Nemeth et al, arXiv:1...

  17. Rotation-vibrational spectra of diatomic molecules and nuclei with Davidson interactions

    CERN Document Server

    Rowe, D J

    1998-01-01

    Complete rotation-vibrational spectra and electromagnetic transition rates are obtained for Hamiltonians of diatomic molecules and nuclei with Davidson interactions. Analytical results are derived by dynamical symmetry methods for diatomic molecules and a liquid-drop model of the nucleus. Numerical solutions are obtained for a many-particle nucleus with quadrupole Davidson interactions within the framework of the microscopic symplectic model. (author)

  18. Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of mannitol.

    Science.gov (United States)

    Moorthi, P P; Gunasekaran, S; Swaminathan, S; Ramkumaar, G R

    2015-02-25

    A collective experimental and theoretical study was conducted on the molecular structure and vibrational spectra of mannitol. The FT-IR and FT-Raman spectra of mannitol were recorded in the solid phase. The molecular geometry, vibrational frequencies, thermodynamic functions and atomic charges of mannitol in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking cc-pVDZ basis set. The complete vibrational assignments were performed on the basis of Total Energy Distribution (TED) of the vibrational modes. The UV absorption spectra of the title compound dissolved in water. Natural bond orbital analysis has been carried out to explain the charge transfer or delocalization of charge due to the intra-molecular interactions. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO methods. The first order hyperpolarizability (β0) of this novel molecular system and related properties (β, α0 and Δα) of mannitol are calculated using B3LYP/cc-pVDZ and HF/cc-pVDZ methods on the finite-field approach. By using TD-DFT calculation, electronic absorption spectra of the title compound have been predicted and a good agreement with experimental one is established. In addition, the molecular electrostatic potential (MEP) have been investigated using theoretical calculations, the calculated HOMO and LUMO energies shows that the charge transfer within the molecule.

  19. Ab initio and DFT studies of the structure and vibrational spectra of anhydrous caffeine.

    Science.gov (United States)

    Srivastava, Santosh K; Singh, Vipin B

    2013-11-01

    Vibrational spectra and molecular structure of anhydrous caffeine have been systematically investigated by second order Moller-Plesset (MP2) perturbation theory and density functional theory (DFT) calculations. Vibrational assignments have been made and many previous ambiguous assignments in IR and Raman spectra are amended. The calculated DFT frequencies and intensities at B3LYP/6-311++G(2d,2p) level, were found to be in better agreement with the experimental values. It was found that DFT with B3LYP functional predicts harmonic vibrational wave numbers more close to experimentally observed value when it was performed on MP2 optimized geometry rather than DFT geometry. The calculated TD-DFT vertical excitation electronic energies of the valence excited states of anhydrous caffeine are found to be in consonance to the experimental absorption peaks.

  20. Vibrational Spectra, Assignments and Ab initio/DFT Analysis for 2-Methyl-3-nitrophenyl isocyanate

    Science.gov (United States)

    Prasannakumar, Sushanti; Yenagi, Jayashree; Tonannavar, J.

    2008-11-01

    The FT-IR (4000-400 cm-1) and Raman (3200-100 cm-1) spectral measurements have been made for 2-Methyl-3-nitrophenyl isocyanate. Electronic energy, optimized geometry and harmonic vibrational spectra have been computed using ab initio and DFT methods, namely, at RHF/6-311G* and B3LYP/6-311G* levels of theory. The methyl, nitro and isocyanate vibrations observed in their characteristic regions, have been accurately computed by the B3LYP/6-311G* level. Computed low frequencies have been assigned to out-of-plane, wagging and torsional vibrations of these groups. A complete assignment of the observed as well as computed spectra has been proposed.

  1. Ab initio and DFT studies of the structure and vibrational spectra of anhydrous caffeine

    Science.gov (United States)

    Srivastava, Santosh K.; Singh, Vipin B.

    2013-11-01

    Vibrational spectra and molecular structure of anhydrous caffeine have been systematically investigated by second order Moller-Plesset (MP2) perturbation theory and density functional theory (DFT) calculations. Vibrational assignments have been made and many previous ambiguous assignments in IR and Raman spectra are amended. The calculated DFT frequencies and intensities at B3LYP/6-311++G(2d,2p) level, were found to be in better agreement with the experimental values. It was found that DFT with B3LYP functional predicts harmonic vibrational wave numbers more close to experimentally observed value when it was performed on MP2 optimized geometry rather than DFT geometry. The calculated TD-DFT vertical excitation electronic energies of the valence excited states of anhydrous caffeine are found to be in consonance to the experimental absorption peaks.

  2. Calculation of Raman optical activity spectra for vibrational analysis.

    Science.gov (United States)

    Mutter, Shaun T; Zielinski, François; Popelier, Paul L A; Blanch, Ewan W

    2015-05-01

    By looking back on the history of Raman Optical Activity (ROA), the present article shows that the success of this analytical technique was for a long time hindered, paradoxically, by the deep level of detail and wealth of structural information it can provide. Basic principles of the underlying theory are discussed, to illustrate the technique's sensitivity due to its physical origins in the delicate response of molecular vibrations to electromagnetic properties. Following a short review of significant advances in the application of ROA by UK researchers, we dedicate two extensive sections to the technical and theoretical difficulties that were overcome to eventually provide predictive power to computational simulations in terms of ROA spectral calculation. In the last sections, we focus on a new modelling strategy that has been successful in coping with the dramatic impact of solvent effects on ROA analyses. This work emphasises the role of complementarity between experiment and theory for analysing the conformations and dynamics of biomolecules, so providing new perspectives for methodological improvements and molecular modelling development. For the latter, an example of a next-generation force-field for more accurate simulations and analysis of molecular behaviour is presented. By improving the accuracy of computational modelling, the analytical capabilities of ROA spectroscopy will be further developed so generating new insights into the complex behaviour of molecules.

  3. CO ro-vibrational lines in HD100546: A search for disc asymmetries and the role of fluorescence

    CERN Document Server

    Bertelsen, R P Hein; Goto, M; van der Plas, G; Thi, W -F; Waters, L B F M; Ancker, M E van den; Woitke, P

    2013-01-01

    We have studied the emission of CO ro-vibrational lines in the disc around the Herbig Be star HD100546 with the final goal of using these lines as a diagnostic to understand inner disc structure in the context of planet formation. High-resolution IR spectra of CO ro-vibrational emission at eight different position angles were taken with CRIRES at the VLT. From these spectra flux tables, CO ro-vibrational line profiles, and population diagrams were produced. We have investigated variations in the line profile shapes and line strengths as a function of slit position angle. We used the thermochemical disc modelling code ProDiMo based on the chemistry, radiation field, and temperature structure of a previously published model for HD100546. Comparing observations and the model, we investigated the possibility of disc asymmetries, the excitation mechanism (UV fluorescence), the geometry, and physical conditions of the inner disc. The observed CO ro-vibrational lines are largely emitted from the inner rim of the out...

  4. Electronic and Vibrational Spectra of InP Quantum Dots Formed by Sequential Ion Implantation

    Science.gov (United States)

    Hall, C.; Mu, R.; Tung, Y. S.; Ueda, A.; Henderson, D. O.; White, C. W.

    1997-01-01

    We have performed sequential ion implantation of indium and phosphorus into silica combined with controlled thermal annealing to fabricate InP quantum dots in a dielectric host. Electronic and vibrational spectra were measured for the as-implanted and annealed samples. The annealed samples show a peak in the infrared spectra near 320/cm which is attributed to a surface phonon mode and is in good agreement with the value calculated from Frolich's theory of surface phonon polaritons. The electronic spectra show the development of a band near 390 nm that is attributed to quantum confined InP.

  5. Investigation on Vibrational Spectra and Structures of 4-Mercaptopyridine Monomer and Its Dihydrate

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The optimized molecular structures and vibrational frequencies of 4-mercaptopyridine(4MPY) monomer and its dihydrate were studied by means of the density functional theory(DFT), viz. B3LYP method with the 6-311++G(d,p) basis set. On the basis of the calculations, the assignments of the vibrational spectra of the monomer and the dihydrate were performed, and so were investigated the changes in the structure and the vibrational spectrum of the dihydrate as well as the intermolecular force resulting in the formation of the dihydrate. The calculated results show that each of the water molecule planes is vertical to the pyridine ring plane in the dihydrate that is formed via the H-bonds between 4MPY and water molecules. Furthermore, the structure and the vibrational spectrum of 4MPY can be consi-derably affected by the water molecules.

  6. Nonnegative matrix factorization: a blind spectra separation method for in vivo fluorescent optical imaging.

    Science.gov (United States)

    Montcuquet, Anne-Sophie; Hervé, Lionel; Navarro, Fabrice; Dinten, Jean-Marc; Mars, Jérôme I

    2010-01-01

    Fluorescence imaging in diffusive media is an emerging imaging modality for medical applications that uses injected fluorescent markers that bind to specific targets, e.g., carcinoma. The region of interest is illuminated with near-IR light and the emitted back fluorescence is analyzed to localize the fluorescence sources. To investigate a thick medium, as the fluorescence signal decreases with the light travel distance, any disturbing signal, such as biological tissues intrinsic fluorescence (called autofluorescence) is a limiting factor. Several specific markers may also be simultaneously injected to bind to different molecules, and one may want to isolate each specific fluorescent signal from the others. To remove the unwanted fluorescence contributions or separate different specific markers, a spectroscopic approach is explored. The nonnegative matrix factorization (NMF) is the blind positive source separation method we chose. We run an original regularized NMF algorithm we developed on experimental data, and successfully obtain separated in vivo fluorescence spectra.

  7. Vibrational circular dichroism and IR absorption spectra of amino acids: a density functional study.

    Science.gov (United States)

    Ji, Zhi; Santamaria, Rubén; Garzón, Ignacio L

    2010-03-18

    With density functional theory, vibrational circular dichroism (VCD) and infrared absorption (IR) spectra are obtained at the B3LYP/CC-pVTZ level of theory for 20 alpha-amino acids. The contribution of different vibration modes to the IR and VCD spectra is analyzed. Overall agreement between calculated results for amino acids in gas phase with the available experimental VCD data for matrix-assisted amino acid films is found. The analysis of the calculated IR and VCD spectra indicates that the functional groups in the backbones and side chains of amino acids contribute differently to the spectra line shape. It is obtained that molecular torsions are the characteristic vibrations of the amino acids at the low-frequency regime, whereas the bending of bond angles, the out-of-plane wagging of individual atoms, and some stretching modes dominate the intermediate frequency range. Specific modes like NH(2) scissoring, CO bond stretching, and the (symmetric and asymmetric) stretching of the hydrogen atoms in the NH(2) and OH groups characterize the high-frequency regime. A general trend emerging from these calculations indicates that the rho(OH) rocking and nu(C=O) stretching modes have the highest intensity in the VCD spectra of most amino acids.

  8. The Vibrational Spectra of Bactericide molecules: Terahertz Spectroscopy and Density Functional Theory Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Wang Xiaowei; Wang Qiang, E-mail: qiangwang@cjlu.edu.cn [Department of Quality and Safety Engineering, China Jiliang University, Hangzhou, 310018 (China)

    2011-02-01

    In the room temperature and nitrogen conditions, we presented well-resolved absorption spectra and indexes of refraction of bactericide molecules in the far infrared radiation (FIR) spectral region recorded by terahertz time-domain spectroscopy (THz-TDS). As illustrative examples we discussed the absorption spectra of captan and folpet in THz region. The absorption coefficient and index of refraction of them were obtained. Meanwhile, density functional theory (DFT) with software package Gaussian 03 using B3LYP theory was employed for optimization and vibration analysis. With the help of Gaussian View 3.09, the distinct absorption peaks of those molecules were assigned with reliable accuracy. They were caused by intermolecular hydrogen-bonding, molecular torsion or vibration modes, absorption of water molecules, etc. As the absorption spectra are highly sensitive to the overall structure and configuration of the molecules, the THz-TDS procedure can provide a direct fingerprint of the molecular structure or conformational state of a compound.

  9. Analysis of laser-induced fluorescence spectra of in vitro plant tissue cultures

    Science.gov (United States)

    Muñoz-Muñoz, Ana Celia; Gutiérrez-Pulido, Humberto; Rodríguez-Domínguez, José Manuel; Gutiérrez-Mora, Antonia; Rodríguez-Garay, Benjamín; Cervantes-Martínez, Jesús

    2007-04-01

    We demonstrate the effectiveness of laser-induced fluorescence (LIF) for monitoring the development and stress detection of in vitro tissue cultures in a nondestructive and noninvasive way. The changes in LIF spectra caused by the induction of organogenesis, the increase of the F690/F740 ratio as a result of the stress originated in the organogenic explants due to shoot emergence, and the relationship between fluorescence spectra and shoot development were detected by LIF through closed containers of Saintpaulia ionantha.

  10. Vibronic-structure tracking: A shortcut for vibrationally resolved UV/Vis-spectra calculations

    Energy Technology Data Exchange (ETDEWEB)

    Barton, Dennis; König, Carolin; Neugebauer, Johannes, E-mail: j.neugebauer@uni-muenster.de [Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster (Germany)

    2014-10-28

    The vibrational coarse structure and the band shapes of electronic absorption spectra are often dominated by just a few molecular vibrations. By contrast, the simulation of the vibronic structure even in the simplest theoretical models usually requires the calculation of the entire set of normal modes of vibration. Here, we exploit the idea of the mode-tracking protocol [M. Reiher and J. Neugebauer, J. Chem. Phys. 118, 1634 (2003)] in order to directly target and selectively calculate those normal modes which have the largest effect on the vibronic band shape for a certain electronic excitation. This is achieved by defining a criterion for the importance of a normal mode to the vibrational progressions in the absorption band within the so-called “independent mode, displaced harmonic oscillator” (IMDHO) model. We use this approach for a vibronic-structure investigation for several small test molecules as well as for a comparison of the vibronic absorption spectra of a truncated chlorophyll a model and the full chlorophyll a molecule. We show that the method allows to go beyond the often-used strategy to simulate absorption spectra based on broadened vertical excitation peaks with just a minimum of computational effort, which in case of chlorophyll a corresponds to about 10% of the cost for a full simulation within the IMDHO approach.

  11. Rotation-Vibration Spectra of Malonaldehyde Obtained with Far-Infrared Synchrotron Radiation

    Science.gov (United States)

    Tokaryk, D. W.; Ross, S. C.; Forthomme, D.; Prescott, J. E.; Yamada, K. M. T.; Ito, F.

    2011-06-01

    Malonaldehyde is an open 5-membered ring molecule which exhibits interesting quantum-mechancial effects due to tunnelling of one of its protons. This results in a 21 Cm-1 tunnelling-splitting in the ground vibrational state, which has been well-studied by microwave spectroscopy. We have taken far-infrared Fourier transform spectra of malonaldehyde at the Canadian Light Source synchrotron, and have recorded a number of rotation-vibration fundamental bands between 100-1000 Cm-1 at 0.00096 Cm-1 resolution. The data permit us to determine with high precision the changes in the tunnelling-splitting induced by vibrational excitation. We have also observed spectra at 240 and 219 Cm-1 that appear to be transitions from the two components of the ground vibrational state to a common upper state that is not mentioned in conventional vibrational analyses of malonaldehyde. We will offer suggestions as to the nature of the newly-observed state. P. Turner, S. L. Baughcum, S. L. Coy and Z. Smith, J. Am. Chem. Soc. 106 (1984) 2265-2267 T. Baba, T. Tanaka, I. Morino, K. M. T. Yamada and K. Tanaka, J. Chem. Phys. 110 (1999) 4131-4133. A. Alparone and S. Millefiori, Chem. Phys. 290 (2003) 15-25.

  12. Measurements of the Ultraviolet Fluorescence Cross Sections and Spectra of Bacillus Anthracis Simulants

    Energy Technology Data Exchange (ETDEWEB)

    Stephens, J.R.

    1998-09-01

    Measurements of the ultraviolet autofluorescence spectra and absolute cross sections of the Bacillus anthracis (Ba) simulants Bacillus globigii (Bg), Bacillus megaterium (Bm), Bacillus subtilis (Bs), and Bacillus cereus (Bc) were measured. Fluorescence spectra and cross sections of pine pollen (Pina echinata) were measured for comparison. Both dried vegetative cells and spores separated from the sporulated vegetative material were studied. The spectra were obtained by suspending a small number (<10) of particles in air in our Single Particle Spectroscopy Apparatus (SPSA), illuminating the particles with light from a spectrally filtered arc lamp, and measuring the fluorescence spectra of the particles. The illumination was 280 nm (20 nm FWHM) and the fluorescence spectra was measured between 300 and 450 nm. The fluorescence cross section of vegetative Bg peaks at 320 nm with a maximum cross section of 5 X 10{sup -14} cm{sup 2}/sr-nm-particle while the Bg spore fluorescence peaks at 310 nm with peak fluorescence of 8 X 10{sup -15} cm{sup 2}/sr-nm-particle. Pine pollen particles showed a higher fluorescence peaking at 355 nm with a cross section of 1.7 X 10{sup -13} cm{sup 2}/sr-nm-particle. Integrated cross sections ranged from 3.0 X 10{sup -13} for the Bg spores through 2.25 X 10{sup -12} (cm{sup 2}/sr-particle) for the vegetative cells.

  13. Vibrational circular dichroism spectra for large molecules and molecules with heavy elements

    Science.gov (United States)

    Reiter, Kevin; Kühn, Michael; Weigend, Florian

    2017-02-01

    We present an implementation of vibrational circular dichroism (VCD) spectra in TURBOMOLE. We mainly followed the route proposed by Cheeseman [Chem. Phys. Lett. 252, 211 (1996)] and extended the modules for calculating the magnetic response and vibrational frequencies accordingly. The implementation allows for gauge origin invariant employment of effective core potentials, as demonstrated for Co(ppy)3, ppy = 2-Phenylpyridine. In this way, scalar relativistic effects are covered and heavy elements can be treated. Further, with the present implementation molecular symmetry may be efficiently exploited, which makes the calculation of large (symmetric) systems feasible. The calculation of the VCD spectrum of icosahedral C6202+ is shown as an illustrative application.

  14. Effects of vibrational motion on core-level spectra of prototype organic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Uejio, Janel S.; Schwartz, Craig P.; Saykally, Richard J.; Prendergast, David

    2008-08-21

    A computational approach is presented for prediction and interpretation of core-level spectra of complex molecules. Applications are presented for several isolated organic molecules, sampling a range of chemical bonding and structural motifs. Comparison with gas phase measurements indicate that spectral lineshapes are accurately reproduced both above and below the ionization potential, without resort to ad hoc broadening. Agreement with experiment is significantly improved upon inclusion of vibrations via molecular dynamics sampling. We isolate and characterize spectral features due to particular electronic transitions enabled by vibrations, noting that even zero-point motion is sufficient in some cases.

  15. A novel detecting system with full fluorescent spectra for pesticides

    Science.gov (United States)

    Wang, Zhong dong; Zheng, Ya Juan; Ruan, Gui cai; Wang, Yu tian

    2006-11-01

    A detecting system is developed applying the technologies of fiber-optic sensing, grating dispersion and multi-channel image sensing (Charge Coupled Device) based on the fluorescence mechanism of carbaryl. In this system, a pulsed xenon lamp is used as an excitation light source, optical fibers are selected to transmit and detect fluorescence, fluorescence dispersion is implemented with a small-sized flat field grating spectrometer and data gathering and A/D conversion are conducted with a high speed signal processing module. Moreover, the system is used to measure the fluorescence characteristics of carbaryl. The results show that a full fluorescence spectrum of carbaryl can be obtained in a single exposure under a UV excitation wavelength of 319nm, has a good linear relationship in the range of 4.0~100.0 ng/mL of carbaryl liquor and the minimum detecting limit is 4.0ng/mL with the linear correlation coefficient r being 0.9986. When this instrument is likewise applied for measuring carbaryl in river and ground water,the recovery may approach 100 %.

  16. Fluorescence Spectra and Enzymatic Property of Hemoglobin as Mimetic Peroxidase

    Institute of Scientific and Technical Information of China (English)

    Li De-jia; Li Hai-cheng; Zou Guo-lin

    2003-01-01

    Intrinsic fluorescence emission maxima of hemoglobin(Hb) was investigated in relation to peroxidase property of Hb. The peroxidase activity of Hb was based on its catalytic activity for oxidation of o-phenylenediamine by hydrogen peroxide. Hb was treated in the condition (temperature,ethanol and salt) that tetramer-dimer equilibrium of Hb is shifted to the dimer state and its fluorescence spectrum was measured. When Hb treated in temperature (60-70 ℃ ), ethanol concentration (60 %-70 % ) and NaCl concentration (2.5-3.0 mol/L), the fluorescence emission maxima of Hb shifted towards red wavelength and its activity decreased quickly.Experimental results revealed that the activity and stability of Hb as mimetic peroxidase was closely relative to the hydrophobic environment of active center of Hb, and when Hb (FeⅡ) converted into met Hb (FeⅢ ), its activity was 1. 6times as much as that of Hb.

  17. Fluorescence Spectra and Enzymatic Property of Hemoglobin as Mimetic Peroxidase

    Institute of Scientific and Technical Information of China (English)

    LiDe-jia; LiHai-cheng; ZouGuo-lin

    2003-01-01

    Intrinsic fluorescence emission maxima of hemo-lobin(Hb) was investigated in relation to peroxidase property of Hb. The peroxidase activity of Hb was based on its catalytic activity for oxidation of o-phenylenediamine by hydrogen peroxide. Hb was treated in the condition (temperature,ethanol and salt) that tetramer-dimer equilibrium of Hb is shifted to the dimer state and its fluorescence spectrum was measured. When Hb treated in temperature (60-70 ℃), ethanol concentration (60%-70%) and NaCl concentration (2. 5-3.0 mol/L), the fluorescence emission maxima of Hb shifted towards red wavelength and its activity decreased quickly.Experimental results revealed that the activity and stability of Hb as mimetic peroxidase was closely relative to the hydrophobic environment of active center of Hb, and when Hb (FeⅡ) converted into met Hb (FeⅢ ), its activity was 1. 6 times as much as that of Hb.

  18. Attempt to separate the fluorescence spectra of adrenaline and noradrenaline using chemometrics

    DEFF Research Database (Denmark)

    Nikolajsen, Rikke P; Hansen, Åse Marie; Bro, R

    2000-01-01

    An investigation was conducted on whether the fluorescence spectra of the very similar catecholamines adrenaline and noradrenaline could be separated using chemometric methods. The fluorescence landscapes (several excitation and emission spectra were measured) of two data sets with respectively 16...... regression (Unfold-PLSR) on the larger data set and parallel factor analysis (PARAFAC) of the six samples of the smaller set showed that there was no difference between the fluorescence landscapes of adrenaline and noradrenaline. It can be concluded that chemometric separation of adrenaline and noradrenaline...

  19. CN and C2 vibrational spectra analysis in molecular LIBS of organic materials

    Science.gov (United States)

    Mousavi, S. J.; Hemati Farsani, M.; Darbani, S. M. R.; Mousaviazar, A.; Soltanolkotabi, M.; Eslami Majd, A.

    2016-05-01

    With the objective of investigation of the influence of molecular structure on CN violet and C2 Swan bands system spectra, plasma emissions from different organic materials, including polycyclic aromatic hydrocarbons, aromatic carboxylic acid, aliphatic carboxylic acid, amides and polymers, have been analyzed by laser-induced breakdown spectroscopy (LIBS) technique in air. To evaluate the influence of N2 and O2 molecules concentration on the CN and C2 molecular emissions, LIB spectra of four different samples have been recorded in air (approximately 80 % N2 and 20 % O2), nitrogen, oxygen and argon atmospheres. Experimental results indicate that the main reason for the absence of C2 emission in LIB spectra of samples which do not contain C-C bonds, when measurements were taken in air, is the presence of oxygen which could potentially deplete C2 emission rather than the absence of C-C bonds in their structure. Also, comparisons between experiment and theory spectra are made using a Nelder-Mead temperature program for CN and C2 bands with the ∆ν = 0 sequences from LIB spectra of different samples in various atmospheres. Furthermore, CN and C2 vibrational temperatures in Kelvin (K) are calculated from these spectral fittings. Both CN and C2 vibrational temperatures have highest values in argon atmosphere, and increasing the oxygen concentration in ambient atmosphere decreased those in most cases.

  20. Ab initio path integral ring polymer molecular dynamics: Vibrational spectra of molecules

    Science.gov (United States)

    Shiga, Motoyuki; Nakayama, Akira

    2008-01-01

    The path integral ring polymer molecular dynamics method is combined with 'on-the-fly' ab initio electronic structure calculations and applied to vibrational spectra of small molecules, LiH and H 2O, at the room temperature. The results are compared with those of the numerically exact solution and ab initio path integral centroid molecular dynamics calculation. The peak positions in the calculated spectra are found to be reasonable, showing the red-shift due to potential anharmonicity. This unification enables the investigation of real-time quantum dynamics of chemically complex molecular systems on the ab initio Born-Oppenheimer potential energy surface.

  1. Theoretical Study on the Vibrational Spectra and Thermodynamic Properties for Nitro Derivatives of Benzene and Anilines

    Institute of Scientific and Technical Information of China (English)

    WANG Gui-Xiang; GONG Xue-Dong; XIAO He-Ming

    2008-01-01

    Nitro derivatives of benzene and anilines were optimized to obtain their molecular geometries and electronic structures at a DFT-B3LYP/6-31G* level. Their IR spectra were obtained and assigned by vibrational analysis. Comparing the calculated IR spectra with these of experiments known, all the IR data obtained in this paper were considered to be reliable. Based on the frequencies scaled by 0.96 and the principle of statistic thermodynamics, the thermodynamic properties were evaluated, which were linearly related with the number of nitro and amino groups as well as the temperature, obviously showing good group additivity.

  2. Study on vibrational modes by group theory and infrared spectra by D FT for calcite crystal

    Institute of Scientific and Technical Information of China (English)

    Danhua Lou; Fengjiu Sun; Lijuan Li

    2007-01-01

    The factor group symmetry analysis (FSA) method and position symmetry analysis (PSA) method are used to analyze the vibrational modes of calcite (CaCO3) crystal, respectively. With the activated results of infrared and Raman spectra presented, strong points of each method are concluded. The infrared spectra are studied by using dynamics calculations based on density-functional theory (DFT) with the supercell model of calcite crystal. The frequencies of 27 normal modes are achieved, which are consistent with that by the group symmetry analysis very well, and fit with the experimental results better than the lattice dynamical methods.

  3. Vibrational Energy-Spectra and Infrared Absorption of α-Helical Protein Molecules

    Institute of Scientific and Technical Information of China (English)

    庞晓峰; 陈相容

    2002-01-01

    The quantum energy spectra, including high excited states, of vibrational amide-I or of intramolecular excitations in a-helical protein molecules, are calculated by the discrete nonlinear Schrodinger equation together with the parameters appropriate to the systems. The distribution of energy levels obtained is basically consistent with the experimental values obtained by infrared absorption and Raman scattering. Utilizing the energy spectra we explain the laser Raman spectrum from metabolically active escherichia coli and we present some further features of the infrared absorption of the protein molecules.

  4. Vibrational spectra, DFT calculations, conformational stabilities and assignments of the fundamentals of the 1-butylpiperazine

    Science.gov (United States)

    Bağlayan, Özge; Kaya, Mehmet Fatih; Güneş, Esma; Şenyel, Mustafa

    2016-10-01

    FT-IR and FT-Raman spectra of 1-butylpiperazine (1bpa) were experimentally recorded in the region of 4000-10 cm-1 and 4000-100 cm-1, respectively. The optimized geometric parameters, conformational equilibria, normal mode frequencies and corresponding vibrational assignments of 1bpa (C8H18N2) are theoretically examined by means of B3LYP hybrid density functional theory (DFT) method together with 6-31++G(d,p) basis set. Also, reliable conformational investigation and vibrational assignments have been performed by the potential energy surface (PES) and potential energy distribution (PED) analysis, respectively. Calculations are made for four possible conformations. According to the experimental and theoretical data, density functional B3LYP method provides reliable results for predicting vibrational wavenumbers and equatorial-equatorial conformer is considered to be the most stable form of 1bpa.

  5. Experimental and DFT studies on the vibrational, electronic spectra and NBO analysis of thiamethoxam

    Science.gov (United States)

    Zhang, Fang; Zhang, Yu; Ni, Haiwei; Ma, Kuirong; Li, Rongqing

    2014-01-01

    Vibrational and electronic spectral measurements were performed for 3-(2-chloro-1,3-thiazol-5-ylmethyl)-5-methyl-1,3,5-oxadiazinan-4-ylidene(nitro) amine (thiamethoxam). Optimized geometrical structure and harmonic vibrational frequencies were calculated with ab initio RHF and DFT (B3LYP, CAMB3LYP, M06 and PBE1PBE) methods with 6-311++G (d, p) basis set. Complete assignments of the observed spectra were proposed. The absorption spectra of the compound were computed in gas-phase using TD-B3LYP/6-311++G (d, p) approach and H2O solution using PCM-TD-B3LYP/6-311++G (d, p) approach. The calculated results matched well with the experimental values. Temperature dependence of thermodynamic parameters in the range of 100-1000 K were determined. The bond orbital occupancies, contribution from parent natural bond orbital (NBO), the natural atomic hybrids was discussed.

  6. Anharmonic Franck-Condon simulation of the absorption and fluorescence spectra for the low-lying S1 and S2 excited states of pyridine.

    Science.gov (United States)

    Wang, Huan; Zhu, Chaoyuan; Yu, Jian-Guo; Lin, Sheng Hsien

    2009-12-31

    Anharmonic effects of the absorption and fluorescence spectra of pyridine molecule are studied and analyzed for the two-low lying singlet excited states S(1)((1)B(1)) and S(2)((1)B(2)). The complete active space self-consistent field (CASSCF) method is utilized to compute equilibrium geometries and all 27 vibrational normal-mode frequencies for the ground state and the two excited states. The present calculations show that the frequency differences between the ground and two excited states are small for the ten totally symmetric vibrational modes so that the displaced oscillator approximation can be used for spectrum simulations. The Franck-Condon factors within harmonic approximation basically grasp the main features of molecular spectra, but simulated 0-0 transition energy position and spectrum band shapes are not satisfactorily good for S(1)((1)B(1)) absorption and fluorescence spectra in comparison with experiment observation. As the first-order anharmonic correction added to Franck-Condon factors, both spectrum positions and band shapes can be simultaneously improved for both absorption and fluorescence spectra. It is concluded that the present anharmonic correction produces a significant dynamic shifts for spectrum positions and improves spectrum band shapes as well. The detailed structures of absorption spectrum of S(2)((1)B(2)) state observed from experiment can be also reproduced with anharmonic Franck-Condon simulation, and these were not shown in the harmonic Franck-Condon simulation with either distorted or Duschinsky effects in the literature.

  7. Correlation of critical temperature with the vibrational spectra of high-temperature superconducters

    Energy Technology Data Exchange (ETDEWEB)

    Bush, A.A.; Dubenko, I.S.; Limonov, M.F.; Markov, IU.F.; Panfilov, A.G. (Moskovskii Institut Radiotekhniki, Elektroniki i Avtomatiki, Moscow (USSR) Fiziko-Tekhnicheskii Institut, Moscow (USSR))

    1989-09-01

    An empirical relation between an increase in Tc and an increase in the frequencies of the vibrational spectra of different high-temperature superconducters of perovskite type is established. Taking this relation into account, a new system (Y{sub 1-x}Sc{sub x})(Ba{sub 1-y}Sr{sub y})2 Cu{sub 3}O(delta) is proposed, in which an increase in Tc is observed at intermediate concentrations. 13 refs.

  8. Structure and intermolecular vibrations of 7-azaindole-water 2:1 complex in a supersonic jet expansion: Laser-induced fluorescence spectroscopy and quantum chemistry calculation

    Indian Academy of Sciences (India)

    Montu K Hazra; Moitrayee Mukherjee; V Ramanathan; Tapas Chakraborty

    2012-01-01

    Laser-induced fluorescence spectra of a 2:1 complex between 7-azaindole and water, known as `non-reactive dimer’ of the molecule, have been measured in a supersonic jet expansion. The dispersed fluorescence spectrum of the electronic origin band of the complex shows a very large number of low-frequency vibrational features corresponding to different intermolecular modes of the complex in the ground electronic state. Geometries of several possible isomeric structures of the complex and their vibrational frequencies at harmonic approximation were calculated by electronic structure theory method at MP2/6-31G∗∗ level. An excellent agreement is observed between the measured and calculated intermolecular vibrational mode frequencies for the energetically most favoured structure of the complex, where the water molecule is inserted within one of the two N$\\cdots$H-N hydrogen bonds of the 7AI dimer.

  9. Assigning the Vibration-Rotation Spectra Using the Lww Program Package

    Science.gov (United States)

    Lodyga, Wieslaw; Kreglewski, Marek

    2016-06-01

    The LWW program package is based on traditional methods used in assigning rotationally resolved IR molecular spectra. The Loomis-Wood diagrams, which are used to visualize spectral branches and facilitate their identification, are combined with the power of interactive lower state combination difference (LSCD) checking, which provides immediate verification of correct assignments of quantum numbers to spectral lines. The traditional Giessen/Cologne type Loomis-Wood algorithm is also implemented. Predictions of vibration-rotation wavenumbers are calculated from a table of vibration-rotation energies, which can be imported from any external fitting program. Program includes many additional tools like simulation of a spectrum from a catalog file (list of transitions with intensities), build-up of a vibration-rotation band from individual branches and simultaneous displaying of two IR spectra - active one used for assignments and a reference one, both with full link to their peak-list files. Importing energies as well as exporting assigned data for fitting in an external program is made easy and flexible by a user-programmed import/export interface, which facilitates iterative refining of energy levels and gives a possibility of using directly exact vibration-rotation energies. Program is available in tree versions: for symmetric top, asymmetric top and molecules with large amplitude motions. The program is designed for the Windows operating systems and is available with full documentation on www.lww.amu.edu.pl .

  10. Vibrational spectra and non linear optical proprieties of L-histidine oxalate: DFT studies

    Science.gov (United States)

    Ahmed, A. Ben; Elleuch, N.; Feki, H.; Abid, Y.; Minot, C.

    2011-08-01

    This paper presents the results of our calculations on the geometric parameters, vibrational spectra and hyperpolarizability of a nonlinear optical material L-histidine oxalate. Due to the lack of sufficiently precise information on geometric structure in literature, theoretical calculations were preceded by re-determination of the crystal X-ray structure. Single crystal of L-histidine oxalate has been growing by slow evaporation of an aqueous solution at room temperature. The compound crystallizes in the non-Centro symmetric space group P2 12 12 1 of orthorhombic system. The FT-IR and Raman spectra of L-histidine oxalate were recorded and analyzed. The vibrational wave numbers were examined theoretical with the aid of Gaussian98 package of programs using the DFT//B3LYP/6-31G(d) level of theory. The data obtained from vibrational wave number calculations are used to assign vibrational bands obtained in IR and Raman spectroscopy of the studied compound. The geometrical parameters of the title compound are in agreement with the values of similar structures. To investigate microscopic second order non-linear optical NLO behaviour of the examined complex, the electric dipole μtot, the polarizability αtot and the hyperpolarizability βtot were computed using DFT//B3LYP/6-31G(d) method. According to our calculation, the title compound exhibits non-zero βtot value revealing microscopic second order NLO behaviour.

  11. Vibrational spectra and normal coordinate analysis of 2-hydroxy-3-(2-methoxyphenoxy) propyl carbamate

    Science.gov (United States)

    Muthu, S.; Renuga, S.

    2014-11-01

    In this work, the vibrational spectral analysis was carried out by using FT-Raman and FTIR spectroscopy in the range 50-4000 cm-1 and 450-4000 cm-1 respectively, for 2-hydroxy-3-(2-methoxyphenoxy) propyl carbamate (2H3MPPLC) molecule. The molecular structure, fundamental vibrational frequencies and intensities of the vibrational bands were interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) and ab initio HF methods with 6-31G(d,p) basis set. The complete vibrational assignments of wave numbers were made on the basis of potential energy distribution (PED). The results of the calculations were applied to simulated spectra of the title compound, which show excellent agreement with observed spectra. The scaled B3LYP/6-31G(d,p) results show the best agreement with the experimental values over the other method. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The results confirm the occurrence of intramolecular charge-transfer (ICT) within the molecule. The dipole moment (μ), polarizability (α) and hyperpolarizability (β) of the investigated molecule has been computed using B3LYP/6-31G(d,p) method. Mulliken population analysis on atomic charges was also calculated. Besides, frontier molecular orbitals, molecular electrostatic potential (MEP) and thermodynamic properties were performed.

  12. Evidence for covalent binding of epicocconone with proteins from synchronous fluorescence spectra and fluorescence lifetimes

    Indian Academy of Sciences (India)

    Debashis Panda; Anindya Datta

    2007-03-01

    Synchronous fluorescence and time-resolved fluorescence spectroscopic studies that reveal the interaction of epicocconone with human serum albumin is significantly different from its interaction with surfactant assemblies. This observation, along with steady-state fluorescence data, indicates groundstate interaction between the fluorophore epicocconone and the protein. Similarity in fluorescence properties with the adduct of the fluorophore with -butylamine indicates that bonding occurs at the Nterminus of the protein.

  13. Resonant soft X-ray fluorescence spectra of molecules

    Energy Technology Data Exchange (ETDEWEB)

    Nordgren, J.; Glans, P.; Gunnelin, K.; Guo, J.; Skytt, P.; Saathe, C.; Wassdahl, N. [Uppsala Univ. (Sweden). Dept. of Phys.

    1997-08-01

    A review is presented of some recent advancements in resonant soft X-ray fluorescence spectroscopy applied to molecules. The concept of inelastic scattering is discussed for molecules with an element of symmetry, which introduces degeneracy or near-degeneracy of core excited states. The potential of the symmetry selection rules associated with resonant X-ray fluorescence is illustrated in studies of electronic structure as well as molecular dynamics. The use of polarized photons for exciting X-ray emission is discussed, and examples are presented where anisotropy of X-ray emission provides more detailed information. A brief section discusses the experimental considerations relevant for the spectroscopic technique. (orig.) With 013 figs., 28 refs.

  14. Vibrational spectra, NBO, HOMO-LUMO and conformational stability studies of 4-hydroxythiobenzamide.

    Science.gov (United States)

    Sambathkumar, Kuppusamy

    2015-08-05

    In this work, the experimental and theoretical study on molecular structure, vibrational spectral analysis of 4-hydroxythiobenzamide (HTB) have been reported. The solid phase FTIR (4000-400 cm(-1)) and FT-Raman spectra (3500-50 cm(-1)) were recorded. The molecular geometry, harmonic vibrational frequencies and bonding features of HTB in the ground-state have been calculated by the density functional method (B3LYP) with 6-311+G(d,p) and 6-311++G(d,p) as basis sets. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. Stability of the molecule arising from hyperconjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The results show that the value of electron density (ED) in the σ(∗) antibonding orbitals and E((2)) energies confirms the occurrence of ICT (intra-molecular charge transfer) within the molecule. The UV spectrum was measured in ethanol solution. The energy and oscillator strength calculated by time-dependent density functional theory (TD-DFT) correlates with the experimental findings. The calculated molecular electrostatic potential (MESP), HOMO and LUMO energies show that charge transfer occurs within the molecule. Besides, the simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Crystal structure, vibrational spectra and theoretical studies of L-histidinium dihydrogen phosphate-phosphoric acid

    Science.gov (United States)

    Ahmed, A. Ben; Feki, H.; Abid, Y.; Boughzala, H.; Minot, C.; Mlayah, A.

    2009-02-01

    In this work, we report a combined experimental and theoretical study on molecular structure and vibrational spectra of L-histidinium dihydrogen phosphate-phosphoric acid, with particular emphasize on the correlation between the intermolecular hydrogen bonds and the hyperpolarizability. Single crystal of L-histidinium dihydrogen phosphate-phosphoric acid has been subjected to X-ray diffraction and Raman spectroscopy. The title compound crystallises in the non-centrosymmetric space group P2 1. Raman spectra have been recorded in the frequency range [150-3350 cm -1]. To obtain a more reliable assignment of the Raman and IR spectra, we have calculated the geometry and the frequencies using HF and DFT methods. All the experimental vibrational bands have been discussed and assigned to normal mode or to combinations and overtones on the basis of our calculations. The optimized geometric bond lengths and bond angles obtained by using HF and DFT (B3LYP and BLYP) are in well agreement with the experimental data. The results of DFT-B3LYP method have shown better fit to experimental ones than HF in evaluating vibrational frequencies. To investigate microscopic second order non-linear optical behaviour of the examined complex, the electric dipole μ, the polarizability α and the hyperpolarizability β were computed using DFT//B3LYP/6-31 G(d) method. According to our calculation, the title compound exhibits non-zero β value revealing microscopic second order NLO behaviour.

  16. Applicability of the SQM force field method to the vibrational spectra of sodium acetate.

    Science.gov (United States)

    Keresztury, Gabor; Istvan, Krisztina; Sundius, Tom

    2005-09-08

    The applicability of the scaled quantum mechanical force field (SQM FF) method to the prediction of the vibrational spectra of a charged molecule has been studied by the example of the acetate ion (CH3CO2-) in sodium acetate for which an efficient empirical valence force field (SVFF) based on observed IR spectra of six isotopomers of sodium acetate is available in the literature. Standard SQM FF calculations done on a free acetate ion at the B3LYP/6-31G level failed to give an acceptable estimation of even the most characteristic features of the observed spectra, which can be exemplified by the gross overestimation of the frequency separation of the nu(a)CO2- and nu(s)CO2- vibrations. In search for a better description, SQM calculations were done for three simple structural models of sodium acetate, testing different QM methods. The results indicate that in addition to taking into account the dielectric field effect of the surrounding medium, incorporation of a Na+ counterion is necessary to achieve a realistic simulation of the IR and Raman spectra. Satisfactory results were obtained with a bidentate Na-acetate complex by the SQM method coupled with a continuum model at the B3LYP/6-31+G level, whereas the use of the Onsager-type spherical cavity model and the polarizable continuum model (PCM) were found preferable over SCI-PCM.

  17. Evaluation of potential emission spectra for the reliable classification of fluorescently coded materials

    Science.gov (United States)

    Brunner, Siegfried; Kargel, Christian

    2011-06-01

    The conservation and efficient use of natural and especially strategic resources like oil and water have become global issues, which increasingly initiate environmental and political activities for comprehensive recycling programs. To effectively reutilize oil-based materials necessary in many industrial fields (e.g. chemical and pharmaceutical industry, automotive, packaging), appropriate methods for a fast and highly reliable automated material identification are required. One non-contacting, color- and shape-independent new technique that eliminates the shortcomings of existing methods is to label materials like plastics with certain combinations of fluorescent markers ("optical codes", "optical fingerprints") incorporated during manufacture. Since time-resolved measurements are complex (and expensive), fluorescent markers must be designed that possess unique spectral signatures. The number of identifiable materials increases with the number of fluorescent markers that can be reliably distinguished within the limited wavelength band available. In this article we shall investigate the reliable detection and classification of fluorescent markers with specific fluorescence emission spectra. These simulated spectra are modeled based on realistic fluorescence spectra acquired from material samples using a modern VNIR spectral imaging system. In order to maximize the number of materials that can be reliably identified, we evaluate the performance of 8 classification algorithms based on different spectral similarity measures. The results help guide the design of appropriate fluorescent markers, optical sensors and the overall measurement system.

  18. [Feature abstraction and spectral reconstruction of three-dimensional fluorescence spectra of oil in water].

    Science.gov (United States)

    Tian, Guang-Jun

    2008-04-01

    In the present paper, spectral reconstruction of three-dimensional fluorescence spectra of oil was studied based on singular value division (SVD) of fluorescence excitation-emission matrix (EEM). Depending on oil components, three-dimensional (3-D) fluorescence spectra of oils can be seen as their "fingerprints". Feature abstraction and selection of 3-D fluorescence spectra is important to oil identification. Statistic parameters such as the average, standard error, centroid, kurtosis, geometrical distribution as well as main-shaft slope selected, forming "apparent statistic feature" vector of 3-D fluorescence spectra of oils, are limited due to their roughness. And the apparent statistic feature vector can not support spectral reconstruction reversely. In this paper, with singular-value features abstracted from EEMs composing the feature chain, reversal spectral reconstruction can be realized, and its information loss can be estimated. In other words, a pan-gene series of 3-D fluorescence spectra consists of singular values and their corresponding accompanying vectors. By SVD operation on EEMs of dozens of oil samples in water, their singular values accompanied with corresponding vectors were calculated showing obviously gathering energy distribution. With singular values being properly cut, principal feature parameters were selected and combined with their accompanying vectors composing the pan-gene series (or singular-value pan-gene chain) and spectral reconstruction was reversely completed. A couple of spectra (original and reconstructed) of diesel as the typical oil in water were presented for comparison. It can be seen that there is no obvious difference between the reconstructed and original spectra. Certainly, information loss exists but in an scheduled extent. It is shown that the singular-value features of fluorescence excitation-emission matrix (EEM) represent spectral gathering energy, and the length-limited pan-gene chain has the ability to reconstruct

  19. Dynamic disorder, phonon lifetimes, and the assignment of modes to the vibrational spectra of methylammonium lead halide perovskites

    CERN Document Server

    Leguy, Aurélien M A; Frost, Jarvist M; Skelton, Jonathan; Brivio, Federico; Rodríguez-Martínez, Xabier; Weber, Oliver J; Pallipurath, Anuradha; Alonso, M Isabel; Campoy-Quiles, Mariano; Weller, Mark T; Nelson, Jenny; Walsh, Aron; Barnes, Piers R F

    2016-01-01

    We present Raman and terahertz absorbance spectra of methylammonium lead halide single crystals (MAPbX3, X = I, Br, Cl) at temperatures between 80 and 370 K. These results show good agreement with density-functional-theory phonon calculations.1 Comparison of experimental spectra and calculated vibrational modes enables confident assignment of most of the vibrational features between 50 and 3500 cm-1. Reorientation of the methylammonium cations, unlocked in their cavities at the orthorhombic-to-tetragonal phase transition, plays a key role in shaping the vibrational spectra of the different compounds. Calculations show that these dynamics effects split Raman peaks and create more structure than predicted from the independent harmonic modes. This explains the presence of extra peaks in the experimental spectra that have been a source of confusion in earlier studies. We discuss singular features, in particular the torsional vibration of the C-N axis, which is the only molecular mode that is strongly influenced b...

  20. Thermo-dynamical contours of electronic-vibrational spectra simulated using the statistical quantum-mechanical methods

    DEFF Research Database (Denmark)

    Pomogaev, Vladimir; Pomogaeva, Anna; Avramov, Pavel

    2011-01-01

    Three polycyclic organic molecules in various solvents focused on thermo-dynamical aspects were theoretically investigated using the recently developed statistical quantum mechanical/classical molecular dynamics method for simulating electronic-vibrational spectra. The absorption bands of estradiol...

  1. Fingerprint vibrational spectra of protonated methyl esters of amino acids in the gas phase.

    Science.gov (United States)

    Simon, Aude; Macaleese, Luke; Maître, Philippe; Lemaire, Joël; McMahon, Terrance B

    2007-03-14

    Infrared spectra of the protonated monomers of glycine, alanine, valine, and leucine methyl esters are presented. These protonated species are generated in the gas phase via matrix assisted laser desorption ionization (MALDI) within the cell of a Fourier transform ion cyclotron resonance spectrometer (FTICR) where they are subsequently mass selected as the only species trapped in the FTICR cell. Alternatively, they have also been generated by electrospray ionization and transferred to a Paul ion-trap mass spectrometer where they are similarly isolated. In both cases IR spectra are then derived from the frequency dependence of the infrared multiple photon dissociation (IRMPD) in the mid-infrared region (1000-2200 cm(-1)), using the free electron laser facility Centre de Laser Infrarouge d'Orsay (CLIO). IR bands are assigned by comparison with the calculated vibrational spectra of the lowest energy isomers using density functional theory (DFT) calculations. There is in general good agreement between experimental IRMPD spectra and calculated IR absorption spectra for the lowest energy conformer which provides evidence for conformational preferences. The two different approaches to ion generation and trapping yield IRMPD spectra that are in excellent agreement.

  2. Vibrational spectra study of phosphorus dendrimer containing azobenzene, ammonium and carbamate groups

    Science.gov (United States)

    Furer, V. L.; Vandyukov, A. E.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

    2013-06-01

    The FTIR and FT Raman spectra of the first generation dendrimers, possessing carbamate (G1) or ammonium (G2) terminal groups were studied. The structural optimization and normal mode analysis were performed for dendrimers on the basis of the density functional theory (DFT). These calculations of G2 gave the frequencies of vibrations, infrared intensities and Raman scattering activities for the E- and Z-forms of azobenzene unit. The energy difference between the E- and Z-forms of G2 is 27.36 kcal/mol. The calculated geometrical parameters and harmonic vibrational frequencies are predicted in a good agreement with the experimental data. It was found that dendrimers molecules have a concave lens structure with planar -O-C6H4-CHdbnd N-N(CH3)Pdbnd S, and -O-C6H4-Ndbnd N-C6H4-CHdbnd N-NH-Cdbnd O-CH2-N fragments and slightly non-planar cyclotriphosphazene core. The experimental IR and Raman spectra of dendrimers G1 and G2 were interpreted by means of potential energy distributions. Relying on DFT calculations a complete vibrational assignment is proposed. The strong band 1605 cm-1 in the IR spectra show marked changes of the optical density in dependence of substituents in the aromatic ring. The differences in the IR and Raman spectra of G2 for the E- and Z-forms of azobenzene units were cleared up. During structural isomerization of azobenzene units, redistribution of band intensities appears to a much higher extent than frequency shifts.

  3. Vibrational spectra study of phosphorus dendrimer containing azobenzene units on the surface

    Science.gov (United States)

    Furer, V. L.; Vandyukov, A. E.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

    2013-08-01

    The FTIR and FT Raman spectra of the first generation dendrimers, possessing oxybenzaldehyde (G1) or oxyphenylazobenzaldehyde (G2) terminal groups and sodium 4-[4-oxyphenyl)azo]-benzaldehyde (SOAB) were studied. The structural optimization and normal mode analysis were performed for dendrimer G2 on the basis of the density functional theory (DFT). These calculations gave the frequencies of vibrations, infrared intensities and Raman scattering activities for the E- and Z-forms of azobenzene unit. The energy differences between the E- and Z-forms are 12.62 and 25.16 kcal/mol for SOAB and G2. The calculated in gas phase dipole moments for the E- and Z-forms are equal to 20.86, 18.28 D (SOAB) and 7.56, 8.88 D (G2). The calculated geometrical parameters and harmonic vibrational frequencies are predicted in a good agreement with the experimental data. It was found that dendrimer G2 molecule has a concave lens structure with planar sbnd Osbnd C6H4sbnd CHdbnd Nsbnd N(CH3)Pdbnd S and sbnd Osbnd C6H4sbnd Ndbnd Nsbnd C6H4sbnd CHdbnd O fragments and slightly non-planar cyclotriphosphazene core. The experimental IR and Raman spectra of dendrimer G2 were interpreted by means of potential energy distributions. Relying on DFT calculations a complete vibrational assignment is proposed. The strong band 1598 cm-1 in the IR spectra show marked changes of the optical density in dependence of substituents in the aromatic ring. The differences in the IR and Raman spectra of SOAB and G2 for the E- and Z-forms of azobenzene units were cleared up. During structural isomerization of azobenzene units, redistribution of band intensities appears to a much higher extent than frequency shifts.

  4. Theoretical simulations for vibrationally-resolved absorption spectra of naphthalenediimide cyclophane derivatives

    Science.gov (United States)

    Song, Ce; Li, Li; Duan, Sai; Luo, Yi; Tian, Guangjun

    2017-08-01

    In the present work we systematically investigated the vibrationally-resolved absorption spectra of three core substituted naphthalenediimide cyclophane derivatives. It has been performed by time-dependent density functional theory calculations using three different exchange-correlation functionals, including the conventional B3LYP functional and two long-range corrected functionals: CAM-B3LYP and ωB97XD. The solvent effects were also considered with the polarizable continuum model. Calculation results showed that long range corrections are needed to correctly describe the optical properties of the three molecules because of the strong charge transfer characteristic of the excited states. The core substitution induced red shift to the first absorption band is nicely explained by the theoretical calculations. It is found that this band mainly involves the transitions within the core substituted naphthalenediimide chromophore. The high energy absorption band, on the other hand, is generated mainly from the un-substituted chromophore. These characters result in different substitution dependence for those two main absorption bands. Furthermore, the simulated vibrational profiles of the first two absorption bands nicely reproduce the observed vibrational features in the measured spectra. The accuracy of the calculated results from different functionals and basis sets has been discussed.

  5. Comparative studies on molecular structure, vibrational spectra and hyperpolarizabilies of NLO chromophore Ethyl 4-Dimethylaminobenzoate

    Science.gov (United States)

    Amalanathan, M.; Jasmine, G. Femina; Roy, S. Dawn Dharma

    2017-08-01

    The molecular structure, vibrational spectra and polarizabilities of Ethyl 4-Dimethylaminobenzoate (EDAB) was investigated by density functional theory employing Becke's three parameter hybrid exchange functional with Lee-Yang-Parr (B3LYP) co-relational functional involving 6-311++G(d,p) basis set and compared with some other levels. A detailed interpretation of the IR and Raman spectra of EDBA have been reported and analyzed. Complete vibrational assignments of the vibrational modes have been done on the basis of the potential energy distribution (TED) using VEDA software. The molecular electrostatic potential mapped onto total density surface has been obtained. A study on the electronic properties, such as absorption wavelength, and frontier molecular orbitals energy, was performed using DFT approach. The stability of the molecule arising from hyper conjugative interactions and accompanying charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The natural and Mulliken charge also calculated and compared with different level of calculation. The dipole moment, polarizability and first, second order hyperpolarizabilities of the title molecule were calculated and compared with the experimental values. The energy gap between frontier orbitals has been used along with electric moments and first order hyperpolarizability, to understand the non linear optical (NLO) activity of the molecule. The NLO activity of molecule was confirmed by SHG analysis.

  6. Vibrational absorption spectra from vibrational coupled cluster damped linear response functions calculated using an asymmetric Lanczos algorithm

    DEFF Research Database (Denmark)

    Thomsen, Bo; Hansen, Mikkel Bo; Seidler, Peter

    2012-01-01

    We report the theory and implementation of vibrational coupled cluster (VCC) damped response functions. From the imaginary part of the damped VCC response function the absorption as function of frequency can be obtained, requiring formally the solution of the now complex VCC response equations....... The absorption spectrum can in this formulation be seen as a matrix function of the characteristic VCC Jacobian response matrix. The asymmetric matrix version of the Lanczos method is used to generate a tridiagonal representation of the VCC response Jacobian. Solving the complex response equations...... in the relevant Lanczos space provides a method for calculating the VCC damped response functions and thereby subsequently the absorption spectra. The convergence behaviour of the algorithm is discussed theoretically and tested for different levels of completeness of the VCC expansion. Comparison is made...

  7. Spectral investigations of 2,5-difluoroaniline by using mass, electronic absorption, NMR, and vibrational spectra

    Science.gov (United States)

    Kose, Etem; Karabacak, Mehmet; Bardak, Fehmi; Atac, Ahmet

    2016-11-01

    One of the most significant aromatic amines is aniline, a primary aromatic amine replacing one hydrogen atom of a benzene molecule with an amino group (NH2). This study reports experimental and theoretical investigation of 2,5-difluoroaniline molecule (2,5-DFA) by using mass, ultraviolet-visible (UV-vis), 1H and 13C nuclear magnetic resonance (NMR), Fourier transform infrared and Raman (FT-IR and FT-Raman) spectra, and supported with theoretical calculations. Mass spectrum (MS) of 2,5-DFA is presented with their stabilities. The UV-vis spectra of the molecule are recorded in the range of 190-400 nm in water and ethanol solvents. The 1H and 13C NMR chemical shifts are recorded in CDCl3 solution. The vibrational spectra are recorded in the region 4000-400 cm-1 (FT-IR) and 4000-10 cm-1 (FT-Raman), respectively. Theoretical studies are underpinned the experimental results as described below; 2,5-DFA molecule is optimized by using B3LYP/6-311++G(d,p) basis set. The mass spectrum is evaluated and possible fragmentations are proposed based on the stable structure. The electronic properties, such as excitation energies, oscillator strengths, wavelengths, frontier molecular orbitals (FMO), HOMO and LUMO energies, are determined by time-dependent density functional theory (TD-DFT). The electrostatic potential surface (ESPs), density of state (DOS) diagrams are also prepared and evaluated. In addition to these, reduced density gradient (RDG) analysis is performed, and thermodynamic features are carried out theoretically. The NMR spectra (1H and 13C) are calculated by using the gauge-invariant atomic orbital (GIAO) method. The vibrational spectra of 2,5-DFA molecule are obtained by using DFT/B3LYP method with 6-311++G(d,p) basis set. Fundamental vibrations are assigned based on the potential energy distribution (PED) of the vibrational modes. The nonlinear optical properties (NLO) are also investigated. The theoretical and experimental results give a detailed description of

  8. Enhancement of Vibronic and Ground-State Vibrational Coherences in 2D Spectra of Photosynthetic Complexes

    CERN Document Server

    Chenu, Aurélia; Kauffmann, Harald F; Mančal, Tomáš

    2013-01-01

    A vibronic-exciton model is applied to investigate the mechanism of enhancement of coherent oscillations due to mixing of electronic and nuclear degrees of freedom recently proposed as the origin of the long-lived oscillations in 2D spectra of the FMO complex [Christensson et al. J. Phys. Chem. B 116 (2012) 7449]. We reduce the problem to a model BChl dimer to elucidate the role of resonance coupling, site energies, nuclear mode and energy disorder in the enhancement of vibronic-exciton and ground-state vibrational coherences, and to identify regimes where this enhancement is significant. For a heterodimer representing the two coupled BChls 3 and 4 of the FMO complex, the initial amplitude of the vibronic-exciton and vibrational coherences are enhanced by up to 15 and 5 times, respectively, compared to the vibrational coherences in the isolated monomer. This maximum initial amplitude enhancement occurs when there is a resonance between the electronic energy gap and the frequency of the vibrational mode. The b...

  9. First principles study on the molecular structure and vibrational spectra of ketoprofen

    Science.gov (United States)

    Liu, Lekun; Gao, Hongwei

    2012-11-01

    The aim of this work was to compare the performance of different DFT methods at different basis sets in predicting geometry and vibration spectrum of ketoprofen. The molecular geometry and vibrational frequencies of ketoprofen have been calculated using five different density function theory (DFT) methods, including LSDA, B3LYP, mPW1PW91, B3PW91 and HCTH, with various basis sets, including 6-311G, 6-311+G, 6-311++G, 6-311+G (d, p) and 6-311++G (2d, 2p). The results indicate that mPW1PW91/6-311++G (2d, 2p) level is clearly superior to all the remaining density functional methods in predicting the bond lengths and bond angles of ketoprofen. Mean absolute deviations between the calculated harmonic and observed fundamental vibration frequencies for each method shows that LSDA/6-311G method is the best to predict vibrational spectra of ketoprofen comparing other DFT methods.

  10. Experimental and DFT studies on the vibrational spectra of 1H-indene-2-boronic acid

    Science.gov (United States)

    Alver, Özgur; Kaya, Mehmet Fatih

    2014-11-01

    Stable conformers and geometrical molecular structures of 1H-indene-2-boronic acid (I-2B(OH)2) were studied experimentally and theoretically using FT-IR and FT-Raman spectroscopic methods. FT-IR and FT-Raman spectra were recorded in the region of 4000-400 cm-1, and 3700-400 cm-1, respectively. The optimized geometric structures were searched by Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional theory method with 6-31++G(d,p) basis set. Vibrational wavenumbers of I-2B(OH)2 were calculated using B3LYP density functional methods including 6-31++G(d,p) basis set. Experimental and theoretical results show that density functional B3LYP method gives satisfactory results for predicting vibrational wavenumbers except OH stretching modes which is probably due to increasing unharmonicity in the high wave number region and possible intra and inter molecular interaction at OH edges. To support the assigned vibrational wavenumbers, the potential energy distribution (PED) values were also calculated using VEDA 4 (Vibrational Energy Distribution Analysis) program.

  11. Vibrational spectra of the steroid hormones, estradiol and estriol, calculated by density functional theory. The role of low-frequency vibrations.

    Science.gov (United States)

    Minaeva, V A; Minaev, B F; Hovorun, D M

    2008-01-01

    The structure of estrogen receptors and their interaction with 17beta-estradiol and estriol are of particular interest today because the treatment of breast cancer and the cause of the disease are intricately linked to the activity of the estrogen receptor and the normal blood serum level of these hormones. Molecular geometry and vibration frequencies of these steroid hormones are calculated by density functional theory with the B3LYP/ 6-31G** approximation. Intensities of infrared absorption and Raman spectra for estradiol are in an agreement with the experiment data. The assignments of all vibrational bands in the spectra of these hormones are presented on the basis of quantum chemical calculations of frequencies and normal modes. For the large number of bands such an assignment is made for the first time. The analysis of infrared spectra of both hormones indicates some nontrivial structure-spectra correlations. A series of specific vibrations is predicted in the low-frequency region of the IR spectra; their role in hormone-receptor interaction and in energy transfer processes are discussed. The search of the optimized geometrical structure by minimization of the total energy gradient is accompanied by the second derivatives calculation; diagonalization of the Hessian matrix leads finally to solution of vibration problem. The 17beta-estradiol molecule consists of 44 atoms and has 126 normal modes of internal vibrations. All these normal modes are presented together with their analysis and comparison with experimental data. From this comparison we have obtained an assignment of all absorption IR bands of 17beta-estradiol recorded earlier in KBr. For all stretching vibrations our assignment is in agreement with the previous one, obtained on the basis of the empirical rules. Direct DFT calculation of vibrational frequencies cannot provide a 100% agreement with the experimental IR spectra and scaling factors in the range of 0.95-0.97 are used in order to fit

  12. Franck-Condon factors perturbed by damped harmonic oscillators: Solvent enhanced X 1Ag ↔ A1B1u absorption and fluorescence spectra of perylene

    Science.gov (United States)

    Wang, Chen-Wen; Yang, Ling; Zhu, Chaoyuan; Yu, Jian-Guo; Lin, Sheng-Hsien

    2014-08-01

    Damped harmonic oscillators are utilized to calculate Franck-Condon factors within displaced harmonic oscillator approximation. This is practically done by scaling unperturbed Hessian matrix that represents local modes of force constants for molecule in gaseous phase, and then by diagonalizing perturbed Hessian matrix it results in direct modification of Huang-Rhys factors which represent normal modes of solute molecule perturbed by solvent environment. Scaling parameters are empirically introduced for simulating absorption and fluorescence spectra of an isolated solute molecule in solution. The present method is especially useful for simulating vibronic spectra of polycyclic aromatic hydrocarbon molecules in which hydrogen atom vibrations in solution can be scaled equally, namely the same scaling factor being applied to all hydrogen atoms in polycyclic aromatic hydrocarbons. The present method is demonstrated in simulating solvent enhanced X 1Ag ↔ A1B1u absorption and fluorescence spectra of perylene (medium-sized polycyclic aromatic hydrocarbon) in benzene solution. It is found that one of six active normal modes v10 is actually responsible to the solvent enhancement of spectra observed in experiment. Simulations from all functionals (TD) B3LYP, (TD) B3LYP35, (TD) B3LYP50, and (TD) B3LYP100 draw the same conclusion. Hence, the present method is able to adequately reproduce experimental absorption and fluorescence spectra in both gas and solution phases.

  13. Electronic and vibrational spectra and thermodynamic functions of 3- and 4-methoxy benzonitriles

    Science.gov (United States)

    Goel, R. K.; Agarwal, M. L.

    The i.r. absorption spectra of 3- and 4- methoxy benzonitriles have been recorded on a Perkin—Elmer 521 spectrophotometer, while the Raman spectrum of 4-methoxybenzonitrile was recorded on CODERG Raman spectrometer T800 triple monochromator. The near ultraviolet absorption spectra of both the molecules in vapour phase have been recorded on Medium Quartz Hilger spectrograph and that of 4-methoxybenzonitrile on DK-2A ratio recording spectrophotometer also. The assignment of fundamental frequencies to various modes of vibration have been proposed and on the basis of free internal rotation and assigned vibrational frequencies, the thermodynamic functions of the molecules have been computed on a VAX-11/780 computer. The analysis of the electronic spectra has been given in terms of fundamentals, their combinations and overtones. 4-Methoxy benzonitrile has exhibited two band systems corresponding to 1A1 g- 1B2 u(2600 Å) and 1A1 g- 1B1 u(2100 Å) system of benzene, while 3-methoxybenzonitrile exhibited only the former system. The red shift of 0,0 bands has been discussed.

  14. Simulation of Vibrational Spectra of Large Molecules by Arbitrary Time Propagation.

    Science.gov (United States)

    Kubelka, Jan; Bouř, Petr

    2009-01-13

    Modern ab initio and multiscale methods enable the simulation of vibrational properties of very large molecules. Within the harmonic approximation, the traditional generation of the spectra based on the force field diagonalization can become inefficient due to the excessive demands on computer time and memory. The present study proposes to avoid completely the matrix diagonalization with a direct generation of the spectral shapes. For infrared absorption (IR) and vibrational circular dichroism (VCD) electric and magnetic dipole moments are propagated in a fictitious time and spectral intensities are obtained by Fourier transformation. The algorithm scales quasi-linearly, and for model polypeptide molecules the method was found numerically stable and faithfully reproduced exact transition frequencies and relative intensities.

  15. Intrinsic and collective structure of an algebraic model of molecular rotation-vibration spectra

    Energy Technology Data Exchange (ETDEWEB)

    Leviatan, A.; Kirson, M.W.

    1988-11-15

    A geometrical framework is provided for a recently proposed interacting boson model of molecular rotation-vibration spectra. An intrinsic state is defined by way of a boson condensate parametrized in terms of shape variables and is used to generate an energy surface. The global minimum of the energy surface determines an equilibrium condensate which serves as the basis for an exact separation of the Hamiltonian into intrinsic and collective parts. A Bogoliubov treatment of the intrinsic part produces, in leading order, the normal modes of vibration and their frequencies, the collective degrees of freedom being represented by zero-frequency Goldstone modes associated with spontaneous symmetry breaking in the condensate. The method is very useful in interpreting numerical results of the algebraic model, in identifying the capabilities and inadequacies of the Hamiltonian, and in constructing appropriate algebraic Hamiltonians for specific molecules. copyright 1988 Academic Press, Inc.

  16. Nightmare from which you will never awake: Electronic to vibrational spectra!

    Energy Technology Data Exchange (ETDEWEB)

    De Silva, Nuwon [Iowa State Univ., Ames, IA (United States)

    2013-01-01

    The theoretical background of ab initio methods and density functional theory is provided. The anharmonicity associated with weakly bound metal cation dihydrogen complexes is examined using the vibrational self-consistent field (VSCF) method and the interaction between a hydrogen molecule and a metal cation is characterized. A study of molecular hydrogen clustering around the lithium cation and their accompanied vibrational anharmonicity employing VSCF is illustrated. A qualitative interpretation is provided of solvent-induced shifts of amides and simulated electronic absorption spectra using the combined time-dependent density functional theory/effective fragment potential method (TDDFT/EFP). An excited-state solvent assisted quadruple hydrogen atom transfer reaction of a coumarin derivative is elucidated using micro solvated quantum mechanical (QM) water and macro solvated EFP water. A dispersion correction to the QM-EFP1 interaction energy is presented.

  17. Vibrational wave packet induced oscillations in two-dimensional electronic spectra. I. Experiments

    CERN Document Server

    Nemeth, Alexandra; Mancal, Tomas; Lukes, Vladimir; Hauer, Juergen; Kauffmann, Harald F; Sperling, Jaroslaw

    2010-01-01

    This is the first in a series of two papers investigating the effect of electron-phonon coupling in two-dimensional Fourier transformed electronic spectroscopy. We present a series of one- and two-dimensional nonlinear spectroscopic techniques for studying a dye molecule in solution. Ultrafast laser pulse excitation of an electronic transition coupled to vibrational modes induces a propagating vibrational wave packet that manifests itself in oscillating signal intensities and line-shapes. For the two-dimensional electronic spectra we can attribute the observed modulations to periodic enhancement and decrement of the relative amplitudes of rephasing and non-rephasing contributions to the total response. Different metrics of the two-dimensional signals are shown to relate to the frequency-frequency correlation function which provides the connection between experimentally accessible observations and the underlying microscopic molecular dynamics. A detailed theory of the time-dependent two-dimensional spectral li...

  18. Vibrational Spectra and Potential Energy Surface for Electronic Ground State of Jet-Cooled Molecule S2O

    Institute of Scientific and Technical Information of China (English)

    WANG Xiao-Yan; DING Shi-Liang

    2004-01-01

    The vibration states of transition molecule S2O, including both bending and stretching vibrations, are studied in the framework of dynamical symmetry groups U1(4) U2(4). We get all the vibration spectra of S2O by fitting 22 spectra data with 10 parameters. The fitting rms of the Hamiltonian is 2.12 cm-1. With the parameters and Lie algebraic theory, we give the analytical expression of the potential energy surface, which helps us to calculate the dissociation energy and force constants of S2O in the electronic ground state.

  19. Fluorescence spectra of Rhodamine 6G for high fluence excitation laser radiation

    CERN Document Server

    Hung, J; Olaizola, A M

    2003-01-01

    Fluorescence spectral changes of Rhodamine 6G in ethanol and glycerol solutions and deposited as a film on a silica surface have been studied using a wide range of pumping field fluence at 532 nm at room temperature. Blue shift of the fluorescence spectra and fluorescence quenching of the dye molecule in solution are observed at high excitation fluence values. Such effects are not reported for the film sample. The effects are interpreted as the result of population redistribution in the solute-solvent molecular system induced by the high fluence field and the fluence dependence of the radiationless decay mechanism.

  20. Selective nonspecific solvation under dielectric saturation and fluorescence spectra of dye solutions in binary solvents.

    Science.gov (United States)

    Bakhshiev, N G; Kiselev, M B

    1991-09-01

    The influence of selective nonspecific solvation on the fluorescence spectra of three substitutedN-methylphthalimides in a binary solvent system consisting of a nonpolar (n-heptane) and a polar (pyridine) component has been studied under conditions close to dielectric saturation. The substantially nonlinearity of the effect is confirmation that the spectral shifts of fluorescence bands depend on the number of polar solvent molecules involved in solvating the dye molecule. The measured fluorescence spectral shifts determined by substituting one nonpolar solvent molecula with a polar one in the proximity of the dye molecule agree quantitatively with the forecasts of the previously proposed semiempirical theory which describes this nonlinear solvation phenomenon.

  1. Vibrational spectra and non linear optical proprieties of L-histidine oxalate: DFT studies.

    Science.gov (United States)

    Ben Ahmed, A; Elleuch, N; Feki, H; Abid, Y; Minot, C

    2011-08-01

    This paper presents the results of our calculations on the geometric parameters, vibrational spectra and hyperpolarizability of a nonlinear optical material L-histidine oxalate. Due to the lack of sufficiently precise information on geometric structure in literature, theoretical calculations were preceded by re-determination of the crystal X-ray structure. Single crystal of L-histidine oxalate has been growing by slow evaporation of an aqueous solution at room temperature. The compound crystallizes in the non-Centro symmetric space group P2(1)2(1)2(1) of orthorhombic system. The FT-IR and Raman spectra of L-histidine oxalate were recorded and analyzed. The vibrational wave numbers were examined theoretical with the aid of Gaussian98 package of programs using the DFT//B3LYP/6-31G(d) level of theory. The data obtained from vibrational wave number calculations are used to assign vibrational bands obtained in IR and Raman spectroscopy of the studied compound. The geometrical parameters of the title compound are in agreement with the values of similar structures. To investigate microscopic second order non-linear optical NLO behaviour of the examined complex, the electric dipole μ(tot), the polarizability α(tot) and the hyperpolarizability β(tot) were computed using DFT//B3LYP/6-31G(d) method. According to our calculation, the title compound exhibits non-zero β(tot) value revealing microscopic second order NLO behaviour. Crown Copyright © 2011. Published by Elsevier B.V. All rights reserved.

  2. Applicability of Density Functional Theory in Reproducing Accurate Vibrational Spectra of Surface Bound Species

    Energy Technology Data Exchange (ETDEWEB)

    Matanovic, Ivana; Atanassov, Plamen; Kiefer, Boris; Garzon, Fernando; Henson, Neil J.

    2014-10-05

    The structural equilibrium parameters, the adsorption energies, and the vibrational frequencies of the nitrogen molecule and the hydrogen atom adsorbed on the (111) surface of rhodium have been investigated using different generalized-gradient approximation (GGA), nonlocal correlation, meta-GGA, and hybrid functionals, namely, Perdew, Burke, and Ernzerhof (PBE), Revised-RPBE, vdW-DF, Tao, Perdew, Staroverov, and Scuseria functional (TPSS), and Heyd, Scuseria, and Ernzerhof (HSE06) functional in the plane wave formalism. Among the five tested functionals, nonlocal vdW-DF and meta-GGA TPSS functionals are most successful in describing energetics of dinitrogen physisorption to the Rh(111) surface, while the PBE functional provides the correct chemisorption energy for the hydrogen atom. It was also found that TPSS functional produces the best vibrational spectra of the nitrogen molecule and the hydrogen atom on rhodium within the harmonic formalism with the error of 22.62 and 21.1% for the NAN stretching and RhAH stretching frequency. Thus, TPSS functional was proposed as a method of choice for obtaining vibrational spectra of low weight adsorbates on metallic surfaces within the harmonic approximation. At the anharmonic level, by decoupling the RhAH and NAN stretching modes from the bulk phonons and by solving one- and two-dimensional Schr€odinger equation associated with the RhAH, RhAN, and NAN potential energy we calculated the anharmonic correction for NAN and RhAH stretching modes as 231 cm21 and 277 cm21 at PBE level. Anharmonic vibrational frequencies calculated with the use of the hybrid HSE06 function are in best agreement with available experiments.

  3. Investigation of formalin influence over hard and soft biological tissues fluorescent spectra in vitro

    Science.gov (United States)

    Borisova, E.; Uzunov, Tz.; Vladimirov, B.; Avramov, L.

    2007-05-01

    In order to investigate the formalin influence over fluorescence properties of hard and soft biological tissues during conservation, emission spectra have been registered. Nitrogen laser at 337 nm and light-emitting diode with maximum at 405 nm have been used as excitation sources. For investigation of formalin influence over hard tissues, an experiment was made on teeth samples. Sound teeth were demineralized with a phosphoric acid for 10 seconds to obtain enamel structure near to the tooth lesion, and were fixed in formalin. Before and after teeth treatment spectra from the areas of interest were detected. There were not observed changes in the shape of the teeth spectra, related to the introduction of formalin fluorescence. Samples from mucosa of esophagus and stomach, where initially an ALA/Protoporphyrin IX diagnosis was applied, were used as soft tissue specimens. After fluorescent diagnosis in vivo biopsy samples were obtained from normal and cancerous areas and were conserved in formalin. Initially, spectrum observed has one autofluorescence maximum from the mucous tissue at 500-600 nm and secondary maxima from the protoporphyrin fluorescence at 635 nm and 720 nm, as well as pronounced minima at 540 and 575 nm related to hemoglobin absorption. After formalin conservation hemoglobin absorption was strongly reduced that increases mucous emission signal in green-yellow spectral region. Simultaneously the maxima at 635 nm and 720 nm were reduced. As conclusion we could say that formalin has negligible influence over fluorescence spectra of conserved hard tissues and has more pronounced influence over fluorescence spectra obtained in the case of soft tissue conservation, which has to be taking into account in measurements in vitro.

  4. Time-resolved fluorescence spectra of cis-stilbene in hexane and acetonitrile

    Science.gov (United States)

    Sajadi, M.; Dobryakov, A. L.; Garbin, E.; Ernsting, N. P.; Kovalenko, S. A.

    2010-04-01

    Transient fluorescence spectra from cis-stilbene in solution are recorded with 0.24 ps instrument response by a Kerr-Shutter upon excitation at 283 and 267 nm. The fluorescence decay shows no dependence on the excitation wavelength and proceeds monoexponentially with 0.21 ps in acetonitrile and 0.75 ps in hexane. No spectral shift or distortion of the fluorescence band is observed during the decay. Fluorescence contribution from 4a,4b-dihydrophenanthrene (DHP), produced in a competing reaction channel, was not detectable. From comparison with trans-fluorescence, the emission oscillator strength of cis-stilbene is determined to be 0.19 in hexane and 0.21 in acetonitrile.

  5. 锕系化合物荧光光谱理论研究进展%Theoretical Studies on Fluorescence Spectra of Actinide Complexes

    Institute of Scientific and Technical Information of China (English)

    苏静; 李隽

    2011-01-01

    本文对锕系化合物荧光光谱的实验研究进行了系统总结,并在此基础上重点介绍了锕酰(actinyl)化合物的电子结构以及荧光光谱模拟的原理。结合我们关于铀酰-甘氨酸水合物结构、稳定性和荧光光谱模拟的研究工作,本文对锕系化合物荧光光谱理论研究的现状、理论方法和计算结果进行了综述。铀酰配合物中O—U—O单元的对称伸缩振动决定了其荧光特征,通过理论研究,结合计算化学模拟,可以解释铀酰-甘氨酸水溶液中振动分辨的实验光谱图,并阐明热带(hot band)峰强度异常高的成因。上述研究结果表明,现代计算化学和实验技术相结合,%In this mini-review,we have briefly summarized the experimental research on fluorescence spectra of actinide complexes,the electronic structures of actinyl complexes,and the basic principle for computational simulations of fluorescence spectra.Although numerous fluorescence spectroscopy data had been available experimentally,there were no theoretical investigations on vibrationally resolved fluorescence spectra of actinide complexes.Recently we have performed for the first time computational modeling of vibrationally resolved fluorescence spectra of uranyl complexes using Heller's time-dependent theory for electronic spectroscopy.Herein reviewed are the theoretical results from computational chemistry modeling on the coordination structures,stabilization energies and fluorescence properties of uranyl-glycine-water complexes.Our research has shown that the vibrationally resolved electronic spectra and the unusually high intensity of the illustrious uranyl hot-band can be interpreted by combining state-of-the-art computational chemistry and contemporary experimental techniques.This integrated theory and experiment approach can lead to a detailed understanding of the geometries,energetics,and luminescence properties of actinide compounds,including those with bio-ligands.

  6. Using symmetry-adapted optimized sum-of-products basis functions to calculate vibrational spectra

    CERN Document Server

    Leclerc, Arnaud

    2016-01-01

    Vibrational spectra can be computed without storing full-dimensional vectors by using low-rank sum-of-products (SOP) basis functions. We introduce symmetry constraints in the SOP basis functions to make it possible to separately calculate states in different symmetry subgroups. This is done using a power method to compute eigenvalues and an alternating least squares method to optimize basis functions. Owing to the fact that the power method favours the convergence of the lowest states, one must be careful not to exclude basis functions of some symmetries. Exploiting symmetry facilitates making assignments and improves the accuracy. The method is applied to the acetonitrile molecule.

  7. Semiempirical models in theory of intensities of rotation—vibration spectra of polyatomic molecules

    Science.gov (United States)

    Berezin, V. I.; El'kin, M. D.

    1992-10-01

    Two fundamental models in the theory of intensities of rotation—vibration spectra of polyatomic molecules are considered: a valence-optical scheme (Volkenstein—Elyashevitch—Stepanov scheme) and the Mayants—Averbukh method. The mathematics of the tensor analysis are proposed for the reception of the calculated formulae of overtonic spectroscopy in the limit of the debated models. It is shown that the difference in these formulae is conditioned by the form of the system of curvilinear coordinates, which are used to describe the different kinds of molecular motion.

  8. High-precision evaluation of the Vibrational spectra of long-range molecules

    CERN Document Server

    Tannous, C

    2001-01-01

    Vibrational spectra of long-range molecules are determined accurately and to arbitrary accuracy with the Canonical Function Method. The energy levels of the $0^-_g$ and $1_u$ electronic states of the $^{23}{\\rm Na}_2$ molecule are determined from the Ground state up to the continuum limit. The method is validated by comparison with previous results obtained by Stwalley et al. using the same potential and Trost et al. whose work is based on the Lennard-Jones potential adapted to long-range molecules.

  9. The influence of the long-range order on the vibrational spectra of structures based on sodalite cage.

    Science.gov (United States)

    Mikuła, A; Król, M; Koleżyński, A

    2015-06-05

    Zeolites are a group of tecto-aluminosilicates with numerous practical applications, e.g. gas separators, molecular sieves and sorbents. The unique properties result from porous structure of channels and cages which are built from smaller units - the so-called Secondary Building Units (SBU), and sometimes also larger groups (Breck, 1974; Ciciszwili et al., 1974; Mozgawa, 2008; Čejka and van Bekkum, 2005). The aim of this study was the examination of the influence of long-range order on vibrational spectra of sodalite and zeolite A. Ab initio calculations (geometry optimizations and vibrational spectra calculations) of sodalite cage and selected SBU were carried out by means of Gaussian09 (Frisch et al., 2009) (in the case of isolated clusters) and Crystal09 (Dovesi et al., 2005, 2009) (for periodic structures). The obtained results were compared with the experimental spectra of sodalite and zeolite A crystal structures, synthesized under hydrothermal conditions. These results allowed analyzing of the long-range ordering influence on the vibrational spectra, as well as the identification of the characteristic vibrations in β cage based frameworks. It has been found, that based on small structural fragment (SBU) models a characteristic vibrations can be identify. However, full spectra analysis and especially the interpretation of far-infrared region of the spectra require using periodic models under the influence of translational crystal lattice.

  10. On the purported "backbone fluorescence" in protein three-dimensional fluorescence spectra

    DEFF Research Database (Denmark)

    Bortolotti, Annalisa; Wong, Yin How; Korsholm, Stine S.

    2016-01-01

    as any traditional protein emission spectrum. The many papers in reputable journals erroneously reporting this peak assignment, contradicting 5 decades of prior knowledge, have led to the creation of a new dogma, where many authors and reviewers now take the purported backbone fluorescence......In this study, several proteins (albumin, lysozyme, insulin) and model compounds (Trp, Tyr, homopolypeptides) were used to demonstrate the origin of the fluorescence observed upon their excitation at 220-230 nm. In the last 10 years we have observed a worrying increase in the number of articles...... claiming that this fluorescence originates from the protein backbone, contrary to the established knowledge that UV protein emission is due to aromatic amino acids only. Overall, our data clearly demonstrate that the observed emission upon excitation at 220-230 nm is due to the excitation of Tyr and/or Trp...

  11. Vibrationally high-resolved electronic spectra of MCl2 (M = C, Si, Ge, Sn, Pb) and photoelectron spectra of MCl2-

    Science.gov (United States)

    Ran, Yibin; Pang, Min; Shen, Wei; Li, Ming; He, Rongxing

    2016-10-01

    We systematically studied the vibrational-resolved electronic spectra of group IV dichlorides using the Franck-Condon approximation combined with the Duschinsky and Herzberg-Teller effects in harmonic and anharmonic frameworks (only the simulation of absorption spectra includes the anharmonicity). Calculated results showed that the band shapes of simulated spectra are in accordance with those of the corresponding experimental or theoretical ones. We found that the symmetric bend mode in progression of absorption is the most active one, whereas the main contributor in photoelectron spectra is the symmetric stretching mode. Moreover, the Duschinsky and anharmonic effects exert weak influence on the absorption spectra, except for PbCl2 molecule. The theoretical insights presented in this work are significant in understanding the photophysical properties of MCl2 (M = C, Si, Ge, Sn, Pb) and studying the Herzberg-Teller and the anharmonic effects on the absorption spectra of new dichlorides of this main group.

  12. Changes in the Vibrational Spectra of Zeolites Due to Sorption of Heavy Metal Cations

    Science.gov (United States)

    Król, M.; Mozgawa, W.; Barczyk, K.; Bajda, T.; Kozanecki, M.

    2013-11-01

    This work presents the results of spectroscopic (MIR and Raman) studies of zeolite structures after immobilization of heavy metal cations from aqueous solutions. The sorption of Ag+, Cu2+, Cd2+, Pb2+, Zn2+, and Cr3+ ions has been conducted on zeolites belonging to different structural groups, i.e., sodium forms of natural chabazite, mordenite, ferrierite, and clinoptilolite, as well as on synthetic zeolite Y. Systematic changes in intensities and positions of the bands corresponding to the characteristic ring vibrations have been observed in the measured spectra. The most visible changes are observed in the FT-IR spectra of the samples in the range of 850-450 cm-1, and in the Raman spectra in the range of 600-250 cm-1. Depending on the zeolite structure, the bands, which can be regarded as a kind of indicator of ion exchange, were indentifi ed. For example, in the case of IR spectra, these bands are at 766, 703, 648, 578, and 506 cm-1 for zeolite Y, at 733 and 560 cm-1 for mordenite, at 675 cm-1 for clinoptilolite, etc. The degree of changes depends on both the type of cation and its concentration in the initial solution. This is connected with the way of binding of metal ions to the zeolite aluminosilicate framework, i.e., a proportion of the ion exchange and chemisorption in the process. Cations mainly undergoing ion exchange, such as Cd2+ or Pb2+, have the greatest impact on the character of the spectra. On the other hand, Cr3+ ions practically do not modify the spectra of zeolites. Results of IR and Raman spectroscopic studies have been compared with those obtained by atomic absorption spectroscopy (AAS), from which the proportion of ion exchange to chemisorption in the process and the effective cation exchange capacity of the individual samples have been estimated.

  13. Experimental and theoretical investigation of vibrational spectra of coordination polymers based on TCE-TTF.

    Science.gov (United States)

    Olejniczak, Iwona; Lapiński, Andrzej; Swietlik, Roman; Olivier, Jean; Golhen, Stéphane; Ouahab, Lahcène

    2011-08-01

    The room-temperature infrared and Raman spectra of a series of four isostructural polymeric salts of 2,3,6,7-tetrakis(2-cyanoethylthio)-tetrathiafulvalene (TCE-TTF) with paramagnetic (Co(II), Mn(II)) and diamagnetic (Zn(II), Cd(II)) ions, together with BF(4)(-) or ClO(4)(-) anions are reported. Infrared and Raman-active modes are identified and assigned based on theoretical calculations for neutral and ionized TCE-TTF using density functional theory (DFT) methods. It is confirmed that the TCE-TTF molecules in all the materials investigated are fully ionized and interact in the crystal structure through cyanoethylthio groups. The vibrational modes related to the C=C stretching vibrations of TCE-TTF are analyzed assuming the occurrence of electron-molecular vibration coupling (EMV). The presence of the antisymmetric C=C dimeric mode provides evidence that charge transfer takes place between TCE-TTF molecules belonging to neighboring polymeric networks.

  14. Vibrationally resolved high-resolution NEXAFS and XPS spectra of phenanthrene and coronene

    Energy Technology Data Exchange (ETDEWEB)

    Fronzoni, Giovanna; Baseggio, Oscar; Stener, Mauro, E-mail: stener@univ.trieste.it [Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via L. Giorgieri 1, I-34127 Trieste (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali, INSTM, Unita’ di Trieste, I-34127 Trieste (Italy); Hua, Weijie; Tian, Guangjun [Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm (Sweden); Luo, Yi [Department of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm (Sweden); National Synchrotron Radiation Laboratory and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); Apicella, Barbara; Alfé, Michela [Istituto di Ricerche sulla Combustione, IRC-CNR, P.le Tecchio, 80, 80125 Napoli (Italy); Simone, Monica de; Kivimäki, Antti [CNR-IOM, Laboratorio TASC, 34149 Trieste (Italy); Coreno, Marcello [CNR-IMIP, 00016 Montelibretti (Italy)

    2014-07-28

    We performed a combined experimental and theoretical study of the C1s Near-Edge X-ray Absorption Fine-Structure (NEXAFS) spectroscopy and X-ray Photoelectron Spectroscopy in the gas phase of two polycyclic aromatic hydrocarbons (phenanthrene and coronene), typically formed in combustion reactions. In the NEXAFS of both molecules, a double-peak structure appears in the C1s → LUMO region, which differ by less than 1 eV in transition energies. The vibronic coupling is found to play an important role in such systems. It leads to weakening of the lower-energy peak and strengthening of the higher-energy one because the 0 − n (n > 0) vibrational progressions of the lower-energy peak appear in nearly the same region of the higher-energy peak. Vibrationally resolved theoretical spectra computed within the Frank-Condon (FC) approximation and linear coupling model agree well with the high-resolution experimental results. We find that FC-active normal modes all correspond to in-plane vibrations.

  15. Intermolecular interaction studies in ammonium squarate: crystal structure and vibrational spectra

    Science.gov (United States)

    Georgopoulos, Stéfanos L.; Diniz, Renata; Rodrigues, Bernardo L.; Yoshida, Maria I.; de Oliveira, Luiz Fernando C.

    2005-10-01

    Ammonium squarate salt [(NH 4) 2C 4O 4] crystallizes in the monoclinic space group P2 1/c. The crystal presents the squarate ions displayed in layers parallel to a crystallographic axis and forming hydrogen bonds interactions with NH4+ cations, localized between squarate anions layers. The squarate anion presents similar CC and CO bond distances which indicate a degree of electronic delocalization in the rings. A π-stacking interaction is observed between squarate rings separated by interplanar distance and centroid ring distance of respectively 3.41 and 3.71 Å. The electron delocalization was also observed in the vibrational spectra. The infrared spectrum shows a narrow band around 1530 cm -1, assigned to a coupled stretching mode of CO and CC groups, indicating the high symmetry of the squarate ion. The Raman spectrum also shows this effect in the 1000 to 1200 cm -1 region (related to CC stretching mode), where it is expected a decrease of the number of bands if compared to squarate ion in aqueous solution, where the symmetry is actually D4 h; in the (NH 4) 2C 4O 4 Raman spectrum just one strong band is observed at 1120 cm -1. All the vibrational results indicate the symmetry is very close to the one observed for the solvated ion in aqueous solution; once again the vibrational analysis appears as an important tool in recognizing the oxocarbon ion geometry in the solid state.

  16. Infrared and Raman spectra, adjusted r0 structural parameters, and vibrational assignment of isopropyl isocyanide

    Science.gov (United States)

    Sawant, Dattatray K.; Klaassen, Joshua J.; Panikar, Savitha S.; Durig, James R.

    2014-09-01

    Infrared spectra (3200-220 cm-1) of gaseous and Raman spectra (3200-40 cm-1) of liquid isopropyl isocyanide ((CH3)2CHNC) have been recorded. By utilizing the microwave rotational constants combined with the structural parameters predicted from MP2(full)/6-311+G(d,p) calculations, adjusted r0 parameters have been obtained for isopropyl isocyanide. The heavy atom distances in Å are: r (C1tbnd N2) = 1.176(3), r (N2sbnd C3) = 1.437(3), r (C3sbnd C4,5) = 1.525(5) and the angles in (°) are ∠C1N2C3 = 178.6(5); ∠N2C3C4,5 = 109.4(5); ∠C4C3C5 = 113.0(5). A complete vibrational assignment is proposed for isopropyl isocyanide based on infrared band contours, relative intensities, depolarization values, and group frequencies. The vibrational assignments were supported by normal coordinate calculation utilizing the force constants from ab inito MP2(full)/6-31G(d). The results are discussed and compared to those obtained for some similar molecules.

  17. Importance of backbone angles versus amino acid configurations in peptide vibrational Raman optical activity spectra

    Science.gov (United States)

    Herrmann, Carmen; Ruud, Kenneth; Reiher, Markus

    2008-01-01

    In this work, we investigate whether the differential scattering of right- and left-circularly polarized light in peptide Raman optical activity spectra are uniquely dominated by the backbone conformation, or whether the configurations of the individual amino acid also play a significant role. This is achieved by calculating Raman optical activity spectra using density functional theory for four structurally related peptides with a common backbone conformation, but with different sequences of amino acid configurations. Furthermore, the ROA signals of the amide normal modes are decomposed into contributions from groups of individual atoms. It is found that the amino acid configuration has a considerable influence on the ROA peaks in the amide I, II, and III regions, although the local decomposition reveals that the side-chain atoms only contribute to those peaks directly in the case of the amide II vibrations. Furthermore, small changes in the amide normal modes may lead to large and irregular modifications in the ROA intensity differences, making it difficult to establish transferable ROA intensity differences even for structurally similar vibrations.

  18. Crystal studies, vibrational spectra and non-linear optical properties of L-histidine chloride monohydrate.

    Science.gov (United States)

    Ben Ahmed, A; Feki, H; Abid, Y; Boughzala, H; Minot, C

    2010-01-01

    This paper presents the results of our calculations on the geometric parameters, vibrational spectra and hyperpolarizability of a non-linear optical material L-histidine chloride monohydrate. Due to the lack of sufficiently precise information on geometric parameters available in literature, theoretical calculations were preceded by re-determination of the crystal X-ray structure. Single crystal of L-histidine chloride monohydrate has been growing by slow evaporation of an aqueous solution at room temperature. The compound crystallizes in the non-Centro-symmetric space group P2(1)2(1)2(1) of orthorhombic system. IR spectrum has been recorded in the range [400-4000 cm(-1)]. All the experimental vibrational bands have been discussed and assigned to normal mode or to combinations on the basis of our calculations. The optimized geometric bond lengths and bond angles obtained by using DFT//B3LYP/6-31G (d) method show a good agreement with the experimental data. The calculated vibrational spectra are in well agreement with the experimental one. To investigate microscopic second-order non-linear optical NLO behavior of the examined complex, the electric dipole mu, the polarizability alpha and the hyperpolarizability beta were computed using DFT//B3LYP/6-31G (d) method. The time-dependent density functional theory (TD-DFT) was employed to descript the molecular electron structure of the title compound using the B3LYP/6-31G (d) method. According to our calculations, L-histidine chloride monohydrate exhibits non-zero beta value revealing microscopic second-order NLO behavior. Copyright 2009 Elsevier B.V. All rights reserved.

  19. Crystal studies, vibrational spectra and non-linear optical properties of L-histidine chloride monohydrate

    Science.gov (United States)

    Ahmed, A. Ben; Feki, H.; Abid, Y.; Boughzala, H.; Minot, C.

    2010-01-01

    This paper presents the results of our calculations on the geometric parameters, vibrational spectra and hyperpolarizability of a non-linear optical material L-histidine chloride monohydrate. Due to the lack of sufficiently precise information on geometric parameters available in literature, theoretical calculations were preceded by re-determination of the crystal X-ray structure. Single crystal of L-histidine chloride monohydrate has been growing by slow evaporation of an aqueous solution at room temperature. The compound crystallizes in the non-Centro-symmetric space group P2 12 12 1 of orthorhombic system. IR spectrum has been recorded in the range [400-4000 cm -1]. All the experimental vibrational bands have been discussed and assigned to normal mode or to combinations on the basis of our calculations. The optimized geometric bond lengths and bond angles obtained by using DFT//B3LYP/6-31G (d) method show a good agreement with the experimental data. The calculated vibrational spectra are in well agreement with the experimental one. To investigate microscopic second-order non-linear optical NLO behavior of the examined complex, the electric dipole μ, the polarizability α and the hyperpolarizability β were computed using DFT//B3LYP/6-31G (d) method. The time-dependent density functional theory (TD-DFT) was employed to descript the molecular electron structure of the title compound using the B3LYP/6-31G (d) method. According to our calculations, L-histidine chloride monohydrate exhibits non-zero β value revealing microscopic second-order NLO behavior.

  20. Research on the discrimination methods of algae based on the fluorescence excitation spectra

    Institute of Scientific and Technical Information of China (English)

    HU Xupeng; SU Rongguo; ZOU Weiming; REN Shijun; WANG Hongtao; CHAI Xiaoping; WANG Yiming

    2010-01-01

    The excitation spectra of chlorophyll(Chl)fluorescence can be used to differentiate phytoplankton populations at phylum level in vivo and in situ within a few minutes.The investigated phytoplankton divisions(Dinophyta,Bacillariophyta,Chrysophyta,Cyanophyta,Cryptophyta,Chlorophyta)are each characterized by a specific composition of photosynthetic antenna pigments and,consequently,by a specific excitation spectrum of the Chl fluorescence.Norm excitation spectra(emission of 680 nm and excitation of 400-600 nm)of every division were obtained from several species per division by a F4500 fluorescence spectrophotometer.Fisher's linear discriminant analysis of the norm spectra shows that the divisions could be discriminated.The discrimination method,established by multivariate linear regression and weighted least squares,was used to differentiate the phytoplankton samples cultured in the laboratory and samples collected from the Jiaozhao Bay at division level.The correctly discriminated samples were more than 94% for single algal species ones,more than 84% for simulatively mixed ones,more than 83% for real mixed ones and 100% for samples collected from the Jiaozhou Bay for the dominant species.The method for phytoplankton differentiation described here can be applied to routine checking by fluorescence spectrophotometer,and benefit the monitoring and supervision tasks related to phytoplankton populations in the marine environments.

  1. On the potential usefulness of Fourier spectra of delayed fluorescence from plants.

    Science.gov (United States)

    Guo, Ya; Tan, Jinglu

    2014-12-09

    Delayed fluorescence (DF) from photosystem II (PSII) of plants can be potentially used as a biosensor for the detection of plant physiological status and environmental changes. It has been analyzed mainly in the time domain. Frequency-domain analysis through Fourier transform allows viewing a signal from another angle, but the usefulness of DF spectra has not been well studied. In this work, experiments were conducted to show the differences and similarities in DF spectra of different plants with short pulse excitation. The DF spectra show low-pass characteristics with first-order attenuation of high frequencies. The results also show that the low-frequency components differ while the high-frequency components are similar. These may imply the potential usefulness of Fourier spectra of DF to analyze photoelectron transport in plants and classify samples.

  2. On the Potential Usefulness of Fourier Spectra of Delayed Fluorescence from Plants

    Directory of Open Access Journals (Sweden)

    Ya Guo

    2014-12-01

    Full Text Available Delayed fluorescence (DF from photosystem II (PSII of plants can be potentially used as a biosensor for the detection of plant physiological status and environmental changes. It has been analyzed mainly in the time domain. Frequency-domain analysis through Fourier transform allows viewing a signal from another angle, but the usefulness of DF spectra has not been well studied. In this work, experiments were conducted to show the differences and similarities in DF spectra of different plants with short pulse excitation. The DF spectra show low-pass characteristics with first-order attenuation of high frequencies. The results also show that the low-frequency components differ while the high-frequency components are similar. These may imply the potential usefulness of Fourier spectra of DF to analyze photoelectron transport in plants and classify samples.

  3. Vibrational infrared and Raman spectra of polypeptides: Fragments-in-fragments within molecular tailoring approach

    Science.gov (United States)

    Sahu, Nityananda; Gadre, Shridhar R.

    2016-03-01

    The present work reports the calculation of vibrational infrared (IR) and Raman spectra of large molecular systems employing molecular tailoring approach (MTA). Further, it extends the grafting procedure for the accurate evaluation of IR and Raman spectra of large molecular systems, employing a new methodology termed as Fragments-in-Fragments (FIF), within MTA. Unlike the previous MTA-based studies, the accurate estimation of the requisite molecular properties is achieved without performing any full calculations (FC). The basic idea of the grafting procedure is implemented by invoking the nearly basis-set-independent nature of the MTA-based error vis-à-vis the respective FCs. FIF has been tested out for the estimation of the above molecular properties for three isomers, viz., β-strand, 310- and α-helix of acetyl(alanine)nNH2 (n = 10, 15) polypeptides, three conformers of doubly protonated gramicidin S decapeptide and trpzip2 protein (PDB id: 1LE1), respectively, employing BP86/TZVP, M06/6-311G**, and M05-2X/6-31G** levels of theory. For most of the cases, a maximum difference of 3 cm-1 is achieved between the grafted-MTA frequencies and the corresponding FC values. Further, a comparison of the BP86/TZVP level IR and Raman spectra of α-helical (alanine)20 and its N-deuterated derivative shows an excellent agreement with the existing experimental spectra. In view of the requirement of only MTA-based calculations and the ability of FIF to work at any level of theory, the current methodology provides a cost-effective solution for obtaining accurate spectra of large molecular systems.

  4. Jet-cooled fluorescence excitation spectra and carbonyl wagging potential energy functions of several cyclic ketones in their S 1(n, π*) electronic excited states

    Science.gov (United States)

    Zhang, J.; Chiang, W. Y.; Sagear, P.; Laane, J.

    1992-08-01

    The jet-cooled fluorescence excitation spectra of the n→π* transitions of cyclopentanone, 3-cyclopenten-1-one, and cyclobutanone have been analyzed to determine the vibrational energy spacings in the S 1(n, π*) electronic excited states for the out-of-plane carbonyl wagging motions. A double-minimum potential energy function was determined for each and the barriers were found to be 680, 926, and 1940 cm -1, respectively. The carbonyl wagging angles were determined to be 22°, 26°, and 41°, respectively.

  5. Study on the interaction between diphenhydramine and erythrosin by absorption, fluorescence and resonance Rayleigh scattering spectra

    Institute of Scientific and Technical Information of China (English)

    TANG XiaoLing; LIU ZhongFang; LIU ShaoPu; HU XiaoLi

    2007-01-01

    In pH 4.5 Britton-Robinson (BR) buffer solution, erythrosin (ET) can react with diphenhydramine (DP) to form a 1:1 ion-association complex, which not only results in the change of the absorption spectra, but also results in the great enhancement of resonance Rayleigh scattering (RRS) and the quenching of fluorescence. Furthermore, a new RRS spectrum will appear, and the maximum RRS wavelength was located at about 580 nm.In this work, the spectral characteristics of the absorption, fluorescence and RRS, the optimum conditions of the reaction and the properties of an analytical chemistry were investigated. A sensitive, simple and new method for the determination of DP by using erythrosin as a probe has been developed. The detection limits for DP were 0.0020 μg/mL for RRS method, 0.088 μg/mL for absorption method and 0.094 μg/mL for fluorophotometry. There was a linear relationship between the absorbance, RRS and fluorescence intensities and the drug concentration in the range of 0.0067-2.0, 0.29-6.4 and 0.31-3.2 μg/mL, respectively. The effects of the interaction of diphenhydramine and erythrosin on the absorption, fluorescence and resonance Rayleigh scattering spectra were discussed. In light polarization experiment, the polarization of RRS at maximum wavelength was measured to be P = 0.9779, and it revealed that the RRS spectrum of DP-ET complex consists mostly of resonance scattering and few resonance fluorescence. In this study, enthalpy of formation and mean polarizability were calculated by AM1 quantum chemistry method. In addition, the reaction mechanism and the reasons for the enhancement of scattering spectra and the energy transfer between absorption, fluorescence and RRS were discussed.

  6. Effect of arsenic on reflectance spectra and chlorophyll fluorescence of aquatic plants.

    Science.gov (United States)

    Iriel, Analia; Dundas, Gavin; Fernández Cirelli, Alicia; Lagorio, Maria G

    2015-01-01

    Arsenic pollution of groundwater is a serious problem in many regions of Latin America that causes severe risks to human health. As a consequence, non-destructive monitoring methodologies, sensitive to arsenic presence in the environment and able to perform a rapid screening of large polluted areas, are highly sought-after. Both chlorophyll - a fluorescence and reflectance of aquatic plants may be potential indicators to sense toxicity in water media. In this work, the effects of arsenic on the optical and photophysical properties of leaves of different aquatic plants (Vallisneria gigantea, Azolla filiculoides and Lemna minor) were evaluated. Reflectance spectra were recorded for the plant leaves from 300 to 2400 nm. The spectral distribution of the fluorescence was also studied and corrected for light re-absorption processes. Photosynthetic parameters (Fv/Fm and ΦPSII) were additionally calculated from the variable chlorophyll fluorescence recorded with a pulse amplitude modulated fluorometer. Fluorescence and reflectance properties for V. gigantea and A. filiculoides were sensitive to arsenic presence in contrast to the behaviour of L. minor. Observed changes in fluorescence spectra could be interpreted in terms of preferential damage in photosystem II. The quantum efficiency of photosystem II for the first two species was also affected, decreasing upon arsenic treatment. As a result of this research, V. gigantea and A. filiculoides were proposed as bioindicators of arsenic occurrence in aquatic media.

  7. Fluorescence Spectra of Model Compounds for Light-emitting Alternating Copolymers in Heterogeneous Environments

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    In this paper, the fluorescence spectra of model compounds of light-emitting alternating copolymers, M (TPA-PPV) and M (TPA-PAV) (Scheme 1) were studied and the effect of KNO3 on the interaction between model compounds and ionic micelle-water interface was also investigated. It is found that (I) The fluorescence changes of M (TPA-PPV) are related to the state of CTAB and SDS solution. (II) Aggregated state can be formed in M (TPA-PAV) solution at low concentration of CTAB. (III) Higher concentration of KNO3 may affect the interaction between model compounds and ionic micelle-water interface.

  8. Vibrational spectra of chemical and isotopic variants of oxyluciferin, the light emitter of firefly bioluminescence.

    Science.gov (United States)

    Maltsev, Oleg V; Yue, Ling; Rebarz, Mateusz; Hintermann, Lukas; Sliwa, Michel; Ruckebusch, Cyril; Pejov, Ljupčo; Liu, Ya-Jun; Naumov, Panče

    2014-08-18

    The chemical complexity of oxyluciferin (OxyLH2), the light-emitting molecule in the bioluminescence of fireflies, originates from the possibility of keto/enol tautomerism and single or double deprotonation. Herein, we present detailed infrared spectroscopic analysis of OxyLH2 and several of its chemical isomers and isotopomers. To facilitate the future characterization of its biogenic forms, we provide accurate assignments of the solid-state and solution FTIR spectra of OxyLH2 based on comparison to six isotopically labeled variants ([2-(13)C]-OxyLH2, [3-(15)N]-OxyLH2, [4-(13)C]-OxyLH2, [5-(13)C]-OxyLH2, [2'-(13)C]-OxyLH2, [3'-(15)N]-OxyLH2), five closely related structural analogues, and theoretically computed spectra. The computed DFT harmonic vibrational force fields (B3LYP and M06 functionals with basis sets of varying flexibility up to 6-311++G**) reproduce well the observed shifts in the IR spectra of both isotopically labeled and structurally related analogues.

  9. Vibrational spectra, quantum chemical calculations and spectral assignments of 1,1-difluoro-1-silacyclohexane.

    Science.gov (United States)

    Guirgis, Gamil A; Dukes, Horace W; Wyatt, Justin K; Nielsen, Claus J; Horn, Anne; Aleksa, Valdemaras; Klaeboe, Peter

    2015-02-05

    Raman spectra of 1,1-difluoro-1-silacyclohexane as a liquid, and as a solid at 78 K were recorded and depolarization data obtained. The infrared spectra of the vapour, liquid and amorphous and crystalline solids have been studied. In the low temperature IR and Raman spectra eight and three bands, respectively, were shifted a few cm(-1) when the sample crystallized. No bands vanished after crystallization in agreement with the assumption that only one conformer (chair) was present in all the states of aggregation. The compound exists in the stable chair conformation, whereas in the parent silacyclohexane a possible twist form should have more than 15 kJ mol(-1) higher energies than the chair, as derived from various calculations. The wavenumbers of the vibrational modes were calculated in the harmonic and anharmonic approximation employing B3LYP/cc-pVTZ calculations. The 27 A' and 21 A″ fundamentals were assigned on the basis of the calculations, infrared vapour contours, Raman depolarization measurements and infrared and Raman band intensities. An average, relative deviation of 1.5% was found between the observed and the anharmonic wavenumbers for the 48 modes.

  10. Vibrational coherence and energy transfer in two-dimensional spectra with the optimized mean-trajectory approximation

    Energy Technology Data Exchange (ETDEWEB)

    Alemi, Mallory; Loring, Roger F., E-mail: roger.loring@cornell.edu [Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 (United States)

    2015-06-07

    The optimized mean-trajectory (OMT) approximation is a semiclassical method for computing vibrational response functions from action-quantized classical trajectories connected by discrete transitions that represent radiation-matter interactions. Here, we extend the OMT to include additional vibrational coherence and energy transfer processes. This generalized approximation is applied to a pair of anharmonic chromophores coupled to a bath. The resulting 2D spectra are shown to reflect coherence transfer between normal modes.

  11. Predicting accurate fluorescent spectra for high molecular weight polycyclic aromatic hydrocarbons using density functional theory

    Science.gov (United States)

    Powell, Jacob; Heider, Emily C.; Campiglia, Andres; Harper, James K.

    2016-10-01

    The ability of density functional theory (DFT) methods to predict accurate fluorescence spectra for polycyclic aromatic hydrocarbons (PAHs) is explored. Two methods, PBE0 and CAM-B3LYP, are evaluated both in the gas phase and in solution. Spectra for several of the most toxic PAHs are predicted and compared to experiment, including three isomers of C24H14 and a PAH containing heteroatoms. Unusually high-resolution experimental spectra are obtained for comparison by analyzing each PAH at 4.2 K in an n-alkane matrix. All theoretical spectra visually conform to the profiles of the experimental data but are systematically offset by a small amount. Specifically, when solvent is included the PBE0 functional overestimates peaks by 16.1 ± 6.6 nm while CAM-B3LYP underestimates the same transitions by 14.5 ± 7.6 nm. These calculated spectra can be empirically corrected to decrease the uncertainties to 6.5 ± 5.1 and 5.7 ± 5.1 nm for the PBE0 and CAM-B3LYP methods, respectively. A comparison of computed spectra in the gas phase indicates that the inclusion of n-octane shifts peaks by +11 nm on average and this change is roughly equivalent for PBE0 and CAM-B3LYP. An automated approach for comparing spectra is also described that minimizes residuals between a given theoretical spectrum and all available experimental spectra. This approach identifies the correct spectrum in all cases and excludes approximately 80% of the incorrect spectra, demonstrating that an automated search of theoretical libraries of spectra may eventually become feasible.

  12. Size variation of infrared vibrational spectra from molecules to hydrogenated diamond nanocrystals: a density functional theory study

    Directory of Open Access Journals (Sweden)

    Mudar A. Abdulsattar

    2013-04-01

    Full Text Available Infrared spectra of hydrogenated diamond nanocrystals of one nanometer length are calculated by ab initio methods. Positions of atoms are optimized via density functional theory at the level of the generalized gradient approximation of Perdew, Burke and Ernzerhof (PBE using 3-21G basis states. The frequencies in the vibrational spectrum are analyzed against reduced masses, force constants and intensities of vibration. The spectrum can be divided into two regions depending on the properties of the vibrations or the gap separating them. In the first region, results show good matching to several experimentally obtained lines. The 500 cm−1 broad-peak acoustical branch region is characterized by pure C–C vibrations. The optical branch is centered at 1185 cm−1. Calculations show that several C–C vibrations are mixed with some C–H vibrations in the first region. In the second region the matching also extends to C–H vibration frequencies that include different modes such as symmetric, asymmetric, wagging, scissor, rocking and twisting modes. In order to complete the picture of the size dependence of the vibrational spectra, we analyzed the spectra of ethane and adamantane. The present analysis shows that acoustical and optical branches in diamond nanocrystals approach each other and collapse at 963 cm−1 in ethane. Variation of the highest reduced-mass-mode C–C vibrations from 1332 cm−1 of bulk diamond to 963 cm−1 for ethane (red shift is shown. The analysis also shows the variation of the radial breathing mode from 0 cm−1 of bulk diamond to 963 cm−1 for ethane (blue shift. These variations compare well with experiment. Experimentally, the above-mentioned modes appear shifted from their exact positions due to overlap with neighboring modes.

  13. Effects of ozone and relative humidity on fluorescence spectra of octapeptide bioaerosol particles

    Science.gov (United States)

    Pan, Yong-Le; Santarpia, Joshua L.; Ratnesar-Shumate, Shanna; Corson, Elizabeth; Eshbaugh, Jonathan; Hill, Steven C.; Williamson, Chatt C.; Coleman, Mark; Bare, Christopher; Kinahan, Sean

    2014-01-01

    The effects of ozone and relative humidity (RH) at common atmospheric levels on the properties of single octapeptide bioaerosol particles were studied using an improved rotating reaction chamber, an aerosol generator, an ultraviolet aerodynamic particle sizer (UVAPS), an improved single particle fluorescence spectrometer (SPFS), and equipments to generate, monitor and control the ozone and RH. Aerosol particles (mean diameter 2 μm) were generated from a slurry of octapeptide in phosphate buffered saline, injected into the rotating chamber, and kept airborne for hours. Bioaerosols were sampled from the chamber hourly for the measurements of particle-size distribution, concentration, total fluorescence excited at 355-nm, and single particle fluorescence spectra excited at 266-nm and 351-nm under different controlled RH (20%, 50%, or 80%) and ozone concentration (0 or 150 ppb). The results show that: (1) Particle size, concentration, and the 263-nm-excited fluorescence intensity decrease at different rates under different combinations of the RH and ozone concentrations used. (2) The 263-nm-excited UV fluorescence (280-400 nm) decreased more rapidly than the 263-nm-excited visible fluorescence (400-560 nm), and decreased most rapidly when ozone is present and RH is high. (3) The UV fluorescence peak near 340 nm slightly shifts to the shorter wavelength (blue-shift), consistent with a more rapid oxidation of tryptophan than tyrosine. (4) The 351/355-nm-excited fluorescence (430-580 nm/380-700 nm) increases when ozone is present, especially when the RH is high. (5) The 351/355-nm-excited fluorescence increase that occurs as the tryptophan emission in the UV decreases, and the observation that these changes occur more rapidly at higher RH with the present of ozone, are consistent with the oxidation of tryptophan by ozone and the conversion of the resulting ozonides to N-formyl kynurenine and kynurenine.

  14. The Photochemical Study of HSA and BSA with Resonance Light-Scattering and Fluorescence Spectra

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The resonance light-scattering (RLS) of human serum albumin (HSA) and bovine serum albumin (BSA) is reported for the first time, and applied to study photochemical reaction of HSA and BSA. The fact of photocrosslinking self-association effect in HSA and BSA solutions is identified by the enhancement of RLS. The fluorescence quenching at about 350 nm and 700 nm proves that tryptophan (Trp) residues are one of the photochemical activity sites in HSA and BSA molecules. The Rayleigh scattering (RS) spectra of HSA and BSA that were neglected in fluorescence spectra before are found at about 296 nm, 592 nm and 888 nm for the first time, and are of adventageous to studying the aggregation of HSA or BSA. The possible photochemical reaction mechanism is also proposed.

  15. Identification of lactobacillus casei-BDI and Streptococcus thermophilus by fluorescence spectra

    Institute of Scientific and Technical Information of China (English)

    Hao Wu; Tuo Zhu; Wei Chen; Hao Zhang; Jianlei Yang

    2009-01-01

    Fluorescence analysis applied in the study of lactic acid bacteria (LAB) provides a new method and theory to study probiotics and realize the detection and identification of the strains.It is also possible to achieve automation and computerization.In this letter,the differences between the fluorescence spectra of lactobacillus casei-BDI (Lc-BDI) and Streptococcus thermophilus (St) are shown,and the second-order derivative spectra are used to further study the diversity of these two strains.According to the results,with thc excitation wavelengths of 285 and 340 nm,there are significant differences between them.The experiment is repeated for 6 times,showing good repetitiveness.

  16. Characterization of excited-state reactions with instant spectra of fluorescence kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Tomin, Vladimir I., E-mail: tomin@apsl.edu.pl; Ushakou, Dzmitryi V.

    2015-10-15

    Comprehensible knowledge of the excited-state proton transfer processes in organic compounds is overwhelmingly important not only for physics, but also chemistry and Life Sciences, since they play a key role in main processes of photosynthesis and functioning of biological organisms. Moreover compounds with Excited-State Intramolecular Proton Transfer (ESIPT) are in the focus of the interest of scientists throughout the world, because dual fluorescence spectra of such objects corresponding to two forms of molecular structure (normal and photoproduct) are very sensitive to characteristics of molecular microenvironment. This property allows to use such substances as fluorescent probes for diverse applications in chemistry and Life Sciences. But at the same time studying of proton transfer processes is not simple, because this process is characterized by extremely fast times (on picoseconds time scale and less order) and very often contribution of reverse reactions is essentially complicates an interpretation of observed properties of dual fluorescence. Hence, understanding of a role of reversible reactions is crucial for a comprehensive description of all processes accompanying excited state reactions. We discuss new approach for treatment ESIPT reaction on the basis of experimentally measured instant spectra of dual fluorescence and temporal behavior of ratiometric signal of normal to tautomer form intensities. Simple analytical expressions show in transparent way how to distinguish a degree of reverse reaction contribution to ratiometric signal. A validation of the approach under consideration is fulfilled with two different flavonols – 3-hydroxyflavone and 4′-(Dimethylamino)-3-hydroxyflavone – representing two extreme cases in affecting reversible reaction on dual emission. A comparing of new approach and traditional method when we analyze kinetics of separate the N* and T* fluorescence bands decays, has been carried out. - Highlights: • The excited

  17. Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field.

    Science.gov (United States)

    Thaunay, Florian; Dognon, Jean-Pierre; Ohanessian, Gilles; Clavaguéra, Carine

    2015-10-21

    The calculation of infrared spectra by molecular dynamics simulations based on the AMOEBA polarizable force field has recently been demonstrated [Semrouni et al., J. Chem. Theory Comput., 2014, 10, 3190]. While this approach allows access to temperature and anharmonicity effects, band assignment requires additional tools, which we describe in this paper. The Driven Molecular Dynamics approach, originally developed by Bowman, Kaledin et al. [Bowman et al. J. Chem. Phys., 2003, 119, 646, Kaledin et al. J. Chem. Phys., 2004, 121, 5646] has been adapted and associated with AMOEBA. Its advantages and limitations are described. The IR spectrum of the Ac-Phe-Ala-NH2 model peptide is analyzed in detail. In addition to differentiation of conformations by reproducing frequency shifts due to non-covalent interactions, DMD allows visualizing the temperature-dependent vibrational modes.

  18. [Vibrational spectra of black species of hetian nephrite (tremolite jade) and its color genesis].

    Science.gov (United States)

    Yang, Xiao-dan; Shi, Guang-hai; Liu, Yan

    2012-03-01

    Black nephrite is a very uncommon jade type currently found only at Karakashi. In order to study the spectral characteristics and color-genetic mechanism of the black nephrite, samples collected from Karakashi were studied using EMPA, IR, Raman and XRD. The results are as follows: nephrite with different color has nearly the same major chemical compostions, while the black ones contain higher carbon; nephrite with different color has similar vibration spectrum, while the black ones show characteristic peak of graphite. It is speculated that the color of black nephrite is not only related with actinolite, but also related with the graphite inclusions. Obviously, Raman spectra is a very important nondestructive method to identify the color genesis and the origin of the black nephrite.

  19. Vibrational spectra and molecular structure of isomeric 1-(adamantan-1-ylcarbonyl)-3-(dichlorophenyl)thioureas

    Science.gov (United States)

    Saeed, Aamer; Ashraf, Zaman; Erben, Mauricio F.; Simpson, Jim

    2017-02-01

    1-(adamantan-1-ylcarbonyl)-3-(2,3-dichlorophenyl)thiourea, 1, and 1-(adamantan-1-ylcarbonyl)-3-(2,5-dichlorophenyl)thiourea, 2, were synthesized in reasonable yields from admanantyl-1-carbonyl chloride and ammonium thiocyanate followed by treatment of the resulting adamantane-1-carbonylisothiocyanate with the 2,3- and 2,5-dichloroanilines. A complete vibrational analysis was performed on the basis of FTIR and Raman spectra. The formation of intramolecular Nsbnd H⋯O and intermolecular Nsbnd H⋯S hydrogen bonds in the solids affect vibrational modes, with low frequency values observed for the ν(Cdbnd O) and ν(Cdbnd S) stretching modes. Structural data obtained by single-crystal X-ray diffraction at low temperature confirm this picture. Compound 1 crystallizes in the triclinic system and compound 2 crystallizes with two unique molecules in the asymmetric unit of the orthorhombic unit cell. The molecular structures reveal that the carbonylthiourea units in 1 and both molecules of 2 are planar due in part to the formation of intramolecular Nsbnd H⋯Odbnd C hydrogen bonds that generate S (6) rings. Moreover, the crystal structures are stabilized by an extensive series of classical and non-classical hydrogen bonds and, in the case of 1 by an intermolecular Cl⋯Cl halogen bond.

  20. CF₃CF₂N=S(F)CF₃: vibrational spectra and conformational properties.

    Science.gov (United States)

    Robles, Norma L; Oberhammer, Heinz; Mews, Rüdiger; Cutin, Edgardo H

    2014-05-05

    The structural, conformational, and configurational properties of 1,1,1-trifluoro-N-(1,1,2,2,2-pentafluoroethyl) methanesulfinimidoyl fluoride, CF3CF2N=S(F)CF3 have been studied by vibrational spectroscopy [IR (vapor) and Raman (liquid)] and quantum chemical calculations [B3LYP, MP2 and B3PW91 levels of theory (using the 6-311+G(d) and 6-311+G(2df) basis sets). According to these theoretical approximations, CF3CF2N=S(F)CF3 might be found in the gas phase as a mixture of a favoured anticlinal form (C-N bond anticlinal with respect to the C-S-F bisector angle) and a less abundant syn conformer showing C1 symmetry as well (ΔG°≈1.5 kcal mol(-1)). However, corresponding vibrational modes for these conformers show only small shifts which would not allow confidently detecting the rather small contribution of this second form in the experimental spectra.

  1. Structural and vibrational characterization of sugar arabinitol structures employing micro-Raman spectra and DFT calculations

    Science.gov (United States)

    Hédoux, Alain; Guinet, Yannick; Carpentier, Laurent; Paccou, Laurent; Derollez, Patrick; Brandán, Silvia Antonia

    2017-06-01

    In this work, three monomeric forms of arabinitol, usually named arabitol, and their dimeric species have been structural and vibrationally studied by using the micro-Raman spectra in the solid phase accomplished with theoretical calculations based on the theory of the functional of the density (DFT). The hybrid B3LYP method was used for all the calculations together with the 6-31G* and 6-311++g** basis sets. Two different L structures with minima energies were predicted in accordance to the two polymorphic structures revealed by recent X-ray diffraction experiments. The studies by natural bond orbital (NBO) calculations reveals high stabilities of the L form as compared with the D one but the topological properties by using the atoms in molecules (AIM) suggest a higher stability of the D form due to a strong H bond interactions. The scaled mechanical force fields (SQMFF) procedure was used to perform the complete vibrational assignments for the monomeric forms and their dimer. On the other hand, the similarity in the gap values computed for the three forms of arabitol with those observed for sucrose, trehalose, maltose and lactose in gas phase at the same level of theory could partially explain the sweetening property of this alcohol. In addition, the influences of the size of the basis set on some properties were evidenced.

  2. First Detection of Vibrational Spectra of the Vinyl and Hexatriynyl Radicals

    Science.gov (United States)

    Doyle, Timothy John

    The first vibrational spectrum of the C _2H_3 (vinyl) radical has been identified in an FTIR study of the vacuum ultraviolet (VUV) photolysis products of ethylene (C_2 H_4) and its D- and ^{13}C-substituted isotopomers and acetylene (C_2H_2) + HI trapped in Ar at 10 K. Absorptions at 900.2 and 685.4 cm^{-1} have been assigned to the nu_8(a^ {''}), out-of-plane wagging and the nu_7(a^'), in-plane asymmetric CH_2 bending - alphaCH bending modes. The assignments are supported by the isotopic data and by comparison with the results of a GVB ab initio calculation by Dupuis and Wendoloski, and an MBPT(2) ab initio calculation. A similar FTIR study of the products of the VUV photolysis of acetylene (C_2H _2) and 1,3-butadiene (C_4 H_6) trapped in solid Ar has resulted in the first identification of a vibration of the C_6H (hexatriynyl) radical at 1953.4 cm^{-1}. Various D and ^{13}C isotopomers have been observed. The complex, overlapping spectra resulting from partial ^{13}C substitution have been fitted using a force constant adjustment calculation and support the assignment of the 1953.4 cm^ {-1} absorption to a Cequiv C stretching fundamental of linear C_6 H.

  3. Study on the violet LED-induced fluorescence spectra of thioredoxin reductase from human brain

    Institute of Scientific and Technical Information of China (English)

    Xiufeng Lan(兰秀风); Tao Yang(杨涛); Shumei Gao(高淑梅); Xiaosen Luo(骆晓森); Zhonghua Shen(沈中华); Jian Lu(陆建); Xiaowu Ni(倪晓武); Lin Xu(许琳)

    2003-01-01

    The technique of fluorescence spectroscopy is applied to study thioredoxin reductase (TrxR) in the ce;lsof human brain. Experimental results show that, by the violet light emitting diode (LED, λmax=407 nm)light irradiation, TrxR is able to emit three striking spectral bands (528 - 582 nm; 588 - 660 nm; 683 - 700nm). The fluorescence intensity is linear to the concentration of TrxR. The spectrum of denatured TrxR israther different from that of organized TrxR, which reflects the structure change between denatured TrxRand organized TrxR. Furthermore, physical and biochemical mechanisms of fluorescence production forLED light-induced TrxR spectra and its characteristics are analyzed. This paper may be useful to betterunderstand the structure of TrxR, and to provide new spectroscopic information to improve the resolutionfor this kind of biology structure.

  4. Fluorescence line-narrowing spectra of Zn-cytochrome c. Temperature dependence

    Science.gov (United States)

    Koloczek, Henryk; Fidy, Judit; Vanderkooi, Jane M.

    1987-10-01

    Fluorescence site selection spectra of Zn-substituted cytochrome c and Zn-mesoporphyrin were measured as a function of excitation energy and temperature within 5-60 K. The emission energies determined for Zn-cytochrome c were comparable with those of Zn-mesoporphyrin and mesoporphyrin in polar glassy matrices and with resonance Raman spectra of heme proteins. In the site selection spectra of both Zn-cytochrome c and Zn-mesoporphyrin in polar organic glass an increase in the intensity of zero phonon emission lines was observed with an increase of temperature between 5 and 30 K. The irregular spectral changes were interpreted on the basis of the temperature dependence of the linewidth as well as possible hole-burning phenomena.

  5. Use of laser fluorescence in dental caries diagnosis: a fluorescence x biomolecular vibrational spectroscopic comparative study.

    Science.gov (United States)

    Carvalho, Fabíola Bastos de; Barbosa, Artur Felipe Santos; Zanin, Fátima Antonia Aparecida; Brugnera Júnior, Aldo; Silveira Júnior, Landulfo; Pinheiro, Antonio Luiz Barbosa

    2013-01-01

    The aim of this work was to verify the existence of correlation between Raman spectroscopy readings of phosphate apatite (~960 cm-1), fluoridated apatite (~575 cm-1) and organic matrix (~1450 cm-1) levels and Diagnodent® readings at different stages of dental caries in extracted human teeth. The mean peak value of fluorescence in the carious area was recorded and teeth were divided in enamel caries, dentin caries and sound dental structure. After fluorescence readings, Raman spectroscopy was carried out on the same sites. The results showed significant difference (ANOVA, pcaries. There was significant negative correlation (pcaries. It may be concluded that the higher the fluorescence detected by Diagnodent the lower the peaks of phosphate apatite and fluoridated apatite. As the early diagnosis of caries is directly related to the identification of changes in the inorganic tooth components, Raman spectroscopy was more sensitive to variations of these components than Diagnodent.

  6. Vibrationally resolved translational energy release spectra from the ultraviolet photodissociation of methyl mercaptan

    Science.gov (United States)

    Segall, J.; Wen, Y.; Singer, R.; Dulligan, M.; Wittig, C.

    1993-11-01

    Product translational energy release spectra resulting from 248 and 193 nm photodissociation of methyl mercaptan are obtained for the hydrogen atom channels (CH3SH+hν→CH3S+H) by using the high-n Rydberg time-of-flight technique. The spectra exhibit vibrational structure that is assigned to a CH3-S stretch progression. At 248 nm, the progression extends only to v=2, while at 193 nm levels up to approximately v=17 are populated. The progression observed at 193 nm is bimodal, with the higher kinetic energy component showing greater spatial anisotropy than the lower energy component, suggesting that two different processes occurring on different time scales are responsible for the two components. The results at 248 nm are consistent with excitation to a repulsive electronic surface. For 193 nm excitation, the high kinetic energy component is consistent with direct photoexcitation to a repulsive surface and/or rapid intramolecular access to a repulsive surface. The lower kinetic energy component presumably derives from the molecule spending more time on an excited surface. A simple model is applied to estimate the extent of C-S bond extension for the various processes.

  7. Vibrationally resolved translational energy release spectra from the ultraviolet photodissociation of methyl mercaptan

    Energy Technology Data Exchange (ETDEWEB)

    Segall, J.; Wen, Y.; Singer, R.; Dulligan, M.; Wittig, C. (Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States))

    1993-11-01

    Product translational energy release spectra resulting from 248 and 193 nm photodissociation of methyl mercaptan are obtained for the hydrogen atom channels (CH[sub 3]SH+[ital h][nu][r arrow]CH[sub 3]S+H) by using the high-[ital n] Rydberg time-of-flight technique. The spectra exhibit vibrational structure that is assigned to a CH[sub 3]--S stretch progression. At 248 nm, the progression extends only to [ital v]=2, while at 193 nm levels up to approximately [ital v]=17 are populated. The progression observed at 193 nm is bimodal, with the higher kinetic energy component showing greater spatial anisotropy than the lower energy component, suggesting that two different processes occurring on different time scales are responsible for the two components. The results at 248 nm are consistent with excitation to a repulsive electronic surface. For 193 nm excitation, the high kinetic energy component is consistent with direct photoexcitation to a repulsive surface and/or rapid intramolecular access to a repulsive surface. The lower kinetic energy component presumably derives from the molecule spending more time on an excited surface. A simple model is applied to estimate the extent of C--S bond extension for the various processes.

  8. Vibrational spectra, DFT quantum chemical calculations and conformational analysis of P-iodoanisole.

    Science.gov (United States)

    Arivazhagan, M; Anitha Rexalin, D; Geethapriya, J

    2013-09-01

    The solid phase FT-IR and FT-Raman spectra of P-iodoanisole (P-IA) have been recorded in the regions 400-4000 and 50-4000 cm(-1), respectively. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by ab initio (HF) and density functional theory (B3LYP) methods with LanL2DZ as basis set. The potential energy surface scan for the selected dihedral angle of P-IA has been performed to identify stable conformer. The optimized structure parameters and vibrational wavenumbers of stable conformer have been predicted by density functional B3LYP method with LanL2DZ (with effective core potential representations of electrons near the nuclei for post-third row atoms) basis set. The nucleophilic and electrophilic sites obtained from the molecular electrostatic potential (MEP) surface were calculated. The temperature dependence of thermodynamic properties has been analyzed. Several thermodynamic parameters have been calculated using B3LYP with LanL2DZ basis set.

  9. Ultrabright fluorescent silica particles with a large number of complex spectra excited with a single wavelength for multiplex applications.

    Science.gov (United States)

    Palantavida, S; Peng, B; Sokolov, I

    2017-02-08

    We report on a novel approach to synthesize ultrabright fluorescent silica particles capable of producing a large number of complex spectra. The spectra can be excited using a single wavelength which is paramount in quantitative fluorescence imaging, flow cytometry and sensing applications. The approach employs the physical encapsulation of organic fluorescent molecules inside a nanoporous silica matrix with no dye leakage. As was recently demonstrated, such an encapsulation allowed for the encapsulation of very high concentrations of organic dyes without quenching their fluorescent efficiency. As a result, dye molecules are distanced within ∼5 nm from each other; it theoretically allows for efficient exchange of excitation energy via Förster resonance energy transfer (FRET). Here we present the first experimental demonstration of the encapsulation of fluorescent dyes in the FRET sequence. Attaining a FRET sequence of up to five different dyes is presented. The number of distinguishable spectra can be further increased by using different relative concentrations of encapsulated dyes. Combining these approaches allows for creating a large number of ultrabright fluorescent particles with substantially different fluorescence spectra. We also demonstrate the utilization of these particles for potential multiplexing applications. Though fluorescence spectra of the obtained multiplex probes are typically overlapping, they can be distinguished by using standard linear decomposition algorithms.

  10. Accurate studies on the full vibrational energy spectra and molecular dissociation energies for some electronic states of N2 molecule

    Institute of Scientific and Technical Information of China (English)

    REN; Weiyi; SUN; Weiguo; HOU; Shilin; FENG; Hao

    2005-01-01

    It is usually very difficult to directly obtain molecular dissociation energy De and all accurate high-lying vibrational energies for most diatomic electronic states using modern experimental techniques or quantum theories, and it is also very difficult to give accurate analytical expression for diatomic molecular dissociation energy. This study proposes a new analytical formula for obtaining accurate molecular dissociation energy based on the LeRoy and Bernstein's energy expression in dissociation limit. A set of full vibrational energy spectra for some electronic states of N2 molecule are studied using the algebraic method (AM) suggested recently, and the corresponding accurate molecular dissociation energies are evaluated using the proposed new formula and high-lying AM vibrational energies. The results show that the AM spectra and the new theoretical dissociation energies agree excellently with experimental data, and thereby providing a new physical approach to generating accurate dissociation energies for electronic states of diatomic molecules.

  11. A support vector machine approach to the automatic identification of fluorescence spectra emitted by biological agents

    Science.gov (United States)

    Gelfusa, M.; Murari, A.; Lungaroni, M.; Malizia, A.; Parracino, S.; Peluso, E.; Cenciarelli, O.; Carestia, M.; Pizzoferrato, R.; Vega, J.; Gaudio, P.

    2016-10-01

    Two of the major new concerns of modern societies are biosecurity and biosafety. Several biological agents (BAs) such as toxins, bacteria, viruses, fungi and parasites are able to cause damage to living systems either humans, animals or plants. Optical techniques, in particular LIght Detection And Ranging (LIDAR), based on the transmission of laser pulses and analysis of the return signals, can be successfully applied to monitoring the release of biological agents into the atmosphere. It is well known that most of biological agents tend to emit specific fluorescence spectra, which in principle allow their detection and identification, if excited by light of the appropriate wavelength. For these reasons, the detection of the UVLight Induced Fluorescence (UV-LIF) emitted by BAs is particularly promising. On the other hand, the stand-off detection of BAs poses a series of challenging issues; one of the most severe is the automatic discrimination between various agents which emit very similar fluorescence spectra. In this paper, a new data analysis method, based on a combination of advanced filtering techniques and Support Vector Machines, is described. The proposed approach covers all the aspects of the data analysis process, from filtering and denoising to automatic recognition of the agents. A systematic series of numerical tests has been performed to assess the potential and limits of the proposed methodology. The first investigations of experimental data have already given very encouraging results.

  12. Spectra-resolved technique of a sensitive time-resolved fluorescence immunoassay instrument

    Science.gov (United States)

    Guo, Zhouyi; Tian, Zhen; Jia, Yali

    2004-07-01

    The lanthanide trivalence ion and its chelates are used for marking substance in time-resolved fluorescence immunoassay (TRFIA), marking the protein, hormone, antibody, nucleic acid probe or biologica alive cell, to measure the concentration of the analysis substance inside the reaction system with time-resolved fluorometry after the reaction system occurred, and attain the quantitative analysis's purpose. TRFIA has been become a kind of new and more sensitive measure method after radioisotope marking, enzymatic marking, chemiluminescence, electrochemiluminescence, it primarily is decided by the special physics and chemistry characteristic of lanthanide trivalence ion and its chelates. In this paper, the result of spectroscopic evaluation of europium trivalence ion and its chelate, and the principle of spectra-resolved technology and a sensitive time-resolved fluorescence immunoassay instrument made by ourselves are reported. In the set, a high frequency Xenon pulsed-light was adopted as exciting light, and two special filters was utilized according to spectra-resolved technique. Thus the influence of scattering light and short-lifetime fluorescence was removed. And the sensitivity is 10-12mol/L (when Eu3+ was used for marking substance), examination repeat is CV = 95% (p < 0.01).

  13. Vibrational spectra and ab initio molecular orbital calculations of the novel anti-cancer drug combretastatin A-4 prodrug

    Science.gov (United States)

    James, C.; Pettit, G. R.; Nielsen, O. F.; Jayakumar, V. S.; Joe, I. Hubert

    2008-10-01

    The NIR-FT Raman and FT-IR spectral studies of the novel antineoplastic and antiangiogenesis substance comprestatin A-4 prodrug (CA4P) were carried out. The equilibrium geometry, various bonding features and harmonic vibrational frequencies of CA4P have been investigated with the help of B3LYP density functional theory (DFT) method. The most preferred cis-configuration for its bioactivity has been demonstrated on the basis of torsional potential energy surface (PES) scan studies. Stability of the molecule arising from hyperconjugative interactions leading to its bioactivity, charge delocalization and mesomeric effects have been analyzed using natural bond orbital (NBO) analysis. Detailed assignments of the vibrational spectra have been made with the aid of theoretically predicted vibrational frequencies. The optimized geometry shows near-planarity of phenyl rings and perpendicular conformation of meta substituted methoxy group. The vibrational analysis confirms the differently acting ring modes, steric repulsion, π conjugation and back-donation.

  14. Evaluation of algorithm methods for fluorescence spectra of cancerous and normal human tissues

    Science.gov (United States)

    Pu, Yang; Wang, Wubao; Alfano, Robert R.

    2016-03-01

    The paper focus on the various algorithms on to unravel the fluorescence spectra by unmixing methods to identify cancerous and normal human tissues from the measured fluorescence spectroscopy. The biochemical or morphologic changes that cause fluorescence spectra variations would appear earlier than the histological approach; therefore, fluorescence spectroscopy holds a great promise as clinical tool for diagnosing early stage of carcinomas and other deceases for in vivo use. The method can further identify tissue biomarkers by decomposing the spectral contributions of different fluorescent molecules of interest. In this work, we investigate the performance of blind source un-mixing methods (backward model) and spectral fitting approaches (forward model) in decomposing the contributions of key fluorescent molecules from the tissue mixture background when certain selected excitation wavelength is applied. Pairs of adenocarcinoma as well as normal tissues confirmed by pathologist were excited by selective wavelength of 340 nm. The emission spectra of resected fresh tissue were used to evaluate the relative changes of collagen, reduced nicotinamide adenine dinucleotide (NADH), and Flavin by various spectral un-mixing methods. Two categories of algorithms: forward methods and Blind Source Separation [such as Principal Component Analysis (PCA) and Independent Component Analysis (ICA), and Nonnegative Matrix Factorization (NMF)] will be introduced and evaluated. The purpose of the spectral analysis is to discard the redundant information which conceals the difference between these two types of tissues, but keep their diagnostically significance. The facts predicted by different methods were compared to the gold standard of histopathology. The results indicate that these key fluorophores within tissue, e.g. tryptophan, collagen, and NADH, and flavin, show differences of relative contents of fluorophores among different types of human cancer and normal tissues. The

  15. Time-dependent wave packet averaged vibrational frequencies from femtosecond stimulated Raman spectra

    Science.gov (United States)

    Wu, Yue-Chao; Zhao, Bin; Lee, Soo-Y.

    2016-02-01

    Femtosecond stimulated Raman spectroscopy (FSRS) on the Stokes side arises from a third order polarization, P(3)(t), which is given by an overlap of a first order wave packet, |" separators=" Ψ2 ( 1 ) ( p u , t ) > , prepared by a narrow band (ps) Raman pump pulse, Epu(t), on the upper electronic e2 potential energy surface (PES), with a second order wave packet, resembles the zeroth order wave packet |" separators=" Ψ1 ( 0 ) ( t ) > on the lower PES spatially, but with a force on |" separators=" Ψ2 ( 1 ) ( p u , t ) > along the coordinates of the reporter modes due to displacements in the equilibrium position, so that . The observable FSRS Raman gain is related to the imaginary part of P(3)(ω). The imaginary and real parts of P(3)(ω) are related by the Kramers-Kronig relation. Hence, from the FSRS Raman gain, we can obtain the complex P(3)(ω), whose Fourier transform then gives us the complex P(3)(t) to analyze for ω ¯ j ( t ) . We apply the theory, first, to a two-dimensional model system with one conformational mode of low frequency and one reporter vibrational mode of higher frequency with good results, and then we apply it to the time-resolved FSRS spectra of the cis-trans isomerization of retinal in rhodopsin [P. Kukura et al., Science 310, 1006 (2005)]. We obtain the vibrational frequency up-shift time constants for the C12-H wagging mode at 216 fs and for the C10-H wagging mode at 161 fs which are larger than for the C11-H wagging mode at 127 fs, i.e., the C11-H wagging mode arrives at its final frequency while the C12-H and C10-H wagging modes are still up-shifting to their final values, agreeing with the findings of Yan et al. [Biochemistry 43, 10867 (2004)].

  16. Vibrational-rotational spectra of GaF and global multi-isotopologue analysis

    Science.gov (United States)

    Uehara, Hiromichi; Horiai, Koui; Katsuie, Shunsuke

    2016-07-01

    In total, 521 vibrational-rotational spectral lines of the Δv = 1 transitions of 69GaF and 71GaF up to bands v = 5-4 and 4-3, respectively, were recorded in emission with a Fourier-transform spectrometer at unapodized resolution 0.010 cm-1 in range 625-660 cm-1. The response of a HgCdTe detector enforced the lower limit, 625 cm-1. To calibrate accurately the spectral lines, the absorption spectrum of CO2 was simultaneously recorded, using dual sample cells, to serve as wavenumber standards. A set of 782 spectral lines comprising all present vibrational-rotational spectra of 69GaF and 71GaF, the reported laser-diode measurements of the Δv = 1 band sequence and the reported rotational spectra was subjected to a global multi-isotopologue analysis through fitting with 11 isotopically invariant, irreducible molecular parameters in a single set. Normalized standard deviation 1.093 indicates a satisfactory fit. For the effects of the breakdown of the Born-Oppenheimer approximation on GaF, the values of non-Born-Oppenheimer parameters ΔBGa, ΔωGa and r1qGa(=r1qF) are experimentally determined for the first time. To facilitate the calculations or predictions of spectral frequencies, the values of the Dunham coefficients of 24 Yij and 81 band parameters for both 69GaF and 71GaF were back-calculated with uncertainties using the 11 evaluated molecular parameters. To date, various types of effective Be, re, ωe, and k have been reported for GaF. Because, in the present work, Dunham coefficients Yij are algebraically expressed with the genuine Be, ωe, ai (i = 1, …) and the non-Born-Oppenheimer correction parameters, the exact expressions for the physical significance of effective quantities are derivable. The various effective quantities of Be, re, ωe and k calculated with these expressions for the physical significance and the determined values of the fitted parameters of GaF agree satisfactorily with the reported values. The physical significance of the conventional

  17. Molecular iodine fluorescence spectra generated with helium-neon lasers for spectrometer calibration.

    Science.gov (United States)

    Williamson, J Charles

    2010-12-01

    Gas-phase molecular iodine laser-induced fluorescence (LIF) spectra were recorded out to 815 nm at 1 cm(-1) resolution using green, yellow, and red helium-neon (HeNe) lasers as excitation sources. Nine previously unreported I(2) B←X absorption transitions accessed by these lasers were identified, and specific rovibronic transition assignments were made for two hundred LIF peaks--more than sixty per laser. These I(2) LIF peaks can be used to calibrate the vacuum wavenumber coordinate of spectrometers to better than 0.1 cm(-1) accuracy. In particular, green HeNe excitation of the I(2) R(106) 28-0 transition leads to strong fluorescence well suited for calibration, with a rotational doublet spacing of 15 cm(-1) and a doublet-to-doublet spacing of 190 cm(-1). Calibration by HeNe I(2) LIF may be an especially valuable technique for Raman spectroscopy applications.

  18. Continuous Fluorescence Imaging of Intracellular Calcium by Use of Ion-Selective Nanospheres with Adjustable Spectra.

    Science.gov (United States)

    Yang, Chenye; Qin, Yu; Jiang, Dechen; Chen, Hong-Yuan

    2016-08-10

    Continuous fluorescence imaging of intracellular ions in various spectral ranges is important for biological studies. In this paper, fluorescent calcium-selective nanospheres, including calix[4]arene-functionalized bodipy (CBDP) or 9-(diethylamino)-5-[(2-octyldecyl)imino]benzo[a]phenoxazine (ETH 5350) as the chromoionophore, were prepared to demonstrate intracellular calcium imaging in visible or near-IR regions, respectively. The fluorescence of the nanospheres was controlled by the chromoionophore, and thus the spectral range for detection was adjustable by choosing the proper chromoionophore. The response time of the nanospheres to calcium was typically 1 s, which allowed accurate measurement of intracellular calcium. These nanospheres were loaded into cells through free endocytosis and exhibited fluorescence for 24 h, and their intensity was correlated with the elevation of intracellular calcium upon stimulation. The successful demonstration of calcium imaging by use of ion-selective nanospheres within two spectral ranges in 24 h supported that these nanospheres could be applied for continuous imaging of intracellular ions with adjustable spectra.

  19. Effects of Glycerol on the Fluorescence Spectra and Chloroplast Ultrastructure of Phaeodactylum tricornutum (Bacillariophyta)

    Institute of Scientific and Technical Information of China (English)

    Xiao-Juan Liu; Shun-Shan Duan; Ai-Fen Li; Kai-Feng Sun

    2009-01-01

    Responses of the photosynthetic activity of Phaeodactylum tricornutum (Bacillariophyta) to organic carbon glycerol were investigated. The growth rate, photosynthetic pigments, 77 K fluorescence spectra, and chloroplast ultrastructure of P. tricornutum were examined under photoautotrophic, mixotrophic, and photoheterotrophic conditions. The results showed that the specific growth rate was the fastest under mixotrophic conditions. The cell photosynthetic pigment content and values of Chl a/Chl c were reduced under mixotrophic and photoheterotrophic conditions. The value of carotenoid/Chl a was enhanced under mixotrophic conditions, but was decreased under photoheterotrophic conditions. In comparison with photoautotrophic conditions, the fluorescence emission peaks and fluorescence excitation peaks were not shifted. The relative fluorescence of photosystem (PS) Ⅰ and PS Ⅱ and the values of F6851F710 and F685/F738 were decreased. Chloroplast thylakoid pairs were less packed under mixotrophic and photoheterotrophic conditions. There was a strong correlation between degree of chloroplast thylakoid packing and the excitation energy kept in PS Ⅱ. These results suggested that the PS Ⅱ activity was reduced by glycerol under mixotrophic conditions, thereby leading to repression of the photosynthetic activity.

  20. Study of the Complexation Behavior of Calixarene with Transition Metal Cations by UV—vis and Fluorescent Spectra

    Institute of Scientific and Technical Information of China (English)

    杨俊林; 郑企雨; 等

    2002-01-01

    A new fluorescent compound based on calix[4] arene skeleton was synthesized.Its complexation ability with transition metal ions,such as Fe3+,Co2+,Ni2+,Cu2+,Zn2+ and Ag+,Was investigated by UV-vis and fluorescent spectra.

  1. Study of the Complexation Behavior of Calixarene with Transition Metal Cations by UV-vis and Fluorescent Spectra

    Institute of Scientific and Technical Information of China (English)

    YANG,Jun-Lin(杨俊林); ZHENG,Qi-Yu(郑企雨); AN,Li-Na(安丽娜); CHEN,Chuan-Feng(陈传峰); LIN,Hong-Zhen(蔺洪振); BAI,Feng-Lian(白凤莲); HUANG,Zhi-Tang(黄志镗)

    2002-01-01

    A new fluorescent compound based on calix[4]arene skeleton was synthesized. Its complexation ability with transition metal ions, such as Fe3+, Co2+, Ni2+, Cu2+, Zn2+ and Ag+, was investigated by UV-vis and fluorescent spectra.

  2. Application of direct peak analysis to energy dispersive x-ray fluorescence spectra

    Energy Technology Data Exchange (ETDEWEB)

    Nielson, K.K.

    1977-07-01

    A modified Covell method for direct peak analysis has been applied to energy dispersive x-ray fluorescence spectra. The method is background independent and is well-suited to computerized data reduction. It provides acceptable precision, minimizes errors from instrumental gain shift, and permits peak overlap correction. Peak overlap errors exhibit both positive and negative nodes as a function of peak separation distance, and are corrected using concentration ratios determined from thin, single-element standards. Peak precisions and overlaps are evaluated as a function of window width to aid in width selection. Least-square polynomial smoothing prior to peak analysis significantly improves peak area precisions without significantly affecting their accuracies.

  3. Effect of urea on synchronous fluorescence spectra and electrochemical behaviour of cytochrome

    Institute of Scientific and Technical Information of China (English)

    侴菊; 陆天虹; 吴越

    1996-01-01

    The changes of the synchronous fluorescence spectra and the electrochemical behaviour of cytochrome c with the urea concentration are studied. It has been found that with the increase of urea concentration, there occur sequentially the deaggregation of cytochrome c molecules, the increase of exposure extent of the heme group to the solvent, the disruption of Fe-S bond of the heme group and the change in the electrochemical behaviour of cytochrome c. It is suggested that the reason why the electrochemical reaction of cytochrome c is irreversible is that cytochrome c molecules exist in the concentrated solution as oligomers which are electrochemically inactive.

  4. [Application of PARAFAC method and 3-D fluorescence spectra in petroleum pollutant measurement and analysis].

    Science.gov (United States)

    Pan, Zhao; Wang, Yu-tian; Shao, Xiao-qing; Wu, Xi-jun; Yang, Li-li

    2012-03-01

    A method for identification and concentration measurement of petroleum pollutant by combining three-dimensional (3-D) fluorescence spectra with parallel factor analysis (PARAFAC) was proposed. The main emphasis of research was the measurement of coexisting different kinds of petroleum. The CCl4 solutions of a 0# diesel sample, a 97# gasoline sample, and a kerosene sample were used as measurement objects. The condition of multiple petroleum coexistence was simulated by petroleum solutions with different mixed ratios. The character of PARAFAC in complex mixture coexisting system analysis was studied. The spectra of three kinds of solutions and the spectra of gasoline-diesel mixed samples, diesel-kerosene mixed samples, and gas oline-diesel mixed with small counts of kerosene interference samples were analyzed respectively. The core consistency diagnostic method and residual sum of squares method were applied to calculate the number of factors in PARAFAC. In gasoline-diesel experiment, gasoline or diesel can be identified and measured as a whole respectively by 2-factors parallel factors analysis. In diesel-kerosene experiment, 2-factors parallel factors analysis can only obtain the characters of diesel, and the 3rd factor is needed to separate the kerosene spectral character from the mixture spectrum. When small counts of kerosene exist in gasoline-diesel solution, gasoline and diesel still can be identified and measured as principal components by a 2-factors parallel factor analysis, and the effect of interference on qualitative analysis is not significant. The experiment verified that the PARAFAC method can obtain characteristic spectrum of each kind of petroleum, and the concentration of petroleum in solutions can be predicted simultaneously, with recoveries shown in the paper. The results showed the possibility of petroleum pollutant identification and concentration measurement based on the 3-D fluorescence spectra and PARAFAC.

  5. The Utilization of Low Frequency Raman Spectra of Gases for the Study of Molecules with Large Amplitude Vibration

    Institute of Scientific and Technical Information of China (English)

    James R. Durig; Sarah Xiao-hua Zhou; Joshua Klaassen; Arindam Ganguly

    2009-01-01

    The utilization of the Raman spectra of the low frequency bending mode for three quasi-linear molecules, disiloxane, (SiH3)2 O; methylisocyanate, CH3NCO; and dimethy lisocyanate, (CH3)2SiHNCO for observing the low frequency anharmonic bending vibration is demonstrated which is superior to the corresponding far infrared spectra. From the observed frequencies from the Raman spectra the potential function governing the heavy atom motion to linearity has been obtained from which the barrier has been determined. These experimental values are compared to the ab ini-tio predicted values. Also low frequency Raman spectra of the ring puckering vibration of chlorocy-clobutane, c-C4H7Cl, bromocyclobutane, c-C4H7Br, and aminocyclobutane, c-C4H7NH2, have been utilized to obtain the potential function governing the ring inversion for these molecules. The deter-mined barriers to planarity are compared to those obtained from MP2 (full) ab initio and density functional theory B3LYP calculations by utilizing a variety of basis sets. For all of these studies it is shown that the Raman spectra are superior to the infrared spectra for determining the frequencies of the excited state transitions.

  6. Structures, Vibrational Spectra, and Relative Energetics of CH3COIO3 Isomers

    Institute of Scientific and Technical Information of China (English)

    GE,Mao-Fa; MA,Chun-Ping

    2008-01-01

    The structures,vibrational spectra,relative energetics,and enthalpies of formation of CH3COlO3 isomers have been investigated with B3LYP,B3P86 and B3PW91 methods in conjugation with the 6-31+G(d),6-311+G(d,p)and 6-311++G(3df,3pd) basis sets.The CH3COOIO2 structure was found to be the most stable form among the isomers with an estimated enthalpy of formation of -314.6 kJ·mol-1.The enthalpies of formation for CH3COOOOI,CH3COOOIO and CH3COIO3 are -180.7,-184.9 and -50.6 kJ·mol-1,respectively.The implication of the formation of CH3COIO3 isomers from the atmospheric cross-reactions of the acetylperoxy (CH3COO2) and iodine monoxide (IO) radicals was examined and the possible dissociation products of the most likely CH3COIO3 isomers were determined.

  7. Density functional theory calculations on the molecular structures and vibration spectra of platinum(II) antitumor drugs.

    Science.gov (United States)

    Gao, Hongwei; Xia, FengYi; Huang, ChangJiang; Lin, Kuangfei

    2011-04-01

    A comparison of six density functional theory (DFT) methods and six basis sets for predicting the molecular structures and vibration spectra of cisplatin is reported. The theoretical results are discussed and compared with the experimental data. It is remarkable that LSDA/SDD level is clearly superior to all the remaining density functional methods (including mPW1PW) in predicting the structures of cisplatin. Mean deviation between the calculated harmonic and observed fundamental vibration frequencies for each method is also calculated. The results indicate that PBE1PBE/SDD is the best method to predict all frequencies on average for cisplatin molecule in DFT methods.

  8. Fluorescence Excitation-Emission Matrix Regional Integration to Quantify Spectra for Dissolved Organic Matter

    Science.gov (United States)

    Chen, W.; Westerhoff, P.; Leenheer, J.A.; Booksh, K.

    2003-01-01

    Excitation-emission matrix (EEM) fluorescence spectroscopy has been widely used to characterize dissolved organic matter (DOM) in water and soil. However, interpreting the >10,000 wavelength-dependent fluorescence intensity data points represented in EEMs has posed a significant challenge. Fluorescence regional integration, a quantitative technique that integrates the volume beneath an EEM, was developed to analyze EEMs. EEMs were delineated into five excitation-emission regions based on fluorescence of model compounds, DOM fractions, and marine waters or freshwaters. Volumetric integration under the EEM within each region, normalized to the projected excitation-emission area within that region and dissolved organic carbon concentration, resulted in a normalized region-specific EEM volume (??i,n). Solid-state carbon nuclear magnetic resonance (13C NMR), Fourier transform infrared (FTIR) analysis, ultraviolet-visible absorption spectra, and EEMs were obtained for standard Suwannee River fulvic acid and 15 hydrophobic or hydrophilic acid, neutral, and base DOM fractions plus nonfractionated DOM from wastewater effluents and rivers in the southwestern United States. DOM fractions fluoresced in one or more EEM regions. The highest cumulative EEM volume (??T,n = ????i,n) was observed for hydrophobic neutral DOM fractions, followed by lower ??T,n values for hydrophobic acid, base, and hydrophilic acid DOM fractions, respectively. An extracted wastewater biomass DOM sample contained aromatic protein- and humic-like material and was characteristic of bacterial-soluble microbial products. Aromatic carbon and the presence of specific aromatic compounds (as indicated by solid-state 13C NMR and FTIR data) resulted in EEMs that aided in differentiating wastewater effluent DOM from drinking water DOM.

  9. Component analysis of fluorescence spectra of thiol DAB dendrimer/ZnSe-PEA nanoparticles.

    Science.gov (United States)

    Algarra, M; Radotić, K; Kalauzi, A; Alonso, B; Casado, C M; Esteves da Silva, J C G

    2013-02-15

    The fluorescence spectroscopy technique is an accurate method and has great utility in the interpretation of complex systems based on several emission bands. An interpretation of the system requires determination of the number, positions and intensities of the spectral components. In this work, the emission spectra of the synthesized ZnSe complex coated with O-phosphorylethanolamine (ZnSe-PEA), both with and without thiol DAB dendrimer generation 5 (S-DAB G5), were analyzed using a combination of asymmetric (log-normal) and symmetric (Gaussian) models. The method applied for the deconvolution of fluorescence spectra has proven to be very sensitive for observing the stability of the ZnSe-PEA complex after binding with S-DAB. The ZnSe-PEA emission spectrum contains two components. The positions of the emission maxima of these two components are not significantly affected by the presence of S-DAB G5 in the complex, which revealed the presence of a stable complex at a pH of 7. By applying the spectral deconvolution method, strong evidence was obtained that suggested that the ZnSe-PEA complex is stable after complexation with S-DAB G5. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. Chlorophyll Fluorescence Emissions of Vegetation Canopies From High Resolution Field Reflectance Spectra

    Science.gov (United States)

    Middleton, E. M.; Corp, L. A.; Daughtry, C. S. T.; Campbell, P. K. Entcheva

    2006-01-01

    A two-year experiment was performed on corn (Zea mays L.) crops under nitrogen (N) fertilization regimes to examine the use of hyperspectral canopy reflectance information for estimating chlorophyll fluorescence (ChlF) and vegetation production. Fluorescence of foliage in the laboratory has proven more rigorous than reflectance for correlation to plant physiology. Especially useful are emissions produced from two stable red and far-red chlorophyll ChlF peaks centered at 685V10 nm and 735V5 nm. Methods have been developed elsewhere to extract steady state solar induced fluorescence (SF) from apparent reflectance of vegetation canopies/landscapes using the Fraunhofer Line Depth (FLD) principal. Our study utilized these methods in conjunction with field-acquired high spectral resolution canopy reflectance spectra obtained in 2004 and 2005 over corn crops, as part of an ongoing multi-year experiment at the USDA/Agriculture Research Service in Beltsville, MD. A spectroradiometer (ASD-FR Fieldspec Pro, Analytical Spectral Devices, Inc., Boulder, CO) was used to measure canopy radiances 1 m above plant canopies with a 22deg field of view and a 0deg nadir view zenith angle. Canopy and plant measurements were made at the R3 grain fill reproductive stage on 3-4 replicate N application plots provided seasonal inputs of 280, 140, 70, and 28 kg N/ha. Leaf level measurements were also made which included ChlF, photosynthesis, and leaf constituents (photosynthetic pigment, carbon (C), and N contents). Crop yields were determined at harvest. SIF intensities for ChlF were derived directly from canopy reflectance spectra in specific narrowband regions associated with atmospheric oxygen absorption features centered at 688 and 760 nm. The red/far-red S F ratio derived from these field reflectance spectra successfully discriminated foliar pigment levels (e.g., total chlorophyll, Chl) associated with N application rates in both corn crops. This canopy-level spectral ratio was also

  11. Fluorescence and Raman spectra on surface of K9 glass by high fluence ultraviolet laser irradiation at 355 nm

    Science.gov (United States)

    Zhang, Zhen; Huang, Jin; Geng, Feng; Zhou, Xiaoyan; Feng, Shiquan; Ren, Dahua; Cheng, Xinlu; Jiang, Xiaodong; Wu, Weidong; Zheng, Wanguo; Tang, Yongjian

    2013-11-01

    In order to explore the damage mechanisms of K9 glass irradiated by high energy density ultraviolet laser, laser-induced fluorescence and Raman spectra were investigated. Compared the fluorescence spectra of damaged area, undamaged area and sub-damaged area, it can be conclude that the fluorescence spectrum of sub-damaged area is different from the structure of the other two areas. Especially, the main peak of the spectra at 415 nm reveals the unique characteristics of K9 glass. The structure at the sub-damaged area enhances intensity of the Raman scattering spectra. Three peaks of the spectra at about 500 nm and two characteristic peaks at about 550 nm exhibit the characterization of damaged area. A peak of the Raman scattering spectra at 350 nm which related to water can be observed. The relationship between intensity of Raman scattering and laser intensity at 355 nm is investigated by confocal Raman microscopy. At sub-damage area, signal of Raman scattering is rather high and decreased dramatically with respect to energy density. The major band at about 1470 cm-1 sharpened and moved to higher frequency with densification. These phenomena demonstrate that the structure of sub-damaged area has some characterization compared with the damaged area. The investigation of defect induced fluorescence and Raman spectra on surface of K9 glass is important to explore the damage mechanisms of optical materials irradiated by ultraviolet laser irradiation at 355 nm.

  12. Structural safety criteria for blasting vibration based on wavelet packet energy spectra

    Institute of Scientific and Technical Information of China (English)

    Zhong Guosheng; Li Jiang; Zhao Kui

    2011-01-01

    Given multi-resolution decomposition of wavelet packet transforms, wavelet packet frequency band energy has been deduced from different bands of blasting vibration signals. Our deduction reflects the total effect of all three key elements (intensity, frequency and duration of vibration) of blasting vibration.We considered and discuss the dynamic response of structures and the effect of inherent characteristics of controlled structures to blasting vibration. Frequency band response coefficients for controlled structures by blasting vibration have been obtained. We established multi-factor blasting vibration safety criteria, referred to as response energy criteria. These criteria reflect the total effect of intensity,frequency and duration of vibration and the inherent characteristics (natural frequency and damping ratio) of dynamic responses from controlled structures themselves. Feasibility and reliability of the criteria are validated by an example.

  13. Femtosecond fluorescence spectra of tryptophan in human gamma-crystallin mutants: site-dependent ultrafast quenching.

    Science.gov (United States)

    Xu, Jianhua; Chen, Jiejin; Toptygin, Dmitri; Tcherkasskaya, Olga; Callis, Patrik; King, Jonathan; Brand, Ludwig; Knutson, Jay R

    2009-11-25

    The eye lens Crystallin proteins are subject to UV irradiation throughout life, and the photochemistry of damage proceeds through the excited state; thus, their tryptophan (Trp) fluorescence lifetimes are physiologically important properties. The time-resolved fluorescence spectra of single Trps in human gammaD- and gammaS-Crystallins have been measured with both an upconversion spectrophotofluorometer on the 300 fs to 100 ps time scale, and a time correlated single photon counting apparatus on the 100 ps to 10 ns time scale, respectively. Three Trps in each wild type protein were replaced by phenylalanine, leading to single-Trp mutants: W68-only and W156-only of HgammaD- and W72-only and W162-only of HgammaS-Crystallin. These proteins exhibit similar ultrafast signatures: positive definite decay associated spectra (DAS) for 50-65 ps decay constants that indicate dominance of fast, heterogeneous quenching. The quenched population (judged by amplitude) of this DAS differs among mutants. Trps 68, 156 in human gammaD- and Trp72 in human gammaS-Crystallin are buried, but water can reach amide oxygen and ring HE1 atoms through narrow channels. QM-MM simulations of quenching by electron transfer predict heterogeneous decay times from 50-500 ps that agree with our experimental results. Further analysis of apparent radiative lifetimes allow us to deduce that substantial subpopulations of Trp are fully quenched in even faster (sub-300 fs) processes for several of the mutants. The quenching of Trp fluorescence of human gammaD- and gammaS-Crystallin may protect them from ambient light induced photo damage.

  14. Vibrational spectra of nanowires measured using laser doppler vibrometry and STM studies of epitaxial graphene : an LDRD fellowship report.

    Energy Technology Data Exchange (ETDEWEB)

    Biedermann, Laura Butler

    2009-09-01

    A few of the many applications for nanowires are high-aspect ratio conductive atomic force microscope (AFM) cantilever tips, force and mass sensors, and high-frequency resonators. Reliable estimates for the elastic modulus of nanowires and the quality factor of their oscillations are of interest to help enable these applications. Furthermore, a real-time, non-destructive technique to measure the vibrational spectra of nanowires will help enable sensor applications based on nanowires and the use of nanowires as AFM cantilevers (rather than as tips for AFM cantilevers). Laser Doppler vibrometry is used to measure the vibration spectra of individual cantilevered nanowires, specifically multiwalled carbon nanotubes (MWNTs) and silver gallium nanoneedles. Since the entire vibration spectrum is measured with high frequency resolution (100 Hz for a 10 MHz frequency scan), the resonant frequencies and quality factors of the nanowires are accurately determined. Using Euler-Bernoulli beam theory, the elastic modulus and spring constant can be calculated from the resonance frequencies of the oscillation spectrum and the dimensions of the nanowires, which are obtained from parallel SEM studies. Because the diameters of the nanowires studied are smaller than the wavelength of the vibrometer's laser, Mie scattering is used to estimate the lower diameter limit for nanowires whose vibration can be measured in this way. The techniques developed in this thesis can be used to measure the vibrational spectra of any suspended nanowire with high frequency resolution Two different nanowires were measured - MWNTs and Ag{sub 2}Ga nanoneedles. Measurements of the thermal vibration spectra of MWNTs under ambient conditions showed that the elastic modulus, E, of plasma-enhanced chemical vapor deposition (PECVD) MWNTs is 37 {+-} 26 GPa, well within the range of E previously reported for CVD-grown MWNTs. Since the Ag{sub 2}Ga nanoneedles have a greater optical scattering efficiency than

  15. Modeling structure and spectra of the kindling fluorescent protein asFP595

    Science.gov (United States)

    Collins, Jack R.; Topol, Igor A.; Savitsky, Alexander P.; Nemukhin, Alexander V.

    2011-03-01

    Modern computational approaches based on quantum mechanical methods to characterize structures and optical spectra of biological chromophores in proteins are intensively used to gain knowledge of events occurring upon of their photoexcitation. Primary attention is paid to the species from the family of the green fluorescent protein applied as biomarkers in living cells. We apply quantum chemical approaches for accurate calculations of the structures of the chromophore binding pockets and to estimate spectral bands corresponding to the S0-S1 optical transitions of the intriguing kindling protein asFP595. Its precursor, the chromoprotein asCP from the sea anemony Anemonia sulcata is characterized by distinctive spectral properties: at low light intensities the wild-type protein is weakly fluorescent with the very low quantum yield, however, high intensity irradiation with green light leads to a drastic increase of quantum yield. This phenomenon is now termed "kindling". In simulations, the model system is designed as a molecular cluster constructed on the basis of available crystal structures of the related protein. The equilibrium geometry of the cluster is optimized using density functional theory approximations. The vertical excitation energies corresponding to the S0-S1 transitions are computed by using the semiempirical ZINDO technique. A special attention is paid to evaluate effects of point mutations in the vicinity of the chromophore group. Theoretical data provide important information on the chromophore properties aiming to interpret the results of experimental studies and applications of this fluorescent protein.

  16. Improved Savitzky-Golay-method-based fluorescence subtraction algorithm for rapid recovery of Raman spectra.

    Science.gov (United States)

    Chen, Kun; Zhang, Hongyuan; Wei, Haoyun; Li, Yan

    2014-08-20

    In this paper, we propose an improved subtraction algorithm for rapid recovery of Raman spectra that can substantially reduce the computation time. This algorithm is based on an improved Savitzky-Golay (SG) iterative smoothing method, which involves two key novel approaches: (a) the use of the Gauss-Seidel method and (b) the introduction of a relaxation factor into the iterative procedure. By applying a novel successive relaxation (SG-SR) iterative method to the relaxation factor, additional improvement in the convergence speed over the standard Savitzky-Golay procedure is realized. The proposed improved algorithm (the RIA-SG-SR algorithm), which uses SG-SR-based iteration instead of Savitzky-Golay iteration, has been optimized and validated with a mathematically simulated Raman spectrum, as well as experimentally measured Raman spectra from non-biological and biological samples. The method results in a significant reduction in computing cost while yielding consistent rejection of fluorescence and noise for spectra with low signal-to-fluorescence ratios and varied baselines. In the simulation, RIA-SG-SR achieved 1 order of magnitude improvement in iteration number and 2 orders of magnitude improvement in computation time compared with the range-independent background-subtraction algorithm (RIA). Furthermore the computation time of the experimentally measured raw Raman spectrum processing from skin tissue decreased from 6.72 to 0.094 s. In general, the processing of the SG-SR method can be conducted within dozens of milliseconds, which can provide a real-time procedure in practical situations.

  17. Vibrational spectra of bis(dmit) complexes of main group metals: IR, Raman and ab initio calculations

    OpenAIRE

    Ferreira,Glaucio B.; Nadia M. Comerlato; Wardell, James L.; Hollauer,Eduardo

    2004-01-01

    This work reports a theoretical-experimental investigation of the infrared/Raman vibrational spectra of several metal 1,3-dithole-2-thione-4,5-dithiolate (dmit) complexes; [NEt4]2[Zn(dmit)2], [NEt4][Sb(dmit)2] and [NEt4][Bi(dmit)2]. IR/Raman spectra of all the solids and the solution IR spectrum of [NEt4]2[Zn(dmit)2] were recorded from 4000 to 100 cm-1. Two regions were clearly identified: below 380 cm-1, the modes presented significant metal-ligand contributions, and above, the modes indicat...

  18. Calculation of the vibrational spectra of RDX as a function of pressure using the Grimme DFT potential

    Science.gov (United States)

    Perger, Warren; Flurchick, K. M.; Slough, Wil; Valenzano, Loredana

    2011-06-01

    The density-functional theory (DFT) potential by Grimme has been proposed for describing long-range dispersion corrections. This potential has been implemented into the CRYSTAL09 program and used to calculate the vibrational spectra in RDX at equilibrium and as a function of pressure. The intensities, Born charge tensor, and high-frequency dielectric constant are reported and compared with prior theory and experiment where possible. Supported by ONR-MURI grant N00014-06-1-0459.

  19. Simulated vibrational spectra of aflatoxins and their demethylated products and the estimation of the energies of the demethylation reactions

    Science.gov (United States)

    Billes, Ferenc; Móricz, Ágnes M.; Tyihák, Ernő; Mikosch, Hans

    2006-06-01

    The structure of four natural mycotoxins, the aflatoxin B 1, B 2, G 1 and G 2 and their demethylated products were optimized with quantum chemical method. The energies and the thermodynamic functions of the molecules were calculated and applied to calculation of the reaction energies of the demethylations. Further results of the calculations are the vibrational force constants, the infrared spectra of the molecules and the assignments of the spectral bands.

  20. Fluorescence spectra of atmospheric aerosol at Adelphi, Maryland, USA: measurement and classification of single particles containing organic carbon

    Science.gov (United States)

    Pinnick, Ronald G.; Hill, Steven C.; Pan, Yong-Le; Chang, Richard K.

    We measured laser-induced fluorescence spectra from individual supermicron-sized atmospheric particles drawn into our laboratory at Adelphi, MD, an urban site in the Washington, DC metroplex. A virtural impactor concentrator is used along with an aerodynamic-focusing-nozzle which forms, within an optical chamber, a focused aerosol jet where single aerosol particles can be interrogated on-the-fly with a pulsed 266-nm-wavelength laser. Sample rates are a few liter per minute, and are size dependent. Crossed-diode laser beams indicate when a particle is traversing the sample region and are used to trigger the UV laser to fire and the gated intensified CCD to record the fluorescence spectrum. Our breadboard fluorescence particle spectrometer measures particles in the 3-10 μm diameter size range. Typical trigger rates are a few per second. The usable spectral range is from about 295 to 605 nm. The majority of the particles have very weak fluorescence (on average 8 percent of particles have fluorescence signals above noise). The spectra were grouped using a heirarchical cluster analysis, with parameters chosen so that spectra typically cluster into 4-12 main categories. From the set of all cluster spectra we chose 8 template spectra for reanalyzing all the data. On average, 92 percent (81-94 percent) of the spectra were similar to these templates (using the same thresholds used for the cluster analysis). The major emission bands of the most commonly occurring spectra have peaks: near 460 nm (28 percent of fluorescent particles on average), a very broad hump, and may be humic acids or humic like substances; near 317 nm (on average 24 percent of fluorescent particles); near 321 and 460 nm (a double hump, 12 percent of fluorescent particles); and near 341 nm (8 percent of fluorescent particles). Some of the fluorescence in spectra peaking in the 317-341 nm range is probably from dicyclic aromatics and heterocyclics, including the amino acid tryptophan in biological

  1. Structural, Conformational and Vibrational Studies of Isocyanocyclopentane from Infrared, Raman Spectra and AB Initio Calculations

    Science.gov (United States)

    Sawant, Dattatray K.; Klaassen, Joshua J.; Durig, James R.

    2013-06-01

    The infrared and Raman spectra (3200 to 50 cm^{-1}) of the gas, liquid or solution, and solid have been recorded of isocyanocyclopentane, _{c}-C_{5}H_{9}NC. FT-microwave studies have also been carried out and 23 transitions were recorded for the envelope-axial (Ax) conformer. Variable temperature (-55 to -100°C) studies of the infrared spectra (3200 to 400 cm^{-1}) dissolved in liquid xenon have been carried out. From these data, both the Ax and envelope-equatorial (Eq) conformers have been identified and their relative stabilities obtained. The enthalpy difference has been determined to be 102 ± 10 cm^{-1} (1.21 ± 0.03 kJ mol^{-1}) with the Ax conformer the more stable form. The percentage of the Eq conformer is estimated to be 38 ± 1% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing several different basis sets up to aug-cc-pVTZ from both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been made for the observed bands for both conformers with initial predictions by MP2(full)/6-31G(d) ab initio calculations to obtain harmonic force constants, wavenumbers, infrared intensities, Raman activities and depolarization ratios for both conformers. The heavy atom distances (Å): C≡N = 1.176 ; C_{α}-N≡C= 1.432; C_{α}-C_{β},C_{β}' = 1.534; C_{β}-C_{γ}, C_{γ}' = 1.542; C_{γ}-C_{γ}' = 1.554 and angles (°:angleC_{α}-N≡C = 177.8; angleC_{β}C_{α}-N≡C = 110.4; angleC_{β}C_{α}C_{β}'= 102.9; angleC_{α}C_{β}C_{γ} = 103.6; angleC_{β}C_{γ}C_{γ}' = 105.9. The results are discussed and compared to the corresponding properties of some related molecules.

  2. A complete assignment of the vibrational spectra of sucrose in aqueous medium based on the SQM methodology and SCRF calculations.

    Science.gov (United States)

    Brizuela, Alicia Beatriz; Castillo, María Victoria; Raschi, Ana Beatriz; Davies, Lilian; Romano, Elida; Brandán, Silvia Antonia

    2014-03-31

    In the present study, a complete assignment of the vibrational spectra of sucrose in aqueous medium was performed combining Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology with self-consistent reaction field (SCRF) calculations. Aqueous saturated solutions of sucrose and solutions at different molar concentrations of sucrose in water were completely characterized by infrared, HATR, and Raman spectroscopies. In accordance with reported data of the literature for sucrose, the theoretical structures of sucrose penta and sucrose dihydrate were also optimized in gas and aqueous solution phases by using the density functional theory (DFT) calculations. The solvent effects for the three studied species were analyzed using the solvation PCM/SMD model and, then, their corresponding solvation energies were predicted. The presence of pure water, sucrose penta-hydrate, and sucrose dihydrate was confirmed by using theoretical calculations based on the hybrid B3LYP/6-31G(∗) method and the experimental vibrational spectra. The existence of both sucrose hydrate complexes in aqueous solution is evidenced in the IR and HATR spectra by means of the characteristic bands at 3388, 3337, 3132, 1648, 1375, 1241, 1163, 1141, 1001, 870, 851, 732, and 668cm(-1) while in the Raman spectrum, the groups of bands in the regions 3159-3053cm(-1), 2980, 2954, and 1749-1496cm(-1) characterize the vibration modes of those complexes. The inter and intra-molecular H bond formations in aqueous solution were studied by Natural Bond Orbital (NBO) and Atoms in Molecules theory (AIM) investigation.

  3. A wavelength-dispersive instrument for characterizing fluorescence and scattering spectra of individual aerosol particles on a substrate

    Science.gov (United States)

    Huffman, Donald R.; Swanson, Benjamin E.; Huffman, J. Alex

    2016-08-01

    We describe a novel, low-cost instrument to acquire both elastic and inelastic (fluorescent) scattering spectra from individual supermicron-size particles in a multi-particle collection on a microscope slide. The principle of the device is based on a slitless spectroscope that is often employed in astronomy to determine the spectra of individual stars in a star cluster but had not been applied to atmospheric particles. Under excitation, most commonly by either a 405 nm diode laser or a UV light-emitting diode (LED), fluorescence emission spectra of many individual particles can be determined simultaneously. The instrument can also acquire elastic scattering spectra from particles illuminated by a white-light source. The technique also provides the ability to detect and rapidly estimate the number fraction of fluorescent particles that could contaminate a collection of non-fluorescent material, even without analyzing full spectra. Advantages and disadvantages of using black-and-white cameras compared to color cameras are given. The primary motivation for this work has been to develop an inexpensive technique to characterize fluorescent biological aerosol particles, especially particles such as pollen and mold spores that can cause allergies. An example of an iPhone-enabled device is also shown as a means for collecting data on biological aerosols at lower cost or by utilizing citizen scientists for expanded data collection.

  4. Characteristics of blood fluorescence spectra using low-level, 457.9-nm excitation from Ar+ laser

    Institute of Scientific and Technical Information of China (English)

    Shumei Gao(高淑梅); Xiufeng Lan(兰秀风); Ying Liu(刘莹); Zhonghua Shen(沈中华); Jian Lu(陆建); Xiaowu Ni(倪晓武)

    2004-01-01

    We measured the fluorescence spectra of the whole blood, the red blood cell (RBC) and the hemoglobin using 457.9-nm Ar+ laser excitation. It was found that the fluorescence spectra of the whole blood and the RBC have much similarities in the intensity, the emission peaks and the emitting region, and abundant peaks can be found. But for the hemoglobin, fluorescence could only be found in the wavelength range 580-650 nm. It was concluded that in the wavelength range of 650-850 nm, the fluorescence spectra were emitted by the new fluorophores generated by the breakdown of some weak bonds on the RBC membrane,such as the C-C bond and the C-N bond. In the wavelength range of 590 - 650 nm, the fluorescence spectra are mainly emitted by the hemoglobin, but the hemoglobin solution of cracked RBC has a strong quencher effect on the fluorescence spectrum. The experimental result and the theoretical analysis are meaningful for the medical diagnostics and the therapy.

  5. Decomposition of the fluorescence spectra of two FAD molecules in electron-transferring flavoprotein from Megasphaera elsdenii.

    Science.gov (United States)

    Sato, Kyosuke; Nishina, Yasuzo; Shiga, Kiyoshi

    2013-07-01

    Electron-transferring flavoprotein (ETF) from Megasphaera elsdenii contains two FAD molecules, FAD-1 and FAD-2. FAD-2 shows an unusual absorption spectrum with a 400-nm peak. In contrast, ETFs from other sources such as pig contain one FAD and one AMP with the FAD showing a typical flavin absorption spectrum with 380- and 440-nm peaks. It is presumed that FAD-2 is the counterpart of the FAD in other ETFs. In this study, the FAD-1 and FAD-2 fluorescence spectra were determined by titration of FAD-1-bound ETF with FAD using excitation-emission matrix (EEM) fluorescence spectroscopy. The EEM data were globally analysed, and the FAD fluorescence spectra were calculated from the principal components using their respective absorption spectra. The FAD-2 fluorescence spectrum was different from that of pig ETF, which is more intense and blue-shifted. AMP-free pig ETF in acidic solution, which has a comparable absorption spectrum to FAD-2, also had a similar fluorescence spectrum. This result suggests that FAD-2 in M. elsdenii ETF and the FAD in acidic AMP-free pig ETF share a common microenvironment. A review of published ETF fluorescence spectra led to the speculation that the majority of ETF molecules in solution are in the conformation depicted by the crystal structure.

  6. Analysis of the vibronic structure of the trans-stilbene fluorescence and excitation spectra: the S0 and S1 PES along the Ce[double bond, length as m-dash]Ce and Ce-Cph torsions.

    Science.gov (United States)

    Orlandi, Giorgio; Garavelli, Marco; Zerbetto, Francesco

    2017-09-20

    We analyze the highly resolved vibronic structure of the low energy (≤200 cm(-1)) region of the fluorescence and fluorescence excitation spectra of trans-stilbene in supersonic beams. In this spectral region the vibronic structure is associated mainly with vibrational levels of the Ce-Ce torsion (τ) and the au combination of the two Ce-Cph bond twisting (ϕ). We base this analysis on the well-established S0(τ, ϕ) two-dimensional potential energy surface (PES) and on a newly refined S1(τ, ϕ) PES. We obtain vibrational eigenvalues and eigenvectors of the anharmonic S0(τ, ϕ) and S1(τ, ϕ) PES using a numerical procedure based on the Meyer's flexible model [R. Meyer, J. Mol. Spectrosc., 1979, 76, 266]. Then we derive Franck-Condon factors and therefore intensities of the relevant vibronic bands for the S0 → S1 excitation and S1 → S0 fluorescence spectra. Furthermore, we assess the role of the bg combination of the two Ce-Cph bond twisting (ν48) in the structure of the S1 → S0 fluorescence spectra. By the use of these results we are able to assign most of the low energy vibrational levels of the S0 → S1 excitation spectra and of the fluorescence spectra of the emission from several low energy S1 vibronic levels. The good agreement between the observed and the computed vibrational structure of the S0 → S1 and S1 → S0 spectra suggests that the proposed picture of the E1(τ, ϕ) and E0(τ, ϕ) PES, in particular along the coordinate τ governing trans-cis photo-isomerization in S1, is accurate. In S0, the barriers for the Ce[double bond, length as m-dash]Ce torsion and for the au type Ce-Cph bond twisting are 16 080 cm(-1) and 3125 cm(-1), respectively, while in S1, where the bond orders of the Ce[double bond, length as m-dash]Ce and Ce-Cph bonds are reversed, the two barriers become 1350 cm(-1) and 8780 cm(-1), respectively.

  7. Rotation-vibration interactions in the spectra of polycyclic aromatic hydrocarbons: Quinoline as a test-case species

    Energy Technology Data Exchange (ETDEWEB)

    Pirali, O.; Gruet, S. [AILES Beamline, Synchrotron SOLEIL, l’Orme des Merisiers, Saint-Aubin, 91192 Gif-sur-Yvette cedex (France); Institut des Sciences Moléculaires d’Orsay, UMR8214 CNRS – Université Paris-Sud, Bât. 210, 91405 Orsay cedex (France); Kisiel, Z. [Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw (Poland); Goubet, M. [Laboratoire de Physique des Lasers, Atomes et Molécules, UMR 8523 CNRS - Université Lille 1, Bâtiment P5, F-59655 Villeneuve d’Ascq Cedex (France); Martin-Drumel, M. A.; Cuisset, A.; Hindle, F.; Mouret, G. [Laboratoire de Physico-Chimie de l’Atmosphère, EA-4493, Université du Littoral – Côte d’Opale, 59140 Dunkerque (France)

    2015-03-14

    Polycyclic aromatic hydrocarbons (PAHs) are highly relevant for astrophysics as possible, though controversial, carriers of the unidentified infrared emission bands that are observed in a number of different astronomical objects. In support of radio-astronomical observations, high resolution laboratory spectroscopy has already provided the rotational spectra in the vibrational ground state of several molecules of this type, although the rotational study of their dense infrared (IR) bands has only recently become possible using a limited number of experimental set-ups. To date, all of the rotationally resolved data have concerned unperturbed spectra. We presently report the results of a high resolution study of the three lowest vibrational states of quinoline C{sub 9}H{sub 7}N, an N-bearing naphthalene derivative. While the pure rotational ground state spectrum of quinoline is unperturbed, severe complications appear in the spectra of the ν{sub 45} and ν{sub 44} vibrational modes (located at about 168 cm{sup −1} and 178 cm{sup −1}, respectively). In order to study these effects in detail, we employed three different and complementary experimental techniques: Fourier-transform microwave spectroscopy, millimeter-wave spectroscopy, and Fourier-transform far-infrared spectroscopy with a synchrotron radiation source. Due to the high density of states in the IR spectra of molecules as large as PAHs, perturbations in the rotational spectra of excited states should be ubiquitous. Our study identifies for the first time this effect and provides some insights into an appropriate treatment of such perturbations.

  8. DFT studies on the vibrational and electronic spectra of acetylsalicylic acid

    Science.gov (United States)

    Ye, Yunfeng; Tang, Guodong; Han, Yonghong; Culnane, Lance F.; Zhao, Jianyin; Zhang, Yu

    2016-05-01

    The following is a theoretical and experimental study on the vibrational and electronic properties of acetylsalicylic acid (ASA). Vibrational information was obtained by FT-IR and Raman spectroscopy which agree well with harmonic vibrational frequency calculations. The calculations were carried out using density functional theory B3LYP methods with 6-311G** and LANL2DZ basis sets. The vibrational assignments were calculated by Gaussview. Absorption UV-Vis experiments of ASA reveal three maximum peaks at 203, 224 and 277 nm, which are in agreement with calculated electronic transitions using TD-B3LYP/6-311G**.

  9. Theoretical studies on vibrational spectra of mixed cyanide-halide complexes of platinum(IV) and palladium(IV)

    Science.gov (United States)

    Zhang, Yu; Zhang, Lin; Tao, Hanbing; Sun, Xiaojuan; Zhu, Longgen

    2003-02-01

    The vibrational spectra of mixed cyanide-halide complexes, M(CN) 4X 22- and M(CN) 5X 2- (M=Pt and Pd; X=F, Cl, Br and I), have been systematically investigated by ab initio RHF, B3LYP and MP2 methods with LanL2DZ and SDD basis sets. The calculated vibrational frequencies of platinum complexes are evaluated via comparison with the experimental values. In the infrared frequency region, the CN stretching vibrational frequencies calculated at B3LYP level with two basis sets are in good agreement with the observed values with deviations, -16-4 cm -1 for Pt(CN) 4X 22- and -18 to -2 cm -1 for Pt(CN) 5X 2-. However, in far-infrared region, the results obtained at RHF level are better than those calculated at B3LYP and MP2 levels. For RHF/SDD method, the deviations for PtX and PtC stretching vibrational frequencies are -14-1 and -12 to -2 cm -1 in the complex Pt(CN) 4X 22-, -19 to -11 and -15-14 cm -1 in the Pt(CN) 5X 2- complex, respectively. The vibrational frequencies of palladium(IV) and some platinum(IV) complexes that have not been experimentally reported are predicted.

  10. Effect of excitation intensity on fluorescence spectra in ZnO nanostructures and its origin

    Institute of Scientific and Technical Information of China (English)

    ZHANG YuGang; ZHANG LiDe

    2009-01-01

    ZnO nanostructures with three kinds of morphologies, namely, tetrapod-, rod-, and sheet-like shape, are synthesized by chemical vapor deposition, conventional solution-phase, and hydrothermal meth-ods, respectively. The fluorescence measurements display that the spectra of these nanostructures exhibit similar unexpected change laws with the altering excitation intensity. It is observed that when the excitation intensity increases, for the green emission band, the peak position shows a small blue-shift, the width turns broader, and the intensity grows first stronger and then weaker; for the UV emission band, the peak position exhibits a significant red-shift, and the width and intensity have the similar behaviors with those of the green band. Additionally, the relative intensity of green emission to UV emission decreases gradually. It is clarified that the origin of this abnormal phenomenon is as-cribed to the local laser heating effect and the high sensitivity of nanostructures to this heating effect.

  11. Effect of excitation intensity on fluorescence spectra in ZnO nanostructures and its origin

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    ZnO nanostructures with three kinds of morphologies, namely,tetrapod-,rod-,and sheet-like shape, are synthesized by chemical vapor deposition, conventional solution-phase,and hydrothermal methods, respectively.The fluorescence measurements display that the spectra of these nanostructures exhibit similar unexpected change laws with the altering excitation intensity. It is observed that when the excitation intensity increases, for the green emission band,the peak position shows a small blue-shift, the width turns broader,and the intensity grows first stronger and then weaker;for the UV emission band, the peak position exhibits a significant red-shift,and the width and intensity have the similar behaviors with those of the green band.Additionally,the relative intensity of green emission to UV emission decreases gradually.It is clarified that the origin of this abnormal phenomenon is ascribed to the local laser heating effect and the high sensitivity of nanostructures to this heating effect.

  12. Computation and interpretation of vibrational spectra on the structure of Losartan using ab initio and Density Functional methods

    Science.gov (United States)

    Latha, B.; Gunasekaran, S.; Srinivasan, S.; Ramkumaar, G. R.

    2014-11-01

    The solid phase FTIR and FT-Raman spectra of Losartan have been recorded in the region 400-4000 cm-1. The spectra were interpreted in terms of fundamental modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by Quantum chemical methods. The vibrational frequencies yield good agreement between observed and calculated values. The infrared and Raman spectra were also predicted from the calculated intensities. (1)H and (13)C NMR spectra were recorded and resonance chemical shifts of the molecule were calculated. UV-Visible spectrum of the compound was recorded in the region 200-600 nm and the electronic properties HOMO and LUMO energies calculated by TD-HF approach. NBO atomic charges of the molecules and second order perturbation theory analysis of Fock matrix also calculated and interpreted. The geometrical parameters, energies, harmonic vibrational frequencies, IR intensities, Raman intensities, and absorption wavelengths were compared with experimental and theoretical data of the molecule.

  13. Effects of high pressure on the Raman and fluorescence emission spectra of two novel 1,3,4-oxadiazole derivatives

    Institute of Scientific and Technical Information of China (English)

    Luo Ji-Feng; Tang Ben-Chen; Gao Chun-Xiao; Li Min; Han Yong-Hao; Zou Guang-Tian

    2005-01-01

    The effects of pressure on the fluorescence emission and Raman spectra of 1,4-bis[(4-methyloxyphenyl)-1,3,4-oxadiazolyl]- 2,5-bisheptyloxyphenylene (OXD-2) and on the fluorescence emission spectra of 1,4-bis[(4-methylphenyl)-1,3,4-oxadiazolyl]phenylene (OXD-1) are investigated using a diamond anvil cell. With the increase of pressure, the intensity of the fluorescence emission increases and reaches maxima at 13GPa for OXD-1 and at 9.6GPa for OXD-2.The effect of pressure on the peak position of the emission shows a similar trend, red shift with the increase of pressure.But at higher pressures, the intensity of emission drops down dramatically. The Raman spectra of OXD-2 indicate that there appears a structural change at ca 3GPa.

  14. Theoretical vibrational spectra and thermodynamics of organic semiconductive tetrathiafulvalene and its cation radical.

    Science.gov (United States)

    Mukherjee, V; Singh, N P

    2014-01-03

    Molecular structure in optimum geometry and vibrational frequencies of pentafulvalene [bicyclopentyliden-2,4,2',4'-tetraene], tetrathiafulvalene [2,2'-bis(1,3-dithiolylidene)] and its cation are calculated. All the calculations are carried out by employing density functional theory incorporated with a suitable basis set. Normal coordinate analysis is also employed to scale the DFT calculated frequencies and to calculate potential energy distributions. The molecular structures and vibrational frequencies are compared for both the pentafulvalene and tetrathiafulvalene molecules. The effect upon geometry and vibrational frequencies of TTF due to charge transfer has also been studied. The vibrational partition function and hence, the thermodynamical properties, such as Helmholtz free energy, entropy, specific heat at constant volume and enthalpy are also calculated and compared for the title molecules. The reason of conductivity of tetrathiafulvalene has been tried to explain on the basis of molecular geometry and normal modes. Study of vibrational partition function exhibits that below 109 K, PFV starts to condense.

  15. Infrared and vibrational CD spectra of partially solvated alpha-helices: DFT-based simulations with explicit solvent.

    Science.gov (United States)

    Turner, David R; Kubelka, Jan

    2007-02-22

    Theoretical simulations are used to investigate the effects of aqueous solvent on the vibrational spectra of model alpha-helices, which are only partly exposed to solvent to mimic alpha-helices in proteins. Infrared absorption (IR) and vibrational circular dichroism (VCD) amide I' spectra for 15-amide alanine alpha-helices are simulated using density functional theory (DFT) calculations combined with the property transfer method. The solvent is modeled by explicit water molecules hydrogen bonded to the solvated amide groups. Simulated spectra for two partially solvated model alpha-helices, one corresponding to a more exposed and the other to a more buried structure, are compared to the fully solvated and unsolvated (gas phase) simulations. The dependence of the amide I spectra on the orientation of the partially solvated helix with respect to the solvent and effects of solvation on the amide I' of 13C isotopically substituted alpha-helices are also investigated. The partial exposure to solvent causes significant broadening of the amide I' bands due to differences in the vibrational frequencies of the explicitly solvated and unsolvated amide groups. The different degree of partial solvation is reflected primarily in the frequency shifts of the unsolvated (buried) amide group vibrations. Depending on which side of the alpha-helix is exposed to solvent, the simulated IR band-shapes exhibit significant changes, from broad and relatively featureless to distinctly split into two maxima. The simulated amide I' VCD band-shapes for the partially solvated alpha-helices parallel the broadening of the IR and exhibit more sign variation, but generally preserve the sign pattern characteristic of the alpha-helical structures and are much less dependent on the alpha-helix orientation with respect to the solvent. The simulated amide I' IR spectra for the model peptides with explicitly hydrogen-bonded water are consistent with the experimental data for small alpha-helical proteins

  16. [Excitation-Emission Matrix Fluorescence Spectra Characteristics of DOM in Integrated Verical Flow Constructed Wetland for Treating Eutrophic Water].

    Science.gov (United States)

    Li, Shu-juan; Ge, Li-yun; Deng, Huan-huan

    2015-04-01

    Three-dimensional fluorescence parameters can reflect classification, properties and content change of pollutants in wastewater treatment. In the present paper, by using three-dimensional fluorescence characteristic analysis, comparative analysis of conventional organic pollutants such as COD, TN and TP, and three dimensional fluorescence spectrum analysis, the classification and content of dissolved organic pollutants were identified. We studied fluorescence spectra, fluorescence peak (R. U.), fluorescence index (FI), humification index (HIX) of DOM's four components in the entrance and effluent water and interstitial water, as well as the correlation between these four components and COD, TN and TP. The results showed that the position and intensity of the characteristic fluorescence peak center changed significantly before and after sewage treatment, indicating that the relative composition and content of the organic wastewater varied with wastewater treatment. Furthermore, the test results presented that humic-like composition was not degraded significantly, while protein-like composition was degraded significantly. And the protein-like component and COD, TN and TP presented significant positive correlation. This paper analyzed the fluorescence characteristics changes of dissolved organic matter in sewage treatment by using three-dimensional fluorescence spectrometry, and discussed the feasibility of three-dimensional fluorescence technique applied for description of dissolved organic pollutant degradation rule in the wastewater treatment process.

  17. Correlation of structure and vibrational spectra of the zwitterion ?-alanine in the presence of water: an experimental and density functional analysis

    Science.gov (United States)

    Ellzy, Michael W.; Jensen, James O.; Hameka, Hendrik F.; Kay, Jack G.

    2003-09-01

    Infrared vibrational spectra were collected along with the vibrational circular dichroism (VCD) spectra for the zwitterions α- D-alanine, α- L-alanine, α- D-mannose and α- L-mannose as potassium bromide (KBr) pressed samples. VCD for D- and L-alanine dissolved in water was also measured and compared against the spectra resulting from KBr pressed samples. The experimental data were compared against the ab initio B3LYP/6-31G* optimized geometry. The zwitterion structure of α- L-alanine was stabilized by the addition of water molecules. Computationally, β- L-mannose was studied and resulting expected VCD bands assigned. We present the molecular structures resulting VCD spectra and infrared vibrational spectra from experimentation as compared with the computed results.

  18. Infrared vibration-rotation spectra of the ClO radical using tunable diode laser spectroscopy. [ozone destruction in stratosphere

    Science.gov (United States)

    Rogowski, R. S.; Bair, C. H.; Wade, W. R.; Hoell, J. M.; Copeland, G. E.

    1978-01-01

    Tunable diode laser spectroscopy is used to measure the infrared vibration-rotation spectra of the ClO radical. The radical is generated in a flow system where a Cl2-He mixture passes through a microwave discharge to dissociate the Cl2. An O3-O2 mixture from an ozone generator is injected into the system downstream of the microwave discharge where O3 combines with Cl to form ClO. By adjusting the gas flow rates to yield an excess of Cl atoms, all the ozone is combined. ClO concentration is measured with UV absorption at 2577 and 2772 A and a deuterium lamp as a continuous source. Total cell pressure is 5.5 torr. The diode laser spectrometer is calibrated with ammonia lines as a reference where possible. The frequency of vibration-rotation lines is expressed as a function of rotational quantum number, fundamental vibrational frequency, and the rotational constants of the upper and lower vibrational states.

  19. Vibrational spectra and normal coordinate analysis on structure of chlorambucil and thioguanine

    Indian Academy of Sciences (India)

    S Gunasekaran; S Kumaresan; R Arun Balaji; G Anand; S Seshadri

    2008-12-01

    A normal coordinate analysis on chlorambucil and thioguanine has been carried out with a set of symmetry coordinates following Wilson's – matrix method. The potential constants evaluated for these molecules are found to be in good agreement with literature values thereby confirming the vibrational assignments. To check whether the chosen set of vibrational frequencies contribute maximum to the potential energy associated with the normal coordinates of the molecule, the potential energy distribution has been evaluated.

  20. Vibrational spectra and DFT calculations of the vibrational modes of Schiff base C18H17N3O2

    Science.gov (United States)

    Antunes, J. A.; Silva, L. E.; Bento, R. R. F.; Teixeira, A. M. R.; Freire, P. T. C.; Faria, J. L. B.; Ramos, R. J.; Silva, C. B.; Lima, J. A.

    2012-04-01

    The Schiff base 4-{[(1E)-(2-Hydroxyphenyl)methylidene]amino}-1,5-dimethyl-2-phenyl-1,2-dihydro-3H-pyrazol-3-one (C18H17N3O2) is a synthetic compound with a variety of scientific and technological applications, such as clinic, analytic and pharmacologic. In this work FT-Raman spectrum and FT-infrared spectrum of C18H17N3O2 were investigated at 300 K. Vibrational wavenumber and wave vector have been predicted using Density Functional Theory (B3LYP) calculations with the 6-31 G(d,p) basis set. The description of the normal modes was performed by means of the potential energy distribution. A comparison with experiment allowed us to assign most of the normal modes of the crystal.

  1. Comparison of different eigensolvers for calculating vibrational spectra using low-rank, sum-of-product basis functions

    CERN Document Server

    Leclerc, Arnaud; Carrington, Tucker

    2016-01-01

    Vibrational spectra and wavefunctions of polyatomic molecules can be calculated at low memory cost using low-rank sum-of-product (SOP) decompositions to represent basis functions generated using an iterative eigensolver. Using a SOP tensor format does not determine the iterative eigensolver. The choice of the interative eigensolver is limited by the need to restrict the rank of the SOP basis functions at every stage of the calculation. We have adapted, implemented and compared different reduced-rank algorithms based on standard iterative methods (block-Davidson algorithm, Chebyshev iteration) to calculate vibrational energy levels and wavefunctions of the 12-dimensional acetonitrile molecule. The effect of using low-rank SOP basis functions on the different methods is analyzed and the numerical results are compared with those obtained with the reduced rank block power method introduced in J. Chem. Phys. 140, 174111 (2014). Relative merits of the different algorithms are presented, showing that the advantage o...

  2. Computational Study of Absorption Spectra of the Photoconvertible Fluorescent Protein EosFP in Different Protonation States.

    Science.gov (United States)

    Imhof, Petra

    2012-11-13

    Absorption spectra of the green-to-red convertible fluorescent protein EosFP have been computed in a hybrid quantum mechanical/molecular mechanical (QM/MM) framework. The experimentally observed absorption maximum at ∼390 nm is well reproduced by the protein with a neutral chromophore, and the anionic form is computed to absorb close to the experimentally determined maximum at ∼500 nm. Absorption of a zwitterionic form is calculated to lie in the same spectral region; however, this species cannot be unambiguously assigned to the experimental spectra. Variation of the protonation states of residues surrounding the chromophore do not have significant impact on the positions of the absorption maxima. In particular, protonation of Glu212 leaves the calculated spectra largely unaffected. This is consistent with the spectra of the E212Q mutant, which differ from the wild-type spectra only in the intensities but not in the positions of the absorption bands.

  3. Franck-Condon profiles in photodetachment-photoelectron spectra of ? and ? based on vibrational configuration interaction wavefunctions

    Science.gov (United States)

    Huh, Joonsuk; Neff, Michael; Rauhut, Guntram; Berger, Robert

    2010-02-01

    Explicitly electron correlating coupled cluster calculations, CCSD(T)-F12a, were performed to determine three-dimensional potential energy hypersurfaces of disulphanide and disulphanyl in an automated approach. Surfaces for different electronic states were used in a Watson rovibrational Hamiltonian ansatz to obtain the correlated anharmonic vibrational wavefunctions. Subsequently the anharmonic Franck-Condon overlap integrals were evaluated. The computed Franck-Condon profiles were compared to experimental photodetachment-photoelectron spectra and confirm essentially the assignments made previously. The profiles indicate, however, additional weaker, and as of yet unresolved, additional features.

  4. Investigation on the spectral properties of 2D asynchronous fluorescence spectra generated by using variable excitation wavelengths as a perturbation

    Science.gov (United States)

    Wang, Jingdan; He, Anqi; Guo, Ran; Wei, Yongju; Feng, Juan; Xu, Yizhuang; Noda, Isao; Wu, Jinguang

    2016-11-01

    Properties of 2D asynchronous spectra generated from a series of fluorescence emission spectra are investigated. Variable excitation wavelengths are utilized as an external perturbation. Based on the results of mathematical analysis and computer simulation, we find that no cross peak will be produced on the 2D asynchronous spectrum if the fluorescent solute under investigation occurs in a single micro-environment. The observation of cross peaks implies that the fluorescent molecule may occur in different micro-environments in a solution. Based on these results, we use 2D asynchronous spectra to investigate the emission spectra of anthracene dissolved in cyclohexane. When the concentration of anthracene is low, no cross peak is produced in the resultant 2D asynchronous spectrum, confirming that anthracene is dissolved as single molecule in the solution. As the concentration elevated, cross peaks appear in the corresponding 2D asynchronous spectra. A plausible explanation of this phenomenon is that anthracene may undergo aggregation via π-π interaction or π-C-H interaction.

  5. Study of vibrational spectra of NH sub 4 Cl and NH sub 4 Br at high pressure

    CERN Document Server

    Glazkov, V P; Syrykh, G F; Kozlenko, D P; Savenko, B N; Telepnev, A S

    2002-01-01

    The NH sub 4 Cl vibrational spectra at the pressures up to 2.6 GPa and the NH sub 4 Br spectra at the pressures up to 7 GPa are studied through the method of the neutrons inelastic incoherent scattering. It is established that the linear baric dependence of the libration mode changes its inclination in the area above the pressure of transition from the disordered cubic phase to the ordered cubic phase with the CsCl-type structure. The baric dependence inclination of the cross-sectional optical translation mode remains unchanged. The evaluations of the Grueneisen parameters are presented in the one-dimensional approximation and the form of the potential function for the libration oscillations in the disordered and ordered cubic phases with the CsCl-type structure is calculated. It is shown that the observed effects are related to the high anharmonism of the potential in the disordered phase

  6. Regio-Regular Oligo and Poly(3-hexyl thiophene): Precise Structural Markers from the Vibrational Spectra of Oligomer Single Crystals.

    KAUST Repository

    Brambilla, Luigi

    2014-10-14

    © 2014 American Chemical Society. In this work, we report a comparative analysis of the infrared and Raman spectra of octa(3-hexylthiophene) (3HT)8, trideca(3-hexylthiophene) (3HT)13, and poly(3-hexylthiophene) P3HT recorded in various phases, namely, amorphous, semicrystalline, polycrystalline and single crystal. We have based our analysis on the spectra of the (3HT)8 single crystal (whose structure has been determined by selected area electron diffraction) taken as reference and on the results of DFT calculations and molecular vibrational dynamics. New and precise spectroscopic markers of the molecular structures show the existence of three phases, namely: hairy (phase 1), ordered (phase 2), and disordered/amorphous (phase 3). Conceptually, the identified markers can be used for the molecular structure analysis of other similar systems.

  7. Vibrational spectra and the structure peculiarity of TiO2 different polycrystalline forms

    Science.gov (United States)

    Shimanovskaya, V. V.; Khalyavka, T. A.; Puchkovska, Galina A.; Bezrodna, T. V.; Strelko, V. V.; Veblaya, T. S.; Baran, J.; Ratajczak, H.

    2002-12-01

    Particularly pure samples of titanium dioxide with a different crystalline structure and a different construction of TiO2 polycrystaline particles which were produced by thermal hydrolysis of TiCl4 hydrochloric acid solutions, were studied by methods of IR and Raman spectroscopy. The assignment of IR and Raman spectral bands to vibrations of different symmetry types has been performed. In accordance with positions and half-width of Raman lattice vibrational band 'ν=143 cm-1'. The stoichiometric composition estimation of TiO2 different crystalline phases has been carried out according to data obtained about the position and half-width of the lattice Raman vibrational band. The intensity and frequency of IR bands in the region of 1250-900 cm-1 were shown to be sensitive to a type of TiO2 crystalline composition and to the physically adsorbed water content.

  8. Theoretical study of potential energy surface and vibrational spectra of ArF2 system

    Institute of Scientific and Technical Information of China (English)

    杨明晖; 谢代前; 鄢国森

    2000-01-01

    An ab initio potential energy surface (PES) of ArF2 system has been obtained by using MP4 calculation with a large basis set including bond functions. There are two local minimums on the PES: one is T-shaped and the other is L-shaped. The L-shaped minimum is the global minimum with a well depth of -119.62 cm- 1 at R = 0.3883nm. The T-shaped minimum has a well depth of -85.93cm -1 at R = 0.3486 nm. A saddle point is found at R = 0.3486 and θ = 61° with the well depth of -61.53 cm-1. The vibrational energy levels have been calculated by using VSCF-CI method. The results show that this PES supports 27 vibrational bound states, and the ground states are two degenerate states assigned to the L-type vibration.

  9. Theoretical study of potential energy surface and vibrational spectra of ArF2 system

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    An ab initio potential energy surface (PES) of ArF2 system has been obtained by using MP4 calculation with a large basis set including bond functions. There are two local minimums on the PES: one is T-shaped and the other is L-shaped. The L-shaped minimum is the global minimum with a well depth of -119.62 cm-1 at R = 0.3883nm. The T-shaped minimum has a well depth of -85.93cm-1 at R = 0.3486 nm. A saddle point is found at R = 0.3486 and q = 61° with the well depth of -61.53 cm-1. The vibrational energy levels have been calculated by using VSCF-CI method. The results show that this PES supports 27 vibrational bound states, and the ground states are two degenerate states assigned to the L-type vibration.

  10. FT-IR, FT-Raman, UV/Vis spectra and fluorescence imaging studies on 2-(bromoacetyl)benzo(b)furan by ab initio DFT calculations.

    Science.gov (United States)

    Veeraiah, A

    2015-08-05

    The vibrational and electronic properties of 2-(bromoacetyl)benzo(b)furan have been studied in the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-31G(d,p) basis set. The theoretically calculated optimized parameters, vibrational frequencies etc., were compared with the experimental values, which yield good agreement between the observed and calculated values. The complete assignments of fundamental modes were performed on the basis of the potential energy distribution (PED). UV-visible spectrum of the compound was recorded in the region 300-600 nm and compared with the theoretical spectrum obtained from SAC-CI calculations. A good agreement is observed between the experimental and theoretical spectra. Fluorescence microscopic imaging studies proved that the compound can be used as one of the potential light sources in the yellow region with suitable excitation. Further, the predicted electronic transitions between the MOs 47→64, 52→62, 56→65, 56→72, 56→77 of the compound show a strong line at 569.8 nm. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Chemometric modelling based on 2D-fluorescence spectra without a calibration measurement.

    Science.gov (United States)

    Solle, D; Geissler, D; Stärk, E; Scheper, T; Hitzmann, B

    2003-01-22

    2D fluorescence spectra provide information from intracellular compounds. Fluorophores like trytophan, tyrosine and phenylalanin as well as NADH and flavins make the corresponding measurement systems very important for bioprocess supervision and control. The evaluation is usually based on chemometric modelling using for their calibration procedure off-line measurements of the desired process variables. Due to the data driven approach lots of off-line measurements are required. Here a methodology is presented, which enables to perform a calibration procedure of chemometric models without any further measurement. The necessary information for the calibration procedure is provided by means of the a priori knowledge about the process, i.e. a mathematical model, whose model parameters are estimated during the calibration procedure, as well as the fact that the substrate should be consumed at the end of the process run. The new methodology for chemometric calibration is applied for a batch cultivation of aerobically grown S. cerevisiae on the glucose Schatzmann medium. As will be presented the chemometric models, which are determined by this method, can be used for prediction during new process runs. The MATHLAB routine is free available on request from the authors.

  12. Quantum-mechanical study of energies, structures, and vibrational spectra of the H(D)Cl complexed with dimethyl ether

    Energy Technology Data Exchange (ETDEWEB)

    Boda, Łukasz, E-mail: lboda@chemia.uj.edu.pl; Boczar, Marek; Gług, Maciej; Wójcik, Marek J. [Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków (Poland)

    2015-11-28

    Interaction energies, molecular structure and vibrational frequencies of the binary complex formed between H(D)Cl and dimethyl ether have been obtained using quantum-chemical methods. Equilibrium and vibrationally averaged structures, harmonic and anharmonic wavenumbers of the complex and its deuterated isotopomer were calculated using harmonic and anharmonic second-order perturbation theory procedures with Density Functional Theory B3LYP and B2PLYP-D and ab initio Møller-Plesset second-order methods, and a 6-311++G(3d,3p) basis set. A phenomenological model describing anharmonic-type vibrational couplings within hydrogen bonds was developed to explain the unique broadening and fine structure, as well as the isotope effect of the Cl–H and Cl–D stretching IR absorption bands in the gaseous complexes with dimethyl ether, as an effect of hydrogen bond formation. Simulations of the rovibrational structure of the Cl–H and Cl–D stretching bands were performed and the results were compared with experimental spectra.

  13. Density functional theory calculations of the molecular structure and the vibrational spectra of bis-tetrapropyl-ammonium hexachloro-dizincate

    Science.gov (United States)

    Ben Gzaiel, M.; Oueslati, A.; Chaabane, I.; Gargouri, M.

    2016-10-01

    The molecular structure and vibrational spectra of bis-tetrapropyl-ammonium hexachloro-dizincate in the ground state have been investigated by density functional method (DFT) using the B3LYP method with the LanL2DZ and LanL2MB basis set. Infrared and Raman spectroscopes of the [N(C3H7)4]2Zn2Cl6 compound have been measured at room temperature in the frequencies range (3500-400 cm-1) and (3500-100 cm-1), respectively. The optimized geometric shows that the calculated values obtained by B3LYP/LanL2DZ basis are in much better agreement with the experimental data than those obtained by B3LYP/LanL2MB. Actually the theoretical vibrational spectra (B3LYP/LanL2DZ) of the title compound have been interpreted by means of potential energy distribution (PED) which is in good agreement with the experimental data. The comparison of the infrared spectrum of the tetrapropyl-ammonium chloride ligand with those of the bis-tetrapropyl-ammonium hexachloro-dizincate compound confirms an increase of the wavenumber in the [N(C3H7)4]2Zn2Cl6 compound. This can be explained by an increase of the electrostatic interactions of the [N(C3H7)4]Cl ligand.

  14. Vibrational spectra of an RDX film over an aluminum substrate from molecular dynamics simulations and density functional theory.

    Science.gov (United States)

    Martínez de la Hoz, Julibeth M; Balbuena, Perla B

    2013-07-01

    We report calculated vibrational spectra in the range of 0-3,500 cm(-1) of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) molecules adsorbed on a model aluminum surface. A molecular film was modeled using two approaches: (1) density functional theory (DFT) was used to optimize a single RDX molecule interacting with its periodic images, and (2) a group of nine molecules extracted from the crystal structure was deposited on the surface and interacted with its periodic images via molecular dynamics (MD) simulations. In both cases, the molecule was initialized in the AAA conformer geometry having the three nitro groups in axial positions, and kept that conformation in the DFT examination, but some molecules were found to change to the AAE conformer (two nitro groups in axial and one in equatorial position) in the MD analysis. The vibrational spectra obtained from both methods are similar to each other, except in the regions where collective RDX intermolecular interactions (captured by MD simulations) are important, and compare fairly well with experimental findings.

  15. A strong NH…Br vibrational behaviour studied through X-ray, vibrational spectra and quantum chemical studies in an isomorphous crystal: 2-Nitroanilinium bromide.

    Science.gov (United States)

    Anitha, R; Athimoolam, S; Gunasekaran, M

    2015-03-05

    A needle shaped transparent light brown crystals of 2-nitroanilinium bromide were successfully synthesized and crystallized from an aqueous mixture by slow evaporation technique. Single crystal XRD studies confirm the crystalline phase of this isomorphous compound which contains a positively charge 2-nitroanilinium cation and a negatively charged bromide anion. The solid phase FT-IR and FT-Raman spectra of the compound have been recorded in the range of 4000-400cm(-1). The observed modes are correlated by the factor group theory analysis and different IR and Raman active species were identified. Geometrical optimisations were carried out and harmonic vibrational wave numbers were computed for the minimum energy molecular structure at RHF level invoking 6-311++G(d,p) and SDD basis sets. Optimised molecular geometry was compared with the crystallographic data. The calculated wavenumbers were compared with the experimental values. The NH vibrational bands are shifted from its normal range and the shifting is associated with the influence of the intermolecular hydrogen bonds in the crystal. A strong intensity peak in theoretical and corresponding band in experimental confirms the presence of NH…Br interaction as predicted in crystalline state.

  16. Binding phenomena and fluorescence quenching. II: Photophysics of aromatic residues and dependence of fluorescence spectra on protein conformation

    Science.gov (United States)

    Callis, Patrik R.

    2014-12-01

    The three amino acids with aromatic ring side chains-phenylalanine (Phe), tyrosine (Tyr), and especially tryptophan (Trp) have played a long and productive role in helping unlock the secrets of protein behavior by optical spectroscopy (absorption, fluorescence, circular dichroism, etc.) In principle, an appropriately placed Trp will undergo fluorescence wavelength and/or intensity changes upon whatever functional process a protein performs. Although perceived to be enigmatic and not well understood, Trp is arguably now better understood than many of the extrinsic probes currently in use. Basic principles of intrinsic tryptophan fluorescence quenching and wavelength shifts in proteins are presented, with strong emphasis on the importance of electrostatics. The condensed description of findings from recent experiments and simulations of tryptophan fluorescence and intrinsic quenching in proteins is designed to help authors in planning and interpreting experimental results of ligand binding studies.

  17. Vibrational spectra and fragmentation pathways of size-selected, D2-tagged ammonium/methylammonium bisulfate clusters.

    Science.gov (United States)

    Johnson, Christopher J; Johnson, Mark A

    2013-12-19

    Particles consisting of ammonia and sulfuric acid are widely regarded as seeds for atmospheric aerosol nucleation, and incorporation of alkylamines has been suggested to substantially accelerate their growth. Despite significant efforts, little direct experimental evidence exists for the structures and chemical processes underlying multicomponent particle nucleation. Here we are concerned with the positively charged clusters of ammonia and sulfuric acid with compositions H(+)(NH3)m(H2SO4)n (2 ≤ m ≤ 5, 1 ≤ n ≤ 4), for which equilibrium geometry structures have been reported in recent computational searches. The computed harmonic vibrational spectra of such minimum energy structures can be directly compared with the experimental spectra of each cluster composition isolated in the laboratory using cryogenic ion chemistry methods. We present one-photon (i.e., linear) infrared action spectra of the isolated gas phase ions cryogenically cooled to 10 K, allowing us to resolve the characteristic vibrational signatures of these clusters. Because the available calculated spectra for different structural candidates have been obtained using different levels of theory, we reoptimized the previously reported structures with several common electronic structure methods and find excellent agreement can be achieved for the (m = 3, n = 2) cluster using CAM-B3LYP with only minor structural differences from the previously identified geometries. At the larger sizes, the experimental spectra strongly resemble that observed for 180 nm ammonium bisulfate particles. The characteristic ammonium- and bisulfate-localized bands are clearly evident at all sizes studied, indicating that the cluster structures are indeed ionic in nature. With the likely (3,2) structure in hand, we then explore the spectral and structural changes caused when methylamine is substituted for ammonia. This process is found to occur with minimal perturbation of the unsubstituted cluster. The thermal

  18. Analyzing pH-induced changes in a myofibril model system with vibrational and fluorescence spectroscopy.

    Science.gov (United States)

    Andersen, Petter Vejle; Veiseth-Kent, Eva; Wold, Jens Petter

    2017-03-01

    The decline of pH and ultimate pH in meat postmortem greatly influences meat quality (e.g. water holding capacity). Four spectroscopic techniques, Raman, Fourier transform infrared (FT-IR), near infrared (NIR) and fluorescence spectroscopy, were used to study protein and amino acid modifications to determine pH-related changes in pork myofibril extracts at three different pH-levels, 5.3, 5.8 and 6.3. Protonation of side-chain carboxylic acids of aspartic and glutamic acid and changes in secondary structure, mainly the amide I-III peaks, were the most important features identified by Raman and FT-IR spectroscopy linked to changes in pH. Fluorescence spectroscopy identified tryptophan interaction with the molecular environment as the most important contributor to changes in the spectra. NIR spectroscopy gave no significant contributions to interpreting protein structure related to pH. Results from our study are useful for interpreting spectroscopic data from meat where pH is an important variable.

  19. Influence of weak vibrational-electronic couplings on 2D electronic spectra and inter-site coherence in weakly coupled photosynthetic complexes

    Energy Technology Data Exchange (ETDEWEB)

    Monahan, Daniele M.; Whaley-Mayda, Lukas; Fleming, Graham R., E-mail: grfleming@lbl.gov [Department of Chemistry, University of California, Berkeley, California 94720 (United States); Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Kavli Energy NanoSciences Institute at Berkeley, Berkeley, California 94720 (United States); Ishizaki, Akihito [Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585 (Japan)

    2015-08-14

    Coherence oscillations measured in two-dimensional (2D) electronic spectra of pigment-protein complexes may have electronic, vibrational, or mixed-character vibronic origins, which depend on the degree of electronic-vibrational mixing. Oscillations from intrapigment vibrations can obscure the inter-site coherence lifetime of interest in elucidating the mechanisms of energy transfer in photosynthetic light-harvesting. Huang-Rhys factors (S) for low-frequency vibrations in Chlorophyll and Bacteriochlorophyll are quite small (S ≤ 0.05), so it is often assumed that these vibrations influence neither 2D spectra nor inter-site coherence dynamics. In this work, we explore the influence of S within this range on the oscillatory signatures in simulated 2D spectra of a pigment heterodimer. To visualize the inter-site coherence dynamics underlying the 2D spectra, we introduce a formalism which we call the “site-probe response.” By comparing the calculated 2D spectra with the site-probe response, we show that an on-resonance vibration with Huang-Rhys factor as small as S = 0.005 and the most strongly coupled off-resonance vibrations (S = 0.05) give rise to long-lived, purely vibrational coherences at 77 K. We moreover calculate the correlation between optical pump interactions and subsequent entanglement between sites, as measured by the concurrence. At 77 K, greater long-lived inter-site coherence and entanglement appear with increasing S. This dependence all but vanishes at physiological temperature, as environmentally induced fluctuations destroy the vibronic mixing.

  20. Vibrational spectra and density functional theoretical calculations on the anti-neurodegenerative drug: Orphenadrine hydrochloride.

    Science.gov (United States)

    Edwin, Bismi; Hubert Joe, I

    2012-11-01

    Vibrational spectral analysis and quantum chemical computations based on density functional theory have been performed on the anti-neuro-degenerative drug Orphenadrine hydrochloride. The geometry, intermolecular hydrogen bond, and harmonic vibrational frequencies of the title molecule have been investigated with the help of B3LYP method. The calculated molecular geometry has been compared with the experimental data. The various intramolecular interactions have been exposed by natural bond orbital analysis. The distribution of Mulliken atomic charges and bending of natural hybrid orbitals also reflect the presence of intramolecular hydrogen bonding. The analysis of the electron density of HOMO and LUMO gives an idea of the delocalization and low value of energy gap indicates electron transport in the molecule and thereby bioactivity. Effective docking of the drug molecule with NMDA receptor subunit 3A also enhances its bioactive nature. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. A Monte Carlo calculation of subexcitation and vibrationally-relaxing electron spectra in irradiated liquid water

    Energy Technology Data Exchange (ETDEWEB)

    Cobut, V.; Frongillo, Y.; Jay-Gerin, J.-P. (Sherbrooke Univ., PQ (Canada). Faculte de Medecine); Patau, J.-P. (Toulouse-3 Univ., 31 (France))

    1992-12-01

    An energy spectrum of ''subexcitation electrons'' produced in liquid water by electrons with initial energies of a few keV is obtained by using a Monte Carlo transport simulation calculation. It is found that the introduction of vibrational-excitation cross sections leads to the appearance of a sharp peak in the probability density function near the electronic-excitation threshold. Electrons contributing to this peak are shown to be more naturally described if a novel energy spectrum, that we propose to name ''vibrationally-relaxing electron'' spectrum, is introduced. The corresponding distribution function is presented, and an empirical expression of it is given. (author).

  2. Electronic spectra of 2- and 3-tolunitrile in the gas phase. II. Geometry changes from Franck-Condon fits of fluorescence emission spectra

    Science.gov (United States)

    Gmerek, Felix; Stuhlmann, Benjamin; Álvarez-Valtierra, Leonardo; Pratt, David W.; Schmitt, Michael

    2016-02-01

    We determined the changes of the geometries of 2- and 3-tolunitrile upon excitation to the lowest excited singlet states from Franck-Condon fits of the vibronic intensities in several fluorescence emission spectra and of the rotational constant changes upon excitation. These structural changes can be connected to the altered electron distribution in the molecules and are compared to the results of ab initio calculations. We show how the torsional barriers of the methyl groups in both components are used as probe of the molecular changes upon electronic excitation.

  3. Vibrational spectra of trimethylsilanol. The problem of the assignment of the SiOH group frequencies.

    Science.gov (United States)

    Ignatyev, Igor S; Partal, F; López González, J J; Sundius, Tom

    2004-04-01

    The assignment of the SiOH group vibrations of trimethylsilanol, which is still controversial, is proposed. This assignment is based on theoretical B3LYP force field scaled using the constants of the (CH3)3Si group optimized to fit experimental vibrational frequencies of (CH3)3SiF and (CD3)3SiF molecules as well as the OH stretching scale factor from methanol. The ab initio force field defined in this way gives a good agreement of the theoretical vibrational frequencies of trimethylsilanol with the positions of IR and Raman bands observed in the gas phase. This force field predicts the greatest contribution of the delta SiOH coordinates to the vibration with frequency of 804 cm(-1). The elimination of the coupling of the SiOH deformation with methyl rocking modes by the normal coordinate treatment of (CD3)3SiOH gives 832 cm(-1) for silanol deformation which is in a good agreement with the 834 cm(-1) value proposed earlier for the bending mode of free silanol groups. The geometry and force field of the open chain H3SiOH trimer is computed to model the change of the delta SiOH frequencies upon formation of the hydrogen-bonded polymers. This model predicts a significant shift of SiOH bending frequencies to the 1000-1200 cm(-1) range while those of SiOD to the 800-850 cm(-1) range. These predictions allow us to ascribe the 1087 cm(-1) band observed in the IR spectrum of crystalline (CH3)3SiOH and the Raman 775 cm(-1) band of the liquid (CH3)3SiOD to deformations of the hydrogen-bonded silanol groups. Copyright 2003 Elsevier B.V.

  4. A-VCI: A flexible method to efficiently compute vibrational spectra.

    Science.gov (United States)

    Odunlami, Marc; Le Bris, Vincent; Bégué, Didier; Baraille, Isabelle; Coulaud, Olivier

    2017-06-07

    The adaptive vibrational configuration interaction algorithm has been introduced as a new method to efficiently reduce the dimension of the set of basis functions used in a vibrational configuration interaction process. It is based on the construction of nested bases for the discretization of the Hamiltonian operator according to a theoretical criterion that ensures the convergence of the method. In the present work, the Hamiltonian is written as a sum of products of operators. The purpose of this paper is to study the properties and outline the performance details of the main steps of the algorithm. New parameters have been incorporated to increase flexibility, and their influence has been thoroughly investigated. The robustness and reliability of the method are demonstrated for the computation of the vibrational spectrum up to 3000 cm(-1) of a widely studied 6-atom molecule (acetonitrile). Our results are compared to the most accurate up to date computation; we also give a new reference calculation for future work on this system. The algorithm has also been applied to a more challenging 7-atom molecule (ethylene oxide). The computed spectrum up to 3200 cm(-1) is the most accurate computation that exists today on such systems.

  5. Molecular structure, vibrational spectra and DFT computational studies of melaminium N-acetylglycinate dihydrate

    Science.gov (United States)

    Tanak, H.; Pawlus, K.; Marchewka, M. K.

    2016-10-01

    Melaminium N-acetylglycinate dihydrate, an organic material has been synthesized and characterized by X-ray diffraction, FT-IR, and FT-Raman spectroscopies for the protiated and deuteriated crystals. The title complex crystallizes in the triclinic system, and the space group is P-1 with a = 5.642(1) Å, b = 7.773(2) Å, c = 15.775(3) Å, α = 77.28(1)°, β = 84.00(1)°, γ = 73.43(1)° and Z = 2. The molecular geometry, vibrational frequencies and intensity of the vibrational bands have been interpreted with the aid of structure optimization based on density functional method (B3LYP) with the 6-311++G(d,p) basis set. The obtained vibrational wavenumbers and optimized geometric parameters were seen to be in good agreement with the experimental data. The intermolecular hydrogen bonding interactions of the title compound have been investigated using the natural bonding orbital analysis. It reveals that the O-H···O, N-H···N and N-H···O intermolecular interactions significantly influence crystal packing of this molecule. The non-linear optical properties are also addressed theoretically. The predicted NLO properties of the title compound are much greater than ones of urea. In addition, DFT calculations of the title compound, molecular electrostatic potential, thermodynamic properties, frontier orbitals and chemical reactivity descriptors were also performed at 6-311++G(d,p) level of theory.

  6. A-VCI: A flexible method to efficiently compute vibrational spectra

    Science.gov (United States)

    Odunlami, Marc; Le Bris, Vincent; Bégué, Didier; Baraille, Isabelle; Coulaud, Olivier

    2017-06-01

    The adaptive vibrational configuration interaction algorithm has been introduced as a new method to efficiently reduce the dimension of the set of basis functions used in a vibrational configuration interaction process. It is based on the construction of nested bases for the discretization of the Hamiltonian operator according to a theoretical criterion that ensures the convergence of the method. In the present work, the Hamiltonian is written as a sum of products of operators. The purpose of this paper is to study the properties and outline the performance details of the main steps of the algorithm. New parameters have been incorporated to increase flexibility, and their influence has been thoroughly investigated. The robustness and reliability of the method are demonstrated for the computation of the vibrational spectrum up to 3000 cm-1 of a widely studied 6-atom molecule (acetonitrile). Our results are compared to the most accurate up to date computation; we also give a new reference calculation for future work on this system. The algorithm has also been applied to a more challenging 7-atom molecule (ethylene oxide). The computed spectrum up to 3200 cm-1 is the most accurate computation that exists today on such systems.

  7. Quantum chemical prediction of vibrational spectra of large molecular systems with radical or metallic electronic structure

    Science.gov (United States)

    Nishimoto, Yoshio; Irle, Stephan

    2017-01-01

    Quantum chemical simulation of infrared (IR) and Raman spectra for molecules with open-shell, radical, or multiradical electronic structure represents a major challenge. We report analytic second-order geometrical derivatives of the Mermin free energy for the second-order self-consistent-charge density-functional tight-binding (DFTB2) method with fractional occupation numbers (FONs). This new method is applied to the evaluation of Nsbnd O radical stretching modes in various open-shell molecules and to the prediction of the evolution of IR and Raman spectra of graphene nanoribbons with increasing molecular size.

  8. IR Vibrational spectra of H-bonded complexes of adenine, 2-aminopurine and 2-aminopurine+ with cytosine and thymine: Quantum-chemical study

    Science.gov (United States)

    Brovarets', O. O.; Hovorun, D. M.

    2011-11-01

    Using theoretical study on the B3LYP/6-311++G(d,p) level of theory, we have compared vibrational spectra of 2-aminopurine (as neutral or protonated at N1 atom species) with adenine and H-bonded complexes of 2-aminopurine (as neutral or protoned at N1 atom species) · cytosine or 2-aminopurine · thymine with adenine · cytosine and adenine · thymine base pairs. The nature of the base pairing between adenine, 2-aminopurine, 2-aminopurine+ and cytosine or thymine have been investigated by means of quantum-mechanical calculations. We have investigated the effect of the hydrogen bond formation on the vibrational spectra of the investigated base pairs. The main differences in the vibrational spectra as for bases so for base pairs have been observed in the high-frequency region.

  9. Impact of environmentally induced fluctuations on quantum mechanically mixed electronic and vibrational pigment states in photosynthetic energy transfer and 2D electronic spectra

    Energy Technology Data Exchange (ETDEWEB)

    Fujihashi, Yuta; Ishizaki, Akihito, E-mail: ishizaki@ims.ac.jp [Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585 (Japan); Fleming, Graham R. [Department of Chemistry, University of California, Berkeley and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)

    2015-06-07

    Recently, nuclear vibrational contribution signatures in two-dimensional (2D) electronic spectroscopy have attracted considerable interest, in particular as regards interpretation of the oscillatory transients observed in light-harvesting complexes. These transients have dephasing times that persist for much longer than theoretically predicted electronic coherence lifetime. As a plausible explanation for this long-lived spectral beating in 2D electronic spectra, quantum-mechanically mixed electronic and vibrational states (vibronic excitons) were proposed by Christensson et al. [J. Phys. Chem. B 116, 7449 (2012)] and have since been explored. In this work, we address a dimer which produces little beating of electronic origin in the absence of vibronic contributions, and examine the impact of protein-induced fluctuations upon electronic-vibrational quantum mixtures by calculating the electronic energy transfer dynamics and 2D electronic spectra in a numerically accurate manner. It is found that, at cryogenic temperatures, the electronic-vibrational quantum mixtures are rather robust, even under the influence of the fluctuations and despite the small Huang-Rhys factors of the Franck-Condon active vibrational modes. This results in long-lasting beating behavior of vibrational origin in the 2D electronic spectra. At physiological temperatures, however, the fluctuations eradicate the mixing, and hence, the beating in the 2D spectra disappears. Further, it is demonstrated that such electronic-vibrational quantum mixtures do not necessarily play a significant role in electronic energy transfer dynamics, despite contributing to the enhancement of long-lived quantum beating in 2D electronic spectra, contrary to speculations in recent publications.

  10. Impact of environmentally induced fluctuations on quantum mechanically mixed electronic and vibrational pigment states in photosynthetic energy transfer and 2D electronic spectra.

    Science.gov (United States)

    Fujihashi, Yuta; Fleming, Graham R; Ishizaki, Akihito

    2015-06-07

    Recently, nuclear vibrational contribution signatures in two-dimensional (2D) electronic spectroscopy have attracted considerable interest, in particular as regards interpretation of the oscillatory transients observed in light-harvesting complexes. These transients have dephasing times that persist for much longer than theoretically predicted electronic coherence lifetime. As a plausible explanation for this long-lived spectral beating in 2D electronic spectra, quantum-mechanically mixed electronic and vibrational states (vibronic excitons) were proposed by Christensson et al. [J. Phys. Chem. B 116, 7449 (2012)] and have since been explored. In this work, we address a dimer which produces little beating of electronic origin in the absence of vibronic contributions, and examine the impact of protein-induced fluctuations upon electronic-vibrational quantum mixtures by calculating the electronic energy transfer dynamics and 2D electronic spectra in a numerically accurate manner. It is found that, at cryogenic temperatures, the electronic-vibrational quantum mixtures are rather robust, even under the influence of the fluctuations and despite the small Huang-Rhys factors of the Franck-Condon active vibrational modes. This results in long-lasting beating behavior of vibrational origin in the 2D electronic spectra. At physiological temperatures, however, the fluctuations eradicate the mixing, and hence, the beating in the 2D spectra disappears. Further, it is demonstrated that such electronic-vibrational quantum mixtures do not necessarily play a significant role in electronic energy transfer dynamics, despite contributing to the enhancement of long-lived quantum beating in 2D electronic spectra, contrary to speculations in recent publications.

  11. Study on the interaction between diphenhydramine and erythrosin by absorption,fluorescence and resonance Rayleigh scattering spectra

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In pH 4.5 Britton-Robinson(BR)buffer solution,erythrosin(ET)can react with diphenhydramine(DP)to form a 1:1 ion-association complex,which not only results in the change of the absorption spectra,but also results in the great enhancement of resonance Rayleigh scattering(RRS)and the quenching of fluorescence.Furthermore,a new RRS spectrum will appear,and the maximum RRS wavelength was located at about 580 nm.In this work,the spectral characteristics of the absorption,fluorescence and RRS,the optimum conditions of the reaction and the properties of an analytical chemistry were inves- tigated.A sensitive,simple and new method for the determination of DP by using erythrosin as a probe has been developed.The detection limits for DP were 0.0020μg/mL for RRS method,0.088μg/mL for absorption method and 0.094μg/mL for fluorophotometry.There was a linear relationship between the absorbance,RRS and fluorescence intensities and the drug concentration in the range of 0.0067-2.0, 0.29-6.4 and 0.31-3.2μg/mL,respectively.The effects of the interaction of diphenhydramine and erythrosin on the absorption,fluorescence and resonance Rayleigh scattering spectra were discussed. In light polarization experiment,the polarization of RRS at maximum wavelength was measured to be P =0.9779,and it revealed that the RRS spectrum of DP-ET complex consists mostly of resonance scat- tering and few resonance fluorescence.In this study,enthalpy of formation and mean polarizability were calculated by AM1 quantum chemistry method.In addition,the reaction mechanism and the rea- sons for the enhancement of scattering spectra and the energy transfer between absorption,fluores- cence and RRS were discussed.

  12. Classification of different kinds of pesticide residues on lettuce based on fluorescence spectra and WT-BCC-SVM algorithm

    Science.gov (United States)

    Zhou, Xin; Jun, Sun; Zhang, Bing; Jun, Wu

    2017-07-01

    In order to improve the reliability of the spectrum feature extracted by wavelet transform, a method combining wavelet transform (WT) with bacterial colony chemotaxis algorithm and support vector machine (BCC-SVM) algorithm (WT-BCC-SVM) was proposed in this paper. Besides, we aimed to identify different kinds of pesticide residues on lettuce leaves in a novel and rapid non-destructive way by using fluorescence spectra technology. The fluorescence spectral data of 150 lettuce leaf samples of five different kinds of pesticide residues on the surface of lettuce were obtained using Cary Eclipse fluorescence spectrometer. Standard normalized variable detrending (SNV detrending), Savitzky-Golay coupled with Standard normalized variable detrending (SG-SNV detrending) were used to preprocess the raw spectra, respectively. Bacterial colony chemotaxis combined with support vector machine (BCC-SVM) and support vector machine (SVM) classification models were established based on full spectra (FS) and wavelet transform characteristics (WTC), respectively. Moreover, WTC were selected by WT. The results showed that the accuracy of training set, calibration set and the prediction set of the best optimal classification model (SG-SNV detrending-WT-BCC-SVM) were 100%, 98% and 93.33%, respectively. In addition, the results indicated that it was feasible to use WT-BCC-SVM to establish diagnostic model of different kinds of pesticide residues on lettuce leaves.

  13. ab initio calculation study on vibrational spectra of C2B10H12,NB11H12 and C2B10H11Cl

    Institute of Scientific and Technical Information of China (English)

    于微舟; 张明瑜; 孙家钟

    1996-01-01

    Geometrical optimization and theoretical calculation of the vibrational frequencies have been performed for C2B10H12, NB11H12 and C2B10Cl by using Gaussian 92 program at 6-31G basis set. The results obtained in this work are in agreement with experimental ones. The optimized geometry and vibrational spectra show that the icosahedral configuration remains unchanged upon converting from B12H122- to the title compounds. The vibrational spectrum of C2B10H11Cl features the absence of C-Cl stretching vibration. But the (C2B10H11)-Cl vibration mode in the low frequency region is as the case for two-atom molecules if the group (C2B10H11) is considered as a pseudoatom

  14. Synthesis, infrared and fluorescence spectra of lanthanide complexes with a new amide-based 1,3,4-oxadiazole derivative

    Science.gov (United States)

    Tang, Xiao-Liang; Dou, Wei; Chen, Su-Wen; Dang, Fang-Fang; Liu, Wei-Sheng

    2007-10-01

    A new amide-based 1,3,4-oxadiazole derivative ligand 2,5-bis[2-( N, N-diethyl-1'-oxopropylamide)phenyl]-1,3,4-oxadiazole (L) and its complexes, Ln(NO 3) 3L (Ln = La, Eu, Gd, Tb, Er), were synthesized. The complexes were characterized by elemental analysis, infrared spectra and conductivity. The lanthanide ions were coordinated by O atoms from C dbnd O. The fluorescence properties of Eu(NO 3) 3L and Tb(NO 3) 3L in the solid state and in different solvents were investigated. Under the excitation of UV light, these complexes exhibit characteristic fluorescence of europium and terbium ions. The solvent factors influencing the fluorescent intensity were discussed.

  15. Using violet laser-induced chlorophyll fluorescence emission spectra for crop yield assessment of cowpea (Vigna unguiculata (L) Walp) varieties

    Science.gov (United States)

    Anderson, Benjamin; Buah-Bassuah, Paul K.; Tetteh, Jonathan P.

    2004-07-01

    The use of violet laser-induced chlorophyll fluorescence (LICF) emission spectra to monitor the growth of five varieties of cowpea in the University of Cape Coast Botanical Garden is presented. Radiation from a continuous-wave violet laser diode emitting at 396 nm through a fibre is closely incident on in vivo leaves of cowpea to excite chlorophyll fluorescence, which is detected by an integrated spectrometer with CCD readout. The chlorophyll fluorescence spectra with peaks at 683 and 731 nm were used for growth monitoring of the cowpea plants over three weeks and analysed using Gaussian spectral functions with curve fitted parameters to determine the peak positions, area under the spectral curve and the intensity ratio F683/F731. The variation in the intensity ratio of the chlorophyll bands showed sensitive changes indicating the photosynthetic activity of the cowpea varieties. A discussion of the fluorescence result as compared to conventional assessment is presented with regard to discrimination between the cowpea varieties in terms of crop yield performance.

  16. Intrinsic fluorescence spectra characteristics of vitamin B1, B2, and B6

    Science.gov (United States)

    Yang, Hui; Xiao, Xue; Zhao, Xuesong; Hu, Lan; Lv, Caofang; Yin, Zhangkun

    2015-11-01

    This paper presents the intrinsic fluorescence characteristics of vitamin B1, B2 and B6 measured with 3D fluorescence Spectrophotometer. Three strong fluorescence areas of vitamin B2 locate at λex/λem=270/525nm, 370/525nm and 450/525nm, one fluorescence areas of vitamin B1 locates at λex/λem=370/460nm, two fluorescence areas of vitamin B6 locates at λex/λem=250/370nm and 325/370nm were found. The influence of pH of solution to the fluorescence profile was also discussed. Using the PARAFAC algorithm, 10 vitamin B1, B2 and B6 mixed solutions were successfully decomposed, and the emission profiles, excitation profiles, central wavelengths and the concentration of the three components were retrieved precisely through about 5 iteration times.

  17. A study of internal rotations and vibrational spectra of oxiranemethanol ( glycidol)

    Science.gov (United States)

    Badawi, Hassan M.; Ali, Shaikh A.

    2009-10-01

    The conformational stability and the C-O and O-H internal rotations in oxiranemethanol were investigated at the DFT-B3LYP/6-311G**, MP2/6-311G** and MP4(SDQ)/6-311G** levels of theory. Three minima were predicted in the CCOH potential energy scans of the molecule to have relative energies of about 2 kcal/mol or less and all were calculated to have real frequencies upon full optimization of structural parameters at the DFT and the MP2 levels of calculations. The Cg1 ( H bond inner) conformation was predicted to be the lowest energy conformation for oxiranemethanol in excellent agreement with an earlier microwave study. The equilibrium mixture was calculated from Gibb's free-energy changes to be about 79% Cg1, 17 % G1g and 3% Gg1 at the B3LYP/6-311G** level and about 87% Cg1, 11 % G1g and 2% Gg1 at the MP2/6-311G** level for oxiranemethanol at 298.15 K. No conclusive evidence was obtained for the presence of high-energy form in the liquid phase of oxiranemethanol. The vibrational frequencies of oxiranemethanol in its three stable forms were computed at the B3LYP level and complete vibrational assignments were made for the lowest energy Cg1 form on basis of calculated and experimental data of the molecule.

  18. Thermally and vibrationally induced conformational isomerizations, infrared spectra, and photochemistry of gallic acid in low-temperature matrices

    Science.gov (United States)

    Justino, Licínia L. G.; Reva, Igor; Fausto, Rui

    2016-07-01

    Near-infrared (near-IR) narrowband selective vibrational excitation and annealing of gallic acid (3,4,5-trihydroxybenzoic acid) isolated in cryogenic matrices were used to induce interconversions between its most stable conformers. The isomerizations were probed by infrared spectroscopy. An extensive set of quantum chemical calculations, carried out at the DFT(B3LYP)/6-311++G(d,p) level of approximation, was used to undertake a detailed analysis of the ground state potential energy surface of the molecule. This investigation of the molecule conformational space allowed extracting mechanistic insights into the observed annealing- or near-IR-induced isomerization processes. The infrared spectra of the two most stable conformers of gallic acid in N2, Xe, and Ar matrices were fully assigned. Finally, the UV-induced photochemistry of the matrix isolated compound was investigated.

  19. Calculations of the electronic levels, spin-Hamiltonian parameters and vibrational spectra for the CrCl3 layered crystals

    Science.gov (United States)

    Avram, C. N.; Gruia, A. S.; Brik, M. G.; Barb, A. M.

    2015-12-01

    Calculations of the Cr3+ energy levels, spin-Hamiltonian parameters and vibrational spectra for the layered CrCl3 crystals are reported for the first time. The crystal field parameters and the energy level scheme were calculated in the framework of the Exchange Charge Model of crystal field. The spin-Hamiltonian parameters (zero-field splitting parameter D and g-factors) for Cr3+ ion in CrCl3 crystals were obtained using two independent techniques: i) semi-empirical crystal field theory and ii) density functional theory (DFT)-based model. In the first approach, the spin-Hamiltonian parameters were calculated from the perturbation theory method and the complete diagonalization (of energy matrix) method. The infrared (IR) and Raman frequencies were calculated for both experimental and fully optimized geometry of the crystal structure, using CRYSTAL09 software. The obtained results are discussed and compared with the experimental available data.

  20. Optimized geometry, vibration (IR and Raman spectra and nonlinear optical activity of p-nitroanilinium perchlorate molecule: A theoretical study

    Directory of Open Access Journals (Sweden)

    Tamer Ömer

    2016-03-01

    Full Text Available The molecular modeling of p-nitroanilinium perchlorate molecule was carried out by using B3LYP and HSEH1PBE levels of density functional theory (DFT. The IR and Raman spectra were simulated and the assignments of vibrational modes were performed on the basis of relative contribution of various internal co-ordinates. NBO analysis was performed to demonstrate charge transfer, conjugative interactions and the formation of intramolecular hydrogen bonding interactions within PNAPC. Obtained large dipole moment values showed that PNAPC is a highly polarizable complex, and the charge transfer occurs within PNAPC. Hydrogen bonding and charge transfer interactions were also displayed by small HOMO-LUMO gap and molecular electrostatic potential (MEP surface. The strong evidences that the material can be used as an efficient nonlinear optical (NLO material of PNAPC were demonstrated by considerable polarizability and hyperpolarizability values obtained at DFT levels.

  1. Vibrational absorption spectra, DFT and SCC-DFTB conformational study and analysis of [Leu]enkephalin

    DEFF Research Database (Denmark)

    Abdali, Salim; Niehaus, T.A.; Jalkanen, Karl J.

    2003-01-01

    . Ab initio (DFT at the B3LYP/6-31G* level of theory) and semi-empirical (SCC-DFTB) with and without dispersion correction were applied to simulate the VA spectra of [Leu] enkephalin. In these calculations structures taken from X-ray measurements for different conformers of the molecule were used...... as initial structures for SCC-DFTB geometry optimizations, while the optimized SCC-DFTB geometries were used as initial structures for the DFT geometry optimizations. The experimental VA spectrum and the VA spectra calculated for the low energy conformers at each level of theory are then compared...... for different conformers of this peptide. This comparison allowed structural study of this molecule as it is here presented....

  2. FT-IR and Raman spectra and vibrational investigation of bis (4-acetylanilinium) hexachlorostannate using DFT (B3LYP) calculation

    Science.gov (United States)

    Tarchouna, S.; Chaabane, I.; Rahaiem, A. Ben

    2016-09-01

    4-acetylanilinium was used as a ligand for the synthesis of the organic/inorganic compound bis (4-acetylanilinium) hexachlorostannate. Vibrational study in the solid state was performed by FT-Raman of the free 4-acetylanilinium ligand C8H9ON+ and by FT-IR and FT-Raman spectroscopies of the [C8H10NO]2 SnCl6 compound. The comparative analysis of the Raman spectra of the title compound with that of the free ligand was discussed. The structure of the [C8H10NO]2SnCl6 was optimized by density functional theory (DFT) using B3LYP method and shows that the calculated values obtained by B3LYP/LanL2DZ basis are in a better agreement with the experimental data reported by Song et al. (2011) [1] than those obtained by B3LYP/LanL2MB basis. The vibrational frequencies are calculated using density functional theory (DFT) with the B3LYP/LanL2DZ basis, and scaled by various factors. Root mean square (RMS) value was calculated and the small difference between experimental and calculated modes has been interpreted by intermolecular interactions in the crystal.

  3. Electronic and vibrational spectra of novel Lanreotide peptide capped gold nanoparticles

    Science.gov (United States)

    Molina-Trinidad, E. M.; Estévez-Hernández, O.; Rendón, L.; Garibay-Febles, V.; Reguera, E.

    2011-11-01

    Lanreotide, a somatostatin analogue peptide used for peptide receptor mediated therapy in metastatic neuroendocrine tumors, was used as capping agent of gold nanoparticles (GNPs) obtained by citrate reduction method. The displacement of the citrate groups from the GNPs surface by Lanreotide (LAN) molecules was evidenced by infrared and Raman spectra. The nanoparticles system, Au@LAN, was also characterized from HRTEM (High-Resolution Transmission Electron Microscopy) and Z-contrast images, UV-vis and EDS spectra. The stability on aging in water solution of the composite is discussed from the UV-vis spectra. The affinity constant of Au@LAN conjugate, calculated from Capillary Zone Electrophoresis data, was found to be 0.52. All the experimental evidence supports that the gold nanoparticles are effectively capped by the Lanreotide molecules through relatively strong covalent interactions. This result opens the possibility of combining the optical properties of gold nanoparticles and of Lanreotide molecule to form a bifunctional system for potential biomedical applications.

  4. On the Consistency of Approximate Quantum Dynamics Simulation Methods for Vibrational Spectra in the Condensed Phase

    CERN Document Server

    Rossi, Mariana; Paesani, Francesco; Bowman, Joel; Ceriotti, Michele

    2014-01-01

    Including quantum mechanical effects on the dynamics of nuclei in the condensed phase is challenging, because the complexity of exact methods grows exponentially with the number of quantum degrees of freedom. Efforts to circumvent these limitations can be traced down to two approaches: methods that treat a small subset of the degrees of freedom with rigorous quantum mechanics, considering the rest of the system as a static or classical environment, and methods that treat the whole system quantum mechanically, but using approximate dynamics. Here we perform a systematic comparison between these two philosophies for the description of quantum effects in vibrational spectroscopy, taking the Embedded Local Monomer (LMon) model and a mixed quantum-classical (MQC) model as representatives of the first family of methods, and centroid molecular dynamics (CMD) and thermostatted ring polymer molecular dynamics (TRPMD) as examples of the latter. We use as benchmarks D$_2$O doped with HOD and pure H$_2$O at three distinc...

  5. An analytical derivative procedure for the calculation of vibrational Raman optical activity spectra

    Science.gov (United States)

    Liégeois, Vincent; Ruud, Kenneth; Champagne, Benoît

    2007-11-01

    We present an analytical time-dependent Hartree-Fock algorithm for the calculation of the derivatives of the electric dipole-magnetic dipole polarizability with respect to atomic Cartesian coordinates. Combined with analogous procedures to determine the derivatives of the electric dipole-electric dipole and electric dipole-electric quadrupole polarizabilities, it enables a fully analytical evaluation of the three frequency-dependent vibrational Raman optical activity (VROA) invariants within the harmonic approximation. The procedure employs traditional non-London atomic orbitals, and the gauge-origin dependence of the VROA intensities has, therefore, been assessed for the commonly used aug-cc-pVDZ and rDPS:3-21G basis sets.

  6. A comparative study of MP2, B3LYP, RHF and SCC-DFTB force fields in predicting the vibrational spectra of N-acetyl-L-alanine-N'-methyl amide: VA and VCD spectra

    DEFF Research Database (Denmark)

    Bohr, Henrik; Jalkanen, Karl J.; Elstner, M.

    1999-01-01

    Recently we have looked for spectroscopic probes for secondary structural elements in the vibrational spectra of N-acetyl-L-alanine N'-methyl amide (NALANMA), L-alanine (LA), N-acetyl-L-alanyl-L-alanine N'-methyl amide (NALALANMA) and L-alanyl-L-alanine (LALA). Our goal has been to identify...

  7. In vivo fluorescence spectra unmixing and autofluorescence removal by sparse nonnegative matrix factorization.

    Science.gov (United States)

    Montcuquet, Anne-Sophie; Hervé, Lionel; Navarro, Fabrice; Dinten, Jean-Marc; Mars, Jérôme I

    2011-09-01

    Fluorescence imaging locates fluorescent markers that specifically bind to targets; like tumors, markers are injected to a patient, optimally excited with near-infrared light, and located thanks to backward-emitted fluorescence analysis. To investigate thick and diffusive media, as the fluorescence signal decreases exponentially with the light travel distance, the autofluorescence of biological tissues comes to be a limiting factor. To remove autofluorescence and isolate specific fluorescence, a spectroscopic approach, based on nonnegative matrix factorization (NMF), is explored. To improve results on spatially sparse markers detection, we suggest a new constrained NMF algorithm that takes sparsity constraints into account. A comparative study between both algorithms is proposed on simulated and in vivo data.

  8. Infrared spectra of rubidium and cesium diaquatetrachloro-manganates. II. External vibrations of the water molecules

    Science.gov (United States)

    Stefov, Viktor; Šoptrajanov, Bojan; Petruševski, Vladimir

    1992-03-01

    Three bands of librational origin are found in the infrared spectra of Rb 2[MnCl 4 (H 2O) 2] and of its cesium analogue. On the basis of the behaviour on partial deuteration, the band having the lowest frequency can be attributed to a mode which is essentially rocking in character. The remaining two librations are the result of the partial mixing of the twisting and wagging modes. For the HDO molecules the out-of-plane ( oop) modes are mixed to a much higher degree, giving rise to modes which are best described as oop motions of the proton (H-motion) and the deuteron (D-motion) respectively.

  9. Vibrational Circular Dichroism Spectra of Methyl Glycidate in Chloroform and Water: Application of the Clusters-In Model

    Science.gov (United States)

    Perera, Angelo Shehan; Thomas, Javix; Merten, Christian; Xu, Yunjie

    2017-06-01

    Infrared and vibrational circular dichroism (VCD) spectra of methyl glycidate, a chiral epoxy ester, were measured in CCl_{4} and water in the 1000 cm^{-1} - 1800 cm^{-1} region. The experimental VCD spectra of methyl glycidate in water and in CCl_{4} show noticeable differences. In particular, there are strong VCD signatures at the water bending mode region, which can be attributed to chirality transfer from chiral methyl glycidate to water through hydrogen-bonding interactions. We applied the clusters-in-a-liquid model^{1} where both implicit and explicit solute-solvent interactions are considered to simulate the experimental infrared and VCD features of methyl glycidate in CCl_{4} and water. All final geometry optimizations, frequency calculations, infrared and VCD intensity calculations were performed at the B3LYP-D3BJ/6-311++G(2d,p) level of theory where D3BJ is Grimme's empirical dispersion correction with damping factor.^{2} We emphasize the link between the small methyl glycidate hydrates and the main long-lived species which exist in aqueous solution. 1 A. S. Perera, J. Thomas, M. R. Poopari, Y. Xu, Front. Chem. 2016, 4, 1-17. 2 S. Grimme, S. Ehrlich, L. Goerigk, J. Comp. Chem. 2011, 32, 1456-1465.

  10. Potential of hydrogen bond in water. Comparison of the theory with vibrational spectra and results of molecular dynamics simulations.

    Science.gov (United States)

    Efimov, Yuri Ya; Naberukhin, Yuri I

    2011-02-01

    Potential of hydrogen bond is the function which relates its energy to geometrical parameters of hydrogen bridge: its length R(O…O) and angles between direction O…O and OH group [φ (H-O…O)] and/or lone pair of proton accepting oxygen atom [χ(-O…O)]. Previously we have suggested an approach to design such potentials based on the approximate numerical solution of a reverse problem of the spectrum band shape in the frames of the fluctuation theory of hydrogen bonding. In the given work this method is applied to construction of the two-parameter potentials that depend on parameters {R(O…O), φ (H-O…O} or {φ (H-O…O), χ (-O…O)}. Using them, the spectra of OH vibrations of HOD molecules in a liquid phase are calculated theoretically in good agreement with experiment in the temperature range up to 200 °C. Distributions of angles P(φ, T), P(χ, T), and energies P(E) are calculated also. The same distributions and spectra are independently calculated on the basis of the geometrical parameters of the hydrogen bridges obtained from molecular dynamics models of water. The shapes of the spectral contours and their temperature evolution calculated for computer models turned out to be similar to experimental ones only for the potential that includes the length of H-bond R(O…O).

  11. Exploring the effect of vibronic contributions on light harvesting efficiency of NKX-2587 derivatives through vibrationally resolved electronic spectra

    Science.gov (United States)

    Yang, Pan; Shen, Wei; Li, Ming; He, Rongxing

    2017-01-01

    The vibrationally resolved electronic spectra of five metal-free NKX-2587 derivatives containing heteroatom with different atomic sizes and electronegativity, were simulated within the Franck-Condon approximation including the Herzberg-Teller and Duschinsky effects, aimed at exploring the correlation of vibronic structure associated with the spectrum and efficiency of dye sensitized solar cells (DSSCs). The parameters of short-circuit current density (Jsc) and open circuit voltage (Voc) involving efficiency of DSSCs, such as total dipole moments (μnormal), the light harvesting efficiency (LHE), injection driving force (∆ Ginject), and the number of electrons in the conduction band (nc), were calculated and discussed in detail. Results showed that the heteroatoms in the same period with large size and weak electronegativity and the ones in the same main group with large size and weak electronegativity are beneficial to Voc. The sizes and electronegativity of the heteroatoms have a weak effect on Jsc. The low-frequency modes play important roles in enhancing the intensities of the electronic spectra and structures can affect light harvesting efficiency (LHE). In this sense, our results provided guidance for understanding the sources of spectral intensities of dye molecules, and a valuable help for rational design of new molecules to improve the energy conversion efficiency (η) of DSSCs.

  12. Simulation of Vacuum UV Absorption and Electronic Circular Dichroism Spectra of Methyl Oxirane: the Role of Vibrational Effects

    Science.gov (United States)

    Hodecker, Manuel; Biczysko, Malgorzata; Dreuw, Andreas; Barone, Vincenzo

    2017-01-01

    Vibrationally resolved one-photon absorption and electronic circular dichroism spectra of (R)-methyl oxirane were calculated with different electronic and vibronic models selecting, through an analysis of the convergence of the results, the best compromise between reliability and computational cost. Linear-response TD-DFT/CAM-B3LYP/SNST electronic computations in conjunction with the simple vertical gradient vibronic model were chosen and employed for systematic comparison with the available experimental data. Remarkable agreement between simulated and experimental spectra was achieved for both one photon absorption and circular dichroism concerning peak positions, relative intensities, and general spectral shapes considering the computational efficiency of the chosen theoretical approach. The significant improvement of the results with respect to smearing of vertical electronic transitions by phenomenological Gaussian functions and the possible inclusion of solvent effects by polarizable continuum models at a negligible additional cost paves the route toward the simulation and analysis of spectral shapes of complex molecular systems in their natural environment. PMID:27159495

  13. On 2:1 melamine - Squaric acid dihydrate complex: The structure and vibrational spectra

    Science.gov (United States)

    Nowicka-Scheibe, J.; Pawlukojć, A.; Sobczyk, L.; Jański, J.

    2017-01-01

    In the present paper we would like to describe the structural and dynamical properties of crystalline dihydrated complex of melamine (2,4,6-triamino-1,3,5-triazin-1-ium) with squaric acid (3,4-dihydroxycyclobut-3-ene-1,2-dione) abbreviated as MH·SQ. The X-ray diffraction studies show the presence of deprotonated units (C4O4)2- and single protonated melamine cations surrounded by tetrameric water assemblies (H2O)4. The formation of the water tetramers deserves a special attention. IR absorption and Raman spectra reflect a richness of structural units and numerous hydrogen bonds. The presence of the continua in the IR spectra, with a characteristic presence of the Hadži's trio enriched by a numerous submaxima, may be ascribed to the structural units and to the various types of hydrogen bonds. The density functional theory calculation with the periodic boundary conditions was use to precise analysis of experimental data.

  14. Ultrafast Time-Resolved Emission and Absorption Spectra of meso-Pyridyl Porphyrins upon Soret Band Excitation Studied by Fluorescence Up-Conversion and Transient Absorption Spectroscopy.

    Science.gov (United States)

    Venkatesh, Yeduru; Venkatesan, M; Ramakrishna, B; Bangal, Prakriti Ranjan

    2016-09-08

    A comprehensive study of ultrafast molecular relaxation processes of isomeric meso-(pyridyl) porphyrins (TpyPs) has been carried out by using femtosecond time-resolved emission and absorption spectroscopic techniques upon pumping at 400 nm, Soret band (B band or S2), in 4:1 dichloromethane (DCM) and tetrahydrofuran (THF) solvent mixture. By combined studies of fluorescence up-conversion, time-correlated single photon counting, and transient absorption spectroscopic techniques, a complete model with different microscopic rate constants associated with elementary processes involved in electronic manifolds has been reported. Besides, a distinct coherent nuclear wave packet motion in Qy state is observed at low-frequency mode, ca. 26 cm(-1) region. Fluorescence up-conversion studies constitute ultrafast time-resolved emission spectra (TRES) over the whole emission range (430-710 nm) starting from S2 state to Qx state via Qy state. Careful analysis of time profiles of up-converted signals at different emission wavelengths helps to reveal detail molecular dynamics. The observed lifetimes are as indicated: A very fast decay component with 80 ± 20 fs observed at ∼435 nm is assigned to the lifetime of S2 (B) state, whereas being a rise component in the region of between 550 and 710 nm emission wavelength pertaining to Qy and Qx states, it is attributed to very fast internal conversion (IC) occurring from B → Qy and B → Qx as well. Two distinct components of Qy emission decay with ∼200-300 fs and ∼1-1.5 ps time constants are due to intramolecular vibrational redistribution (IVR) induced by solute-solvent inelastic collisions and vibrational redistribution induced by solute-solvent elastic collision, respectively. The weighted average of these two decay components is assigned as the characteristic lifetime of Qy, and it ranges between 0.3 and 0.5 ps. An additional ∼20 ± 2 ps rise component is observed in Qx emission, and it is assigned to the formation time of

  15. Study on the interaction between fluoroquinolones and erythrosine by absorption, fluorescence and resonance Rayleigh scattering spectra and their application

    Science.gov (United States)

    Wang, Jian; Liu, Zhongfang; Liu, Jiangtao; Liu, Shaopu; Shen, Wei

    2008-03-01

    In pH 4.4-4.5 Britton-Robinson (BR) buffer solution, fluoroquinolone antibiotics (FLQs) including ciprofloxacin (CIP), norfloxacin (NOR), levofloxacin (LEV) and lomefloxacin (LOM) could react with erythrosine (Ery) to form 1:1 ion-association complexes, which not only resulted in the changes of the absorption spectra and the quenching of fluorescence, but also resulted in the great enhancement of resonance Rayleigh scattering (RRS). These offered some indications of the determination of fluoroquinolone antibiotics by spectrophotometric, fluorescence and resonance Rayleigh scattering methods. The detection limits for fluoroquinolone antibiotics were in the range of 0.097-0.265 μg/mL for absorption methods, 0.022-0.100 μg/mL for fluorophotometry and 0.014-0.027 μg/mL for RRS method, respectively. Among them, the RRS method had the highest sensitivity. In this work, the spectral characteristics of the absorption, fluorescence and RRS, the optimum conditions of the reactions and the properties of the analytical chemistry were investigated. The methods have been successfully applied to determination of some fluoroquinolone antibiotics in human urine samples and tablets. Taking CIP-Ery system as an example, the charge distribution, the enthalpy of formation and the mean polarizability were calculated by density function theory (DFT) method. In addition, the reasons for the enhancement of scattering spectra were discussed.

  16. DVR3D: a program suite for the calculation of rotation-vibration spectra of triatomic molecules

    Science.gov (United States)

    Tennyson, Jonathan; Kostin, Maxim A.; Barletta, Paolo; Harris, Gregory J.; Polyansky, Oleg L.; Ramanlal, Jayesh; Zobov, Nikolai F.

    2004-11-01

    The DVR3D program suite calculates energy levels, wavefunctions, and where appropriate dipole transition moments, for rotating and vibrating triatomic molecules. Potential energy and, where necessary, dipole surfaces must be provided. Expectation values of geometrically defined functions can be calculated, a feature which is particularly useful for fitting potential energy surfaces. The programs use an exact (within the Born-Oppenheimer approximation) Hamiltonian and offer a choice of Jacobi or Radau internal coordinates and several body-fixed axes. Rotationally excited states are treated using an efficient two-step algorithm. The programs uses a Discrete Variable Representation (DVR) based on Gauss-Jacobi and Gauss-Laguerre quadrature for all 3 internal coordinates and thus yields a fully point-wise representation of the wavefunctions. The vibrational step uses successive diagonalisation and truncation which is implemented for a number of possible coordinate orderings. The rotational, expectation value and transition dipole programs exploit the savings offered by performing integrals on a DVR grid. The new version has been rewritten in FORTRAN 90 to exploit the dynamic array allocations and the algorithm for dipole and spectra calculations have been substantially improved. New modules allow the z-axis to be embedded perpendicular to the plane of the molecule and for the calculation of expectation values. Program summaryTitle of the program: DVR3D suite Catalogue number: ADTI Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTI Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Programming language: Fortran 90 No. of lines in distributed program, including test data, etc.: 61 574 No. of bytes in distributed program, including test data, etc.: 972 404 Distribution format: tar.gz New version summaryTitle of program: DVR3DRJZ Catalogue number: ADTB Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTB Program obtainable

  17. Intramolecular charge delocalization and nonlinear optical properties of push-pull chromophore 1-(4-N,N-dimethylaminopyridinium) acetic acid bromide monohydrate from vibrational spectra.

    Science.gov (United States)

    John, C Jesintha; Amalanathan, M; Sajan, D; Lakshmi, K Udaya; Joe, I Hubert

    2011-01-01

    FT-Raman and FT-IR spectra of the nonlinear optical crystal 1-(4-N,N-dimethylaminopyridinium) acetic acid bromide monohydrate have been recorded and analyzed. The equilibrium geometry, vibrational wavenumbers and the first order hyperpolarizability of the crystal have been calculated with the help of density functional theory computations. The assignments of the vibrational spectra have been carried out with the help of Scaled Quantum Mechanic force field theory. Optimized geometry gives the charge transfer interaction of the pyridine ring and the amino group in the electron-donor side of the nonlinear optic chromophore. Electron-phonon coupling and O-H⋯O interactions in making the molecule nonlinear optical active have been analyzed based on the vibrational spectral features. The Natural Bond Orbital analysis confirms the occurrence of strong intermolecular O-H⋯O hydrogen bonding. Copyright © 2010 Elsevier B.V. All rights reserved.

  18. Impact of environmentally induced fluctuations on quantum mechanically mixed electronic and vibrational pigment states in photosynthetic energy transfer and 2D electronic spectra

    CERN Document Server

    Fujihashi, Yuta; Ishizaki, Akihito

    2015-01-01

    Recently, nuclear vibrational contribution signatures in 2D electronic spectroscopy have attracted considerable interest, in particular as regards interpretation of the oscillatory transients observed in light-harvesting complexes. These transients have dephasing times that persist for much longer than theoretically predicted electronic coherence lifetime. As a plausible explanation for this long-lived spectral beating in 2D electronic spectra, quantum-mechanically mixed electronic and vibrational states (vibronic excitons) were proposed by Christensson et al. [J. Phys. Chem. B 116, 7449 (2012)] and have since been explored. In this work, we address a dimer which produces little beating of electronic origin in the absence of vibronic contributions, and examine the impact of protein-induced fluctuations upon electronic-vibrational quantum mixtures by calculating the electronic energy transfer dynamics and 2D electronic spectra in a numerically accurate manner. It is found that, at cryogenic temperatures, the e...

  19. Quantum chemical and experimental studies on the structure and vibrational spectra of an alkaloid-Corlumine

    Science.gov (United States)

    Mishra, Rashmi; Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha

    2014-01-01

    The study concentrates on an important natural product, phthalide isoquinoline alkaloid Corlumine (COR) [(6R)-6-[(1S)-1,2,3,4-Tetrahydro-6,7-dimethoxy-2-methylisoquinolin-1-yl] furo [3,4-e]-1,3-benzodioxol-8(6H)-one] well known to exhibit spasmolytic and GABA antagonist activity. It was fully characterized by a variety of experimental methods including vibrational spectroscopy (IR and Raman), thermal analysis (DSC), UV and SEM. For a better interpretation and analysis of the results quantum chemical calculations employing DFT were also performed. TD-DFT was employed to elucidate electronic properties for both gaseous and solvent environment using IEF-PCM model. Graphical representation of HOMO and LUMO would provide a valuable insight into the nature of reactivity and some of the structural and physical properties of the title molecule. The structure-activity relationship have been interpreted by mapping electrostatic potential surface (MEP), which is valuable information for the quality control of medicines and drug-receptor interactions. Stability of the molecule arising from hyper conjugative interactions, charge delocalisation has been analyzed using natural bond orbital (NBO) analysis. Computation of thermodynamical properties would help to have a deep insight into the molecule for further applications.

  20. Reliable HPLC separation, vibrational circular dichroism spectra, and absolute configurations of isoborneol enantiomers.

    Science.gov (United States)

    Gao, Rui-Qi; Fan, Jun; Tan, Qi; Guo, Dong; Chen, Tao; He, Ru-Jian; Li, Dan; Zhang, Hui; Zhang, Wei-Guang

    2017-09-01

    Resolution of chiral compounds has played an important role in the pharmaceutical field, involving detailed studies of pharmacokinetics, physiological, toxicological, and metabolic activities of enantiomers. Herein, a reliable method by high-performance liquid chromatography (HPLC) coupled with an optical rotation detector was developed to separate isoborneol enantiomers. A cellulose tris(3, 5-dimethylphenylcarbamate)-coated chiral stationary phase showed the best separation performance for isoborneol enantiomers in the normal phase among four polysaccharide chiral packings. The effects of alcoholic modifiers and column temperature were studied in detail. Resolution of the isoborneol racemate displayed a downward trend along with an increase in the content of ethanol and column temperature, indicating that less ethanol in the mobile phase and lower temperature were favorable to this process. Moreover, two isoborneol enantiomers were obtained via a semipreparative chiral HPLC technique under optimum conditions, and further characterized by analytical HPLC, and experimental and calculated vibrational circular dichroism (VCD) spectroscopy, respectively. The solution VCD spectrum of the first-eluted component was consistent with the Density Functional Theory (DFT) calculated pattern based on the SSS configuration, indicating that this enantiomer should be (1S, 2S, 4S)-(+)-isoborneol. Briefly, these results have provided reliable information to establish a method for analysis, preparative separation, and absolute configuration of chiral compounds without typical chromophoric groups. © 2017 Wiley Periodicals, Inc.

  1. Stabilizing the PARAFAC decomposition of fluorescence spectra by insertion of zeros outside the data area

    DEFF Research Database (Denmark)

    Thygesen, Lisbeth Garbrecht; Rinnan, Åsmund; Barsberg, Søren

    2004-01-01

    The use of fluorescence spectroscopy for recording multiple excitation and corresponding emission wavelengths and the subsequent technique of analyzing the resulting fluorescence landscapes is a rather new method as opposed to the use of just a single excitation wavelength. In a fluorescence...... landscape, several light-scatter effects are usually present, and often the part of the landscape containing information on the chemical and/or physical characteristics of the sample is surrounded by two Rayleigh scatter lines. When such landscapes are decomposed using parallel factor analysis (PARAFAC...... by PARAFAC. In this paper, we introduce a novel pretreatment method applicable for two-dimensional fluorescence landscapes, where instead of inserting only missing values a mixture of zeros and missing values are inserted close to and outside the Rayleigh scatter lines. It is shown that, by the use...

  2. Driving the atom by atomic fluorescence: Analytic results for the power and noise spectra

    OpenAIRE

    2000-01-01

    We study how the spectral properties of resonance fluorescence propagate through a two-atom system. Within the weak-driving-field approximation we find that, as we go from one atom to the next, the power spectrum exhibits both subnatural linewidth narrowing and large asymmetries while the noise spectrum of the squeezed quadrature narrows but remains otherwise unchanged. Analytical results for the observed spectral features of the fluorescence are provided and their origin is thoroughly discus...

  3. Application of the Modified Urey-Bradley-Shimanouchi Force field of α-D-Glucopyranose and β-D-Fructopyranose to Predict the Vibrational Spectra of Disaccharides

    Science.gov (United States)

    Gafour, H. M.; Sekkal-Rahal, M.; Sail, K.

    2014-01-01

    The vibrational frequencies of the disaccharide isomaltulose in the solid state have been reproduced in the 50-4000 cm-1 range. The modified Urey-Bradley-Shimanouchi force field was used, combined with an inter molecular potential energy function that includes van der Waals interactions, electrostatic terms, and an explicit hydrogen bond function. The force constants previously established for α-D-glucopyranose and β-D-fructo pyranose, as well as the crystallographic data of isomaltulose monohydrate, were the starting parameters for the present work. The vibrational frequencies of isomaltulose were calculated and assigned to the experimentally observed vibrational frequencies. Overall, there was good agreement between the observed and calculated frequencies with an average error of 4 cm-1. Furthermore, good agreement was found between our calculated results and the vibration spectra of other disaccharides and monosaccharides.

  4. Influences of quantum mechanically mixed electronic and vibrational pigment states in 2D electronic spectra of photosynthetic systems: Strong electronic coupling cases

    CERN Document Server

    Fujihashi, Yuta; Ishizaki, Akihito

    2015-01-01

    In 2D electronic spectroscopy studies, long-lived quantum beats have recently been observed in photosynthetic systems, and it has been suggested that the beats are produced by quantum mechanically mixed electronic and vibrational states. Concerning the electronic-vibrational quantum mixtures, the impact of protein-induced fluctuations was examined by calculating the 2D electronic spectra of a weakly coupled dimer with vibrational modes in the resonant condition [J. Chem. Phys. 142, 212403 (2015)]. This analysis demonstrated that quantum mixtures of the vibronic resonance are rather robust under the influence of the fluctuations at cryogenic temperatures, whereas the mixtures are eradicated by the fluctuations at physiological temperatures. However, this conclusion cannot be generalized because the magnitude of the coupling inducing the quantum mixtures is proportional to the inter-pigment coupling. In this study, we explore the impact of the fluctuations on electronic-vibrational quantum mixtures in a strongl...

  5. Research of fluorescent spectra of oleic acid-stabilized ZnSe nanocrystals based on UV light modification

    Science.gov (United States)

    Hao, Licai; Bai, Zhongchen; Huang, Zhaoliang; Liao, Sha; Zhang, Zhengping

    2016-11-01

    The non-aqueous synthesized and post-preparative treatment of oleic acid (OA)-stabilized ZnSe nanocrystals were studied systematically. ZnSe nanocrystals were successfully synthesized via paraffin liquid and oleic acid system by using OA as stabilizer. Synthesized nanocrystals were characterized by means of absorption and fluorescent spectra, Fourier transform infrared spectrometer, transmission electron microscopy and selected area electron diffraction. Furthermore, solutions of ZnSe nanocrystals were illuminated with UV light. The experimental results showed that the fluorescent peak was red-shifted from 445 to 510 nm. The results suggested that, when the solution under illumination, OA was removed from the surface of ZnSe nanocrystals and the surface of ZnSe nanocrystals was oxidized to ZnO nanocrystals. ZnSe/ZnO core/shell nanocrystals were formed when the solution of ZnSe nanocrystals illuminated with UV light.

  6. Extension of the MIRS computer package for the modeling of molecular spectra : from effective to full ab initio ro-vibrational hamiltonians in irreducible tensor form

    CERN Document Server

    Nikitin, Andrei; Champion, Jean Paul; Tyuterev, Vladimir

    2012-01-01

    The MIRS software for the modeling of ro-vibrational spectra of polyatomic molecules was considerably extended and improved. The original version (Nikitin, et al. JQSRT, 2003, pp. 239--249) was especially designed for separate or simultaneous treatments of complex band systems of polyatomic molecules. It was set up in the frame of effective polyad models by using algorithms based on advanced group theory algebra to take full account of symmetry properties. It has been successfully used for predictions and data fitting (positions and intensities) of numerous spectra of symmetric and spherical top molecules within the vibration extrapolation scheme. The new version offers more advanced possibilities for spectra calculations and modeling by getting rid of several previous limitations particularly for the size of polyads and the number of tensors involved. It allows dealing with overlapping polyads and includes more efficient and faster algorithms for the calculation of coefficients related to molecular symmetry ...

  7. Vibrational Spectra of 3-(Adamantan-1-YL)-4-(2-Propen-1-YL)-1 H-1,2,4-Triazole-5(4 H)-Thione

    Science.gov (United States)

    Gladkov, L. L.; Matsukovich, A. S.; Pavich, T. A.; Gaponenko, S. V.; El-Emam, A. A.

    2017-01-01

    Vibrational spectra of 3-(adamantan-1-yl)-4-(2-propen-1-yl)-1H-1,2,4-triazole-5(4H)-thione (C15H21N3S), which was promising for drug development, were studied experimentally and theoretically. The geometric structure and normal modes of the molecule and its dimer were calculated using quantum-mechanical density functional theory. It was shown that the experimentally obtained vibrational spectra were due to dimeric C15H21N3S structures. This conclusion was confirmed by spectra of the isotopically substituted compound with a deuterated imine. Bands at 1496 and 1549 cm-1 were identified as markers of dimer formation. Bands at 936 and 1244 cm-1 were found to be markers of intermolecular interactions of adamantane fragments.

  8. Theoretical Investigation of C-H Vibrational Spectroscopy. 2. Unified Assignment Method of IR, Raman, and Sum Frequency Generation Spectra of Ethanol.

    Science.gov (United States)

    Wang, Lin; Ishiyama, Tatsuya; Morita, Akihiro

    2017-09-14

    Using the flexible and polarizable model in the preceding paper, we performed comprehensive analysis of C-H stretching vibrations of ethanol and partially deuterated ones by molecular dynamics (MD) simulation. The overlapping band structures of the C-H stretching region including (i) methyl and methylene, (ii) the number of modes with Fermi resonances, and (iii) different trans/gauche conformers are disentangled by various analysis methods, such as isotope exchange, empirical potential parameter shift analysis, and separate calculations of conformers. The present analysis with MD simulation revealed unified assignment of infrared, Raman, and sum frequency generation (SFG) spectra. The analysis confirmed that the different conformers have significant influence on the assignment of CH2 vibrations. Band components and their signs in the imaginary χ((2)) spectra of SFG under various polarizations are also understood from the common assignment with the infrared and Raman spectra.

  9. Synthesis, structure, infrared and fluorescence spectra of new rare earth complexes with 6-hydroxy chromone-3-carbaldehyde benzoyl hydrazone

    Science.gov (United States)

    Wang, Bao-Dui; Yang, Zheng-Yin; Zhang, Ding-Wa; Wang, Yan

    2006-01-01

    A novel 6-hydroxy chromone-3-carbaldehyde benzoyl hydrazone ligand and its four complexes, [LnL2(NO3)2]NO3 [Ln = Eu(1), Sm(2), Tb(3), Dy(4)], were synthesized. The complexes were characterized by the elemental analyses, molar conductivity and IR spectra. The crystal and molecular structure of Sm(III) complex was determined by single-crystal X-ray diffraction: crystallized in the triclinic system, space group P-1, Z = 1, a = 11.037(4) Å, b = 14.770(5) Å, c = 15.032(7) Å, α = 60.583(4), β = 75.528(7), γ = 88.999(4), R1 = 0.0349. The fluorescence properties of complexes in the solid state and in the organic solvent were studied in detail, respectively. Under the excitation of ultraviolet light, strong red fluorescence of solid europium complex was observed. But the green fluorescence of solid terbium complex was not observed. These observations show that the ligand favor energy transfers to the emitting energy level of Eu3+. Some factors that influence the fluorescent intensity were also discussed.

  10. A study of hydrogen bonded vibrational spectra of (R)-(+)-Methylsuccinic acid, as aided by DFT dimer analysis

    Science.gov (United States)

    Tonannavar, J.; Chavan, Yashaswita B.; Yenagi, Jayashree

    2016-05-01

    Infrared and Raman spectral measurements in the region 4000-400 cm- 1 have been carried out for (R)-(+)-Methylsuccinic acid. The vibrational band structures near 3100-3040 cm- 1 in the IR and near 1650 cm- 1 in the Raman spectra have indicated the presence of an inter-molecular hydrogen bonding. A DFT dimer model has been proposed that involves O-H ⋯ OC type of hydrogen bonding. The proposed dimer model has been derived from the three stable monomers computed at RHF/3-21G and B3LYP/6-311 + G(d,p) levels of theory. A total of six dimer structures have been considered with a Boltzmann population of 38% for the most stable dimer and 62% for the remaining five dimer populations. A Boltzmann population weighted vibration spectrum has predicted bands, among others, for O-H ⋯ OC group that are in very good agreement with experiment. All the dimers have the same structure in that the two pairs of -O-H and -OC form a closed cyclic structure with a local center of inversion. This dimer geometry has given rise to one asymmetric mode at 1683 and one symmetric -CO mode at 1637 cm- 1 corresponding to mutually exclusive an experimental IR band at 1700 and a Raman band at 1651 cm- 1. Further, the bond length, H ⋯ O, for the most stable dimer is 1.686 Å, being shorter than the sums of van der Waals radii, 2.72 Å and the angle between O-H and H ⋯ O is almost linear (179°) suggesting that the hydrogen bonding is fairly strong.

  11. ATR-FTIR and density functional theory study of the structures, energetics, and vibrational spectra of phosphate adsorbed onto goethite.

    Science.gov (United States)

    Kubicki, James D; Paul, Kristian W; Kabalan, Lara; Zhu, Qing; Mrozik, Michael K; Aryanpour, Masoud; Pierre-Louis, Andro-Marc; Strongin, Daniel R

    2012-10-16

    Periodic plane-wave density functional theory (DFT) and molecular cluster hybrid molecular orbital-DFT (MO-DFT) calculations were performed on models of phosphate surface complexes on the (100), (010), (001), (101), and (210) surfaces of α-FeOOH (goethite). Binding energies of monodentate and bidentate HPO(4)(2-) surface complexes were compared to H(2)PO(4)(-) outer-sphere complexes. Both the average potential energies from DFT molecular dynamics (DFT-MD) simulations and energy minimizations were used to estimate adsorption energies for each configuration. Molecular clusters were extracted from the energy-minimized structures of the periodic systems and subjected to energy reminimization and frequency analysis with MO-DFT. The modeled P-O and P---Fe distances were consistent with EXAFS data for the arsenate oxyanion that is an analog of phosphate, and the interatomic distances predicted by the clusters were similar to those of the periodic models. Calculated vibrational frequencies from these clusters were then correlated with observed infrared bands. Configurations that resulted in favorable adsorption energies were also found to produce theoretical vibrational frequencies that correlated well with experiment. The relative stability of monodentate versus bidentate configurations was a function of the goethite surface under consideration. Overall, our results show that phosphate adsorption onto goethite occurs as a variety of surface complexes depending on the habit of the mineral (i.e., surfaces present) and solution pH. Previous IR spectroscopic studies may have been difficult to interpret because the observed spectra averaged the structural properties of three or more configurations on any given sample with multiple surfaces.

  12. Infrared and NMR spectra, tautomerism, vibrational assignment, normal coordinate analysis, and quantum mechanical calculations of 4-amino-5-pyrimidinecarbonitrile.

    Science.gov (United States)

    Afifi, Mahmoud S; Farag, Rabei S; Shaaban, Ibrahim A; Wilson, Lee D; Zoghaib, Wajdi M; Mohamed, Tarek A

    2013-07-01

    The infrared (4000-200 cm(-1)) spectrum for 4-amino-5-pyrimidinecarbonitrile (APC, C5H4N4) was acquired in the solid phase. In addition, the (1)H and (13)C NMR spectra of APC were obtained in DMSO-d6 along with its mass spectrum. Initially, six isomers were hypothesized and then investigated by means of DFT/B3LYP and MP2(full) quantum mechanical calculations using a 6-31G(d) basis set. Moreover, the (1)H and (13)C NMR chemical shifts were predicted using a GIAO approximation at the 6-311+G(d,p) basis set and the B3LYP method with (and without) solvent effects using PCM method. The correlation coefficients showed good agreement between the experimental/theoretical chemical shift values of amino tautomers (1 and 2) rather than the eliminated imino tautomers (3-6), in agreement with the current quantum mechanical calculations. Structures 3-6 are less stable than the amino tautomers (1 and 2) by about 5206-8673 cm(-1) (62.3-103.7 kJ/mol). The MP2(full)/6-31G(d) computational results favor the amino structure 1 with a pyramidal NH2 moiety and calculated real vibrational frequencies, however; structure 2 is considered a transition state owing to the calculated imaginary frequency. It is worth mentioning that, the calculated structural parameters suggest a strong conjugation between the amino nitrogen and pyrimidine ring. Aided by frequency calculations, normal coordinate analysis, force constants and potential energy distributions (PEDs), a complete vibrational assignment for the observed bands is proposed herein. Finally, NH2 internal rotation barriers for the stable non-planar isomer (1) were carried out using MP2(full)/6-31G(d) optimized structural parameters. Our results are discussed herein and compared to structural parameters for similar molecules whenever appropriate.

  13. Principal component analysis (PCA)-based k-nearest neighbor (k-NN) analysis of colonic mucosal tissue fluorescence spectra.

    Science.gov (United States)

    Kamath, Sudha D; Mahato, Krishna K

    2009-08-01

    The objective of this study was to verify the suitability of principal component analysis (PCA)-based k-nearest neighbor (k-NN) analysis for discriminating normal and malignant autofluorescence spectra of colonic mucosal tissues. Autofluorescence spectroscopy, a noninvasive technique, has high specificity and sensitivity for discrimination of diseased and nondiseased colonic tissues. Previously, we assessed the efficacy of the technique on colonic data using PCA Match/No match and Artificial Neural Networks (ANNs) analyses. To improve the classification reliability, the present work was conducted using PCA-based k-NN analysis and was compared with previously obtained results. A total of 115 fluorescence spectra (69 normal and 46 malignant) were recorded from 13 normal and 10 malignant colonic tissues with 325 nm pulsed laser excitation in the spectral region 350-600 nm in vitro. We applied PCA to extract the relevant information from the spectra and used a nonparametric k-NN analysis for classification. The normal and malignant spectra showed large variations in shape and intensity. Statistically significant differences were found between normal and malignant classes. The performance of the analysis was evaluated by calculating the statistical parameters specificity and sensitivity, which were found to be 100% and 91.3%, respectively. The results obtained in this study showed good discrimination between normal and malignant conditions using PCA-based k-NN analysis.

  14. Probing the photoreaction mechanism of phytochrome through analysis of resonance Raman vibrational spectra of recombinant analogues.

    Science.gov (United States)

    Andel, F; Murphy, J T; Haas, J A; McDowell, M T; van der Hoef, I; Lugtenburg, J; Lagarias, J C; Mathies, R A

    2000-03-14

    Resonance Raman spectra of native and recombinant analogues of oat phytochrome have been obtained and analyzed in conjunction with normal mode calculations. On the basis of frequency shifts observed upon methine bridge deuteration and vinyl and C(15)-methine bridge saturation of the chromophore, intense Raman lines at 805 and 814 cm(-)(1) in P(r) and P(fr), respectively, are assigned as C(15)-hydrogen out-of-plane (HOOP) wags, lines at 665 cm(-)(1) in P(r) and at 672 and 654 cm(-)(1) in P(fr) are assigned as coupled C=C and C-C torsions and in-plane ring twisting modes, and modes at approximately 1300 cm(-)(1) in P(r) are coupled N-H and C-H rocking modes. The empirical assignments and normal mode calculations support proposals that the chromophore structures in P(r) and P(fr) are C(15)-Z,syn and C(15)-E,anti, respectively. The intensities of the C(15)-hydrogen out-of-plane, C=C and C-C torsional, and in-plane ring modes in both P(r) and P(fr) suggest that the initial photochemistry involves simultaneous bond rotations at the C(15)-methine bridge coupled to C(15)-H wagging and D-ring rotation. The strong nonbonded interactions of the C- and D-ring methyl groups in the C(15)-E,anti P(fr) chromophore structure indicated by the intense 814 cm(-1) C(15) HOOP mode suggest that the excited state of P(fr) and its photoproduct states are strongly coupled.

  15. Identifying the Assembly Configuration and Fluorescence Spectra of Nanoscale Zinc-Tetraphenylporphyrin Aggregates with Scanning Tunneling Microscopy

    Science.gov (United States)

    Zhang, Xiao-Lei; Jiang, Jian-Wei; Liu, Yi-Ting; Lou, Shi-Tao; Gao, Chun-Lei; Jin, Qing-Yuan

    2016-03-01

    ZnTPP (Zinc-Tetraphenylporphyrin) is one of the most common nanostructured materials, having high stability and excellent optoelectronic properties. In this paper, the fluorescence features of self-assembled ZnTPP monomers and aggregates on Au(111) surface are investigated in detail on the nanometer scale with scanning tunneling microscopy (STM). The formation of ZnTPP dimers is found in thick layers of a layer-by-layer molecular assembly on Au substrate with its specific molecular arrangement well characterized. Tip-induced luminescence shows a red shift from tilted dimers comparing with the behavior from monomers, which can be attributed to the change of vibrational states due to the intermolecular interaction and the increasing dielectric effect. The nanoscale configuration dependence of electroluminescence is demonstrated to provide a powerful tool aiding the design of functional molecular photoelectric devices.

  16. Fo-spectra of chlorophyll fluorescence for the determination of zooplankton grazing

    NARCIS (Netherlands)

    Lürling, M.F.L.L.W.; Verschoor, A.M.

    2003-01-01

    In the PHYTO-PAM phytoplankton analyzer the minimal fluorescence of dark-adapted samples (F-0) was assessed, which gives direct information on the chlorophyll-a content. Clearance rates (CR) of Daphnia and Brachionus were calculated from a decrease in chlorophyll-a concentration using the PHYTO-PAM

  17. FO-spectra of chlorophyll fluorescence for the determination of zooplankton grazing

    NARCIS (Netherlands)

    Lürling, M.; Verschoor, A.M.

    2003-01-01

    In the PHYTO-PAM phytoplankton analyzer the minimal fluorescence of dark-adapted samples (F0) was assessed, which gives direct information on the chlorophyll- a content. Clearance rates (CR) of Daphnia and Brachionus were calculated from a decrease in chlorophyll-a concentration using the PHYTO-PAM

  18. Temperature dependence of absorption and fluorescence spectra of bacteriochlorophylls in vivo and in vitro

    NARCIS (Netherlands)

    Goedheer, J.C.

    1972-01-01

    The “short wave” far-red absorption bands (795–825 nm) of bacteriochlorophyll in photosynthetic red bacteria are sharpened but not shifted upon cooling, the “long wave” far-red bands (840–890 nm) are sharpened less but shifted appreciably towards longer wavelengths. The fluorescence bands are shifte

  19. Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of Gallic acid imprinted polymers

    Science.gov (United States)

    Pardeshi, Sushma; Dhodapkar, Rita; Kumar, Anupama

    2013-12-01

    Gallic acid (GA) is known by its antioxidant, anticarcinogenic properties and scavenger activity against several types of harmful free radicals. Molecularly imprinted polymers (MIPs) are used in separation of a pure compound from complex matrices. A stable template-monomer complex generates the MIPs with the highest affinity and selectivity for the template. The quantum chemical computations based on density functional theory (DFT) was used on the template Gallic acid (GA), monomer acrylic acid (AA) and GA-AA complex to study the nature of interactions involved in the GA-AA complex. B3LYP/6-31+G(2d,2p) model chemistry was used to optimize their structures and frequency calculations. The effect of porogen acetonitrile (ACN) on complex formation was included by using polarizable continuum model (PCM). The results demonstrated the formation of a stable GA-AA complex through the intermolecular hydrogen bonding between carboxylic acid groups of GA and AA. The Mulliken atomic charge analysis and simulated vibrational spectra also supported the stable hydrogen bonding interaction between the carboxylic acid groups of GA and AA with minimal interference of porogen ACN. Further, simulations on GA-AA mole ratio revealed that 1:4 GA-AA was optimum for synthesis of MIP for GA.

  20. Study of vibrational spectra and hydrogen bonding network in dimeric and tetrameric model of ampicillin using DFT and AIM approach

    Science.gov (United States)

    Shukla, Anuradha; Khan, Eram; Tandon, Poonam; Sinha, Kirti

    2017-03-01

    Ampicillin is a β-lactam antibiotic that is active against both gram-positive and gram-negative bacteria and is widely used for the treatment of infections. In this work, molecular properties of ampicillin are calculated on the basis of calculations on its dimeric and tetrameric models using DFT/B3LYP/6-311G(d,p). HOMO-LUMO energy gap shows that chemical reactivity of tetrameric model of ampicillin is higher than the dimeric and monomeric model of ampicillin. To get a better understanding of intra and intermolecular bonding and interactions among bonds, NBO analysis is carried out with tetrameric model of ampicillin, and is further finalized with an 'quantum theory of atoms-in-molecules' (QTAIM) analysis. The binding energy of dimeric model of ampicillin is calculated as -26.84 kcal/mol and -29.34 kcal/mol using AIM and DFT calculations respectively. The global electrophilicity index (ω = 2.8118 eV) of tetrameric model of ampicillin shows that this behaves as a strong electrophile in comparison to dimeric and monomeric model of ampicillin. The FT-Raman and FT-IR spectra were recorded in the solid phase, and interpreted in terms of potential energy distribution analysis. A collective theoretical and experimental vibrational analysis approves the presence of hydrogen bonds in the ampicillin molecule.

  1. Study of molecular structure, vibrational, electronic and NMR spectra of oncocalyxone A using DFT and quantum chemical calculations

    Science.gov (United States)

    Joshi, Bhawani Datt; Srivastava, Anubha; Honorato, Sara Braga; Tandon, Poonam; Pessoa, Otília Deusdênia Loiola; Fechine, Pierre Basílio Almeida; Ayala, Alejandro Pedro

    2013-09-01

    Oncocalyxone A (C17H18O5) is the major secondary metabolite isolated from ethanol extract from the heartwood of Auxemma oncocalyx Taub popularly known as “pau branco”. Oncocalyxone A (Onco A) has many pharmaceutical uses such as: antitumor, analgesic, antioxidant and causative of inhibition of platelet activation. We have performed the optimized geometry, total energy, conformational study, molecular electrostatic potential mapping, frontier orbital energy gap and vibrational frequencies of Onco A employing ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d, p) basis set. Stability of the molecule arising from hyperconjugative interactions and/or charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis spectrum of the compound was recorded in DMSO and MeOH solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using IEF-PCM and 6-31G basis set. The 13C NMR chemical shifts have been calculated with the B3LYP/6-311++G(d, p) basis set and compared with the experimental values. These methods have been used as tools for structural characterization of Onco A.

  2. Calculating vibrational spectra with sum of product basis functions without storing full-dimensional vectors or matrices

    CERN Document Server

    Leclerc, Arnaud

    2014-01-01

    We propose an iterative method for computing vibrational spectra that significantly reduces the memory cost of calculations. It uses a direct product primitive basis, but does not require storing vectors with as many components as there are product basis functions. Wavefunctions are represented in a basis each of whose functions is a sum of products (SOP) and the factorizable structure of the Hamiltonian is exploited. If the factors of the SOP basis functions are properly chosen, wavefunctions are linear combinations of a small number of SOP basis functions. The SOP basis functions are generated using a shifted block power method. The factors are refined with a rank reduction algorithm to cap the number of terms in a SOP basis function. The ideas are tested on a 20-D model Hamiltonian and a realistic CH$_3$CN (12 dimensional) potential. For the 20-D problem, to use a standard direct product iterative approach one would need to store vectors with about $10^{20}$ components and would hence require about $8 \\tim...

  3. Study of molecular structure, vibrational, electronic and NMR spectra of oncocalyxone A using DFT and quantum chemical calculations.

    Science.gov (United States)

    Joshi, Bhawani Datt; Srivastava, Anubha; Honorato, Sara Braga; Tandon, Poonam; Pessoa, Otília Deusdênia Loiola; Fechine, Pierre Basílio Almeida; Ayala, Alejandro Pedro

    2013-09-01

    Oncocalyxone A (C17H18O5) is the major secondary metabolite isolated from ethanol extract from the heartwood of Auxemma oncocalyx Taub popularly known as "pau branco". Oncocalyxone A (Onco A) has many pharmaceutical uses such as: antitumor, analgesic, antioxidant and causative of inhibition of platelet activation. We have performed the optimized geometry, total energy, conformational study, molecular electrostatic potential mapping, frontier orbital energy gap and vibrational frequencies of Onco A employing ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. Stability of the molecule arising from hyperconjugative interactions and/or charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis spectrum of the compound was recorded in DMSO and MeOH solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using IEF-PCM and 6-31G basis set. The (13)C NMR chemical shifts have been calculated with the B3LYP/6-311++G(d,p) basis set and compared with the experimental values. These methods have been used as tools for structural characterization of Onco A.

  4. [Determination of carmine in carbonated beverages using 3-D fluorescence spectra coupled with second-order calibration algorithm].

    Science.gov (United States)

    Li, Run; Chen, Guo-qing; Zhu, Chun; Kong, Fan-biao; Hu, Yang-jun

    2014-12-01

    Three-dimensional fluorescence spectra combined with second-order calibration algorithm based on alternate a weighted residual (ANWE) was applied to the direct concentration determination of carmine in carbonated beverages. Firstly, 3-D fluorescence spectra of carmine and sunset yellow mixed solutions with different concentrations were obtained by employing spectrometer, and analyzed by using ANWE, the correlation coefficient between calibration concentration and the actual concentration was 0.9917, and the average recovery was 100.92%±2.71%. The results show that the ANWE algorithm is reliable. Then, the commercial carbonated soft drinks in 8, 9, 12 and 13 times diluted concentration were detected by using ANWE algorithm, the correlation coefficient between relative concentration and the actual concentration were 0.9930, 0.9930, 0.9932 and 0.7932, respectively, and the contents of carmine in beverage were 38.88, 37.71, 37.68 and 39.65 μg · mL(-1), respectively. The average concentration was (38.48±0.96) μg · mL(-1). Finally, the standard addition method was applied to estimate the prediction accuracy between calibration concentration and the actual concentration was 0.9935, and the average recovery was 102.99%±2.15%. The results can provide a new idea for the rapid content determination of food pigments in commercial beverages.

  5. Simulation of infrared spectra for beta-hairpin peptides stabilized by an Aib-Gly turn sequence: correlation between conformational fluctuation and vibrational coupling.

    Science.gov (United States)

    Kim, Joohyun; Huang, Rong; Kubelka, Jan; Bou Rcaron, Petr; Keiderling, Timothy A

    2006-11-23

    Vibrational spectra of a 12-residue beta-hairpin peptide, RYVEVBGKKILQ (HBG), stabilized by an Aib-Gly turn sequence (B = Aib) were investigated theoretically using a combination of molecular dynamics (MD) and density functional theory (DFT) calculations. Selected conformations of HBG were extracted from a classical MD trajectory and used for spectral simulations. DFT calculations, based on the Cartesian coordinate spectral property transfer protocol, were carried out for peptide structures in which all residues are replaced with Ala, except for the Aib and Gly residues, but the backbone (phi, psi, omega) structure of the original configuration is retained. The simulations provide a basis for interpretation of the HBG amide I infrared spectra in terms of structural variables such as detailed secondary structure and thermal conformational fluctuation as well as vibrational coupling as indicated by spectra of 13C isotope-labeled variants. The characteristic amide I band shape of such small beta-hairpin peptides appears to arise from the structure of the short antiparallel beta-sheet strands. The role of structural parameter fluctuation in vibrational coupling is evaluated by comparison of DFT-derived amide coupling constants for selected configurations and from transition dipole coupling calculations of coupling parameters between (13)C isotopically labeled residues for a MD-derived ensemble of configurations. Calculated results were compared with the experimentally obtained spectra for several (13)C isotope-labeled peptides of this sequence.

  6. Computer simulations on resonant fluorescence spectra in atomic gases in two monochromatic laser fields of arbitrary intensity and magnetic field

    Science.gov (United States)

    Karagodova, Tamara Y.

    1996-03-01

    In the intense radiation fields with power density from 104W/cm2 to 109W/cm2 the essential modification of electronic states of atoms occurs displaying, in particular, in modifications of resonant fluorescence (rf) spectra. We use 'Fermi golden rule' for calculations of relative intensities and frequencies for rf multiplet for real multilevel initially unexcited atoms in two monochromatic laser fields of arbitrary intensity resonant to adjacent transitions of (Xi) or (Lambda) types and magnetic field, giving the level splittings of different values from Zeeman to Paschen-Back effect. The dependence of quasienergies on parameters obtained with the help of a sorting program permits us to define the values of parameters for which the states of the system are mixed and so to receive the correct probability amplitudes for instantaneous or adiabatic regimes of switching the perturbation. The analysis of the quasienergies and form of rf spectra permits us to get relations between the form of the spectra and modifications of electronic structure of the atom due to radiation fields and external magnetic field.

  7. Influence of the emission-reception geometry in laser-induced fluorescence spectra from turbid media.

    Science.gov (United States)

    Avrillier, S; Tinet, E; Ettori, D; Tualle, J M; Gélébart, B

    1998-05-01

    Routine clinical detection of precancerous lesions by laser-inducedautofluorescence was recently demonstrated in several medicalfields. This technique is based on the analysis of complex spectrawith overlapping broad structures. However, in biological tissues, scattering and absorption are wavelength dependent, and the observedfluorescence signals are distorted when the illumination and detectiongeometry varies, making comparison of results from different groupsdifficult. We study this phenomenon experimentally in human tissuein a simple experiment: A fiber is used for the excitation and anidentical fiber is used for reception of the signal; both fibers aremaintained in contact with the tissue. We study the distortion ofthe spectra as a function of the distance between the twofibers. For correction of the spectra we show that it is possibleto use a fast and accurate ab initio Monte Carlo simulationwhen the spectral variations of the optical properties of the mediumare known. The main advantage of this simulation is itsapplicability even for complex boundary conditions or when the sampleconsists of several layers.

  8. Effect of CdSe nanoparticles on the fluorescence spectra of conjugate polymer P3HT: An experimental and theoretical study

    Science.gov (United States)

    Mastour, Nouha; Bouchriha, Habib

    2016-11-01

    In this work we have investigated the effect of CdSe nanoparticles (Nps) on the fluorescence spectra of conjugate polymer Poly(3-hexylthiophene-2,5-diyl) (P3HT). The fluorescence intensity is significantly decreased in both solution and solid films by the incorporation of CdSe Nps. This observed effect in the nanocomposite P3HT-CdSe is analyzed by using the Franck-Condon theory which reproduces correctly the decrease of the fluorescence with the Nps concentration and permits to reach the Huang-Rhys factor and the relaxation energy which are shown efficient to explain the fluorescence quenching.

  9. Multi-Photon Absorption Spectra: A Comparison Between Transmittance Change and Fluorescence Methods

    Science.gov (United States)

    2015-05-21

    AFRL-OSR-VA-TR-2015-0134 multi-photon absorption spectra Cleber Mendonca INSTITUTO DE FISICA DE SAO CARLOS Final Report 05/21/2015 DISTRIBUTION A...5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Instituto de Fisica de Sao Carlos - Universidade de Sao Paulo Av...of this project is to determine the multi-photon absorption spectrum of organic compounds, in order to establish its correlation with the molecular

  10. The photodissociation and reaction dynamics of vibrationally excited molecules

    Energy Technology Data Exchange (ETDEWEB)

    Crim, F.F. [Univ. of Wisconsin, Madison (United States)

    1993-12-01

    This research determines the nature of highly vibrationally excited molecules, their unimolecular reactions, and their photodissociation dynamics. The goal is to characterize vibrationally excited molecules and to exploit that understanding to discover and control their chemical pathways. Most recently the author has used a combination of vibrational overtone excitation and laser induced fluorescence both to characterize vibrationally excited molecules and to study their photodissociation dynamics. The author has also begun laser induced grating spectroscopy experiments designed to obtain the electronic absorption spectra of highly vibrationally excited molecules.

  11. Microwave, infrared and Raman spectra, r0 structural parameters, ab initio calculations and vibrational assignment of 1-fluoro-1-silacyclopentane.

    Science.gov (United States)

    Durig, James R; Panikar, Savitha S; Obenchain, Daniel A; Bills, Brandon J; Lohan, Patrick M; Peebles, Rebecca A; Peebles, Sean A; Groner, Peter; Guirgis, Gamil A; Johnston, Michael D

    2012-01-28

    The microwave spectrum (6500-18 ,500 MHz) of 1-fluoro-1-silacyclopentane, c-C(4)H(8)SiHF has been recorded and 87 transitions for the (28)Si, (29)Si, (30)Si, and (13)C isotopomers have been assigned for a single conformer. Infrared spectra (3050-350 cm(-1)) of the gas and solid and Raman spectrum (3100-40 cm(-1)) of the liquid have also been recorded. The vibrational data indicate the presence of a single conformer with no symmetry which is consistent with the twist form. Ab initio calculations with a variety of basis sets up to MP2(full)/aug-cc-pVTZ predict the envelope-axial and envelope-equatorial conformers to be saddle points with nearly the same energies but much lower energy than the planar conformer. By utilizing the microwave rotational constants for seven isotopomers ((28)Si, (29)Si, (30)Si, and four (13)C) combined with the structural parameters predicted from the MP2(full)/6-311+G(d,p) calculations, adjusted r(0) structural parameters have been obtained for the twist conformer. The heavy atom distances in Å are: r(0)(SiC(2)) = 1.875(3); r(0)(SiC(3)) = 1.872(3); r(0)(C(2)C(4)) = 1.549(3); r(0)(C(3)C(5)) = 1.547(3); r(0)(C(4)C(5)) = 1.542(3); r(0)(SiF) = 1.598(3) and the angles in degrees are: [angle]CSiC = 96.7(5); [angle]SiC(2)C(4) = 103.6(5); [angle]SiC(3)C(5) = 102.9(5); [angle]C(2)C(4)C(5) = 108.4(5); [angle]C(3)C(5)C(4) = 108.1(5); [angle]F(6)Si(1)C(2) = 110.7(5); [angle]F(6)Si(1)C(3) = 111.6(5). The heavy atom ring parameters are compared to the corresponding r(s) parameters. Normal coordinate calculations with scaled force constants from MP2(full)/6-31G(d) calculations were carried out to predict the fundamental vibrational frequencies, infrared intensities, Raman activities, depolarization values, and infrared band contours. These experimental and theoretical results are compared to the corresponding quantities of some other five-membered rings.

  12. First-principles calculation of geometry and anharmonic vibrational spectra of thioformamide and thioformamide-d2

    Science.gov (United States)

    Kowal, Andrzej T.

    2006-01-01

    The equilibrium geometry of thioformamide HCSNH2 has been determined at the MP2 and CCSD (T) electron correlation levels under Cs symmetry constraints using triple-zeta basis sets up to cc-pVTZ. All optimized planar structures are true minima on the potential-energy surface and are characterized by the C-N bond length within 1.353-1.343Å, C-S distances of 1.656-1.628Å, and NCS angle between 125.7° and 125.9°. The wave number of the NH2 out-of-plane wagging mode computed in the harmonic approximation shows stronger dependence on the basis set rather than the electron correlation level and varies from 85.9cm-1 at CCSD (T)/cc-pVDZ level to 335cm-1 at MP2/aug-cc-pVTZ level. Anharmonic vibrational spectra of HCSNH2 and HCSND2 have been determined directly from the potential-energy surfaces computed at MP2 level in triple-zeta valence (TZV)(2df,2p) and TZV +(2df,2p) basis sets using vibrational self-consistent-field (VSCF) and correlation-corrected VSCF (CC-VSCF) methods. CC-VSCF wave numbers of fundamental, first overtone, and most intense combination transitions are reported for thioformamide and those of fundamentals for thioformamide-d2. The NH2 wagging (ν12) mode is strongly anharmonic and its fundamentals have been computed at 406.9cm-1[TZV(2df,2p)] and 399.5cm-1[TZV+(2df,2p)], which is remarkably close to the experimental energy of 393cm-1. Anharmonically computed fundamentals of this mode in thioformamide-d2, 299.7cm-1[TZV(2df,2p)] and 299.6cm-1[TZV+(2df,2p)], are only ˜7cm-1 higher than the transition energy (293cm-1) observed in the gas phase spectrum of HCSND2. The first overtone of the NH2 wagging mode of thioformamide (ν1202) has been calculated by CC-VSCF procedure at 830.8cm-1[TZV(2df,2p)] and 880.0cm-1[TZV+(2df,2p)], which implies "negative" (ν1202>2*ν1201) anharmonicity of this mode.

  13. Density functional theory study, FT-IR and FT-Raman spectra and SQM force field calculation for vibrational analysis of 1, 3-Bis (hydroxymethyl) benzimidazolin-2-one.

    Science.gov (United States)

    Joseph, Lynnette; Sajan, D; Chaitanya, K; Devarajegowda, H C; Isac, Jayakumary

    2013-10-01

    FT-IR and FT-Raman spectra of 1, 3-Bis (hydroxymethyl) benzimidazolin-2-one were recorded and analyzed in the solid phase. The optimized molecular geometry and vibrational wavenumbers have also been calculated in optimized structure by using DFT method. Scaled quantum mechanical force fields have also been used to calculate potential energy distributions in order to make conspicuous vibrational assignments. The red shifting of the O-H stretching wavenumber is due to the formation of O-H···O intermolecular hydrogen bonding. The lowering and splitting of the carbonyl stretching vibrational modes is assigned to the intermolecular association based on C=O···H type hydrogen bonding in the molecule. Chemical interpretation of hyperconjugative interactions was done by natural bond orbital analysis.

  14. Comparison of the performance of different DFT methods in the calculations of the molecular structure and vibration spectra of serotonin (5-hydroxytryptamine, 5-HT)

    Science.gov (United States)

    Yang, Yue; Gao, Hongwei

    2012-04-01

    Serotonin (5-hydroxytryptamine, 5-HT) is a monoamine neurotransmitter which plays an important role in treating acute or clinical stress. The comparative performance of different density functional theory (DFT) methods at various basis sets in predicting the molecular structure and vibration spectra of serotonin was reported. The calculation results of different methods including mPW1PW91, HCTH, SVWN, PBEPBE, B3PW91 and B3LYP with various basis sets including LANL2DZ, SDD, LANL2MB, 6-31G, 6-311++G and 6-311+G* were compared with the experimental data. It is remarkable that the SVWN/6-311++G and SVWN/6-311+G* levels afford the best quality to predict the structure of serotonin. The results also indicate that PBEPBE/LANL2DZ level show better performance in the vibration spectra prediction of serotonin than other DFT methods.

  15. The giant frequency shift of intramolecular O-H vibration band in the raman spectra of water on the silver surface

    CERN Document Server

    Kompan, Mikhail

    2016-01-01

    The giant frequency shift was observed in Raman spectra for inramolecular O-H vibration band. The effect was observed in SERS-condition experiment, when exciting light was focused by short-focus objective on the Ag-surface, merged in water. The shift was detected relatively to the regularl position of band, measured from the bulk of water under the same other conditions.

  16. Hexamethylenetetramine (urotropine) C6H12N2: Interpreting the vibrational spectra of -d0 and -d12 isotopomers by scaling the quantum-chemical force field

    Science.gov (United States)

    Khaikin, L. S.; Grikina, O. E.; Kochikov, I. V.; Stepanov, N. F.

    2014-03-01

    The equilibrium structure and quadratic and cubic force fields of the urotropine molecule are calculated at the MP2 (full)/cc-pVTZ level. Pulay scaling of the quadratic force field allows unambiguous interpretation of the vibrational spectra of -d0 and -d12 urotropines. A reliable matrix for the quadratic force constants of urotropine is obtained which may be used to determine the parameters of the equilibrium structure of the urotropine molecule by means of gas-phase electron diffraction.

  17. Vibrational spectra, UV-vis spectral analysis and HOMO-LUMO studies of 2,4-dichloro-5-nitropyrimidine and 4-methyl-2-(methylthio)pyrimidine.

    Science.gov (United States)

    Arivazhagan, M; Anitha Rexalin, D

    2013-04-15

    The FT-IR and FT-Raman vibrational spectra of 2,4-dichloro-5-nitropyrimidine (DCNP) and 4-methyl-2-(methylthio)pyrimidine (MTP) have been recorded in the range 4000-400 and 3600-50 cm(-1), respectively. A detailed vibrational spectral analysis has been carried out and assignments of the observed fundamental bands have been proposed on the basis of peak positions and relative intensities. The optimized molecular geometry and vibrational frequencies in the ground state are calculated using density functional B3LYP method with 6-31+G(d,p) and 6-311++G(d,p) basis set combinations. With the help of specific scaling procedures, the observed vibrational wavenumbers in FT-IR and FT-Raman spectra are analyzed and assigned to different normal modes of the molecules. The predicted first hyperpolarizability reveals that the molecules are an attractive object for future studies of non-linear optical properties. And also HOMO-LUMO energy gap explains the eventual charge transfer interaction taking place within the molecules. UV-vis spectral analysis of the title compounds has been researched by theoretical calculations. The frontier orbital energies, absorption wavelengths (λ), oscillator strengths (f) and excitation energies (E) studied using TD-DFT (B3LYP) with 6-311++G(d,p) basis set are calculated in this work.

  18. High-resolution spectroscopy in superfluid helium droplets. Investigation of vibrational fine structures in electronic spectra of phthalocyanine and porphyrin derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Riechers, Ricarda Eva Friederike Elisabeth

    2011-03-22

    Since a considerably large variety of substituted compounds is commercially available and the electronic excitation spectra fit well into the spectral range covered by the continuous wave dye laser used for this study several porphyrin and phthalocyanine derivatives substituted with different types and numbers of alkyl and aryl groups were chosen as molecular probes. Recording fluorescence excitation and dispersed emission spectra revealed exclusively sharp transitions for all species. A change of the molecule's electrostatic moments, primarily and most effectively, a change of the molecular dipole moment regarding both magnitude and orientation, was identified as the main contribution for line broadening effects. Apart from the sharp lines presented in their fluorescence excitation spectra, the phthalocyanine derivatives investigated for this study, namely chloro-aluminium-phthalocyanine (AlClPc) and tetra-tertbutyl-phthalocyanine (TTBPc), exhibited more than one emission spectrum.

  19. Calculated Rotational and Vibrational g Factors of LiH X (1)Sigma(+) and Evaluation of Parameters in Radial Functions from Rotational and Vibration-Rotational Spectra

    DEFF Research Database (Denmark)

    Sauer, S. P. A.; Paidarová, I.; Oddershede, J.

    2011-01-01

    The vibrational g factor, that is, the nonadiabatic correction to the vibrational reduced mass, of LiH has been calculated for internuclear distances over a wide range. Based on multiconfigurational wave functions with a large complete active space and an extended set of gaussian type basis...... functions, these calculations yielded also the rotational g factor, the electric dipolar moment, and its gradient with internuclear distance for LiH in its electronic ground state X (1)Sigma(+). The vibrational g factor g(v) exhibits a pronounced minimum near internuclear distance R = 3.65 x 10(-10) m...... state A (1)Sigma(+). The irreducible contribution g(r)(irr)(R) to the rotational g factor increases monotonically over the calculated domain, whereas the irreducible contribution g(v)(irr)(R) to the vibrational g factor has a minimum at the same location as that of g(v) itself. From these calculated...

  20. Vibrational spectra (FT-IR, FT-Raman), frontier molecular orbital, first hyperpolarizability, NBO analysis and thermodynamics properties of Piroxicam by HF and DFT methods.

    Science.gov (United States)

    Suresh, S; Gunasekaran, S; Srinivasan, S

    2015-03-05

    The solid phase FT-IR and FT-Raman spectra of 4-Hydroxy-2-methyl-N-(2-pyridinyl)-2H-1,2-benzothiazine-3-carboxamide-1,1-dioxide (Piroxicam) have been recorded in the region 4000-400 and 4000-100cm(-1) respectively. The molecular geometry, harmonic vibrational frequencies and bonding features of piroxicam in the ground state have been calculated by Hartree-Fock (HF) and density functional theory (DFT) methods using 6-311++G(d,p) basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimental obtained by FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of the title compound has been made on the basis of the calculated potential energy distribution (PED). The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) are also performed. The linear polarizability (α) and the first order hyper polarizability (β) values of the title compound have been computed. The molecular stability arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

  1. Vibrational spectra (FT-IR, FT-Raman), frontier molecular orbital, first hyperpolarizability, NBO analysis and thermodynamics properties of Piroxicam by HF and DFT methods

    Science.gov (United States)

    Suresh, S.; Gunasekaran, S.; Srinivasan, S.

    2015-03-01

    The solid phase FT-IR and FT-Raman spectra of 4-Hydroxy-2-methyl-N-(2-pyridinyl)-2H-1,2-benzothiazine-3-carboxamide-1,1-dioxide (Piroxicam) have been recorded in the region 4000-400 and 4000-100 cm-1 respectively. The molecular geometry, harmonic vibrational frequencies and bonding features of piroxicam in the ground state have been calculated by Hartree-Fock (HF) and density functional theory (DFT) methods using 6-311++G(d,p) basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimental obtained by FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of the title compound has been made on the basis of the calculated potential energy distribution (PED). The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) are also performed. The linear polarizability (α) and the first order hyper polarizability (β) values of the title compound have been computed. The molecular stability arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

  2. Studies of the molecular geometry, vibrational spectra, frontier molecular orbital, nonlinear optical and thermodynamics properties of aceclofenac by quantum chemical calculations.

    Science.gov (United States)

    Suresh, S; Gunasekaran, S; Srinivasan, S

    2014-05-05

    The solid phase FT-IR and FT-Raman spectra of 2-[2-[2-[(2,6-dichlorophenyl)amino]phenyl]acetyl] oxyacetic acid (Aceclofenac) have been recorded in the region 4000-400 and 4000-100 cm(-1) respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies were scaled and have been compared with experimental by obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method employed to study its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) were also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

  3. A comparative study of the vibrational spectra of the anticancer drug melphalan and its fundamental molecules 3-phenylpropionic acid and L-phenylalanine

    Science.gov (United States)

    Badawi, Hassan M.; Khan, Ibrahim

    2016-04-01

    The structural stability and the vibrational spectra of the anticancer drug melphalan and its parent compounds 3-phenylpropionic acid and L-phenylalanine were investigated by the DFT B3LYP/6-311G** calculations. Melphalan and its fundamental compounds were predicted to exist predominantly in non-planar structures. The vibrational frequencies of the low energy structures of melphalan, 3-phenylpropionic acid, and phenylalanine were computed at the DFT B3LYP level of theory. Complete vibrational assignments of the normal modes of melphalan, 3-phenylpropionic acid, and phenylalanine were provided by combined theoretical and experimental data of the molecules. The experimental infrared spectra of phenylalanine and melphalan show a significantly different pattern of the Cdbnd O stretching mode as compared to those of normal carboxylic acids. A comparison of the 3700-2000 cm-1 infrared spectral region of the three molecules suggests the presence of similar intermolecular H-bonding in their condensed phases. The observed infrared and Raman spectra are consistent with the presence of one predominant melphalan conformation at room temperature.

  4. The vibrational spectra of N-phenylpyrrole in the gas phase, in argon matrices and in single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Schweke, D. [Department of Physical Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Farkas Center for Light-Induced Processes, Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Brauer, B. [Department of Physical Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Fritz Haber Research Center, Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Gerber, R.B. [Department of Physical Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Fritz Haber Research Center, Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Department of Chemistry, University of California, Irvine, CA 92697 (United States); Haas, Y. [Department of Physical Chemistry, Hebrew University of Jerusalem, Jerusalem 91904 (Israel); Farkas Center for Light-Induced Processes, Hebrew University of Jerusalem, Jerusalem 91904 (Israel)], E-mail: yehuda@chem.ch.huji.ac.il

    2007-03-30

    The infrared spectrum of N-phenylpyrrole (PP) was measured in the gas phase and in an argon matrix, and the Raman spectrum was obtained in a single crystal. The measured matrix shifts are found to be small: many bands are not split, and the shifts from the gas phase values are less than 1%. Splitting to two sub-bands is observed for some bands, indicating the presence of two major trapping sites, in agreement with previous predictions. The spectra are analyzed with the help of harmonic calculations on the free molecule and on its adduct with one or two argon atoms, and anharmonic frequency calculations on the free molecule. Harmonic frequencies were obtained at the MP2/cc-pVDZ and DFT-B3LYP/cc-pVDZ levels. Anharmonic frequencies were obtained by the correlation-corrected vibrational self-consistent field (CC-VSCF) method with a variant of the PM3 semiempirical electronic structure method, calibrated for much improved spectroscopic accuracy. The potential surfaces used in the CC-VSCF calculation obtained by adjusting standard PM3 surfaces so that they provide harmonic frequencies that are comparable to those obtained at the DFT-B3LYP/cc-pVDZ level. Agreement between the experimental and theoretical results is in general very good, allowing the assignments of most bands. The harmonic frequency calculations of PP-Ar clusters, at the MP2/cc-pVDZ level show that the environment can greatly affect the intensities of some of the transitions, which is in accord with experiment.

  5. Microwave and infrared spectra, adjusted r0 structural parameters, conformational stabilities, vibrational assignments, and theoretical calculations of cyclobutylcarboxylic acid chloride.

    Science.gov (United States)

    Klaassen, Joshua J; Darkhalil, Ikhlas D; Deodhar, Bhushan S; Gounev, Todor K; Gurusinghe, Ranil M; Tubergen, Michael J; Groner, Peter; Durig, James R

    2013-08-01

    The FT-microwave spectrum of cyclobutylcarboxylic acid chloride, c-C4H7C(O)Cl, has been recorded and 153 transitions for the (35)Cl and (37)Cl isotopologues have been assigned for the gauche-equatorial (g-Eq) conformation. The ground state rotational constants were determined for (35)Cl [(37)Cl]: A = 4349.8429(25) [4322.0555(56)] MHz, B = 1414.8032(25) [1384.5058(25)] MHz, and C = 1148.2411(25) [1126.3546(25)] MHz. From these rotational constants and ab initio predicted parameters, adjusted r0 parameters are reported with distances (Å) rCα-C = 1.491(4), rC═O = 1.193(3), rCα-Cβ = 1.553(4), rCα-Cβ' = 1.540(4), rCγ-Cβ = 1.547(4), rCγ-Cβ' = 1.546(4), rC-Cl = 1.801(3) and angles (deg) τCγCβCβ'Cα = 30.9(5). Variable temperature (-70 to -100 °C) infrared spectra (4000 to 400 cm(-1)) were recorded in liquid xenon and the g-Eq conformer was determined the most stable form, with enthalpy differences of 91 ± 9 cm(-1) (1.09 ± 0.11 kJ/mol) for the gauche-axial (g-Ax) form and 173 ± 17 cm(-1) (2.07 ± 0.20 kJ/mol) for the trans-equatorial (t-Eq) conformer. The relative amounts at ambient temperature are 54% g-Eq, 35 ± 1% g-Ax, and 12 ± 1% t-Eq forms. Vibrational assignments have been provided for the three conformers and theoretical calculations were carried out. The results are discussed and compared to corresponding properties of related molecules.

  6. Temperature measurements using a projection to latent structures of fluorescence spectra of potassium-aluminum borate glasses with copper-containing molecular clusters

    Science.gov (United States)

    Babkina, A. N.; Khodasevich, M. A.; Shirshnev, P. S.

    2017-02-01

    Luminescence spectra of a potassium-aluminum borate glass with copper-containing molecular clusters are presented in the temperature range of 295-624 K. Two methods of temperature measurement are compared with the aim of evaluating the possibility of their further application in optical temperature sensors: specifically, the classical method of measuring a temperature based on the spectral position of the fluorescence band peak and the measurement method based on projection to latent structures of fluorescence spectra in the visible range. It is shown that, concerning the accuracy of measuring a temperature, the fourdimensional space of latent structures is preferred for the case under consideration; it allows one to determine (using a training set of fluorescence spectra) a temperature with the relative error of no more than 1.2%.

  7. X-ray spectra of Hercules X-1. I - Iron line fluorescence from a subrelativistic shell

    Science.gov (United States)

    Pravdo, S. H.; Becker, R. H.; Boldt, E. A.; Holt, S. S.; Serlemitsos, P. J.; Swank, J. H.

    1977-01-01

    The X-ray spectrum of Her X-1 was observed in the energy range from 2 to 24 keV from August 29 to September 3, 1975. Emission features are observed near the K-alpha iron-line energy which exhibit both broadening and a double line structure. The total luminosity in these features is about 4 by 10 to the 35th power ergs/s. Iron line fluorescence from an opaque cool (not exceeding 1 million K) shell of material at the Alfven surface provides the necessary luminosity in this feature. The double line structure and the line energy width can be due to Doppler shifts if the shell is forced to corotate with the pulsar at a radius of at least 800 million cm. Implications of this model regarding physical conditions near Her X-1 are discussed.

  8. UV and fluorescent spectra study the reaction between 1, 8-Naphthalimide derivative and hypochlorite their applications

    Science.gov (United States)

    Li, Jiawei; Liu, Tao; Huo, Fangjun; Chao, Jianbin; Zhang, Yongbin; Yin, Caixia

    2017-03-01

    Two simple, efficient turn-on fluorescent probes for hypochlorite have been rationally designed and developed by utilizing the oxidation of hypochlorite. Notably, probe 1 and 2 displayed rapid and remarkable turn-on responses to ClO- in PBS buffer solution (pH 7.4). Further, the optical properties of two probes and their ClO--addition products were confirmed by density functional theory calculations. And detection limits of two probes for ClO- based on the definition by IUPAC were calculated for 2.882 nM and 0.354 μM. More importantly, cell imaging experiments demonstrated that probe 1 was more suitable for detecting the ClO- in living A549 cells. And both two probes had the possibility of potentially applied in practical applications such as detecting the hypochlorite concentration of tap water and river water.

  9. Evaluation of Silver and Gold Nanoparticles on Polyester Fibers by Fluorescent Polarization Raman Spectra

    Directory of Open Access Journals (Sweden)

    V.M. Emelyanov

    2014-07-01

    Full Text Available The results of the validation of identification nanoparticle colloidal silver and gold on the polyester fibers on the background component of the Raman spectra in the control based on the polarization characteristics. The accuracy of identification of nanoparticles was evaluated by the joint probability of crossing normal scatter intensity distributions Raman spectrograms as silver nanoparticles and gold nanoparticles on polyester fibers, depending on the longitudinal and transverse polarization of the laser radiation on the entire range of wave numbers. Defined generalized parameter values common to distributions over the entire range for each wave numbers with the polarization of the laser and across the grain, and generalized reliability of the control and identification of nanoparticles of silver, gold for assessing the likelihood of the complete group of events. Set the sensitivity of detection reliability.

  10. A novel quantitative analysis method of three-dimensional fluorescence spectra for vegetable oils contents in edible blend oil

    Science.gov (United States)

    Xu, Jing; Wang, Yu-Tian; Liu, Xiao-Fei

    2015-04-01

    Edible blend oil is a mixture of vegetable oils. Eligible blend oil can meet the daily need of two essential fatty acids for human to achieve the balanced nutrition. Each vegetable oil has its different composition, so vegetable oils contents in edible blend oil determine nutritional components in blend oil. A high-precision quantitative analysis method to detect the vegetable oils contents in blend oil is necessary to ensure balanced nutrition for human being. Three-dimensional fluorescence technique is high selectivity, high sensitivity, and high-efficiency. Efficiency extraction and full use of information in tree-dimensional fluorescence spectra will improve the accuracy of the measurement. A novel quantitative analysis is proposed based on Quasi-Monte-Carlo integral to improve the measurement sensitivity and reduce the random error. Partial least squares method is used to solve nonlinear equations to avoid the effect of multicollinearity. The recovery rates of blend oil mixed by peanut oil, soybean oil and sunflower are calculated to verify the accuracy of the method, which are increased, compared the linear method used commonly for component concentration measurement.

  11. Determination of the in vivo redox potential using roGFP and fluorescence spectra obtained from one-wavelength excitation

    Science.gov (United States)

    Wierer, S.; Elgass, K.; Bieker, S.; Zentgraf, U.; Meixner, A. J.; Schleifenbaum, F.

    2011-02-01

    The analysis of molecular processes in living (plant) cells such as signal transduction, DNA replication, carbon metabolism and senescence has been revolutionized by the use of green fluorescent protein (GFP) and its variants as specific cellular markers. Many cell biological processes are accompanied by changes in the intracellular redox potential. To monitor the redox potential, a redox-sensitive mutant of GFP (roGFP) was created, which shows changes in its optical properties in response to changes in the redox state of its surrounding medium. For a quantitative analysis in living systems, it is essential to know the optical properties of roGFP in vitro. Therefore, we applied spectrally resolved fluorescence spectroscopy on purified roGFP exposed to different redox potentials to determine shifts in both the absorption and the emission spectra of roGFP. Based on these in vitro findings, we introduce a new approach using one-wavelength excitation to use roGFP for the in vivo analysis of cell biological processes. We demonstrate the ability this technique by investigating chloroplast-located Grx1-roGFP2 expressing Arabidopsis thaliana cells as example for dynamically moving intracellular compartments. This is not possible with the two-wavelength excitation technique established so far, which hampers a quantitative analysis of highly mobile samples due to the time delay between the two measurements and the consequential displacement of the investigated area.

  12. TEMPERATURE DEPENDENCE OF THE FLUORESCENCE SPECTRA OF LADDERLIKE POLYPHENYLSILSESQUIOXANE AND LADDERLIKE 1,4- PHENYLENE-BRIDGED POLYVINYLSILOXANE

    Institute of Scientific and Technical Information of China (English)

    Jun-lin Yang; Feng-lian Bai; Chun-qing Liu; Yang Liu; Ping Xie; Rong-ben Zhang

    2002-01-01

    Fluorescence spectra of ladderlike polyphenylsilsesquioxane (LPPS) and ladderlike 1,4-phenylene-bridged polyvinylsiloxane (LPPVS) have been measured as a function of temperature (4-55℃), in dilute tetrahydrofuran solution.The excimer (IE) to monomer (IM) intensity ratio (IE/IM) of LPPS dilute solution shows a double linear Arrhenius plot with a break point ascribable to a transition temperature Tr. This behavior has not been found for single chain polyorganosiloxanes.When In/E of LPPS was plotted against 1/T, it also gave a double linear plot with one break point, which was found in single chain polyorganosiloxanes. The different behaviors between LPPS and single chain polyorganosiloxanes may be mainly attributed to the relatively rigid double-chain macromolecular backbone of LPPS. However, the ln(IE/IM) of dilute LPPVS solution versus 1/T shows a simple linear variation with a positive slope which confirms our proposition. The difference between the fluorescence results of LPPS and those of LPPVS may possibly derive from their structure differences and cooperative motion in backbone chain bonds.

  13. A band Lanczos approach for calculation of vibrational coupled cluster response functions: simultaneous calculation of IR and Raman anharmonic spectra for the complex of pyridine and a silver cation.

    Science.gov (United States)

    Godtliebsen, Ian H; Christiansen, Ove

    2013-07-07

    We describe new methods for the calculation of IR and Raman spectra using vibrational response theory. Using damped linear response functions that incorporate a Lorentzian line-shape function from the outset, it is shown how the calculation of Raman spectra can be carried out through the calculation of a set of vibrational response functions in the same manner as described previously for IR spectra. The necessary set of response functions can be calculated for both vibrational coupled cluster (VCC) and vibrational configuration interaction (VCI) anharmonic vibrational wave-functions. For the efficient and simultaneous calculation of the full set of necessary response functions, a non-hermitian band Lanczos algorithm is implemented for VCC, and a hermitian band Lanczos algorithm is implemented for VCI. It is shown that the simultaneous calculation of several response functions is often advantageous. Sample calculations are presented for pyridine and the complex between pyridine and the silver cation.

  14. Solvents effect on the absorption and fluorescence spectra of 7-diethylamino-3-thenoylcoumarin: evaluation and correlation between solvatochromism and solvent polarity parameters.

    Science.gov (United States)

    Basavaraja, Jana; Inamdar, S R; Suresh Kumar, H M

    2015-02-25

    Effect of solvents of varying polarities on absorption and fluorescence spectra and dipole moment of laser dye: 7-diethylamino-3-thenoylcoumarin (DETC) has been investigated. A small band shift is obtained in the absorption spectra compared to emission spectra. The spectral shifts were correlated with Catalan's parameters using linear solvation energy relationship. It reveals that non-specific interaction measured by solvent polarity has more influence on absorption and solvent dipolarity contribution is significant in case of fluorescence. A bathochromic shift observed in absorption and emission spectra with increasing solvent polarity, which implied that the transition involved is π→π(∗). The solvatochromic correlations were used to estimate the excited state dipole moment using experimentally determined ground state dipole moment. The observed single-state excited state dipole moment is found to be greater than the ground state.

  15. A Structural Basis for Reversible Photoswitching of Absorbance Spectra in Red Fluorescent Protein rsTagRFP

    Energy Technology Data Exchange (ETDEWEB)

    Pletnev, Sergei; Subach, Fedor V.; Dauter, Zbigniew; Wlodawer, Alexander; Verkhusha, Vladislav V. (Einstein); (NCI)

    2012-09-05

    rsTagRFP is the first monomeric red fluorescent protein (FP) with reversibly photoswitchable absorbance spectra. The switching is realized by irradiation of rsTagRFP with blue (440 nm) and yellow (567 nm) light, turning the protein fluorescence ON and OFF, respectively. It is perhaps the most useful probe in this color class that has yet been reported. Because of the photoswitchable absorbance, rsTagRFP can be used as an acceptor in photochromic Foerster resonance energy transfer. Yellow FPs, YPet and mVenus, are demonstrated to be excellent photochromic Foerster resonance energy transfer donors for the rsTagRFP acceptor in its fusion constructs. Analysis of X-ray structures has shown that photoswitching of rsTagRFP is accompanied by cis-trans isomerization and protonation/deprotonation of the chromophore, with the deprotonated cis- and protonated trans-isomers corresponding to its ON and OFF states, respectively. Unlike in other photoswitchable FPs, both conformers of rsTagRFP chromophore are essentially coplanar. Two other peculiarities of the rsTagRFP chromophore are an essentially hydrophobic environment of its p-hydroxyphenyl site and the absence of direct hydrogen bonding between this moiety and the protein scaffold. The influence of the immediate environment on rsTagRFP chromophore was probed by site-directed mutagenesis. Residues Glu145 and His197 were found to participate in protonation/deprotonation of the chromophore accompanying the photoswitching of rsTagRFP fluorescence, whereas residues Met160 and Leu174 were shown to spatially restrict chromophore isomerization, favoring its radiative decay.

  16. CdSe/ZnS quantum dot fluorescence spectra shape-based thermometry via neural network reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Munro, Troy [Multiscale Thermal-Physics Lab, Department of Mechanical and Aerospace Engineering, Utah State University, 4130 Old Main Hill, Logan, Utah 84322 (United States); Laboratory of Soft Matter and Biophysics, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, B-3001 Heverlee (Belgium); Liu, Liwang; Glorieux, Christ [Laboratory of Soft Matter and Biophysics, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, B-3001 Heverlee (Belgium); Ban, Heng [Multiscale Thermal-Physics Lab, Department of Mechanical and Aerospace Engineering, Utah State University, 4130 Old Main Hill, Logan, Utah 84322 (United States)

    2016-06-07

    As a system of interest gets small, due to the influence of the sensor mass and heat leaks through the sensor contacts, thermal characterization by means of contact temperature measurements becomes cumbersome. Non-contact temperature measurement offers a suitable alternative, provided a reliable relationship between the temperature and the detected signal is available. In this work, exploiting the temperature dependence of their fluorescence spectrum, the use of quantum dots as thermomarkers on the surface of a fiber of interest is demonstrated. The performance is assessed of a series of neural networks that use different spectral shape characteristics as inputs (peak-based—peak intensity, peak wavelength; shape-based—integrated intensity, their ratio, full-width half maximum, peak normalized intensity at certain wavelengths, and summation of intensity over several spectral bands) and that yield at their output the fiber temperature in the optically probed area on a spider silk fiber. Starting from neural networks trained on fluorescence spectra acquired in steady state temperature conditions, numerical simulations are performed to assess the quality of the reconstruction of dynamical temperature changes that are photothermally induced by illuminating the fiber with periodically intensity-modulated light. Comparison of the five neural networks investigated to multiple types of curve fits showed that using neural networks trained on a combination of the spectral characteristics improves the accuracy over use of a single independent input, with the greatest accuracy observed for inputs that included both intensity-based measurements (peak intensity) and shape-based measurements (normalized intensity at multiple wavelengths), with an ultimate accuracy of 0.29 K via numerical simulation based on experimental observations. The implications are that quantum dots can be used as a more stable and accurate fluorescence thermometer for solid materials and that use of

  17. CdSe/ZnS quantum dot fluorescence spectra shape-based thermometry via neural network reconstruction

    Science.gov (United States)

    Munro, Troy; Liu, Liwang; Glorieux, Christ; Ban, Heng

    2016-06-01

    As a system of interest gets small, due to the influence of the sensor mass and heat leaks through the sensor contacts, thermal characterization by means of contact temperature measurements becomes cumbersome. Non-contact temperature measurement offers a suitable alternative, provided a reliable relationship between the temperature and the detected signal is available. In this work, exploiting the temperature dependence of their fluorescence spectrum, the use of quantum dots as thermomarkers on the surface of a fiber of interest is demonstrated. The performance is assessed of a series of neural networks that use different spectral shape characteristics as inputs (peak-based—peak intensity, peak wavelength; shape-based—integrated intensity, their ratio, full-width half maximum, peak normalized intensity at certain wavelengths, and summation of intensity over several spectral bands) and that yield at their output the fiber temperature in the optically probed area on a spider silk fiber. Starting from neural networks trained on fluorescence spectra acquired in steady state temperature conditions, numerical simulations are performed to assess the quality of the reconstruction of dynamical temperature changes that are photothermally induced by illuminating the fiber with periodically intensity-modulated light. Comparison of the five neural networks investigated to multiple types of curve fits showed that using neural networks trained on a combination of the spectral characteristics improves the accuracy over use of a single independent input, with the greatest accuracy observed for inputs that included both intensity-based measurements (peak intensity) and shape-based measurements (normalized intensity at multiple wavelengths), with an ultimate accuracy of 0.29 K via numerical simulation based on experimental observations. The implications are that quantum dots can be used as a more stable and accurate fluorescence thermometer for solid materials and that use of

  18. Removal of the free cysteine residue reduces irreversible thermal inactivation of feruloyl esterase: evidence from circular dichroism and fluorescence spectra.

    Science.gov (United States)

    Li, Jingjing; Zhang, Shuaibing; Yi, Zhuolin; Pei, Xiaoqiong; Wu, Zhongliu

    2015-08-01

    Feruloyl esterase A from Aspergillus niger (AnFaeA) contains three intramolecular disulfide bonds and one free cysteine at position 235. Saturated mutagenesis at Cys235 was carried out to produce five active mutants, all of which displayed unusual thermal inactivation patterns with the most residual activity achieved at 75°C, much higher than the parental AnFaeA. But their optimal reaction temperatures were lower than the parental AnFaeA. Extensive investigation into their free thiol and disulfide bond, circular dichroism spectra and fluorescence spectra revealed that the unfolding of the parental enzyme was irreversible on all the tested conditions, while that of the Cys235 mutants was reversible, and their ability to refold was highly dependent on the denaturing temperature. Mutants denatured at 75°C were able to efficiently reverse the unfolding to regain native structure during the cooling process. This study provided valid evidence that free cysteine substitutions can reduce irreversible thermal inactivation of proteins. © The Author 2015. Published by ABBS Editorial Office in association with Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.

  19. Jet-cooled fluorescence excitation spectra and carbonyl wagging and ring-puckering potential energy functions of cyclobutanone and its 2,2,4,4-d4 isotopomer in the S1(n,π*) electronic excited state

    Science.gov (United States)

    Zhang, Jian; Chiang, Whe-Yi; Laane, Jaan

    1994-03-01

    The jet-cooled fluorescence excitation spectra of cyclobutanone and its 2,2,4,4-d4 isotopomer have been recorded in the 305-335 nm region. The electronic band origin of the d0 molecule for the S1(n,π*) state of A2 symmetry occurs at 30 292 cm-1 (30 265 cm-1 for the d4 molecule). The observed spectra consisting of more than 50 bands for each isotopomer involve ν7, ν8, and ν9 (the three A1 ring vibrations) as well as ν20(C=O in-plane wag), ν26 (C=O out-of-plane wag), and ν27 (ring puckering). Five bands associated with the excited vibrational states of ν26 in the S1(n,π*) electronic state were observed for each isotopic species, and these were used to determine the one-dimensional potential energy functions for the C=O out-of-plane wagging. The C=O wagging angle was determined to be 39° and the barrier to inversion is 2149 cm-1 (2188 cm-1 for the deuteride). For the ring-puckering in the S1 state the lowest three vibrational energy spacings were found to be 106, 166, and 185 cm-1 as compared to values of 35, 57, and 65 cm-1 in the S0 ground state. Several ring-puckering potential energy functions with varying degrees of asymmetry are capable of reproducing the observed results. In all cases, however, the v=0 puckering state lies above any barrier to planarity. A two-dimensional potential function which fits the observed data was also determined in terms of the wagging and puckering coordinates.

  20. Towards understanding the stabilization process in vermicomposting using PARAFAC analysis of fluorescence spectra.

    Science.gov (United States)

    Lv, Baoyi; Xing, Meiyan; Zhao, Chunhui; Yang, Jian; Xiang, Liang

    2014-12-01

    In this study, fluorescence excitation-emission matrix (EEM) combined with parallel factor analysis (PARAFAC) was employed to trace the behavior of water extractable organic matter and assess the stabilization process during vermicomposting of sewage sludge and cattle dung. Experiments using different mixing ratios of sewage sludge and cattle dung were conducted using Eisenia fetida. The results showed that vermicomposting reduced the DOC, DOC/DON ratio and ammonia, while increased the nitrate content. A three-component model containing two humic-like materials (components 1 and 2) and a protein-like material (component 3) was successfully developed using PARAFAC analysis. Moreover, the initial waste composition had a significant effect on the distribution of each component and the addition of cattle dung improved the stability of sewage sludge in vermicomposting. The PARAFAC results also indicated that protein-like materials were degraded and humic acid-like compounds were evolved during vermicomposting. Pearson correlation analysis showed that components 2 and 3 are more suitable to assess vermicompost maturity than component 1. In all, EEM-PARAFAC can be used to track organic transformation and assess biological stability during the vermicomposting process.

  1. Vibrational, X-ray absorption, and Mössbauer spectra of sulfate minerals from the weathered massive sulfide deposit at Iron Mountain, California

    Science.gov (United States)

    Majzlan, Juraj; Alpers, Charles N.; Bender Koch, Christian; McCleskey, R. Blaine; Myneni, Satish B.C.; Neil, John M.

    2011-01-01

    The Iron Mountain Mine Superfund site in California is a prime example of an acid mine drainage (AMD) system with well developed assemblages of sulfate minerals typical for such settings. Here we present and discuss the vibrational (infrared), X-ray absorption, and M??ssbauer spectra of a number of these phases, augmented by spectra of a few synthetic sulfates related to the AMD phases. The minerals and related phases studied in this work are (in order of increasing Fe2O3/FeO): szomolnokite, rozenite, siderotil, halotrichite, r??merite, voltaite, copiapite, monoclinic Fe2(SO4)3, Fe2(SO4)3??5H2O, kornelite, coquimbite, Fe(SO4)(OH), jarosite and rhomboclase. Fourier transform infrared spectra in the region 750-4000cm-1 are presented for all studied phases. Position of the FTIR bands is discussed in terms of the vibrations of sulfate ions, hydroxyl groups, and water molecules. Sulfur K-edge X-ray absorption near-edge structure (XANES) spectra were collected for selected samples. The feature of greatest interest is a series of weak pre-edge peaks whose position is determined by the number of bridging oxygen atoms between Fe3+ octahedra and sulfate tetrahedra. M??ssbauer spectra of selected samples were obtained at room temperature and 80K for ferric minerals jarosite and rhomboclase and mixed ferric-ferrous minerals r??merite, voltaite, and copiapite. Values of Fe2+/[Fe2++Fe3+] determined by M??ssbauer spectroscopy agree well with those determined by wet chemical analysis. The data presented here can be used as standards in spectroscopic work where spectra of well-characterized compounds are required to identify complex mixtures of minerals and related phases. ?? 2011 Elsevier B.V.

  2. Vibrational, X-ray absorption, and Mössbauer spectra of sulfate minerals from the weathered massive sulfide deposit at Iron Mountain, California

    Science.gov (United States)

    Majzlan, Juraj; Alpers, Charles N.; Bender Koch, Christian; McCleskey, R. Blaine; Myneni, Satish B.C.; Neil, John M.

    2014-01-01

    The Iron Mountain Mine Superfund site in California is a prime example of an acid mine drainage (AMD) system with well developed assemblages of sulfate minerals typical for such settings. Here we present and discuss the vibrational (infrared), X-ray absorption, and Mössbauer spectra of a number of these phases, augmented by spectra of a few synthetic sulfates related to the AMD phases. The minerals and related phases studied in this work are (in order of increasing Fe2O3/FeO): szomolnokite, rozenite, siderotil, halotrichite, römerite, voltaite, copiapite, monoclinic Fe2(SO4)3, Fe2(SO4)3·5H2O, kornelite, coquimbite, Fe(SO4)(OH), jarosite and rhomboclase. Fourier transform infrared spectra in the region 750–4000 cm−1 are presented for all studied phases. Position of the FTIR bands is discussed in terms of the vibrations of sulfate ions, hydroxyl groups, and water molecules. Sulfur K-edge X-ray absorption near-edge structure (XANES) spectra were collected for selected samples. The feature of greatest interest is a series of weak pre-edge peaks whose position is determined by the number of bridging oxygen atoms between Fe3+ octahedra and sulfate tetrahedra. Mössbauer spectra of selected samples were obtained at room temperature and 80 K for ferric minerals jarosite and rhomboclase and mixed ferric–ferrous minerals römerite, voltaite, and copiapite. Values of Fe2+/[Fe2+ + Fe3+] determined by Mössbauer spectroscopy agree well with those determined by wet chemical analysis. The data presented here can be used as standards in spectroscopic work where spectra of well-characterized compounds are required to identify complex mixtures of minerals and related phases.

  3. The study of laser induced dispersive fluorescence spectra of SO2 by time tomographic scanning%SO2气体激光诱导色散荧光时间断层扫描研究

    Institute of Scientific and Technical Information of China (English)

    张连水; 陈思远; 李明; 党伟; 赵魁芳

    2011-01-01

    The paper presented one study on the complicated de-excitation process of the first-excited band of SO2 molecule, including fluorescence radiation and collision relaxation, using gated enhanced optical multi-channel spectrum analyzer (OMA) and the quadruple harmonic output (266 nm) of a nanosecond pulsed Nd: YAG laser as excitation source.The time tomographic scanning results showed that the fluorescence spectrum envelopes centered in 305.6 nm and 337.2 nm and the regular fluorescence lines centered in 424.7 nm in the laser induced dispersive fluorescence spectra (LIDFS) were attributed to transitions to the different vibrational levels of ground electronic state X1A1 from low vibrational levels of B1B1, A1A2 and the ground vibrational level a3B1 respectively.The sensitive detection wavelength (425 nm) of SO2 gas was confirmed by the experiment.The harmonic frequencies of the symmetry stretch vibration (ω1 =1151.8 cm-1 ±0.6cm-1) and the bend vibration (ω2=517.8 cm-1 ±0.6 cm-1) of X1A1 state were also calculated from the experimental data.The anharmonic constants of stretch vibration mode and the bend vibration mode arex11 = 8±0.6 cm-1 andx22 = 9.2±0.6 cm-1 respectively.%以纳秒Nd:YAG激光器的四倍频(266 nm)为激发源,利用门选通增强光学多通道光谱分析仪(OMA),研究了SO2分子第一激发带粒子的荧光辐射与碰撞弛豫相结合的复杂退激发过程.通过对SO2分子第一激发带的激发及碰撞弛豫过程的时间断层扫描分析,可以将激光诱导色散荧光谱中以305.6 rnm、337.2 nm为中心的荧光包络和以424.7 nm为中心的规则序列分别归属于B1B1、A1A2低振动能级和a3B1基振动能级到基电子态X1A1不同振动能级的荧光跃迁,由此可以确定大气污染气体SO2的诱导荧光的灵敏检测波长为425 nm由规则序列的实验数据可以计算出SO2分子基电子态X1A1的对称振动和弯曲振动模式的基振动角频率分别为ω1=1151.8士0.6 cm-1和ω2=517.8

  4. Development of a trans-rotational temperature diagnostic for vibrationally-excited carbon monoxide using single- photon laser-induced fluorescence

    Science.gov (United States)

    Leiweke, Robert John

    2004-09-01

    A new trans-rotational temperature diagnostic with ±50K accuracy has been developed for use in nonequilibrium, low temperature, monatomic gases seeded with carbon monoxide (CO). The scheme utilizes single- photon laser induced fluorescence (LIF) of CO under vibrationally-excited conditions in which single-photon transitions from the CO X1Σ + ground electronic state to upper electronic A1Π or D'1Σ+ states become accessible to a tunable, narrowband ArF excimer laser at 193 nm. Two vibrationally excited environments in which the chemistry is well understood were used as a testbed; an optically-pumped 3% CO/Ar plasma at 100 torr and a 4% CO/He d.c. glow discharge at 8 torr. The LIF saturation limit was experimentally investigated and diagnostic advantages of either regime discussed. For the optically-pumped CO/Ar plasma, a spatially-averaged LIF temperature of 536 ± 103 K (2σ) was obtained from rotationally resolved X 1Σ+ (v' = 20) → D '1Σ+ (v' = 2) LIF excitation spectra. Temperature measurements pumping the X 1Σ+ (v' = 7) → A 1Π (v' = 1) 4th Positive (528 ± 51 K) were also found to compare well with line-of-sight Fourier Transform-InfraRed (FT-IR) emission measurements (536 ± 10 K). Spatially averaged FT- IR spectroscopy of the CO 1st overtone was used to verify that an adequate vibrational population (˜0.1%) existed within the positive column of the CO/He d.c. glow discharge. The A-X (7,1) transition was pumped and subsequent (8,1) emission at 200.8 nm collected. The resulting rotational spectral peaks were assigned and a subset used to determine a spatially averaged rotational temperature of 432 ± 44 K on the discharge centerline. This was found to be in good agreement with FT-IR spectroscopy measurements (395 ± 10 K). As a prelude to Planar-LIF (PLIF) temperature measurements, vibrationally-resolved emission from laser excitation of various rotational lines within the A-X and D'-X bands were used to investigate spectral interferences. This

  5. Conformational studies of 3-[(2,2-dimethylhydrazinyl)methylene]-pentane-2,4-dione using vibrational and NMR spectra, X-ray analysis and ab initio calculations

    Science.gov (United States)

    Gatial, Anton; Herich, Peter; Tarabová, Denisa; Milata, Viktor; Prónayová, Nadežda

    2017-07-01

    The conformers of push-pull 3-[(2,2-dimethylhydrazinyl)methylene]-pentane-2,4-dione (CH3)2Nsbnd NHsbnd CHdbnd C(COCH3)2 (DMHMP) have been studied experimentally by NMR and vibrational spectroscopy and theoretically by ab initio calculations at MP2 and DFT B3LYP levels in various basis sets. The NMR spectra were obtained in chloroform and dimethylsulfoxide and the IR and Raman spectra of DMHMP as a solid and as a solute in various less and more polar solvents at room temperature have been recorded. DMHMP was prepared as a pure solid and the data from X-ray analysis revealed that DMHMP exists in solid state as EZa conformer with an intramolecular hydrogen bond. The geometries and relative energies of possible conformers of DMHMP were evaluated at the both levels of theory in several basis sets and compared with the data from X-ray analysis. According to the NMR spectra the studied compound exists as a single entity. On the other hand vibrational spectra revealed that in less polar DMHMP solutions the presence of the second less polar ZZa conformer is possible, whereas in more polar solvent only one EZa conformer is observed. The influence of the environment polarity on this conformational equilibrium is discussed with respect to the SCRF solvent effect calculations using IEFPCM model. The observed IR and Raman bands were compared with calculated MP2/cc-pVTZ harmonic vibrational frequencies and assigned on the basis of potential energy distribution.

  6. Synthesis and infrared and fluorescence spectra of new europium and terbium polynuclear complexes with an amide-based 1,10-phenanthroline derivative

    Science.gov (United States)

    Zhang, Yu-Liang; Liu, Wei-Sheng; Dou, Wei; Qin, Wen-Wu

    2004-07-01

    An amide-based 1,10-phenanthroline (phen) derivative and its complexes with europium(III) and terbium(III) ions were synthesized. The complexes were characterized by elemental analysis, infrared spectra and conductivity. The europium and terbium ions were coordinated by O atoms of CO, Ar-O-C and N atoms of phen. The fluorescence properties of the complexes in THF, dioxane, MeCN and DMF were investigated. Under the excitation of UV light, these complexes exhibited characteristic fluorescence of europium and terbium ions. The solvent factors influencing the fluorescent intensity were discussed.

  7. Non-equilibrium effects evidenced by vibrational spectra during the coil-to-globule transition in poly(N-isopropylacrylamide) subjected to an ultrafast heating-cooling cycle.

    Science.gov (United States)

    Deshmukh, Sanket A; Kamath, Ganesh; Suthar, Kamlesh J; Mancini, Derrick C; Sankaranarayanan, Subramanian K R S

    2014-03-14

    Molecular dynamics simulations in conjunction with finite element calculations are used to explore the conformational dynamics of a thermo-sensitive oligomer, namely poly(N-isopropylacrylamide) (PNIPAM), subjected to an ultra-fast heating-cooling cycle. Finite element (FE) calculations were used to predict the temperature profile resulting from laser-induced heating of the polymer-aqueous system. The heating rate (∼0.6 K ps(-1)) deduced from FE calculations was used to heat an aqueous solution of PNIPAM consisting of 30 monomeric units (30-mer) from 285 K to 315 K. Non-equilibrium effects arising from the ultra-fast heating-cooling cycle results in a hysteresis during the coil-to-globule transition. The corresponding atomic scale conformations were characterized by monitoring the changes in the vibrational spectra, which provided a reliable metric to study the coil-to-globule transition in PNIPAM and vice-versa across the LCST. The vibrational spectra of bonds involving atoms from the oligomer backbone and the various side-groups (amide I, amide II, and the isopropyl group of PNIPAM) of the oligomers were analyzed to study the conformational changes in the oligomer corresponding to the observed hysteresis. The differences in the vibrational spectra calculated at various temperatures during heating and cooling cycles were used to understand the coil-to-globule and globule-to-coil transitions in the PNIPAM oligomer and identify the changes in the relative interactions between various atoms in the backbone and in the side groups of the oligomer with water. The shifts in the computed vibrational spectral peaks and the changes in the intensity of peaks for the different regions of PNIPAM, seen across the LCST during the heating cycle, are in good agreement with previous experimental studies. The changes in the radius of gyration (Rg) and vibrational spectra for amide I and amide II regions of PNIPAM suggest a clear coil-to-globule transition at ∼301 K during the

  8. Molecular structure, vibrational spectra, NBO, UV and first order hyperpolarizability, analysis of 4-Chloro-dl-phenylalanine by density functional theory.

    Science.gov (United States)

    Govindarasu, K; Kavitha, E

    2014-12-10

    The Fourier transform infrared (4000-400cm(-1)) and Fourier transform Raman (3500-50cm(-1)) spectra of 4-Chloro-dl-phenylalanine (4CLPA) were recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational wavenumbers were investigated with the help of density functional theory (DFT) method using B3LYP/6-31G(d,p) as basis set. The observed vibrational wavenumbers were compared with the calculated results. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction. Predicted electronic absorption spectra from TD-DFT calculation have been analyzed comparing with the UV-Vis (200-800nm) spectrum. The effects of chlorine and ethylene group substituent in benzene ring in the vibrational wavenumbers have been analyzed. The HOMO-LUMO energy gap explains the charge interaction taking place within the molecule. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of 4CLPA were calculated. The Chemical reactivity and chemical potential of 4CLPA is calculated. In addition, molecular electrostatic potential (MEP), frontier molecular orbital (FMO) analysis were investigated using theoretical calculations. Published by Elsevier B.V.

  9. Experimental determinations and quantum-chemical calculations of the vibrational spectra of β-ZnB4O7 and β-CaB4O7.

    Science.gov (United States)

    Kaindl, Reinhard; Sohr, Gerhard; Huppertz, Hubert

    2013-12-01

    The two oxoborates β-ZnB4O7 and β-CaB4O7 were synthesized and investigated by FTIR- and Raman spectroscopy and ab initio quantum chemical calculations. Maximum and mean deviations between experimentally determined bands and calculated modes ranged between 15-36 cm(-1) and 5-7 cm(-1), respectively, allowing band assignments to vibrational modes in most cases. The complex network structures with tetrahedral BO4 and planar OB3 groups are mirrored by the spectra and numerous vibrational modes, not assignable by standard borates classification schemes. It was confirmed that OB3 units, despite similar force constants and geometry, do not absorb in the same range as BO3 units. Bands in the high wavenumber range are rather caused by B-O-(Zn/Ca), O-B-O, B-O-B, and B-O stretching and bending vibrations. The experimental observation of inactive or Raman-active modes in the absorption spectra indicates defects or structural distortions in both compounds.

  10. Vibrational spectra, DFT calculations, unusual structure, anomalous CH2 wagging and twisting modes, and phase-dependent conformation of 1,3-disilacyclobutane.

    Science.gov (United States)

    Rishard, Mohamed Z M; Irwin, Richard M; Laane, Jaan

    2007-02-08

    Our previously published infrared and Raman spectra of 1,3-disilacyclobutane (13DSCB) and its 1,1,3,3-d4 isotopomer have been reexamined and partially reassigned on the basis of DFT and ab initio calculations. The calculations confirm previous microwave work that the CSiC angles in the ring are unexpectedly larger than the SiCSi angles. This may arise from the partial charges on the ring atoms. The calculations are in excellent agreement with the observed spectra in both frequency and intensity. They also demonstrate that this molecule has CH2 wagging and twisting vibrations with frequencies below 1000 cm-1, about 200 cm-1 lower than expected. These unprecedented low values can be explained by the decreased slope in the potential energy curves for these vibrations as the sideways motions of the CH2 groups result in attractive forces between the positively charged hydrogens on the carbon atoms and the negatively charged hydrogens on the silicon atoms. The theoretical calculations also confirm the previous conclusions that the individual molecules (vapor) have C2v symmetry whereas in the solid the molecules become planar with D2h symmetry. The vibrational coupling between the ring-angle bending mode and the SiH2 in-phase rocking, which is present for the C2v structure, is forbidden for D2h and hence disappears.

  11. Molecular structure, vibrational spectra, NBO, UV and first order hyperpolarizability, analysis of 4-Chloro-DL-phenylalanine by density functional theory

    Science.gov (United States)

    Govindarasu, K.; Kavitha, E.

    2014-12-01

    The Fourier transform infrared (4000-400 cm-1) and Fourier transform Raman (3500-50 cm-1) spectra of 4-Chloro-DL-phenylalanine (4CLPA) were recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational wavenumbers were investigated with the help of density functional theory (DFT) method using B3LYP/6-31G(d,p) as basis set. The observed vibrational wavenumbers were compared with the calculated results. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction. Predicted electronic absorption spectra from TD-DFT calculation have been analyzed comparing with the UV-Vis (200-800 nm) spectrum. The effects of chlorine and ethylene group substituent in benzene ring in the vibrational wavenumbers have been analyzed. The HOMO-LUMO energy gap explains the charge interaction taking place within the molecule. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of 4CLPA were calculated. The Chemical reactivity and chemical potential of 4CLPA is calculated. In addition, molecular electrostatic potential (MEP), frontier molecular orbital (FMO) analysis were investigated using theoretical calculations.

  12. The influence of visible light and inorganic pigments on fluorescence excitation emission spectra of egg-, casein- and collagen-based painting media

    Science.gov (United States)

    Nevin, A.; Anglos, D.; Cather, S.; Burnstock, A.

    2008-07-01

    Spectrofluorimetric analysis of proteinaceous binding media is particularly promising because proteins employed in paintings are often fluorescent and media from different sources have significantly different fluorescence spectral profiles. Protein-based binding media derived from eggs, milk and animal tissue have been used for painting and for conservation, but their analysis using non-destructive techniques is complicated by interferences with pigments, their degradation and their low concentration. Changes in the fluorescence excitation emission spectra of films of binding media following artificial ageing to an equivalent of 50 and 100 years of museum lighting include the reduction of bands ascribed to tyrosine, tryptophan and Maillard reaction products and an increase in fluorescent photodegradation. Fluorescence of naturally aged paint is dependent on the nature of the pigment present and, with egg-based media, in comparison with un-pigmented films, emissions ascribed to amino acids are more pronounced.

  13. Vibrational spectra of silatranes and germatranes XM(OCH2CH2)3N (X = F,Cl,H; M = Si,Ge). The problem of the theoretical prediction of condensed phase spectra

    Science.gov (United States)

    Ignatyev, Igor S.; Sundius, Tom

    2012-09-01

    The structures of silatranes and germatranes XM(OCH2CH2)3N (X = F,Cl,H; M = Si,Ge) were optimized and their vibrational spectra were calculated at the B3LYP/aug-cc-pVDZ level of theory. Theoretical frequencies of vibrations perpendicular to the C3 axis (E type) are in good agreement with experimental values, while the axial vibrations (MX and M…N stretchings) demonstrate a significant discrepancy with experimental spectra recorded for the crystalline state. This discrepancy stems from the well-known difference in the MX and M…N bond lengths in gas and solid state. The force constant scaling procedure was used to compensate for this difference. As a result a set of scaling factors was refined for 1-Cl-germatrane (the unique atrane for which the distinction between A and E modes was experimentally established). This set was transferred to the theoretical force fields of other atranes, which provided a fair reproduction of their experimental frequencies. The analysis of the normal modes allowed us to assign the ν M…N mode to bands in the 180-270 cm-1 frequency range, although large contributions of these coordinates are in two other modes in the 450-500 cm-1 and 600-800 cm-1 frequency ranges. The frequencies of degenerate vibrations (with vectors perpendicular to the C3 axis) do not depend substantially on the axial atom (X and M) substitution, while those of A-type in the 200-700 cm-1 frequency range vary significantly.

  14. Vibration-rotation pattern in acetylene. II. Introduction of Coriolis coupling in the global model and analysis of emission spectra of hot acetylene around 3 microm.

    Science.gov (United States)

    Amyay, Badr; Robert, Séverine; Herman, Michel; Fayt, André; Raghavendra, Balakrishna; Moudens, Audrey; Thiévin, Jonathan; Rowe, Bertrand; Georges, Robert

    2009-09-21

    A high temperature source has been developed and coupled to a high resolution Fourier transform spectrometer to record emission spectra of acetylene around 3 mum up to 1455 K under Doppler limited resolution (0.015 cm(-1)). The nu(3)-ground state (GS) and nu(2)+nu(4)+nu(5) (Sigma(u) (+) and Delta(u))-GS bands and 76 related hot bands, counting e and f parities separately, are assigned using semiautomatic methods based on a global model to reproduce all related vibration-rotation states. Significantly higher J-values than previously reported are observed for 40 known substates while 37 new e or f vibrational substates, up to about 6000 cm(-1), are identified and characterized by vibration-rotation parameters. The 3 811 new or improved data resulting from the analysis are merged into the database presented by Robert et al. [Mol. Phys. 106, 2581 (2008)], now including 15 562 lines accessing vibrational states up to 8600 cm(-1). A global model, updated as compared to the one in the previous paper, allows all lines in the database to be simultaneously fitted, successfully. The updates are discussed taking into account, in particular, the systematic inclusion of Coriolis interaction.

  15. Submillimeter-wave rotational spectra of DNC in highly excited vibrational states observed in an extended negative glow discharge

    Science.gov (United States)

    Amano, T.

    2011-05-01

    Rotational transitions of DNC have been observed in the submillimeter-wave region in an extended negative glow discharge in a gas mixture of CD 4 and N 2. The dissociative recombination reaction of DCND + with electrons is thought to be a dominant channel to produce DNC in highly excited vibrational states. The vibrational temperature for the ν3 vibrational mode is found to be about 4000 K, and the rotational lines in levels up to (0 0 8) are observed. The rotational and centrifugal distortion constants are determined for these states along with those for the (1 0 0) state. The measurement accuracy is high enough to determine some higher order vibration-rotation interaction constants.

  16. Determination of Enantiomeric Compositions of Tryptophan by Chemometric Analysis of the Fluorescence Spectra of Bovine Serum Albumin Receptor-ligand Mixtures

    Institute of Scientific and Technical Information of China (English)

    Yun Xia WANG; Fang ZHANG; Jing LIANG; Hua LI; Ji Lie KONG

    2006-01-01

    In this work, a novel method was constructed to determine the enantiomeric composition of tryptophan (Trp) by bovine serum albumin (BSA) based on the fluorescence spectra of the receptor-ligand mixtures coupled with partial least squares (PLS-1) analysis. As a result the enantiomeric composition of Trp was accurately determined.

  17. Data of fluorescence, UV–vis absorption and FTIR spectra for the study of interaction between two food colourants and BSA

    Directory of Open Access Journals (Sweden)

    Tian Li

    2016-09-01

    Full Text Available In this data article, the fluorescence, UV–vis absorption and FTIR spectra data of BSA-AR1/AG50 system were presented, which were used for obtaining the binding characterization (such as binding constant, binding distance, binding site, thermodynamics, and structural stability of protein between BSA and AR1/AG50.

  18. Molecular structure, vibrational spectra, natural bond orbital and thermodynamic analysis of 3,6-dichloro-4-methylpyridazine and 3,6-dichloropyridazine-4-carboxylic acid by dft approach.

    Science.gov (United States)

    Prabavathi, N; Senthil Nayaki, N; Venkatram Reddy, B

    2015-02-05

    Vibrational spectral analysis of the molecules 3,6-dichloro-4-methylpyridazine (DMP) and 3,6-dichloropyridazine-4-carboxylic acid (DPC) was carried out using FT-IR and FT-Raman spectroscopic techniques. The molecular structure and vibrational spectra of DMP and DPC were obtained by the density functional theory (DFT) method, using B3LYP functional, with 6-311++G(d,p) basis set. A detailed interpretation of the Infrared and Raman spectra of the two molecules were reported based on potential energy distribution (PED). The theoretically predicted FTIR and FT-Raman spectra of the titled molecules have been simulated and were compared with the experimental spectra. Determination of electric dipole moment (μ) and hyperpolarizability β0 helps to study the non-linear optical (NLO) behavior of DMP and DPC. Stability of the molecules arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. (13)C and (1)H NMR spectra were recorded and (13)C and (1)H NMR chemical shifts of the molecules were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compounds was also recorded in the region 200-1100 nm and electronic properties, HOMO (Highest Occupied Molecular Orbitals) and LUMO (Lowest Unoccupied Molecular Orbitals) energies were measured by time-dependent TD-DFT approach. Charge density distribution and site of chemical reactivity of the molecule have been studied by mapping electron density isosurface with molecular electrostatic potential (MESP). Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Comparative analysis of the vibrational structure of the absorption spectra of acrolein in the excited ( S 1) electronic state

    Science.gov (United States)

    Koroleva, L. A.; Tyulin, V. I.; Matveev, V. K.; Pentin, Yu. A.

    2012-04-01

    The assignments of absorption bands of the vibrational structure of the UV spectrum are compared with the assignments of bands obtained by the CRDS method in a supersonic jet from the time of laser radiation damping for the trans isomer of acrolein in the excited ( S 1) electronic state. The ν00 trans = 25861 cm-1 values and fundamental frequencies, including torsional vibration frequency, obtained by the two methods were found to coincide in the excited electronic state ( S 1) for this isomer. The assignments of several absorption bands of the vibrational structure of the spectrum obtained by the CRDS method were changed. Changes in the assignment of (0-v') transition bands of the torsional vibration of the trans isomer in the Deslandres table from the ν00 trans trans origin allowed the table to be extended to high quantum numbers v'. The torsional vibration frequencies up to v' = 5 were found to be close to the frequencies found by analyzing the vibrational structure of the UV spectrum and calculated quantum-mechanically. The coincidence of the barrier to internal rotation (the cis-trans transition) in the one-dimensional model with that calculated quantum-mechanically using the two-dimensional model corresponds to a planar structure of the acrolein molecule in the excited ( S 1) electronic state.

  20. Molecular structure, vibrational spectra and HOMO, LUMO analysis of yohimbine hydrochloride by density functional theory and ab initio Hartree-Fock calculations

    Science.gov (United States)

    Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha

    2011-11-01

    Yohimbine hydrochloride (YHCl) is an aphrodisiac and promoted for erectile dysfunction, weight loss and depression. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of yohimbine hydrochloride have been determined using ab initio, Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and IR spectra of YHCl. The UV absorption spectrum was examined in ethanol solvent and compared with the calculated one in gas phase as well as in solvent environment (polarizable continuum model, PCM) using TD-DFT/6-31G basis set. These methods are proposed as a tool to be applied in the structural characterization of YHCl. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap are presented.

  1. FLUORESCENCE EMISSION SPECTRA OF MARINE AND BRACKISH-WATER ECOTYPES OF FUCUS VESICULOSUS AND FUCUS RADICANS (PHAEOPHYCEAE) REVEAL DIFFERENCES IN LIGHT-HARVESTING APPARATUS(1).

    Science.gov (United States)

    Maria Gylle, Anna; Rantamäki, Susanne; Ekelund, Nils G A; Tyystjärvi, Esa

    2011-02-01

    The Bothnian Sea in the northerly part of the Baltic Sea is a geologically recent brackish-water environment, and rapid speciation is occurring in the algal community of the Bothnian Sea. We measured low-temperature fluorescence emission spectra from the Bothnian Sea and the Norwegian Sea ecotypes of Fucus vesiculosus L., a marine macroalga widespread in the Bothnian Sea. Powdered, frozen thallus was used to obtain undistorted emission spectra. The spectra were compared with spectra measured from the newly identified species Fucus radicans Bergström et L. Kautsky, which is a close relative of F. vesiculosus and endemic to the Bothnian Sea. The spectrum of variable fluorescence was used to identify fluorescence peaks originating in PSI and PSII in this chl c-containing alga. The spectra revealed much higher PSII emission, compared to PSI emission, in the Bothnian Sea ecotype of F. vesiculosus than in F. radicans or in the Norwegian Sea ecotype of F. vesiculosus. The results suggest that more light-harvesting chl a/c proteins serve PSII in the Bothnian Sea ecotype of F. vesiculosus than in the two other algal strains. Treatment of the Bothnian Sea ecotype of F. vesiculosus in high salinity (10, 20, and 35 practical salinity units) for 1 week did not lead to spectral changes, indicating that the measured features of the Bothnian Sea F. vesiculosus are stable and not simply a direct result of exposure to low salinity.

  2. Influence of Gamma-Ray Irradiation on Absorption and Fluorescent Spectra of Nd:YAG and Yb:YAG Laser Crystals

    Institute of Scientific and Technical Information of China (English)

    SUN Dun-Lu; ZHANG Qing-Li; XIAO Jing-Zhong; LUO Jian-Qiao; JIANG Hai-He; YIN Shao-Tang

    2008-01-01

    We investigate the influence of gamma-ray irradiation on the absorption and fluorescent spectra of Nd3+ : Y3Al5O12 (Nd:YAG) and Yb3+ :Y3Al5O12 (Yb:YAG) crystals grown by the Czochralski method. Two additional absorption (AA) bands induced by gamma-ray irradiation appear at 255nm and 340nm. The former is eontributed due to Fe3+ impurity, the latter is due to Fe2+ ions and F-type colour centres. The intensity of the excitation and emission spectra as well as the fluorescent lifetime of Nd:YAG crystal decrease after the irradiation of 100 Mrad gamma-ray. In contrast, the same dose irradiation does not impair the fluorescent properties of Yb: YA G crystal. These results indicate that Yb: YA G crystal possesses the advantage over Nd: YA G crystal that has better reliability for applications in harsh radiant environment.

  3. Resolution of complex fluorescence spectra of lipids and nicotinic acetylcholine receptor by multivariate analysis reveals protein-mediated effects on the receptor's immediate lipid microenvironment

    CERN Document Server

    Wenz, Jorge J; 10.1186/1757-5036-1-6

    2009-01-01

    Analysis of fluorescent spectra from complex biological systems containing various fluorescent probes with overlapping emission bands is a challenging task. Valuable information can be extracted from the full spectra, however, by using multivariate analysis (MA) of measurements at different wavelengths. We applied MA to spectral data of purified Torpedo nicotinic acetylcholine receptor (AChR) protein reconstituted into liposomes made up of dioleoylphosphatidic acid (DOPA) and dioleoylphosphatidylcholine (DOPC) doped with two extrinsic fluorescent probes (NBD-cholesterol/pyrene-PC). Forster resonance energy transfer (FRET) was observed between the protein and pyrene-PC and between pyrene-PC and NBD-cholesterol, leading to overlapping emission bands. Partial least squares analysis was applied to ...

  4. Anharmonic Vibrational Analysis of the Infrared and Raman Gas-Phase Spectra of s-trans- and s-gauche-1,3-Butadiene.

    Science.gov (United States)

    Krasnoshchekov, Sergey V; Craig, Norman C; Boopalachandran, Praveenkumar; Laane, Jaan; Stepanov, Nikolay F

    2015-10-29

    A quantum-mechanical (hybrid MP2/cc-pVTZ and CCSD(T)/cc-pVTZ) full quartic potential energy surface (PES) in rectilinear normal coordinates and the second-order operator canonical Van Vleck perturbation theory (CVPT2) are employed to predict the anharmonic vibrational spectra of s-trans- and s-gauche-butadiene (BDE). These predictions are used to interpret their infrared and Raman scattering spectra. New high-temperature Raman spectra in the gas phase are presented in support of assignments for the gauche conformer. The CVPT2 solution is based on a PES and electro-optical properties (EOP; dipole moment and polarizability) expanded in Taylor series. Higher terms than those routinely available from Gaussian09 software were calculated by numerical differentiation of quadratic force fields and EOP using the MP2/cc-pVTZ model. The integer coefficients of the polyad quantum numbers were derived for both conformers of BDE. Replacement of harmonic frequencies by their counterparts from the CCSD(T)/cc-pVTZ model significantly improved the agreement with experimental data for s-trans-BDE (root-mean-square deviation ≈ 5.5 cm(-1)). The accuracy in predicting the rather well-studied spectrum of fundamentals of s-trans-BDE assures good predictions of the spectrum of s-gauche-BDE. A nearly complete assignment of fundamentals was obtained for the gauche conformer. Many nonfundamental transitions of the BDE conformers were interpreted as well. The predictions of multiple Fermi resonances in the complex CH-stretching region correlate well with experiment. It is shown that solving a vibrational anharmonic problem through a numerical-analytic implementation of CVPT2 is a straightforward and computationally advantageous approach for medium-size molecules in comparison with the standard second-order vibrational perturbation theory (VPT2) based on analytic expressions.

  5. Effect of CdSe nanoparticles on the fluorescence spectra of conjugate polymer P3HT: An experimental and theoretical study

    Energy Technology Data Exchange (ETDEWEB)

    Mastour, Nouha, E-mail: mastournouha@yahoo.fr; Bouchriha, Habib

    2016-11-25

    In this work we have investigated the effect of CdSe nanoparticles (Nps) on the fluorescence spectra of conjugate polymer Poly(3-hexylthiophene-2,5-diyl) (P3HT). The fluorescence intensity is significantly decreased in both solution and solid films by the incorporation of CdSe Nps. This observed effect in the nanocomposite P3HT-CdSe is analyzed by using the Franck–Condon theory which reproduces correctly the decrease of the fluorescence with the Nps concentration and permits to reach the Huang–Rhys factor and the relaxation energy which are shown efficient to explain the fluorescence quenching. - Highlights: • The effects of CdSe nanoparticles concentration on the fluorescence spectra of conjugate polymer P3HT are investigated. • Theoretical approach based on Franck–Condon analysis is proposed. • The Huang–Rhys factor and the relaxation energy as a function of the CdSe Nps are determined. • The fluorescence quenching has been explained.

  6. Infrared spectra of metal complexes with -x,5-dimethylpyrazole and 1,2,4-triazole in frequency range of valent vibrations of metal-ligand bond

    Energy Technology Data Exchange (ETDEWEB)

    Oglezneva, I.M.; Lavrenova, L.G.; Larionov, S.V. (AN SSSR, Novosibirsk. Inst. Neorganicheskoj Khimii)

    1984-06-01

    In the range 200-600 cm/sup -1/ IR absorption spectra of complexes of halides and nitrates of Cu/sup 2/, Ni/sup 2/, Co/sup 2/, Zn/sup 2/, Cd/sup 2/ with two heterocyclic nitrogen-containing ligands: 3,5-dimethylpyrazole and 1,2,4-triazole, have been investigated. Taking into account the structure of coordination polyhedron (according to the data of electron spectroscopy and magnetic measurements), the interpretation of frequencies of valent vibrations of metal-nitrogen and metal-helide bonds is made. Regularities of ..nu.. (MN) change depending on metal and ligand are pointed out.

  7. Tautomeric conversion, vibrational spectra, and density functional studies on peripheral sulfur derivatives of benzothiazole and benzothiazoline isomers

    Science.gov (United States)

    Altun, Ahmet; Kuliyev, Eziz; Aghatabay, Naz M.

    2016-01-01

    The room temperature structural (tautomerism, dimerization, conformational preference, geometry parameters) and vibrational spectral (IR and Raman) analyses have been performed on benzothiazoline (benzothiazoline-2-thione, 3-methyl-benzothiazoline-2-thione) and benzothiazole [2-mercaptobenzothiazole, 2-methylthiobenzothiazole, and bis(benzothiazole-2-ylthio)ethane] derivatives at the B3LYP/6-311++G∗∗ level of theory. Although the keto to enol transition barriers are too high over the most stable benzothiazoline isomers, vibrational spectral analyses reveal some major bands of benzothiazole isomers in the present room temperature experimental FT-IR and FT-Raman specta. Therefore, benzothiazole isomers exist at rare amounts in the powdered samples that are mainly composed of benzothiazoline isomers. The benzothiazole isomers have two stable conformations due to the orientation of their SH and SCH3 moieties. The energetic and vibrational spectral analyses suggest that the benzothiazoline-2-thione molecules can be stabilized further through the NH⋯S intermolecular hydrogen bonds in solid phase. All observed fundamental vibrational bands of the molecules have been assigned based on the calculated mode frequencies and IR/Raman intensities. The mode assignments have been expressed in terms of internal coordinates and their percent potential energy distributions. The effects of substitution at the nitrogen and peripheral sulfur atoms have been analyzed for the geometries and vibrational bands of the molecules.

  8. Structures, vibrational absorption and vibrational circular dichroism spectra of L-alanine in aqueous solution: a density functional theory and RHF study

    DEFF Research Database (Denmark)

    Frimand, Kenneth; Bohr, Henrik; Jalkanen, Karl J.;

    2000-01-01

    at the density functional theory level using the B3LYP functional with the 6-31G* basis set. The Hessians and atomic polar tensors and atomic axial tensors were all calculated at the B3LYP/6-31G* level of theory. An important result is the method of treating solvent effects by both adding explicit water....... The calculated VA and VCD spectra of this conformer are in better agreement with experimentally measured VA and VCD spectra previously reported. (C) 2000 Elsevier Science B.V. All rights reserved....

  9. The Far-Ultraviolet Spectra of TW Hya. II. Models of H2 Fluorescence in a Disk

    CERN Document Server

    Herczeg, G J; Linsky, J L; Valenti, J A; Johns-Krull, C M; Herczeg, Gregory J.; Wood, Brian E.; Linsky, Jeffrey L.; Valenti, Jeff A.; Johns-Krull, Chris M.

    2004-01-01

    We measure the temperature of warm gas at planet-forming radii in the disk around the classical T Tauri star (CTTS) TW Hya by modelling the H2 fluorescence observed in HST/STIS and FUSE spectra. Strong Ly-alpha emission irradiates a warm disk surface within 2 AU of the central star and pumps certain excited levels of H2. We simulate a 1D plane-parallel atmosphere to estimate fluxes for the 140 observed H2 emission lines and to reconstruct the Ly-alpha emission profile incident upon the warm H2. The excitation of H2 can be determined from relative line strengths by measuring self-absorption in lines with low-energy lower levels, or by reconstructing the Ly-alpha profile incident upon the warm H2 using the total flux from a single upper level and the opacity in the pumping transition. Based on those diagnostics, we estimate that the warm disk surface has a column density of log N(H2)=18.5^{+1.2}_{-0.8}, a temperature T=2500^{+700}_{-500} K, and a filling factor of H2, as seen by the source of Ly-alpha emission,...

  10. Origin of long-lived oscillations in 2D-spectra of a Quantum Vibronic Model: Electronic vs Vibrational coherence

    CERN Document Server

    Plenio, M B; Huelga, S F

    2013-01-01

    We demonstrate that the coupling of excitonic and vibrational motion in biological complexes can provide mechanisms to explain the long-lived oscillations that have been obtained in non linear spectroscopic signals of different photosynthetic pigment protein complexes and we discuss the contributions of excitonic versus purely vibrational components to these oscillatory features. Considering a dimer model coupled to a structured spectral density we exemplify the fundamental aspects of the electron-phonon dynamics, and by analyzing separately the different contributions to the non linear signal, we show that for realistic parameter regimes purely electronic coherence is of the same order as purely vibrational coherence in the electronic ground state. Moreover, we demonstrate how the latter relies upon the excitonic interaction to manifest. These results link recently proposed microscopic, non-equilibrium mechanisms to support long lived coherence at ambient temperatures with actual experimental observations of...

  11. Vibration-insensitive temperature sensing system based on fluorescence decay and using a digital processing approach

    Science.gov (United States)

    Dong, H.; Zhao, W.; Sun, T.; Grattan, K. T. V.; Al-Shamma'a, A. I.; Wei, C.; Mulrooney, J.; Clifford, J.; Fitzpatrick, C.; Lewis, E.; Degner, M.; Ewald, H.; Lochmann, S. I.; Bramann, G.; Merlone Borla, E.; Faraldi, P.; Pidria, M.

    2006-07-01

    A fluorescence-based temperature sensor system using a digital signal processing approach has been developed and evaluated in operation on a working automotive engine. The signal processing approach, using the least-squares method, makes the system relatively insensitive to intensity variations in the probe and thus provides more precise measurements when compared to a previous system designed using analogue phase-locked detection. Experiments carried out to determine the emission temperatures of a running car engine have demonstrated the effectiveness of the sensor system in monitoring exhaust temperatures up to 250 °C, and potentially higher. This paper was presented at the 13th International Conference on Sensors and Their Applications, held in Chatham, Kent, on 6-7 September 2005.

  12. The fluorescence and dynamics properties in phenoxy-phthalocyanines liquid

    Science.gov (United States)

    Yao, Cheng-Bao; Yan, Xiao-Yan; Tan, Ming-Yue; Li, Jin; Sun, Wen-Jun; Yang, Shou-Bin

    2015-06-01

    We investigated the one/two-photon fluorescence and excited state dynamics properties of two synthesized phenoxy-phthalocyanines (Pc1 and Pc2) using mild reaction coordination method. The results show that the fast decay component in the time-resolved fluorescence technique dynamics comes from the intramolecular vibrational relaxation, the slower ones from the internal conversion. Furthermore, in comparison with one-photon fluorescence spectra, the red shift of two-photon fluorescence spectra can be explained by the reabsorption effect of molecules. The samples are expected to be a potential candidate for optical applications and photodynamic therapy.

  13. Prediction of the hydrophilic antioxidant capacity of tomato pastes from the IR and fluorescence excitation-emission spectra of extracts and intact samples.

    Science.gov (United States)

    Orzel, Joanna; Stanimirova, Ivana; Czarnik-Matusewicz, Boguslawa; Daszykowski, Michal

    2015-06-01

    The performance of the recently proposed excitation-emission fluorescence method was compared to the method using infrared measurements for the evaluation of the antioxidant properties of intact samples and extracts that had been obtained from tomato pastes. The oxygen radical absorbance capacity assay (ORAC) was applied in order to estimate the antioxidant capacity of the extracts, while the Folin-Ciocalteu reagent was adopted for the evaluation of the total phenolic content. The optimal extraction conditions for tomato pastes (three minutes of sonication under 80°C) were determined using the central composite design. Chemometric models such as the partial least squares regression and its N-way variant were further constructed in order to predict the antioxidant capacity or total phenolic content of the samples using either the IR or fluorescence spectra. The prediction errors that were obtained for the total antioxidant content were evaluated as the Trolox equivalents from the ORAC assay and were found to be equal to 2.011 (14.21%) for the fluorescence and 2.426 (17.15%) for the IR spectra, respectively. The prediction errors of the total phenolic content expressed as gallic acid equivalents were 0.067 (10.78%) for the fluorescence and 0.033 (5.36%) for the IR spectra, which were used as independent variables in the regression models.

  14. Origin of long-lived oscillations in 2D-spectra of a quantum vibronic model: electronic versus vibrational coherence.

    Science.gov (United States)

    Plenio, M B; Almeida, J; Huelga, S F

    2013-12-21

    We demonstrate that the coupling of excitonic and vibrational motion in biological complexes can provide mechanisms to explain the long-lived oscillations that have been obtained in nonlinear spectroscopic signals of different photosynthetic pigment protein complexes and we discuss the contributions of excitonic versus purely vibrational components to these oscillatory features. Considering a dimer model coupled to a structured spectral density we exemplify the fundamental aspects of the electron-phonon dynamics, and by analyzing separately the different contributions to the nonlinear signal, we show that for realistic parameter regimes purely electronic coherence is of the same order as purely vibrational coherence in the electronic ground state. Moreover, we demonstrate how the latter relies upon the excitonic interaction to manifest. These results link recently proposed microscopic, non-equilibrium mechanisms to support long lived coherence at ambient temperatures with actual experimental observations of oscillatory behaviour using 2D photon echo techniques to corroborate the fundamental importance of the interplay of electronic and vibrational degrees of freedom in the dynamics of light harvesting aggregates.

  15. Origin of long-lived oscillations in 2D-spectra of a quantum vibronic model: Electronic versus vibrational coherence

    Energy Technology Data Exchange (ETDEWEB)

    Plenio, M. B.; Almeida, J.; Huelga, S. F. [Institute for Theoretical Physics, Albert-Einstein-Allee 11, University Ulm, D-89069 Ulm (Germany)

    2013-12-21

    We demonstrate that the coupling of excitonic and vibrational motion in biological complexes can provide mechanisms to explain the long-lived oscillations that have been obtained in nonlinear spectroscopic signals of different photosynthetic pigment protein complexes and we discuss the contributions of excitonic versus purely vibrational components to these oscillatory features. Considering a dimer model coupled to a structured spectral density we exemplify the fundamental aspects of the electron-phonon dynamics, and by analyzing separately the different contributions to the nonlinear signal, we show that for realistic parameter regimes purely electronic coherence is of the same order as purely vibrational coherence in the electronic ground state. Moreover, we demonstrate how the latter relies upon the excitonic interaction to manifest. These results link recently proposed microscopic, non-equilibrium mechanisms to support long lived coherence at ambient temperatures with actual experimental observations of oscillatory behaviour using 2D photon echo techniques to corroborate the fundamental importance of the interplay of electronic and vibrational degrees of freedom in the dynamics of light harvesting aggregates.

  16. Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

    Science.gov (United States)

    Sumner, Isaiah; Iyengar, Srinivasan S

    2007-10-18

    We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

  17. Quantum Chemical Studies on the Prediction of Structures, Charge Distributions and Vibrational Spectra of Some Ni(II), Zn(II), and Cd(II) Iodide Complexes

    Science.gov (United States)

    Bardakci, Tayyibe; Kumru, Mustafa; Altun, Ahmet

    2016-06-01

    Transition metal complexes play an important role in coordination chemistry as well as in the formation of metal-based drugs. In order to obtain accurate results for studying these type of complexes quantum chemical studies are performed and especially density functional theory (DFT) has become a promising choice. This talk represents molecular structures, charge distributions and vibrational analysis of Ni(II), Zn(II), and Cd(II) iodide complexes of p-toluidine and m-toluidine by means of DFT. Stable structures of the ligands and the related complexes have been obtained in the gas phase at B3LYP/def2-TZVP level and calculations predict Ni(II) complexes as distorted polymeric octahedral whereas Zn(II) and Cd(II) complexes as distorted tetrahedral geometries. Charge distribution analysis have been performed by means of Mulliken, NBO and APT methods and physically most meaningful method for our compounds is explained. Vibrational spectra of the title compounds are computed from the optimized geometries and theoretical frequencies are compared with the previously obtained experimental data. Since coordination occurs via nitrogen atoms of the free ligands, N-H stretching bands of the ligands are shifted towards lower wavenumbers in the complexes whereas NH_2 wagging and twisting vibrations are shifted towards higher wavenumbers.

  18. A complete assignment of the vibrational spectra of 2-furoic acid based on the structures of the more stable monomer and dimer

    Science.gov (United States)

    Ghalla, Houcine; Issaoui, Noureddine; Castillo, María Victoria; Brandán, Silvia Antonia; Flakus, Henryk T.

    2014-03-01

    The structural and vibrational properties of cyclic dimer of 2-furoic acid (2FA) were predicted by combining the available experimental infrared and Raman spectra in the solid phase and ab initio calculations based on density functional theory (DFT) with Pople's basis sets. The calculations show that there are two cyclic dimers for the title molecule that have been theoretically determined in the gas phase, and that only one of them, cis conformer, is present in the solid phase. The complete assignment of the 66 normal vibrational modes for the cis cyclic dimer was performed using the Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology. Four strong bands in the infrared spectrum at 1583, 1427, 1126 and 887 cm-1 and the group of bands in the Raman spectrum at 1464, 1452, 1147, 1030, 885, 873, 848, 715 and 590 cm-1 are characteristic of the dimeric form of 2FA in the solid phase. In this work, the calculated structural and vibrational properties of both dimeric species were analyzed and compared between them. In addition, three types of atomic charges, bond orders, possible charge transfer, topological properties of the furan rings, Natural Bond Orbital (NBO) and Atoms in Molecules (AIM) theory calculations were employed to study the stabilities and intermolecular interactions of the both dimers of 2FA.

  19. Vibrational Spectra of β″-Type BEDT-TTF Salts: Relationship between Conducting Property, Time-Averaged Site Charge and Inter-Molecular Distance

    Directory of Open Access Journals (Sweden)

    Takashi Yamamoto

    2012-07-01

    Full Text Available The relationship between the conducting behavior and the degree of charge fluctuation in the β″-type BEDT-TTF salts is reviewed from the standpoints of vibrational spectroscopy and crystal structure. A group of β″-type ET salts demonstrates the best model compounds for achieving the above relationship because the two-dimensional structure is simple and great diversity in conducting behavior is realized under ambient pressure. After describing the requirement for the model compound, the methodology for analyzing the results of the vibrational spectra is presented. Vibrational spectroscopy provides the time-averaged molecular charge, the charge distribution in the two-dimensional layer, and the inter-molecular interactions, etc. The experimental results applied to 2/3-filled and 3/4-filled β″-type ET salts are reported. These experimental results suggest that the conducting property, the difference in the time-averaged molecular charges between the ionic and neutral-like sites, the alternation in the inter-molecular distances and the energy levels in the charge distributions are relevant to one another. The difference in the time-averaged molecular charges, ∆ρ, is a useful criterion for indicating conducting behavior. All superconductors presented in this review are characterized as small but finite ∆ρ.

  20. A new experimental and theoretical investigation on the structures of aminoethyl phosphonic acid in aqueous medium based on the vibrational spectra and DFT calculations

    Science.gov (United States)

    Roldán, María L.; Ledesma, Ana E.; Raschi, Ana B.; Castillo, María V.; Romano, Elida; Brandán, Silvia A.

    2013-06-01

    A new study on the structural and vibrational properties of the aminoethylphosphonic acid was performed in aqueous solution phase by using the self-consistent reaction field (SCRF) method. We have studied and characterized it by infrared and Raman spectroscopies in solid and aqueous solution phases. The Density Functional Theory (DFT) method with Pople's basis set show that three stable zwitterions for the title molecule have been theoretically determined in aqueous solution and that probably they are present in it medium. Here, the solvent effects were studied by means of the self-consistent reaction field (SCRF) method with the polarized continuum model (PCM). The harmonic vibrational frequencies for the optimized geometries of the three zwitterions were calculated at the B3LYP/6-31G∗ level of the theory. A complete assignment of the IR and Raman spectra of the compound in aqueous solution was performed combining the DFT calculations with Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology in order to fit the theoretical frequency values to the experimental ones. Moreover, Natural Bond Orbital (NBO) and topological properties calculations were performed to analyze the energies and geometrical parameters of its three zwitterions in aqueous medium as well as the magnitude of the intramolecular interactions. The bond orders, atomic charges, solvation energies, dipole moments, molecular electrostatic potentials and force constants parameters calculated for zwitterions in aqueous solution, may be used to gain chemical and vibrational insights into related compounds.

  1. Nightglow vibrational distributions in the A3Σu+ and A'3Δu states of O2 derived from astronomical sky spectra

    Directory of Open Access Journals (Sweden)

    A. M. Widhalm

    2004-09-01

    Full Text Available Astronomical sky spectra from the Keck I telescope on Mauna Kea have been used to obtain vibrational distributions in the O2A3Σu+ and O2(A'3Δu states from rotationally-resolved Herzberg I and Chamberlain band emissions in the terrestrial nightglow. The A3Σu+ distribution is similar to that presented in earlier publications, with the exception that there is significant population in the previously undiscerned v=0 level. The vibrational distributions of the A'3Δu and A3Σu+ states are essentially the same when comparison is made in terms of the level energies. The intensity of Chamberlain band emission at the peak of the distribution is about one-fourth that of the Herzberg I emission, as previously shown, and may be related primarily to radiative efficiency. The peaks in both population distributions are about 0.25eV below the O(3P+O(3P dissociation limit. We compare these Herzberg state distributions with that of the O2(b1Σg+ state, concurring with others that the intense nightglow emission associated with b1Σg+(v=0 is a reflection of direct transfer from the Herzberg states. This process takes place following O2 collisions, with simultaneous production of very high a1Δg and b1Σg+ vibrational levels.

  2. New Cerium(III Complex Of Schiff Base (E-N-Benzylidene-4-Methoxyaniline: Synthesis And Density Functional Theoretical Study Of Vibrational Spectra

    Directory of Open Access Journals (Sweden)

    Imanelakehal

    2016-05-01

    Full Text Available Complex of cerium (III with (E-N-benzylidene-4-methoxyaniline is synthesized through a one-pot three-componentreaction from aromatical dehyde, aromatic amine and the CeCl3· 7 H2O, as an efficient catalyst. This cerium(IIIcom- plexis characterized by IR, 1H, and 13 CNMR-spectros copy and mass-spectraldata. Molecular structure, Mullikan charges, thermodynamic parameters; vibrational frequencies and intensities were calculated by Density Functional theory methods (B3LYP,B3PW91,mPW1PW91 and PBEPBE using the SDD basis set. The comparison between the calculated and experimental data inorder to attain the best quality and to predict the structure, the best perfor-mance in the vibration spectra perfected of the title compound,we have found that the harmonic vibration computed are in a good agreement with the observed in IRspectrum, for closest match we calculated optimal scaling factors can recommend for the IR spectral future predictions for unknown compounds of this class. In order to better comparison, we also root meansqu are values of the experimental and calculated IR bands are 16.64,16.64,17.45,17.66 and the mean absolute percentage error values are1.33,1.39,1.40, and 1.5forB3LYP, B3PW91,mPW1PW91, and PBEPBE methods respectively

  3. Application of high-resolution photoelectron spectroscopy: Vibrational resolved C 1s and O 1s spectra of CO adsorbed on Ni(100)

    Energy Technology Data Exchange (ETDEWEB)

    Foehlisch, A.; Nilsson, A.; Martensson, N. [Uppsala Univ. (Sweden)] [and others

    1997-04-01

    There are various effects which determine the line shape of a core-level electron spectrum. These are due to the finite life-time of the core hole, inelastic scattering of the outgoing photoelectron, electronic shake-up and shake-off processes and vibrational excitations. For free atoms and molecules the different contributions to the observed line shapes can often be well separated. For solids, surfaces and adsorbates the line shapes are in general much broader and it has in the past been assumed that no separation of the various contributions can be made. In the present report the authors will show that this is indeed not the case. Surprisingly, the vibrational fine structure of CO adsorbed on Ni(100) can be resolved in the C 1s and O 1s electron spectra. This was achieved by the combination of highly monochromatized soft X-rays from B18.0 with a high resolution Scienta 200 mm photoelectron spectrometer. X-ray photoelectron spectroscopy (XPS) with tunable excitation energy yields as a core level spectroscopy atomic and site-specific information. The presented measurements allow for a determination of internuclear distances and potential energy curves in corehole ionized adsorbed molecules. The authors analysis of the c(2x2) phase CO/Ni(100) on {open_quotes}top{close_quotes} yielded a vibrational splitting of 217 +/- 2 meV for C 1s ionization. For O 1s ionization a splitting of 173 +/- 8 meV was found.

  4. Calculation of Vibrational and Electronic Excited-State Absorption Spectra of Arsenic-Water Complexes Using Density Functional Theory

    Science.gov (United States)

    2016-06-03

    IR and UV-visible ranges. The absorption spectrum corresponding to excitation states of As-H2O complexes consisting of relatively small numbers of...complexes consisting of relatively small numbers of water molecules using DFT and TD- DFT. Calculation of excited state resonance structure using DFT and TD...absorption spectra. A significant aspect of using DFT and TD-DFT for the calculation of absorption spectra is that it adopts the perspective of computational

  5. The Change of Reflection Spectra and Fluorescence Spectra of Port Wine Stains During PDT%鲜红斑痣光动力治疗中皮肤光谱特点的变化

    Institute of Scientific and Technical Information of China (English)

    王颖; 廖小华; 顾瑛; 陈荣; 曾晶

    2011-01-01

    尝试利用漫反射光谱和荧光光谱检测鲜红斑痣皮肤在光动力治疗中的变化特点,用于分析治疗中组织光学特性的变化,指导光剂量的制定.在光动力治疗中,采用微型光纤光谱仪监测PWS皮肤的漫反射光谱和荧光光谱,结合PWS结构特点以及皮肤中主要吸光基团的吸收光谱,分析术中、术后相关组织成分变化及对应的光学特性变化.PDT治疗中PWS皮肤的反射光谱的变化主要是血红蛋白和黑色素吸收波段的反射率增加或降低;部分患者伴有反射光谱形态的变化,主要是两种血红蛋白吸收光谱差异明显的波段.PWS组织的荧光光谱也反映了组织中血液含量的信息.漫反射光谱监测可反映组织中血液含量、血氧含量、黑色素含量变化引起的组织光学特性变化,进一步进行深入研究可提供PDT中组织光学特性动态变化的信息.%To analyze the change of optical property of PWS skin during photodynamic therapy, the reflection spectra and fluorescence spectra of PWS skin during PDT treatment were measured using mini-optical fiber spectrograph. The change of reflection spectra and fluorescence spectra were analyzed according to the histological structure of PWS skin and the absorption spectra of the main chromophores in skin (melanin and hemoglobin). The result showed that the spectra changed significantly at the wavelength at which melanin and hemoglobin have high absorption, or at which obvious difference existed in the absorption between HbO2 and Hb. The monitoring of reflection spectra and fluorescence spectra during PDT can provide information about the dynamic change of the optical property of PWS tissue.

  6. Interpretation of DNA vibration modes: IV--A single-helical approach to assign the phosphate-backbone contribution to the vibrational spectra in A and B conformations.

    Science.gov (United States)

    Letellier, R; Ghomi, M; Taillandier, E

    1989-02-01

    A calculated approach based on the Higgs method for assigning the vibration modes of an infinite helicoidal polymeric chain has been performed on the basis of a reliable valence force field. The calculated results allowed the phosphate-backbone marker modes of the A and B forms, to be interpreted. In the dynamic models used, the bases have been omitted and no interchain interaction was considered. The calculation can also interprete quite satisfactorily the characteristic Raman peaks and infrared bands in the 1250-700 cm-1 spectral region arising from the sugar or sugar-phosphate association and reproduce their evolution upon the B----A DNA conformational transition. They clearly show that the phosphate-backbone modes in the above mentioned spectral region constitute the optical branches of the phonon dispersion curves with no detectable variation in the first Brillouin-zone.

  7. Improved Assignments of the Vibrational Fundamental Modes of ortho-, meta-, and para-xylene Using Gas- and Liquid-Phase Infrared and Raman Spectra Combined with ab initio Calculations: Quantitative Gas-Phase Infrared Spectra for Detection

    Energy Technology Data Exchange (ETDEWEB)

    Lindenmaier, Rodica; Scharko, Nicole K.; Tonkyn, Russell G.; Nguyen, Kiet T.; Williams, Stephen D.; Johnson, Timothy J.

    2017-12-05

    Xylenes contain a blend of the ortho-, meta-, and para- isomers, and all are abundant contaminants in the ground, surface waters, and air. To better characterize xylene and to better enable its detection, we report high quality quantitative vapor-phase infrared spectra of all three isomers over the 540˗6500 cm-1 range. All fundamental vibrational modes are assigned based on these vapor-phase infrared spectra, liquid-phase infrared and Raman spectra, along with density functional theory (DFT), ab initio MP2 and high energy-accuracy compound theoretical model (W1BD) calculations. Both MP2 and DFT predict a single conformer with C2v symmetry for ortho-xylene, and two conformers each for meta- and para-xylene, depending on the preferred orientations of the methyl groups. For meta-xylene the two conformers have Cs and C2 symmetry, and for para-xylene these conformers have C2v or C2h symmetry. Since the relative population of the two conformers is approximately 50% for both isomers and predicted frequencies and intensities are very similar for each conformer, we made an arbitrary choice to discuss the Cs conformer for meta-xylene and the C2v conformer for para-xylene. We report integrated band intensities for all isomers. Using the quantitative infrared data, we determine the global warming potential values of each isomer and discuss potential bands for atmospheric monitoring.

  8. Dispersed fluorescence spectroscopy of the SiCN A ˜ 2 Δ - X ˜ 2 Π system: Observation of some vibrational levels with chaotic characteristics

    Science.gov (United States)

    Fukushima, Masaru; Ishiwata, Takashi

    2016-12-01

    The laser induced fluorescence (LIF) spectrum of the A ˜ 2Δ - X ˜ 2Π transition was obtained for SiCN generated by laser ablation under supersonic free jet expansion. The vibrational structures of the dispersed fluorescence (DF) spectra from single vibronic levels (SVL's) were analyzed with consideration of the Renner-Teller (R-T) interaction. Analysis of the pure bending (ν2) structure by a perturbation approach including R-T, anharmonicity, spin-orbit (SO), and Herzberg-Teller (H-T) interactions indicated considerably different spin splitting for the μ and κ levels of the X ˜ 2Π state of SiCN, in contrast to identical spin splitting for general species derived from the perturbation approach, where μ and κ specify the lower and upper levels, respectively, separated by R-T. Further analysis of the vibrational structure including R-T, anharmonicity, SO, H-T, Fermi, and Sears interactions was carried out via a direct diagonalization procedure, where Sears resonance is a second-order interaction combined from SO and H-T interactions with Δ K = ± 1, ΔΣ = ∓1, and Δ P = 0, and where P is a quantum number, P = K + Σ. The later numerical analysis reproduced the observed structure, not only the pure ν2 structure but also the combination structure of the ν2 and the Si-CN stretching (ν3) modes. As an example, the analysis demonstrates Sears resonance between vibronic levels, (0110) κ Σ(+) and ( 0 2 0 0 ) μ Π /1 2 , with Δ K = ± 1 and Δ P = 0. On the basis of coefficients of their eigen vectors derived from the numerical analysis, it is interpreted as an almost one-to-one mixing between the two levels. The mixing coefficients of the two vibronic levels agree with those obtained from computational studies. The numerical analysis also indicates that some of the vibronic levels show chaotic characteristics in view of the two-dimensional harmonic oscillator (2D-HO) basis which is used as the basis function in the present numerical analysis; i.e., the

  9. NBO analysis and vibrational spectra of 2,6-bis(p-methyl benzylidene cyclohexanone) using density functional theory

    Science.gov (United States)

    Padmaja, L.; Amalanathan, M.; Ravikumar, C.; Hubert Joe, I.

    2009-10-01

    Vibrational analysis of the 2,6-bis(p-methyl benzylidene cyclohexanone) [PMBC] compound was carried out by using NIR FT-Raman and FT-IR spectroscopic techniques. The equilibrium geometry, various bonding features and harmonic vibrational frequencies of PMBC have been investigated with the help of B3LYP/6-31G(d) density functional theory method. The optimized geometry clearly demonstrates cyclohexanone ring chair conformation is changed into half-chair conformation. The shortening of C-H bond length and blue shifting of the CH stretching wavenumber suggest the existence of improper weak C-H⋯O hydrogen bonding, which is confirmed by the natural bond orbital analysis. The Mulliken population analysis on atomic charges and the HOMO-LUMO energy are also calculated.

  10. Structure and vibrational spectra of melaminium bis(trifluoroacetate) trihydrate: FT-IR, FT-Raman and quantum chemical calculations.

    Science.gov (United States)

    Sangeetha, V; Govindarajan, M; Kanagathara, N; Marchewka, M K; Gunasekaran, S; Anbalagan, G

    2014-05-05

    Melaminium bis(trifluoroacetate) trihydrate (MTFA), an organic material has been synthesized and single crystals of MTFA have been grown by the slow solvent evaporation method at room temperature. X-ray powder diffraction analysis confirms that MTFA crystal belongs to the monoclinic system with space group P2/c. The molecular geometry, vibrational frequencies and intensity of the vibrational bands have been interpreted with the aid of structure optimization based on density functional theory (DFT) B3LYP method with 6-311G(d,p) and 6-311++G(d,p) basis sets. The X-ray diffraction data have been compared with the data of optimized molecular structure. The theoretical results show that the crystal structure can be reproduced by optimized geometry and the vibrational frequencies show good agreement with the experimental values. The nuclear magnetic resonance (NMR) chemical shift of the molecule has been calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. HOMO-LUMO, and other related molecular and electronic properties are calculated. The Mulliken and NBO charges have also been calculated and interpreted.

  11. Neural-network analysis of the vibrational spectra of N-acetyl L-alanyl N '-methyl amide conformational states

    DEFF Research Database (Denmark)

    Bohr, Henrik; Frimand, Kenneth; Jalkanen, Karl J.

    2001-01-01

    data for a given conformer of the molecule by interpolation. Finally the neural network performances are used to monitor a sensitivity analysis of the importance of secondary structures and the influence of the solvent. The neural network is shown to be good in distinguishing the different conformers...... dichroism (VCD), Raman spectra, and Raman optical activity (ROA) intensities. The large changes due to hydration in the structures, and the relative stability of the conformer, reflected in the VA, VCD, Raman spectra, and ROA spectra observed experimentally, are reproduced by the DFT calculations. A neural...... network has been constructed for reproducing the inverse scattering data (we infer the structural coordinates from spectroscopic data) that the DFT method could produce. The purpose of the network has also been to generate the large set of conformational states associated with each set of spectroscopic...

  12. First principles and DFT supported investigations on vibrational spectra and electronic structure of 2-((phenylamino)methyl)isoindoline-1,3-dione - An antioxidant active Mannich base

    Science.gov (United States)

    Boobalan, Maria susai; Amaladasan, M.; Ramalingam, S.; Tamilvendan, D.; Venkatesa Prabhu, G.; Bououdina, M.

    2015-02-01

    The 2-((phenylamino)methyl)isoindoline-1,3-dione (PID) is a synthesized Mannich base which has significant antioxidant activity and biological importance. Quantum mechanical calculations on energy, geometry and vibrational wavenumber of PID were computed using ab initio HF and density functional theory (DFT/B3LYP) methods with 6-31+G/6-311++G(d,p) basis sets. Optimized geometrical parameters obtained by HF and DFT calculations were indicatively agreement with experimental crystal geometry. The experimental FT-Raman and FT-IR spectra of PID has been recorded and analyzed by comparing with simulated spectra. The 1H and 13C NMR spectra of title molecule records the chemical shift resulted from shielding and deshielding effects. Natural bond orbital (NBO) analysis has been carried out to calculate various intramolecular interactions that are accountable for the stabilization of this Mannich base. The predicted HOMO-LUMO gap offers interesting information on intramolecular charge transfer and reactivity of the molecular system. Molecular electrostatic potential (MEP) imprint visualize the reactive sites in PID, which is also supported by Mulliken, ESP, Hirshfeld and NBO charges. Thermodynamic properties of PID at various temperatures have been calculated at B3LYP/6-311++G(d,p) in gas phase and the correlations between standard entropies (S), internal energy (E or U) and standard heat capacity (C) with different temperatures.

  13. Effect of anthocyanins, carotenoids, and flavonols on chlorophyll fluorescence excitation spectra in apple fruit: signature analysis, assessment, modelling, and relevance to photoprotection.

    Science.gov (United States)

    Merzlyak, Mark N; Melø, Thor Bernt; Naqvi, K Razi

    2008-01-01

    Whole apple fruit (Malus domestica Borkh.) widely differing in pigment content and composition has been examined by recording its chlorophyll fluorescence excitation and diffuse reflection spectra in the visible and near UV regions. Spectral bands sensitive to the pigment concentration have been identified, and linear models for non-destructive assessment of anthocyanins, carotenoids, and flavonols via chlorophyll fluorescence measurements are put forward. The adaptation of apple fruit to high light stress involves accumulation of these protective pigments, which absorb solar radiation in broad spectral ranges extending from UV to the green and, in anthocyanin-containing cultivars, to the red regions of the spectrum. In ripening apples the protective effect in the blue region could be attributed to extrathylakoid carotenoids. A simple model, which allows the simulation of chlorophyll fluorescence excitation spectra in the visible range and a quantitative evaluation of competitive absorption by anthocyanins, carotenoids, and flavonols, is described. Evidence is presented to support the view that anthocyanins, carotenoids, and flavonols play, in fruit with low-to-moderate pigment content, the role of internal traps (insofar as they compete with chlorophylls for the absorption of incident light in specific spectral bands), affecting thereby the shape of the chlorophyll fluorescence excitation spectrum.

  14. Isotopomer-selective spectra of a single intact H2O molecule in the Cs+(D2O)5H2O isotopologue: Going beyond pattern recognition to harvest the structural information encoded in vibrational spectra

    Science.gov (United States)

    Wolke, Conrad T.; Fournier, Joseph A.; Miliordos, Evangelos; Kathmann, Shawn M.; Xantheas, Sotiris S.; Johnson, Mark A.

    2016-02-01

    We report the vibrational signatures of a single H2O molecule occupying distinct sites of the hydration network in the Cs+(H2O)6 cluster. This is accomplished using isotopomer-selective IR-IR hole-burning on the Cs+(D2O)5(H2O) clusters formed by gas-phase exchange of a single, intact H2O molecule for D2O in the Cs+(D2O)6 ion. The OH stretching pattern of the Cs+(H2O)6 isotopologue is accurately recovered by superposition of the isotopomer spectra, thus establishing that the H2O incorporation is random and that the OH stretching manifold is largely due to contributions from decoupled water molecules. This behavior enables a powerful new way to extract structural information from vibrational spectra of size-selected clusters by explicitly identifying the local environments responsible for specific infrared features. The Cs+(H2O)6 structure was unambiguously assigned to the 4.1.1 isomer (a homodromic water tetramer with two additional flanking water molecules) from the fact that its computed IR spectrum matches the observed overall pattern and recovers the embedded correlations in the two OH stretching bands of the water molecule in the Cs+(D2O)5(H2O) isotopomers. The 4.1.1 isomer is the lowest in energy among other candidate networks at advanced (e.g., CCSD(T)) levels of theoretical treatment after corrections for (anharmonic) zero-point energy. With the structure in hand, we then explore the mechanical origin of the various band locations using a local electric field formalism. This approach promises to provide a transferrable scheme for the prediction of the OH stretching fundamentals displayed by water networks in close proximity to solute ions.

  15. Isotopomer-selective spectra of a single intact H2O molecule in the Cs(+)(D2O)5H2O isotopologue: Going beyond pattern recognition to harvest the structural information encoded in vibrational spectra.

    Science.gov (United States)

    Wolke, Conrad T; Fournier, Joseph A; Miliordos, Evangelos; Kathmann, Shawn M; Xantheas, Sotiris S; Johnson, Mark A

    2016-02-21

    We report the vibrational signatures of a single H2O molecule occupying distinct sites of the hydration network in the Cs(+)(H2O)6 cluster. This is accomplished using isotopomer-selective IR-IR hole-burning on the Cs(+)(D2O)5(H2O) clusters formed by gas-phase exchange of a single, intact H2O molecule for D2O in the Cs(+)(D2O)6 ion. The OH stretching pattern of the Cs(+)(H2O)6 isotopologue is accurately recovered by superposition of the isotopomer spectra, thus establishing that the H2O incorporation is random and that the OH stretching manifold is largely due to contributions from decoupled water molecules. This behavior enables a powerful new way to extract structural information from vibrational spectra of size-selected clusters by explicitly identifying the local environments responsible for specific infrared features. The Cs(+)(H2O)6 structure was unambiguously assigned to the 4.1.1 isomer (a homodromic water tetramer with two additional flanking water molecules) from the fact that its computed IR spectrum matches the observed overall pattern and recovers the embedded correlations in the two OH stretching bands of the water molecule in the Cs(+)(D2O)5(H2O) isotopomers. The 4.1.1 isomer is the lowest in energy among other candidate networks at advanced (e.g., CCSD(T)) levels of theoretical treatment after corrections for (anharmonic) zero-point energy. With the structure in hand, we then explore the mechanical origin of the various band locations using a local electric field formalism. This approach promises to provide a transferrable scheme for the prediction of the OH stretching fundamentals displayed by water networks in close proximity to solute ions.

  16. Isotopomer-selective spectra of a single intact H2O molecule in the Cs+(D2O)5H2O isotopologue: Going beyond pattern recognition to harvest the structural information encoded in vibrational spectra

    Energy Technology Data Exchange (ETDEWEB)

    Wolke, Conrad T.; Fournier, Joseph A.; Miliordos, Evangelos; Kathmann, Shawn M.; Xantheas, Sotiris S.; Johnson, Mark A.

    2016-02-21

    We report the vibrational signatures of a single H2O water molecule occupying distinct sites of the hydration network in the Cs+(H2O)6 cluster. This is accomplished using isotopomer selective IR-IR hole-burning on the Cs+(D2O)5(H2O) clusters formed by gas-phase exchange of a single, intact H2O molecule for D2O in the Cs+(D2O)6 ion. The OH stretching pattern of the Cs+(H2O)6 isotopologue is accurately recovered by superposition of the isotopomer spectra, thus establishing that the H2O incorporation is random and that the OH stretching manifold is largely due to contributions from decoupled water molecules. This behavior enables a powerful new way to extract structural information from vibrational spectra of size-selected clusters by explicitly identifying the local environments responsible for specific infrared features. The Cs+(H2O)6 structure was unambiguously assigned to the 4.1.1 isomer (a homodromic water tetramer with two additional flanking water molecules) from the fact that its computed IR spectrum matches the observed overall pattern and recovers the embedded correlations in the two OH stretching bands of the water molecule in the Cs+(D2O)5(H2O) isotopomers. The 4.1.1 isomer is the lowest in energy among other candidate networks at advanced (e.g., CCSD(T)) levels of theoretical treatment after corrections for (anharmonic) zero-point energy (ZPE). With the structure in hand, we then explore the mechanical origin of the various band locations using a local electric field formalism. This approach promises to provide a transferrable scheme for the prediction of the OH stretching fundamentals displayed by water networks in close proximity to solute ions.

  17. Parallel β-sheet vibrational couplings revealed by 2D IR spectroscopy of an isotopically labeled macrocycle: quantitative benchmark for the interpretation of amyloid and protein infrared spectra.

    Science.gov (United States)

    Woys, Ann Marie; Almeida, Aaron M; Wang, Lu; Chiu, Chi-Cheng; McGovern, Michael; de Pablo, Juan J; Skinner, James L; Gellman, Samuel H; Zanni, Martin T

    2012-11-21

    Infrared spectroscopy is playing an important role in the elucidation of amyloid fiber formation, but the coupling models that link spectra to structure are not well tested for parallel β-sheets. Using a synthetic macrocycle that enforces a two stranded parallel β-sheet conformation, we measured the lifetimes and frequency for six combinations of doubly (13)C═(18)O labeled amide I modes using 2D IR spectroscopy. The average vibrational lifetime of the isotope labeled residues was 550 fs. The frequencies of the labels ranged from 1585 to 1595 cm(-1), with the largest frequency shift occurring for in-register amino acids. The 2D IR spectra of the coupled isotope labels were calculated from molecular dynamics simulations of a series of macrocycle structures generated from replica exchange dynamics to fully sample the conformational distribution. The models used to simulate the spectra include through-space coupling, through-bond coupling, and local frequency shifts caused by environment electrostatics and hydrogen bonding. The calculated spectra predict the line widths and frequencies nearly quantitatively. Historically, the characteristic features of β-sheet infrared spectra have been attributed to through-space couplings such as transition dipole coupling. We find that frequency shifts of the local carbonyl groups due to nearest neighbor couplings and environmental factors are more important, while the through-space couplings dictate the spectral intensities. As a result, the characteristic absorption spectra empirically used for decades to assign parallel β-sheet secondary structure arises because of a redistribution of oscillator strength, but the through-space couplings do not themselves dramatically alter the frequency distribution of eigenstates much more than already exists in random coil structures. Moreover, solvent exposed residues have amide I bands with >20 cm(-1) line width. Narrower line widths indicate that the amide I backbone is solvent

  18. Optical Absorption of Impurities and Defects in Semiconducting Crystals Electronic Absorption of Deep Centres and Vibrational Spectra

    CERN Document Server

    Pajot, Bernard

    2013-01-01

    This book outlines, with the help of several specific examples, the important role played by absorption spectroscopy in the investigation of deep-level centers introduced in semiconductors and insulators like diamond, silicon, germanium and gallium arsenide by high-energy irradiation, residual impurities, and defects produced during crystal growth. It also describes the crucial role played by vibrational spectroscopy to determine the atomic structure and symmetry of complexes associated with light impurities like hydrogen, carbon, nitrogen and oxygen, and as a tool for quantitative analysis of these elements in the materials.

  19. Jet-cooled fluorescence excitation spectra, conformation, and carbonyl wagging potential energy function of cyclopentanone and its deuterated isotopomers in the S1 (n,π*) electronic excited states

    Science.gov (United States)

    Zhang, Jian; Chiang, Whe-Yi; Laane, Jaan

    1993-04-01

    The jet-cooled fluorescence excitation spectra of cyclopentanone and its 2,2,5,5-d4 isotopomer have been recorded in the 305-335 nm region. In addition, the spectra of d1, d2, and d3 species were obtained from isotopic mixtures. The electronic band origin of the d0 molecule for the S1 (n,π*) state of A2 symmetry occurs at 30 276 cm-1, while that of the d4 molecule is at 30 265 cm-1. More than 100 fluorescence bands were assigned for each species. These arise from combinations of ν3 (C=O stretch), ν11 (ring-angle bending), ν18 (ring twisting), ν25 (C=O out-of-plane wag), ν26 (ring bending), and ν36 (C=O in-plane wag) and their vibrational excited states. The vibrational frequencies for ν3, ν11, and ν36 are significantly lower in the S1 state than the S0 ground state. However, the out-of-plane ring modes ν18 and ν26 are only slightly shifted. A progression observed for ν26 does indicate that in the S1 state, the bent ring conformation lies about 500 cm-1 above the ring-twisting minimum and corresponds to a saddle point in the two-dimensional ring-twisting/ring-bending potential energy surface. Band progressions for ν18 can be used to calculate the ring-twisting barriers (the barriers to planarity) for the d0 and d4 isotopomers to be 1433 and 1240 cm-1, respectively. Because of limited data, however, these values may be as much as several hundred cm-1 too high. The energies for the C=O out-of-plane wagging states up to v25=9 for each isotopomer were determined for the S1 state and these were used to calculate the C=O wagging potential energy functions for each. In the S1 state, the barrier to inversion of the C=O group is 672±10 cm-1 and the wagging angle is 22°±1°.

  20. Vibrational spectra of Mg2KH(XO4)2·15H2O (X = P, As) containing dimer units [H(XO4)2

    Science.gov (United States)

    Stefov, V.; Koleva, V.; Najdoski, M.; Abdija, Z.; Cahil, A.; Šoptrajanov, B.

    2017-08-01

    Infrared and Raman spectra of Mg2KH(PO4)2·15H2O and Mg2KH(AsO4)2·15H2O and a series of their partially deuterated analogues were recorded and analyzed. Compounds of the type Mg2KH(XO4)2·15H2O (X = P, As) are little-known and a rare case of phosphate and arsenate salts containing dimer units [H(XO4)2] in the crystal structure. The analysis of their IR spectra (recorded at room and liquid nitrogen temperature) and Raman spectra showed that the spectral characteristics of the XO4 groups connected in a dimer through a proton are not consistent with the presence of X-O-H covalent linkage and C1 crystallographic symmetry of the XO4 groups. The observation of a singlet Raman band for the ν1(XO4) mode as well as the absence of substantial splitting of the ν3(XO4) modes and IR activation of the ν1(XO4) mode suggest that the dimer units [H(XO4)2] are most probably symmetric rather than non-symmetric ones. It was found that, in the vibrational spectra of Mg2KH(AsO4)2·15H2O, both ν1(AsO4) and ν3(AsO4) modes have practically the same wavenumber around 830 cm- 1. It was also established that the ν4(PO4) modes in the deuterated hydrogendiphosphate compound are strongly coupled, most probably with HDO and/or D2O librations. As a whole, the spectral picture of Mg2KH(XO4)2·15H2O (X = P, As) very much resembles that observed for the struvite type compounds with the formula KMgXO4·6H2O (X = P, As) which do not contain X-OH groups. This means that vibrations of the dimers [H(XO4)2] play a relatively small part in the general spectral appearance.

  1. Temperature dependent analysis of three classes of fluorescence spectra from p-6P nanofiber films

    DEFF Research Database (Denmark)

    Balzer, F.; Pogantsch, Alexander; Rubahn, Horst-Günter

    2009-01-01

    Discontinuous nanofiber films of para-hexaphenylene molecules can be routinely fabricated via vacuum deposition on muscovite mica. The fibers emit upon UV illumination blue fluorescence with excitonic spectral peaks. Their intense fluorescence makes them very attractive for the use in photonic de...

  2. PARAFAC modeling of fluorescence excitation - Emission spectra of fish bile for rapid en route screening of PAC exposure

    DEFF Research Database (Denmark)

    Christensen, Jan H.; Tomasi, Giorgio; Strand, Jakob

    2009-01-01

    with parallel factor analysis (PARAFAC) and may constitute an alternative to fixed wavelength fluorescence and synchronous fluorescence spectroscopy (M). PARAFAC was applied to excitation-emission matrices (EEMs) of bile samples of shorthorn sculpins and European eels collected in Greenland and Denmark...

  3. Structures and vibrational spectra of the N-benzoyl N‧-dialkylthiourea derivative and their complexes with Hg(II)

    Science.gov (United States)

    Weiqun, Zhou; Wen, Yang; Lihua, Qiu; Yong, Zhang; Zhengfeng, Yu

    2005-07-01

    The complex Hg (MTCB) 2 (MTCB= N-(morpholinothiocarbonyl) benzamide) and Hg (PTCB) 2 (PTCB= N-(piperidylthiocarbonyl) benzamide) have been synthesized and characterized by elemental analysis, FT-IR, FT-Raman spectra and NMR methods. The complex, Hg (MTCB) 2, crystallizes in the triclinic space group P1¯, with Z=2. Unit cell parameters, a=10.3621(11) Å, b=11.5738(11) Å, c=12.7722(7) Å, α=64.493(8)°, β=66.132(8)°, γ=85.811(11)°, V=1254.7(2) Å 3. The FT-Infrared and FT-Raman spectra were used in study of the structures of MTCB, PTCB and their complexes with mercury cation, which were agreement with the result of X-ray diffraction.

  4. Communication: He-tagged vibrational spectra of the SarGlyH{sup +} and H{sup +}(H{sub 2}O){sub 2,3} ions: Quantifying tag effects in cryogenic ion vibrational predissociation (CIVP) spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Christopher J.; Wolk, Arron B.; Fournier, Joseph A.; Johnson, Mark A. [Sterling Chemistry Laboratory, Yale University, 225 Prospect St., New Haven, Connecticut 06520 (United States); Sullivan, Erin N. [Department of Chemistry and Biochemistry, Fairfield University, 1073 North Benson Rd., Fairfield, Connecticut 06824 (United States); Weddle, Gary H. [Sterling Chemistry Laboratory, Yale University, 225 Prospect St., New Haven, Connecticut 06520 (United States); Department of Chemistry and Biochemistry, Fairfield University, 1073 North Benson Rd., Fairfield, Connecticut 06824 (United States)

    2014-06-14

    To assess the degree to which more perturbative, but widely used “tag” species (Ar, H{sub 2}, Ne) affect the intrinsic band patterns of the isolated ions, we describe the extension of mass-selective, cryogenic ion vibrational spectroscopy to the very weakly interacting helium complexes of three archetypal ions: the dipeptide SarGlyH{sup +} and the small protonated water clusters: H{sup +}(H{sub 2}O){sub 2,3}, including the H{sub 5}O{sub 2}{sup +} “Zundel” ion. He adducts were generated in a 4.5 K octopole ion trap interfaced to a double-focusing, tandem time-of-flight photofragmentation mass spectrometer to record mass-selected vibrational predissociation spectra. The H{sub 2} tag-induced shift (relative to that by He) on the tag-bound NH stretch of the SarGlyH{sup +} spectrum is quite small (12 cm{sup −1}), while the effect on the floppy H{sub 5}O{sub 2}{sup +} ion is more dramatic (125 cm{sup −1}) in going from Ar (or H{sub 2}) to Ne. The shifts from Ne to He, on the other hand, while quantitatively significant (maximum of 10 cm{sup −1}), display the same basic H{sub 5}O{sub 2}{sup +} band structure, indicating that the He-tagged H{sub 5}O{sub 2}{sup +} spectrum accurately represents the delocalized nature of the vibrational zero-point level. Interestingly, the He-tagged spectrum of H{sup +}(H{sub 2}O){sub 3} reveals the location of the non-bonded OH group on the central H{sub 3}O{sup +} ion to fall between the collective non-bonded OH stretches on the flanking water molecules in a position typically associated with a neutral OH group.

  5. Ab initio molecular orbital studies of the vibrational spectra of the van der Waals complexes of boron trifluoride with the noble gases.

    Science.gov (United States)

    Ford, Thomas A

    2005-05-01

    The molecular structures, interaction energies, charge transfer properties and vibrational spectra of the van der Waals complexes formed between boron trifluoride and the noble gases neon, argon, krypton and xenon have been computed using second and fourth order Møller-Plesset perturbation theory and the Los Alamos National Laboratory LANL2DZ basis set. The complexes are all symmetric tops, with the noble gas atom acting as a sigma electron donor along the C3 axis of the BF3 molecule. The interaction energies are all vanishingly small, and the amount of charge transferred in each case is of the order of 0.01e. The directions of the wavenumber shifts of the symmetric bending (nu2) and antisymmetric stretching (nu3) modes of the BF3 fragment confirm those determined experimentally, and the shifts are shown to correlate well with the polarizability of the noble gas atom and the inverse sixth power of the intermonomer separation. The nu2 mode is substantially more sensitive to complexation than the nu3 vibration.

  6. A New, Dispersion-Driven Intermolecular Arrangement for the Benzene-Water Octamer Complex: Isomers and Analysis of their Vibrational Spectra.

    Science.gov (United States)

    Miliordos, Evangelos; Aprà, Edoardo; Xantheas, Sotiris S

    2016-08-01

    The anharmonic spectra of the gas phase cubic water octamer (W8, D2d and S4 isomers) have been theoretically calculated at the second order Møller-Plesset perturbation (MP2) and the coupled cluster with single, double and a perturbative estimate of triple replacements [CCSD(T)] theories. The CCSD(T) harmonic frequencies are the first ones reported for this cluster. An additional band at ∼3500 cm(-1) is reported, in a spectral area that was not previously accessible experimentally due to technical reasons. The IR spectra of the S4 isomer have a larger number of fundamental bands than the spectra of the D2d isomer, in accordance with the presence of lower symmetry in the former compared to the latter. When W8 interacts with benzene (BZ), the dispersion interaction plays a major role in determining the resulting intermolecular arrangement. Calculations at the MP2, DFT (with the ωB97XD functional which includes dispersion corrections) and CCSD(T) levels of theory suggest an optimal arrangement in which BZ is almost parallel to one of the faces of the W8 cube. This structure differs from the previously reported one in which one of the "free" OH bonds of the W8 cube pointed toward the center of BZ (Science 276, 1678 (1997)) that was determined at the DFT level with the dispersionless B3LYP functional and was used to assign the experimentally measured IR spectra. Five low-lying isomers, three of the S4-like and two of the D2d-like type, were determined, and their spectra were assigned. The perturbation of BZ to the W8 vibrational bands amounts to (i) the localization of the normal modes of W8 thus resulting in more IR active bands and (ii) the lowering of the overall symmetry of the complex that results in the splitting of the doubly degenerate bands of the bare W8. Our results further suggest that a future recording of the IR spectra in the HOH bending region can definitively aid in the assignment of the various isomers of both the BZ and the BZ-W8 complexes.

  7. Fluorescence spectra and biological activity of aerosolized bacillus spores and MS2 bacteriophage exposed to ozone at different relative humidities in a rotating drum

    Science.gov (United States)

    Ratnesar-Shumate, Shanna; Pan, Yong-Le; Hill, Steven C.; Kinahan, Sean; Corson, Elizabeth; Eshbaugh, Jonathan; Santarpia, Joshua L.

    2015-03-01

    Biological aerosols (bioaerosols) released into the environment may undergo physical and chemical transformations when exposed to atmospheric constituents such as solar irradiation, reactive oxygenated species, ozone, free radicals, water vapor and pollutants. Aging experiments were performed in a rotating drum chamber subjecting bioaerosols, Bacillus thuringiensis Al Hakam (BtAH) spores and MS2 bacteriophages to ozone at 0 and 150 ppb, and relative humidities (RH) at 10%, 50%, and 80+%. Fluorescence spectra and intensities of the aerosols as a function of time in the reaction chamber were measured with a single particle fluorescence spectrometer (SPFS) and an Ultra-Violet Aerodynamic Particle Sizer® Spectrometer (UV-APS). Losses in biological activity were measured by culture and quantitative polymerase chain reaction (q-PCR) assay. For both types of aerosols the largest change in fluorescence emission was between 280 and 400 nm when excited at 263 nm followed by fluorescence emission between 380 and 700 nm when excited at 351 nm. The fluorescence for both BtAH and MS2 were observed to decrease significantly at high ozone concentration and high RH when excited at 263 nm excitation. The decreases in 263 nm excited fluorescence are indicative of hydrolysis and oxidation of tryptophan in the aerosols. Fluorescence measured with the UV-APS (355-nm excitation) increased with time for both BtAH and MS2 aerosols. A two log loss of MS2 bacteriophage infectivity was observed in the presence of ozone at ~50% and 80% RH when measured by culture and normalized for physical losses by q-PCR. Viability of BtAH spores after exposure could not be measured due to the loss of genomic material during experiments, suggesting degradation of extracelluar DNA attributable to oxidation. The results of these studies indicate that the physical and biological properties of bioaerosols change significantly after exposure to ozone and water vapor.

  8. Rotational spectra of isotopic species of methyl cyanide, CH3CN, in their v8 = 1 excited vibrational states

    CERN Document Server

    Müller, H S P; Pearson, J C; Ordu, M H; Wehres, N; Lewen, F

    2016-01-01

    Methyl cyanide is an important trace molecule in space, especially in star-forming regions where it is one of the more common molecules used to derive kinetic temperatures. We want to obtain accurate spectroscopic parameters of minor isotopologs of methyl cyanide in their lowest excited v8 = 1 vibrational states to support astronomical observations, in particular, with interferometers such as ALMA. The laboratory rotational spectrum of methyl cyanide in natural isotopic composition has been recorded from the millimeter to the terahertz regions. Transitions with good signal-to-noise ratios could be identified for the three isotopic species CH3(13)CN, (13)CH3CN, and CH3C(15)N up to about 1.2 THz (J" <= 66). Accurate spectroscopic parameters were obtained for all three species. The present data were already instrumental in identifying v8 = 1 lines of methyl cyanide with one (13)C in IRAM 30 m and ALMA data toward Sagittarius B2(N).

  9. DFT calculations of 2,6-dimethylpyrazine (26DMP) and its complex with chloranilic acid (CLA): Comparison to INS, IR and Raman vibration spectra

    Science.gov (United States)

    Pawlukojć, A.; Sobczyk, L.; Prager, M.; Bator, G.; Grech, E.; Nowicka-Scheibe, J.

    2008-12-01

    The inelastic neutron scattering (INS), infrared and Raman spectra of crystalline 2,6-dimethylpyrazine (26DMP) and its complex with chloranilic acid (26DMP·CLA) were measured. Simultaneously the DFT calculations of the molecular structures and frequencies of the normal vibrations were performed by using various functionals. The INS spectra were simulated in the energy range up to 1200 cm -1, on the basis of the calculated frequencies. A very good conformity was obtained between experimental and calculated data with respect to the structure as well as to frequencies, with exception, however, of the CH 3 torsional modes. The structural analysis based on the deviation from the sum of the van der Waals radii showed that the packing of the methyl groups in the 26DMP·CLA complex was markedly stronger than that in the neat 26DMP. However, the DFT calculations overestimated the role of this effect that may be due to a limitation of the applied methods. In addition the anharmonicity of the rotational potential led to the librational energies different from those obtained using a harmonic potential.

  10. The vibrational spectra of amides—II. The force field and isotopic shifts of N, N-dimethyl formamide

    Science.gov (United States)

    Steele, D.; Quatermain, A.

    The effects of 16O → 18O substitution on the vibrational frequencies of N, N-dimethylformamide have been studied. To understand these and the effects of previously measured shift data due to 13C, 2H and 15N ab initio calculations of frequencies and intensities have been carried out at the 3-21G level. Accord between theory and experiment is generally good. A surprising result is the prediction of a weak band near 2000 cm -1 in DMF due to in-plane interaction between the methyl umbrella modes and the anti-symmetric CN stretch. This abnormally high frequency is explained as arising due to the planar trigonal C 3N entity. Previous problems in reproducing isotope shifts are shown to be due to this mode being previously assigned near 1500 cm -1. The effects of suppressing reference to one of a set of internal valence angles involved in a redundancy are explored. It is shown that the principal effect is to add the diagonal quadratic constant for that coordinate to all other quadratic terms involving pairs of the angles involved in the redundancy. This results in large, almost equal, interaction constants amongst this set. Such effects are seen in the present work. The ab initio field is shown to be compatible with ab initio fields of mono N-methyl amides extant in the literature.

  11. Crystal and molecular structure of N-(4-nitrophenyl)-β-alanine—Its vibrational spectra and theoretical calculations

    Science.gov (United States)

    Marchewka, M. K.; Drozd, M.; Janczak, J.

    2011-08-01

    The N-(4-nitrophenyl)-β-alanine in crystalline form directly by the addition of 4-nitroaniline to the acrylic acid in aqueous solution has been obtained. The title β-alanine derivative crystallizes in the P2 1/ c space group of monoclinic system with four molecules per unit cell. The X-ray geometry of β-alanine derivative molecule has been compared with those obtained by molecular orbital calculations corresponding to the gas phase. In the crystal the molecules related by an inversion center interact via symmetrically equivalent O-H⋯O hydrogen bonds with O⋯O distance of 2.656(2) Å forming a dimeric structure. The dimers of β-alanine derivative weakly interact via N-H⋯O hydrogen bonds between the H atom of β-amine groups and one of O atom of nitro groups. The room temperature powder vibrational (infrared and Raman) measurements are in accordance with the X-ray analysis. In aqueous solution of 4-nitroaniline and acrylic acid, the double C dbnd C bond of vinyl group of acrylic acid breaks as result of 4-nitroaniline addition.

  12. Crystal and molecular structure of N-(4-nitrophenyl)-β-alanine--its vibrational spectra and theoretical calculations.

    Science.gov (United States)

    Marchewka, M K; Drozd, M; Janczak, J

    2011-08-15

    The N-(4-nitrophenyl)-β-alanine in crystalline form directly by the addition of 4-nitroaniline to the acrylic acid in aqueous solution has been obtained. The title β-alanine derivative crystallizes in the P2(1)/c space group of monoclinic system with four molecules per unit cell. The X-ray geometry of β-alanine derivative molecule has been compared with those obtained by molecular orbital calculations corresponding to the gas phase. In the crystal the molecules related by an inversion center interact via symmetrically equivalent O-H···O hydrogen bonds with O···O distance of 2.656(2) Å forming a dimeric structure. The dimers of β-alanine derivative weakly interact via N-H···O hydrogen bonds between the H atom of β-amine groups and one of O atom of nitro groups. The room temperature powder vibrational (infrared and Raman) measurements are in accordance with the X-ray analysis. In aqueous solution of 4-nitroaniline and acrylic acid, the double CC bond of vinyl group of acrylic acid breaks as result of 4-nitroaniline addition.

  13. Molecular structure and vibrational spectra of 2,6-bis(benzylidene)cyclohexanone: A density functional theoretical study

    Science.gov (United States)

    Sajan, D.; Udaya Lakshmi, K.; Erdogdu, Y.; Hubert Joe, I.

    2011-01-01

    The near-infrared Fourier transform (NIR-FT) Raman and Fourier transform infrared (FT-IR) spectral analyses of 2,6-bis(benzylidene)cyclohexanone (BBC) molecule, a potential drugs for the treatment of P388 leukemia cells, were carried out along with density functional computations. The optimized geometry of BBC using density functional theory shows that the energetically favored chair conformation is not observed for central cyclohexanone ring and is found to possess a nearly 'half chair' conformation and shows less expansion of the angles and more rotation about the bonds. The existence of intramolecular C-H⋯O improper, blue-shifted hydrogen bond was investigated by means of the NBO analysis. The lowering of carbonyl stretching vibration can be attributed to the mesomeric effect and the π-orbital conjugation induced by the unsaturation in the α-carbon atoms and co-planarity of the (-CH dbnd C-(C dbnd O)-C dbnd CH-) group.

  14. Rotational spectra of isotopic species of methyl cyanide, CH3CN, in their v8 = 1 excited vibrational states

    Science.gov (United States)

    Müller, Holger S. P.; Drouin, Brian J.; Pearson, John C.; Ordu, Matthias H.; Wehres, Nadine; Lewen, Frank

    2016-02-01

    Context. Methyl cyanide is an important trace molecule in space, especially in star-forming regions where it is one of the more common molecules used to derive kinetic temperatures. Aims: We want to obtain accurate spectroscopic parameters of minor isotopologs of methyl cyanide in their lowest excited ν8 = 1 vibrational states to support astronomical observations, in particular, with interferometers such as ALMA. Methods: The laboratory rotational spectrum of methyl cyanide in natural isotopic composition has been recorded from the millimeter to the terahertz regions. Results: Transitions with good signal-to-noise ratios could be identified for the three isotopic species CH313CN, 13CH3CN, and CH3C15N up to about 1.2 THz (J'' ≤ 66). Accurate spectroscopic parameters were obtained for all three species. Conclusions: The present data were already instrumental in identifying ν8 = 1 lines of methyl cyanide with one 13C in IRAM 30 m and ALMA data toward Sagittarius B2(N).

  15. Theoretical Study on Vibrational Spectra, Detonation Properties and Pyrolysis Mechanism for Cyclic 2-Diazo-4,6-dinitrophenol

    Institute of Scientific and Technical Information of China (English)

    Xiao-hong Li; Geng-xin Yin; Xian-zhou Zhang

    2012-01-01

    Based on the full optimized molecular geometrical structures at the DFT-B3LYP/6-311+G** level,there exists intramolecular hydrogen bond interaction for cyclic 2-diazo-4,6-dinitrophenol.The assigned infrared spectrum is obtained and used to compute the thermodynamic properties.The results show that there are four main characteristic regions in the calculated IR spectra of the title compound.The detonation velocities and pressures are also evaluated by using Kamlet-Jacobs equations based on the calculated density and condensed phase heat of formation.Thermal stability and the pyrolysis mechanism of 2-diazo-4,6-dinitrophenol are investigated by calculating the bond dissociation energies at the B3LYP/6-311+G** level.

  16. Comparison of experimental proton-induced fluorescence spectra for a selection of thin high-Z samples with Geant4 Monte Carlo simulations

    Energy Technology Data Exchange (ETDEWEB)

    Incerti, S., E-mail: sebastien.incerti@tdt.edu.vn [Division of Nuclear Physics, Ton Duc Thang University, Ho Chi Minh City (Viet Nam); Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City (Viet Nam); Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Barberet, Ph.; Dévès, G.; Michelet, C. [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Francis, Z. [Université Saint Joseph, Science Faculty, Department of Physics, Beirut (Lebanon); Ivantchenko, V. [Ecoanalytica, Moscow (Russian Federation); Geant4 Associates International Ltd, Hebden Bridge (United Kingdom); Mantero, A. [SWHARD srl, via Greto di Cornigliano 6r, 16152 Genova (Italy); El Bitar, Z. [Institut Pluridisciplinaire Hubert Curien, CNRS/IN2P3, 67037 Strasbourg Cedex (France); Bernal, M.A. [Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, SP (Brazil); Tran, H.N. [Division of Nuclear Physics, Ton Duc Thang University, Ho Chi Minh City (Viet Nam); Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City (Viet Nam); Karamitros, M.; Seznec, H. [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France)

    2015-09-01

    The general purpose Geant4 Monte Carlo simulation toolkit is able to simulate radiative and non-radiative atomic de-excitation processes such as fluorescence and Auger electron emission, occurring after interaction of incident ionising radiation with target atomic electrons. In this paper, we evaluate the Geant4 modelling capability for the simulation of fluorescence spectra induced by 1.5 MeV proton irradiation of thin high-Z foils (Fe, GdF{sub 3}, Pt, Au) with potential interest for nanotechnologies and life sciences. Simulation results are compared to measurements performed at the Centre d’Etudes Nucléaires de Bordeaux-Gradignan AIFIRA nanobeam line irradiation facility in France. Simulation and experimental conditions are described and the influence of Geant4 electromagnetic physics models is discussed.

  17. Absorption,fluorescence and resonance Rayleigh scattering spectra of hydrophobic hydrogen bonding of eosin Y/Triton X-100 nanoparticles and their analytical applications

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    In a weak acidic medium(pH 2.4-2.8),eosin Y molecules(H2L) could replace water molecules to associate with Triton X-100 to form hydrophobic hydrogen bonding complexes.These complexes could further aggregate to form nanoparticles through the squeezing action of the water phase and Van Der Waals force,resulting in changes in the absorption spectrum and fluorescence quenching of EY as well as the significant enhancement of resonance Rayleigh scattering.This enables the sensitive determination of Triton X-100 using the fading spectrophotometry,fluorescence quenching method and RRS method.Among them,the RRS method shows the highest sensitivity with a detection limit of 20.6 ng mL-1 for Triton X-100.The optimum experimental conditions and factors that affect the absorption,fluorescence and RRS spectra were tested.The effects of coexisting substances were investigated and the results showed good selectivity.Based on these results,new spectrophotometric methods,fluorescence quenching method and RRS method for the determination of Triton X-100,were established.The hydrogen bonding association of eosin Y with Triton X-100 and the formation of nanoparticles as well as their effects on related spectral characteristics were discussed utilizing infrared,transmission electron microscope technique and quantum chemical method.

  18. Vibrational spectra of the ML/sub 2/Cl/sub 2/ complexes (M=Zn,Cd,Co,Ni; L=5-methyl-1-phenylhexahydro-1,3-5-triazine-2-thion)

    Energy Technology Data Exchange (ETDEWEB)

    Zakharova, O.S.; Dobreva, D.D.; Ignatova, L.A.; Kravchenko, V.V.; Petrov, K.I. (Moskovskij Inst. Tonkoj Khimicheskoj Tekhnologii (USSR))

    1984-01-01

    IR absorption spectra of the complexes ML/sub 2/Cl/sub 2/ (M=Zn, Cd, Co, Ni, L=5 - methyl-1-phenylhexahydro-1, 3, 5-triazine-2-thion) in the range from 4000 to 200 cm/sup -1/ and Raman laser spectra of the complexes ML/sub 2/Cl/sub 2/ (M=Zn, Cd) in crystal state are recorded. Qualitative interpretation of vibrational frequencies in the spectra has been carried out. It is established that ligand molecules are coordinated via sulphur atom. The structure of the complexes is briefly outlined.

  19. Absorption and fluorescence lineshape theory for polynomial potentials

    DEFF Research Database (Denmark)

    Anda, Andre; De Vico, Luca; Hansen, Thorsten

    2016-01-01

    and fluorescence spectra. The first method, which constructs vibrational wave functions as linear combinations of the harmonic oscillator wave functions, is shown to be extremely robust and can handle large anharmonicities. The second method uses the cumulant expansion, which is readily solved, even at high orders...

  20. Raman and DRIFT spectra, vibrational assignments and quantum mechanical calculations of centrosymmetric meso-2,3-Dimercaptosuccinic acid

    Science.gov (United States)

    Shaaban, Ibrahim A.; Karoyo, Abdalla; Wilson, Lee D.; Mohamed, Tarek A.

    2017-08-01

    The Raman spectrum (3700-100 cm- 1) of meso-2,3-Dimercaptosuccinic acid (meso-DMSA; C4H6O4S2) was recorded in the solid phase using 514.5 and 785 nm excitation lines. Whereas, the DRIFT spectrum (4000-400 cm- 1) of the sample powdered in KBr was obtained. Moreover, DFT-B3LYP/6-31G(d) geometry optimization and frequency calculations were carried out for centrosymmetric trans (Ci), gauche (C1; G+/G-) and eclipsed (Cs; Ef and C1; E+/E-) rotational isomers in favor of a trans conformation, the least energy with real frequencies. However, other conformers were found at either local minima or local maxima as a result of the rotation of carboxyl, hydroxyl and thiol groups according to a potential energy surface scan. Moreover, an imaginary wavenumber was predicted; therefore, they are considered transition states. On the other hand, the mass spectrum of the sample dissolved in an acetonitrile/methanol mixture reveal 4-6% dimer through intermolecular hydrogen bonding interactions via the dicarboxylic groups. Therefore, we have modeled the complex structure obeying Ci restricted symmetry for an isolated dimer unit using DFT-B3LYP/6-31G(d) and for two molecules per unit cell in the solid phase implementing DFT-PBE functional. Thus, the meso-DMSA forms long strands in which individual molecules are bonded together at each termini through hydrogen bonding. Aided by normal coordinate analysis, complete vibrational assignments were provided herein which support Ci configuration of meso-DMSA in the solid state which found consistent with the observed broadening, composite, split bands, and the mutual exclusion rule.

  1. Interaction of 4-aminosalieylic Acid and Surfactants in Aqueous Solutions Using UV-Vis Spectra and Steady-state Fluorescence Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    XU Dongying; REN Jiaoyan; LIAO Zhengfu; WANG Hui; ZHAO Mouming; LI Guangji

    2011-01-01

    The interactions of 4-aminosalicylic acid (4-ASA) and surfactants in aqueous solutions were investigated by using UV-Vis spectra and steady-state fluorescence spectroscopy.The results showed that the strongest peak at UV-vis spectra of 4-ASA aqueous solution in the presence of cationic surfactant and cetyltrimethyl ammonium bromide (CTAB) appeared at 206 nm and took.a red shift from 206 nm to 221 nm with the increase of 4-ASA concentrations from 0.8× 10-5 to 4.4× 10-4 mol/L.Similarly,the strongest peak at UV-vis spectra of 4-ASA aqueous solution in the presence of nonionic surfactant and polyvinylpyrrolidone (PVP)appeared at 206 nm and took a red shift from 206 nm to 219 nm with the increase of 4-ASA concentrations from 0.8× 10-5 to 4.4x 10-4 mol/L.However,the similar phenomena did not appeared in the presence of anion surfactant,sodium dodecyl sulfate (SDS),the UV-vis spectra of 4-ASA aqueous solution remained the same peak position and the peak value increased with the 4-ASA concentration increase.The results could be attributed to the electrostatic attraction between 4-ASA and CTAB or PVP,as well as the electrostatic repulsion between 4-ASA and SDS.Furthermore,the value of critical micelle concentration (CMC) of surfactants in the presence of 4-ASA was determined with Fluorescence method.The first and second CMC of CTAB was 1.2×10-4 M and 2.4x10-4 M,respectively.The first and second CMC of PVP was 1.2×10 4 M and 2.8x 10 4 M.SDS realized the multiple micellizations to form multiple CMC.

  2. A novel coordination polymer of 7-azaindole-3-carboxylic acid with sodium ions: crystal and molecular structures, vibrational spectra and DFT calculations

    Science.gov (United States)

    Morzyk-Ociepa, Barbara; Szmigiel, Ksenia; Petrus, Rafał; Turowska-Tyrk, Ilona; Michalska, Danuta

    2017-09-01

    A novel two-dimensional coordination polymer, catena-poly[(μ2-7-azaindole-3-carboxylato-O:N)-di-aqua-sodium], [Na(7AI3CAH)(H2O)2]n has been synthesized and investigated by a single crystal X-ray diffraction, vibrational spectroscopy and DFT calculations. The sodium complex crystallizes in the triclinic system, space group Pī with a = 7.2226 (4), b = 7.4342 (7), c = 8.8428 (8) Å, α = 103.568 (8), β = 93.425 (6), γ = 91.233 (6)°, V = 460.42 (7) A3 and Z = 2. The asymmetric unit contains two crystallographically independent, half occupied sodium cations surrounded by one 7AI3CAH anion and two water molecules. The O-deprotonated 7-azaindole-3-carboxylate ligand (7AI3CAH) bridges the adjacent Na ions via one oxygen atom of the carboxylate group and via the pyridine nitrogen atom of the 7-azaindole group, which is quite unusual. The sodium cations are six-coordinated in a distorted octahedral geometry, where two apical positions are occupied by two water molecules. Extensive intermolecular Nsbnd H⋯O and Osbnd H⋯O hydrogen bonds stabilize the crystal structure of the complex. The infrared and Raman spectra of [Na(7AI3CAH)(H2O)2]n were recorded in the solid state. The theoretical wavenumbers, infrared intensities, Raman scattering activities and Raman intensities were calculated at the B3LYP/6-311++G(d,p) level for a theoretical model of the title compound including an inter ligand Nsbnd H⋯O(aqua) interaction. A detailed vibrational assignment has been made on the basis of the calculated potential energy distribution.

  3. The crystal structure, vibrational spectra, thermal behaviour and second harmonic generation of aminoguanidinium(1+) hydrogen L-tartrate monohydrate

    Science.gov (United States)

    Macháčková, Zorka; Němec, Ivan; Teubner, Karel; Němec, Petr; Vaněk, Přemysl; Mička, Zdeněk

    2007-04-01

    Aminoguanidinium(1+) hydrogen L-tartrate monohydrate was prepared by crystallisation from aqueous solution and X-ray structural analysis was carried out. The substance crystallises in the orthorhombic system in space group P2 12 12 1, a = 7.1380(2) Å, b = 9.9700(4) Å, c = 14.0790(6) Å, V = 1001.94(7) Å 3, Z = 4, R = 0.0271 for 2272 observed reflections. The crystal structure consists of a 3D framework formed by hydrogen tartrate anions and water molecules with incorporated aminoguanidinium(1+) cations connected by a system of hydrogen bonds. The FTIR and FT Raman spectra of natural and N,O-deuterated compounds were measured and discussed at laboratory temperature. DSC measurements were carried out in the temperature range from 95 to 380 K. A weak anomaly was observed at a temperature of 268 K. Quantitative measurements of second harmonic generation of powdered aminoguanidinium(1+) hydrogen tartrate monohydrate at 800 nm were performed relative to KDP and a relative efficiency of 14% was observed.

  4. Microwave, infrared, and Raman spectra, structural parameters, vibrational assignments and theoretical calculations of 1,1,3,3-tetrafluoro-1,3-disilacyclopentane

    Energy Technology Data Exchange (ETDEWEB)

    Pate, Brooks H.; Seifert, Nathan A. [Department of Chemistry, University of Virginia, Charlottesville, VA 22904 (United States); Guirgis, Gamil A. [Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424 (United States); Deodhar, Bhushan S.; Klaassen, Joshua J.; Darkhalil, Ikhlas D. [Department of Chemistry, University of Missouri-Kansas City, Kansas City, MO 64110 (United States); Crow, Joseph A. [Department of Physics, University of Missouri-Kansas City, Kansas City, MO 64110 (United States); Wyatt, Justin K.; Dukes, Horace W. [Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424 (United States); Durig, James R., E-mail: durigj@umkc.edu [Department of Chemistry, University of Missouri-Kansas City, Kansas City, MO 64110 (United States)

    2013-04-18

    Highlights: • Structural parameters have been determined for the stable twist conformer. • Rotational constants for the six isotopologues for the twist conformer were determined from the microwave spectra. • Vibrational assignments are given for the molecule. • Ab intio and density functional theory calculations have been carried out for all possible conformers. - Abstract: The FT-microwave spectrum of 1,1,3,3-tetrafluoro-1,3-disilacyclopentane (c-C{sub 3}H{sub 6}Si{sub 2}F{sub 4}) has been recorded and 339 transitions for 6 isotopologues have been assigned for the twist conformation. The ground state rotational constants were determined with values for the normal species: A = 2102.74026(68), B = 751.34319(32), C = 736.51478(31). Adjusted r{sub 0} parameters are reported with distances (Å): rC{sub α}–Si = 1.859(2), rSi–C{sub β} = 1.864(2), rSi–F{sub 1} = 1.583(3), rSi–F{sub 2} = 1.578(3), and rC{sub β}–C{sub β} = 1.559(3), and angles (°): ∠SiC{sub α}Si = 102.8(3), ∠C{sub α}SiC{sub β} = 104.3(3), ∠SiC{sub β}C{sub β′} = 106.6(3), τC{sub β}SiC{sub α}Si = 10.7(3), and τ SiC{sub β}C{sub β′}Si = 40.8(3). The conformational stabilities have been predicted from ab initio calculations utilizing several various basis sets. Vibrational assignments have been provided for the observed bands for the twist conformer which are supported by ab initio calculations to predict harmonic force constants, vibrational wavenumbers, infrared intensities, Raman activities and depolarization ratios. The results are discussed and compared to the corresponding properties of some related molecules.

  5. Metal-organic frameworks in cadmium(II) complexes with 5-methoxyindole-2-carboxylic acid: structure, vibrational spectra and DFT calculations

    Science.gov (United States)

    Morzyk-Ociepa, Barbara; Szmigiel, Ksenia; Dysz, Karolina; Turowska-Tyrk, Ilona; Michalska, Danuta

    2016-11-01

    Two new complexes of Cd(II) with an O-deprotonated anion of 5-methoxyindole-2-carboxylic acid (5-MeOI2CA), of the formulas [Cd(5-MeOI2CA)2(H2O)2]n (1) and [Cd3(5-MeOI2CA)6(H2O)4(DMSO)4]ṡ2DMSO (2) were synthesized. In the polymeric complex 1, the 5-MeOI2CA anion acts as a bidentate bridging ligand and the coordination environment around the Cd(II) ion can be described as a distorted octahedron. Single crystal X-ray diffraction analysis of 2 has revealed that this complex is a trimer and it crystallizes in the monoclinic system (space group P21/c with a = 20.3403(4), b = 14.3079(2), c = 15.0603(3) Å, β = 92.4341(17)°, V = 4379.00(14) Å3 and Z = 2). In 2, the 5-MeOI2CA anions act as bidentate bridging and bidentate chelating ligands. The asymmetric unit of 2 contains two crystallographically independent Cd(II) cations. One of the cations is coordinated to six oxygen atoms and shows an octahedral geometry with a rhombic deformation. The other Cd(II) cation adopts a distorted seven-coordinate pentagonal-bipyramidal geometry involving seven oxygen atoms. In 2, the DMSO solvent molecules play a key role in the formation of metal-organic frameworks by filling voids, which are created by the bridging and chelating 5-MeOI2CA anions, the cadmium cations and the other DMSO molecules coordinated to cadmium. Comprehensive theoretical calculations (including the optimized structural parameters, harmonic frequencies and vibrational intensities) were performed for 2 using the B3LYP method with the 6-311++G(d,p)/LanL2DZ basis sets. The infrared and Ramana spectra were measured and a detailed assignment of the experimental spectra of 2 was performed. All cadmium-oxygen stretching vibrations occur in the range below 400 cm-1.

  6. Twisted intramolecular charge transfer states : rotationally resolved fluorescence excitation spectra of 4,4 '-dimethylaminobenzonitrile in a molecular beam

    NARCIS (Netherlands)

    Nikolaev, A.E.; Myszkiewicz, G.; Berden, G.; Meerts, W.L.; Pfanstiel, J.F.; Pratt, D.W.

    2005-01-01

    We report the observation at high resolution of seven vibronic bands that appear within similar to200 cm(-1) of the electronic origin in the S-1-S-0 fluorescence excitation spectrum of 4,4(')-dimethylaminobenzonitrile (DMABN) in a molecular beam. Surprisingly, each band is found to be split into two

  7. Constructing Periodic Phase Space Orbits from ab Initio Molecular Dynamics Trajectories to Analyze Vibrational Spectra: Case Study of the Zundel (H5O2(+)) Cation.

    Science.gov (United States)

    Dietrick, Scott M; Iyengar, Srinivasan S

    2012-12-11

    A method of analysis is introduced to probe the spectral features obtained from ab initio molecular dynamics simulations. Here, the instantaneous mass-weighted velocities are projected onto irreducible representations constructed from discrete time translation groups comprising operations that invoke the time-domain symmetries (or periodic phase space orbits) reflected in the spectra. The projected velocities are decomposed using singular value decomposition (SVD) to construct a set of "modes" pertaining to a given frequency domain. These modes now include all anharmonicities, as sampled during the dynamics simulations. In this approach, the underlying motions are probed in a manner invariant with respect to coordinate transformations, operations being performed along the time axis rather than coordinate axes, making the analysis independent of choice of reference frame. The method is used to probe the underlying motions responsible for the doublet at ∼1000 cm(-1) in the vibrational spectrum of the H5O2(+), Zundel cation. The associated analysis results are confirmed by projecting the Fourier transformed velocities onto the harmonic normal mode coordinates and a set of mass-weighted, symmetrized Jacobi coordinates. It is found that the two peaks of the doublet are described and differentiated by their respective contributions from the proton transfer, water-water stretch, and water wag coordinates, as these are defined. Temperature dependent effects are also briefly noted.

  8. Effect of solvent on absorption and fluorescence spectra of a typical fluorinated azo dye for its acidic and basic structures

    Science.gov (United States)

    Abdel-Halim, Shakir T.

    2011-11-01

    The effect of 15 polar solvents on absorption and fluorescence energies of a typical fluorinated azo dye, 4-(2,3,5,6-tetrafluoro-pyridin-4-yl azo)-phenol, was reported for its acidic, MH, and basic, M, structures. For MH, the absorption energy is described on the basis of multi-linear equation with Taft's π* (solvent polarity) and β (hydrogen bond acceptor) parameters while the fluorescence energy varies rectilinearly with free energy of transferring the proton to the surrounding solvent, Δ Gt°. For M, the hydrogen bonding donor ability of protic solvent, α, is a predominant factor which affects the absorption energy while in aprotic solvents, the absorption energy correlates linearly with Kirkwood function. As the ability of the solvent for hydrogen bonding increases, the absorption band width will increase in parallel with the transition energy.

  9. Vibrational Spectra of Hetian Nephrite from Xinjiang%新疆和田透闪石软玉的振动光谱

    Institute of Scientific and Technical Information of China (English)

    张永旺; 刘琰; 刘涛涛; 木合塔尔·扎日; 刘元晴

    2012-01-01

    In previous studies, EMPA, PIXE and others were employed to study the chemical compositions of nephrite separately without a systematical measurement. In the present study, XRF, XRD, IR and LR were used together to examine chemical and spectra characteristics of white, green and black nephrite from Hetian, Xinjiang. XRD results indicate that all nephrite samples consist of tremolite. Then IR spectra of nephrite samples suggest that the M-OH stretching vibration bands show that the M1 and M3 sites are not only occupied by Mg2+ and Fe2+ , but also by Fe3+ , which is consistent with the chemical compositions of these samples. This information might be useful to understanding the variety of nephrite. Their Raman spectra are almost the same, while some differences exist because of different content of FeO/Fe2O3.%采用X荧光光谱、X光粉晶衍射、红外光谱和拉曼光谱等对新疆和田地区的白色、青色和黑色透闪石软玉进行了化学成份和振动光谱研究.在通过X光粉晶衍射判定所采样品全部属于透闪石质软玉后,采用红外光谱仪和拉曼光谱仪对样品进行振动光谱测试,并结合化学成分测试结果分析白玉、青玉和墨玉等不同颜色的软玉中透闪石晶体结构M1、M3位置中阳离子占位情况.红外光谱中M-OH吸收谱带显示样品在M1及M3位置不仅有Mg2+和Fe2+,还有Fe3+.M-OH的吸收谱带和振动光谱特征与化学成分测试结果一致.在此基础之上,总结了新疆和田透闪石软玉中阳离子的种类和含量对振动光谱的影响.

  10. 人血液及其组分的荧光光谱研究%Study on Fluorescence Spectra of Human Blood and Its Components

    Institute of Scientific and Technical Information of China (English)

    降雨强; 李昌勇; 周源; 张临杰; 肖连团; 贾锁堂; 马存根; 周国生

    2001-01-01

    A 532 nm laser was used as exciting source to measure the fluorescence spectra of human blood and its components (red blood cell, blood platelet and blood plasma). The spectra of blood have peaks near 630 nm and 710 nm, and the spectra of blood components are obviously different from them. The spectrum of plasma has a clear peak at 738 nm. Contrary to the normal blood plasma, the plasma spectrum of HBsAg positive blood has a very strong peak at 738 nm,which can be used for diagnosis of hepatitis B.%用532 nm的激光作为激发光源,分别测量正常人血液及血液组分(血浆、血小板、红细胞)的荧光光谱。结果显示,全血在630 nm及710 nm附近出现荧光峰值,其各组分的荧光光谱有明显差异,其中血浆的荧光光谱可作为临床诊断依据。另外,比较正常人及乙型肝炎患者血浆标本的荧光光谱发现,其738 nm处的峰值强度有显著差异。

  11. Effects of solvent polarity on the absorption and fluorescence spectra of chlorogenic acid and caffeic acid compounds: determination of the dipole moments.

    Science.gov (United States)

    Belay, Abebe; Libnedengel, Ermias; Kim, Hyung Kook; Hwang, Yoon-Hwae

    2016-02-01

    The effects of solvent polarity on absorption and fluorescence spectra of biologically active compounds (chlorogenic acid (CGA) and caffeic acids (CA)) have been investigated. In both spectra pronounced solvatochromic effects were observed with shift of emission peaks larger than the corresponding UV-vis electronic absorption spectra. From solvatochromic theory the ground and excited-state dipole moments were determined experimentally and theoretically. The differences between the excited and ground state dipole moment determined by Bakhshiev, Kawski-Chamma-Viallet and Reichardt equations are quite similar. The ground and excited-state dipole moments were determined by theoretical quantum chemical calculation using density function theory (DFT) method (Gaussian 09) and were also similar to the experimental results. The HOMO-LUMO energy band gaps for CGA and CFA were calculated and found to be 4.1119 and 1.8732 eV respectively. The results also indicated the CGA molecule is more stable than that of CFA. It was also observed that in both compounds the excited state possesses a higher dipole moment than that of the ground state. This confirms that the excited state of the hydroxycinnamic compounds is more polarized than that of the ground state and therefore is more sensitive to the solvent.

  12. Theoretical study of enhancement and suppression of the fluorescent spectra of dye molecules in a photonic crystal with a pseudogap

    Institute of Scientific and Technical Information of China (English)

    刘晓东; 许兴胜; 王义全; 张道中; 程丙英

    2003-01-01

    We have investigated the analytical forms of the photonic density of states(DOS)in a photonic crystal in the interested frequency regime according to the rule of state conservation in a photonic crystal with pseudogaps,which states that,if a valley of the DOS appears in some range of frequencies,it must be compensated for by increasing over some other ranges.By using a model DOS with a state-conservative photonic pseudogap,we have also investigated the enhancement and suppression of spontaneous emission of two-level atoms with different frequency positions and widths of emission spectra in a state-conservative electromagnetic reservoir; and the DOS-induced suppression,enhancement,narrowing and redshifting or blueshifting of spontaneous emission spectra are naturally obtained.

  13. Vapor Phase Vibrational Spectra for Re(2)O(7) and the Infrared Spectrum of Gaseous HReO(4). Molecular Shapes of Mn(2)O(7), Tc(2)O(7), and Re(2)O(7).

    Science.gov (United States)

    Beattie, I. R.; Gilson, T. R.; Jones, P. J.

    1996-02-28

    The Raman and infrared spectra of gas phase Re(2)O(7) are reported. The experimental vibrational spectra of molecular Tc(2)O(7) and Re(2)O(7) are compared with calculated spectra. The results of these studies agree with a nonlinear M-O-M bridge for Tc(2)O(7) and Re(2)O(7). For infrared intensity calculations, the point charge approximation is used, while for the Raman calculations a combination of bond and atom polarizabilities is adopted. Pure Re(2)O(7) was prepared from rhenium wire, but attempts to prepare it from rhenium powder and oxygen always led to infrared spectra showing serious contamination from a species containing an -OH linkage. Detailed experiments identified this molecule as HReO(4), a unique transition metal analogue of the perhalic acids, and a partial infrared spectrum of this molecule is reported.

  14. Molecular structure and vibrational spectra of spin-crossover complexes in solution and colloidal media: resonance Raman and time-resolved resonance Raman studies.

    Science.gov (United States)

    Brady, Clare; Callaghan, Philip L; Ciunik, Zbigniew; Coates, Colin G; Døssing, Anders; Hazell, Alan; McGarvey, John J; Schenker, Sabine; Toftlund, Hans; Trautwein, Alfred X; Winkler, Heiner; Wolny, Juliusz A

    2004-07-12

    The spin-crossover system [Fe(btpa)](PF(6))(2) (btpa = N,N,N',N'-tetrakis(2-pyridylmethyl)-6,6'-bis(aminomethyl)-2,2'-bipyridine) and the predominantly low-spin species [Fe(b(bdpa))](PF(6))(2) ((b(bdpa) = N,N'-bis(benzyl)-N,N'-bis(2-pyridylmethyl)-6,6'-bis(aminomethyl)-2,2'-bipyridine) have been characterized by means of X-ray diffraction. The unit cell of [Fe(btpa)](PF(6))(2) contains two crystallographically independent molecules revealing octahedral low-spin and quasi-seven-coordinated high-spin structures. The unit cell of [Fe(b(bdpa))](PF(6))(2) contains two crystallographically independent molecules one of which corresponds to a low-spin structure, while the other reveals a disordering. On the basis of magnetic susceptibility and Mössbauer measurements, it has been proposed that this disorder involves low-spin and high-spin six-coordinated molecules. The structures of [Zn(btpa)](PF(6))(2) and [Ru(btpa)](PF(6))(2) have been determined also. Pulsed laser photoperturbation, coupled here with time-resolved resonance Raman spectroscopy (TR(3)), has been used to investigate, for the first time by this technique, the relaxation dynamics in solution on nanosecond and picosecond time scales of low-spin, LS ((1)A) --> high-spin, HS ((5)T) electronic spin-state crossover in these Fe(II) complexes. For the nanosecond experiments, use of a probe wavelength at 321 nm, falling within the pi-pi transition of the polypyridyl backbone of the ligands, enabled the investigation of vibrational modes of both LS and HS isomers, through coupling to spin-state-dependent angle changes of the backbone. Supplementary investigations of the spin-crossover (SCO) equilibrium in homogeneous solution and in colloidal media assisted the assignment of prominent features in the Raman spectra of the LS and HS isomers. The relaxation data from the nanosecond studies confirm and extend earlier spectrophotometric findings, (Schenker, S.; Stein, P. C.; Wolny, J. A.; Brady, C.; McGarvey, J. J

  15. Optical pathology using oral tissue fluorescence spectra: classification by principal component analysis and k-means nearest neighbor analysis.

    Science.gov (United States)

    Kamath, Sudha D; Mahato, K K

    2007-01-01

    The spectral analysis and classification for discrimination of pulsed laser-induced autofluorescence spectra of pathologically certified normal, premalignant, and malignant oral tissues recorded at a 325-nm excitation are carried out using MATLAB@R6-based principal component analysis (PCA) and k-means nearest neighbor (k-NN) analysis separately on the same set of spectral data. Six features such as mean, median, maximum intensity, energy, spectral residuals, and standard deviation are extracted from each spectrum of the 60 training samples (spectra) belonging to the normal, premalignant, and malignant groups and they are used to perform PCA on the reference database. Standard calibration models of normal, premalignant, and malignant samples are made using cluster analysis. We show that a feature vector of length 6 could be reduced to three components using the PCA technique. After performing PCA on the feature space, the first three principal component (PC) scores, which contain all the diagnostic information, are retained and the remaining scores containing only noise are discarded. The new feature space is thus constructed using three PC scores only and is used as input database for the k-NN classification. Using this transformed feature space, the centroids for normal, premalignant, and malignant samples are computed and the efficient classification for different classes of oral samples is achieved. A performance evaluation of k-NN classification results is made by calculating the statistical parameters specificity, sensitivity, and accuracy and they are found to be 100, 94.5, and 96.17%, respectively.

  16. Low temperature vibrational spectra, lattice dynamics, and phase transitions in some potassium hexahalometallates: K2[XY6] with X=Sn or Te and Y=Cl or Br

    DEFF Research Database (Denmark)

    Chodos, Steven L.; Berg, Rolf W.

    1979-01-01

    This paper deals with the observation and identification of phonon frequencies resulting from the low temperature phase transitions in K2XY6 crystals. By means of a simple lattice dynamical model, the vibrational Raman and IR data available in the literature and obtained here have been analyzed....... The model used is an extension of one previously used to explain the vibronic spectra of several related compounds. The Journal of Chemical Physics is copyrighted by The American Institute of Physics....

  17. Effect of surfactants on the fluorescence spectra of water-soluble MEHPPV derivatives having grafted polyelectrolyte chains

    Indian Academy of Sciences (India)

    Nagesh Kolishetti; S Ramakrishnan

    2007-03-01

    Poly(2-methoxy-5-[2'-ethylhexyoxy]-1,4-phenylenevinylene) (MEHPPV) derivatives with polyacrylic acid (PAA) chains grafted onto their backbone were found to be water soluble, and they exhibited a dramatic increase in their fluorescence intensity in the presence of a variety of surfactants, even at concentrations far below their critical micelle concentrations (CMC). This increase was accompanied by a blue-shift in the emission maximum. These observations are rationalized based on the postulate that the backbone conformation of the conjugated polymer is modulated upon interaction of the surfactant molecules with the polyelectrolytic tethers, which in turn results in a significant depletion of intra-chain interchromophore interactions that are known to cause red-shifted emission bands with significantly lower emission yields.

  18. Molecular structure, vibrational spectroscopic (FT-IR, FT-Raman), UV-vis spectra, first order hyperpolarizability, NBO analysis, HOMO and LUMO analysis, thermodynamic properties of benzophenone 2,4-dicarboxylic acid by ab initio HF and density functional method.

    Science.gov (United States)

    Chaitanya, K

    2012-02-01

    The FT-IR (4000-450 cm(-1)) and FT-Raman spectra (3500-100 cm(-1)) of benzophenone 2,4-dicarboxylic acid (2,4-BDA) have been recorded in the condensed state. Density functional theory calculation with B3LYP/6-31G(d,p) basis set have been used to determine ground state molecular geometries (bond lengths and bond angles), harmonic vibrational frequencies, infrared intensities, Raman activities and bonding features of the title compounds. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) following the scaled quantum mechanical force field (SQMFF) methodology. The first order hyperpolarizability (β0) and related properties (β, α0 and Δα) of 2,4-BDA is calculated using HF/6-31G(d,p) method on the finite-field approach. The stability of molecule has been analyzed by using NBO analysis. The calculated first hyperpolarizability shows that the molecule is an attractive molecule for future applications in non-linear optics. The calculated HOMO and LUMO energies show that charge transfer occurs within these molecules. Mulliken population analysis on atomic charges is also calculated. Because of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated. Finally, the UV-vis spectra and electronic absorption properties were explained and illustrated from the frontier molecular orbitals.

  19. Raman and IR studies and DFT calculations of the vibrational spectra of 2,4-Dithiouracil and its cation and anion

    Science.gov (United States)

    Singh, R.; Yadav, R. A.

    2014-09-01

    Raman and FTIR spectra of solid 2,4-Dithiouracil (DTU) at room temperature have been recorded. DFT calculations were carried out to compute the optimized molecular geometries, GAPT charges and fundamental vibrational frequencies along with their corresponding IR intensities, Raman activities and depolarization ratios of the Raman bands for the neutral DTU molecule and its cation (DTU+) and anion (DTU-) using the Gaussian-03 software. Addition of one electron leads to increase in the atomic charges on the sites N1 and N3 and decrease in the atomic charges on the sites S8 and S10. Due to ionization of DTU molecule, the charge at the site C6 decreases in the cationic and anionic radicals of DTU as compared to its neutral species. As a result of anionic radicalization, the C5sbnd C6 bond length increases and loses its double bond character while the C4sbnd C5 bond length decreases. In the case of the DTU+ ion the IR and Raman band corresponding to the out-of-phase coupled Nsbnd H stretching mode is strongest amongst the three species. The anionic DTU radical is found to be the most stable. The two NH out-of-plane bending modes are found to originate due to out-of-phase and in-phase coupling of the two NH bonds in the anion and cation contrary to the case of the neutral DTU molecule in which the out-of-plane bending motions of the two NH bonds are not coupled.

  20. Effects of high pressure on the fluorescence spectra of Cr sup 3 sup + in GdAlO sub 3

    CERN Document Server

    Jovanic, B R

    1998-01-01

    The effect of high hydrostatic pressure, up to 100 kbar, on the emission spectra of Cr sup 3 sup + ions in GdAlO sub 3 hosts was studied. A linear shifting (red-shift) of the single-ion line (the R line), the left-hand side (LS) line, right-hand side (RS) line and the neighbouring-pair line (NPL) was observed. The R line shows a pressure-induced shift of 0.082 nm kbar sup - sup 1 , nearly 2.25 times that of ruby. The LS line, RS line and NPL show pressure-induced shifts of 0.0779 nm kbar sup - sup 1 , 0.0864 nm kbar sup - sup 1 and 0.0933 nm kbar sup - sup 1 , respectively. (author)

  1. Study on the absorption and fluorescence and resonance Rayleigh scattering spectra of Cu (Ⅱ)-fluoroquinolone chelates with erythrosine and their applications

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    In pH 4.2-5.0 Britton-Robinson buffer solution medium, fluoroquinolone antibiotics (FLQs), such as ciprofloxacin (CIP), norfloxacin (NOR), ofloxacin (OF), levofloxacin (LEV), lomefloxacin (LOM), and sparfloxacin (SPA), react with Cu (Ⅱ) to form chelate cations, which further bind with erythrosine to form the ion association complexes. They can result in the changes of the absorption spectra. Simultaneously, erythrosine fades obviously and the maximum fading wavelength is located at 526 nm. The fading reactions have high sensitivities. Thus, new spectrophotometries of determination for these drugs are developed. The ion-association reactions result in the quenching of fluorescence, which also have high sensitivities. The detection limits for six antibiotics are in the range of 7.1-12.2 μg·L-1. Furthermore, the reactions can result in the enhancement of resonance Rayleigh scattering (RRS). The maximum scattering peaks of six ion-association complexes are located at 566 nm, and there are two small RRS peaks at 333 nm and 287 nm. The detection limits for fluoroquinolone antibiotics are in the range of 1.70-3.10 μg·L-1 for RRS method. Among the above three methods, the RRS method has the highest sensitivity. In this work, we investigated the spectral characteristics of the absorption, fluorescence and RRS, the optimum conditions of the reactions, and the properties of the analytical chemistry. In addition, the mechanism of reactions were discussed by density function theory (DFT) and AM1 methods.

  2. Estimation of ground and excited state dipole moment of laser dyes C504T and C521T using solvatochromic shifts of absorption and fluorescence spectra.

    Science.gov (United States)

    Basavaraja, Jana; Kumar, H M Suresh; Inamdar, S R; Wari, M N

    2016-02-05

    The absorption and fluorescence spectra of laser dyes: coumarin 504T (C504T) and coumarin 521T (C521T) have been recorded at room temperature in a series of non-polar and polar solvents. The spectra of these dyes showed bathochromic shift with increasing in solvent polarity indicating the involvement of π→π⁎ transition. Kamlet-Taft and Catalan solvent parameters were used to analyze the effect of solvents on C504T and C521T molecules. The study reveals that both general solute-solvent interactions and specific interactions are operative in these two systems. The ground state dipole moment was estimated using Guggenheim's method and also by quantum mechanical calculations. The solvatochromic data were used to determine the excited state dipole moment (μ(e)). It is observed that dipole moment value of excited state (μ(e)) is higher than that of the ground state in both the laser dyes indicating that these dyes are more polar in nature in the excited state than in the ground state.

  3. Solvent effect in implicit/explicit model on FT-IR, 1H, 13C and 19F NMR, UV-vis and fluorescence spectra, linear, second- and third-nonlinear optical parameters of 2-(trifluoromethyl)benzoic acid: Experimental and computational study

    Science.gov (United States)

    Avcı, Davut; Altürk, Sümeyye; Tamer, Ömer; Kuşbazoğlu, Mustafa; Atalay, Yusuf

    2017-09-01

    FT-IR, 1H, 13C and 19F NMR, UV-vis and fluorescence spectra for 2-(trifluoromethyl)benzoic acid (2-TFMBA) were recorded. DFT//B3LYP/6-31++G(d,p) calculations were used to determine the optimized molecular geometry, vibrational frequencies, 1H, 13C and 19F GIAO-NMR chemical shifts of 2-TFMBA. The detailed assignments of vibrational frequencies were carried out on the basis of potential energy distribution (PED) by using VEDA program. TD-DFT/B3LYP/6-31++G(d,p) calculations with the PCM (polarizable continuum model) in ethanol and DMSO solvents based on implicit/explicit model and gas phase in the excited state were employed to investigate UV-vis absorption and fluorescence emission wavelengths. The UV-vis and emission spectra were given in ethanol and DMSO solvents, and the major contributions to the electronic transitions were obtained. In addition, the NLO parameters (β, γ and χ(3)) and frontier molecular orbital energies of 2-TFMBA were calculated by using B3LYP/6-31++G(d,p) level. The NLO parameters of 2-TFMBA were compared with that of para-Nitroaniline (pNA) and urea which are the typical NLO materials. The refractive index (n) is calculated by using the Lorentz-Lorenz equation to observe polarization behavior of 2-TFMBA in DMSO and ethanol solvents. In order to investigate intramolecular and hydrogen bonding interactions, NBO calculations were also performed by the same level. To sum up, considering the well-known biological role, photochemical properties of 2-TFMBA were discussed.

  4. Morphology-based automated baseline removal for Raman spectra of artistic pigments.

    Science.gov (United States)

    Perez-Pueyo, Rosanna; Soneira, Maria Jose; Ruiz-Moreno, Sergio

    2010-06-01

    The interpretation of a Raman spectrum is based on the identification of its characteristic molecular bands. However, the assignment of the vibrational modes is often compromised by the presence in the spectrum of an intense fluorescence background that covers the measured spectra. Several techniques have been employed to minimize the presence of this fluorescence in order to resolve and analyze Raman spectra. In this paper a new automated method for fluorescence subtraction is described, based on morphology operations. This method is compared with the most commonly used polynomial fitting methods. Results indicate that the proposed automated method is efficient in fluorescence subtraction and retains the line shapes and positions of the Raman bands in the spectra.

  5. Investigating the effect of landfill leachates on the characteristics of dissolved organic matter in groundwater using excitation-emission matrix fluorescence spectra coupled with fluorescence regional integration and self-organizing map.

    Science.gov (United States)

    He, Xiao-Song; Fan, Qin-Dong

    2016-11-01

    For the purpose of investigating the effect of landfill leachate on the characteristics of organic matter in groundwater, groundwater samples were collected near and in a landfill site, and dissolved organic matter (DOM) was extracted from the groundwater samples and characterized by excitation-emission matrix (EEM) fluorescence spectra combined with fluorescence regional integration (FRI) and self-organizing map (SOM). The results showed that the groundwater DOM comprised humic-, fulvic-, and protein-like substances. The concentration of humic-like matter showed no obvious variation for all groundwater except the sample collected in the landfill site. Fulvic-like substance content decreased when the groundwater was polluted by landfill leachates. There were two kinds of protein-like matter in the groundwater. One kind was bound to humic-like substances, and its content did not change along with groundwater pollution. However, the other kind was present as "free" molecules or else bound in proteins, and its concentration increased significantly when the groundwater was polluted by landfill leachates. The FRI and SOM methods both can characterize the composition and evolution of DOM in the groundwater. However, the SOM analysis can identify whether protein-like moieties was bound to humic-like matter.

  6. 橙汁饮品的荧光光谱特性及模式识别%Fluorescence Spectra Characteristics and Pattern Recognition of Orange Juice Beverages

    Institute of Scientific and Technical Information of China (English)

    胡扬俊; 陈国庆; 朱纯; 张咏; 孔凡标; 李润

    2013-01-01

    Three dimensional fluorescence spectra of fresh orange juice and orange juice beverages (8 brands) were obtained by employing FLS920 spectrometer.The fluorescence mechanism and characters of fresh orange juice and different kinds of pure food additives in beverage foods were analyzed.The optimal excitation wavelength and fluorescence peak wavelength of orange juice are 470 nm and 526 nm,respectively.The characteristic peak of orange juice is 470/526 nm,and other peaks belong to food additives.Meanwhile,By extracting the center of gravity of three dimensional fluorescence spectroscopy,and combining the robust Mahalanobis distance based on MCD estimator,the orange juice beverages were classified,and the classification results were ideal.The results indicate that the combination of spectral detection and pattern recognition can contribute to the classification of beverages.%应用FLS920型荧光光谱仪测得鲜榨橙汁、市售橙汁饮品(8种品牌)的三维荧光光谱,通过分析鲜榨橙汁与饮品中常见食品添加剂纯物质的荧光机理与特性,得到橙汁饮品中橙汁成分的最佳激发波长为470nm,荧光峰值波长为526 nm,其荧光特征峰为470/526 nm,其余荧光峰的归属均为食品添加剂.同时,采用三维荧光光谱重心法与基于MCD估计的稳健马氏距离相结合的方法对市售橙汁饮品进行筛选与分类,分类效果良好.结果表明:将荧光光谱技术与光谱模式识别方法相结合,可为饮料类食品的鉴别提供帮助.

  7. Fluorescence spectra and elastic scattering characteristics of atmospheric aerosol in Las Cruces, New Mexico, USA: Variability of concentrations and possible constituents and sources of particles in various spectral clusters

    Science.gov (United States)

    Pinnick, R. G.; Fernandez, E.; Rosen, J. M.; Hill, S. C.; Wang, Y.; Pan, Y. L.

    2013-02-01

    The UV-excited laser-induced-fluorescence (UV-LIF) spectra of single atmospheric particles and the three-band integrating-nephelometer elastic scattering of atmospheric aerosol were measured during four approximately 24-h periods on May 2007 in Las Cruces, New Mexico, USA. Aerosol scattering measurements in the nephelometer red channel (50-nm band centered at 700-nm) ranged from around 3-10 times the molecular (Rayleigh) scattering background. On average 22.8% of particles with size greater than about 1 μm diameter have fluorescence above a preset fluorescence threshold. A hierarchical cluster analysis indicates that most of the single-particle UV-LIF spectra fall into about 10 categories (spectral clusters) as found previously at other geographic sites (Pinnick et al., 2004; Pan et al., 2007). The clusters include spectra characteristic of various humic/fulvic acids, humic-like-substances (HULIS), chemically aged terpenes, fungal spores, polycyclic aromatic hydrocarbons, bacteria, cellulose/pollens, and mixtures of various organic carbon compounds. By far the most populated cluster category is similar to those of chemically aged terpenes/humic-materials; on average this population comprises about 62% of fluorescent particles. Clusters with spectra similar to that of some HULIS aerosol contain on average 10.0% of particles; those characteristic of some fungal spores (or perhaps mixtures of aromatic organic compounds) 8.4% of particles; bacteria-like spectra 1.6% of particles; and cellulose/pollen-like spectra 0.8% of particles. Measurements of fluorescent particles over relatively short (24 min) periods reveal that the concentrations of particles in the most populated clusters are highly correlated, suggesting that the particles populating them derive from the same region; these particles might be composed of crustal material coated with secondary organic carbon. On the other hand, concentrations of particles having cellulose-like spectra are generally

  8. Vibrational (FT-IR and FT-Raman), electronic (UV-Vis), NMR (1H and 13C) spectra and reactivity analyses of 4,5-dimethyl-o-phenylenediamine.

    Science.gov (United States)

    Atac, Ahmet; Karaca, Caglar; Gunnaz, Salih; Karabacak, Mehmet

    2014-09-15

    The structure of 4,5-dimethyl-o-phenylenediamine (C8H12N2, DMPDA) was investigated on the basis of spectroscopic data and theoretical calculations. The sterochemical structure was determined by FT-IR, FT-Raman, UV, 1H and 13C NMR spectra. An experimental study and a theoretical analysis were associated by using the B3LYP method with Gaussian09 package program. FT-IR and FT-Raman spectra were recorded in the region of 4000-400 cm(-1) and 4000-10 cm(-1), respectively. The vibrational spectra were calculated by DFT method and the fundamental vibrations were assigned on the basis of the total energy distribution (TED), calculated with scaled quantum mechanics (SQM) method with Parallel Quantum Solutions (PQS) program. The UV absorption spectrum of the compound that dissolved in ethanol solution were recorded in the range of 190-400 nm. Total density of state (TDOS) and partial density of state (PDOS) of the DMPDA in terms of HOMOs and LUMOs were calculated and analyzed. Chemical shifts were reported in ppm relative to tetramethylsilane (TMS) for 1H and 13C NMR spectra. The compound was dissolved in dimethyl sulfoxide (DMSO). Also, 1H and 13C chemical shifts calculated using the gauge independent atomic orbital (GIAO) method. Mullikan atomic charges and other thermo-dynamical parameters were investigated with the help of B3LYP (DFT) method using 6-311++G** basis set. On the basis of the thermodynamic properties of the title compound at different temperatures have been carried out, revealing the correlations between heat capacity (C), entropy (S), enthalpy changes (H) and temperatures. The optimized bond lengths, bond angles, chemical shifts and vibrational wavenumbers showed the best agreement with the experimental results. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Vibrational analysis using FT-IR, FT-Raman spectra and HF-DFT methods and NBO, NLO, NMR, HOMO-LUMO, UV and electronic transitions studies on 2,2,4-trimethyl pentane

    Science.gov (United States)

    Suvitha, A.; Periandy, S.; Govindarajan, M.; Gayathri, P.

    2015-03-01

    In this work, the vibrational spectral analysis was carried out by using Raman and infrared spectroscopy in the range 100-4000 cm-1and 50-4000 cm-1, respectively, for 2,2,4-Trimethyl Pentane, TMP (C8H18) molecule. The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimizations and geometrical parameter calculations based on Hartree Fock (HF) and density functional theory (DFT) method with 6-311++G(d,p) basis set. The scaled B3LYP/6-311++G(d,p) results shows the best agreement with the experimental values over the other method. The calculated HOMO and LUMO energies shows that charge transfer within the molecule. The physical reactions of single bond hydrocarbon TMP were investigated. The results of the calculations were applied to simulate spectra of the title compound, which shows the excellent agreement with observed spectra. Besides, Mulliken atomic charges, UV, frontier molecular orbital (FMO), MEP, NLO activity, Natural Bond-Orbital (NBO) analysis, NMR and thermodynamic properties of title molecule were also performed.

  10. Study on the absorption and fluorescence and resonance Rayleigh scattering spectra of Cu (II)-fluoroquinolone chelates with erythrosine and their applications

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    In pH 4.2-5.0 Britton-Robinson buffer solution medium, fluoroquinolone antibiotics (FLQs), such as ciprofloxacin (CIP), norfloxacin (NOR), ofloxacin (OF), levofloxacin (LEV), lomefloxacin (LOM), and sparfloxacin (SPA), react with Cu (II) to form chelate cations, which further bind with erythrosine to form the ion association complexes. They can result in the changes of the absorption spectra. Simultane- ously, erythrosine fades obviously and the maximum fading wavelength is located at 526 nm. The fad- ing reactions have high sensitivities. Thus, new spectrophotometries of determination for these drugs are developed. The ion-association reactions result in the quenching of fluorescence, which also have high sensitivities. The detection limits for six antibiotics are in the range of 7.1-12.2 μg·L?1. Furthermore, the reactions can result in the enhancement of resonance Rayleigh scattering (RRS). The maximum scattering peaks of six ion-association complexes are located at 566 nm, and there are two small RRS peaks at 333 nm and 287 nm. The detection limits for fluoroquinolone antibiotics are in the range of 1.70 -3.10 μg·L?1 for RRS method. Among the above three methods, the RRS method has the highest sen- sitivity. In this work, we investigated the spectral characteristics of the absorption, fluorescence and RRS, the optimum conditions of the reactions, and the properties of the analytical chemistry. In addi- tion, the mechanism of reactions were discussed by density function theory (DFT) and AM1 methods.

  11. Monitoring Disinfection Byproduct Forming Potential with Simultaneous Absorbance Spectra and Fluorescence Excitation-Emission Mapping: Supporting Stage 2 EPA Regulation Monitoring Compliance

    Science.gov (United States)

    Gilmore, A. M.

    2011-12-01

    Water treatment plants in the United States will soon (by 2013 to 2013) be required to initialize enhanced monitoring for reducing disinfection by-products (DBPs) to meet the Stage 2 levels enforced by the EPA. The key to successfully meeting these requirements lies in the treatment plant's ability to deal with often dramatic source-water variations in natural organic matter (NOM) content. Whereas the regulated levels of NOM must be determined by measuring total organic carbon (TOC) often this parameter does not provide rapid or cost-effective qualitative or quantitative assessment of the various humic, fulvic and other aromatic NOM components. However, 2 main optical techniques namely UV absorbance and fluorescence excitation-emission mapping can be used for rapid assessment with precise identification of humic and fulvic components. This study presents data from a new type of instrument which simultaneously measures the UV-VIS absorbance spectrum and EEM. The rapid absorbance-EEM is facilitated by a single system that is more than 100 time faster than conventional scanning absorbance and fluoresence optical benches. The new system can continuously collect EEMs and absorbance spectra at a rate often greater than 1 per min with the extra capacity to monitor the UV254 absorbance and fluorescence emission spectrum excited at 254 nm in 4 ms intervals (an equivalent scan rate of 5.5 million nm/min). The EEM spectral data is corrected for all instrumental response factors including concentration dependent inner-filter effects. The accumulated EEM data sets can be modeled using conventional peak identification, PARAFAC and or PCA analysis of the fractionated samples to predict the trihalomethane forming potential (THMFP). This study compares the effectiveness of THFMP predictive models based on these three techniques and explains how these can be readily employed to facilitate the Stage 2 regulation compliance for DBP monitoring.

  12. Analysis of the major chiral compounds of Artemisia herba-alba essential oils (EOs) using reconstructed vibrational circular dichroism (VCD) spectra: En route to a VCD chiral signature of EOs.

    Science.gov (United States)

    Said, Mohammed El-Amin; Vanloot, Pierre; Bombarda, Isabelle; Naubron, Jean-Valère; Dahmane, El Montassir; Aamouche, Ahmed; Jean, Marion; Vanthuyne, Nicolas; Dupuy, Nathalie; Roussel, Christian

    2016-01-15

    An unprecedented methodology was developed to simultaneously assign the relative percentages of the major chiral compounds and their prevailing enantiomeric form in crude essential oils (EOs). In a first step the infrared (IR) and vibrational circular dichroism (VCD) spectra of the crude essential oils were recorded and in a second step they were modelized as a linear weighted combination of the IR and VCD spectra of the individual spectra of pure enantiomer of the major chiral compounds present in the EOs. The VCD spectra of enantiomer of known enantiomeric excess shall be recorded if they are not yet available in a library of VCD spectra. For IR, the spectra of pure enantiomer or racemic mixture can be used. The full spectra modelizations were performed using a well known and powerful mathematical model (least square estimation: LSE) which resulted in a weighting of each contributing compound. For VCD modelization, the absolute value of each weighting represented the percentage of the associate compound while the attached sign addressed the correctness of the enantiomeric form used to build the model. As an example, a model built with the non-prevailing enantiomer will show a negative sign of the weighting value. For IR spectra modelization, the absolute value of each weighting represented the percentage of the compounds without of course accounting for the chirality of the prevailing enantiomers. Comparison of the weighting values issuing from IR and VCD spectra modelizations is a valuable source of information: if they are identical, the EOs are composed of nearly pure enantiomers, if they are different the chiral compounds of the EOs are not in an optically pure form. The method was applied on four samples of essential oil of Artemisia herba-alba in which the three major compounds namely (-)-α-thujone, (+)-β-thujone and (-)-camphor were found in different proportions as determined by GC-MS and chiral HPLC using polarimetric detector. In order to validate the

  13. Measurement of magic-wavelength optical dipole trap by using the laser-induced fluorescence spectra of trapped single cesium atoms

    Science.gov (United States)

    Liu, Bei; Jin, Gang; Sun, Rui; He, Jun; Wang, Junmin

    2017-07-01

    Based on the multi-level model, we have calculated light shifts for Zeeman states of hyperfine levels of cesium (Cs) 6S1/2 ground state and 6P3/2 excited state.The magic-wavelength linearly-polarized optical dipole trap (ODT) for Cs 6S1/2 F=4, mF=+4 - 6P3/2 F'=5, mF=+5 transition is experimentally constructed and characterized by using the laser-induced fluorescence spectra of trapped single Cs atoms. The magic wavelength is 937.7 nm which produces almost the same light shift for 6S1/2 F=4, mF=+4 ground state and 6P3/2 F'=5, mF=+5 excited state with linearly-polarized ODT laser beam. Compared to undisturbed Cs 6S1/2 F=4, mF=+4 - 6P3/2 F'=5, mF=+5 transition frequency in free space, the differential light shift is less than 0.7 MHz in a linearly-polarized 937.7 nm ODT, which is less than 1.2% of the trap depth. We also discussed influence of the trap depth and the bias magnetic field on the measurement results.

  14. Quantitative Infrared Absorption Spectra and Vibrational Assignments of Crotonaldehyde and Methyl Vinyl Ketone Using Gas-Phase Mid-Infrared, Far-Infrared, and Liquid Raman Spectra: s-cis vs s-trans Composition Confirmed via Temperature Studies and ab Initio Methods

    Energy Technology Data Exchange (ETDEWEB)

    Lindenmaier, Rodica; Williams, Stephen D.; Sams, Robert L.; Johnson, Timothy J.

    2016-12-16

    Methyl vinyl ketone (MVK) and crotonaldehyde are chemical isomers; both are also important species in tropospheric chemistry. We report quantitative vapor-phase infrared spectra of crotonaldehyde and MVK vapors over the 540-6500 cm-1 range. Vibrational assignments of all fundamental modes are made for both molecules based on far- and mid-infrared vapor-phase spectra, liquid Raman spectra, along with density functional theory and ab initio MP2 and high energy-accuracy compound theoretical models (W1BD). Theoretical results indicate that at room temperature the crotonaldehyde equilibrium mixture is approximately 97% s-trans and only 3% s-cis conformer. Nearly all observed bands are thus associated with the s-trans conformer, but a few appear to be uniquely associated the s-cis conformer, notably ν16c at 730.90 cm-1, which displays a substantial intensity increase with temperature (62% upon going from 5 to 50 oC). The intensity of the corresponding mode of the s-trans conformer decreases with temperature. Under the same conditions, the MVK equilibrium mixture is approximately 69% s-trans conformer and 31% s-cis. W1BD calculations indicate that for MVK this is one of those (rare) cases where there are comparable populations of both conformers, ~doubling the number of observed bands and exacerbating the vibrational assignments. We uniquely assign the bands associated with both the MVK s-cis conformer as well as those of the s-trans, thus completing the vibrational analyses of both conformers from the same set of experimental spectra. Integrated band intensities are reported for both molecules along with global warming potential values. Using the quantitative IR data, potential bands for atmospheric monitoring are also discussed.

  15. Path integral molecular dynamics combined with discrete-variable-representation approach: the effect of solvation structures on vibrational spectra of Cl 2 in helium clusters

    Science.gov (United States)

    Takayanagi, Toshiyuki; Shiga, Motoyuki

    2002-08-01

    The structures and vibrational frequencies of Cl 2-helium clusters have been studied using the path integral molecular dynamics method combined with the discrete-variable-representation approach. It is found that the Cl 2-helium clusters form clear shell structures comprised of rings around the Cl 2 bond. The vibrational frequencies calculated show a monotonically increasing red shift with an increase in cluster size. It can be concluded that the first solvation shell and its density around T-shaped configurations play the most important role in the observed frequency shifts.

  16. Responses of epidermal phenolic compounds to light acclimation: in vivo qualitative and quantitative assessment using chlorophyll fluorescence excitation spectra in leaves of three woody species.

    Science.gov (United States)

    Bidel, L P R; Meyer, S; Goulas, Y; Cadot, Y; Cerovic, Z G

    2007-09-25

    Chlorophyll fluorescence (ChlF) excitation spectra were measured to assess the UV-sunscreen compounds accumulated in fully expanded leaves of three woody species belonging to different chemotaxons, (i.e. Morus nigra L., Prunus mahaleb L. and Lagerstroemia indica L.), grown in different light microclimates. The logarithm of the ratio of ChlF excitation spectra (logFER) between two leaves acclimated to different light microclimates was used to assess the difference in epidermal absorbance (EAbs). EAbs increased with increasing solar irradiance intercepted for the three species. This epidermal localisation of UV-absorbers was confirmed by the removal of the epidermis. It was possible to simulate EAbs as a linear combination of major phenolic compounds (Phen) identified in leaf methanol extracts by HPLC-DAD. Under UV-free radiation conditions, shaded leaves of M. nigra accumulated chlorogenic acid. Hydroxybenzoic acid (HBA) derivatives and hydroxycinnamic acid (HCA) derivatives greatly increased with increasing PAR irradiance under the low UV-B conditions found in the greenhouse. These traits were also observed for the HCA of the two other species. Flavonoid (FLAV) accumulation started under low UV-A irradiance, and became maximal in the adaxial epidermis of sun-exposed leaves outdoors. A decrease in the amount of HCA was observed concomitantly to the intense accumulation of FLAV for both leaf sides of the three species. Judging from the logFER, under low UV-B conditions, larger amounts of HCA are present in the epidermis in comparison to FLAV for the three species. Upon transition from the greenhouse to full sunlight outdoors, there was a decrease in leaf-soluble HCA that paralleled FLAV accumulation in reaction to increasing solar UV-B radiation in the three species. In M. nigra, that contains large amounts of HCA, the logFER analysis showed that this decrease occurred in the adaxial epidermis, whereas the abaxial epidermis, which is protected from direct UV

  17. 橙汁中卡拉胶的荧光光谱检测%Detection of Carrageenan in the Orange Juice Using Fluorescence Spectra Methods

    Institute of Scientific and Technical Information of China (English)

    孔凡标; 陈国庆; 黄奇峰; 陈超; 李润

    2013-01-01

    应用多功能荧光光谱仪测得三种市售100%橙汁和鲜榨橙汁的三维荧光光谱并提取其特征参数,比较发现其三维荧光光谱及特征参数存在较为明显的差异,特别是在683 nm处.推断可能是三种市售100%橙汁中加入了食品添加剂的原因.在鲜榨橙汁中加入卡拉胶,检测得卡拉胶及加入卡拉胶的鲜榨橙汁的三维荧光光谱,发现卡拉胶为荧光物质.将加入卡拉胶的鲜榨橙汁的三维荧光光谱与三种市售100%橙汁的三维荧光光谱相比较,发现它们基本一致,并且其特征参数也基本一致,由此可推断三种市售100%橙汁均含有卡拉胶.本实验可为卡拉胶在橙汁中的定量检测提供一定帮助.%Using the FLS920P spectrometer of Edinburgh Instruments the three-dimensional fluorescence spectra of the fresh orange juice and the three samples of 100% orange juice bought in the supermarket were studied and their characteristic parameters were obtained. The comparison of the spectra and the characteristic parameters shows that they are apparently different, especially at the emission wavelength of 683 nm. This might be caused by the food additives added into the orange juice bought The three-dimensional spectrum of the fresh orange juice with carrageenan was obtained. The comparison of the samples bought and the one with carrageenan shows that they are with little difference. The characteristic parameters of them are almost of no difference. Thus the conclusion can be drawn that the samples bought all have carrageenaa The results of the paper can somewhat help quantitatively study carrageenan in the orange juice.

  18. The fluorescence and resonance Rayleigh scattering spectra study on the interactions of palladium (II)-Nootropic chelate with Congo red and their analytical applications

    Science.gov (United States)

    Chen, Fang; Peng, Jingdong; Liu, Shaopu; Peng, Huanjun; Pan, Ziyu; Bu, Lingli; Xiao, Huan; Zhang, Ruiwen

    2017-04-01

    A highly sensitive detection approach of resonance Rayleigh scattering spectra (RRS) is firstly applied to analyzing nootropic drugs including piracetam (PIR) and oxiracetam (OXI). In HCl-NaAc buffer solution (pH = 3.0), the OXI chelated with palladium (II) to form the chelate cation [Pd2·OXI]2 +, and then reacted with Congo red (CGR) by virtue of electrostatic attraction and hydrophobic force to form binary complex [Pd2·OXI]. CGR2, which could result in the great enhancement of RRS. The resonance Rayleigh scattering signal was recorded at λex = λem = 375 nm. This mixture complex not only has higher RRS, but also makes contribution to significant increase of fluorescence, and the same phenomena also were discovered in PIR. The enhanced RRS intensity is in proportion to the PIR and OXI concentration in the range of 0.03-3.0 μg mL- 1, and the detection limit (DL) of RRS method for PIR and OXI is 2.3 ng mL- 1 and 9.7 ng mL- 1. In addition, the DL of fluorescence method for PIR and OXI is 8.4 μg mL- 1 and 19.5 μg mL- 1. Obviously, the RRS is the highly sensitive method, and the recoveries of the two kinds of nootropic drugs were range from 100.4% to 101.8.0% with RSD (n = 5) from 1.1% to 3.1% by RRS method. This paper not only investigated the optimum conditions for detecting nootropics with using RRS method, but also focused on the reasons for enhancing RRS intensity and the reaction mechanism, which in order to firm and contract the resultant. Finally, The RRS method has been applied to detect nootropic drugs in human urine samples with satisfactory results. Fig. S2. The effect of ionic strength: Pd (II)-CGR system (curve a); Pd (II)-OXI-CGR system (curve b); Pd (II)-PIR- CGR system (curve c). Pd (II): 2.0 × 10- 4 mol L- 1; CGR: 1.0 × 10- 5 mol L- 1; OXI: 1.5 μg mL- 1; PIR: 2 μg mL- 1; NaCl: 1 mol L- 1. Fig. S3. The effect of time: Pd (II)-OXI-CGR system (curve a); Pd (II)-PIR-CGR system (curve b). Pd (II): 2.0 × 10- 4 mol L- 1; CGR: 1.0 × 10- 5 mol L- 1

  19. Electronic structures of organometallic complexes of f elements LXXVI: Correlation of experimental and calculated (on the basis of density functional theory) vibrational spectra of bis(η5-cyclopentadienyl)ruthenium and bis(η5-pentamethylcyclopentadienyl)ruthenium.

    Science.gov (United States)

    Prosenc, Marc Heinrich; Reddmann, Hauke; Amberger, Hanns-Dieter

    2012-02-15

    Previous empirical assignments of the normal modes of Ru(η(5)-C(5)H(5))(2) were checked against the results of a calculation applying density functional theory (DFT). After some reassignments, following those recently suggested for Fe(η(5)-C(5)H(5))(2) (after theoretical model calculations), a satisfactory agreement was observed. Recently communicated polarized Raman spectra of an oriented Ru(η(5)-C(5)Me(5))(2) single crystal were used here for the identification of the irreducible representations of a number of Raman active normal modes (assuming molecular D(5h) symmetry) which agree well with the results of the DFT calculation. The energies of IR active fundamental vibrations, extracted from recently communicated FIR/MIR spectra (pellets), were correlated with comparable energies of IR allowed irreducible representations of the DFT calculation and assigned. Both the skeletal and the intra-ligand normal modes could be correlated with the idealized standard motions (ν(i)s) of the model sandwich complex Ru(C(5)C(5))(2), and previous assignments had to be revised. Neglecting the νCH vibrations (which are off by ca. 50cm(-1)) an r.m.s. deviation of 9.8cm(-1) (for 47 assignments) of the remaining normal modes could be achieved.

  20. Crystal and molecular structures, temperature dependence of the IR and Raman spectra and vibrational dynamics of aquo 4,6-dimethyl-5H-[1,2,3]triazolo[4,5-c]pyridine in a new zwitterionic form

    Science.gov (United States)

    Dymińska, Lucyna; Janczak, Jan; Sheweshen, Khalil Salem M.; Lorenc, Jadwiga; Hanuza, Jerzy

    2017-09-01

    The crystal and molecular structures of aquo 4,6-dimethyl-5H-[1,2,3]triazolo[4,5-c]pyridine in a zwitterionic form have been determined by X-ray diffraction and DFT quantum chemical calculations. The compound adopts a triclinic crystal structure, space group P-1 = Ci1 (No. 2) with Z = 2 and the unit cell parameters: a = 6.7452 Å, b = 9.5292 Å, c = 9.5554 Å and α = 69.279°, β = 73.951°, γ = 74.242°. The temperature dependence of its IR and Raman spectra have been measured and discussed in terms of proton transfer dynamics. The molecular structure and simulated vibrational spectra of the studied compound have been determined using the DFT B3LYP/6-311G(2d,2p) approach. Vibrational characteristics of a triazolo-pyridinium system in the studied compound has been proposed. A role of water molecules in stabilization of the compound space structure has been considered.