WorldWideScience

Sample records for anharmonic vibrational spectroscopy

  1. Anharmonic vibrations in nuclei

    CERN Document Server

    Fallot, M; Andrés, M V; Catara, F; Lanza, E G; Scarpaci, J A; Chomaz, Ph.

    2003-01-01

    In this letter, we show that the non-linearitites of large amplitude motions in atomic nuclei induce giant quadrupole and monopole vibrations. As a consequence, the main source of anharmonicity is the coupling with configurations including one of these two giant resonances on top of any state. Two-phonon energies are often lowered by one or two MeV because of the large matrix elements with such three phonon configurations. These effects are studied in two nuclei, 40Ca and 208Pb.

  2. Anharmonic quantum contribution to vibrational dephasing

    OpenAIRE

    Barik, Debashis; Ray, Deb Shankar

    2004-01-01

    Based on a quantum Langevin equation and its corresponding Hamiltonian within a c-number formalism we calculate the vibrational dephasing rate of a cubic oscillator. It is shown that leading order quantum correction due to anharmonicity of the potential makes a significant contribution to the rate and the frequency shift. We compare our theoretical estimates with those obtained from experiments for small diatomics $N_2$, $O_2$ and $CO$.

  3. High energy conformers of M(+)(APE)(H2O)(0-1)Ar(0-1) clusters revealed by combined IR-PD and DFT-MD anharmonic vibrational spectroscopy.

    Science.gov (United States)

    Brites, V; Nicely, A L; Sieffert, N; Gaigeot, M-P; Lisy, J M

    2014-07-14

    IR-PD vibrational spectroscopy and DFT-based molecular dynamics simulations are combined in order to unravel the structures of M(+)(APE)(H2O)0-1 ionic clusters (M = Na, K), where APE (2-amino-1-phenyl ethanol) is commonly used as an analogue for the noradrenaline neurotransmitter. The strength of the synergy between experiments and simulations presented here is that DFT-MD provides anharmonic vibrational spectra that unambiguously help assign the ionic clusters structures. Depending on the interacting cation, we have found that the lowest energy conformers of K(+)(APE)(H2O)0-1 clusters are formed, while the lowest energy conformers of Na(+)(APE)(H2O)0-1 clusters can only be observed through water loss channel (i.e. without argon tagged to the clusters). Trapping of higher energy conformers is observed when the argon loss channel is recorded in the experiment. This has been rationalized by transition state energies. The dynamical anharmonic vibrational spectra unambiguously provide the prominent OH stretch due to the OH···NH2 H-bond, within 10 cm(-1) of the experiment, hence reproducing the 240-300 cm(-1) red-shift (depending on the interacting cation) from bare neutral APE. When this H-bond is not present, the dynamical anharmonic spectra provide the water O-H stretches as well as the rotational motion of the water molecule at finite temperature, as observed in the experiment.

  4. Optimized coordinates for anharmonic vibrational structure theories.

    Science.gov (United States)

    Yagi, Kiyoshi; Keçeli, Murat; Hirata, So

    2012-11-28

    A procedure to determine optimal vibrational coordinates is developed on the basis of an earlier idea of Thompson and Truhlar [J. Chem. Phys. 77, 3031 (1982)]. For a given molecule, these coordinates are defined as the unitary transform of the normal coordinates that minimizes the energy of the vibrational self-consistent-field (VSCF) method for the ground state. They are justified by the fact that VSCF in these coordinates becomes exact in two limiting cases: harmonic oscillators, where the optimized coordinates are normal, and noninteracting anharmonic oscillators, in which the optimized coordinates are localized on individual oscillators. A robust and general optimization algorithm is developed, which decomposes the transformation matrix into a product of Jacobi matrices, determines the rotation angle of each Jacobi matrix that minimizes the energy, and iterates the process until a minimum in the whole high dimension is reached. It is shown that the optimized coordinates are neither entirely localized nor entirely delocalized (or normal) in any of the molecules (the water, water dimer, and ethylene molecules) examined (apart from the aforementioned limiting cases). Rather, high-frequency stretching modes tend to be localized, whereas low-frequency skeletal vibrations remain normal. On the basis of these coordinates, we introduce two new vibrational structure methods: optimized-coordinate VSCF (oc-VSCF) and optimized-coordinate vibrational configuration interaction (oc-VCI). For the modes that become localized, oc-VSCF is found to outperform VSCF, whereas, for both classes of modes, oc-VCI exhibits much more rapid convergence than VCI with respect to the rank of excitations. We propose a rational configuration selection for oc-VCI when the optimized coordinates are localized. The use of the optimized coordinates in VCI with this configuration selection scheme reduces the mean absolute errors in the frequencies of the fundamentals and the first overtones

  5. Effective harmonic oscillator description of anharmonic molecular vibrations

    Indian Academy of Sciences (India)

    Tapta Kanchan Roy; M Durga Prasad

    2009-09-01

    The validity of an effective harmonic oscillator approximation for anharmonic molecular vibrations is tested and compared with vibrational self consistent field and vibrational configurational interaction results. The effective harmonic oscillator is constructed variationally, by taking the trial wave function as a harmonic oscillator eigenfunction with the centroid and width parameter as variational paraeters. It is found that the effective harmonic oscillator approximation provides a description of the anharmonic eigenstates very similar to the vibrational self consistent field results. Coriolis coupling is also included in these studies.

  6. 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.

  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. Stochastic many-body perturbation theory for anharmonic molecular vibrations

    Energy Technology Data Exchange (ETDEWEB)

    Hermes, Matthew R. [Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 (United States); Hirata, So, E-mail: sohirata@illinois.edu [Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801 (United States); CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan)

    2014-08-28

    A new quantum Monte Carlo (QMC) method for anharmonic vibrational zero-point energies and transition frequencies is developed, which combines the diagrammatic vibrational many-body perturbation theory based on the Dyson equation with Monte Carlo integration. The infinite sums of the diagrammatic and thus size-consistent first- and second-order anharmonic corrections to the energy and self-energy are expressed as sums of a few m- or 2m-dimensional integrals of wave functions and a potential energy surface (PES) (m is the vibrational degrees of freedom). Each of these integrals is computed as the integrand (including the value of the PES) divided by the value of a judiciously chosen weight function evaluated on demand at geometries distributed randomly but according to the weight function via the Metropolis algorithm. In this way, the method completely avoids cumbersome evaluation and storage of high-order force constants necessary in the original formulation of the vibrational perturbation theory; it furthermore allows even higher-order force constants essentially up to an infinite order to be taken into account in a scalable, memory-efficient algorithm. The diagrammatic contributions to the frequency-dependent self-energies that are stochastically evaluated at discrete frequencies can be reliably interpolated, allowing the self-consistent solutions to the Dyson equation to be obtained. This method, therefore, can compute directly and stochastically the transition frequencies of fundamentals and overtones as well as their relative intensities as pole strengths, without fixed-node errors that plague some QMC. It is shown that, for an identical PES, the new method reproduces the correct deterministic values of the energies and frequencies within a few cm{sup −1} and pole strengths within a few thousandths. With the values of a PES evaluated on the fly at random geometries, the new method captures a noticeably greater proportion of anharmonic effects.

  9. Stochastic many-body perturbation theory for anharmonic molecular vibrations.

    Science.gov (United States)

    Hermes, Matthew R; Hirata, So

    2014-08-28

    A new quantum Monte Carlo (QMC) method for anharmonic vibrational zero-point energies and transition frequencies is developed, which combines the diagrammatic vibrational many-body perturbation theory based on the Dyson equation with Monte Carlo integration. The infinite sums of the diagrammatic and thus size-consistent first- and second-order anharmonic corrections to the energy and self-energy are expressed as sums of a few m- or 2m-dimensional integrals of wave functions and a potential energy surface (PES) (m is the vibrational degrees of freedom). Each of these integrals is computed as the integrand (including the value of the PES) divided by the value of a judiciously chosen weight function evaluated on demand at geometries distributed randomly but according to the weight function via the Metropolis algorithm. In this way, the method completely avoids cumbersome evaluation and storage of high-order force constants necessary in the original formulation of the vibrational perturbation theory; it furthermore allows even higher-order force constants essentially up to an infinite order to be taken into account in a scalable, memory-efficient algorithm. The diagrammatic contributions to the frequency-dependent self-energies that are stochastically evaluated at discrete frequencies can be reliably interpolated, allowing the self-consistent solutions to the Dyson equation to be obtained. This method, therefore, can compute directly and stochastically the transition frequencies of fundamentals and overtones as well as their relative intensities as pole strengths, without fixed-node errors that plague some QMC. It is shown that, for an identical PES, the new method reproduces the correct deterministic values of the energies and frequencies within a few cm(-1) and pole strengths within a few thousandths. With the values of a PES evaluated on the fly at random geometries, the new method captures a noticeably greater proportion of anharmonic effects.

  10. Effects of vibrational anharmonicity on molecular electronic conduction and thermoelectric efficiency

    Science.gov (United States)

    Friedman, Hava Meira; Agarwalla, Bijay Kumar; Segal, Dvira

    2017-03-01

    We study inelastic vibration-assisted charge transfer effects in two-site molecular junctions, focusing on signatures of vibrational anharmonicity on the electrical characteristics and the thermoelectric response of the junction. We consider three types of oscillators: harmonic, anharmonic-Morse allowing bond dissociation, and harmonic-quartic, mimicking a confinement potential. Using a quantum master equation method which is perturbative in the electron-vibration interaction, we find that the (inelastic) electrical and thermal conductances can be largely affected by the nature of the vibrational potential. In contrast, the Seebeck coefficient, the thermoelectric figure-of-merit, and the thermoelectric efficiency beyond linear response conceal this information, showing a rather weak sensitivity to vibrational anharmonicity. Our work illustrates that anharmonic (many-body) effects, consequential to the current-voltage characteristics, are of little effect for the thermoelectric performance in the present model.

  11. Anharmonic double-{gamma} vibrations in nuclei and their description in the interacting boson model

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Ramos, J.E.; Alonso, C.E.; Arias, J.M. [Sevilla Univ. (Spain). Departamento de Fisica Atomica, Molecular y Nuclear; Van Isacker, P. [Grand Accelerateur National d`Ions Lourds, 14 - Caen (France)

    1998-07-01

    Double-{gamma} vibrations in deformed nuclei are studied in the context of the interacting boson model with special reference to their anharmonic character. It is shown that large anharmonicities can be obtained with interactions that are (at least) of three-body nature between the bosons. As an example the {gamma} vibrations of the nucleus {sub 68}{sup 166}Er{sub 98} are studied in detail. (author) 28 refs.

  12. Anharmonicity of lattice vibrations induced by charged nickel additions in A sup 2 B sup 6 semiconductors

    CERN Document Server

    Sokolov, V I; Shirokov, E A; Kislov, A N

    2002-01-01

    Paper presents the results of investigations into lattice vibrations induced by nickel impurities charged negatively as to the lattice in ZnSe:Ni, ZnO:Ni, ZnS:Ni, CdS:Ni semiconductors. To investigate into vibrations one applies a sensitive technique of field exciton-oscillation spectroscopy. One observes experimentally oscillating reiterations of the impurity exciton head line including the intensive peaks of combined repetitions up to the 8-th order. The experimental results are discussed on the basis of the model estimations of oscillations of a lattice with a charged impurity centre, as well as, on the ground of calculations for oscillations of monoatomic chain with high anharmonicity. Charged impurity centres are shown to induce new oscillations of lattice - impurity anharmonic modes

  13. Anharmonic Vibrational Frequency Calculations Are Not Worthwhile for Small Basis Sets.

    Science.gov (United States)

    Jacobsen, Ruth L; Johnson, Russell D; Irikura, Karl K; Kacker, Raghu N

    2013-02-12

    Anharmonic calculations using vibrational perturbation theory are known to provide near-spectroscopic accuracy when combined with high-level ab initio potential energy functions. However, performance with economical, popular electronic structure methods is less well characterized. We compare the accuracy of harmonic and anharmonic predictions from Hartree-Fock, second-order perturbation, and density functional theories combined with 6-31G(d) and 6-31+G(d,p) basis sets. As expected, anharmonic frequencies are closer than harmonic frequencies to experimental fundamentals. However, common practice is to correct harmonic predictions using multiplicative scaling. The surprising conclusion is that scaled anharmonic calculations are no more accurate than scaled harmonic calculations for the basis sets we used. The data used are from the Computational Chemistry Comparison and Benchmark Database (CCCBDB), maintained by the National Institute of Standards and Technology, which includes more than 3939 independent vibrations for 358 molecules.

  14. Exploring Anharmonic Nuclear Dynamics and Spectroscopy Using the Kratzer Oscillator.

    Science.gov (United States)

    Toutounji, Mohamad

    2011-06-14

    The Kratzer oscillator is useful in modeling anharmonic molecular vibrations; therefore, its underlying theory is briefly explored in this study. The linear dipole moment time correlation function, within the Condon approximation, is analytically evaluated, and linear absorption lineshapes are calculated at different temperatures. An important integral formula of Landau and Liftshitz is, for the first time, utilized to evaluate the anharmonic Franck-Condon factor (FCF) resulting from modeling the initial and final states by Kratzer potentials. In addition, an exact closed-form expression of the FCF for the linearly displaced and shape-distorted final state energy curve, with respect to the ground state, is reported. Within the context of Mukamel formalism, nonlinear spectral/temporal lineshapes, such as hole-burning, photon echo, and pump-probe signals, may not be calculated without nonlinear response theory using the so-called "four-point dipole moment time correlation function". The above FCFs will be employed to calculate optical linear and nonlinear spectra at different temperatures utilizing a previously developed formula [Toutounji, M. J. Phys. Chem. C2010, in press], whereby a hole-burned absorption lineshape may be found using a linear dipole moment time correlation function.

  15. Vibration-translation energy transfer in anharmonic diatomic molecules. II - The vibrational quantum-number dependence

    Science.gov (United States)

    Mckenzie, R. L.

    1976-01-01

    A semiclassical model of the inelastic collision between a vibrationally excited anharmonic oscillator and a structureless atom is used to predict the variation of thermally averaged vibrational-translational rate coefficients with temperature and initial-state quantum number. Multiple oscillator states are included in a numerical solution for collinear encounters. The results are compared with CO-He experimental values for both ground and excited initial states using several simplified forms of the interaction potential. The numerical model is also used as a basis for evaluating several less complete, but analytic, models. Two computationally simple analytic approximations are found that successfully reproduce the numerical rate coefficients for a wide range of molecular properties and collision partners. Their limitations are identified, and the relative rates of multiple-quantum transitions from excited states are evaluated for several molecular types.

  16. Vibration-translation energy transfer in anharmonic diatomic molecules. 2: The vibrational quantum number dependence

    Science.gov (United States)

    Mckenzie, R. L.

    1975-01-01

    A semiclassical model of the inelastic collision between a vibrationally excited anharmonic oscillator and a structureless atom was used to predict the variation of thermally averaged vibration-translation rate coefficients with temperature and initial-state quantum number. Multiple oscillator states were included in a numerical solution for collinear encounters. The results are compared with CO-He experimental values for both ground and excited initial states using several simplified forms of the interaction potential. The numerical model was also used as a basis for evaluating several less complete but analytic models. Two computationally simple analytic approximations were found that successfully reproduced the numerical rate coefficients for a wide range of molecular properties and collision partners. Their limitations were also identified. The relative rates of multiple-quantum transitions from excited states were evaluated for several molecular types.

  17. Transition from the Seniority to the Anharmonic Vibrator Regime in Nuclei

    CERN Document Server

    Bijker, R; Pittel, S

    1996-01-01

    A recent analysis of experimental energy systematics suggests that all collective nuclei fall into one of three classes -- seniority, anharmonic vibrational, or rotational -- with sharp phase transitions between them. We investigate the transition from the seniority to the anharmonic vibrator regime within a shell model framework involving a single large j-orbit. The calculations qualitatively reproduce the observed transitional behavior, both for U(5) like and O(6) like nuclei. They also confirm the preeminent role played by the neutron-proton interaction in producing the phase transition.

  18. Vibrational Spectroscopy of Biomembranes

    Science.gov (United States)

    Schultz, Zachary D.; Levin, Ira W.

    2011-07-01

    Vibrational spectroscopy, commonly associated with IR absorption and Raman scattering, has provided a powerful approach for investigating interactions between biomolecules that make up cellular membranes. Because the IR and Raman signals arise from the intrinsic properties of these molecules, vibrational spectroscopy probes the delicate interactions that regulate biomembranes with minimal perturbation. Numerous innovative measurements, including nonlinear optical processes and confined bilayer assemblies, have provided new insights into membrane behavior. In this review, we highlight the use of vibrational spectroscopy to study lipid-lipid interactions. We also examine recent work in which vibrational measurements have been used to investigate the incorporation of peptides and proteins into lipid bilayers, and we discuss the interactions of small molecules and drugs with membrane structures. Emerging techniques and measurements on intact cellular membranes provide a prospective on the future of vibrational spectroscopic studies of biomembranes.

  19. Local anharmonic vibrations strong correlations and superconductivity : a quantum simulation study

    NARCIS (Netherlands)

    Frick, M.; Linden, W. von der; Morgenstern, I.; Raedt, H. de

    1990-01-01

    We investigate the importance of local anharmonic vibrations of the bridging oxygen in the copper oxide high-Tc materials in the context of superconductivity. For the numerical simulation we employ the projector quantum Monte Carlo method to study the ground state properties of the coupled electron-

  20. Probing anharmonic properties of nuclear surface vibration by heavy-ion fusion reactions

    CERN Document Server

    Takigawa, N; Kuyucak, S

    1997-01-01

    Describing fusion reactions between ^{16}O and ^{154}Dy and, between ^{16}O and ^{144}Sm by the $sd-$ and $sdf-$ interacting boson model, we show that heavy-ion fusion reactions are strongly affected by anharmonic properties of nuclear surface vibrations and nuclear shape, and thus provide a powerful method to study details of nuclear structure and dynamics.

  1. Anharmonic vibrations of the dicarbon antisite defect in 4H-SiC

    Energy Technology Data Exchange (ETDEWEB)

    Yan, F.; Devaty, R. P.; Choyke, W. J. [Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 (United States); Gali, A. [Research Institute for Solid State Physics and Optics, Hungarian Academy of Sciences, P.O. Box 49, H-1525 Budapest (Hungary); Kimoto, T. [Department of Electronic Science and Engineering, Kyoto University, Katsura, Nishikyo, Kyoto 615-8510 (Japan); Ohshima, T. [Japan Atomic Energy Agency, 1233 Watanuki, Takasaki, Gunma 370-1292 (Japan); Pensl, G. [Lehrstuhl fuer Angewandte Physik, Universitaet Erlangen-Nuernberg, Staudstr. 7/A3 Erlangen (Germany)

    2012-03-26

    Dicarbon antisite defects were created by either electron irradiation or ion implantation into 4H-SiC. The no-phonon lines from the dicarbon antisite defect center were observed with their phonon replicas. The stretch frequencies of the defect were observed up to the fifth harmonic. The Morse potential model accounts for the anharmonicity quite well and gives a very good prediction of the vibration energies up to the fifth harmonic with an error of less than 1%. First principles calculations show that the model of a dicarbon antisite defect along with its four nearest neighboring carbon atoms can explain the observed anharmonicity.

  2. 2008 Vibrational Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Philip J. Reid

    2009-09-21

    The conference focuses on using vibrational spectroscopy to probe structure and dynamics of molecules in gases, liquids, and interfaces. The goal is to bring together a collection of researchers who share common interests and who will gain from discussing work at the forefront of several connected areas. The intent is to emphasize the insights and understanding that studies of vibrations provide about a variety of systems.

  3. Vibrational Spectroscopy of Methyl benzoate

    CERN Document Server

    Maiti, Kiran Sankar

    2014-01-01

    Methyl benzoate (MB) is studied as a model compound for the development of new IR pulse schemes with possible applicability to biomolecules. Anharmonic vibrational modes of MB are calculated on different level (MP2, SCS, CCSD(T) with varying basis sets) ab-initio PESs using the vibrational self-consistent field (VSCF) method and its correlation corrected extensions. Dual level schemes, combining different quantum chemical methods for diagonal and coupling potentials, are systematically studied and applied successfully to reduce the computational cost. Isotopic substitution of {\\beta}-hydrogen by deuterium is studied to obtain a better understanding of the molecular vibrational coupling topology.

  4. Anharmonic Vibrational Analysis for the Propadienylidene Molecule (H2C═C═C:).

    Science.gov (United States)

    Wu, Qunyan; Hao, Qiang; Wilke, Jeremiah J; Simmonett, Andrew C; Yamaguchi, Yukio; Li, Qianshu; Fang, De-Cai; Schaefer, Henry F

    2010-10-12

    Maier et al. found that photolysis of singlet cyclopropenylidene (1S) in a matrix yields triplet propargylene (2T), which upon further irradiation is converted to singlet propadienylidene (vinylidenecarbene, 3S). Their discovery was followed by interstellar identification of 3S by Cernicharo et al. An accurate quartic force field for propadienylidene (3S) has been determined employing the ab initio coupled-cluster (CC) with single and double excitations and perturbative triple excitations [CCSD(T)] method and the correlation-consistent core-valence quadruple-ζ (cc-pCVQZ) basis set. Utilizing vibrational second-order perturbation theory (VPT2), vibration-rotation coupling constants, rotational constants, centrifugal distortion constants, vibrational anharmonic constants, and fundamental vibrational frequencies are determined. The predicted fundamental frequencies for 3S as well as its (13)C and deuterium isotopologues are in good agreement with experimental values. The theoretical zero-point vibration corrected rotational constants B0 are consistent with experimental values within 0.3% of errors. The isotopic shifts of B0 are in close to exact agreement with experimental observations. The mean absolute deviation between theoretical anharmonic and experimental fundamental vibrational frequencies for 24 modes (excluding CH2 s-str.) is only 2.6 cm(-1). The isotopic shifts of the vibrational frequencies are also in excellent agreement with the available experimental values. However, a large discrepancy is observed for the CH2 symmetric stretch, casting doubt on the experimental assignment for this mode.

  5. Anharmonic vibrational studies of L-aspartic acid using HF and DFT calculations

    Science.gov (United States)

    Alam, Mohammad Jane; Ahmad, Shabbir

    2012-10-01

    The experimental and theoretical studies on the structure, molecular properties and vibrational spectra of L-aspartic acid are presented. The molecular structure, harmonic and anharmonic vibrational frequencies, molecular properties, MEP mapping, NBO analysis and electronic spectra of L-aspartic acid have been reported. Computed geometrical parameters and anharmonic frequencies of fundamental, combination and overtone transitions were found in satisfactory agreement with the experimental data. The UV-Vis spectrum of present molecule has been recorded and the electronic properties such as HOMO and LUMO energies and few low lying excited states were carried out by using time dependent density functional theory (TD-DFT) approach. Natural Bond Orbital (NBO) analysis has been performed for analyzing charge delocalization throughout the molecule. Molecular electrostatic potential map has also been used for quantitative measure of the chemical activities of various sites of the molecule.

  6. High-resolution IR absorption spectroscopy of polycyclic aromatic hydrocarbons: the realm of anharmonicity

    CERN Document Server

    Maltseva, Elena; Candian, Alessandra; Mackie, Cameron J; Huang, Xinchuan; Lee, Timothy J; Tielens, Alexander G G M; Oomens, Jos; Buma, Wybren Jan

    2015-01-01

    We report on an experimental and theoretical investigation of the importance of anharmonicity in the 3 micron CH stretching region of Polycyclic Aromatic Hydrocarbon (PAH) molecules. We present mass-resolved, high-resolution spectra of the gas-phase cold (~4K) linear PAH molecules naphthalene, anthracene, and tetracene. The measured IR spectra show a surprisingly high number of strong vibrational bands. For naphthalene, the observed bands are well separated and limited by the rotational contour, revealing the band symmetries. Comparisons are made to the harmonic and anharmonic approaches of the widely used Gaussian software. We also present calculated spectra of these acenes using the computational program SPECTRO, providing anharmonic predictions enhanced with a Fermi-resonance treatment that utilises intensity redistribution. We demonstrate that the anharmonicity of the investigated acenes is strong, dominated by Fermi resonances between the fundamental and double combination modes, with triple combination ...

  7. Anharmonic exciton dynamics and energy dissipation in liquid water from two-dimensional infrared spectroscopy

    Science.gov (United States)

    De Marco, Luigi; Fournier, Joseph A.; Thämer, Martin; Carpenter, William; Tokmakoff, Andrei

    2016-09-01

    Water's extended hydrogen-bond network results in rich and complex dynamics on the sub-picosecond time scale. In this paper, we present a comprehensive analysis of the two-dimensional infrared (2D IR) spectrum of O-H stretching vibrations in liquid H2O and their interactions with bending and intermolecular vibrations. By exploring the dependence of the spectrum on waiting time, temperature, and laser polarization, we refine our molecular picture of water's complex ultrafast dynamics. The spectral evolution following excitation of the O-H stretching resonance reveals vibrational dynamics on the 50-300 fs time scale that are dominated by intermolecular delocalization. These O-H stretch excitons are a result of the anharmonicity of the nuclear potential energy surface that arises from the hydrogen-bonding interaction. The extent of O-H stretching excitons is characterized through 2D depolarization measurements that show spectrally dependent delocalization in agreement with theoretical predictions. Furthermore, we show that these dynamics are insensitive to temperature, indicating that the exciton dynamics alone set the important time scales in the system. Finally, we study the evolution of the O-H stretching mode, which shows highly non-adiabatic dynamics suggestive of vibrational conical intersections. We argue that the so-called heating, commonly observed within ˜1 ps in nonlinear IR spectroscopy of water, is a nonequilibrium state better described by a kinetic temperature rather than a Boltzmann distribution. Our conclusions imply that the collective nature of water vibrations should be considered in describing aqueous solvation.

  8. Role of anharmonicities of nuclear vibrations in fusion reactions at subbarrier energies

    CERN Document Server

    Hagino, K; Kuyucak, S

    1997-01-01

    We discuss the effects of double octupole and quadrupole phonon excitations in $^{144}$Sm on fusion reactions between $^{16}$O and $^{144}$Sm at subbarrier energies. The effects of anharmonicities of the vibrational states are taken into account by using the $sdf$-interacting boson model. We compare the results with those in the harmonic limit to show that anharmonicities play an essential role in reproducing the experimental fusion barrier distribution. From the analysis of the high quality fusion data available for this system, we deduce negative static quadrupole moments for both the first 2$^{+}$ and 3$^{-}$ states in $^{144}$Sm. This is the first time that the sign of static quadrupole moments of phonon states in a spherical nucleus is determined from the data of subbarrier fusion reactions.

  9. Perturbative treatment of anharmonic vibrational effects on bond distances: an extended Langevin dynamics method.

    Science.gov (United States)

    Shen, Tonghao; Su, Neil Qiang; Wu, Anan; Xu, Xin

    2014-03-05

    In this work, we first review the perturbative treatment of an oscillator with cubic anharmonicity. It is shown that there is a quantum-classical correspondence in terms of mean displacement, mean-squared displacement, and the corresponding variance in the first-order perturbation theory, provided that the amplitude of the classical oscillator is fixed at the zeroth-order energy of quantum mechanics EQM (0). This correspondence condition is realized by proposing the extended Langevin dynamics (XLD), where the key is to construct a proper driving force. It is assumed that the driving force adopts a simple harmonic form with its amplitude chosen according to EQM (0), while the driving frequency chosen as the harmonic frequency. The latter can be improved by using the natural frequency of the system in response to the potential if its anharmonicity is strong. By comparing to the accurate numeric results from discrete variable representation calculations for a set of diatomic species, it is shown that the present method is able to capture the large part of anharmonicity, being competitive with the wave function-based vibrational second-order perturbation theory, for the whole frequency range from ∼4400 cm(-1) (H2 ) to ∼160 cm(-1) (Na2 ). XLD shows a substantial improvement over the classical molecular dynamics which ceases to work for hard mode when zero-point energy effects are significant.

  10. High-Resolution IR Absorption Spectroscopy of Polycyclic Aromatic Hydrocarbons: The Realm of Anharmonicity

    Science.gov (United States)

    Maltseva, Elena; Petrignani, Annemieke; Candian, Alessandra; Mackie, Cameron J.; Huang, Xinchuan; Lee, Timothy J.; Tielens, Alexander G. G. M.; Oomens, Jos; Buma, Wybren Jan

    2016-01-01

    We report on an experimental and theoretical investigation of the importance of anharmonicity in the 3 micrometers CH stretching region of Polycyclic Aromatic Hydrocarbon (PAH) molecules. We present mass-resolved, high-resolution spectra of the gas-phase cold ((is) approximately 4K) linear PAH molecules naphthalene, anthracene, and tetracene. The measured IR spectra show a surprisingly high number of strong vibrational bands. For naphthalene, the observed bands are well separated and limited by the rotational contour, revealing the band symmetries. Comparisons are made to the harmonic and anharmonic approaches of the widely used Gaussian software. We also present calculated spectra of these acenes using the computational program SPECTRO, providing anharmonic predictions enhanced with a Fermi-resonance treatment that utilizes intensity redistribution. We demonstrate that the anharmonicity of the investigated acenes is strong, dominated by Fermi resonances between the fundamental and double combination modes, with triple combination bands as possible candidates to resolve remaining discrepancies. The anharmonic spectra as calculated with SPECTRO lead to predictions of the main modes that fall within 0.5% of the experimental frequencies. The implications for the Aromatic Infrared Bands, specifically the 3-m band are discussed.

  11. HIGH-RESOLUTION IR ABSORPTION SPECTROSCOPY OF POLYCYCLIC AROMATIC HYDROCARBONS: THE REALM OF ANHARMONICITY

    Energy Technology Data Exchange (ETDEWEB)

    Maltseva, Elena; Buma, Wybren Jan [University of Amsterdam, Science Park 904, 1098 XH Amsterdam (Netherlands); Petrignani, Annemieke; Candian, Alessandra; Mackie, Cameron J.; Tielens, Alexander G. G. M. [Leiden Observatory, Niels Bohrweg 2, 2333 CA Leiden (Netherlands); Huang, Xinchuan; Lee, Timothy J. [SETI Institute, 189 Bernardo Avenue, Suite 100, Mountain View, CA 94043 (United States); Oomens, Jos, E-mail: w.j.buma@uva.nl, E-mail: petrignani@strw.leidenuniv.nl [Radboud University, Toernooiveld 7, 6525 ED Nijmegen (Netherlands)

    2015-11-20

    We report on an experimental and theoretical investigation of the importance of anharmonicity in the 3-μm CH stretching region of polycyclic aromatic hydrocarbon (PAH) molecules. We present mass-resolved, high-resolution spectra of the gas-phase cold (∼4 K) linear PAH molecules naphthalene, anthracene, and tetracene. The measured IR spectra show a surprisingly high number of strong vibrational bands. For naphthalene, the observed bands are well separated and limited by the rotational contour, revealing the band symmetries. Comparisons are made to the harmonic and anharmonic approaches of the widely used Gaussian software. We also present calculated spectra of these acenes using the computational program SPECTRO, providing anharmonic predictions with a Fermi-resonance treatment that utilizes intensity redistribution. We demonstrate that the anharmonicity of the investigated acenes is strong, dominated by Fermi resonances between the fundamental and double combination modes, with triple combination bands as possible candidates to resolve remaining discrepancies. The anharmonic spectra as calculated with SPECTRO lead to predictions of the main bands that fall within 0.5% of the experimental frequencies. The implications for the aromatic infrared bands, specifically the 3-μm band, are discussed.

  12. Lattice dynamics and anharmonicity of CaZrF{sub 6} from Raman spectroscopy and ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Sanson, Andrea, E-mail: andrea.sanson@unipd.it [Department of Physics and Astronomy, University of Padova, Padova (Italy); Giarola, Marco; Mariotto, Gino [Department of Computer Science, University of Verona, Verona (Italy); Hu, Lei; Chen, Jun; Xing, Xianran [Department of Physical Chemistry, University of Science and Technology Beijing, Beijing (China)

    2016-09-01

    Very recently it has been found that CaZrF{sub 6} exhibits a very large and isotropic negative thermal expansion (NTE), even greater than the current most popular NTE materials. In this work, the vibrational dynamics of CaZrF{sub 6} has been investigated by temperature-dependent Raman spectroscopy combined with ab initio calculations. As expected on the basis of the group theory for CaZrF{sub 6}, three Raman-active modes were identified: the F{sub 2g} mode peaked at about 236 cm{sup −1}, the E{sub g} mode at around 550–555 cm{sup −1}, and the A{sub g} mode peaked at about 637 cm{sup −1}. The temperature dependence of their frequencies follows an unusual trend: the F{sub 2g} mode, due to bending vibrations of fluorine atoms in the linear Ca-F-Zr chain, is hardened with increasing temperature, while the A{sub g} mode, corresponding to Ca-F-Zr bond stretching vibrations, is softened. We explain this anomalous behavior by separating implicit and explicit anharmonicity for both F{sub 2g} and A{sub g} modes. In fact, cubic anharmonicity (three-phonon processes) is observed to dominate the higher-frequency A{sub g} phonon-mode, quartic anharmonicity (four-phonon processes) is found to dominate the lower-frequency F{sub 2g} phonon-mode. As a result, the large NTE of CaZrF{sub 6} cannot be accurately predicted through the quasi-harmonic approximation. - Highlights: • A Raman and ab initio study of the lattice dynamics of CaZrF{sub 6} was performed. • All the Raman-active modes expected on the basis of the group theory were identified. • The temperature-dependence of the CaZrF{sub 6} Raman frequencies follows an unusual trend. • Explicit anharmonicity dominates for both F{sub 2g} and A{sub g} Raman modes. • The NTE of CaZrF{sub 6} cannot be accurately predicted by the quasi-harmonic approximation.

  13. Vibrational spectroscopy at electrified interfaces

    CERN Document Server

    Wieckowski, Andrzej; Braunschweig, Björn

    2013-01-01

    Reviews the latest theory, techniques, and applications Surface vibrational spectroscopy techniques probe the structure and composition of interfaces at the molecular level. Their versatility, coupled with their non-destructive nature, enables in-situ measurements of operating devices and the monitoring of interface-controlled processes under reactive conditions. Vibrational Spectroscopy at Electrified Interfaces explores new and emerging applications of Raman, infrared, and non-linear optical spectroscopy for the study of charged interfaces. The book draws from hu

  14. On the benefits of localized modes in anharmonic vibrational calculations for small molecules

    CERN Document Server

    Panek, Pawel T

    2016-01-01

    Anharmonic vibrational calculations can already be computationally demanding for relatively small molecules. The main bottlenecks lie in the construction of the potential energy surface and in the size of the excitation space in the vibrational configuration interaction (VCI) calculations. To address these challanges, we use localized-mode coordinates to construct potential energy surfaces and perform vibrational self-consistent field (L-VSCF) and L-VCI calculations [P. T. Panek, Ch. R. Jacob, ChemPhysChem 15, 3365 (2014)] for all vibrational modes of two prototypical test cases, the ethene and furan molecules. We find that the mutual coupling between modes is reduced when switching from normal-mode coordinates to localized-mode coordinates. When using such localized-mode coordinates, we observe a faster convergence of the $n$-mode expansion of the potential energy surface. This makes it possible to neglect higher-order contributions in the $n$-mode expansion of the potential energy surface or to approximate ...

  15. Anharmonic vibrational effects of thermoelectric Cu-Sb-Se ternary semiconductors: Density-functional theory studies

    Science.gov (United States)

    Zhang, Yongsheng; Skoug, Eric; Cain, Jeffrey; Morelli, Donald; Ozolins, Vidvuds; Wolverton, Christopher

    2012-02-01

    Strong anharmonicity can lead to intrinsically minimal thermal conductivity even in defect-free single crystals. In an effort to understand this behavior, we have investigated two Cu-Sb-Se ternary semiconductors, Cu3SbSe4 and Cu3SbSe3, by both experimental measurements and density functional theory (DFT) calculations. The experimental lattice thermal conductivity measurements show that while Cu3SbSe4 exhibits classical behavior, the lattice thermal conductivity in Cu3SbSe3 is anomalously low and nearly temperature independent. The vibrational properties of these two semiconductors are calculated by DFT phonon calculations within the quasi-harmonic approximation. The average of the Gr"uneisen parameters of the acoustic mode in Cu3SbSe3 is larger than that of Cu3SbSe4, which theoretically confirms that Cu3SbSe3 has a stronger lattice anharmonicity than Cu3SbSe4. Using our DFT-determined longitudinal and transverse Gr"uneisen parameters, Debye temperatures, and phonon velocities, we calculate the lattice the lattice thermal conductivity using the Debye-Callaway model (without the use of any adjustable parameters). The calculated thermal conductivity is in good agreement with the experimental measurements.

  16. Comparison of the local binding motifs in the imidazolium-based ionic liquids [EMIM][BF{sub 4}] and [EMMIM][BF{sub 4}] through cryogenic ion vibrational predissociation spectroscopy: Unraveling the roles of anharmonicity and intermolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Fournier, Joseph A.; Wolke, Conrad T.; Johnson, Christopher J.; Johnson, Mark A., E-mail: mark.johnson@yale.edu, E-mail: mccoy@chemistry.ohio-state.edu [Sterling Chemistry Laboratory, Yale University, New Haven, Connecticut 06520 (United States); McCoy, Anne B., E-mail: mark.johnson@yale.edu, E-mail: mccoy@chemistry.ohio-state.edu [Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210 (United States)

    2015-02-14

    We clarify the role of the critical imidazolium C{sub (2)}H position (the central C between N atoms in the heterocycle) in the assembly motif of the [EMIM][BF{sub 4}] ionic liquid by analyzing the vibrational spectra of the bare EMIM{sup +} ion as well as that of the cationic [EMIM]{sub 2}[BF{sub 4}]{sup +} (EMIM{sup +} = 1-ethyl-3-methylimidazolium, C{sub 6}H{sub 11}N{sub 2}{sup +}) cluster. Vibrational spectra of the cold, mass-selected ions are obtained using cryogenic ion vibrational predissociation of weakly bound D{sub 2} molecules formed in a 10 K ion trap. The C{sub (2)}H behavior is isolated by following the evolution of key vibrational features when the C{sub (2)} hydrogen, the proposed binding location of the anion to the imidazolium ring, is replaced by either deuterium or a methyl group (i.e., in the EMMIM{sup +} analogue). Strong features in the ring CH stretching region of the bare ion are traced to Fermi resonances with overtones of lower frequency modes. Upon incorporation into the EMIM{sup +} ⋅ ⋅ ⋅ BF{sub 4}{sup −} ⋅ ⋅ ⋅ EMIM{sup +} ternary complex, the C{sub (2)}H oscillator strength is dramatically increased, accounting for the much more complicated patterns derived from the EMIM{sup +} ring CH stretches in the light isotopomer, which are strongly suppressed in the deuterated analogue. Further changes in the spectra that occur when the C{sub (2)}H is replaced by a methyl group are consistent with BF{sub 4}{sup −} attachment directly to the imidazolium ring in an arrangement that maximizes the electrostatic interaction between the molecular ions.

  17. Automatic generation of force fields and property surfaces for use in variational vibrational calculations of anharmonic vibrational energies and zero-point vibrational averaged properties.

    Science.gov (United States)

    Kongsted, Jacob; Christiansen, Ove

    2006-09-28

    An automatic and general procedure for the calculation of geometrical derivatives of the energy and general property surfaces for molecular systems is developed and implemented. General expressions for an n-mode representation are derived, where the n-mode representation includes only the couplings between n or less degrees of freedom. The general expressions are specialized to derivative force fields and property surfaces, and a scheme for calculation of the numerical derivatives is implemented. The implementation is interfaced to electronic structure programs and may be used for both ground and excited electronic states. The implementation is done in the context of a vibrational structure program and can be used in combination with vibrational self-consistent field (VSCF), vibrational configuration interaction (VCI), vibrational Moller-Plesset, and vibrational coupled cluster calculations of anharmonic wave functions and calculation of vibrational averaged properties at the VSCF and VCI levels. Sample calculations are presented for fundamental vibrational energies and vibrationally averaged dipole moments and frequency dependent polarizabilities and hyperpolarizabilities of water and formaldehyde.

  18. Phonon-state mixing in the lowest two $I^{\\pi}=2^+$ states of anharmonic vibration nuclei

    CERN Document Server

    Qin, Z Z

    2016-01-01

    The phonon-configuration mixing in $2^+_1$ and $2^+_2$ states beyond the anharmonic-vibration collectivity explains the universal correlations of $Q(2^+_1)=-Q(2^+_2)$. It also suggests another strong magnetic-moment correlation of $\\mu(2^+_1)=\\mu(2^+_2)$ for the anharmonic-vibration nuclei, which is further confirmed by our experimental-data survey. The global relation between $|Q(2^+)|$, $E_{2^+_1}$ and $E_{2^+_2}$ is analytically established according to the phonon-configuration mixing scheme, and roughly agrees with experiments. This relation may provide a convenient estimation of $|Q(2^+)|$ only with spectral input. The $N_pN_n$ scheme suggests that the phonon-configuration mixing may be driven by the neutron-proton interaction.

  19. Vibrational spectroscopy of resveratrol

    Science.gov (United States)

    Billes, Ferenc; Mohammed-Ziegler, Ildikó; Mikosch, Hans; Tyihák, Ernő

    2007-11-01

    In this article the authors deal with the experimental and theoretical interpretation of the vibrational spectra of trans-resveratrol (3,5,4'-trihydroxy- trans-stilbene) of diverse beneficial biological activity. Infrared and Raman spectra of the compound were recorded; density functional calculations were carried out resulting in the optimized geometry and several properties of the molecule. Based on the calculated force constants, a normal coordinate analysis yielded the character of the vibrational modes and the assignment of the measured spectral bands.

  20. Catalytic mechanism of LENR in quasicrystals based on localized anharmonic vibrations and phasons

    CERN Document Server

    Dubinko, Volodymyr; Irwin, Klee

    2016-01-01

    Quasicrystals (QCs) are a novel form of matter, which are neither crystalline nor amorphous. Among many surprising properties of QCs is their high catalytic activity. We propose a mechanism explaining this peculiarity based on unusual dynamics of atoms at special sites in QCs, namely, localized anharmonic vibrations (LAVs) and phasons. In the former case, one deals with a large amplitude (~ fractions of an angstrom) time-periodic oscillations of a small group of atoms around their stable positions in the lattice, known also as discrete breathers, which can be excited in regular crystals as well as in QCs. On the other hand, phasons are a specific property of QCs, which are represented by very large amplitude (~angstrom) oscillations of atoms be-tween two quasi-stable positions determined by the geometry of a QC. Large amplitude atomic motion in LAVs and phasons results in time-periodic driving of adjacent potential wells occupied by hydrogen ions (protons or deuterons) in case of hydrogenated QCs. This drivin...

  1. Ultrafast infrared vibrational spectroscopy

    CERN Document Server

    Fayer, Michael D

    2013-01-01

    The past ten years or so have seen the introduction of multidimensional methods into infrared and optical spectroscopy. The technology of multidimensional spectroscopy is developing rapidly and its applications are spreading to biology and materials science. Edited by a recognized leader in the field and with contributions from top researchers, including experimentalists and theoreticians, this book presents the latest research methods and results and will serve as an excellent resource for other researchers.

  2. Global dynamical analysis of vibrational manifolds of HOCl and HOBr under anharmonicity and Fermi resonance: the dynamical potential approach

    Science.gov (United States)

    Fang, Chao; Wu, Guo-Zhen

    2010-01-01

    The vibrational dynamics of HOCl and HOBr between bending and OCl/OBr stretching coordinates with anharmonicity and Fermi coupling is studied with the classical dynamical potential approach. The quantal vibrational dynamics is mostly mapped out by the classical nonlinear variables such as fixed points, except for the state energies, which are quantized. This approach is global in the sense that the focus is on a set of levels instead of individual ones. The dynamics of HOBr is demonstrated to be less complicated. The localized modes along the OCl/OBr stretching coordinates are also shown to have O-Br bonds more prone to dissociation.

  3. TIME-RESOLVED VIBRATIONAL SPECTROSCOPY

    Energy Technology Data Exchange (ETDEWEB)

    Andrei Tokmakoff, MIT (Conference Chair); Paul Champion, Northeastern University; Edwin J. Heilweil, NIST; Keith A. Nelson, MIT; Larry Ziegler, Boston University

    2009-05-14

    This document contains the Proceedings from the 14th International Conference on Time-Resolved Vibrational Spectroscopy, which was held in Meredith, NH from May 9-14, 2009. The study of molecular dynamics in chemical reaction and biological processes using time-resolved spectroscopy plays an important role in our understanding of energy conversion, storage, and utilization problems. Fundamental studies of chemical reactivity, molecular rearrangements, and charge transport are broadly supported by the DOE’s Office of Science because of their role in the development of alternative energy sources, the understanding of biological energy conversion processes, the efficient utilization of existing energy resources, and the mitigation of reactive intermediates in radiation chemistry. In addition, time-resolved spectroscopy is central to all five of DOE’s grand challenges for fundamental energy science. The Time-Resolved Vibrational Spectroscopy conference is organized biennially to bring the leaders in this field from around the globe together with young scientists to discuss the most recent scientific and technological advances. The latest technology in ultrafast infrared, Raman, and terahertz spectroscopy and the scientific advances that these methods enable were covered. Particular emphasis was placed on new experimental methods used to probe molecular dynamics in liquids, solids, interfaces, nanostructured materials, and biomolecules.

  4. Time-resolved vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tokmakoff, Andrei [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Champion, Paul [Northeastern Univ., Boston, MA (United States); Heilweil, Edwin J. [National Inst. of Standards and Technology (NIST), Boulder, CO (United States); Nelson, Keith A. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Ziegler, Larry [Boston Univ., MA (United States)

    2009-05-14

    This document contains the Proceedings from the 14th International Conference on Time-Resolved Vibrational Spectroscopy, which was held in Meredith, NH from May 9-14, 2009. The study of molecular dynamics in chemical reaction and biological processes using time-resolved spectroscopy plays an important role in our understanding of energy conversion, storage, and utilization problems. Fundamental studies of chemical reactivity, molecular rearrangements, and charge transport are broadly supported by the DOE's Office of Science because of their role in the development of alternative energy sources, the understanding of biological energy conversion processes, the efficient utilization of existing energy resources, and the mitigation of reactive intermediates in radiation chemistry. In addition, time-resolved spectroscopy is central to all fiveof DOE's grand challenges for fundamental energy science. The Time-Resolved Vibrational Spectroscopy conference is organized biennially to bring the leaders in this field from around the globe together with young scientists to discuss the most recent scientific and technological advances. The latest technology in ultrafast infrared, Raman, and terahertz spectroscopy and the scientific advances that these methods enable were covered. Particular emphasis was placed on new experimental methods used to probe molecular dynamics in liquids, solids, interfaces, nanostructured materials, and biomolecules.

  5. Anharmonic bend-stretch coupling in neat liquid water

    NARCIS (Netherlands)

    Lindner, Joerg; Cringus, Dan; Pshenichnikov, Maxim S.; Voehringer, Peter

    2007-01-01

    Femtosecond mid-IR spectroscopy is used to study the vibrational relaxation dynamics in neat liquid water. By exciting the bending vibration and probing the stretching mode, it is possible to reliably determine the bending and librational lifetimes of water. The anharmonic coupling between the bendi

  6. Probing zeolites by vibrational spectroscopies.

    Science.gov (United States)

    Bordiga, Silvia; Lamberti, Carlo; Bonino, Francesca; Travert, Arnaud; Thibault-Starzyk, Frédéric

    2015-10-21

    This review addresses the most relevant aspects of vibrational spectroscopies (IR, Raman and INS) applied to zeolites and zeotype materials. Surface Brønsted and Lewis acidity and surface basicity are treated in detail. The role of probe molecules and the relevance of tuning both the proton affinity and the steric hindrance of the probe to fully understand and map the complex site population present inside microporous materials are critically discussed. A detailed description of the methods needed to precisely determine the IR absorption coefficients is given, making IR a quantitative technique. The thermodynamic parameters of the adsorption process that can be extracted from a variable-temperature IR study are described. Finally, cutting-edge space- and time-resolved experiments are reviewed. All aspects are discussed by reporting relevant examples. When available, the theoretical literature related to the reviewed experimental results is reported to support the interpretation of the vibrational spectra on an atomic level.

  7. Anharmonic OH vibrations in Mg(OH)2 (brucite): two-dimensional calculations and crystal-induced blueshift.

    Science.gov (United States)

    Hermansson, Kersti; Probst, Michael M; Gajewski, Grzegorz; Mitev, Pavlin D

    2009-12-28

    A two-dimensional quantum-mechanical vibrational model has been used to calculate the anharmonic OH vibrational frequencies in the layered Mg(OH)(2) (brucite) crystal. The underlying potential energy surface was generated by density functional theory (DFT) calculations. The resulting OH frequencies are upshifted (blueshifted) by about +75 cm(-1) with respect to the gas-phase OH frequency (+120 cm(-1) in experiments; the discrepancy is mainly due to inadequacies in the DFT and pseudopotential models). The Raman-IR split is about 50 cm(-1), both in the calculations and in experiments. We find that the blueshift phenomenon in brucite can qualitatively be explained by a parabolalike "OH frequency versus electric field" correlation curve pertaining to an OH(-) ion exposed to an electric field. We also find that it is primarily the neighbors within the Mg(OH)(2) layer that induce the blueshift while the interlayer interaction gives a smaller (and redshifting) contribution.

  8. Interpreting nonlinear vibrational spectroscopy with the classical mechanical analogs of double-sided Feynman diagrams.

    Science.gov (United States)

    Noid, W G; Loring, Roger F

    2004-10-15

    Observables in coherent, multiple-pulse infrared spectroscopy may be computed from a vibrational nonlinear response function. This response function is conventionally calculated quantum-mechanically, but the challenges in applying quantum mechanics to large, anharmonic systems motivate the examination of classical mechanical vibrational nonlinear response functions. We present an approximate formulation of the classical mechanical third-order vibrational response function for an anharmonic solute oscillator interacting with a harmonic solvent, which establishes a clear connection between classical and quantum mechanical treatments. This formalism permits the identification of the classical mechanical analog of the pure dephasing of a quantum mechanical degree of freedom, and suggests the construction of classical mechanical analogs of the double-sided Feynman diagrams of quantum mechanics, which are widely applied to nonlinear spectroscopy. Application of a rotating wave approximation permits the analytic extraction of signals obeying particular spatial phase matching conditions from a classical-mechanical response function. Calculations of the third-order response function for an anharmonic oscillator coupled to a harmonic solvent are compared to numerically correct classical mechanical results.

  9. A study of anharmonic al and nonlinear behaviours of vibrations of atomic nuclei; Etude des comportements anharmonioques et non lineaires des vibrations des noyaux atomiques

    Energy Technology Data Exchange (ETDEWEB)

    Volpe, M.C. [Caen Univ., 14 (France)

    1997-12-31

    Double Giant Resonances, vibrational states in which a Giant Resonance is excited on top of another Giant Resonance, have been in the last years the object of many theories and studies. Whereas the measured energies and widths of these states agree with a theoretical predictions, the measured excitation cross sections on the other hand are almost always larger than the calculated ones. The standard theoretical approaches are based both on a harmonic approximation for the collective motion on the nucleus and on its linear response to an external field. In this work the influence of anharmonicities and non-linearities in the external field on the excitation of Double Giant Resonances are studied. First, an oscillator model and an extension of the Lipkin-Meshkow-Glick model are used to study the effects of anharmonicities and non-linearities on the excitation probabilities. The results show that these terms can influence the excitation probability of the second excited state in a significant way. Secondly, these exactly soluble schematic models are used to study some of the approximations made in microscopic calculations based on boson expansion methods and also some aspects on the time-dependent mean field approach. Finally, a microscopic calculation of the Coulomb excitation cross sections of Double Giant Resonances is presented for several nuclei. It is found that, for {sup 208} Pb, the inclusion of anharmonicities and non-linearities and the consideration of many states that play a role in the excitation process give a satisfactory agreement between calculated and observed cross sections. (author). 113 refs.

  10. Systematic studies of molecular vibrational anharmonicity and vibration-rotation interaction by self-consistent-field higher derivative methods: Applications to asymmetric and symmetric top and linear polyatomic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Clabo, D.A. Jr.

    1987-04-01

    Inclusion of the anharmonicity normal mode vibrations (i.e., the third and fourth (and higher) derivatives of a molecular Born-Oppenheimer potential energy surface) is necessary in order to theoretically reproduce experimental fundamental vibrational frequencies of a molecule. Although ab initio determinations of harmonic vibrational frequencies may give errors of only a few percent by the inclusion of electron correlation within a large basis set for small molecules, in general, molecular fundamental vibrational frequencies are more often available from high resolution vibration-rotation spectra. Recently developed analytic third derivatives methods for self-consistent-field (SCF) wavefunctions have made it possible to examine with previously unavailable accuracy and computational efficiency the anharmonic force fields of small molecules.

  11. Vibrational spectroscopy of water interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Du, Quan [Univ. of California, Berkeley, CA (United States)

    1994-12-01

    The second order nonlinear optical processes of second harmonic generation and sum frequency generation are powerful and versatile tools for studying all kinds of surfaces. They possess unusual surface sensitivity due to the symmetry properties of the second order nonlinear susceptibility. The technique of infrared-visible sum frequency generation (SFG) is particularly attractive because it offers a viable way to do vibrational spectroscopy on any surfaces accessible to light with submonolayer sensitivity. In this thesis, the author applies SFG to study a number of important water interfaces. At the air/water interface, hydrophobic solid/water and liquid/water interfaces, it was found that approximately 25% of surface water molecules have one of their hydrogen pointing away from the liquid water. The large number of unsatisfied hydrogen bonds contributes significantly to the large interfacial energy of the hydrophobic surfaces. At the hydrophilic fused quartz/water interface and a fatty acid monolayer covered water surface, the structure and orientation of surface water molecules are controlled by the hydrogen bonding of water molecules with the surface OH groups and the electrostatic interaction with the surface field from the ionization of surface groups. A change of pH value in the bulk water can significantly change the relative importance of the two interactions and cause a drastic change in orientation of the surface water molecules. SFG has also been applied to study the tribological response of some model lubricant films. Monolayers of Langmuir-Blodgett films were found to disorder orientationaly under mildly high pressure and recover promptly upon removal of the applied pressure.

  12. Unexpected red shift of C-H vibrational band of Methyl benzoate

    CERN Document Server

    Maiti, Kiran Sankar; Scheurer, Christoph

    2016-01-01

    The C-H vibrational bands become more and more important in the structural determination of biological molecules with the development of CARS microscopy and 2DIR spectroscopy. Due to the congested pattern, near degeneracy, and strong anharmonicity of the C-H stretch vibrations, assignment of the C-H vibrational bands are often misleading. Anharmonic vibrational spectra calculation with multidimensional potential energy surface interprets the C-H vibrational spectra more accurately. In this article we have presented the importance of multidimensional potential energy surface in anharmonic vibrational spectra calculation and discuss the unexpected red shift of C-H vibrational band of Methyl benzoate.

  13. Alcohol dimers--how much diagonal OH anharmonicity?

    Science.gov (United States)

    Kollipost, Franz; Papendorf, Kim; Lee, Yu-Fang; Lee, Yuan-Pern; Suhm, Martin A

    2014-08-14

    The OH bond of methanol, ethanol and t-butyl alcohol becomes more anharmonic upon hydrogen bonding and the infrared intensity ratio between the overtone and the fundamental transition of the bridging OH stretching mode decreases drastically. FTIR spectroscopy of supersonic slit jet expansions allows to quantify these effects for isolated alcohol dimers, enabling a direct comparison to anharmonic vibrational predictions. The diagonal anharmonicity increase amounts to 15-18%, growing with increasing alkyl substitution. The overtone/fundamental IR intensity ratio, which is on the order of 0.1 or more for isolated alcohols, drops to 0.004-0.001 in the hydrogen-bonded OH group, making overtone detection very challenging. Again, alkyl substitution enhances the intensity suppression. Vibrational second order perturbation theory appears to capture these effects in a semiquantitative way. Harmonic quantum chemistry predictions for the hydrogen bond-induced OH stretching frequency shift (the widely used infrared signature of hydrogen bonding) are insufficient, and diagonal anharmonicity corrections from experiment make the agreement between theory and experiment worse. Inclusion of anharmonic cross terms between hydrogen bond modes and the OH stretching mode is thus essential, as is a high level electronic structure theory. The isolated molecule results are compared to matrix isolation data, complementing earlier studies in N2 and Ar by the more weakly interacting Ne and p-H2 matrices. Matrix effects on the hydrogen bond donor vibration are quantified.

  14. Anharmonic Vibrational Treatment Exclusively in Curvilinear Valence Coordinates: The Case of Formamide.

    Science.gov (United States)

    Richter, F; Thaunay, F; Lauvergnat, D; Carbonnière, P

    2015-12-01

    A highly correlated approach using curvilinear valence coordinates is applied to calculate the vibrational fundamentals and some combination modes of the formamide molecule with high accuracy. A series of potential energy surfaces (PESs) has been generated by AGAPES, a program for adaptive generation of adiabatic PESs, at various electronic structure qualities until excellent nonaccidental agreement with the experimentally assigned fundamental transitions was reached at the CCSDT(T)-F12a/aug-cc-pVTZ level of theory using the improved relaxation method of the Heidelberg multiconfiguration time-dependent Hartree (MCTDH) package in connection with an exact expression for the kinetic energy in valence coordinates generated by the TANA program. By comparison of the overtone series ν1-3ν1 to experiment, we demonstrate that the known problems concerning the floppy ν1 wagging motion are solved within this approach. The potential energy coupling as well as the vibrational coupling in curvilinear coordinates is discussed together with the efficiency of this approach.

  15. Vibrational Spectroscopy of Chromatographic Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Jeanne E. Pemberton

    2011-03-10

    Chromatographic separations play a central role in DOE-supported fundamental research related to energy, biological systems, the environment, and nuclear science. The overall portfolio of research activities in the Separations and Analysis Program within the DOE Office of Basic Energy Sciences includes support for activities designed to develop a molecular-level understanding of the chemical processes that underlie separations for both large-scale and analytical-scale purposes. The research effort funded by this grant award was a continuation of DOE-supported research to develop vibrational spectroscopic methods to characterize the interfacial details of separations processes at a molecular level.

  16. Getting down to the Fundamentals of Hydrogen Bonding: Anharmonic Vibrational Frequencies of (HF)2 and (H2O)2 from Ab Initio Electronic Structure Computations.

    Science.gov (United States)

    Howard, J Coleman; Gray, Jessica L; Hardwick, Amanda J; Nguyen, Linh T; Tschumper, Gregory S

    2014-12-09

    This work presents a systematic investigation into the basis set convergence of harmonic vibrational frequencies of (H2O)2 and (HF)2 computed with second-order Møller-Plesset perturbation theory (MP2) and the coupled-cluster singles and doubles method with perturbative connected triples, CCSD(T), while employing correlation-consistent basis sets as large as aug-cc-pV6Z. The harmonic vibrational frequencies presented here are expected to lie within a few cm(-1) of the complete basis set (CBS) limit. For these important hydrogen-bonding prototype systems, a basis set of at least quadruple-ζ quality augmented with diffuse functions is required to obtain harmonic vibrational frequencies within 10 cm(-1) of the CBS limit. In addition, second-order vibrational perturbation theory (VPT2) anharmonic corrections yield CCSD(T) vibrational frequencies in excellent agreement with experimental spectra, differing by no more than a few cm(-1) for the intramonomer fundamental vibrations. D0 values predicted by CCSD(T) VPT2 computations with a quadruple-ζ basis set reproduce the experimental values of (HF)2 and (H2O)2 to within 2 and 21 cm(-1), respectively.

  17. Electron hybridization and anharmonic thermal vibration effect on structure transition of SrTiO3 at high-pressure and low-temperature

    Science.gov (United States)

    Yamanaka, Takamitsu; Ahart, Muhtar; Mao, Ho-kwang; Suzuki, Takeyuki

    2017-01-01

    We execute electron density analysis of SrTiO3 at low temperatures up 80 K and high pressures up to 11.88 GPa using X-ray single-crystal diffraction and ab initio quantum chemical molecular orbital (MO) calculation. By changing pressures, the cubic SrTiO3 with perovskite structure goes through a antiferroelastic distortion to tetragonal symmetry above the critical pressure Pc=7 GPa with c/a1 and increasing with lowering temperature. Difference Fourier (D-F) synthesis experimentally proves the residual electron densities Δρ(xyz) are associated with two different effects: electron hybridization bonding electron and anharmonic thermal vibration atoms. The d-p-π hybridization between Ti(3d) and O(2p) orbitals is confirmed in the residual electron density, which is deformed from the ideal spherical density conducted by the atomic scattering factor fi using Hartree-Fock (HF) approximation. MO calculation also reveals the electron hybridization. Anharmonic thermal vibration of atoms yields a large effect to the structure transition. Mulliken charges analysis of MO calculation indicates much smaller charges than their formal ionic charges. Their ionicity increases from cubic to tetragonal above Pc and below Tc.

  18. Predicting the structure and vibrational frequencies of ethylene using harmonic and anharmonic approaches at the Kohn-Sham complete basis set limit.

    Science.gov (United States)

    Buczek, Aneta; Kupka, Teobald; Broda, Małgorzata A; Żyła, Adriana

    2016-01-01

    In this work, regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn-Sham complete basis set (KS CBS) limit are demonstrated for the first time. The performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with two Pople basis sets (6-311++G** and 6-311++G(3df,2pd)), the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n = 0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X = D, T, Q, 5, 6) was tested.The BLYP-calculated harmonic frequencies were found to be markedly closer than the B3LYP-calculated harmonic frequencies to the experimentally derived values, while the calculated anharmonic frequencies consistently underestimated the observed wavenumbers. The different basis set families gave very similar estimated values for the CBS parameters. The anharmonic frequencies calculated with B3LYP/aug-pc-3 were consistently significantly higher than those obtained with the pc-3 basis set; applying the aug-pcseg-n basis set family alleviated this problem. Utilization of B3LYP/aug-pcseg-n basis sets instead of B3LYP/aug-cc-pVXZ, which is computationally less expensive, is suggested for medium-sized molecules. Harmonic BLYP/pc-2 calculations produced fairly accurate ethylene frequencies. Graphical Abstract In this study, the performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n = 0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X = D, T, Q, 5, and 6) was tested. For the first time, we demonstrated regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn-Sham complete basis set (KS CBS) limit.

  19. New developments in IR surface vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Hirschmugl, C.J.; Lamont, C.L.A.; Williams, G.P. [Brookhaven National Lab., Upton, NY (United States). National Synchrotron Light Source

    1995-12-31

    Low frequency dynamics at surfaces, particularly in the region of the adsorbate-substrate vibrational modes is of fundamental importance in areas as varied as sliding friction, catalysis, corrosion and epitaxial growth. This paper reviews the new developments in low frequency Infrared Reflection Absorption Spectroscopy using synchrotron radiation as the source. Absolute changes induced in the far infrared for several adsorbate systems on Cu, including CO and H, are dominated by broadband reflectance changes and dipole forbidden vibrational modes which in some cases are an order of magnitude stronger than the dipole allowed modes. The experimental data can be explained by a theory developed by Persson, in which the dielectric response of the substrate is seen as playing a crucial role in the dynamics. In particular the relationships between the wavelength of the light, the penetration depth and the electron mean-free path, are critical.

  20. 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.

  1. Vibrational spectroscopy in diagnosis and screening

    CERN Document Server

    Severcan, F

    2012-01-01

    In recent years there has been a tremendous growth in the use of vibrational spectroscopic methods for diagnosis and screening. These applications range from diagnosis of disease states in humans, such as cancer, to rapid identification and screening of microorganisms. The growth in such types of studies has been possible thanks to advances in instrumentation and associated computational and mathematical tools for data processing and analysis. This volume of Advances in Biomedical Spectroscopy contains chapters from leading experts who discuss the latest advances in the application of Fourier

  2. Frequency and zero-point vibrational energy scale factors for double-hybrid density functionals (and other selected methods): can anharmonic force fields be avoided?

    Science.gov (United States)

    Kesharwani, Manoj K; Brauer, Brina; Martin, Jan M L

    2015-03-05

    We have obtained uniform frequency scaling factors λ(harm) (for harmonic frequencies), λ(fund) (for fundamentals), and λ(ZPVE) (for zero-point vibrational energies (ZPVEs)) for the Weigend-Ahlrichs and other selected basis sets for MP2, SCS-MP2, and a variety of DFT functionals including double hybrids. For selected levels of theory, we have also obtained scaling factors for true anharmonic fundamentals and ZPVEs obtained from quartic force fields. For harmonic frequencies, the double hybrids B2PLYP, B2GP-PLYP, and DSD-PBEP86 clearly yield the best performance at RMSD = 10-12 cm(-1) for def2-TZVP and larger basis sets, compared to 5 cm(-1) at the CCSD(T) basis set limit. For ZPVEs, again, the double hybrids are the best performers, reaching root-mean-square deviations (RMSDs) as low as 0.05 kcal/mol, but even mainstream functionals like B3LYP can get down to 0.10 kcal/mol. Explicitly anharmonic ZPVEs only are marginally more accurate. For fundamentals, however, simple uniform scaling is clearly inadequate.

  3. The far infrared spectrum of naphthalene characterized by high resolution synchrotron FTIR spectroscopy and anharmonic DFT calculations.

    Science.gov (United States)

    Pirali, O; Goubet, M; Huet, T R; Georges, R; Soulard, P; Asselin, P; Courbe, J; Roy, P; Vervloet, M

    2013-07-07

    Using synchrotron radiation, we performed the rotationally resolved Fourier transform infrared absorption spectroscopy of three bands of naphthalene C10H8, namely ν(46)-0 (centered at 782 cm(-1), 12.7 μm), ν(47)-0 (centered at 474 cm(-1), 21 μm), and ν(48)-0 (centered at 167 cm(-1), 60 μm). The intense CH bending out of plane ν(46)-0 band was recorded under supersonic jet-cooled conditions using a molecular beam (the Jet-AILES apparatus) and the low frequency ν(47)-0 and ν(48)-0 bands were measured at room temperature in a long absorption path cell. The simultaneous rotational analysis of these bands permitted us to refine the ground state (GS) and ν(46) rotational spectroscopic constants and to provide the first sets of constants for the ν(47) and ν(48) modes. The experimental rotational constants were then used as reference data to calibrate theoretical models in order to provide new insights into the accuracy of anharmonic calculations. The B97-1 functional associated with the cc-pVTZ and ANO-RCC basis sets gave a consistent set of results, for rotational constants and fundamental frequencies. The data presented here pave the way for the search of naphthalene through its far-infrared spectrum in different objects of the interstellar medium.

  4. Origin of the large anharmonicity in the phonon modes of LiBH{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Gremaud, R.; Züttel, A. [Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory 505 (Hydrogen and Energy), Überlandstrasse 129, CH-8600 Dübendorf (Switzerland); Borgschulte, A., E-mail: andreas.borgschulte@empa.ch [Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory 505 (Hydrogen and Energy), Überlandstrasse 129, CH-8600 Dübendorf (Switzerland); Ramirez-Cuesta, A.J.; Refson, K. [Chemical and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, PO Box 2008, MS 6473 Oak Ridge (United States); Colognesi, D. [Istituto dei Sistemi Complessi – sezione di Firenze, Consiglio Nazionale delle Ricerche, via Madonna del piano 10, 50019 Sesto Fiorentino (Italy)

    2013-12-12

    Highlights: • IR, Raman, and INS spectroscopy data and corresponding DFT-calculations on LiBH4. • Mismatch between experiment and theory are due to anharmonicity. • Strong anharmonic effects can be expected for vibrations with high H amplitude. - Abstract: The dynamics and bonding of the complex hydride LiBH{sub 4} have been investigated by vibrational spectroscopy and density functional theory (DFT). The combination of infrared, Raman, and inelastic neutron-scattering (INS) spectroscopies on hydrided and deuterated samples reveals a complete picture of the dynamics of the BH{sub 4}{sup −} ions as well as of the lattice. Particular emphasis is laid on a comparison between experiment and theory, revealing significant discrepancy between the two approaches for vibrations with high anharmonicity, which is related to large vibrational amplitudes. The latter is typical for librational modes in molecular crystals and pseudo-ionic crystals such as complex hydrides. The presented strategy for anharmonic frequency corrections might thus be generally applicable for this kind of materials.

  5. Multidimensional Time-Resolved Spectroscopy of Vibrational Coherence in Biopolyenes

    Science.gov (United States)

    Buckup, Tiago; Motzkus, Marcus

    2014-04-01

    Multidimensional femtosecond time-resolved vibrational coherence spectroscopy allows one to investigate the evolution of vibrational coherence in electronic excited states. Methods such as pump-degenerate four-wave mixing and pump-impulsive vibrational spectroscopy combine an initial ultrashort laser pulse with a nonlinear probing sequence to reinduce vibrational coherence exclusively in the excited states. By carefully exploiting specific electronic resonances, one can detect vibrational coherence from 0 cm-1 to over 2,000 cm-1 and map its evolution. This review focuses on the observation and mapping of high-frequency vibrational coherence for all-trans biological polyenes such as β-carotene, lycopene, retinal, and retinal Schiff base. We discuss the role of molecular symmetry in vibrational coherence activity in the S1 electronic state and the interplay of coupling between electronic states and vibrational coherence.

  6. Multidimensional time-resolved spectroscopy of vibrational coherence in biopolyenes.

    Science.gov (United States)

    Buckup, Tiago; Motzkus, Marcus

    2014-01-01

    Multidimensional femtosecond time-resolved vibrational coherence spectroscopy allows one to investigate the evolution of vibrational coherence in electronic excited states. Methods such as pump-degenerate four-wave mixing and pump-impulsive vibrational spectroscopy combine an initial ultrashort laser pulse with a nonlinear probing sequence to reinduce vibrational coherence exclusively in the excited states. By carefully exploiting specific electronic resonances, one can detect vibrational coherence from 0 cm(-1) to over 2,000 cm(-1) and map its evolution. This review focuses on the observation and mapping of high-frequency vibrational coherence for all-trans biological polyenes such as β-carotene, lycopene, retinal, and retinal Schiff base. We discuss the role of molecular symmetry in vibrational coherence activity in the S1 electronic state and the interplay of coupling between electronic states and vibrational coherence.

  7. Reactivity, vibrational spectroscopy, internal rotation and thermochemical aspects of methylarsine

    Science.gov (United States)

    Viana, Rommel B.

    2017-01-01

    The aim of this investigation was to perform a characterization of the spectroscopic and thermodynamic properties of methylarsine (CH3AsH2). Post-Hartree-Fock, 29 DFT methods and eight different composite methodologies were employed in these analyses. A comparison between harmonic and anharmonic frequency accuracies in reproducing the observable frequencies was performed here. In addition, the CH3AsH2 → CH2AsH3 isomerization barrier energy was estimated in 100 kcal mol- 1, whereas the H2-release routes barrier heights were in the 45-107 kcal mol- 1 range. A rate constant of 10- 66 s- 1 was predicted regarding the isomerization route, while the CH2AsH3 hydrogen elimination mechanism is faster than the methylarsine one. The transition state structure of the CH3AsH2 internal rotational barrier energy varied between 1.0 and 1.4 kcal mol- 1. For the CH2AsH3 internal rotation the estimated barrier heights varied 0.6-2.5 kcal mol- 1. The adiabatic ionization energy and the heat of formation each structure was also calculated here. Table S2 Mean absolute error (MAE, in cm- 1) based in the harmonic frequencies calculated for each method in the prediction of the methylarsine experimental vibrational modes. Table S3 Calculated harmonic (ν, in cm- 1) and anharmonic (ω, in cm- 1) vibrational frequencies in reproducing the methylarsine observed frequencies using the cc-pVTZ basis sets. Table S4. Calculated harmonic (ZPVEHARM, in kcal mol- 1) and anharmonic (ZPVEANHARM, in kcal mol- 1) methylarsine zero-point vibrational energy values (ZPVE) and the difference (∆ZPVE) between both values. Table S5. Arsenic-Carbon bond order indexes for each molecule. Table S6 Properties at As-C bond critical points (BCPs) as electronic charge density [ρ(r)] and its Laplacian [∇2ρ(r)], total energy density [H(r)], ellipticity (ε) and the relationship between local potential energy and local energy density [V(r)/G(r)]. Table S7 Carbon [q(C)] and arsenic [q(As)] atomic charge distribution

  8. 2010 GRC VIBRATIONAL SPECTROSCOPY AUGUST 1 - AUGUST 6, 2010

    Energy Technology Data Exchange (ETDEWEB)

    Brooks Pate

    2010-08-06

    The Vibrational Spectroscopy conference focuses on using vibrational spectroscopy to probe structure and dynamics of molecules in gases, liquids, and at interfaces. The conference explores the wide range of state-of-the-art techniques based on vibrational motion. These techniques span the fields of time-domain, high-resolution frequency-domain, spatially-resolved, nonlinear and multidimensional spectroscopies. The conference highlights the application of these techniques in chemistry, materials, biology, and medicine. The theory of molecular vibrational motion and its connection to spectroscopic signatures and chemical reaction dynamics is the third major theme of the meeting. The goal is to bring together a collection of researchers who share common interests and who will gain from discussing work at the forefront of several connected areas. The intent is to emphasize the insights and understanding that studies of vibrations provide about a variety of molecular systems ranging from small polyatomic molecules to large biomolecules and nanomaterials.

  9. The road to medical vibrational spectroscopy--a history.

    Science.gov (United States)

    Mantsch, Henry H

    2013-07-21

    The present Editorial chronicles the journey from classical infrared and Raman spectroscopy to medical vibrational spectroscopy, as experienced by a contemporary witness of the times. During the second half of the last century vibrational biospectroscopy became a topic of increasing global interest and has spawned a number of international conferences of which the most recent, SPEC 2012 - Shedding New Light on Disease, constitutes the basis of the present themed issue.

  10. 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.

  11. Spectroscopy and reactions of vibrationally excited transient molecules

    Energy Technology Data Exchange (ETDEWEB)

    Dai, H.L. [Univ. of Pennsylvania, Philadelphia (United States)

    1993-12-01

    Spectroscopy, energy transfer and reactions of vibrationally excited transient molecules are studied through a combination of laser-based excitation techniques and efficient detection of emission from the energized molecules with frequency and time resolution. Specifically, a Time-resolved Fourier Transform Emission Spectroscopy technique has been developed for detecting dispersed laser-induced fluorescence in the IR, visible and UV regions. The structure and spectroscopy of the excited vibrational levels in the electronic ground state, as well as energy relaxation and reactions induced by specific vibronic excitations of a transient molecule can be characterized from time-resolved dispersed fluorescence in the visible and UV region. IR emissions from highly vibrational excited levels, on the other hand, reveal the pathways and rates of collision induced vibrational energy transfer.

  12. Vibrational properties and phonon anharmonicity in ZnS{sub 1−x}Se{sub x}: Inelastic neutron scattering, Raman scattering, X-ray diffraction measurements and lattice dynamical studies

    Energy Technology Data Exchange (ETDEWEB)

    Basak, Tista, E-mail: tistabasak1@gmail.com [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra (India); Rao, Mala N.; Chaplot, S.L.; Salke, Nilesh; Rao, Rekha [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra (India); Dhanasekaran, R. [Crystal Growth Centre, Anna University, SP Road, Chennai 600025 (India); Rajarajan, A.K. [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra (India); Rols, S. [Institut Laue-Langevin, BP 156, 38042 Grenoble Cedex 9, Grenoble (France); Mittal, R.; Jayakrishnan, V.B.; Sastry, P.U. [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, Maharashtra (India)

    2014-01-15

    Inelastic neutron scattering, Raman and X-ray diffraction measurements coupled with lattice dynamical calculations (employing a semi-empirical transferable potential model) have been carried out to gain a detailed understanding of the peculiar vibrational spectrum exhibited by the mixed crystal ZnS{sub 1−x}Se{sub x}. Raman scattering measurements performed over a varying range of temperature (100–800 K) and pressure (up to 13 GPa) have confirmed that the additional mode observed in the spectra are visible over the entire range of temperature and pressure. Correlation of the individual motions of atoms (obtained from computed total and partial phonon density of states) with the inelastic neutron scattering measurements (carried out over the entire Brillouin zone) have then indicated that the existence of the additional mode in ZnS{sub 1−x}Se{sub x} is due to the vibrations of the Se atom being in resonance with that of the S atom. Further, it has been shown that the presence of this additional mode can be tuned by varying the mass of the atom at the Se site. In addition, an analysis of bond-length distribution with increasing Se concentration have elucidated that bond-length spread is not responsible for the presence of the additional mode. An analysis of the peak shifts of the Raman modes with temperature and pressure indicate that the anharmonicity of the vibrational modes increases with increasing compositional disorder. This is attributed to the fact that increasing Se concentration gives rise to a distribution of bond-lengths in ZnS{sub 1−x}Se{sub x}, which is responsible for this compositional disorder induced anharmonicity. Our computations have thus revealed that mass of the anion is responsible for the presence of additional mode while bond-length distribution gives rise to the existence of compositional disorder induced anharmonicity in ZnS{sub 1−x}Se{sub x}. Further, it is observed that the contribution of explicit anharmonicity to the total

  13. Seventh international conference on time-resolved vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Dyer, R.B.; Martinez, M.A.D.; Shreve, A.; Woodruff, W.H. [comps.

    1997-04-01

    The International Conference on Time-Resolved Vibrational Spectroscopy (TRVS) is widely recognized as the major international forum for the discussion of advances in this rapidly growing field. The 1995 conference was the seventh in a series that began at Lake Placid, New York, 1982. Santa Fe, New Mexico, was the site of the Seventh International Conference on Time-Resolved Vibrational Spectroscopy, held from June 11 to 16, 1995. TRVS-7 was attended by 157 participants from 16 countries and 85 institutions, and research ranging across the full breadth of the field of time-resolved vibrational spectroscopy was presented. Advances in both experimental capabilities for time-resolved vibrational measurements and in theoretical descriptions of time-resolved vibrational methods continue to occur, and several sessions of the conference were devoted to discussion of these advances and the associated new directions in TRVS. Continuing the interdisciplinary tradition of the TRVS meetings, applications of time-resolved vibrational methods to problems in physics, biology, materials science, and chemistry comprised a large portion of the papers presented at the conference.

  14. Anharmonicity and Confinement in Zeolites: Structure, Spectroscopy and Adsorption Free Energy of Ethanol in H-ZSM-5

    Energy Technology Data Exchange (ETDEWEB)

    Alexopoulos, Konstantinos; Lee, Mal Soon; Liu, Yue; Zhi, Yuchun; Liu, Yuanshuai; Reyniers, Marie-Francoise; Marin, Guy B.; Glezakou, Vassiliki Alexandra; Rousseau, Roger J.; Lercher, Johannes A.

    2016-04-07

    To account for thermal and entropic effects caused by the dynamics of the motion of the reaction intermediates, ethanol adsorption on the Brønsted acid site of the H-ZSM-5 catalyst has been studied at different temperatures and ethanol loadings using ab initio molecular dynamics (AIMD) simulations, infrared (IR) spectroscopy and calorimetric measurements. At low temperatures (T ≤ 400 K) and ethanol loading, a single ethanol molecule adsorbed in H-ZSM-5 forms a Zundel-like structure where the proton is equally shared between the oxygen of the zeolite and the oxygen of the alcohol. At higher ethanol loading, a second ethanol molecule helps to stabilize the protonated ethanol at all temperatures by acting as a solvating agent. The vibrational density of states (VDOS), as calculated from the AIMD simulations, are in excellent agreement with measured IR spectra for C2H5OH, C2H5OD and C2D5OH isotopomers and support the existence of both monomers and dimers. A quasi-harmonic approximation (QHA), applied to the VDOS obtained from the AIMD simulations, provides estimates of adsorption free energy within ~10 kJ/mol of the experimentally determined quantities, whereas the traditional approach, employing harmonic frequencies from a single ground state minimum, strongly overestimates the adsorption free energy by at least ~30 kJ/mol. This discrepancy is traced back to the inability of the harmonic approximation to represent the contributions to the vibrational motions of the ethanol molecule upon confinement in the zeolite. KA, MFR, GBM were supported by the Long Term Structural Methusalem Funding by the Flemish Government – grant number BOF09/01M00409. MSL, VAG, RR and JAL were supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. PNNL is a multiprogram national laboratory operated for DOE by Battelle. Computational resources were provided at W. R. Wiley Environmental

  15. Vibrational spectroscopy on intermolecular interactions in solutions and at interfaces

    NARCIS (Netherlands)

    Nissink, Johannes Wilhelmus Maria

    2001-01-01

    In recent years, considerable progress has been made in the areas of molecular recognition and surface analysis. These fields meet in the field of sensor development, where the interaction between molecules and a suitably modified surface is of utmost importance. Vibrational spectroscopy is quite us

  16. Breathers in strongly anharmonic lattices.

    Science.gov (United States)

    Rosenau, Philip; Pikovsky, Arkady

    2014-02-01

    We present and study a family of finite amplitude breathers on a genuinely anharmonic Klein-Gordon lattice embedded in a nonlinear site potential. The direct numerical simulations are supported by a quasilinear Schrodinger equation (QLS) derived by averaging out the fast oscillations assuming small, albeit finite, amplitude vibrations. The genuinely anharmonic interlattice forces induce breathers which are strongly localized with tails evanescing at a doubly exponential rate and are either close to a continuum, with discrete effects being suppressed, or close to an anticontinuum state, with discrete effects being enhanced. Whereas the D-QLS breathers appear to be always stable, in general there is a stability threshold which improves with spareness of the lattice.

  17. Vibrational dynamics and solvatochromism of the label SCN in various solvents and hemoglobin by time dependent IR and 2D-IR spectroscopy.

    Science.gov (United States)

    van Wilderen, Luuk J G W; Kern-Michler, Daniela; Müller-Werkmeister, Henrike M; Bredenbeck, Jens

    2014-09-28

    We investigated the characteristics of the thiocyanate (SCN) functional group as a probe of local structural dynamics for 2D-IR spectroscopy of proteins, exploiting the dependence of vibrational frequency on the environment of the label. Steady-state and time-resolved infrared spectroscopy are performed on the model compound methylthiocyanate (MeSCN) in solvents of different polarity, and compared to data obtained on SCN as a local probe introduced as cyanylated cysteine in the protein bovine hemoglobin. The vibrational lifetime of the protein label is determined to be 37 ps, and its anharmonicity is observed to be lower than that of the model compound (which itself exhibits solvent-independent anharmonicity). The vibrational lifetime of MeSCN generally correlates with the solvent polarity, i.e. longer lifetimes in less polar solvents, with the longest lifetime being 158 ps. However, the capacity of the solvent to form hydrogen bonds complicates this simplified picture. The long lifetime of the SCN vibration is in contrast to commonly used azide labels or isotopically-labeled amide I and better suited to monitor structural rearrangements by 2D-IR spectroscopy. We present time-dependent 2D-IR data on the labeled protein which reveal an initially inhomogeneous structure around the CN oscillator. The distribution becomes homogeneous after 5 picoseconds so that spectral diffusion has effectively erased the 'memory' of the CN stretching frequency. Therefore, the 2D-IR data of the label incorporated in hemoglobin demonstrate how SCN can be utilized to sense rearrangements in the local structure on a picosecond timescale.

  18. Elucidating low-frequency vibrational dynamics in calcite and water with time-resolved third-harmonic generation spectroscopy.

    Science.gov (United States)

    Wang, Liang; Liu, Weimin; Fang, Chong

    2015-07-14

    Low-frequency vibrations are foundational for material properties including thermal conductivity and chemical reactivity. To resolve the intrinsic molecular conformational dynamics in condensed phase, we implement time-resolved third-harmonic generation (TRTHG) spectroscopy to unravel collective skeletal motions in calcite, water, and aqueous salt solution in situ. The lifetime of three Raman-active modes in polycrystalline calcite at 155, 282 and 703 cm(-1) is found to be ca. 1.6 ps, 1.3 ps and 250 fs, respectively. The lifetime difference is due to crystallographic defects and anharmonic effects. By incorporating a home-built wire-guided liquid jet, we apply TRTHG to investigate pure water and ZnCl2 aqueous solution, revealing ultrafast dynamics of water intermolecular stretching and librational bands below 500 cm(-1) and a characteristic 280 cm(-1) vibrational mode in the ZnCl4(H2O)2(2-) complex. TRTHG proves to be a compact and versatile technique that directly uses the 800 nm fundamental laser pulse output to capture ultrafast low-frequency vibrational motion snapshots in condensed-phase materials including the omnipresent water, which provides the important time dimension to spectral characterization of molecular structure-function relationships.

  19. Probing electronic lifetimes and phonon anharmonicities in high-quality chemical vapor deposited graphene by magneto-Raman spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Neumann, Christoph, E-mail: cneumann@physik.rwth-aachen.de; Stampfer, Christoph [JARA-FIT and 2nd Institute of Physics, RWTH Aachen University, 52074 Aachen (Germany); Peter Grünberg Institute (PGI-9), Forschungszentrum Jülich, 52425 Jülich (Germany); Halpaap, Donatus; Banszerus, Luca; Schmitz, Michael; Beschoten, Bernd [JARA-FIT and 2nd Institute of Physics, RWTH Aachen University, 52074 Aachen (Germany); Reichardt, Sven [JARA-FIT and 2nd Institute of Physics, RWTH Aachen University, 52074 Aachen (Germany); Physics and Materials Science Research Unit, Université du Luxembourg, 1511 Luxembourg (Luxembourg); Watanabe, Kenji; Taniguchi, Takashi [National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044 (Japan)

    2015-12-07

    We present a magneto-Raman study on high-quality single-layer graphene grown by chemical vapor deposition (CVD) that is fully encapsulated in hexagonal boron nitride by a dry transfer technique. By analyzing the Raman D, G, and 2D peaks, we find that the structural quality of the samples is comparable with state-of-the-art exfoliated graphene flakes. From B-field dependent Raman measurements, we extract the broadening and associated lifetime of the G peak due to anharmonic effects. Furthermore, we determine the decay width and lifetime of Landau level (LL) transitions from magneto-phonon resonances as a function of laser power. At low laser power, we find a minimal decay width of 140 cm{sup −1} highlighting the high electronic quality of the CVD-grown graphene. At higher laser power, we observe an increase of the LL decay width leading to a saturation, with the corresponding lifetime saturating at a minimal value of 18 fs.

  20. Vibrational spectroscopy at high external pressures the diamond anvil cell

    CERN Document Server

    Ferraro, John R

    1984-01-01

    Vibrational Spectroscopy at High External Pressures: The Diamond Anvil Cell presents the effects of high pressure on the vibrational properties of materials as accomplished in a diamond anvil cell (DAC). The DAC serves the dual purpose of generating the pressures and being transparent to infrared radiation, allowing the observation of changes caused by pressure. The optical probes highlighted will deal principally with infrared and Raman scattering, although some observations in the visible region will also be presented. The book begins with a discussion of the effects of pressure and pres

  1. Structural characterization of chiral molecules using vibrational circular dichroism spectroscopy

    DEFF Research Database (Denmark)

    Lassen, Peter Rygaard

    2006-01-01

    compounds of pharmaceutical interest. Others are transition metal complexes relevant for the search for parity-violation effects in vibrational spectroscopy (rhenium complexes), for asymmetric catalysis (Schiff-base complexes), or as model systems for metal centres in biology (Schiff-bases and heme....... Currently, only part of the enhancement can be reproduced theoretically, as demonstrated for the Schiff-bases. Their conformers and absolute configurations were also identified. As for proteins, the interpretation of their spectra is different, because the immense number of overlapping vibrational modes...... chiral molecules. This project is about application of one such technique, circular dichroism (CD) spectroscopy, which measures the difference in absorption of left- and right circularly polarized light - hence the name circular dichroism. This study has focused on the infrared (IR) range because...

  2. Vibrational characterization of pheomelanin and trichochrome F by Raman spectroscopy

    Science.gov (United States)

    Galván, Ismael; Jorge, Alberto; Solano, Francisco; Wakamatsu, Kazumasa

    2013-06-01

    We characterize for the first time the vibrational state of natural pheomelanin using Raman spectroscopy and model pigment synthesized from 5-S-cysteinyldopa. The shape of the Raman spectrum was very different from that of eumelanin. Four Raman bands were visible in the 500-2000 cm-1 wavenumber region about 500, 1150, 1490 and 2000 cm-1, which we assigned to the out-of-plane deformation and the stretching vibration of the phenyl rings, to the stretching vibration of C-N bonds or the stretching and wagging vibration of CH2, and to overtone or combination bands. Interestingly, we also show that the Raman spectrum of synthetic trichochrome F, a pigment that may be produced along with pheomelanin during pheomelanogenesis, is different from that of pheomelanin and similar to the spectrum of eumelanin. We could detect Raman signal of both eumelanin and pheomelanin in feathers and hairs where both pigments simultaneously occur without the need of isolating the pigment. This indicates that Raman spectroscopy represents a non-invasive method to detect pheomelanin and distinguish it from other pigments. This may be especially relevant to detect pheomelanin in animal skin including humans, where it has been associated with animal appearance and classification, human phototypes, prevention of skin diseases and cancer risk.

  3. Vibrational spectroscopy of microhydrated conjugate base anions.

    Science.gov (United States)

    Asmis, Knut R; Neumark, Daniel M

    2012-01-17

    Conjugate-base anions are ubiquitous in aqueous solution. Understanding the hydration of these anions at the molecular level represents a long-standing goal in chemistry. A molecular-level perspective on ion hydration is also important for understanding the surface speciation and reactivity of aerosols, which are a central component of atmospheric and oceanic chemical cycles. In this Account, as a means of studying conjugate-base anions in water, we describe infrared multiple-photon dissociation spectroscopy on clusters in which the sulfate, nitrate, bicarbonate, and suberate anions are hydrated by a known number of water molecules. This spectral technique, used over the range of 550-1800 cm(-1), serves as a structural probe of these clusters. The experiments follow how the solvent network around the conjugate-base anion evolves, one water molecule at a time. We make structural assignments by comparing the experimental infrared spectra to those obtained from electronic structure calculations. Our results show how changes in anion structure, symmetry, and charge state have a profound effect on the structure of the solvent network. Conversely, they indicate how hydration can markedly affect the structure of the anion core in a microhydrated cluster. Some key results include the following. The first few water molecules bind to the anion terminal oxo groups in a bridging fashion, forming two anion-water hydrogen bonds. Each oxo group can form up to three hydrogen bonds; one structural result, for example, is the highly symmetric, fully coordinated SO(4)(2-)(H(2)O)(6) cluster, which only contains bridging water molecules. Adding more water molecules results in the formation of a solvent network comprising water-water hydrogen bonding in addition to hydrogen bonding to the anion. For the nitrate, bicarbonate, and suberate anions, fewer bridging sites are available, namely, three, two, and one (per carboxylate group), respectively. As a result, an earlier onset of water

  4. Nanomechanical Infrared Spectroscopy with Vibrating Filters for Pharmaceutical Analysis

    DEFF Research Database (Denmark)

    Kurek, Maksymilian; Carnoy, Matthias; Larsen, Peter Emil

    2017-01-01

    Standard infrared spectroscopy techniques are well-developed and widely used. However, they typically require milligrams of sample and can involve time-consuming sample preparation. A promising alternative is represented by nanomechanical infrared spectroscopy (NAM-IR) based on the photothermal...... response of a nanomechanical resonator, which enables the chemical analysis of picograms of analyte directly from a liquid solution in only a few minutes. Herein, we present NAM-IR using perforated membranes (filters). The method was tested with the pharmaceutical compound indomethacin to successfully...... perform a chemical and morphological analysis on roughly 100 pg of sample. With an absolute estimated sensitivity of 109±15 fg, the presented method is suitable for ultrasensitive vibrational spectroscopy....

  5. Enhanced Vibrational Spectroscopies as Tools for Small Molecule Biosensing

    Directory of Open Access Journals (Sweden)

    Souhir Boujday

    2015-08-01

    Full Text Available In this short summary we summarize some of the latest developments in vibrational spectroscopic tools applied for the sensing of (small molecules and biomolecules in a label-free mode of operation. We first introduce various concepts for the enhancement of InfraRed spectroscopic techniques, including the principles of Attenuated Total Reflection InfraRed (ATR-IR, (phase-modulated InfraRed Reflection Absorption Spectroscopy (IRRAS/PM-IRRAS, and Surface Enhanced Infrared Reflection Absorption Spectroscopy (SEIRAS. Particular attention is put on the use of novel nanostructured substrates that allow for the excitation of propagating and localized surface plasmon modes aimed at operating additional enhancement mechanisms. This is then be complemented by the description of the latest development in Surface- and Tip-Enhanced Raman Spectroscopies, again with an emphasis on the detection of small molecules or bioanalytes.

  6. Transient grating spectroscopy of SF6 molecular vibrations

    CERN Document Server

    Ferré, Amélie; Burgy, Frédéric; Dagan, Michal; Descamps, Dominique; Dudovich, Nirit; Petit, Stéphane; Soifer, Hadas; Blanchet, Valérie; Mairesse, Yann

    2014-01-01

    Strong field transient grating spectroscopy has shown to be a very versatile tool in time-resolved molecular spectroscopy. Here we use this technique to investigate the high-order harmonic generation from SF6 molecules vibrationally excited by impulsive stimulated Raman scattering. Transient grating spectroscopy enables us to reveal clear modulations of the harmonic emission. This heterodyne detection shows that the harmonic emission generated between 14 to 26 eV is mainly sensitive to two among the three active Raman modes in SF6, i.e. the strongest and fully symmetric nu 1-A1g mode (774 cm-1, 43 fs) and the slowest mode nu5-T2g (524 cm-1, 63 fs). A time-frequency analysis of the harmonic emission reveals additional dynamics: the strength and central frequency of the nu 1 mode oscillate with a frequency of 52 cm-1 (640 fs). This could be a signature of the vibration of dimers in the generating medium. Harmonic 11 shows a remarkable behavior, oscillating in opposite phase, both on the fast (774 cm-1) and slow...

  7. Direct anharmonic correction method by molecular dynamics

    Science.gov (United States)

    Liu, Zhong-Li; Li, Rui; Zhang, Xiu-Lu; Qu, Nuo; Cai, Ling-Cang

    2017-04-01

    The quick calculation of accurate anharmonic effects of lattice vibrations is crucial to the calculations of thermodynamic properties, the construction of the multi-phase diagram and equation of states of materials, and the theoretical designs of new materials. In this paper, we proposed a direct free energy interpolation (DFEI) method based on the temperature dependent phonon density of states (TD-PDOS) reduced from molecular dynamics simulations. Using the DFEI method, after anharmonic free energy corrections we reproduced the thermal expansion coefficients, the specific heat, the thermal pressure, the isothermal bulk modulus, and the Hugoniot P- V- T relationships of Cu easily and accurately. The extensive tests on other materials including metal, alloy, semiconductor and insulator also manifest that the DFEI method can easily uncover the rest anharmonicity that the quasi-harmonic approximation (QHA) omits. It is thus evidenced that the DFEI method is indeed a very efficient method used to conduct anharmonic effect corrections beyond QHA. More importantly it is much more straightforward and easier compared to previous anharmonic methods.

  8. Influence of water on anharmonicity, stability, and vibrational energy distribution of hydrogen-bonded adducts in atmospheric reactions: case study of the OH + isoprene reaction intermediate using ab initio molecular dynamics.

    Science.gov (United States)

    Dietrick, Scott M; Pacheco, Alexander B; Phatak, Prasad; Stevens, Philip S; Iyengar, Srinivasan S

    2012-01-12

    The effect of water on the stability and vibrational states of a hydroxy-isoprene adduct is probed through the introduction of 1-15 water molecules. It is found that when a static nuclear harmonic approximation is invoked there is a substantial red-shift of the alcohol O-H stretch (of the order of 800 cm(-1)) as a result of introduction of water. When potential energy surface sampling and associated anharmonicities are introduced through finite temperature ab initio dynamics, this hydroxy-isoprene OH stretch strongly couples with all the water vibrational modes as well as the hydroxy-isoprene OH bend modes. A new computational technique is introduced to probe the coupling between these modes. The method involves a two-dimensional, time-frequency analysis of the finite temperature vibrational properties. Such an analysis not only provides information about the modes that are coupled as a result of finite-temperature analysis, but also the temporal evolution of such coupling.

  9. [Structure analysis of disease-related proteins using vibrational spectroscopy].

    Science.gov (United States)

    Hiramatsu, Hirotsugu

    2014-01-01

    Analyses of the structure and properties of identified pathogenic proteins are important for elucidating the molecular basis of diseases and in drug discovery research. Vibrational spectroscopy has advantages over other techniques in terms of sensitivity of detection of structural changes. Spectral analysis, however, is complicated because the spectrum involves a substantial amount of information. This article includes examples of structural analysis of disease-related proteins using vibrational spectroscopy in combination with additional techniques that facilitate data acquisition and analysis. Residue-specific conformation analysis of an amyloid fibril was conducted using IR absorption spectroscopy in combination with (13)C-isotope labeling, linear dichroism measurement, and analysis of amide I band features. We reveal a pH-dependent property of the interacting segment of an amyloidogenic protein, β2-microglobulin, which causes dialysis-related amyloidosis. We also reveal the molecular mechanisms underlying pH-dependent sugar-binding activity of human galectin-1, which is involved in cell adhesion, using spectroscopic techniques including UV resonance Raman spectroscopy. The decreased activity at acidic pH was attributed to a conformational change in the sugar-binding pocket caused by protonation of His52 (pKa 6.3) and the cation-π interaction between Trp68 and the protonated His44 (pKa 5.7). In addition, we show that the peak positions of the Raman bands of the C4=C5 stretching mode at approximately 1600 cm(-1) and the Nπ-C2-Nτ bending mode at approximately 1405 cm(-1) serve as markers of the His side-chain structure. The Raman signal was enhanced 12 fold using a vertical flow apparatus.

  10. Structural dynamics in complex liquids studied with multidimensional vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tokmakoff, Andrei [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

    2013-08-31

    The development of new sustainable energy sources is linked to our understanding of the molecular properties of water and aqueous solutions. Energy conversion, storage, and transduction processes, particularly those that occur in biology, fuel cells, and batteries, make use of water for the purpose of moving energy in the form of charges and mediating the redox chemistry that allows this energy to be stored as and released from chemical bonds. To build our fundamental knowledge in this area, this project supports work in the Tokmakoff group to investigate the molecular dynamics of water’s hydrogen bond network, and how these dynamics influence its solutes and the mechanism of proton transport in water. To reach the goals of this grant, we developed experiments to observe molecular dynamics in water as directly as possible, using ultrafast multidimensional vibrational spectroscopy. We excite and probe broad vibrational resonances of water, molecular solutes, and protons in water. By correlating how molecules evolve from an initial excitation frequency to a final frequency, we can describe the underlying molecular dynamics. Theoretical modeling of the data with the help of computational spectroscopy coupled with molecular dynamics simulations provided the atomistic insight in these studies.

  11. Vibrational and photoionization spectroscopy of biomolecules: aliphatic amino acid structures.

    Science.gov (United States)

    Hu, Yongjun; Bernstein, Elliot R

    2008-04-28

    The aliphatic amino acids glycine, valine, leucine, and isoleucine are thermally placed into the gas phase and expanded into a vacuum system for access by time of flight mass spectroscopy and infrared (IR) spectroscopy in the energy range of 2500-4000 cm(-1) (CH, NH, OH, and stretching vibrations). The isolated neutral amino acids are ionized by a single photon of 10.5 eV energy (118 nm), which exceeds by less than 2 eV their reported ionization thresholds. As has been reported for many hydrogen bonded acid-base systems (e.g., water, ammonia, alcohol, acid clusters, and acid molecules), the amino acids undergo a structural rearrangement in the ion state (e.g., in simplest form, a proton transfer) that imparts sufficient excess vibrational energy to the ion to completely fragment it. No parent ions are observed. If the neutral ground state amino acids are exposed to IR radiation prior to ionization, an IR spectrum of the individual isomers for each amino acid can be determined by observation of the ion intensity of the different fragment mass channels. Both the IR spectrum and fragmentation patterns for individual isomers can be qualitatively identified and related to a particular isomer in each instance. Thus, each fragment ion detected presents an IR spectrum of its particular parent amino acid isomer. In some instances, the absorption of IR radiation by the neutral amino acid parent isomer increases a particular fragmentation mass channel intensity, while other fragmentation mass channel intensities decrease. This phenomenon can be rationalized by considering that with added energy in the molecule, the fragmentation channel populations can be modulated by the added vibrational energy in the rearranged ions. This observation also suggests that the IR absorption does not induce isomerization in the ground electronic state of these amino acids. These data are consistent with theoretical predictions for isolated amino acid secondary structures and can be related to

  12. Highly Resolved Sub-Terahertz Vibrational Spectroscopy of Biological Macromolecules and Bacteria Cells

    Science.gov (United States)

    2016-07-01

    HIGHLY RESOLVED SUB-TERAHERTZ VIBRATIONAL SPECTROSCOPY OF BIOLOGICAL MACROMOLECULES AND BACTERIA CELLS ECBC...SUBTITLE Highly Resolved Sub-Terahertz Vibrational Spectroscopy of Biological Macromolecules and Bacteria Cells 5a. CONTRACT NUMBER W911SR-14-P...22 4.3 Bacteria THz Study

  13. Vibrational and Rotational Spectroscopy of CD_2H^+

    Science.gov (United States)

    Asvany, Oskar; Jusko, Pavol; Brünken, Sandra; Schlemmer, Stephan

    2016-06-01

    The lowest rotational levels (J=0-5) of the CD_2H^+ ground state have been probed by high-resolution rovibrational and pure rotational spectroscopy in a cryogenic 22-pole ion trap. For this, the ν_1 rovibrational band has been revisited, detecting 107 transitions, among which 35 are new. The use of a frequency comb system allowed to measure the rovibrational transitions with high precision and accuracy, typically better than 1 MHz. The high precision has been confirmed by comparing combination differences in the ground and vibrationally excited state. For the ground state, this allowed for equally precise predictions of pure rotational transitions, 24 of which have been measured directly by a novel IR - mm-wave double resonance method. M.-F. Jagod et al, J. Molec. Spectrosc. 153, 666, 1992 S. Gartner et al, J. Phys. Chem. A 117, 9975, 2013

  14. Cross-Propagation Sum-Frequency Generation Vibrational Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Li; Chen, Shunli; Gan, Wei; Wang, Hongfei

    2016-02-01

    Here we report the theory formulation and the experiment realization of sum-frequency generation vibrational spectroscopy (SFG-VS) in the cross-propagation (XP) geometry or configuration. In the XP geometry, the visible and the infrared (IR) beams in the SFG experiment are delivered to the same location on the surface from visible and IR incident planes perpendicular to each other, avoiding the requirement to have windows or optics to be transparent to both the visible and IR frequencies. Therefore, the XP geometry is applicable to study surfaces in the enclosed vacuum or high pressure chambers with far infrared (FIR) frequencies that can directly access the metal oxide and other lower frequency surface modes, with much broader selection of visible and IR transparent window materials.

  15. Liquid Space Lubricants Examined by Vibrational Micro-Spectroscopy

    Science.gov (United States)

    Street, Kenneth W., Jr.

    2008-01-01

    Considerable effort has been expended to develop liquid lubricants for satellites and space exploration vehicles. These lubricants must often perform under a range of harsh conditions such as vacuum, radiation, and temperature extremes while in orbit or in transit and in extremely dusty environments at destinations such as the Moon and Mars. Historically, oil development was guided by terrestrial application, which did not provide adequate space lubricants. Novel fluids such as the perfluorinated polyethers provided some relief but are far from ideal. With each new fluid proposed to solve one problem, other problems have arisen. Much of the work performed at the National Aeronautics and Space Administration (NASA) Glenn Research Center (GRC) in elucidating the mechanisms by which chemical degradation of space oils occur has been done by vibrational micro-spectroscopic techniques such as infrared and Raman, which this review details. Presented are fundamental lubrication studies as well as actual case studies in which vibrational spectroscopy has led to millions of dollars in savings and potentially prevented loss of mission.

  16. Millimetre-wave spectroscopy of HC{sub 4}Cl in ground and excited vibrational states

    Energy Technology Data Exchange (ETDEWEB)

    Bizzocchi, Luca [Dipartimento di Chimica ' G. Ciamician' , Universita di Bologna, via F. Selmi 2, 40126 Bologna (Italy)], E-mail: luca.bizzocchi@unibo.it; Degli Esposti, Claudio [Dipartimento di Chimica ' G. Ciamician' , Universita di Bologna, via F. Selmi 2, 40126 Bologna (Italy)], E-mail: claudio.degliesposti@unibo.it

    2008-05-04

    The semi-stable HC{sub 4}Cl molecule has been detected in the pyrolysis products of propyne and carbon tetrachloride mixtures. The rotational spectrum of the most abundant isotopologue HC{sub 4}{sup 35}Cl has been investigated in the millimetre- and sub-millimetre-wave regions for the ground and 12 vibrationally excited states which approximately lie below 630 cm{sup -1}, namely ({nu}{sub 5}{nu}{sub 6}{nu}{sub 7}{nu}{sub 8}{nu}{sub 9})=(10000), (01000), (00100), (00010), (00001), (00020), (00002), (00003), (00004), (00101), (00011) and (00012). Transitions up to J=151 <- 150 were measured for the ground state, allowing for a precise evaluation of the quartic and sextic centrifugal distortion constants D and H. The l-type resonances between the different sublevels of the bending states and the anharmonic resonance which couples the states {nu}{sub 5}=1, {nu}{sub 8}=2 and {nu}{sub 9}=4 have been taken into account in the analysis of the spectra, which yielded precise determinations of the x{sub L(99)}, x{sub L(88)}, x{sub L(89)} and x{sub L(79)} anharmonicity constants and of the {phi}{sub 588} normal coordinate cubic force constant. Extensive measurements have also been performed for the HC{sub 4}{sup 37}Cl isotopologue.

  17. On the Use of Quantum Algebras in Rotation-Vibration Spectroscopy

    OpenAIRE

    1995-01-01

    A two-parameter deformation of the Lie algebra u$_2$ is used, in conjunction with the rotor system and the oscillator system, to generate a model for rotation-vibration spectroscopy of molecules and nuclei.

  18. Low temperature vibrational spectroscopy. III. Structural aspects and detection of phase transitions in crystalline alkali metal and tetramethylammonium hexabromotellurates and platinates

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    1979-01-01

    that the methyl groups are not pseudo freely rotating. The anharmonicity of the vibrations in tetramethylammonium hexabromotellurate seems to increase abnormally at lower temperatures, possibly due to enhanced methyl–bromine interaction. The Journal of Chemical Physics is copyrighted by The American Institute...

  19. Vibrational dynamics of aqueous hydroxide solutions probed using broadband 2DIR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Mandal, Aritra [Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637 (United States); Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Tokmakoff, Andrei, E-mail: tokmakoff@uchicago.edu [Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637 (United States)

    2015-11-21

    We employed ultrafast transient absorption and broadband 2DIR spectroscopy to study the vibrational dynamics of aqueous hydroxide solutions by exciting the O–H stretch vibrations of the strongly hydrogen-bonded hydroxide solvation shell water and probing the continuum absorption of the solvated ion between 1500 and 3800 cm{sup −1}. We observe rapid vibrational relaxation processes on 150–250 fs time scales across the entire probed spectral region as well as slower vibrational dynamics on 1–2 ps time scales. Furthermore, the O–H stretch excitation loses its frequency memory in 180 fs, and vibrational energy exchange between bulk-like water vibrations and hydroxide-associated water vibrations occurs in ∼200 fs. The fast dynamics in this system originate in strong nonlinear coupling between intra- and intermolecular vibrations and are explained in terms of non-adiabatic vibrational relaxation. These measurements indicate that the vibrational dynamics of the aqueous hydroxide complex are faster than the time scales reported for long-range transport of protons in aqueous hydroxide solutions.

  20. Vibrational spectroscopy of –/ – stretching vibrations of copper tetramesityl porphyrin: An algebraic approach

    Indian Academy of Sciences (India)

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

    2010-01-01

    Using Lie algebraic techniques and simpler expressions of the matrix elements of Majorana and Casimir operators given by us, we obtain an effective Hamiltonian operator which conveniently describes stretching vibrations of biomolecules. For a copper tetramesityl porphyrin molecule, the higher excited vibrational levels are calculated by applying the (2) algebraic approach.

  1. "Plug and play" full-dimensional ab initio potential energy and dipole moment surfaces and anharmonic vibrational analysis for CH4-H2O.

    Science.gov (United States)

    Qu, Chen; Conte, Riccardo; Houston, Paul L; Bowman, Joel M

    2015-03-28

    The potential energy surface of the methane-water dimer is represented as the sum of a new intrinsic two-body potential energy surface and pre-existing intramolecular potentials for the monomers. Different fits of the CH4-H2O intrinsic two-body energy are reported. All these fits are based on 30 467 ab initio interaction energies computed at CCSD(T)-F12b/haTZ (aug-cc-pVTZ for C and O, cc-pVTZ for H) level of theory. The benchmark fit is a full-dimensional, permutationally-invariant analytical representation with root-mean-square (rms) fitting error of 3.5 cm(-1). Two other computationally more efficient two-body potentials are also reported, albeit with larger rms fitting errors. Of these a compact permutationally invariant fit is shown to be the best one in combining precision and speed of evaluation. An intrinsic two-body dipole moment surface is also obtained, based on MP2/haTZ expectation values, with an rms fitting error of 0.002 au. As with the potential, this dipole moment surface is combined with existing monomer ones to obtain the full surface. The vibrational ground state of the dimer and dissociation energy, D0, are determined by diffusion Monte Carlo calculations, and MULTIMODE calculations are performed for the IR spectrum of the intramolecular modes. The relative accuracy of the different intrinsic two-body potentials is analyzed by comparing the energetics and the harmonic frequencies of the global minimum well, and the maximum impact parameter employed in a sample methane-water scattering calculation.

  2. 2012 VIBRATIONAL SPECTROSCOPY GORDON RESEARCH CONFERENCE, AUGUST 5-10, 2012

    Energy Technology Data Exchange (ETDEWEB)

    Geiger, Franz

    2012-08-10

    The Vibrational Spectroscopy conference brings together experimentalists and theoreticians working at the frontiers of modern vibrational spectroscopy, with a special emphasis on spectroscopies that probe the structure and dynamics of molecules in gases, liquids, and at interfaces. The conference explores the wide range of state-of-the-art techniques based on vibrational motion. These techniques span the fields of time-domain, high-resolution frequency-domain, spatially-resolved, nonlinear, and multidimensional spectroscopies. The conference highlights both the application of these techniques in chemistry, materials, biology, the environment, and medicine as well as the development of theoretical models that enable one to connect spectroscopic signatures to underlying molecular motions including chemical reaction dynamics. The conference goal is to advance the field of vibrational spectroscopy by bringing together a collection of researchers who share common interests and who will gain from discussing work at the forefront of several connected areas. The intent is to emphasize the insights and understanding that studies of vibrations provide about a variety of molecular systems ranging from small polyatomic molecules to large biomolecules, nanomaterials, and environmental systems.

  3. Thermoelectricity in molecular junctions with harmonic and anharmonic modes

    Directory of Open Access Journals (Sweden)

    Bijay Kumar Agarwalla

    2015-11-01

    Full Text Available We study charge and energy transfer in two-site molecular electronic junctions in which electron transport is assisted by a vibrational mode. To understand the role of mode harmonicity/anharmonicity in transport behavior, we consider two limiting situations: (i the mode is assumed harmonic, (ii we truncate the mode spectrum to include only two levels, to represent an anharmonic mode. Based on the cumulant generating functions of the models, we analyze the linear-response and nonlinear performance of these junctions and demonstrate that while the electrical and thermal conductances are sensitive to whether the mode is harmonic/anharmonic, the Seebeck coefficient, the thermoelectric figure-of-merit, and the thermoelectric efficiency beyond linear response, conceal this information.

  4. 非简谐振动对石墨烯杨氏模量与声子频率的影响∗%Influence of the anharmonic vibration on the Young mo dulus and the phonon frequency of the graphene

    Institute of Scientific and Technical Information of China (English)

    程正富; 郑瑞伦

    2016-01-01

    perpendicular to the bond-length direction and the longitudinal vibrations along the bond-length direction, in which the longitudinal vibrations are dominant. The nonharmonic effect of the longitudinal vibration is much larger than that of the transverse vibration. The first and the second non-harmonic coeffcient of the transverse vibration are both much less than those of the longitudinal vibration, where ε0/ε′0 ≈8.477 and ε2/ε′2 ≈156. The above five physical quantities are constant at different temperatures if the first and second nonhamonic effects are omitted, which does not conform to the experimental results. After the first and second nonhamonic effects are considered, they all increase with temperature and results are in good agreement with experimental data. The anharmonic effect increases with temperature.

  5. Microwave spectroscopy of furfural in vibrationally excited states

    Science.gov (United States)

    Motiyenko, R. A.; Alekseev, E. A.; Dyubko, S. F.

    2007-07-01

    The results of microwave spectrum investigation of the excited vibrational states of furfural in the frequency range between 49 and 149 GHz are reported. In total 15 excited vibrational states (9 for trans-furfural and 6 for cis-furfural) were assigned and analyzed. Six of the 15 investigated states were assigned for the first time. Accurate values of rigid rotor and quartic centrifugal distortion constants of asymmetric top Hamiltonian have been determined for 13 excited states. Also for some states several sextic and octic level constants were needed in order to fit the data within experimental accuracy. The vt = 3 and vs = 1, va = 1 states of trans-furfural were found to be strongly perturbed and only rotational transitions with low Ka values can be reliably identified in this study.

  6. Vibrational Spectroscopy of the CCl[subscript 4] v[subscript 1] Mode: Theoretical Prediction of Isotopic Effects

    Science.gov (United States)

    Gaynor, James D.; Wetterer, Anna M.; Cochran, Rea M.; Valente, Edward J.; Mayer, Steven G.

    2015-01-01

    Raman spectroscopy is a powerful experimental technique, yet it is often missing from the undergraduate physical chemistry laboratory curriculum. Tetrachloromethane (CCl[subscript 4]) is the ideal molecule for an introductory vibrational spectroscopy experiment and the symmetric stretch vibration contains fine structure due to isotopic variations…

  7. Anharmonic effects in neutron cross-section calculation for nuclei in mass range 48 [<=] A [<=] 58

    Energy Technology Data Exchange (ETDEWEB)

    Lubian, J.; Cabezas, R. (Center for Applied Studies to Nuclear Development, Havana (Cuba))

    1993-08-01

    In this paper, a deviation of the target nucleus wavefunction from the harmonic vibrator in the neutron scattering process by medium-mass nuclei at low energies is studied. Two forms of anharmonicities are used: anharmonicities due to the higher-order terms in the Hamiltonians and those due to the different deformation parameters, corresponding to transitions between nuclear states. For calculation of neutron cross sections, combined use of the coupled-channel method and the statistical Hauser-Feshbach-Moldauer theory is applied. It is shown that both kinds of anharmonicities introduced a correction (about 10% in some cases) to the neutron cross sections at low energies. (author).

  8. Vibrational and optical spectroscopies integrated with environmental transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Picher, Matthieu; Mazzucco, Stefano [Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899-6203 (United States); Institute for Research in Electronics and Applied Physics, University of Maryland, College Park, MD 20740 (United States); Blankenship, Steve [Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899-6203 (United States); Sharma, Renu, E-mail: renu.sharma@nist.gov [Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899-6203 (United States)

    2015-03-15

    Here, we present a measurement platform for collecting multiple types of spectroscopy data during high-resolution environmental transmission electron microscopy observations of dynamic processes. Such coupled measurements are made possible by a broadband, high-efficiency, free-space optical system. The critical element of the system is a parabolic mirror, inserted using an independent hollow rod and placed below the sample holder which can focus a light on the sample and/or collect the optical response. We demonstrate the versatility of this optical setup by using it to combine in situ atomic-scale electron microscopy observations with Raman spectroscopy. The Raman data is also used to measure the local temperature of the observed sample area. Other applications include, but are not limited to: cathodo- and photoluminescence spectroscopy, and use of the laser as a local, high-rate heating source. - Highlights: • Broadband, high-efficiency design adaptable to other electron microscopes. • Raman spectroscopy integrated with environmental transmission electron microscopy. • Raman spectra peak frequency shifts enable measurement of local sample temperature. • Multiple types of optical spectroscopy enabled, e.g. cathodoluminescence.

  9. Vibrational Spectroscopy of Intramolecular Hydrogen Bonds in the Infrared and Near-Infrared Regions

    DEFF Research Database (Denmark)

    Schrøder, Sidsel Dahl

    and 1,4-diaminobutane). Experimentally, the hydrogen bonds have been studied with vibrational spectroscopy in the infrared and near-infrared regions. The focus is primarily on spectra recorded in the near-infrared regions, which in these studies are dominated by O-H and N-H stretching overtones...

  10. Anisotropic crystal of the δ-BiB3O6 investigated by vibrational spectroscopy

    Science.gov (United States)

    Strikina, E. A.; Krylov, A. S.; Oreshonkov, A. S.; Vtyurin, A. N.; Maximova, A.

    2016-11-01

    The vibrational spectroscopy has been applied to investigate the structure the BiB3O6 (BIBO) crystal. Based on the experimental results, the total set of phonons mode of the polarized Raman spectra was proposed. To verify the obtained experimental data have been performed theoretical calculation in software package LADY.

  11. Raman-scattering probe of anharmonic effects in GaAs

    Science.gov (United States)

    Verma, Prabhat; Abbi, S. C.; Jain, K. P.

    1995-06-01

    A comparative study of anharmonic effects in various structural forms of GaAs, namely crystalline, disordered and ion-implanted, and pulse laser annealed (PLA), using temperature-dependent Raman scattering, is reported for various phonon modes over the temperature range 10-300 K. The disordered and PLA samples are found to have greater anharmonicity than crystalline GaAs. The localized vibrational mode in PLA GaAs shows shorter relaxation time than the LO-phonon mode.

  12. Double resonant absorption measurement of acetylene symmetric vibrational states probed with cavity ring down spectroscopy

    CERN Document Server

    Karhu, J; Vainio, M; Metsälä, M; Hoekstra, S; Halonen, L

    2016-01-01

    A novel mid-infrared/near-infrared double resonant absorption setup for studying infrared-inactive vibrational states is presented. A strong vibrational transition in the mid-infrared region is excited using an idler beam from a singly resonant continuous-wave optical parametric oscillator, to populate an intermediate vibrational state. High output power of the optical parametric oscillator and the strength of the mid-infrared transition result in efficient population transfer to the intermediate state, which allows measuring secondary transitions from this state with a high signal-to-noise ratio. A secondary, near-infrared transition from the intermediate state is probed using cavity ring down spectroscopy, which provides high sensitivity in this wavelength region. Due to the narrow linewidths of the excitation sources, the rovibrational lines of the secondary transition are measured with sub-Doppler resolution. The setup is used to access a previously unreported symmetric vibrational state of acetylene, $\

  13. Compression and pressure-induced amorphization of Co(OH)2 characterized by infrared vibrational spectroscopy

    Science.gov (United States)

    Nguyen, Jeffrey H.; Kruger, Michael B.; Jeanloz, Raymond

    1994-02-01

    The infrared-active (A2u) O-H vibration of Co(OH)2 decreases in frequency under hydrostatic compression to 51 GPa at 290 K. Similarly, the bond anharmonicity, determined from the ν1-->ν2 absorption-band difference, increases by more than a factor of 2 between 0 and 20 GPa. Both changes are attributed to an increase in the O-H bond length due to enhanced hydrogen bonding under pressure. The full width at half maximum (FWHM) of the fundamental absorption band increases abruptly by ~100 cm-1 at 11.2 (+/-0.3) GPa, and continues to increase at a rate of ~3.3 cm-1/GPa up to 36 GPa. Above 36 (+/-2) GPa and below the onset of amorphization, the FWHM changes at a slower rate, 0.8 (+/-0.1) cm-1/GPa. The abrupt change in FWHM is reversible on decompression, and is interpreted in terms of a pressure-induced crystal-to-glass transition exhibiting a small hysteresis compared to similar compounds. The rapid variation in FWHM above the transition pressure suggests that the amorphous structure is continuously modified between 11.3 and 36 GPa.

  14. Vibration spectroscopy of a sessile drop and its contact line.

    Science.gov (United States)

    Mettu, S; Chaudhury, M K

    2012-10-02

    Resonance frequencies of small sessile liquid drops (1-20 μL) were estimated from the power spectra of their height fluctuations after subjecting them to white noise vibration. Various resonance modes could be identified with this method as a function of the mass of the drop. Studies with water drops on such supports as polystyrene (θ ≈ 80°) and a superhydrophobic surface of microfibrillar silicone rubber (θ ≈ 162°) demonstrated that the resonant frequency decreases with the contact angle, θ. This trend is in remarkable agreement with the current models of the resonant vibration of sessile drops. A novel aspect of this study is the analysis of the modes of a slipping contact line that indicated that its higher frequency modes are more severely damped than its lower ones. Another case is with the glycerol-water solutions, where the resonance frequency decreases with the concentration of glycerol purely due to the capillary effects. The interface fluctuation, on the other hand, is strongly correlated with the kinematic viscosity of the liquid. Thus, these experiments provide a means to measure the surface tension and the viscosity of very small droplets.

  15. Prediction of Milk Quality Parameters Using Vibrational Spectroscopy and Chemometrics

    DEFF Research Database (Denmark)

    Eskildsen, Carl Emil Aae

    Vibrational spectroscopic techniques are widely used throughout all stages of food production. The analysis of raw materials, real-time process control, and end-product quality evaluation are all crucial steps in food production. In order to increase production throughput there is a need for speed...... fatty acids, protein fractions and coagulation properties from Fourier transform infrared measurements. This thesis shows how such predictions are trapped in a cage of covariance with major milk constituents like total fat and protein content. The prediction models for detailed milk composition...... are not based on causal relationships and this may seriously compromise calibration robustness. It is not recommended to implement indirect models for detailed milk composition in milk recording or breeding programs as such model are providing information on, for example, total protein rather than the specific...

  16. Nonlinear vibrational spectroscopy of surfactants at liquid interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Miranda, Paulo B. [Univ. of California, Berkeley, CA (United States)

    1998-12-14

    Surfactants are widely used to modify physical and chemical properties of interfaces. They play an important role in many technological problems. Surfactant monolayer are also of great scientific interest because they are two-dimensional systems that may exhibit a very rich phase transition behavior and can also be considered as a model system for biological interfaces. In this Thesis, we use a second-order nonlinear optical technique (Sum-Frequency Generation - SFG) to obtain vibrational spectra of surfactant monolayer at Iiquidhapor and solid/liquid interfaces. The technique has several advantages: it is intrinsically surface-specific, can be applied to buried interfaces, has submonolayer sensitivity and is remarkably sensitive to the confirmational order of surfactant monolayers.

  17. Vibrational spectroscopy characterization of magnetron sputtered silicon oxide and silicon oxynitride films

    Energy Technology Data Exchange (ETDEWEB)

    Godinho, V., E-mail: godinho@icmse.csic.es [Instituto de Ciencia de Materiales de Sevilla-CSIC/US, Avda. Americo Vespucio no 49, 41092 Seville (Spain); Universite Libre de Bruxelles, Avenue F.D. Roosevelt 50, B 1050 Bruxelles (Belgium); Denisov, V.N.; Mavrin, B.N.; Novikova, N.N.; Vinogradov, E.A.; Yakovlev, V.A. [Institute for Spectroscopy - Russian Academy of Sciences, 142190, Troitsk, Moscow reg. (Russian Federation); Fernandez-Ramos, C. [Instituto de Ciencia de Materiales de Sevilla-CSIC/US, Avda. Americo Vespucio no 49, 41092 Seville (Spain); Institute for Prospective and Technological Studies-JRC European Commission, C/Inca Garcilaso s/n, 41092 Seville (Spain); Jimenez de Haro, M.C.; Fernandez, A. [Instituto de Ciencia de Materiales de Sevilla-CSIC/US, Avda. Americo Vespucio no 49, 41092 Seville (Spain)

    2009-10-15

    Vibrational (infrared and Raman) spectroscopy has been used to characterize SiO{sub x}N{sub y} and SiO{sub x} films prepared by magnetron sputtering on steel and silicon substrates. Interference bands in the infrared reflectivity measurements provided the film thickness and the dielectric function of the films. Vibrational modes bands were obtained both from infrared and Raman spectra providing useful information on the bonding structure and the microstructure (formation of nano-voids in some coatings) for these amorphous (or nanocrystalline) coatings. X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM) analysis have also been carried out to determine the composition and texture of the films, and to correlate these data with the vibrational spectroscopy studies. The angular dependence of the reflectivity spectra provides the dispersion of vibrational and interference polaritons modes, what allows to separate these two types of bands especially in the frequency regions where overlaps/resonances occurred. Finally the attenuated total reflection Fourier transform infrared measurements have been also carried out demonstrating the feasibility and high sensitivity of the technique. Comparison of the spectra of the SiO{sub x}N{sub y} films prepared in various conditions demonstrates how films can be prepared from pure silicon oxide to silicon oxynitride with reduced oxygen content.

  18. The potential of vibrational spectroscopy in the early detection of cervical cancer: an exciting emerging field

    Science.gov (United States)

    O Faolain, Eoghan; Hunter, Mary B.; Byrne, Joe M.; Kelehan, Peter; Byrne, Hugh J.; Lyng, Fiona M.

    2005-06-01

    The application of vibrational spectroscopy to disease diagnosis is a relatively new, rapidly evolving scientific field. Techniques such as Raman and infrared spectroscopy have shown great promise in this regard over the past number of years. This study directly compared Raman spectroscopy and synchrotron infrared (SR-IR) spectroscopy on parallel cervical cancer samples. Both frozen and dewaxed formalin fixed paraffin preserved tissue sections were examined. Both tissue types produced good quality Raman and SR-IR spectra, although the lesser processed, frozen tissue sections displayed the most detailed spectra. Spectroscopy was shown capable of discriminating between different cell types in normal cervical tissue. Spectra recorded from invasive carcinoma showed a marked difference from those recorded from normal cervical epithelial cells. Spectral differences identified with the onset of carcinogenesis include increased nucleic acid contributions and decreased glycogen levels. These investigations pave the way for an enlarged study into this exciting new diagnostic field.

  19. Correlating the motion of electrons and nuclei with two-dimensional electronic-vibrational spectroscopy.

    Science.gov (United States)

    Oliver, Thomas A A; Lewis, Nicholas H C; Fleming, Graham R

    2014-07-15

    Multidimensional nonlinear spectroscopy, in the electronic and vibrational regimes, has reached maturity. To date, no experimental technique has combined the advantages of 2D electronic spectroscopy and 2D infrared spectroscopy, monitoring the evolution of the electronic and nuclear degrees of freedom simultaneously. The interplay and coupling between the electronic state and vibrational manifold is fundamental to understanding ensuing nonradiative pathways, especially those that involve conical intersections. We have developed a new experimental technique that is capable of correlating the electronic and vibrational degrees of freedom: 2D electronic-vibrational spectroscopy (2D-EV). We apply this new technique to the study of the 4-(di-cyanomethylene)-2-methyl-6-p-(dimethylamino)styryl-4H-pyran (DCM) laser dye in deuterated dimethyl sulfoxide and its excited state relaxation pathways. From 2D-EV spectra, we elucidate a ballistic mechanism on the excited state potential energy surface whereby molecules are almost instantaneously projected uphill in energy toward a transition state between locally excited and charge-transfer states, as evidenced by a rapid blue shift on the electronic axis of our 2D-EV spectra. The change in minimum energy structure in this excited state nonradiative crossing is evident as the central frequency of a specific vibrational mode changes on a many-picoseconds timescale. The underlying electronic dynamics, which occur on the hundreds of femtoseconds timescale, drive the far slower ensuing nuclear motions on the excited state potential surface, and serve as a excellent illustration for the unprecedented detail that 2D-EV will afford to photochemical reaction dynamics.

  20. Anharmonic Oscillator Lasers.

    Science.gov (United States)

    laser development ; time dependent solutions of the master kinetic equations; electric discharge stabilization in a supersonic CO/N2 flow; and computations of vibrational pumping rates by electrons including super-elastic collisions. A description of the progress made in each of these areas is

  1. Edge chlorination of hexa-peri-hexabenzocoronene investigated by density functional theory and vibrational spectroscopy.

    Science.gov (United States)

    Maghsoumi, Ali; Narita, Akimitsu; Dong, Renhao; Feng, Xinliang; Castiglioni, Chiara; Müllen, Klaus; Tommasini, Matteo

    2016-04-28

    We investigate the molecular structure and vibrational properties of perchlorinated hexa-peri-hexabenzocoronene (HBC-Cl) by density functional theory (DFT) calculations and IR and Raman spectroscopy, in comparison to the parent HBC. The theoretical and experimental IR and Raman spectra demonstrated very good agreement, elucidating a number of vibrational modes corresponding to the observed peaks. Compared with the parent HBC, the edge chlorination significantly alters the planarity of the molecule. Nevertheless, the results indicated that such structural distortion does not significantly impair the π-conjugation of such polycyclic aromatic hydrocarbons.

  2. Vibrationally resolved UV/Vis spectroscopy with time-dependent density functional based tight binding

    CERN Document Server

    Rüger, Robert; van Lenthe, Erik; Heine, Thomas; Visscher, Lucas

    2016-01-01

    We report a time-dependent density functional based tight-binding (TD-DFTB) scheme for the calculation of UV/Vis spectra, explicitly taking into account the excitation of nuclear vibrations via the harmonic approximation. The theory of vibrationally resolved UV/Vis spectroscopy is first summarized from the viewpoint of TD-DFTB. The method is benchmarked against time-dependent density functional theory (TD-DFT) calculations for strongly dipole allowed excitations in various aromatic and polar molecules. Using the recent 3ob:freq parameter set of Elstner's group, excellent agreement with TD-DFT calculations using local functionals was achieved.

  3. Vibrational spectroscopy and DFT calculations of flavonoid derriobtusone A

    Science.gov (United States)

    Marques, A. N. L.; Mendes Filho, J.; Freire, P. T. C.; Santos, H. S.; Albuquerque, M. R. J. R.; Bandeira, P. N.; Leite, R. V.; Braz-Filho, R.; Gusmão, G. O. M.; Nogueira, C. E. S.; Teixeira, A. M. R.

    2017-02-01

    Flavonoids are secondary metabolites of plants which perform various functions. One subclass of flavonoid is auronol that can present immunostimulating activity. In this work Fourier-Transform Infrared with Attenuated Total Reflectance (FTIR-ATR) and Fourier-Transform Raman (FT-Raman) spectra of an auronol, derriobtusone A (C18H12O4), were obtained at room temperature. Theoretical calculations using Density Functional Theory (DFT) were performed in order to assign the normal modes and to interpret the spectra of the derriobtusone A molecule. The FTIR-ATR and FT-Raman spectra of the crystal, were recorded at room temperature in the regions 600 cm-1 to 4000 cm-1 and 40 cm-1 to 4000 cm-1, respectively. The normal modes of vibrations were obtained using Density Functional Theory with B3LYP functional and 6-31G+ (d,p) basis set. The calculated frequencies are in good agreement with those obtained experimentally. Detailed assignments of the normal modes present in both the Fourier-Transform infrared and the Fourier-Transform Raman spectra of the crystal are given.

  4. Vibrational spectroscopy on protons and deuterons in proton conducting perovskites

    DEFF Research Database (Denmark)

    Glerup, M.; Poulsen, F.W.; Berg, R.W.

    2002-01-01

    A short review of IR-spectroscopy on protons in perovskite structure oxides is given. The nature of possible proton sites, libration and combination tones and degree of hydrogen bonding is emphasised. Three new spectroscopic experiments and/or interpretations are presented. An IR......-microscopy experiment was performed on the protonic conductor Ba-3(Ca1-chiNb2-chi)O9-delta, x = 0.18. The H/D concentration profile of a cross-section of the sample after partial isotopic exchange can be visualised; proton containing La0.9Ca0.1ErO3 was studied up to 200degreesC by Raman spectroscopy. At 200degrees.......8Sr0.2ScO3, La0.9Sr0.1Sc0.9Mg0.1O3 and SrCe0.95Y0.05O3 shows at least three types of proton positions. (C) 2002 Published by Elsevier Science B.V....

  5. Anharmonic densities of states: A general dynamics-based solution

    Science.gov (United States)

    Jellinek, Julius; Aleinikava, Darya

    2016-06-01

    Density of states is a fundamental physical characteristic that lies at the foundation of statistical mechanics and theoretical constructs that derive from them (e.g., kinetic rate theories, phase diagrams, and others). Even though most real physical systems are anharmonic, the vibrational density of states is customarily treated within the harmonic approximation, or with some partial, often limited, account for anharmonicity. The reason for this is that the problem of anharmonic densities of states stubbornly resisted a general and exact, yet convenient and straightforward in applications, solution. Here we formulate such a solution within both classical and quantum mechanics. It is based on actual dynamical behavior of systems as a function of energy and as observed, or monitored, on a chosen time scale, short or long. As a consequence, the resulting anharmonic densities of states are fully dynamically informed and, in general, time-dependent. As such, they lay the ground for formulation of new statistical mechanical frameworks that incorporate time and are ergodic, by construction, with respect to actual dynamical behavior of systems.

  6. Diffusion mobility of the hydrogen atom with allowance for the anharmonic attenuation of migrating atom state

    Science.gov (United States)

    Kashlev, Y. A.

    2017-04-01

    Evolution of vibration relaxation of hydrogen atoms in metals with the close-packed lattice at high and medium temperatures is investigated based on non-equilibrium statistical thermodynamics, in that number on using the retarded two-time Green function method. In accordance with main kinetic equation - the generalized Fokker- Plank- Kolmogorov equation, anharmonism of hydrogen atoms vibration in potential wells does not make any contribution to collision effects. It influences the relaxation processes at the expense of interference of fourth order anharmonism with single-phonon scattering on impurity hydrogen atoms. Therefore, the total relaxation time of vibration energy of system metal-hydrogen is written as a product of two factors: relaxation time of system in harmonic approximation and dimensionless anharmonic attenuation of quantum hydrogen state.

  7. Vibrational ladder-climbing in surface-enhanced, ultrafast infrared spectroscopy.

    Science.gov (United States)

    Kraack, Jan Philip; Hamm, Peter

    2016-06-28

    In a recent work (J. Phys. Chem. C 2016, 120, 3350-3359), we have introduced the concept of surface-enhanced, two-dimensional attenuated total reflectance (2D ATR IR) spectroscopy with modest enhancement factors (450), which allows for multi-quantum IR excitation of adsorbed molecules, a process known as "vibrational ladder-climbing", even for weakly absorbing (ε < 200 M(-1) cm(-1)) nitrile IR labels. We show that it is possible to deposit up to four quanta of vibrational energy in the respective functional group. Based on these results, optical near-fields of plasmonic nanostructures may pave the way for future investigations involving ultrafast dynamics of highly excited vibrational states or surface-sensitive coherent control experiments of ground-state reactions at solid-liquid interfaces.

  8. Communication: Vibrational and vibronic coherences in the two dimensional spectroscopy of coupled electron-nuclear motion

    Energy Technology Data Exchange (ETDEWEB)

    Albert, Julian; Falge, Mirjam; Hildenbrand, Heiko; Engel, Volker [Universität Würzburg, Institut für Physikalische und Theoretische Chemie, Emil-Fischer-Str. 42, Campus Nord, Am Hubland, 97074 Würzburg (Germany); Gomez, Sandra; Sola, Ignacio R. [Departamento de Quimica Fisica, Universidad Complutense, 28040 Madrid (Spain)

    2015-07-28

    We theoretically investigate the photon-echo spectroscopy of coupled electron-nuclear quantum dynamics. Two situations are treated. In the first case, the Born-Oppenheimer (adiabatic) approximation holds. It is then possible to interpret the two-dimensional (2D) spectra in terms of vibrational motion taking place in different electronic states. In particular, pure vibrational coherences which are related to oscillations in the time-dependent third-order polarization can be identified. This concept fails in the second case, where strong non-adiabatic coupling leads to the breakdown of the Born-Oppenheimer-approximation. Then, the 2D-spectra reveal a complicated vibronic structure and vibrational coherences cannot be disentangled from the electronic motion.

  9. Excitonic and vibrational coherence in artificial photosynthetic systems studied by negative-time ultrafast laser spectroscopy.

    Science.gov (United States)

    Han, Dongjia; Xue, Bing; Du, Juan; Kobayashi, Takayoshi; Miyatake, Tomohiro; Tamiaki, Hitoshi; Xing, Xin; Yuan, Wei; Li, Yanyan; Leng, Yuxin

    2016-09-21

    Quantum coherences between excitonic states are believed to have a substantial impact on excitation energy transfer in photosynthetic systems. Here, the excitonic and vibrational coherence relaxation dynamics of artificially synthetic chlorosomes are studied by a sub 7 fs negative-time-delay laser spectroscopy at room temperature. The results provide direct evidence for the quantum coherence of the excitonic dephasing time of 23 ± 1 fs at physiologically relevant temperatures, which is significant in the initial step of energy transfer in chlorosome or chlorosome-like photosynthetic systems. Meanwhile, coherent molecular vibrations in the excited state are also detected without the effect of wave-packet motion in the ground state, which shows that the excited state wave-packet motion contributes greatly to the vibrational modes of ∼150 and ∼1340 cm(-1) in artificial chlorosome systems.

  10. Vibrational Spectroscopy of Transient Dipolar Radicals via Autodetachment of Dipole-Bound States of Cold Anions

    Science.gov (United States)

    Huang, Dao-Ling; Liu, Hong-Tao; Dau, Phuong Diem; Wang, Lai-Sheng

    2014-06-01

    High-resolution vibrational spectroscopy of transient species is important for determining their molecular structures and understanding their chemical reactivity. However, the low abundance and high reactivity of molecular radicals pose major challenges to conventional absorption spectroscopic methods. The observation of dipole-bound states (DBS) in anions extend autodetachment spectroscopy to molecular anions whose corresponding neutral radicals possess a large enough dipole moment (>2.5 D).1,2 However, due to the difficulty of assigning the congested spectra at room temperature, there have been only a limited number of autodetachment spectra via DBS reported. Recently, we have built an improved version of a cold trap3 coupled with high-resolution photoelectron imaging.4 The first observation of mode-specific auotodetachment of DBS of cold phenoxide have shown that not only vibrational hot bands were completely suppressed, but also rotational profile was observed.5 The vibrational frequencies of the DBS were found to be the same as those of the neutral radical, suggesting that vibrational structures of dipolar radicals can be probed via DBS.5 More significantly, the DBS resonances allowed a number of vibrational modes with very weak Frank-Condon factors to be "lightened" up via vibrational autodetachment.5 Recently, our first high-resolution vibrational spectroscopy of the dehydrogenated uracil radical, with partial rotational resolution, via autodetachment from DBS of cold deprotonated uracil anions have been reported.6 Rich vibrational information is obtained for this important radical species. The resolved rotational profiles also allow us to characterize the rotational temperature of the trapped anions for the first time.6 1 K. R. Lykke, D. M. Neumark, T. Andersen, V. J. Trapa, and W. C. Lineberger, J. Chem. Phys. 87, 6842 (1987). 2 D. M. Wetzel, and J. I. Brauman, J. Chem. Phys. 90, 68 (1989). 3 P. D. Dau, H. T. Liu, D. L. Huang, and L. S. Wang, J. Chem. Phys

  11. VSI@ESS: Case study for a vibrational spectroscopy instrument at the european spallation source

    Science.gov (United States)

    Zoppi, Marco; Fedrigo, Anna; Celli, Milva; Colognesi, Daniele

    2015-01-01

    Neutron Vibrational Spectroscopy is a well-established experimental technique where elementary excitations at relatively high frequency are detected via inelastic neutron scattering. This technique attracts a high interest in a large fraction of the scientific community in the fields of chemistry, materials science, physics, and biology, since one of its main applications exploits the large incoherent scattering cross section of the proton with respect to all the other elements, whose dynamics can be spectroscopically detected, even if dissolved in very low concentration in materials composed of much heavier atoms. We have proposed a feasibility study for a Vibrational Spectroscopy Instrument (VSI) at the European Spallation Source ESS. Here, we will summarize the preliminary design calculations and the corresponding McStas simulation results for a possible ToF, Inverted Geometry, VSI beamline.

  12. VSI@ESS: Case study for a vibrational spectroscopy instrument at the european spallation source

    Directory of Open Access Journals (Sweden)

    Zoppi Marco

    2015-01-01

    Full Text Available Neutron Vibrational Spectroscopy is a well-established experimental technique where elementary excitations at relatively high frequency are detected via inelastic neutron scattering. This technique attracts a high interest in a large fraction of the scientific community in the fields of chemistry, materials science, physics, and biology, since one of its main applications exploits the large incoherent scattering cross section of the proton with respect to all the other elements, whose dynamics can be spectroscopically detected, even if dissolved in very low concentration in materials composed of much heavier atoms. We have proposed a feasibility study for a Vibrational Spectroscopy Instrument (VSI at the European Spallation Source ESS. Here, we will summarize the preliminary design calculations and the corresponding McStas simulation results for a possible ToF, Inverted Geometry, VSI beamline.

  13. Spectroscopy

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    This introductory booklet covers the basics of molecular spectroscopy, infrared and Raman methods, instrumental considerations, symmetry analysis of molecules, group theory and selection rules, as well as assignments of fundamental vibrational modes in molecules.......This introductory booklet covers the basics of molecular spectroscopy, infrared and Raman methods, instrumental considerations, symmetry analysis of molecules, group theory and selection rules, as well as assignments of fundamental vibrational modes in molecules....

  14. Vibrational spectroscopy studies of formalin-fixed cervix tissues.

    Science.gov (United States)

    Krishna, C M; Sockalingum, G D; Vadhiraja, B M; Maheedhar, K; Rao, A C K; Rao, L; Venteo, L; Pluot, M; Fernandes, D J; Vidyasagar, M S; Kartha, V B; Manfait, M

    2007-02-15

    Optical histopathology is fast emerging as a potential tool in cancer diagnosis. Fresh tissues in saline are ideal samples for optical histopathology. However, evaluation of suitability of ex vivo handled tissues is necessitated because of severe constraints in sample procurement, handling, and other associated problems with fresh tissues. Among these methods, formalin-fixed samples are shown to be suitable for optical histopathology. However, it is necessary to further evaluate this method from the point of view discriminating tissues with minute biochemical variations. A pilot Raman and Fourier transform infrared (FTIR) microspectroscopic studies of formalin-fixed tissues normal, malignant, and after-2-fractions of radiotherapy from the same malignant cervix subjects were carried out, with an aim to explore the feasibility of discriminating these tissues, especially the tissues after-2-fractions of radiotherapy from other two groups. Raman and FTIR spectra exhibit large differences for normal and malignant tissues and subtle differences are seen between malignant and after-2-fractions of radiotherapy tissues. Spectral data were analyzed by principal component analysis (PCA) and it provided good discrimination of normal and malignant tissues. PCA of data of three tissues, normal, malignant, and 2-fractions after radiotherapy, gave two clusters corresponding to normal and malignant + after-2-fractions of radiotherapy tissues. A second step of PCA was required to achieve discrimination between malignant and after-2-fractions of radiotherapy tissues. Hence, this study not only further supports the use of formalin-fixed tissues in optical histopathology, especially from Raman spectroscopy point of view, it also indicates feasibility of discriminating tissues with minute biochemical differences such as malignant and after-2-fractions of radiotherapy.

  15. Vibrational Spectral Signatures of Crystalline Cellulose Using High Resolution Broadband Sum Frequency Generation Vibrational Spectroscopy (HR-BB-SFG-VS)

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Libing; Lu, Zhou; Velarde Ruiz Esparza, Luis A.; Fu, Li; Pu, Yunqiao; Ding, Shi-You; Ragauskas, Art J.; Wang, Hongfei; Yang, Bin

    2015-03-03

    Here we reported the first sub-wavenumber high-resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS) study on both the C-H and O-H region spectra of crystalline cellulose. HR-BB-SFG-VS has about 10 times better resolution than the conventional scanning SFG-VS and is known to be able to measure the intrinsic spectral lineshape and to resolve much more spectral details. With HR-BB-SFG-VS, we found that in cellulose from different sources, including Avicel and cellulose crystals isolated from algae Valonia (Iα) and tunicates (Iβ), the spectral signatures in the OH regions were unique for different allomorphs, i.e. Iα and Iβ, while the spectral signatures in the C-H regions varied in all samples examined. Even though the origin of the different behaviors of the crystalline cellulose in the O-H and C-H vibrational frequency regions is yet to be correlated to the structure of cellulose, these results provided new spectroscopic methods and opportunities to classify and understand the basic crystalline structure, as well as variations, in polymorphism of the crystalline cellulose structure.

  16. Thermodynamic scaling of relaxation: insights from anharmonic elasticity

    Science.gov (United States)

    Bernini, S.; Puosi, F.; Leporini, D.

    2017-04-01

    Using molecular dynamics simulations of a molecular liquid, we investigate the thermodynamic scaling (TS) of the structural relaxation time {τα} in terms of the quantity T{ρ-{γ\\text{ts}}}} , where T and ρ are the temperature and density, respectively. The liquid does not exhibit strong virial–energy correlations. We propose a method for evaluating both the characteristic exponent {{γ\\text{ts}} and the TS master curve that uses experimentally accessible quantities that characterise the anharmonic elasticity and does not use details about the microscopic interactions. In particular, we express the TS characteristic exponent {γ\\text{ts}} in terms of the lattice Grüneisen parameter {γL} and the isochoric anharmonicity {δL} . An analytic expression of the TS master curve of {τα} with {δL} as the key adjustable parameter is found. The comparison with the experimental TS master curves and the isochoric fragilities of 34 glassformers is satisfying. In a few cases, where thermodynamic data are available, we test (i) the predicted characteristic exponent {γ\\text{ts}} and (ii) the isochoric anharmonicity {δL} , as drawn by the best fit of the TS of the structural relaxation, against the available thermodynamic data. A linear relation between the isochoric fragility and the isochoric anharmonicity {δL} is found and compared favourably with the results of experiments with no adjustable parameters. A relation between the increase of the isochoric vibrational heat capacity due to anharmonicity and the isochoric fragility is derived.

  17. Exciton–vibrational coupling in the dynamics and spectroscopy of Frenkel excitons in molecular aggregates

    Energy Technology Data Exchange (ETDEWEB)

    Schröter, M.; Ivanov, S.D.; Schulze, J. [Institut für Physik, Universität Rostock, D-18051 Rostock (Germany); Polyutov, S.P. [Institut für Physik, Universität Rostock, D-18051 Rostock (Germany); Laboratory for Nonlinear Optics and Spectroscopy, Siberian Federal University, Svobodniy, 79, 660041 Krasnoyarsk (Russian Federation); Yan, Y. [Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Normal College, Guizhou 550018 (China); Pullerits, T. [Department of Chemical Physics, Lund University, P.O. Box 124, S-22100 Lund (Sweden); Kühn, O., E-mail: oliver.kuehn@uni-rostock.de [Institut für Physik, Universität Rostock, D-18051 Rostock (Germany)

    2015-03-18

    The influence of exciton–vibrational coupling on the optical and transport properties of molecular aggregates is an old problem that gained renewed interest in recent years. On the experimental side, various nonlinear spectroscopic techniques gave insight into the dynamics of systems as complex as photosynthetic antennae. Striking evidence was gathered that in these protein–pigment complexes quantum coherence is operative even at room temperature conditions. Investigations were triggered to understand the role of vibrational degrees of freedom, beyond that of a heat bath characterized by thermal fluctuations. This development was paralleled by theory, where efficient methods emerged, which could provide the proper frame to perform non-Markovian and non-perturbative simulations of exciton–vibrational dynamics and spectroscopy. This review summarizes the state of affairs of the theory of exciton–vibrational interaction in molecular aggregates and photosynthetic antenna complexes. The focus is put on the discussion of basic effects of exciton–vibrational interaction from the stationary and dynamics points of view. Here, the molecular dimer plays a prominent role as it permits a systematic investigation of absorption and emission spectra by numerical diagonalization of the exciton–vibrational Hamiltonian in a truncated Hilbert space. An extension to larger aggregates, having many coupled nuclear degrees of freedom, becomes possible with the Multi-Layer Multi-Configuration Time-Dependent Hartree (ML-MCTDH) method for wave packet propagation. In fact it will be shown that this method allows one to approach the limit of almost continuous spectral densities, which is usually the realm of density matrix theory. Real system–bath situations are introduced for two models, which differ in the way strongly coupled nuclear coordinates are treated, as a part of the relevant system or the bath. A rather detailed exposition of the Hierarchy Equations Of Motion (HEOM

  18. Investigation of organometallic reaction mechanisms with one and two dimensional vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Cahoon, James Francis [Univ. of California, Berkeley, CA (United States)

    2008-12-01

    One and two dimensional time-resolved vibrational spectroscopy has been used to investigate the elementary reactions of several prototypical organometallic complexes in room temperature solution. The electron transfer and ligand substitution reactions of photogenerated 17-electron organometallic radicals CpW(CO)3 and CpFe(CO)2 have been examined with one dimensional spectroscopy on the picosecond through microsecond time-scales, revealing the importance of caging effects and odd-electron intermediates in these reactions. Similarly, an investigation of the photophysics of the simple Fischer carbene complex Cr(CO)5[CMe(OMe)] showed that this class of molecule undergoes an unusual molecular rearrangement on the picosecond time-scale, briefly forming a metal-ketene complex. Although time-resolved spectroscopy has long been used for these types of photoinitiated reactions, the advent of two dimensional vibrational spectroscopy (2D-IR) opens the possibility to examine the ultrafast dynamics of molecules under thermal equilibrium conditions. Using this method, the picosecond fluxional rearrangements of the model metal carbonyl Fe(CO)5 have been examined, revealing the mechanism, time-scale, and transition state of the fluxional reaction. The success of this experiment demonstrates that 2D-IR is a powerful technique to examine the thermally-driven, ultrafast rearrangements of organometallic molecules in solution.

  19. Anharmonicity and infrared bands of Polycyclic Aromatic Hydrocarbon (PAH) molecules

    Science.gov (United States)

    Petrignani, Annemieke; Maltseva, Elena; Candian, Alessandra; Mackie, Cameron; Huang, Xinchuan; Lee, Timothy J.; Tielens, Alexander; Oomens, Jos; Buma, Wybren Jan

    2015-08-01

    We present a systematic laboratory study of the CH stretching region in Polycyclic Aromatic Hydrocarbon (PAH) molecules of different shapes and sizes to investigate anharmonic behaviour and address the reliability of the never-validated but universally accepted scaling factors employed in astronomical PAH models. At the same time, new anharmonic theoretical quantum chemistry studies have been performed with the software program Spectro using our experimental data as benchmark. We performed mass and conformational-resolved, high-resolution spectroscopy of cold (~10K) linear and compact PAH molecules starting with naphthalene (C10H8) in the 3-µm CH stretching region. Surprisingly, the measured infrared spectra show many more strong modes than expected. Measurements of the deuterated counterparts demonstrate that these bands are the result of Fermi Resonances. First comparisons with harmonic and anharmonic DFT calculations using Gaussian 09 show that both approximations are not able to reproduce in detail the observed molecular reality. The improved anharmonic calculations performed with Spectro now include the effects of Fermi resonances and have been applied to PAHs for the first time. The analysis of the experimental data is greatly aided by these new theoretical quantum chemistry studies. Preliminary assignments are presented, aided by comparison between the observed rotational contour and the symmetry of candidate bands.

  20. Axial ligand effects on vibrational dynamics of iron in heme carbonyl studied by nuclear resonance vibrational spectroscopy.

    Science.gov (United States)

    Ohta, Takehiro; Liu, Jin-Gang; Saito, Makina; Kobayashi, Yasuhiro; Yoda, Yoshitaka; Seto, Makoto; Naruta, Yoshinori

    2012-11-29

    Nuclear resonance vibrational spectroscopy (NRVS) and density functional theory calculation (DFT) have been applied to illuminate the effect of axial ligation on the vibrational dynamics of iron in heme carbonyl. The analyses of the NRVS data of five- (5c) and six-coordinate (6c) heme-CO complexes indicate that the prominent feature of (57)Fe partial vibrational density of state ((57)FePVDOS) at the 250-300 cm(-1) region is significantly affected by the association of the axial ligand. The DFT calculations predict that the prominent (57)FePVDOS is composed of iron in-plane motions which are coupled with porphyrin pyrrole in-plane (ν(49), ν(50), and ν(53)), an out-of-plane (γ(8)) (two of four pyrrole rings include the in-plane modes, while the rest of pyrrole rings vibrate along the out-of-plane coordinate), and out-of-phase carbonyl C and O atom displacement perpendicular to the Fe-C-O axis. Thus, in the case of the 5c CO-heme the prominent (57)FePVDOS shows sharp and intense feature because of the degeneracy of the e symmetry mode within the framework of C(4v) symmetry molecule, whereas the association of the axial imidazole ligand in the 6c complex with the lowered symmetry results in split of the degenerate vibrational energy as indicated by broader and lower intensity features of the corresponding NRVS peak compared to the 5c structure. The vibrational energy of the iron in-plane motion in the 6c complex is higher than that in 5c, implying that the iron in the 6c complex includes stronger in-plane interaction with the porphyrin compared to 5c. The iron in-plane mode above 500 cm(-1), which is predominantly coupled with the out-of-phase carbonyl C and O atom motion perpendicular to Fe-C-O, called as Fe-C-O bending mode (δ(Fe-C-O)), also suggests that the 6c structure involves a larger force constant for the e symmetry mode than 5c. The DFT calculations along with the NRVS data suggest that the stiffened iron in-plane motion in the 6c complex can be ascribed

  1. Millimeter-wave spectroscopy of syn formyl azide (HC(O)N3) in seven vibrational states

    Science.gov (United States)

    Walters, Nicholas A.; Amberger, Brent K.; Esselman, Brian J.; Woods, R. Claude; McMahon, Robert J.

    2017-01-01

    Millimeter-wave spectra for formyl azide (HC(O)N3) were obtained from 240 to 360 GHz at ambient temperature. For the ground state of syn formyl azide, over 1500 independent rotational transitions were measured and least-squares fit to a complete S-reduced 8th order centrifugal distortion/rigid rotor Hamiltonian. The decomposition of formyl azide was monitored over a period of several hours, the half-life (t½ = 30 min) was determined, and its decomposition products were investigated. Transitions from five vibrational satellites of syn formyl azide (ν9, ν12, 2ν9, ν9 + ν12, and ν11) were observed, measured, and least-squares fit to complete or nearly complete octic centrifugally-distorted, single-state S-reduced models. A less complete single-state fit of 3ν9 (509.3 cm-1) was obtained from an unperturbed subset of its assignable transitions. This state is apparently coupled to the fundamental ν8 (489.4 cm-1) and the overtone 2ν12 (503.6 cm-1), but the coupling remains unanalyzed. Anharmonic CCSD(T)/ANO1 estimates of the vibrational frequencies of syn formyl azide were in close agreement with previously published experimental and computational values. Experimentally determined vibration-rotation interaction (αi) values were in excellent agreement with coupled-cluster predicted αi values for the fundamentals ν9, ν12, and ν11.

  2. Double resonant absorption measurement of acetylene symmetric vibrational states probed with cavity ring down spectroscopy

    Science.gov (United States)

    Karhu, J.; Nauta, J.; Vainio, M.; Metsälä, M.; Hoekstra, S.; Halonen, L.

    2016-06-01

    A novel mid-infrared/near-infrared double resonant absorption setup for studying infrared-inactive vibrational states is presented. A strong vibrational transition in the mid-infrared region is excited using an idler beam from a singly resonant continuous-wave optical parametric oscillator, to populate an intermediate vibrational state. High output power of the optical parametric oscillator and the strength of the mid-infrared transition result in efficient population transfer to the intermediate state, which allows measuring secondary transitions from this state with a high signal-to-noise ratio. A secondary, near-infrared transition from the intermediate state is probed using cavity ring-down spectroscopy, which provides high sensitivity in this wavelength region. Due to the narrow linewidths of the excitation sources, the rovibrational lines of the secondary transition are measured with sub-Doppler resolution. The setup is used to access a previously unreported symmetric vibrational state of acetylene, ν 1 + ν 2 + ν 3 + ν4 1 + ν5 - 1 in the normal mode notation. Single-photon transitions to this state from the vibrational ground state are forbidden. Ten lines of the newly measured state are observed and fitted with the linear least-squares method to extract the band parameters. The vibrational term value was measured to be at 9775.0018(45) cm-1, the rotational parameter B was 1.162 222(37) cm-1, and the quartic centrifugal distortion parameter D was 3.998(62) × 10-6 cm-1, where the numbers in the parenthesis are one-standard errors in the least significant digits.

  3. Analysis of structural transformation in wool fiber resulting from oxygen plasma treatment using vibrational spectroscopy

    Science.gov (United States)

    Barani, Hossein; Haji, Aminoddin

    2015-01-01

    The aim of this study was to investigate the influence of oxygen plasma procedure at different time treatments on wool fiber using the micro-Raman spectroscopy as a non-destructive vibrational spectroscopic technique and Fourier transform infrared spectroscopy. The amide I and III regions, Csbnd C skeletal vibration region, and Ssbnd S and Csbnd S bonds vibration regions were analyzed with the Raman microscope. The Fourier transform infrared spectroscope analysis was employed to find out the effect of oxygen plasma treatment on the cysteic acid residues content of the wool fiber sample. The results indicated that the α-helix structure was the highest component content of wool fiber. Moreover, the protein secondary structure of wool fibers was transformed from α-helical arrangement to the β-pleated sheet configuration during the oxygen plasma treatment. Also, the disulphide bonds content in the treated wool fiber reduced because they were fractured and oxidized during oxygen plasma treatment. The oxygen plasma treated samples presented higher cysteic acid compared to the untreated wool samples due to produce more cleavage of disulfide linkages.

  4. Ultra-sensitive vibrational spectroscopy of protein monolayers with plasmonic nanoantenna arrays.

    Science.gov (United States)

    Adato, Ronen; Yanik, Ahmet A; Amsden, Jason J; Kaplan, David L; Omenetto, Fiorenzo G; Hong, Mi K; Erramilli, Shyamsunder; Altug, Hatice

    2009-11-17

    Infrared absorption spectroscopy enabling direct access to vibrational fingerprints of the molecular structure is a powerful method for functional studies of bio-molecules. Although the intrinsic absorption cross-sections of IR active modes of proteins are nearly 10 orders of magnitude larger than the corresponding Raman cross-sections, they are still small compared to that of fluorescence-label based methods. Here, we developed a new tool based on collective excitation of plasmonic nanoantenna arrays and demonstrated direct detection of vibrational signatures of single protein monolayers. We first tailored the geometry of individual nanoantennas to form resonant structures that match the molecular vibrational modes. The tailored nanoantennas are then arranged in such a way that their in-phase dipolar coupling leads to a collective excitation of the ensemble with strongly enhanced near fields. The combined collective and individual plasmonic responses of the antenna array play a critical role in attaining signal enhancement factors of 10(4)-10(5). We achieved measurement of the vibrational spectra of proteins at zeptomole levels for the entire array, corresponding to only 145 molecules per antenna. The near-field nature of the plasmonic enhancement of the absorption signals is demonstrated with progressive loading of the nanoantennas with varying protein film thicknesses. Finally, an advanced model based on nonequilibrium Green's function formalism is introduced, which explains the observed Fano-type absorption line-shapes and tuning of the absorption strengths with the antenna resonance.

  5. The Microwave Spectroscopy of Aminoacetonitrile in the Vibrational Excited States 2

    Science.gov (United States)

    Fujita, Chiho; Higurashi, Haruka; Ozeki, Hiroyuki; Kobayashi, Kaori

    2016-06-01

    Aminoacetonitrile (NH_2CH_2CN) is a potential precursor of the simplest amino acid, glycine in the interstellar space and was detected toward SgrB2(N). We have extended measurements up to 1.3 THz so that the strongest transitions that may be found in the terahertz region should be covered. Aminoacetonitrile has a few low-lying vibrational excited states and indeed the pure rotational transitions in these vibrational excited states were found. The pure rotational transitions in six vibrational excited states in the 80-180 GHz range have been assigned and centrifugal distortion constants up to the sextic terms were determined. Based on spectral intensities and the vibrational information from Bak et al., They were assigned to the 3 low-lying fundamentals, 1 overtone and 2 combination bands. In the submillimeter wavelength region, perturbations were recognized and some of the lines were off by more than a few MHz. At this moment, these perturbed transitions are not included in our analysis. A. Belloche, K. M. Menten, C. Comito, H. S. P. Müller, P. Schilke, J. Ott, S. Thorwirth, and C. Hieret, 2008, Astronom. & Astrophys. 482, 179 (2008). Y. Motoki, Y. Tsunoda, H. Ozeki, and K. Kobayashi, Astrophys. J. Suppl. Ser. 209, 23 (2013). B. Bak, E. L. Hansen, F. M. Nicolaisen, and O. F. Nielsen, Can. J. Phys. 53, 2183 (1975) C. Fujita, H. Ozeki, and K. Kobayashi, 70th International Symposium on Molecular Spectroscopy (2015), MH14.

  6. Far-field nanoscale infrared spectroscopy of vibrational fingerprints of molecules with graphene plasmons

    CERN Document Server

    Hu, Hai; Zhai, Feng; Hu, Debo; Liu, Ruina; Liu, Kaihui; Sun, Zhipei; Dai, Qing

    2016-01-01

    Infrared spectroscopy, especially for molecular vibrations in the fingerprint region between 600 and 1500 cm-1, is a powerful characterization method for bulk materials. However, molecular fingerprinting at the nanoscale level still remains a significant challenge, due to weak light-matter interaction between micron-wavelengthed infrared light and nano-sized molecules. Here, we demonstrate molecular fingerprinting at the nanoscale level using our specially designed graphene plasmonic structure on CaF2 nanofilm. This structure not only avoids the plasmon-phonon hybridization, but also provides in situ electrically-tunable graphene plasmon covering the entire infrared fingerprint region, which was previously unattainable. In addition, undisturbed and highly-confined graphene plasmon offers simultaneous detection of in-plane and out-of-plane vibrational modes with ultrahigh detection sensitivity down to the sub-monolayer level, significantly pushing the current detection limit of far-field mid-infrared spectrosc...

  7. Vibrationally resolved UV/Vis spectroscopy with time-dependent density functional based tight binding

    Science.gov (United States)

    Rüger, Robert; Niehaus, Thomas; van Lenthe, Erik; Heine, Thomas; Visscher, Lucas

    2016-11-01

    We report a time-dependent density functional based tight-binding (TD-DFTB) scheme for the calculation of UV/Vis spectra, explicitly taking into account the excitation of nuclear vibrations via the adiabatic Hessian Franck-Condon method with a harmonic approximation for the nuclear wavefunction. The theory of vibrationally resolved UV/Vis spectroscopy is first summarized from the viewpoint of TD-DFTB. The method is benchmarked against time-dependent density functional theory (TD-DFT) calculations for strongly dipole allowed excitations in various aromatic and polar molecules. Using the recent 3ob:freq parameter set of Elstner's group, very good agreement with TD-DFT calculations using local functionals was achieved.

  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. Thermal expansion of mullite-type Bi{sub 2}Al{sub 4}O{sub 9}: A study by X-ray diffraction, vibrational spectroscopy and density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Mangir Murshed, M., E-mail: murshed@uni-bremen.de [Chemische Kristallographie fester Stoffe, Institut für Anorganische Chemie, Universität Bremens, Leobener Straße, D-28359 Bremen (Germany); Mendive, Cecilia B.; Curti, Mariano [Departamento de Química, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Dean Funes 3350, B7600AYL Mar del Plata (Argentina); Šehović, Malik [Chemische Kristallographie fester Stoffe, Institut für Anorganische Chemie, Universität Bremens, Leobener Straße, D-28359 Bremen (Germany); Friedrich, Alexandra [Institut für Geowissenschaften, Abteilung Kristallographie, Goethe-Universität Frankfurt, Altenhöferallee 1, D-60438 Frankfurt am Main (Germany); Fischer, Michael [Kristallographie, FB Geowissenschaften, Universität Bremen, Klagenfurter Straße, D-28359 Bremen (Germany); Gesing, Thorsten M. [Chemische Kristallographie fester Stoffe, Institut für Anorganische Chemie, Universität Bremens, Leobener Straße, D-28359 Bremen (Germany)

    2015-09-15

    Polycrystalline Bi{sub 2}Al{sub 4}O{sub 9} powder samples were synthesized using the glycerine method. Single crystals were produced from the powder product in a Bi{sub 2}O{sub 3} melt. The lattice thermal expansion of the mullite-type compound was studied using X-ray diffraction, Raman spectroscopy and density functional theory (DFT). The metric parameters were modeled using Grüneisen approximation for the zero pressure equation of state, where the temperature-dependent vibrational internal energy was calculated from the Debye characteristic frequency. Both the first-order and second-order Grüneisen approximations were applied for modeling the volumetric expansion, and the second-order approach provided physically meaningful axial parameters. The phonon density of states as well as phonon dispersion guided to set the characteristic frequency for simulation. The experimental infrared and Raman phonon bands were compared with those calculate from the DFT calculations. Selective Raman modes were analyzed for the thermal anharmonic behaviors using simplified Klemens model. The respective mode Grüneisen parameters were calculated from the pressure-dependent Raman spectra. - Graphical abstract: Crystal structure of mullite-type Bi{sub 2}Al{sub 4}O{sub 9} showing the edge-sharing AlO{sub 6} octahedra running parallel to the c-axis. - Highlights: • Thermal expansion of Bi{sub 2}Al{sub 4}O{sub 9} was studied using XRD, FTIR, Raman and DFT. • Metric parameters were modeled using Grüneisen approximation. • Phonon DOS and phonon dispersion helped to set the Debye frequency. • Mode Grüneisen parameters were calculated from the pressure-dependent Raman spectra. • Anharmonicity was analyzed for some selective Raman modes.

  10. Vibrational spectroscopy: a tool being developed for the noninvasive monitoring of wound healing

    Science.gov (United States)

    Crane, Nicole J.; Elster, Eric A.

    2012-01-01

    Wound care and management accounted for over 1.8 million hospital discharges in 2009. The complex nature of wound physiology involves hundreds of overlapping processes that we have only begun to understand over the past three decades. The management of wounds remains a significant challenge for inexperienced clinicians. The ensuing inflammatory response ultimately dictates the pace of wound healing and tissue regeneration. Consequently, the eventual timing of wound closure or definitive coverage is often subjective. Some wounds fail to close, or dehisce, despite the use and application of novel wound-specific treatment modalities. An understanding of the molecular environment of acute and chronic wounds throughout the wound-healing process can provide valuable insight into the mechanisms associated with the patient's outcome. Pathologic alterations of wounds are accompanied by fundamental changes in the molecular environment that can be analyzed by vibrational spectroscopy. Vibrational spectroscopy, specifically Raman and Fourier transform infrared spectroscopy, offers the capability to accurately detect and identify the various molecules that compose the extracellular matrix during wound healing in their native state. The identified changes might provide the objective markers of wound healing, which can then be integrated with clinical characteristics to guide the management of wounds.

  11. Ion aggregation in high salt solutions. III. Computational vibrational spectroscopy of HDO in aqueous salt solutions

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jun-Ho; Lim, Sohee; Chon, Bonghwan; Cho, Minhaeng, E-mail: mcho@korea.ac.kr [Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 136-713 (Korea, Republic of); Department of Chemistry, Korea University, Seoul 136-713 (Korea, Republic of); Kim, Heejae; Kim, Seongheun [Department of Chemistry, Korea University, Seoul 136-713 (Korea, Republic of)

    2015-05-28

    The vibrational frequency, frequency fluctuation dynamics, and transition dipole moment of the O—D stretch mode of HDO molecule in aqueous solutions are strongly dependent on its local electrostatic environment and hydrogen-bond network structure. Therefore, the time-resolved vibrational spectroscopy the O—D stretch mode has been particularly used to investigate specific ion effects on water structure. Despite prolonged efforts to understand the interplay of O—D vibrational dynamics with local water hydrogen-bond network and ion aggregate structures in high salt solutions, still there exists a gap between theory and experiment due to a lack of quantitative model for accurately describing O—D stretch frequency in high salt solutions. To fill this gap, we have performed numerical simulations of Raman scattering and IR absorption spectra of the O—D stretch mode of HDO in highly concentrated NaCl and KSCN solutions and compared them with experimental results. Carrying out extensive quantum chemistry calculations on not only water clusters but also ion-water clusters, we first developed a distributed vibrational solvatochromic charge model for the O—D stretch mode in aqueous salt solutions. Furthermore, the non-Condon effect on the vibrational transition dipole moment of the O—D stretch mode was fully taken into consideration with the charge response kernel that is non-local polarizability density. From the fluctuating O—D stretch mode frequencies and transition dipole vectors obtained from the molecular dynamics simulations, the O—D stretch Raman scattering and IR absorption spectra of HDO in salt solutions could be calculated. The polarization effect on the transition dipole vector of the O—D stretch mode is shown to be important and the asymmetric line shapes of the O—D stretch Raman scattering and IR absorption spectra of HDO especially in highly concentrated NaCl and KSCN solutions are in quantitative agreement with experimental results. We

  12. Communication: atomic force detection of single-molecule nonlinear optical vibrational spectroscopy.

    Science.gov (United States)

    Saurabh, Prasoon; Mukamel, Shaul

    2014-04-28

    Atomic Force Microscopy (AFM) allows for a highly sensitive detection of spectroscopic signals. This has been first demonstrated for NMR of a single molecule and recently extended to stimulated Raman in the optical regime. We theoretically investigate the use of optical forces to detect time and frequency domain nonlinear optical signals. We show that, with proper phase matching, the AFM-detected signals closely resemble coherent heterodyne-detected signals. Applications are made to AFM-detected and heterodyne-detected vibrational resonances in Coherent Anti-Stokes Raman Spectroscopy (χ((3))) and sum or difference frequency generation (χ((2))).

  13. Biomolecular interactions in HCV nucleocapsid-like particles as revealed by vibrational spectroscopy

    Science.gov (United States)

    Rodríguez-Casado, Arantxa; Molina, Marina; Carmona, Pedro

    2007-05-01

    Hepatitis C virus (HCV) occurs in the form of 55-65 nm spherical particles, but the structure of the virion remains to be clarified. Structural studies of HCV have been hampered by the lack of an appropriate cell culture system. However, structural analyses of HCV components can provide an essential framework for understanding of the molecular mechanism of virion assembly. This article reviews the potential of vibrational spectroscopy aimed at the knowledge of HCV structural biology, particularly regarding biomolecular interactions in nucleocapsid-like particles obtained in vitro.

  14. Application of Hamilton's Principle to the Study of the Anharmonic Oscillator in Classical Mechanics.

    Science.gov (United States)

    And Others; Gilmartin, Harvey

    1979-01-01

    Presented is a form of Hamilton's principle for classical mechanics appropriate to the study of arbitrary self-sustained vibrations in one dimension. It is applied as an approximate computational tool to the study of several examples of anharmonic oscillation. (Author/GA)

  15. Coherent Two-Dimensional Infrared Spectroscopy of Vibrational Excitons in Hydrogen-Bonded Liquids

    Science.gov (United States)

    Paarmann, Alexander

    The structure and structural dynamics of hydrogen bonded liquids were studied experimentally and theoretically with coherent two-dimensional infrared (2DIR) spectroscopy. The resonant intermolecular interactions within the fully resonant hydrogen bond networks give access to spatial correlations in the dynamics of the liquid structures. New experimental and theoretical tools were developed that significantly reduced the technical challenges of these studies. A nanofluidic flow device was designed and manufactured providing sub-micron thin, actively stabilized liquid sample layers between similarly thin windows. A simulation protocol for nonlinear vibrational response calculations of disordered fluctuating vibrational excitons was developed that allowed for the first treatment of resonant intermolecular interactions in the 2DIR response of liquid water. The 2DIR spectrum of the O-H stretching vibration of pure liquid water was studied experimentally at different temperatures. At ambient conditions the loss of frequency correlations is extremely fast, and is attributed to very efficient modulations of the two-dimensional O-H stretching vibrational potential through librational motions in the hydrogen bond network. At temperatures near freezing, the librational motions are significantly reduced leading to a pronounced slowing down of spectral diffusion dynamics. Comparison with energy transfer time scales revealed the first direct proof of delocalization of the vibrational excitations. This work establishes a fundamentally new view of vibrations in liquid water by providing a spatial length scale of correlated hydrogen-bond motions. The linear and 2DIR response of the amide I mode in neat liquid formamide was found to be dominated by excitonic effects due to largely delocalized vibrational excitations. The spectral response and dynamics are very sensitive to the excitonic mode structure and infrared activity distributions, leading to a pronounced asymmetry of linear

  16. On the applicability of centroid and ring polymer path integral molecular dynamics for vibrational spectroscopy

    Science.gov (United States)

    Witt, Alexander; Ivanov, Sergei D.; Shiga, Motoyuki; Forbert, Harald; Marx, Dominik

    2009-05-01

    Centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD) are two conceptually distinct extensions of path integral molecular dynamics that are able to generate approximate quantum dynamics of complex molecular systems. Both methods can be used to compute quasiclassical time correlation functions which have direct application in molecular spectroscopy; in particular, to infrared spectroscopy via dipole autocorrelation functions. The performance of both methods for computing vibrational spectra of several simple but representative molecular model systems is investigated systematically as a function of temperature and isotopic substitution. In this context both CMD and RPMD feature intrinsic problems which are quantified and investigated in detail. Based on the obtained results guidelines for using CMD and RPMD to compute infrared spectra of molecular systems are provided.

  17. Sub-Thz Vibrational Spectroscopy for Analysis of Ovarian Cancer Cells

    Science.gov (United States)

    Ferrance, Jerome P.; Sizov, Igor; Jazaeri, Amir; Moyer, Aaron; Gelmont, Boris; Globus, Tatiana

    2016-06-01

    Sub-THz vibrational spectroscopy utilizes wavelengths in the submillimeter-wave range ( 1.5-30 wn), beyond those traditionally used for chemical and biomolecular analysis. This low energy radiation excites low-frequency internal molecular motions (vibrations) involving hydrogen bonds and other weak connections within these molecules. The ability of sub-THz spectroscopy to identify and quantify biological molecules is based on detection of signature resonance absorbance at specific frequencies between 0.05 and 1 THz, for each molecule. The long wavelengths of this radiation, mean that it can even pass through entire cells, detecting the combinations of proteins and nucleic acids that exist within the cell. This research introduces a novel sub-THz resonance spectroscopy instrument with spectral resolution sufficient to identify individual resonance absorption peaks, for the analysis of ovarian cancer cells. In vitro cell cultures of SK-OV-3 and ES-2 cells, two human ovarian cancer subtypes, were characterized and compared with a normal non-transformed human fallopian tube epithelial cell line (FT131). A dramatic difference was observed between the THz absorption spectra of the cancer and normal cell sample materials with much higher absorption intensity and a very strong absorption peak at a frequency of 13 wn dominating the cancer sample spectra. Comparison of experimental spectra with molecular dynamic simulated spectroscopic signatures suggests that the high intensity spectral peak could originate from overexpressed mi-RNA molecules specific for ovarian cancer. Ovarian cancer cells are utilized as a proof of concept, but the sub-THz spectroscopy method is very general and could also be applied to other types of cancer.

  18. Anharmonicity and hydrogen bonding in electrooptic sucrose crystal

    Science.gov (United States)

    Szostak, M. M.; Giermańska, J.

    1990-03-01

    The polarized absorption spectra of the sucrose crystal in the 5300 - 7300 cm -1 region have been measured. The assignments of all the eight OH stretching overtones are proposed and their mechanical anharmonicities are estimated. The discrepancies from the oriented gas model (OGM) in the observed relative band intensities, especially of the -CH vibrations, are assumed to be connected with vibronic couplings enhanced by the helical arrangement of molecules joined by hydrogen bondings. It seems that this kind of interactions might be important for the second harmonic generation (SHG) by the sucrose crystal.

  19. Metamaterial-enhanced vibrational absorption spectroscopy for the detection of protein molecules

    Science.gov (United States)

    Bui, Tung S.; Dao, Thang D.; Dang, Luu H.; Vu, Lam D.; Ohi, Akihiko; Nabatame, Toshihide; Lee, YoungPak; Nagao, Tadaaki; Hoang, Chung V.

    2016-01-01

    From visible to mid-infrared frequencies, molecular sensing has been a major successful application of plasmonics because of the enormous enhancement of the surface electromagnetic nearfield associated with the induced collective motion of surface free carriers excited by the probe light. However, in the lower-energy terahertz (THz) region, sensing by detecting molecular vibrations is still challenging because of low sensitivity, complicated spectral features, and relatively little accumulated knowledge of molecules. Here, we report the use of a micron-scale thin-slab metamaterial (MM) architecture, which functions as an amplifier for enhancing the absorption signal of the THz vibration of an ultrathin adsorbed layer of large organic molecules. We examined bovine serum albumin (BSA) as a prototype large protein molecule and Rhodamine 6G (Rh6G) and 3,3′-diethylthiatricarbocyanine iodide (DTTCI) as examples of small molecules. Among them, our MM significantly magnified only the signal strength of bulky BSA. On the other hand, DTTCI and Rh6G are inactive, as they lack low-frequency vibrational modes in this frequency region. The results obtained here clearly demonstrate the promise of MM-enhanced absorption spectroscopy in the THz region for detection and structural monitoring of large biomolecules such as proteins or pathogenic enzymes. PMID:27555217

  20. Metamaterial-enhanced vibrational absorption spectroscopy for the detection of protein molecules

    Science.gov (United States)

    Bui, Tung S.; Dao, Thang D.; Dang, Luu H.; Vu, Lam D.; Ohi, Akihiko; Nabatame, Toshihide; Lee, Youngpak; Nagao, Tadaaki; Hoang, Chung V.

    2016-08-01

    From visible to mid-infrared frequencies, molecular sensing has been a major successful application of plasmonics because of the enormous enhancement of the surface electromagnetic nearfield associated with the induced collective motion of surface free carriers excited by the probe light. However, in the lower-energy terahertz (THz) region, sensing by detecting molecular vibrations is still challenging because of low sensitivity, complicated spectral features, and relatively little accumulated knowledge of molecules. Here, we report the use of a micron-scale thin-slab metamaterial (MM) architecture, which functions as an amplifier for enhancing the absorption signal of the THz vibration of an ultrathin adsorbed layer of large organic molecules. We examined bovine serum albumin (BSA) as a prototype large protein molecule and Rhodamine 6G (Rh6G) and 3,3‧-diethylthiatricarbocyanine iodide (DTTCI) as examples of small molecules. Among them, our MM significantly magnified only the signal strength of bulky BSA. On the other hand, DTTCI and Rh6G are inactive, as they lack low-frequency vibrational modes in this frequency region. The results obtained here clearly demonstrate the promise of MM-enhanced absorption spectroscopy in the THz region for detection and structural monitoring of large biomolecules such as proteins or pathogenic enzymes.

  1. Sum Frequency Generation Vibrational Spectroscopy of Colloidal Platinum Nanoparticle Catalysts: Disordering versus Removal of Organic Capping

    KAUST Repository

    Krier, James M.

    2012-08-23

    Recent work with nanoparticle catalysts shows that size and shape control on the nanometer scale influences reaction rate and selectivity. Sum frequency generation (SFG) vibrational spectroscopy is a powerful tool for studying heterogeneous catalysis because it enables the observation of surface intermediates during catalytic reactions. To control the size and shape of catalytic nanoparticles, an organic ligand was used as a capping agent to stabilize nanoparticles during synthesis. However, the presence of an organic capping agent presents two major challenges in SFG and catalytic reaction studies: it blocks a significant fraction of active surface sites and produces a strong signal that prevents the detection of reaction intermediates with SFG. Two methods for cleaning Pt nanoparticles capped with poly (vinylpyrrolidone) (PVP) are examined in this study: solvent cleaning and UV cleaning. Solvent cleaning leaves more PVP intact and relies on disordering with hydrogen gas to reduce the SFG signal of PVP. In contrast, UV cleaning depends on nearly complete removal of PVP to reduce SFG signal. Both UV and solvent cleaning enable the detection of reaction intermediates by SFG. However, solvent cleaning also yields nanoparticles that are stable under reaction conditions, whereas UV cleaning results in aggregation during reaction. The results of this study indicate that solvent cleaning is more advantageous for studying the effects of nanoparticle size and shape on catalytic selectivity by SFG vibrational spectroscopy. © 2012 American Chemical Society.

  2. Far-field nanoscale infrared spectroscopy of vibrational fingerprints of molecules with graphene plasmons

    Science.gov (United States)

    Hu, Hai; Yang, Xiaoxia; Zhai, Feng; Hu, Debo; Liu, Ruina; Liu, Kaihui; Sun, Zhipei; Dai, Qing

    2016-07-01

    Infrared spectroscopy, especially for molecular vibrations in the fingerprint region between 600 and 1,500 cm-1, is a powerful characterization method for bulk materials. However, molecular fingerprinting at the nanoscale level still remains a significant challenge, due to weak light-matter interaction between micron-wavelengthed infrared light and nano-sized molecules. Here we demonstrate molecular fingerprinting at the nanoscale level using our specially designed graphene plasmonic structure on CaF2 nanofilm. This structure not only avoids the plasmon-phonon hybridization, but also provides in situ electrically-tunable graphene plasmon covering the entire molecular fingerprint region, which was previously unattainable. In addition, undisturbed and highly confined graphene plasmon offers simultaneous detection of in-plane and out-of-plane vibrational modes with ultrahigh detection sensitivity down to the sub-monolayer level, significantly pushing the current detection limit of far-field mid-infrared spectroscopies. Our results provide a platform, fulfilling the long-awaited expectation of high sensitivity and selectivity far-field fingerprint detection of nano-scale molecules for numerous applications.

  3. Vibrational Spectroscopy of Chemical Species in Silicon and Silicon-Rich Nitride Thin Films

    Directory of Open Access Journals (Sweden)

    Kirill O. Bugaev

    2012-01-01

    Full Text Available Vibrational properties of hydrogenated silicon-rich nitride (SiN:H of various stoichiometry (0.6≤≤1.3 and hydrogenated amorphous silicon (a-Si:H films were studied using Raman spectroscopy and Fourier transform infrared spectroscopy. Furnace annealing during 5 hours in Ar ambient at 1130∘C and pulse laser annealing were applied to modify the structure of films. Surprisingly, after annealing with such high-thermal budget, according to the FTIR data, the nearly stoichiometric silicon nitride film contains hydrogen in the form of Si–H bonds. From analysis of the FTIR data of the Si–N bond vibrations, one can conclude that silicon nitride is partly crystallized. According to the Raman data a-Si:H films with hydrogen concentration 15% and lower contain mainly Si–H chemical species, and films with hydrogen concentration 30–35% contain mainly Si–H2 chemical species. Nanosecond pulse laser treatments lead to crystallization of the films and its dehydrogenization.

  4. Far-field nanoscale infrared spectroscopy of vibrational fingerprints of molecules with graphene plasmons

    Science.gov (United States)

    Hu, Hai; Yang, Xiaoxia; Zhai, Feng; Hu, Debo; Liu, Ruina; Liu, Kaihui; Sun, Zhipei; Dai, Qing

    2016-01-01

    Infrared spectroscopy, especially for molecular vibrations in the fingerprint region between 600 and 1,500 cm−1, is a powerful characterization method for bulk materials. However, molecular fingerprinting at the nanoscale level still remains a significant challenge, due to weak light–matter interaction between micron-wavelengthed infrared light and nano-sized molecules. Here we demonstrate molecular fingerprinting at the nanoscale level using our specially designed graphene plasmonic structure on CaF2 nanofilm. This structure not only avoids the plasmon–phonon hybridization, but also provides in situ electrically-tunable graphene plasmon covering the entire molecular fingerprint region, which was previously unattainable. In addition, undisturbed and highly confined graphene plasmon offers simultaneous detection of in-plane and out-of-plane vibrational modes with ultrahigh detection sensitivity down to the sub-monolayer level, significantly pushing the current detection limit of far-field mid-infrared spectroscopies. Our results provide a platform, fulfilling the long-awaited expectation of high sensitivity and selectivity far-field fingerprint detection of nano-scale molecules for numerous applications. PMID:27460765

  5. Photo-vibrational spectroscopy of solid and liquid chemicals using laser Doppler vibrometer.

    Science.gov (United States)

    Hu, Qi; Lim, Jacob Song Kiat; Liu, Huan; Fu, Yu

    2016-08-22

    Photoacoustic/photothermal spectroscopy is an established technique for trace detection of chemicals and explosives. However, prior sample preparation is required and the analysis is conducted in a sealed space with a high-sensitivity microphone or a piezo sensor coupled with a lock-in amplifier, limiting the technique to applications in a laboratory environment. Due to the aforementioned requirements, traditionally this technique may not be suitable for defense and security applications where the detection of explosives or hazardous chemicals is required in an open environment at a safe standoff distance. In this study, chemicals in various forms (membrane, powder and liquid) were excited by an intensity-modulated quantum cascade laser (QCL), while a laser Doppler vibrometer (LDV) based on the Mach-Zehnder interferometer was applied to detect the vibration signal resulting from the photocoustic/photothermal effect. The photo-vibrational spectrum obtained by scanning the QCL's wavelength in MIR range, coincides well with the corresponding spectrum obtained using typical FTIR equipment. The experiment demonstrated that the LDV is a capable sensor for applications in photoacoustic/photothermal spectroscopy, with potential to enable the detection of chemicals in open environment at safe standoff distance.

  6. Absolute Helmholtz free energy of highly anharmonic crystals: theory vs Monte Carlo.

    Science.gov (United States)

    Yakub, Lydia; Yakub, Eugene

    2012-04-14

    We discuss the problem of the quantitative theoretical prediction of the absolute free energy for classical highly anharmonic solids. Helmholtz free energy of the Lennard-Jones (LJ) crystal is calculated accurately while accounting for both the anharmonicity of atomic vibrations and the pair and triple correlations in displacements of the atoms from their lattice sites. The comparison with most precise computer simulation data on sublimation and melting lines revealed that theoretical predictions are in excellent agreement with Monte Carlo simulation data in the whole range of temperatures and densities studied.

  7. Anharmonic-potential-effective-charge approach for computing Raman cross sections of a gas

    Science.gov (United States)

    Kutteh, Ramzi; van Zandt, L. L.

    1993-05-01

    An anharmonic-potential-effective-charge approach for computing relative Raman intensities of a gas is developed. The equations of motion are set up and solved for the driven anharmonic molecular vibrations. An explicit expression for the differential polarizability tensor is derived and its properties discussed. This expression is then used within the context of Placzek's theory [Handbuch der Radiologie (Akademische Verlagsgesellschaft, Leipzig, 1934), Vol. VI] to compute the Raman cross section and depolarization ratio of a gas. The computation is carried out for the small molecules CO2, CS2, SO2, and CCl4; results are compared with experimental measurements and discussed.

  8. The Application of Vibrational Spectroscopy Techniques in the Qualitative Assessment of Material Traded as Ginseng

    Directory of Open Access Journals (Sweden)

    Maxleene Sandasi

    2016-04-01

    Full Text Available The name “ginseng” is collectively used to describe several plant species, including Panax ginseng (Asian/Oriental ginseng, P. quinquefolius (American ginseng, P. pseudoginseng (Pseudoginseng and Eleutherococcus senticosus (Siberian ginseng, each with different applications in traditional medicine practices. The use of a generic name may lead to the interchangeable use or substitution of raw materials which poses quality control challenges. Quality control methods such as vibrational spectroscopy-based techniques are here proposed as fast, non-destructive methods for the distinction of four ginseng species and the identification of raw materials in commercial ginseng products. Certified ginseng reference material and commercial products were analysed using hyperspectral imaging (HSI, mid-infrared (MIR and near-infrared (NIR spectroscopy. Principal component analysis (PCA and (orthogonal partial least squares discriminant analysis models (OPLS-DA were developed using multivariate analysis software. UHPLC-MS was used to analyse methanol extracts of the reference raw materials and commercial products. The holistic analysis of ginseng raw materials revealed distinct chemical differences using HSI, MIR and NIR. For all methods, Eleutherococcus senticosus displayed the greatest variation from the three Panax species that displayed closer chemical similarity. Good discrimination models with high R2X and Q2 cum vales were developed. These models predicted that the majority of products contained either /P. ginseng or P. quinquefolius. Vibrational spectroscopy and HSI techniques in tandem with multivariate data analysis tools provide useful alternative methods in the authentication of ginseng raw materials and commercial products in a fast, easy, cost-effective and non-destructive manner.

  9. Towards vibrational spectroscopy on surface-attached colloids performed with a quartz crystal microbalance

    Directory of Open Access Journals (Sweden)

    Diethelm Johannsmann

    2016-12-01

    Full Text Available Colloidal spheres attached to a quartz crystal microbalance (QCM produce the so-called “coupled resonances”. They are resonators of their own, characterized by a particle resonance frequency, a resonance bandwidth, and a modal mass. When the frequency of the main resonator comes close to the frequency of the coupled resonance, the bandwidth goes through a maximum. A coupled resonance can be viewed as an absorption line in acoustic shear-wave spectroscopy. The known concepts from spectroscopy apply. This includes the mode assignment problem, selection rules, and the oscillator strength. In this work, the mode assignment problem was addressed with Finite Element calculations. These reveal that a rigid sphere in contact with a QCM displays two modes of vibration, termed “slipping” and “rocking”. In the slipping mode, the sphere rotates about its center; it exerts a tangential force onto the resonator surface at the point of contact. In the rocking mode, the sphere rotates about the point of contact; it exerts a torque onto the substrate. In liquids, both axes of rotation are slightly displaced from their ideal positions. Characteristic for spectroscopy, the two modes do not couple to the mechanical excitation equally well. The degree of coupling is quantified by an oscillator strength. Because the rocking mode mostly exerts a torque (rather than a tangential force, its coupling to the resonator's tangential motion is weak; the oscillator strength consequently is small. Recent experiments on surface-adsorbed colloidal spheres can be explained by the mode of vibration being of the rocking type.

  10. Quantum statistics and anharmonicity in the thermodynamics of spin waves in ferromagnetic metals

    Science.gov (United States)

    Wen, Haohua; Woo, C. H.

    2016-09-01

    The average energy needed to create a magnon is high in ferromagnetic metals due to the high-strength spin stiffness, which results in strong quantization effects that could be important even at thousands of degrees. To take into account quantum statistics at such high temperatures, the associated effects of anharmonicity of the spin vibrations must be taken into account. In addition to the complex nature of such effects, anharmonicity also affects the occupation of the density of state of the vibration states in the context of quantum statistics. Thus, an unoccupied vibration state might become occupied when its spring stiffness is substantially reduced with anharmonicity. Combined effects of quantum statistics and anharmonicity are expected. In this regard, the thermodynamics of ferromagnetic metals are investigated in this paper through the example of bcc iron between 10 and 1400 K. Theoretical analysis and spin-lattice dynamic simulations are performed, through which the physics behind the complex and dramatic temperature dependence of the thermodynamic functions of bcc iron is understood.

  11. Anharmonicity effects in Cu-doped ZnO nanocombs by temperature-dependent Raman scattering

    Science.gov (United States)

    Kong, J. F.; Fan, D. H.; Shen, W. Z.

    2016-09-01

    Micro-Raman spectra of E 2(high) phonon mode in Cu-doped ZnO nanocombs have been presented in detail with different Cu compositions under the temperature ranging from 83 to 443 K grown by a simple catalyst-free chemical vapor deposition method. The alloy disorder effect has been investigated by analyzing the asymmetric broadening of E 2(high) phonon mode and Cu-induced localized vibration mode at room temperature. In addition, we resort to a theory model including the lattice thermal expansion and anharmonic phonon-phonon interaction, which can well describe the temperature dependence of Raman shift and linewidth of E 2(high) phonon. In combining with the theory model, we have revealed an increasing anharmonic effect on the Raman shift and linewidth behaviors with increasing Cu composition. Furthermore, it is found that the lifetime of E 2(high) phonon mode shortens with enhancing the anharmonicity.

  12. First-principles analysis of anharmonic nuclear motion and thermal transport in thermoelectric materials

    Energy Technology Data Exchange (ETDEWEB)

    Tadano, Terumasa [Department of Applied Physics, The University of Tokyo, Tokyo 113-8656 (Japan); Tsuneyuki, Shinji [Department of Physics, The University of Tokyo, Tokyo 113-0033 (Japan); Institute for Solid State Physics, The University of Tokyo, Kashiwa 277-8581 (Japan)

    2015-12-31

    We show a first-principles approach for analyzing anharmonic properties of lattice vibrations in solids. We firstly extract harmonic and anharmonic force constants from accurate first-principles calculations based on the density functional theory. Using the many-body perturbation theory of phonons, we then estimate the phonon scattering probability due to anharmonic phonon-phonon interactions. We show the validity of the approach by computing the lattice thermal conductivity of Si, a typical covalent semiconductor, and selected thermoelectric materials PbTe and Bi{sub 2}Te{sub 3} based on the Boltzmann transport equation. We also show that the phonon lifetime and the lattice thermal conductivity of the high-temperature phase of SrTiO{sub 3} can be estimated by employing the perturbation theory on top of the solution of the self-consistent phonon equation.

  13. Simplified generalized-gradient approximation and anharmonicity: Benchmark calculations on molecules

    Science.gov (United States)

    Patton, David C.; Porezag, Dirk V.; Pederson, Mark R.

    1997-03-01

    Recent implementational improvements of the generalized-gradient approximation (GGA) have led to a simplified version which is parametrized entirely from fundamental constants, easier to use, and possibly easier to improve. We have performed detailed calculations on the geometries, atomization energies, vibrational energies, and infrared and Raman spectra of many first- and second-row dimers as well as some polyatomic molecules. For atomization and vibrational energies, we find that the simplified version of GGA leads to results similar to the original version. We comment on the fact that GGA-induced changes of hydrogenic bonding are different than for the other atoms in the periodic table but still an improvement over the local approximations to density-functional theory. In addition to a harmonic treatment of the vibrational modes we include the contributions of anharmonicity as well. With the exception of the light hydrogen containing molecules anharmonic corrections are quite small.

  14. Structure-Dependent Vibrational Dynamics of Mg(BH4)2 Polymorphs Probed with Neutron Vibrational Spectroscopy and First-Principles Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Dimitrievska, Mirjana; White, James L.; Zhou, Wei; Stavila, Vitalie; Klebanoff, Leonard E.; Udovic, Terrence J.

    2016-09-28

    The structure-dependent vibrational properties of different Mg(BH4)2 polymorphs (..alpha.., ..beta.., ..gamma.., and ..delta.. phases) were investigated with a combination of neutron vibrational spectroscopy (NVS) measurements and density functional theory (DFT) calculations, with emphasis placed on the effects of the local structure and orientation of the BH4- anions. DFT simulations closely match the neutron vibrational spectra. The main bands in the low-energy region (20-80 meV) are associated with the BH4- librational modes. The features in the intermediate energy region (80-120 meV) are attributed to overtones and combination bands arising from the lower-energy modes. The features in the high-energy region (120-200 meV) correspond to the BH4- symmetric and asymmetric bending vibrations, of which four peaks located at 140, 142, 160, and 172 meV are especially intense. There are noticeable intensity distribution variations in the vibrational bands for different polymorphs. This is explained by the differences in the spatial distribution of BH4- anions within various structures. An example of the possible identification of products after the hydrogenation of MgB2, using NVS measurements, is presented. These results provide fundamental insights of benefit to researchers currently studying these promising hydrogen-storage materials.

  15. Proton translocation in cytochrome c oxidase: insights from proton exchange kinetics and vibrational spectroscopy.

    Science.gov (United States)

    Ishigami, Izumi; Hikita, Masahide; Egawa, Tsuyoshi; Yeh, Syun-Ru; Rousseau, Denis L

    2015-01-01

    Cytochrome c oxidase is the terminal enzyme in the electron transfer chain. It reduces oxygen to water and harnesses the released energy to translocate protons across the inner mitochondrial membrane. The mechanism by which the oxygen chemistry is coupled to proton translocation is not yet resolved owing to the difficulty of monitoring dynamic proton transfer events. Here we summarize several postulated mechanisms for proton translocation, which have been supported by a variety of vibrational spectroscopic studies. We recently proposed a proton translocation model involving proton accessibility to the regions near the propionate groups of the heme a and heme a3 redox centers of the enzyme based by hydrogen/deuterium (H/D) exchange Raman scattering studies (Egawa et al., PLoS ONE 2013). To advance our understanding of this model and to refine the proton accessibility to the hemes, the H/D exchange dependence of the heme propionate group vibrational modes on temperature and pH was measured. The H/D exchange detected at the propionate groups of heme a3 takes place within a few seconds under all conditions. In contrast, that detected at the heme a propionates occurs in the oxidized but not the reduced enzyme and the H/D exchange is pH-dependent with a pKa of ~8.0 (faster at high pH). Analysis of the thermodynamic parameters revealed that, as the pH is varied, entropy/enthalpy compensation held the free energy of activation in a narrow range. The redox dependence of the possible proton pathways to the heme groups is discussed. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

  16. Polymer Adsorption on Graphite and CVD Graphene Surfaces Studied by Surface-Specific Vibrational Spectroscopy.

    Science.gov (United States)

    Su, Yudan; Han, Hui-Ling; Cai, Qun; Wu, Qiong; Xie, Mingxiu; Chen, Daoyong; Geng, Baisong; Zhang, Yuanbo; Wang, Feng; Shen, Y R; Tian, Chuanshan

    2015-10-14

    Sum-frequency vibrational spectroscopy was employed to probe polymer contaminants on chemical vapor deposition (CVD) graphene and to study alkane and polyethylene (PE) adsorption on graphite. In comparing the spectra from the two surfaces, it was found that the contaminants on CVD graphene must be long-chain alkane or PE-like molecules. PE adsorption from solution on the honeycomb surface results in a self-assembled ordered monolayer with the C-C skeleton plane perpendicular to the surface and an adsorption free energy of ∼42 kJ/mol for PE(H(CH2CH2)nH) with n ≈ 60. Such large adsorption energy is responsible for the easy contamination of CVD graphene by impurity in the polymer during standard transfer processes. Contamination can be minimized with the use of purified polymers free of PE-like impurities.

  17. Vibrational properties of epitaxial Bi4Te3 films as studied by Raman spectroscopy

    Directory of Open Access Journals (Sweden)

    Hao Xu

    2015-08-01

    Full Text Available Bi4Te3, as one of the phases of the binary Bi–Te system, shares many similarities with Bi2Te3, which is known as a topological insulator and thermoelectric material. We report the micro-Raman spectroscopy study of 50 nm Bi4Te3 films on Si substrates prepared by molecular beam epitaxy. Raman spectra of Bi4Te3 films completely resolve the six predicted Raman-active phonon modes for the first time. Structural features and Raman tensors of Bi4Te3 films are introduced. According to the wavenumbers and assignments of the six eigenpeaks in the Raman spectra of Bi4Te3 films, it is found that the Raman-active phonon oscillations in Bi4Te3 films exhibit the vibrational properties of those in both Bi and Bi2Te3 films.

  18. Observation of the low frequency vibrational modes of bacteriophage M13 in water by Raman spectroscopy

    Directory of Open Access Journals (Sweden)

    Tsen Shaw-Wei D

    2006-09-01

    Full Text Available Abstract Background Recently, a technique which departs radically from conventional approaches has been proposed. This novel technique utilizes biological objects such as viruses as nano-templates for the fabrication of nanostructure elements. For example, rod-shaped viruses such as the M13 phage and tobacco mosaic virus have been successfully used as biological templates for the synthesis of semiconductor and metallic nanowires. Results and discussion Low wave number (≤ 20 cm-1 acoustic vibrations of the M13 phage have been studied using Raman spectroscopy. The experimental results are compared with theoretical calculations based on an elastic continuum model and appropriate Raman selection rules derived from a bond polarizability model. The observed Raman mode has been shown to belong to one of the Raman-active axial torsion modes of the M13 phage protein coat. Conclusion It is expected that the detection and characterization of this low frequency vibrational mode can be used for applications in nanotechnology such as for monitoring the process of virus functionalization and self-assembly. For example, the differences in Raman spectra can be used to monitor the coating of virus with some other materials and nano-assembly process, such as attaching a carbon nanotube or quantum dots.

  19. Electronic and vibrational spectroscopy of intermediates in methane-to-methanol conversion by CoO+

    Science.gov (United States)

    Altinay, Gokhan; Kocak, Abdulkadir; Silva Daluz, Jennifer; Metz, Ricardo B.

    2011-08-01

    At room temperature, cobalt oxide cations directly convert methane to methanol with high selectivity but very low efficiency. Two potential intermediates of this reaction, the [HO-Co-CH3]+ insertion intermediate and [H2O-Co=CH2]+ aquo-carbene complex are produced in a laser ablation source and characterized by electronic and vibrational spectroscopy. Reaction of laser-ablated cobalt cations with different organic precursors seeded in a carrier gas produces the intermediates, which subsequently expand into vacuum and cool. Ions are extracted into a time-of-flight mass spectrometer and spectra are measured via photofragment spectroscopy. Photodissociation of [HO-Co-CH3]+ in the visible and via infrared multiple photon dissociation (IRMPD) makes only Co+ + CH3OH, while photodissociation of [H2O-Co=CH2]+ produces CoCH2+ + H2O. The electronic spectrum of [HO-Co-CH3]+ shows progressions in the excited state Co-C stretch (335 cm-1) and O-Co-C bend (90 cm-1); the IRMPD spectrum gives νOH = 3630 cm-1. The [HO-Co-CH3]+(Ar) complex has been synthesized and its vibrational spectrum measured in the O-H stretching region. The resulting spectrum is sharper than that obtained via IRMPD and gives νOH = 3642 cm-1. Also, an improved potential energy surface for the reaction of CoO+ with methane has been developed using single point energies calculated by the CBS-QB3 method for reactants, intermediates, transition states and products.

  20. From Vibrational Spectroscopy to Force Fields and Structures of Saccharides: New Computational Algorithms and Applications

    Energy Technology Data Exchange (ETDEWEB)

    Pincu, Madeleine [UCI; Gerber, Robert Benny [Professor, UCI, Chemistry Dept.

    2013-07-17

    This work was undertaken with the main objective to investigate basic reactions that take place in relatively simple saccharides (mono-saccharides and cellobiose - the building block of cellulose) , in isolation and in cluster with few water molecules or with (gas-phase) clusters of few waters and ionic compounds (salt, isolated ions like H{sup +} or OH{sup -}). Within the context of this work, different potentials were investigated; among them, were the PM3 semi empirical potential, DFT/BLYP and a new hybrid potential constructed from MP2 for the harmonic part and from adjusted Hartree-Fock anharmonic interactions (VSCF-PT2). These potentials were evaluated by comparison with experimental data from published sources and from several collaborating groups. The findings show excellent agreement between experiments and predictions with the hybrid VSCF-PT2 potential and very good agreement with predictions obtained from dynamics with dispersion corrected DFT/BLYP potential. Investigation of hydration of cellobiose, was another topic of interest. Guided by a hydration motif demonstrated by our experimental collaborators (team of Prof J.P. Simons), we demonstrated large energetic and structural differences between the two species of cellobiose: cis and trans. The later, which is dominant in solid and liquid phases, is higher in energy in the gas-phase and compared to pure water, it does not disturb as much the network of H bonds. In contrast, the cis species exhibits asymmetric hydration in cluster with up to 25 waters, indicating that it has surfactant properties. Another highlight of this research effort was the successful first time spectrometric and spectroscopic study of a gas-phase protonated sugar derivative (alpha-D-Galactopyranoside) and its interpretation by Ab Initio molecular dynamics (AIMD) simulations. The findings demonstrate the formation of a motif in which a proton bridges between two Oxygen atoms (belonging to OH groups) at the sugar; The vibrational

  1. Modeling Stretching Modes of Common Organic Molecules with the Quantum Mechanical Harmonic Oscillator: An Undergraduate Vibrational Spectroscopy Laboratory Exercise

    Science.gov (United States)

    Parnis, J. Mark; Thompson, Matthew G. K.

    2004-01-01

    An introductory undergraduate physical organic chemistry exercise that introduces the harmonic oscillator's use in vibrational spectroscopy is developed. The analysis and modeling exercise begins with the students calculating the stretching modes of common organic molecules with the help of the quantum mechanical harmonic oscillator (QMHO) model.

  2. Infrared spectroscopy of methoxyphenols involved as atmospheric secondary organic aerosol precursors: Gas-phase vibrational cross-sections

    Science.gov (United States)

    Cuisset, A.; Coeur, C.; Mouret, G.; Ahmad, W.; Tomas, A.; Pirali, O.

    2016-08-01

    Methoxyphenols are emitted in the atmosphere from biomass burning and recent works have shown the potential role of these oxygenated aromatic species in the formation of secondary organic aerosols. IR spectroscopic data that would enable their remote measurement in the atmosphere remain scarce in the literature. Room temperature Far-IR cross-sections of 4 methoxyphenols (2-methoxyphenol or guaiacol, 3-methoxyphenol, 4-methoxyphenol and 2,6-dimethoxyphenol or syringol) have been determined using the THz synchrotron radiation available at SOLEIL. Mid- and near-IR regions have also been investigated with a conventional Fourier transform IR setup and allowed to provide a set of vibrational cross-sections of the studied methoxyphenols. Finally, gas-phase cross sections of two nitroguaiacol isomers (4-nitroguaiacol and 5-nitroguaiacol), two intermediate products involved in the formation of secondary organic aerosols have been measured in the mid- and near-IR with a heated multi-pass cell. Harmonic and anharmonic density functional theory calculations were carried out for all the studied compounds and allowed a full assignment of the recorded rovibrational bands.

  3. Probing the Vibrational Spectroscopy of the Deprotonated Thymine Radical by Photodetachment and State-Selective Autodetachment Photoelectron Spectroscopy via Dipole-Bound States

    Science.gov (United States)

    Huang, Dao-Ling; Zhu, Guo-Zhu; Wang, Lai-Sheng

    2016-06-01

    Deprotonated thymine can exist in two different forms, depending on which of its two N sites is deprotonated: N1[T-H]^- or N3[T-H]^-. Here we report a photodetachment study of the N1[T-H]^- isomer cooled in a cryogenic ion trap and the observation of an excited dipole-bound state. Eighteen vibrational levels of the dipole-bound state are observed, and its vibrational ground state is found to be 238 ± 5 wn below the detachment threshold of N1[T-H]^-. The electron affinity of the deprotonated thymine radical (N1[T-H]^.) is measured accruately to be 26 322 ± 5 wn (3.2635 ± 0.0006 eV). By tuning the detachment laser to the sixteen vibrational levels of the dipole-bound state that are above the detachment threshold, highly non-Franck-Condon resonant-enhanced photoelectron spectra are obtained due to state- and mode-selective vibrational autodetachment. Much richer vibrational information is obtained for the deprotonated thymine radical from the photodetachment and resonant-enhanced photoelectron spectroscopy. Eleven fundamental vibrational frequencies in the low-frequency regime are obtained for the N1[T-H]^. radical, including the two lowest-frequency internal rotational modes of the methyl group at 70 ± 8 wn and 92 ± 5 wn. D. L. Huang, H. T. Liu, C. G. Ning, G. Z. Zhu and L. S. Wang, Chem. Sci., 6, 3129-3138 (2015)

  4. Linear, third- and fifth-order nonlinear spectroscopy of a charge transfer system coupled to an underdamped vibration

    CERN Document Server

    Dijkstra, Arend G

    2015-01-01

    We study hole, electron and exciton transport in a charge transfer system in the presence of underdamped vibrational motion. We analyze the signature of these processes in the linear and third-, and fifth-order nonlinear electronic spectra. Calculations are performed with a numerically exact hierarchical equations of motion method for an underdamped Brownian oscillator spectral density. We find that combining electron, hole and exciton transfer can lead to non-trivial spectra with more structure than with excitonic coupling alone. Traces taken during the waiting time of a two-dimensional spectrum are dominated by vibrational motion and do not reflect the electron, hole, and exciton dynamics directly. We find that the fifth-order nonlinear response is particularly sensitive to the charge transfer process. While third-order 2D spectroscopy detects the correlation between two coherences, fifth-order 2D spectroscopy (2D population spectroscopy) is here designed to detect correlations between the excited states du...

  5. Anharmonicity effects in the frictionlike mode of graphite

    Science.gov (United States)

    Menéndez, C.; Lobato, A.; Abbasi-Pérez, D.; Fernández-Núñez, J.; Baonza, V. G.; Recio, J. M.

    2016-04-01

    Graphite is a prototypical solid lubricant demanding a thorough understanding of its low-friction behavior. The E2 g(1) Raman active vibrational mode of graphite is associated with the rigid-layer relative movement of its graphene sheets. Thus, this mode can provide a good means of exploring the low resistance of graphene layers to slip with respect to each other. To take advantage of this fact, the anharmonicity of the E2 g(1) mode has to be carefully characterized and evaluated since the atomic arrangement of carbon atoms in the ambient condition ABA stacking of graphite evidences potential asymmetry. The calculated one-dimensional energetic profile of the E2 g(1) mode reveals this local anisotropy around the energy minima and can be microscopically interpreted in terms of electron density interactions. Morse-type potentials accurately fit the energetic profiles at different interlayer separations, and provide simple analytical expressions for evaluating harmonic and anharmonic contributions to the Γ -point E2 g(1) frequency ωE2g(1 ) under a perturbative algebraic treatment. We quantify how the anharmonic contribution increases with the available energy (E ) at zero pressure, and how this contribution decreases as hydrostatic pressure (p ) or uniaxial stress is applied for a given available energy. The calculated ωE2g(1 )-p and ωE2g(1 )-E trends indicate an increasing (decreasing) of frictional forces in graphite with pressure (temperature). Our conclusions are supported by the good agreement of the calculated frequencies with existing Raman experiments under hydrostatic pressure conditions.

  6. Theoretical study of molecular vibrations in electron momentum spectroscopy experiments on furan: An analytical versus a molecular dynamical approach

    Energy Technology Data Exchange (ETDEWEB)

    Morini, Filippo; Deleuze, Michael S., E-mail: michael.deleuze@uhasselt.be [Center of Molecular and Materials Modelling, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek (Belgium); Watanabe, Noboru; Takahashi, Masahiko [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577 (Japan)

    2015-03-07

    The influence of thermally induced nuclear dynamics (molecular vibrations) in the initial electronic ground state on the valence orbital momentum profiles of furan has been theoretically investigated using two different approaches. The first of these approaches employs the principles of Born-Oppenheimer molecular dynamics, whereas the so-called harmonic analytical quantum mechanical approach resorts to an analytical decomposition of contributions arising from quantized harmonic vibrational eigenstates. In spite of their intrinsic differences, the two approaches enable consistent insights into the electron momentum distributions inferred from new measurements employing electron momentum spectroscopy and an electron impact energy of 1.2 keV. Both approaches point out in particular an appreciable influence of a few specific molecular vibrations of A{sub 1} symmetry on the 9a{sub 1} momentum profile, which can be unravelled from considerations on the symmetry characteristics of orbitals and their energy spacing.

  7. Enhanced vibrational spectroscopy, intracellular refractive indexing for label-free biosensing and bioimaging by multiband plasmonic-antenna array.

    Science.gov (United States)

    Chen, Cheng-Kuang; Chang, Ming-Hsuan; Wu, Hsieh-Ting; Lee, Yao-Chang; Yen, Ta-Jen

    2014-10-15

    In this study, we report a multiband plasmonic-antenna array that bridges optical biosensing and intracellular bioimaging without requiring a labeling process or coupler. First, a compact plasmonic-antenna array is designed exhibiting a bandwidth of several octaves for use in both multi-band plasmonic resonance-enhanced vibrational spectroscopy and refractive index probing. Second, a single-element plasmonic antenna can be used as a multifunctional sensing pixel that enables mapping the distribution of targets in thin films and biological specimens by enhancing the signals of vibrational signatures and sensing the refractive index contrast. Finally, using the fabricated plasmonic-antenna array yielded reliable intracellular observation was demonstrated from the vibrational signatures and intracellular refractive index contrast requiring neither labeling nor a coupler. These unique features enable the plasmonic-antenna array to function in a label-free manner, facilitating bio-sensing and imaging development.

  8. Exploring Solvent Shape and Function Using - and Isomer-Selective Vibrational Spectroscopy

    Science.gov (United States)

    Johnson, Mark

    2010-06-01

    We illustrate the new types of information than can be obtained through isomer-selective ``hole-burning'' spectroscopy carried out in the vibrational manifolds of Ar-tagged cluster ions. Three examples of increasing complexity will be presented where the changes in a solute ion are correlated with different morphologies of a surrounding solvent cage. In the first, we discuss the weak coupling limit where different hydration morphologies lead to small distortions of a covalent ion. We then introduce the more interesting case of the hydrated electron, where different shapes of the water network lead to dramatic changes in the extent of delocalization in the diffuse excess electron cloud. We then turn to the most complex case involving hydration of the nitrosonium ion, where different arrangements of the same number of water molecules span the range in behavior from simple solvation to actively causing a chemical reaction. The latter results are particularly interesting as they provide a microscopic, molecular-level picture of the ``solvent coordinate'' commonly used to describe solvent mediated processes.

  9. Chemometrics and vibrational spectroscopy as green tools for mine phytoremediation strategies

    Science.gov (United States)

    Mokgalaka-Matlala, N. S.; Regnier, T.; Combrinck, S.; Kouekam, C. R.; Weiersbye, I. M.

    This study describes the use of near infrared (NIR) spectroscopy in combination with chemometrics to characterise Combretum erythrophyllum plant material to determine differences in the chemical profiles of samples harvested from mine contaminated areas and those of natural populations. The chemometric computation of near infrared vibrational spectra was used to generate principal component analysis and partial least squares models. These models were used to determine seasonal differences in the chemical matrices of samples harvested from the mine sites with different levels of contamination. Principal component analysis scatter plots illustrated clustering of phenolic profiles of samples depending on whether they originated from contaminated or uncontaminated soils. A partial least squares model was developed to link the variations in the chemical composition and levels of contamination in all samples collected in the same season (autumn). The levels of total soluble phenolic compounds in leaf extracts of C. erythrophyllum were measured using the Folin-Ciocalteau assay. Data analysis of the samples revealed that plants harvested from mine sites, particularly in summer, produced a higher level of phenolic compounds than those of the natural population, thereby displaying a good correlation with the chemometric models.

  10. Application of Reed-Vibration Mechanical Spectroscopy for Liquids in Studying Liquid Crystallization

    Science.gov (United States)

    Zhou, Heng-Wei; Wang, Li-Na; Zhang, Li-Li; Huang, Yi-Neng

    2013-08-01

    By using the reed-vibration mechanical spectroscopy for liquids (RMS-L), we measured the complex Young's modulus of dimethyl phthalate (DP) during a cooling and heating circulation starting from room temperature at about 2 KHz. The results show that there is no crystallization in the cooling supercooled liquid (CSL) of DP, but a crystallization process in the heating supercooled liquid (HSL) after the reverse glass transition. Based on the measured modulus, crystal volume fraction (v) during the HSL crystallization was calculated. Moreover, the Avrami exponent (n) was obtained according to the JJMA equation and v data. In view of n versus temperature and v, the nucleation dynamics was analyzed, and especially, there has already existed saturate nuclei in DP HSL before the crystallization. Furthermore, the authors inferred that the nuclei are induced by the random frozen stress in the glass, but there is no nucleus in CSL. The above results indicated that RMS-L might provide a new way to measure and analyze the crystallization of liquids.

  11. Probing QED and fundamental constants through laser spectroscopy of vibrational transitions in HD+

    CERN Document Server

    Biesheuvel, J; Hilico, L; Eikema, K S E; Ubachs, W; Koelemeij, J C J

    2016-01-01

    The simplest molecules in nature, molecular hydrogen ions in the form of H2+ and HD+, provide an important benchmark system for tests of quantum electrodynamics in complex forms of matter. Here, we report on such a test based on a frequency measurement of a vibrational overtone transition in HD+ by laser spectroscopy. We find that the theoretical and experimental frequencies are equal to within 0.6(1.1) parts per billion, which represents the most stringent test of molecular theory so far. Our measurement not only confirms the validity of high-order quantum electrodynamics in molecules, but also enables the long predicted determination of the proton-to-electron mass ratio from a molecular system, as well as improved constraints on hypothetical fifth forces and compactified higher dimensions at the molecular scale. With the perspective of comparisons between theory and experiment at the 0.01 part-per-billion level, our work demonstrates the potential of molecular hydrogen ions as a probe of fundamental physica...

  12. Localised vibrational mode spectroscopy studies of self-interstitial clusters in neutron irradiated silicon

    Energy Technology Data Exchange (ETDEWEB)

    Londos, C. A.; Antonaras, G. [University of Athens, Solid State Physics Section, Panepistimiopolis Zografos, Athens 157 84 (Greece); Chroneos, A. [Materials Engineering, The Open University, Milton Keynes MK7 6AA (United Kingdom); Department of Materials, Imperial College, London SW7 2AZ (United Kingdom)

    2013-07-28

    The evolution of self-interstitial clusters in silicon (Si), produced by fast neutron irradiation of silicon crystals followed by anneals up to 750 °C, is investigated using localised vibrational mode spectroscopy. A band at 582 cm{sup −1} appears after irradiation and is stable up to 550 °C was attributed to small self-interstitial clusters (I{sub n}, n ≤ 4), with the most probable candidate the I{sub 4} structure. Two bands at 713 and 758 cm{sup −1} arising in the spectra upon annealing of the 582 cm{sup −1} band and surviving up to ∼750 °C were correlated with larger interstitial clusters (I{sub n}, 5 ≤ n ≤ 8), with the most probable candidate the I{sub 8} structure or/and with chainlike defects which are precursors of the (311) extended defects. The results illustrate the presence of different interstitial clusters I{sub n}, at the various temperature intervals of the material, in the course of an isochronal anneal sequence. As the annealing temperature increases, they evolve from first-order structures with a small number of self-interstitials (I{sub n}, n ≤ 4) for the temperatures 50 < T < 550 °C, to second order structures (I{sub n}, 5 ≤ n ≤ 8) with a larger number of interstitials, for the temperatures 550 < T < 750 °C.

  13. Energy calibration issues in nuclear resonant vibrational spectroscopy: observing small spectral shifts and making fast calibrations.

    Science.gov (United States)

    Wang, Hongxin; Yoda, Yoshitaka; Dong, Weibing; Huang, Songping D

    2013-09-01

    The conventional energy calibration for nuclear resonant vibrational spectroscopy (NRVS) is usually long. Meanwhile, taking NRVS samples out of the cryostat increases the chance of sample damage, which makes it impossible to carry out an energy calibration during one NRVS measurement. In this study, by manipulating the 14.4 keV beam through the main measurement chamber without moving out the NRVS sample, two alternative calibration procedures have been proposed and established: (i) an in situ calibration procedure, which measures the main NRVS sample at stage A and the calibration sample at stage B simultaneously, and calibrates the energies for observing extremely small spectral shifts; for example, the 0.3 meV energy shift between the 100%-(57)Fe-enriched [Fe4S4Cl4](=) and 10%-(57)Fe and 90%-(54)Fe labeled [Fe4S4Cl4](=) has been well resolved; (ii) a quick-switching energy calibration procedure, which reduces each calibration time from 3-4 h to about 30 min. Although the quick-switching calibration is not in situ, it is suitable for normal NRVS measurements.

  14. Vibrational overtone combination spectroscopy (VOCSY)-a new way of using IR and NIR data.

    Science.gov (United States)

    Alm, Erik; Bro, Rasmus; Engelsen, Søren B; Karlberg, Bo; Torgrip, Ralf J O

    2007-05-01

    This work explores a novel method for rearranging 1st order (one-way) infra-red (IR) and/or near infra-red (NIR) ordinary spectra into a representation suitable for multi-way modelling and analysis. The method is based on the fact that the fundamental IR absorption and the first, second, and consecutive overtones of NIR absorptions represent identical chemical information. It is therefore possible to rearrange these overtone regions of the vectors comprising an IR and NIR spectrum into a matrix where the fundamental, 1st, 2nd, and consecutive overtones of the spectrum are arranged as either rows or columns in a matrix, resulting in a true three-way tensor of data for several samples. This tensorization facilitates explorative analysis and modelling with multi-way methods, for example parallel factor analysis (PARAFAC), N-way partial least squares (N-PLS), and Tucker models. The vibrational overtone combination spectroscopy (VOCSY) arrangement is shown to benefit from the "order advantage", producing more robust, stable, and interpretable models than, for example, the traditional PLS modelling method. The proposed method also opens the field of NIR for true peak decomposition--a feature unique to the method because the latent factors acquired using PARAFAC can represent pure spectral components whereas latent factors in principal component analysis (PCA) and PLS usually do not.

  15. High-resolution monochromator for iron nuclear resonance vibrational spectroscopy of biological samples

    Science.gov (United States)

    Yoda, Yoshitaka; Okada, Kyoko; Wang, Hongxin; Cramer, Stephen P.; Seto, Makoto

    2016-12-01

    A new high-resolution monochromator for 14.4-keV X-rays has been designed and developed for the Fe nuclear resonance vibrational spectroscopy of biological samples. In addition to high resolution, higher flux and stability are especially important for measuring biological samples, because of the very weak signals produced due to the low concentrations of Fe-57. A 24% increase in flux while maintaining a high resolution better than 0.9 meV is achieved in the calculation by adopting an asymmetric reflection of Ge, which is used as the first crystal of the three-bounce high-resolution monochromator. A 20% increase of the exit beam size is acceptable to our biological applications. The higher throughput of the new design has been experimentally verified. A fine rotation mechanics that combines a weak-link hinge with a piezoelectric actuator was used for controlling the photon energy of the monochromatic beam. The resulting stability is sufficient to preserve the intrinsic resolution.

  16. Study of plasmonic nanoparticles interactions with skin layers by vibrational spectroscopy.

    Science.gov (United States)

    Jeništová, Adéla; Dendisová, Marcela; Matějka, Pavel

    2016-12-21

    The healing effects of silver and gold nanoparticles (AgNPs, AuNPs) are already known from ancient times. In addition considering to their antibacterial and anti-inflammatory effects speculations are being lead with respect to these nanoparticles (NPs) also about enhancement of skin penetration properties. In this work the interactions of pig skin (PS) layers and ointments with additions of AgNPs or AuNPs prepared by standard procedures and also by "green" synthesis in a different weight proportion by vibrational spectroscopy were studied. Spectra of untreated skin and skin treated by pure ointment were measured, as well as by ointment modified by vitamins without addition of NPs or with different proportion of NPs. Kinetics of interactions of modified ointments with skin was monitored during two hours with a five-minutes interval between each two consecutive measurements. The obtained series of spectra were analyzed by multivariate statistical methods namely Partial Least Squares (PLS), Principal Component Analysis (PCA) and Soft Independent Modelling of Class Analogy (SIMCA) which revealed observation of spectral changes in time-dependent spectra and variations of the peak intensity ratios. The study showed that the effects of quantity and type of NPs on skin penetration characteristics are evident.

  17. Terahertz Spectroscopy and Global Analysis of the Bending Vibrations of Acetylene 12C2D2

    Science.gov (United States)

    Yu, Shanshan; Drouin, Brian J.; Pearson, John C.; Pickett, Herbert M.; Lattanzi, Valerio; Walters, Adam

    2009-06-01

    Two hundred and fifty-one 12C2D2 transitions have been measured in the 0.2-1.6 THz region of its ν5-ν4 difference band and 202 of them were observed for the first time. The accuracy of these measurements is estimated to be ranging from 50 kHz to 100 kHz. The 12C2D2 molecules were generated under room temperature by passing 120-150 mTorr D2O vapor through calcium carbide (CaC2) powder. A multistate analysis was carried out for the bending vibrational modes ν4 and ν5 of 12C2D2, which includes the lines observed in this work and prior microwave, far-infrared and infrared data on the pure bending levels. Significantly improved molecular parameters were obtained for 12C2D2 by adding the new measurements to the old data set, which had only 10 lines with microwave measurement precision. New frequency and intensity predictions have been made based on the obtained molecular parameters. The more precise measurements and new predictions reported here will support the analyses of astronomical observations by the future high-resolution spectroscopy telescopes such as Herschel, SOFIA, and ALMA, which will work in the terahertz spectral region.

  18. Theoretical vibrational sum-frequency generation spectroscopy of water near lipid and surfactant monolayer interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Roy, S.; Gruenbaum, S. M.; Skinner, J. L. [Theoretical Chemistry Institute and Department of Chemistry, 1101 University Ave., University of Wisconsin-Madison, Madison, Wisconsin 53706 (United States)

    2014-11-14

    Understanding the structure of water near cell membranes is crucial for characterizing water-mediated events such as molecular transport. To obtain structural information of water near a membrane, it is useful to have a surface-selective technique that can probe only interfacial water molecules. One such technique is vibrational sum-frequency generation (VSFG) spectroscopy. As model systems for studying membrane headgroup/water interactions, in this paper we consider lipid and surfactant monolayers on water. We adopt a theoretical approach combining molecular dynamics simulations and phase-sensitive VSFG to investigate water structure near these interfaces. Our simulated spectra are in qualitative agreement with experiments and reveal orientational ordering of interfacial water molecules near cationic, anionic, and zwitterionic interfaces. OH bonds of water molecules point toward an anionic interface leading to a positive VSFG peak, whereas the water hydrogen atoms point away from a cationic interface leading to a negative VSFG peak. Coexistence of these two interfacial water species is observed near interfaces between water and mixtures of cationic and anionic lipids, as indicated by the presence of both negative and positive peaks in their VSFG spectra. In the case of a zwitterionic interface, OH orientation is toward the interface on the average, resulting in a positive VSFG peak.

  19. Molecular order at polymer interfaces measured by broad-bandwidth vibrationally-resolved sum frequency generation spectroscopy.

    Science.gov (United States)

    Wilson, Philip T.; Briggman, Kimberly A.; Stephenson, John C.; Wallace, William E.; Richter, Lee J.

    2001-03-01

    Broad-bandwidth vibrationally-resolved sum frequency generation (VR-SFG)spectroscopy has been used to measure the molecular orientation distribution at polymer/dielectric interfaces. A novel three layer microcavity structure of polystyrene (i.e.,PS)/spin-on hydrogen silsesquioxane dielectric (i.e.,spin-on glass)/Au has been developed in which manipulation of Fresnel factors through the variation of dielectric thickness allows unique spectroscopic study of either the free or buried polymer interface. Chemically specific VR-SFG spectroscopy of the phenyl groups of PS reveals opposite absolute orientations of these groups for the two interfaces, each directed away from the bulk of the PS film.

  20. Study of calcification formation and disease diagnostics utilising advanced vibrational spectroscopy

    Science.gov (United States)

    Kerssens, Marleen Maartje

    The accurate and safe diagnosis of breast cancer is a significant societal issue, with annual disease incidence of 48,000 women and around 370 men in the UK. Early diagnosis of the disease allows more conservative treatments and better patient outcomes. Microcalcifications in breast tissue are an important indicator for breast cancers, and often the only sign of their presence. Several studies have suggested that the type of calcification formed may act as a marker for malignancy and its presence may be of biological significance. In this work, breast calcifications are studied with FTIR, synchrotron FTIR, ATR FTIR, and Raman mapping to explore their disease specific composition. From a comparison between vibrational spectroscopy and routine staining procedures it becomes clear that calcium builds up prior to calcification formation. Raman and FTIR indicate the same size for calcifications and are in agreement with routine staining techniques. From the synchrotron FTIR measurements it can be proven that amide is present in the centre of the calcifications and the intensity of the bands depends on the pathology. Special attention is paid to the type of carbonate substitution in the calcifications relating to different pathology grades. In contrast to mammography, Raman spectroscopy has the capability to distinguish calcifications based on their chemical composition. The ultimate goal is to turn the acquired knowledge from the mapping studies into a clinical tool based on deep Raman spectroscopy. Deep Raman techniques have a considerable potential to reduce large numbers of normal biopsies, reduce the time delay between screening and diagnosis and therefore diminish patient anxiety. In order to achieve this, a deep Raman system is designed and after evaluation of its performance tested on buried calcification standards in porcine soft tissue and human mammary tissue. It is shown that, when the calcification is probed through tissue, the strong 960 cm-1 phosphate band

  1. Vibrational spectroscopy [FTIR and FTRaman] investigation, computed vibrational frequency analysis and IR intensity and Raman activity peak resemblance analysis on 4-chloro 2-methylaniline using HF and DFT [LSDA, B3LYP and B3PW91] calculations.

    Science.gov (United States)

    Ramalingam, S; Periandy, S

    2011-03-01

    In the present study, the FT-IR and FT-Raman spectra of 4-chloro-2-methylaniline (4CH2MA) have been recorded in the range of 4000-100 cm(-1). The fundamental modes of vibrational frequencies of 4CH2MA are assigned. All the geometrical parameters have been calculated by HF and DFT (LSDA, B3LYP and B3PW91) methods with 6-31G (d, p) and 6-311G (d, p) basis sets. Optimized geometries of the molecule have been interpreted and compared with the reported experimental values for aniline and some substituted aniline. The harmonic and anharmonic vibrational wavenumbers, IR intensities and Raman activities are calculated at the same theory levels used in geometry optimization. The calculated frequencies are scaled and compared with experimental values. The scaled vibrational frequencies at LSDA/B3LYP/6-311G (d, p) seem to coincide with the experimentally observed values with acceptable deviations. The impact of substitutions on the benzene structure is investigated. The molecular interactions between the substitutions (Cl, CH(3) and NH(2)) are also analyzed.

  2. Vibrational spectroscopy and solubility study of the mineral stringhamite CaCuSiO₄·H₂O.

    Science.gov (United States)

    Frost, Ray L; Xi, Yunfei

    2012-06-01

    Stringhamite CaCuSiO(4)·H(2)O is a hydrated calcium copper silicate and is commonly known as a significant 'healing' mineral and is potentially a semi-precious jewel. Stringhamite is a neosilicate with Cu(2+) in square planar coordination. Vibrational spectroscopy has been used to characterise the molecular structure of stringhamite. The intense sharp Raman band at 956 cm(-1) is assigned to the ν(1) (A(1g)) symmetric stretching vibration. Raman bands at 980, 997, 1061 cm(-1) are assigned to the ν(3) (A(2u), B(1g)) antisymmetric stretching vibrations. Splitting of the ν(3) vibrational mode supports the concept that the stringhamite SiO(4) tetrahedron is strongly distorted. The intense bands at 505 and 519 cm(-1) and at 570 cm(-1) are assigned to the ν(2) and ν(4) vibrational modes. The question arises as to whether the mineral stringhamite can actually function as a healing mineral. An estimation of the solubility product at pHcopper ion is a very powerful antibiological agent and thus the mineral stringhamite may well function as a healing mineral.

  3. Effects of Plant Cell Wall Matrix Polysaccharides on Bacterial Cellulose Structure Studied with Vibrational Sum Frequency Generation Spectroscopy and X-ray Diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Park, Yong Bum; Lee, Christopher M; Kafle, Kabindra; Park, Sunkyu; Cosgrove, Daniel; Kim, Seong H

    2014-07-14

    The crystallinity, allomorph content, and mesoscale ordering of cellulose produced by Gluconacetobacter xylinus cultured with different plant cell wall matrix polysaccharides were studied with vibrational sum frequency generation (SFG) spectroscopy and X-ray diffraction (XRD).

  4. Structural Variations in Amorphous Silicon and Germanium: a Vibrational Spectroscopy Study

    Science.gov (United States)

    Maley, Nagendranath

    Variations in short range structural order in the tetrahedral amorphous semiconductors Si and Ge have been studied by means of vibrational spectroscopy. Short range order (SRO) in in a-Si and a-Ge can be described by bond length, bond angle and dihedral angle distributions. While the existence of SRO in amorphous (a-) Si and Ge has been known for a long time, it was believed until recently that it was not variable. This notion was, in part, based on the results of conventional diffraction studies which showed negligible changes in the radial distribution function for different samples. Thus the observed variations in physical properties as a function of sample preparation conditions were attributed to extrinsic effects such as voids. However, recent studies in this laboratory showed that SRO is variable, primarily through modifications of P((THETA)), the bond angle distribution, and that Raman scattering can be used to measure small variations in (DELTA)(THETA), the width of P((THETA)). Subsequent studies here and elsewhere have shown strong correlations between Raman and various physical properties suggesting that variations in SRO have important consequences on electronic as well as vibrational properties of both a-Si and a-Ge. A detailed study has been carried out to investigate the extent of variation in SRO and the effect of preparation conditions. The results show the bond angle distribution width to be very sensitive to preparation conditions, particularly, temperature, bombardment and hydrogen incorporation. Phonon spectra of highly ordered and highly disordered samples of a-Ge have been obtained by means of inelastic neutron scattering. Detailed comparisons between theory and experiment for phonon as well as Raman spectra show qualitative agreement. The discrepancies provide suggestions for further improvements in theory. Estimates from a combination of optical, Raman and RDF data and comparisons between theory and experiment suggest that (DELTA

  5. The Complete Molecular Geometry of Salicyl Aldehyde from Rotational Spectroscopy

    Science.gov (United States)

    Dorosh, O.; Bialkowska-Jaworska, E.; Kisiel, Z.; Pszczolkowski, L.; Kanska, M.; Krygowski, T. M.; Maeder, H.

    2013-06-01

    Salicyl aldehyde is a well known planar molecule containing an internal hydrogen bond. In preparing the publication of our previous report of the study of its rotational spectrum we have taken the opportunity to update the structure determination of this molecule to the complete r_e^{SE} geometry. The molecule contains 15 atoms and we have used supersonic expansion FTMW spectroscopy to obtain rotational constants for a total 26 different isotopic species, including all singly substitued species relative to the parent molecule. The ^{13}C and ^{18}O substitutions were measured in natural abundance, while deuterium substitutions were carried out synthetically. The r_e^{SE} determination requires the calculation of vibration-rotation changes in rotational constants from an ab initio anharmonic force field, which necessitates some compromises in the level of calculation for a molecule of the size of salicyl aldehyde. For this reason we studied the five lowest vibrationally excited states, by using the combination of room-temperature mm-wave spectroscopy and waveguide Fourier transform cm-wave spectroscopy. The experimental excited state rotational constants were then used to calibrate the anharmonic force field calculation. The resulting r_e^{SE} geometry is compared with other types of geometry determination possible from this data, with emphasis on the effect of the near zero principal coordinate of the important C_2 atom. Z.Kisiel et al., 61^{st} OSU Symposium on Molecular Spectroscopy, The Ohio State University, Ohio 2006, RI-12.

  6. Enthalpy of formation and anharmonic force field of diacetylene.

    Science.gov (United States)

    Simmonett, Andrew C; Schaefer, Henry F; Allen, Wesley D

    2009-01-28

    The enthalpy of formation of diacetylene (C4H2) is pinpointed using state-of-the-art theoretical methods, accounting for high-order electron correlation, relativistic effects, non-Born-Oppenheimer corrections, and vibrational anharmonicity. Molecular energies are determined from coupled cluster theory with single and double excitations (CCSD), perturbative triples [CCSD(T)], full triples (CCSDT), and perturbative quadruples [CCSDT(Q)], in concert with correlation-consistent basis sets (cc-pVXZ, X=D, T, Q, 5, 6) that facilitate extrapolations to the complete basis set limit. The first full quartic force field of diacetylene is determined at the highly accurate all-electron CCSD(T) level with a cc-pCVQZ basis, which includes tight functions for core correlation. Application of second-order vibrational perturbation theory to our anharmonic force field yields fundamental frequencies with a mean absolute difference of only 3.9 cm(-1) relative to the experimental band origins, without the use of any empirical scale factors. By a focal point approach, we converge on an enthalpy change for the isogyric reaction 2 H-C[triple bond]C-H-->H-C[triple bond]C-C[triple bond]C-H+H2 of (+0.03, +0.81) kcal mol(-1) at (0, 298.15) K. With the precisely established fHdegrees of acetylene, we thus obtain DeltafHdegrees(C4H2)=(109.4,109.7)+/-0.3 kcal mol(-1) at (0, 298.15) K. Previous estimates of the diacetylene enthalpy of formation range from 102 to 120 kcal mol(-1).

  7. Thermodynamic properties of wadsleyite with anharmonic effect

    Institute of Scientific and Technical Information of China (English)

    Zhongqing Wu

    2015-01-01

    The thermodynamic properties of crystals can be routinely calculated by density functional theory calculations combining with quasi-harmonic approximation.Based on the method developed recently by Wu and Wentzcovitch (Phys Rev B 79:104304,2009) and Wu (Phys Rev B 81:172301,2010),we are able to further ab initio include anharmonic effect on thermodynamic properties of crystals by one additional canonical ensemble with numbers of particle,volume and temperature fixed (NVT) molecular dynamic simulations.Our study indicates that phonon-phonon interaction causes the renormalized phonon frequencies of wadsleyite decrease with temperature.This is consistent with the Raman experimental observation.The anharmonic free energy of wadsleyite is negative and its heat capacity at constant pressure can exceed the Dulong-Petit limit at high temperature.The anharmonicity still significantly affects thermodynamic properties of wadsleyite at pressure and temperature conditions correspond to the transition zone.

  8. Two-dimensional Infrared Spectroscopy of vibrational polaritons of molecules in an optical cavity

    CERN Document Server

    Saurabh, Prasoon

    2016-01-01

    Strong coupling of molecular vibrations to an infrared cavity mode affects their nature by creating dressed polariton states. We show how the single and double vibrational polariton manifolds may be controlled by varying the cavity coupling strength, and probed by a time domain 2DIR technique, Double Quantum Coherence (DQC). Applications are made to the amide-I ($CO$) and amide-II ($CN$) bond vibrations of $N-methylacetamide$ (NMA).

  9. Synthesis, characterization and vibrational studies of p-chlorosulfinylaniline

    Science.gov (United States)

    Chemes, Doly M.; Alonso de Armiño, Diego J.; Cutin, Edgardo H.; Oberhammer, Heinz; Robles, Norma L.

    2017-01-01

    p-Cholorosulfinylaniline was prepared by the reaction of p-chloroaniline and SOCl2. The structural, conformational and configurational properties of the obtained liquid compound were studied by Raman and infrared spectroscopy in the liquid state. The assignment of the vibrational spectra was carried out with the help of data obtained by quantum chemical calculations at the harmonic oscillator approximation and using anharmonic vibrational self-consistent field (VSCF) method as well. The 1H and 13C NMR chemical shifts of the molecule were calculated by Gauge including orbital (GIAO) method (DFT/B3LYP approximation using 6-311 + G (df), 6-311++G (df,pd) and cc-pVTZ basis sets) and compared to the experimental values. Natural Bond Orbital analysis provides an explanation of the stability of the molecule and its electronic properties upon charge delocalization.

  10. Peptides as Model Systems for the Unfolded State of Proteins Explored By Vibrational Spectroscopy

    Science.gov (United States)

    Schweitzer-Stenner, Reinhard; Measey, Thomas; Hagarman, Andrew

    2008-11-01

    Unfolded proteins are generally thought to be structurally random with a minimum of non-local interactions. This concept implies that with the exception of glycine and proline the conformational propensities of amino acid residues in polypeptides should be comparable in that they all sample the statistically allowed region of the Ramachandran plot. However, over the last ten years experimental and computational evidence has emerged for the notion that the conformational space of residues might be more restricted than predicted by random or statistical coil models. We have developed several algorithms which can be used to simulate the amide I band profile of the IR, isotropic Raman, anisotropic Raman and Vibrational Circular Dichroism (VCD) spectra of polypeptides based on assumed ensembles of side chain conformations. The simulations are generally restricted by 3JcαHNH coupling constants obtained from NMR spectroscopy. A comparison with experimental results reveals that e.g. alanine has a clear preference for the so called polyproline II (PPII) conformation in short peptides. The situation becomes more complex if longer polyalanines are doped with negatively charged residues. For the so-called XAO-peptide (X2A7O2, X: diaminobutyric acid, O;ornithine) we found a more compact structure owing to multiple turn conformations sampled by the X2A7 interfaces. For Salmon Calcitonin, a 32-residue hormone, we identified a mixture of PPII, β-strand and helical conformations. Currently, we are in the process of investigating short GxG (x; different natural amino acid residues) peptides in terms of conformational distributions obtained from coil libraries. This will enable us obtain the conformational preferences of amino acid residues in the absence of nearest neighbor interactions.

  11. Anharmonicity in GaTe layered crystals

    Energy Technology Data Exchange (ETDEWEB)

    Aydinli, A. [Physics Department, Bilkent University, Ankara (Turkey); Gasanly, N.M.; Uka, A. [Physics Department, Middle East Technical University, Ankara (Turkey); Efeoglu, H. [Physics Department, Atatuerk University, Erzurum (Turkey)

    2002-07-01

    The temperature dependencies (10-300 K) of seven Raman-active mode frequencies in layered semiconductor gallium telluride have been measured in the frequency range from 25 to 300 cm{sup -1}. Softening and broadening of the optical phonon lines are observed with increasing temperature. Comparison between the experimental data and theories of the shift of the phonon lines during heating of the crystal showed that the experimental dependencies can be explained by contributions from thermal expansion and lattice anharmonicity. Lattice anharmonicity is determined to be due to three-phonon processes. (Abstract Copyright [2002], Wiley Periodicals, Inc.)

  12. Binding of Na+ and K+ to the Headgroup of Palmitic Acid Monolayers Studied by Vibrational Sum Frequency Generation Spectroscopy

    Science.gov (United States)

    Huang, Zishuai; Allen, Heather C.

    2012-06-01

    Alkali cations are critical in biological systems due to their electrical interaction with cell membranes. While Na+ and K+ share similar chemical and physical properties, they can exhibit differences when interacting with biological membranes. These phenomena may be modeled using a Langmuir monolayer of surfactant on alkali chloride solutions. Vibrational sum frequency generation (VSFG) spectroscopy is an interface specific technique that is widely employed to study molecular organization at surfaces and interfaces. VSFG spectroscopy was used to probe the CO2- vibrational mode for the carboxylic acid headgroup of palmitic acid (PA) spread on the surface of NaCl and KCl solutions in the vibrational region between 1400 and 1500 cm-1. The ability of Na+ and K+ to bind with the carboxylic headgroup of PA is revealed by observing peak positions (˜1410 cm-1 and ˜1470 cm-1) and relative intensity for the CO2- peaks. These results are compared and discussed with perspective toward elucidating interfacial PA headgroup organization. The time evolution for the PA CO2- peaks is also monitored after monolayer spreading via VSFG and these results are presented as well.

  13. Pushing The Sample-Size Limit Of Infrared Vibrational Nano-Spectroscopy: From Monolayer Towards Single molecule sensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Xiaoji G.; Rang, Matthias; Craig, Ian M.; Rashcke, Markus B.

    2012-06-18

    While scattering-scanning near-field optical microscopy (s-SNOM) has demonstrated its potential to extend infrared (IR) spectroscopy into the nanometer scale, it has not yet reached its full potential in terms of spectroscopic sensitivity. We combine broadband femtosecond mid-IR excitation with an optimized spectral irradiance of 2 W/cm2/ cm–1 (power/area/bandwidth) and a combination of tip- and substrate enhancement to demonstrate single-monolayer sensitivity with exceptional signal-to-noise ratio. Using interferometric time domain detection, the near-field IR s-SNOM spectral phase directly reflects the molecular vibrational resonances and their intrinsic line shapes. We probe the stretching resonance of 1000 carbonyl groups at 1700 cm–1 in a self-assembled monolayer of 16-mercaptohexadecanoic acid (MHDA) on an evaporated gold substrate with spectroscopic contrast and sensitivity of 100 vibrational oscillators. From these results we provide a roadmap for achieving true single-molecule IR vibrational spectroscopy in s-SNOM by implementing optical antenna resonant enhancement, increased spectral pump power, and improved detection schemes.

  14. Anharmonic effects and double giant dipole resonances

    CERN Document Server

    Voronov, V V

    2001-01-01

    A brief review of recent results of the microscopic calculations to describe characteristics of the double giant dipole resonances (DGDR) is presented. A special attention is paid to a microscopic study of the anharmonic properties of the DGDR. It is found that the deviation of the energy centroid of the DGDR from the harmonic limit follows A sup - sup 1 dependence

  15. Anharmonic phonons and high-temperature superconductivity

    Energy Technology Data Exchange (ETDEWEB)

    Crespi, V.H.; Cohen, M.L. (Department of Physics, University of California at Berkeley, and Materials Sciences Division, Lawrence Berkeley Laboratory, Berkeley, California 94720 (United States))

    1993-07-01

    We examine a simple model of anharmonic phonons with application to the superconducting isotope effect. Linear and quadratic electron-phonon coupling are considered for various model potentials. The results of the model calculations are compared with the high-temperature superconductors La[sub 2[minus][ital x

  16. Comparative study of quantum anharmonic potentials

    Energy Technology Data Exchange (ETDEWEB)

    Amore, Paolo [Facultad de Ciencias, Universidad de Colima, Bernal Diaz del Castillo 340, Colima (Mexico)]. E-mail: paolo@ucol.mx; Aranda, Alfredo [Facultad de Ciencias, Universidad de Colima, Bernal Diaz del Castillo 340, Colima (Mexico); De Pace, Arturo [Istituto Nazionale di Fisica Nucleare, Sezione di Torino, via P. Giuria 1, I-10125 Torino (Italy); Lopez, Jorge A. [Physics Department, University of Texas at El Paso, El Paso, TX (United States)

    2004-09-06

    We perform a study of various anharmonic potentials using a recently developed method. We calculate both the wave functions and the energy eigenvalues for the ground and first excited states of the quartic, sextic and octic potentials with high precision, comparing the results with other techniques available in the literature.

  17. Application of vibrational spectroscopy in the in vitro studies of carbon fiber-polylactic acid composite degradation.

    Science.gov (United States)

    Blazewicz, Marta; Gajewska, Maria Chomyszyn; Paluszkiewicz, Czeslawa

    1999-05-01

    Vibrational spectroscopy was used for assessment of new material for stomatology, for guided tissue regeneration (GTR) techniqe.Implants applied in the healing of periodontal defects using GTR technique have to meet stringent requirements concerning their chemical as well physical properties.At present the implants prepared from two layers membranes differing in porosity in their outer and inner layers are studied clinically. Composite plates prepared by us consist of three layers: polylactic acid film, carbon fibres coated with polylactic acid and carbon fabric.Vibrational spectroscopic studies of the material; polylactic acid- carbon fiber have made it possible to analyse chemical reactions occurring between the polymer and carbon surface. Analysis of the IR spectra of samples treated in Ringer solution allowed to describe the phenomena resulting from the composite degradation. It was shown that material biostability is related to the presence of carbon fibers.

  18. Linear and third- and fifth-order nonlinear spectroscopies of a charge transfer system coupled to an underdamped vibration

    Energy Technology Data Exchange (ETDEWEB)

    Dijkstra, Arend G., E-mail: arend.dijkstra@mpsd.mpg.de, E-mail: tanimura@kuchem.kyoto-u.ac.jp [Max Planck Institute for the Structure and Dynamics of Matter, Hamburg (Germany); Tanimura, Yoshitaka, E-mail: arend.dijkstra@mpsd.mpg.de, E-mail: tanimura@kuchem.kyoto-u.ac.jp [Department of Chemistry, Kyoto University, Kyoto (Japan)

    2015-06-07

    We study hole, electron, and exciton transports in a charge transfer system in the presence of underdamped vibrational motion. We analyze the signature of these processes in the linear and third-, and fifth-order nonlinear electronic spectra. Calculations are performed with a numerically exact hierarchical equations of motion method for an underdamped Brownian oscillator spectral density. We find that combining electron, hole, and exciton transfers can lead to non-trivial spectra with more structure than with excitonic coupling alone. Traces taken during the waiting time of a two-dimensional (2D) spectrum are dominated by vibrational motion and do not reflect the electron, hole, and exciton dynamics directly. We find that the fifth-order nonlinear response is particularly sensitive to the charge transfer process. While third-order 2D spectroscopy detects the correlation between two coherences, fifth-order 2D spectroscopy (2D population spectroscopy) is here designed to detect correlations between the excited states during two different time periods.

  19. Linear and third- and fifth-order nonlinear spectroscopies of a charge transfer system coupled to an underdamped vibration.

    Science.gov (United States)

    Dijkstra, Arend G; Tanimura, Yoshitaka

    2015-06-01

    We study hole, electron, and exciton transports in a charge transfer system in the presence of underdamped vibrational motion. We analyze the signature of these processes in the linear and third-, and fifth-order nonlinear electronic spectra. Calculations are performed with a numerically exact hierarchical equations of motion method for an underdamped Brownian oscillator spectral density. We find that combining electron, hole, and exciton transfers can lead to non-trivial spectra with more structure than with excitonic coupling alone. Traces taken during the waiting time of a two-dimensional (2D) spectrum are dominated by vibrational motion and do not reflect the electron, hole, and exciton dynamics directly. We find that the fifth-order nonlinear response is particularly sensitive to the charge transfer process. While third-order 2D spectroscopy detects the correlation between two coherences, fifth-order 2D spectroscopy (2D population spectroscopy) is here designed to detect correlations between the excited states during two different time periods.

  20. Revealing subsurface vibrational modes by atom-resolved damping force spectroscopy.

    Science.gov (United States)

    Ashino, Makoto; Wiesendanger, Roland; Khlobystov, Andrei N; Berber, Savas; Tománek, David

    2009-05-15

    We propose to use the damping signal of an oscillating cantilever in dynamic atomic force microscopy as a noninvasive tool to study the vibrational structure of the substrate. We present atomically resolved maps of damping in carbon nanotube peapods, capable of identifying the location and packing of enclosed Dy@C_{82} molecules as well as local excitations of vibrational modes inside nanotubes of different diameter. We elucidate the physical origin of damping in a microscopic model and provide quantitative interpretation of the observations by calculating the vibrational spectrum and damping of Dy@C_{82} inside nanotubes with different diameters using ab initio total energy and molecular dynamics calculations.

  1. The origin of phonon anharmonicity in MgB{sub 2} and related compounds

    Energy Technology Data Exchange (ETDEWEB)

    Boeri, L [INFM Center for Statistical Mechanics and Complexity and Dipartimento di Fisica, Universita di Roma ' La Sapienza' , Piazzale A. Moro 2, 00185 Rome (Italy); Bachelet, G B [INFM Center for Statistical Mechanics and Complexity and Dipartimento di Fisica, Universita di Roma ' La Sapienza' , Piazzale A. Moro 2, 00185 Rome (Italy); Cappelluti, E [INFM Center for Statistical Mechanics and Complexity and Dipartimento di Fisica, Universita di Roma ' La Sapienza' , Piazzale A. Moro 2, 00185 Rome (Italy); Pietronero, L [INFM Center for Statistical Mechanics and Complexity and Dipartimento di Fisica, Universita di Roma ' La Sapienza' , Piazzale A. Moro 2, 00185 Rome (Italy)

    2003-02-01

    The recent discovery of a superconducting transition at 39 K in MgB{sub 2} - made of alternating Mg and graphene-like B planes - has raised great interest, for both its technological and theoretical implications. It was clear since the very beginning that the properties of this material are related to an anomalous coupling between the charge carriers in the {sigma} bands - due to in-plane bonds between Boron atoms - and the phonon mode (E{sub 2g}) which involves in-plane vibrations of the B ions. Theoretical studies have thus been focused on the search for possible anomalies in the e-ph coupling: one of the first results was the discovery that the E{sub 2g} phonon is highly anharmonic, but the connection between anharmonicity and T{sub c} in this material is still a controversial point. We first present a detailed first-principles study of the E{sub 2g} phonon anharmonicity in MgB{sub 2} and analogous compounds which are not superconducting, AlB{sub 2} and graphite, and in a hypothetical hole-doped graphite (C{sup 2+}{sub 2}); we then introduce an analytical model which allows us to relate the onset of anharmonicity with the small Fermi energy of the carriers in {sigma} bands. Our study suggests a possible relation between anharmonicity and non-adiabaticity; non-adiabatic effects, which can lead to a sensible increase of T{sub c} with respect to values predicted by conventional theory, become in fact relevant when phonon frequencies are comparable to electronic energy scales.

  2. Interactions of L-alanine with alumina as studied by vibrational spectroscopy.

    Science.gov (United States)

    Garcia, Ana R; de Barros, Ricardo Brito; Fidalgo, Alexandra; Ilharco, Laura M

    2007-09-25

    The interactions of L-alanine with gamma- and alpha-alumina have been investigated by diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). L-alanine/alumina samples were dried from aqueous suspensions, at 36.5 degrees C, with two amino acid concentrations (0.4 and 0.8 mmol g-1) and at different pH values (1, 6, and 13). The vibrational spectra proved that the nature of L-alanine interactions with both aluminas is the same (hydrogen bonding), although the groups involved depend on the L-alanine form and on alumina surface groups, both controlled by the pH. For samples prepared at pH 1, cationic L-alanine [CH3CH(NH3+)COOH] displaces physisorbed water from alumina, and strong hydrogen bonds are established between the carbonyl groups of alanine, as electron donors, and the surface Al-OH2+ groups of alumina. This occurs at the expense of alanine dimer dissociation and breaking of intramolecular bonds. When samples are prepared at pH 6, the interacting groups are Al-OH2+ and the carboxylate groups of zwitterionic L-alanine [CH3CH(NH3+)COO-]. The affinity of L-alanine toward alumina decreases, as the strong NH3+...-OOC intermolecular hydrogen bonds prevail over the interactions with alumina. Thus, for a load of 0.8 mmol g-1, phase segregation is observed. On alpha-alumina, crystal deposition is even observed for a load of 0.4 mmol g-1. At pH 13, the carboxylate groups of anionic L-alanine [CH3CH(NH2)COO-] are not affected by alumina. Instead, hydrogen bond interactions occur between NH2 and the Al-OH surface groups of the substrate. Complementary N2 adsorption-desorption isotherms showed that adsorption of L-alanine occurs onto the alumina pore network for samples prepared at pH 1 and 13, whereas at pH 6 the amino acid/alumina interactions are not strong enough to promote adsorption. The mesoporous structure and the high specific surface area of gamma-alumina make it a more efficient substrate for adsorption of L-alanine. For each alumina, however, it is

  3. Electron-vibration entanglement in the Born-Oppenheimer description of chemical reactions and spectroscopy.

    Science.gov (United States)

    McKemmish, Laura K; McKenzie, Ross H; Hush, Noel S; Reimers, Jeffrey R

    2015-10-14

    Entanglement is sometimes regarded as the quintessential measure of the quantum nature of a system and its significance for the understanding of coupled electronic and vibrational motions in molecules has been conjectured. Previously, we considered the entanglement developed in a spatially localized diabatic basis representation of the electronic states, considering design rules for qubits in a low-temperature chemical quantum computer. We extend this to consider the entanglement developed during high-energy processes. We also consider the entanglement developed using adiabatic electronic basis, providing a novel way for interpreting effects of the breakdown of the Born-Oppenheimer (BO) approximation. We consider: (i) BO entanglement in the ground-state wavefunction relevant to equilibrium thermodynamics, (ii) BO entanglement associated with low-energy wavefunctions relevant to infrared and tunneling spectroscopies, (iii) BO entanglement in high-energy eigenfunctions relevant to chemical reaction processes, and (iv) BO entanglement developed during reactive wavepacket dynamics. A two-state single-mode diabatic model descriptive of a wide range of chemical phenomena is used for this purpose. The entanglement developed by BO breakdown correlates simply with the diameter of the cusp introduced by the BO approximation, and a hierarchy appears between the various BO-breakdown correction terms, with the first-derivative correction being more important than the second-derivative correction which is more important than the diagonal correction. This simplicity is in contrast to the complexity of BO-breakdown effects on thermodynamic, spectroscopic, and kinetic properties. Further, processes poorly treated at the BO level that appear adequately treated using the Born-Huang adiabatic approximation are found to have properties that can only be described using a non-adiabatic description. For the entanglement developed between diabatic electronic states and the nuclear motion

  4. Structure and Absolute Configuration of Nyasol and Hinokiresinol via Synthesis and Vibrational Circular Dichroism Spectroscopy

    DEFF Research Database (Denmark)

    Lassen, Peter Rygaard

    2005-01-01

    The absolute configuration of the norlignan (+)-nyasol was determined to be S by comparison of the experimental vibrational circular dichroism data with first-principle calculations taking into account the eight lowest energy conformations. The established absolute configuration of (+)-nyasol...

  5. The Fourteenth International Meeting on Time-Resolved Vibrational Spectroscopy (TRVS XIV)

    Science.gov (United States)

    2010-02-03

    Turton University of Strathclyde United Kingdom david.turton@phys.str Richard Van Duyne Northwestern University United States vanduyne@northwest...Vibrational Excitons in Liquid Formamide Righini, R. J. D. Miller, University of Toronto 2:40 PM C David A. Turton and Klaas Wynne, University of...University of Bonn Vibrational energy relaxation in liquid-to-supercritical ammonia 18 David Turton , Klaas Wynne, University of Strathclyde

  6. Vibrational spectroscopy of SnBr4 and CCl4 using Lie algebraic approach

    Indian Academy of Sciences (India)

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

    2008-09-01

    The stretching and bending vibrational energies of SnBr4 and CCl4 are calculated in the one-dimensional framework. The dynamical symmetry group of tetrahedral molecule was taken into consideration to construct the model Hamiltonian in this frame-work. Casimir and Majorana invariant operators were also determined accordingly. Using the model Hamiltonian so constructed, we reported the vibrational energy levels of SnBr4 and CCl4 molecules accurately.

  7. Temperature dependence of Raman scattering and anharmonic properties in LiNbO{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Kokanyan, Ninel; Chapron, David; Fontana, Marc D. [Universite de Lorraine, Laboratoire Materiaux Optiques, Photonique et Systemes (LMOPS), Metz (France); Supelec, Laboratoire Materiaux Optiques, Photonique et Systemes (LMOPS), Metz (France)

    2014-11-15

    The temperature dependence of the Raman spectrum in LiNbO{sub 3} is investigated from 100 to 700 K. The various sources of asymmetry of Raman bands and artefacts are discussed before analyzing the temperature dependence of A{sub 1} and E first-order phonon lines. The phonon frequency downshift and damping increase on heating are interpreted in terms of normal volume expansion and third- and fourth-order anharmonic potentials. Anharmonic contributions are highly anisotropic and mainly explain the temperature dependences of both frequency and damping of A{sub 1} optical vibrational modes along the ferroelectric axis. Results are consistent with Caciuc et al. (Phys Rev B 61:8806, 2000) predictions. (orig.)

  8. Sum Frequency Generation Vibrational Spectroscopy of Adsorbed Amino Acids, Peptides and Proteins of Hydrophilic and Hydrophobic Solid-Water Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Holinga IV, George Joseph [Univ. of California, Berkeley, CA (United States)

    2010-09-01

    Sum frequency generation (SFG) vibrational spectroscopy was used to investigate the interfacial properties of several amino acids, peptides, and proteins adsorbed at the hydrophilic polystyrene solid-liquid and the hydrophobic silica solid-liquid interfaces. The influence of experimental geometry on the sensitivity and resolution of the SFG vibrational spectroscopy technique was investigated both theoretically and experimentally. SFG was implemented to investigate the adsorption and organization of eight individual amino acids at model hydrophilic and hydrophobic surfaces under physiological conditions. Biointerface studies were conducted using a combination of SFG and quartz crystal microbalance (QCM) comparing the interfacial structure and concentration of two amino acids and their corresponding homopeptides at two model liquid-solid interfaces as a function of their concentration in aqueous solutions. The influence of temperature, concentration, equilibration time, and electrical bias on the extent of adsorption and interfacial structure of biomolecules were explored at the liquid-solid interface via QCM and SFG. QCM was utilized to quantify the biological activity of heparin functionalized surfaces. A novel optical parametric amplifier was developed and utilized in SFG experiments to investigate the secondary structure of an adsorbed model peptide at the solid-liquid interface.

  9. Vibrational spectroscopy of biofluids for disease screening or diagnosis: translation from the laboratory to a clinical setting.

    Science.gov (United States)

    Mitchell, Alana L; Gajjar, Ketan B; Theophilou, Georgios; Martin, Francis L; Martin-Hirsch, Pierre L

    2014-04-01

    There remains a need for objective and cost-effective approaches capable of diagnosing early-stage disease in point-of-care clinical settings. Given an increasingly ageing population resulting in a rising prevalence of chronic diseases, the need for screening to facilitate the personalising of therapies to prevent or slow down pathology development will increase. Such a tool needs to be robust but simple enough to be implemented into clinical practice. There is interest in extracting biomarkers from biofluids (e.g., plasma or serum); techniques based on vibrational spectroscopy provide an option. Sample preparation is minimal, techniques involved are relatively low-cost, and data frameworks are available. This review explores the evidence supporting the applicability of vibrational spectroscopy to generate spectral biomarkers of disease in biofluids. We extend the inter-disciplinary nature of this approach to hypothesise a microfluidic platform that could allow such measurements. With an appropriate lightsource, such engineering could revolutionize screening in the 21(st) century.

  10. Quantum anharmonic oscillator: The airy function approach

    Energy Technology Data Exchange (ETDEWEB)

    Maiz, F., E-mail: fethimaiz@gmail.com [King Khalid University, Faculty of Science, Physics Department, PO Box 9004, Abha 61413, Asseer (Saudi Arabia); University of Cartage, Nabeul Engineering Preparatory Institute, Merazka, 8000 Nabeul (Tunisia); AlFaify, S. [King Khalid University, Faculty of Science, Physics Department, PO Box 9004, Abha 61413, Asseer (Saudi Arabia)

    2014-05-15

    New and simple numerical method is being reported to solve anharmonic oscillator problems. The method is setup to approach the real potential V(x) of the anharmonic oscillator system as a piecewise linear potential u(x) and to solve the Schrödinger equation of the system using the Airy function. Then, solutions continuity conditions lead to the energy quantification condition, and consequently, the energy eigenvalues. For testing purpose, the method was applied on the sextic and octic oscillators systems. The proposed method is found to be realistic, computationally simple, and having high degrees of accuracy. In addition, it can be applied to any form of potential. The results obtained by the proposed method were seen closely agreeing with results reached by other complicated methods.

  11. Solvation of coumarin6 studied by vibrational spectroscopy and density functional theory

    Science.gov (United States)

    Singh, Randhir; Sathe, Vasant; Sharma, Amit; Kaur, Sarvpreet; Saini, G. S. S.

    2016-02-01

    Effect of solvation on coumarin6 dye has been studied with density functional theory (DFT). Optimized structure of the dye has been obtained in various solvents and frequencies of various vibrational bands have been calculated in these solvents. Calculations predict shift in the frequency of certain bands in the solvents. Similar shifts have been observed experimentally in the vibrational spectra of the dye in solvents. In order to ascertain the origin of these shifts, the interactions of solvent molecules with the coumarin6 molecule have been studied using various tools of DFT like donor-acceptor interactions, Molecular Electrostatic potential (MEP) and HOMO-LUMO analysis etc.

  12. Anharmonic properties of potassium halide crystals

    OpenAIRE

    RAJU, Krishna Murti

    2011-01-01

    An effort has been made to obtain the anharmonic properties of potassium halides starting from primary physical parameters viz. nearest neighbor distance and hardness parameters assuming long- and short- range potentials at elevated temperatures. The elastic energy density for a deformed crystal can be expanded as power series of strains for obtaining coefficients of quadratic, cubic and quartic terms which are known as the second, third and fourth order elastic constants respectively...

  13. Study of cancer cell lines with Fourier transform infrared (FTIR)/vibrational absorption (VA) spectroscopy

    DEFF Research Database (Denmark)

    Uceda Otero, E. P.; Eliel, G. S. N.; Fonseca, E. J. S.

    2013-01-01

    vibrational spectroscopic simulations, in addition to the chemometric and statistical tools of PCA, linear and quadratic discriminant analysis, and artificial networks methods that are good at finding correlations, but provide little if any physical, chemical and biochemical insight into the nature...

  14. Vibrational Spectroscopy of CH/CD Stretches in Propadiene: An Algebraic Approach

    Institute of Scientific and Technical Information of China (English)

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

    2009-01-01

    Using Hamiltonian based on Lie algebraic method, the stretching vibrational modes of C3H4 and C3D4 molecules are calculated up to higher overtones. The model appears to describe C-H and C-D stretching modes with less number of parameters. The locality parameter ξ confirms the highly local behaviour of the stretching modes of these molecules.

  15. Time Dependent Coupled Cluster Approach to Resonance Raman Excitation Profiles from General Anharmonic Surfaces

    Directory of Open Access Journals (Sweden)

    M. Durga Prasad

    2002-05-01

    Full Text Available Abstract: A time dependent coupled cluster approach to the calculation of Resonance Raman excitation profiles on general anharmonic surfaces is presented. The vibrational wave functions on the ground electronic surface are obtained by the coupled cluster method (CCM. It is shown that the propagation of the vibrational ground state on the upper surface is equivalent to propagation of the vacuum state by an effective hamiltonian generated by the similarity transformation of the vibrational hamiltonian of that surface by the CCM wave operator of the lower surface up to a normalization constant. This time propagation is carried out by the time-dependent coupled cluster method in a time dependent frame. Numerical studies are presented to asses the validity of the approach.

  16. Comparative Study of Cl-Atom Reactions in Solution Using Time-Resolved Vibrational Spectroscopy.

    Science.gov (United States)

    Shin, Jae Yoon; Case, Amanda S; Crim, F Fleming

    2016-04-28

    A Cl atom can react with 2,3-dimethylbutane (DMB), 2,3-dimethyl-2-butene (DMBE), and 2,5-dimethyl-2,4-hexadiene (DMHD) in solution via a hydrogen-abstraction reaction. The large exoergicity of the reaction between a Cl atom and alkenes (DMBE and DMHD) makes vibrational excitation of the HCl product possible, and we observe the formation of vibrationally excited HCl (v = 1) for both reactions. In CCl4, the branching fractions of HCl (v = 1), Γ (v = 1), for the Cl-atom reactions with DMBE and DMHD are 0.14 and 0.23, respectively, reflecting an increased amount of vibrational excitation in the products of the more exoergic reaction. In addition, Γ (v = 1) for both reactions is larger in the solvent CDCl3, being 0.23 and 0.40, as the less viscous solvent apparently dampens the vibrational excitation of the nascent HCl less effectively. The bimolecular reaction rates for the Cl reactions with DMB, DMBE, and DMHD in CCl4 are diffusion limited (having rate constants of 1.5 × 10(10), 3.6 × 10(10), and 17.5 × 10(10) M(-1) s(-1), respectively). In fact, the bimolecular reaction rate for Cl + DMHD exceeds a typical diffusion-limited reaction rate, implying that the attractive intermolecular forces between a Cl atom and a C═C bond increase the rate of favorable encounters. The 2-fold increase in the reaction rate of the Cl + DMBE reaction from that of the Cl + DMB reaction likely reflects the effect of the C═C bond, while both the number of C═C bonds and the molecular geometry likely play a role in the large reaction rate of the Cl + DMHD reaction.

  17. Vibrational Spectroscopy and Phonon-Related Properties of the L-Aspartic Acid Anhydrous Monoclinic Crystal.

    Science.gov (United States)

    Silva, A M; Costa, S N; Sales, F A M; Freire, V N; Bezerra, E M; Santos, R P; Fulco, U L; Albuquerque, E L; Caetano, E W S

    2015-12-10

    The infrared absorption and Raman scattering spectra of the monoclinic P21 l-aspartic acid anhydrous crystal were recorded and interpreted with the help of density functional theory (DFT) calculations. The effect of dispersive forces was taken into account, and the optimized unit cells allowed us to obtain the vibrational normal modes. The computed data exhibits good agreement with the measurements for low wavenumbers, allowing for a very good assignment of the infrared and Raman spectral features. The vibrational spectra of the two lowest energy conformers of the l-aspartic molecule were also evaluated using the hybrid B3LYP functional for the sake of comparison, showing that the molecular calculations give a limited description of the measured IR and Raman spectra of the l-aspartic acid crystal for wavenumbers below 1000 cm(-1). The results obtained reinforce the need to use solid-state calculations to describe the vibrational properties of molecular crystals instead of calculations for a single isolated molecule picture even for wavenumbers beyond the range usually associated with lattice modes (200 cm(-1) < ω < 1000 cm(-1)).

  18. Vibrational relaxation and vibrational cooling in low temperature molecular crystals

    Science.gov (United States)

    Hill, Jeffrey R.; Chronister, Eric L.; Chang, Ta-Chau; Kim, Hackjin; Postlewaite, Jay C.; Dlott, Dana D.

    1988-01-01

    The processes of vibrational relaxation (VR) and vibrational cooling (VC) are investigated in low temperature crystals of complex molecules, specifically benzene, naphthalene, anthracene, and durene. In the VR process, a vibration is deexcited, while VC consists of many sequential and parallel VR steps which return the crystal to thermal equilibrium. A theoretical model is developed which relates the VR rate to the excess vibrational energy, the molecular structure, and the crystal structure. Specific relations are derived for the vibrational lifetime T1 in each of three regimes of excess vibrational energy. The regimes are the following: Low frequency regime I where VR occurs by emission of two phonons, intermediate frequency regime II where VR occurs by emission of one phonon and one vibration, and high frequency regime III where VR occurs by evolution into a dense bath of vibrational combinations. The VR rate in each regime depends on a particular multiphonon density of states and a few averaged anharmonic coefficients. The appropriate densities of states are calculated from spectroscopic data, and together with available VR data and new infrared and ps Raman data, the values of the anharmonic coefficients are determined for each material. The relationship between these parameters and the material properties is discussed. We then describe VC in a master equation formalism. The transition rate matrix for naphthalene is found using the empirically determined parameters of the above model, and the time dependent redistribution in each mode is calculated.

  19. Quasi-localized low-frequency vibrational modes of disordered solids II. Study by single-molecule spectroscopy

    Science.gov (United States)

    Naumov, A. V.; Vainer, Yu. G.; Bauer, M.; Kador, L.

    2004-12-01

    By means of single molecule (SM) spectroscopy we investigated elementary matrix excitations in a disordered solid, i.e., quasi-localized low-frequency vibrational modes (LFMs). To this end we recorded the spectra of single tetra-tert-butylterrylene molecules embedded in an amorphous polyisobutylene matrix in a temperature region, where the LFM contribution to line broadening dominates. The individual param- eters of LFMs in a polymer glass can be determined from the temperature-dependent linewidths of single molecules. The magnitude of the LFM contribution to SM spectra was obtained by the statistical analysis of the distribution of linewidths of SMs. Pronounced distributions of LFM frequencies and SM-LFM coupling constants were found. This result can be regarded as the first direct experimental proof of the localized nature of LFMs.

  20. Conformational analysis of quinine and its pseudo enantiomer quinidine: a combined jet-cooled spectroscopy and vibrational circular dichroism study.

    Science.gov (United States)

    Sen, Ananya; Bouchet, Aude; Lepère, Valeria; Le Barbu-Debus, Katia; Scuderi, D; Piuzzi, F; Zehnacker-Rentien, A

    2012-08-16

    Laser-desorbed quinine and quinidine have been studied in the gas phase by combining supersonic expansion with laser spectroscopy, namely, laser-induced fluorescence (LIF), resonance-enhanced multiphoton ionization (REMPI), and IR-UV double resonance experiments. Density funtional theory (DFT) calculations have been done in conjunction with the experimental work. The first electronic transition of quinine and quinidine is of π-π* nature, and the studied molecules weakly fluoresce in the gas phase, in contrast to what was observed in solution (Qin, W. W.; et al. J. Phys. Chem. C2009, 113, 11790). The two pseudo enantiomers quinine and quinidine show limited differences in the gas phase; their main conformation is of open type as it is in solution. However, vibrational circular dichroism (VCD) experiments in solution show that additional conformers exist in condensed phase for quinidine, which are not observed for quinine. This difference in behavior between the two pseudo enantiomers is discussed.

  1. Electron diffraction study of the equilibrium structure of hexamethylenetetramine involving data from quantum chemistry and vibrational spectroscopy

    Science.gov (United States)

    Khaikin, L. S.; Grikina, O. E.; Karasev, N. M.; Kovtun, D. M.; Kochikov, I. V.

    2014-04-01

    The equilibrium structure of the urotropine molecule is characterized by means of gas electron diffraction (GED) with the involvement of quantum chemistry and vibrational spectroscopy. A structural analysis of the GED data is performed based on the parameters of the intramolecular potential function using of the program complex SYMM/DISP/ELDIFF/LARGE. The quadratic and cubic force constants of the urotropine molecule were obtained earlier on the basis of calculations at the MP2(full)/cc-pVTZ level and assuming molecular symmetry T d . The values of the equilibrium geometric parameters r e of the urotropine molecule are found. The experimental structural parameters are in good agreement with those calculated at the MP2(full)/cc-pVTZ level.

  2. N-H stretching modes around 3300 wavenumber from peptide backbones observed by chiral sum frequency generation vibrational spectroscopy.

    Science.gov (United States)

    Fu, Li; Wang, Zhuguang; Yan, Elsa C Y

    2014-09-01

    We present a detailed analysis of the molecular origin of the chiral sum frequency generation (SFG) signals of proteins and peptides at interfaces in the N-H stretching vibrational region. The N-H stretching can be a probe for investigating structural and functional properties of proteins, but remains technically difficult to analyze due to the overlapping with the O-H stretching of water molecules. Chiral SFG spectroscopy offers unique tools to study the N-H stretching from proteins at interfaces without interference from the water background. However, the molecular origin of the N-H stretching signals of proteins is still unclear. This work provides a justification of the origin of chiral N-H signals by analyzing the vibrational frequencies, examining chiral SFG theory, studying proton (hydrogen/deuterium) exchange kinetics, and performing optical control experiments. The results demonstrate that the chiral N-H stretching signals at ~3300 cm(-1) originate from the amide group of the protein backbones. This chiral N-H stretching signal offers an in situ, real-time, and background-free probe for interrogating the protein structures and dynamics at interfaces at the molecular level.

  3. Azide-water intermolecular coupling measured by 2-color 2D IR spectroscopy

    Directory of Open Access Journals (Sweden)

    Perakis F.

    2013-03-01

    Full Text Available We present 2-color two-dimensional infrared spectroscopy of intermolecular coupling between azide ions and their solvation shell water molecules. The cross-peak between azide asymmetric stretch vibration and the OD-stretch vibration is a result of low- probability uphill population transfer. Narrow bleach/excited state absorption peak shows selectivity to solvation shell water molecules only and the characteristics of the cross-peak suggest that the solvation shell hydrogen bond potential has similar anharmonic properties as the hydrogen bond in ice Ih. Population and depopulation of the excited state of the OD-stretch vibration happen on 150 fs and 1.7 ps timescales, respectively, with early manifesting heating effects that limit the selectivity to population times up to 1 ps.

  4. Molecular and vibrational structure of diphenylether and its 4,4' -dibromo derivative. Infrared linear dichroism spectroscopy and density functional theory calculations

    DEFF Research Database (Denmark)

    Eriksen, Troels K; Karlsen, Eva; Spanget-Larsen, Jens

    2015-01-01

    The title compounds were investigated by means of Linear Dichroism (LD) IR spectroscopy on samples partially aligned in uniaxially stretched low-density polyethylene and by density functional theory calculations. Satisfactory overall agreement between observed and calculated vibrational wavenumbe...... and IR intensities are obtained, allowing a fairly detailed assignment of the observed transitions in terms of individual nuclear motions....

  5. Electronic Excited State and Vibrational Dynamics of Water Solution of Cytosine Observed by Time-resolved Transient Absorption Spectroscopy with Sub-10fs Deep Ultraviolet Laser Pules

    Directory of Open Access Journals (Sweden)

    Kobayashi Takayoshi.

    2013-03-01

    Full Text Available Time-resolved transient absorption spectroscopy for water solution of cytosine with sub-10fs deep ultraviolet laser pulse is reported. Ultrafast electronic excited state dynamics and coherent molecular vibrational dynamics are simultaneously observed and their relaxation mechanisms are discussed.

  6. Modeling for proximate analysis and heating value of torrefied biomass with vibration spectroscopy.

    Science.gov (United States)

    Via, Brian K; Adhikari, Sushil; Taylor, Steve

    2013-04-01

    The goal of this study was to characterize the changes in biomass with torrefaction for near infrared reflectance (NIR) and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy for sweetgum, loblolly pine, and switchgrass. Calibration models were built for the prediction of proximate analysis after torrefaction. Two dimensional (2D) correlation spectroscopy between NIR and FTIR was found to precisely explain the depolymerization at key functional groups located within hemicellulose, cellulose, and lignin. This novel 2D technique also demonstrated the possibility of assigning key NIR wavenumbers based on mid IR spectra. Hemicellulose based wavenumbers were found to be most sensitive to torrefaction severity with complete degradation at 250-275°C. Lignin associated wavenumbers exhibited the least degradation to severity but was still detected with 2D correlation spectroscopy. Finally, calibration models for proximate analysis were performed and while both systems could be used for rapid monitoring, NIR performed better than FTIR.

  7. Communication: Uncovering correlated vibrational cooling and electron transfer dynamics with multidimensional spectroscopy

    Science.gov (United States)

    Guo, Zhenkun; Giokas, Paul G.; Cheshire, Thomas P.; Williams, Olivia F.; Dirkes, David J.; You, Wei; Moran, Andrew M.

    2016-09-01

    Analogues of 2D photon echo methods in which two population times are sampled have recently been used to expose heterogeneity in chemical kinetics. In this work, the two population times sampled for a transition metal complex are transformed into a 2D rate spectrum using the maximum entropy method. The 2D rate spectrum suggests heterogeneity in the vibrational cooling (VC) rate within the ensemble. In addition, a cross peak associated with VC and back electron transfer (BET) dynamics reveals correlation between the two processes. We hypothesize that an increase in the strength of solute-solvent interactions, which accelerates VC, drives the system toward the activationless regime of BET.

  8. Terahertz Spectroscopy of the Bending Vibrations of Acetylene 12C2H2

    Science.gov (United States)

    Yu, Shanshan; Drouin, Brian J.; Pearson, John C.

    2009-11-01

    Twenty P-branch transitions of 12C2H2 have been measured in the 0.8-1.6 THz region of its bending vibrational difference band. The accuracy of these measurements is estimated to be 100 kHz. The 12C2H2 molecules were generated under room temperature by passing 150 mTorr H2O vapor through calcium carbide (CaC2) powder. The observed transitions were modeled together with prior far-infrared data involving the bending levels with ∑\

  9. Terahertz Vibrations and Hydrogen-Bonded Networks in Crystals

    Directory of Open Access Journals (Sweden)

    Masae Takahashi

    2014-03-01

    Full Text Available The development of terahertz technology in the last few decades has made it possible to obtain a clear terahertz (THz spectrum. THz vibrations clearly show the formation of weak bonds in crystals. The simultaneous progress in the code of first-principles calculations treating noncovalent interactions has established the position of THz spectroscopy as a powerful tool for detecting the weak bonding in crystals. In this review, we are going to introduce, briefly, the contribution of weak bonds in the construction of molecular crystals first, and then, we will review THz spectroscopy as a powerful tool for detecting the formation of weak bonds and will show the significant contribution of advanced computational codes in treating noncovalent interactions. From the second section, following the Introduction, to the seventh section, before the conclusions, we describe: (1 the crystal packing forces, the hydrogen-bonded networks and their contribution to the construction of organic crystals; (2 the THz vibrations observed in hydrogen-bonded molecules; (3 the computational methods for analyzing the THz vibrations of hydrogen-bonded molecules; (4 the dispersion correction and anharmonicity incorporated into the first-principles calculations and their effect on the peak assignment of the THz spectrum (5 the temperature dependence; and (6 the polarization dependence of the THz spectrum.

  10. Vibrational spectroscopy and aromaticity investigation of squarate salts: A theoretical and experimental approach

    Science.gov (United States)

    Georgopoulos, Stéfanos L.; Diniz, Renata; Yoshida, Maria I.; Speziali, Nivaldo L.; Santos, Hélio F. Dos; Junqueira, Geórgia Maria A.; de Oliveira, Luiz F. C.

    2006-08-01

    Experimental and theoretical investigations of squarate salts [M 2(C 4O 4)] (M=Li, Na, K and Rb) were performed aiming to correlate the structures, vibrational analysis and aromaticity. Powder X-ray diffraction data show that these compounds are not isostructural, indicating that the metal-squarate and hydrogen bonds to water molecules interactions play a significant role on the the crystal packing. The infrared and Raman assigments suggest an equalization of the C-C bond lengths with the increasing of the counter-ion size. This result is interpreted as an enhancement in the electronic delocalization and consequently in the degree of aromaticity for salts with larger ions. Quantum mechanical calculations for structures, vibrational spectra and aromaticity index are in agreement with experimental finding, giving insights at molecular level for the role played by distinct complexation modes to the observed properties. Comparison between our results and literature, regarding molecular dynamics in different chemical environments, shows that aromaticity and hydrogen bonds are the most important forces driving the interactions in the solid structures of squarate ion.

  11. Electronic and vibrational spectroscopy of 1-methylthymine and its water clusters: the dark state survives hydration.

    Science.gov (United States)

    Busker, Matthias; Nispel, Michael; Häber, Thomas; Kleinermanns, Karl; Etinski, Mihajlo; Fleig, Timo

    2008-08-04

    Electronic and vibrational gas phase spectra of 1-methylthymine (1MT) and 1-methyluracil (1MU) and their clusters with water are presented. Mass selective IR/UV double resonance spectra confirm the formation of pyrimidine-water clusters and are compared to calculated vibrational spectra obtained from ab initio calculations. In contrast to Y. He, C. Wu, W. Kong; J. Phys. Chem. A, 2004, 108, 94 we are able to detect 1MT/1MU and their water clusters via resonant two-photon delayed ionization under careful control of the applied water-vapor pressure. The long-living dark electronic state of 1MT and 1MU detected by delayed ionization, survives hydration and the photostability of 1MT/1MU cannot be attributed solely to hydration. Oxygen coexpansions and crossed-beam experiments indicate that the triplet state population is probably small compared to the (1)n pi* and/or hot electronic ground state population. Ab initio theory shows that solvation of 1MT by water does not lead to a substantial modification of the electronic relaxation and quenching of the (1)n pi* state. Relaxation pathways via (1)pi pi*(1)-n pi*(1) and (1)pi pi*-S(0) conical intersections and barriers have been identified, but are not significantly altered by hydration.

  12. 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.

  13. Understanding and Manipulating Electrostatic Fields at the Protein-Protein Interface Using Vibrational Spectroscopy and Continuum Electrostatics Calculations.

    Science.gov (United States)

    Ritchie, Andrew W; Webb, Lauren J

    2015-11-05

    Biological function emerges in large part from the interactions of biomacromolecules in the complex and dynamic environment of the living cell. For this reason, macromolecular interactions in biological systems are now a major focus of interest throughout the biochemical and biophysical communities. The affinity and specificity of macromolecular interactions are the result of both structural and electrostatic factors. Significant advances have been made in characterizing structural features of stable protein-protein interfaces through the techniques of modern structural biology, but much less is understood about how electrostatic factors promote and stabilize specific functional macromolecular interactions over all possible choices presented to a given molecule in a crowded environment. In this Feature Article, we describe how vibrational Stark effect (VSE) spectroscopy is being applied to measure electrostatic fields at protein-protein interfaces, focusing on measurements of guanosine triphosphate (GTP)-binding proteins of the Ras superfamily binding with structurally related but functionally distinct downstream effector proteins. In VSE spectroscopy, spectral shifts of a probe oscillator's energy are related directly to that probe's local electrostatic environment. By performing this experiment repeatedly throughout a protein-protein interface, an experimental map of measured electrostatic fields generated at that interface is determined. These data can be used to rationalize selective binding of similarly structured proteins in both in vitro and in vivo environments. Furthermore, these data can be used to compare to computational predictions of electrostatic fields to explore the level of simulation detail that is necessary to accurately predict our experimental findings.

  14. Spectral methods for study of the G-protein-coupled receptor rhodopsin: I. Vibrational and electronic spectroscopy

    Science.gov (United States)

    Struts, A. V.; Barmasov, A. V.; Brown, M. F.

    2015-05-01

    Here we review the application of modern spectral methods for the study of G-protein-coupled receptors (GPCRs) using rhodopsin as a prototype. Because X-ray analysis gives us immobile snapshots of protein conformations, it is imperative to apply spectroscopic methods for elucidating their function: vibrational (Raman, FTIR), electronic (UV-visible absorption, fluorescence) spectroscopies, and magnetic resonance (electron paramagnetic resonance, EPR), and nuclear magnetic resonance (NMR). In the first of the two companion articles, we discuss the application of optical spectroscopy for studying rhodopsin in a membrane environment. Information is obtained regarding the time-ordered sequence of events in rhodopsin activation. Isomerization of the chromophore and deprotonation of the retinal Schiff base leads to a structural change of the protein involving the motion of helices H5 and H6 in a pH-dependent process. Information is obtained that is unavailable from X-ray crystallography, which can be combined with spectroscopic studies to achieve a more complete understanding of GPCR function.

  15. Definition of the intermediates and mechanism of the anticancer drug bleomycin using nuclear resonance vibrational spectroscopy and related methods

    Science.gov (United States)

    Liu, Lei V.; Bell, Caleb B.; Wong, Shaun D.; Wilson, Samuel A.; Kwak, Yeonju; Chow, Marina S.; Zhao, Jiyong; Hodgson, Keith O.; Hedman, Britt; Solomon, Edward I.

    2010-01-01

    Bleomycin (BLM) is a glycopeptide anticancer drug capable of effecting single- and double-strand DNA cleavage. The last detectable intermediate prior to DNA cleavage is a low spin FeIII peroxy level species, termed activated bleomycin (ABLM). DNA strand scission is initiated through the abstraction of the C-4′ hydrogen atom of the deoxyribose sugar unit. Nuclear resonance vibrational spectroscopy (NRVS) aided by extended X-ray absorption fine structure spectroscopy and density functional theory (DFT) calculations are applied to define the natures of FeIIIBLM and ABLM as (BLM)FeIII─OH and (BLM)FeIII(η1─OOH) species, respectively. The NRVS spectra of FeIIIBLM and ABLM are strikingly different because in ABLM the δFe─O─O bending mode mixes with, and energetically splits, the doubly degenerate, intense O─Fe─Nax transaxial bends. DFT calculations of the reaction of ABLM with DNA, based on the species defined by the NRVS data, show that the direct H-atom abstraction by ABLM is thermodynamically favored over other proposed reaction pathways. PMID:21149675

  16. Mixed IR/Vis two-dimensional spectroscopy: chemical exchange beyond the vibrational lifetime and sub-ensemble selective photochemistry.

    Science.gov (United States)

    van Wilderen, Luuk J G W; Messmer, Andreas T; Bredenbeck, Jens

    2014-03-03

    Two-dimensional exchange spectroscopy (2D EXSY) is a powerful method to study the interconversion (chemical exchange) of molecular species in equilibrium. This method has recently been realized in femtosecond 2D-IR spectroscopy, dramatically increasing the time resolution. However, current implementations allow the EXSY signal (and therefore the chemical process of interest) only to be tracked during the lifetime (T1 ) of the observed spectroscopic transition. This is a severe limitation, as typical vibrational T1 are only a few ps. An IR/Vis pulse sequence is presented that overcomes this limit and makes the EXSY signal independent of T1 . The same pulse sequence allows to collect time-resolved IR spectra after electronic excitation of a particular chemical species in a mixture of species with strongly overlapping UV/Vis spectra. Different photoreaction pathways and dynamics of coexisting isomers or of species involved in different intermolecular interactions can thus be revealed, even if the species cannot be isolated because they are in rapid equilibrium.

  17. High resolution IR diode laser study of collisional energy transfer between highly vibrationally excited monofluorobenzene and CO2: the effect of donor fluorination on strong collision energy transfer.

    Science.gov (United States)

    Kim, Kilyoung; Johnson, Alan M; Powell, Amber L; Mitchell, Deborah G; Sevy, Eric T

    2014-12-21

    Collisional energy transfer between vibrational ground state CO2 and highly vibrationally excited monofluorobenzene (MFB) was studied using narrow bandwidth (0.0003 cm(-1)) IR diode laser absorption spectroscopy. Highly vibrationally excited MFB with E' = ∼41,000 cm(-1) was prepared by 248 nm UV excitation followed by rapid radiationless internal conversion to the electronic ground state (S1→S0*). The amount of vibrational energy transferred from hot MFB into rotations and translations of CO2 via collisions was measured by probing the scattered CO2 using the IR diode laser. The absolute state specific energy transfer rate constants and scattering probabilities for single collisions between hot MFB and CO2 were measured and used to determine the energy transfer probability distribution function, P(E,E'), in the large ΔE region. P(E,E') was then fit to a bi-exponential function and extrapolated to the low ΔE region. P(E,E') and the biexponential fit data were used to determine the partitioning between weak and strong collisions as well as investigate molecular properties responsible for large collisional energy transfer events. Fermi's Golden rule was used to model the shape of P(E,E') and identify which donor vibrational motions are primarily responsible for energy transfer. In general, the results suggest that low-frequency MFB vibrational modes are primarily responsible for strong collisions, and govern the shape and magnitude of P(E,E'). Where deviations from this general trend occur, vibrational modes with large negative anharmonicity constants are more efficient energy gateways than modes with similar frequency, while vibrational modes with large positive anharmonicity constants are less efficient at energy transfer than modes of similar frequency.

  18. Interfacial Water Structure in Langmuir Monolayer and Gibbs Layer Probed by Sum Frequency Generation Vibrational Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    张贞; 郭源

    2012-01-01

    Langmuir monolayer and Gibbs layer exhibit surface-active properties and it can be used as simple model systems to investigate the physicochemical properties of biological membranes. In this report, we presented the OH stretching vibration of H2O in the 4"-n-pentyl-4-cyano-p-terphenyl (5CT), nonadecanenitrile (C18CN) Langmuir monolayer and compared them with CH3CN Gibbs layer at the air/water interface with polarization SFG-VS. This study demonstrated that the hydrogen bond network is different in the Langmuir monolayer of 5CT, C18CN from CH3CN Gibbs layer at the air/water interface which showed two different water structures on the different surface layer. The results provided a deeper insight into understanding the hydrogen bond on the interfaces.

  19. Intramolecular hydrogen bonding in myricetin and myricitrin. Quantum chemical calculations and vibrational spectroscopy

    Science.gov (United States)

    Vojta, Danijela; Dominković, Katarina; Miljanić, Snežana; Spanget-Larsen, Jens

    2017-03-01

    The molecular structures of myricetin (3,3‧,4‧,5,5‧,7-hexahydroxyflavone; MCE) and myricitrin (myricetin 3-O-rhamnoside; MCI) are investigated by quantum chemical calculations (B3LYP/6-311G**). Two preferred molecular rotamers of MCI are predicted, corresponding to different conformations of the O-rhamnoside subunit. The rotamers are characterized by different hydrogen bonded cross-links between the hydroxy groups of the rhamnoside substituent and the parent MCE moiety. The predicted OH stretching frequencies are compared with vibrational spectra of MCE and MCI recorded for the sake of this investigation (IR and Raman). In addition, a reassignment of the Cdbnd O stretching bands is suggested.

  20. Vibrational spectroscopy and density functional theory analysis of 3-O-caffeoylquinic acid

    Science.gov (United States)

    Mishra, Soni; Tandon, Poonam; Eravuchira, Pinkie J.; El-Abassy, Rasha M.; Materny, Arnulf

    2013-03-01

    Density functional theory (DFT) calculations are being performed to investigate the geometric, vibrational, and electronic properties of the chlorogenic acid isomer 3-CQA (1R,3R,4S,5R)-3-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-1,4,5-trihydroxycyclohexanecarboxylic acid), a major phenolic compound in coffee. DFT calculations with the 6-311G(d,p) basis set produce very good results. The electrostatic potential mapped onto an isodensity surface has been obtained. A natural bond orbital analysis (NBO) has been performed in order to study intramolecular bonding, interactions among bonds, and delocalization of unpaired electrons. HOMO-LUMO studies give insights into the interaction of the molecule with other species. The calculated HOMO and LUMO energies indicate that a charge transfer occurs within the molecule.

  1. Introduction of a valence space in QRPA: Impact on vibrational mass parameters and spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Lechaftois, F., E-mail: francois.lechaftois@cea.fr; Péru, S. [CEA, DAM, DIF F-91297 Arpajon (France); Deloncle, I. [CEA, DAM, DIF F-91297 Arpajon (France); CSNSM, IN2P3/CNRS, F-91405 Orsay Campus (France)

    2015-10-15

    For the first time, using a unique finite range interaction (D1M Gogny force), a fully coherent and time-feasible calculation of the Bohr Hamiltonian vibrational mass is envisioned in a Hartree-Fock-Bogoliubov + Quasiparticle Random Phase Approximation (QRPA) framework. In order to reach handable computation time, we evaluate the feasibility of this method by considering the insertion of a valence space for QRPA. We validate our approach in the even-even tin isotopes comparing the convergence scheme of the mass parameter with those of built-in QRPA outputs: excited state energy and reduced transition probability. The seeming convergence of these intrinsic quantities is shown to be misleading and the difference with the theoretical expected value is quantified. This work is a primary step towards the systematic calculation of mass parameters.

  2. Solvation Reaction Field at the Interface Measured by Vibrational Sum Frequency Generation Spectroscopy.

    Science.gov (United States)

    Sorenson, Shayne A; Patrow, Joel G; Dawlaty, Jahan M

    2017-02-15

    Interfacial electric fields are important in several areas of chemistry, materials sciences, and device physics. However, they are poorly understood, partly because they are difficult to measure directly and model accurately. We present both a spectroscopic experimental investigation and a theoretical model for the interfacial field at the junction of a conductor and a dielectric. First, we present vibrational sum frequency generation (VSFG) results of the nitrile (CN) stretch of 4-mercaptobenzonitrile (4-MBN) covalently attached to a gold surface and in contact with a variety of liquid dielectrics. It is found that the CN stretch frequency red-shifts with increasing dielectric constant. Second, we build a model in direct analogy to the well-known Onsager reaction field theory, which has been successful in predicting vibrational frequency shifts in bulk dielectric media. Clearly, due to the asymmetric environment, with metal on one side and a dielectric on the other, the bulk Onsager model is not applicable at the interface. To address this, we apply the Onsager model to the interface accounting for the asymmetry. The model successfully explains the red-shift of the CN stretch as a function of the dielectric constant and is used to estimate the reaction field near the interface. We show the similarities and differences between the conventional bulk Onsager model and the interfacial reaction field model. In particular, the model emphasizes the importance of the metal as part of the solvation environment of the tethered molecules. We anticipate that our work will be of fundamental value to understand the crucial and often elusive electric fields at interfaces.

  3. X-ray and vibrational spectroscopy of manganese complexes relevant to the oxygen-evolving complex of photosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Visser, Hendrik [Univ. of California, Berkeley, CA (United States)

    2001-01-01

    Manganese model complexes, relevant to the oxygen-evolving complex (OEC) in photosynthesis, were studied with Mn K-edge X-ray absorption near-edge spectroscopy (XANES), Mn Kb X-ray emission spectroscopy (XES), and vibrational spectroscopy. A more detailed understanding was obtained of the influence of nuclearity, overall structure, oxidation state, and ligand environment of the Mn atoms on the spectra from these methods. This refined understanding is necessary for improving the interpretation of spectra of the OEC. Mn XANES and Kb XES were used to study a di-(mu)-oxo and a mono-(mu)-oxo di-nuclear Mn compound in the (III,III), (III,IV), and (IV,IV) oxidation states. XANES spectra show energy shifts of 0.8 - 2.2 eV for 1-electron oxidation-state changes and 0.4 - 1.8 eV for ligand-environment changes. The shifts observed for Mn XES spectra were approximately 0.21 eV for oxidation state-changes and only approximately 0.04 eV for ligand-environment changes. This indicates that Mn Kb XES i s more sensitive to the oxidation state and less sensitive to the ligand environment of the Mn atoms than XANES. These complimentary methods provide information about the oxidation state and the ligand environment of Mn atoms in model compounds and biological systems. A versatile spectroelectrochemical apparatus was designed to aid the interpretation of IR spectra of Mn compounds in different oxidation states. The design, based on an attenuated total reflection device, permits the study of a wide spectral range: 16,700 (600 nm) - 225

  4. X-ray and vibrational spectroscopy of manganese complexes relevant to the oxygen-evolving complex of photosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Visser, Hendrik

    2001-05-16

    Manganese model complexes, relevant to the oxygen-evolving complex (OEC) in photosynthesis, were studied with Mn K-edge X-ray absorption near-edge spectroscopy (XANES), Mn Kb X-ray emission spectroscopy (XES), and vibrational spectroscopy. A more detailed understanding was obtained of the influence of nuclearity, overall structure, oxidation state, and ligand environment of the Mn atoms on the spectra from these methods. This refined understanding is necessary for improving the interpretation of spectra of the OEC. Mn XANES and Kb XES were used to study a di-(mu)-oxo and a mono-(mu)-oxo di-nuclear Mn compound in the (III,III), (III,IV), and (IV,IV) oxidation states. XANES spectra show energy shifts of 0.8 - 2.2 eV for 1-electron oxidation-state changes and 0.4 - 1.8 eV for ligand-environment changes. The shifts observed for Mn XES spectra were approximately 0.21 eV for oxidation state-changes and only approximately 0.04 eV for ligand-environment changes. This indicates that Mn Kb XES i s more sensitive to the oxidation state and less sensitive to the ligand environment of the Mn atoms than XANES. These complimentary methods provide information about the oxidation state and the ligand environment of Mn atoms in model compounds and biological systems. A versatile spectroelectrochemical apparatus was designed to aid the interpretation of IR spectra of Mn compounds in different oxidation states. The design, based on an attenuated total reflection device, permits the study of a wide spectral range: 16,700 (600 nm) - 225

  5. Anharmonicity of multi-octupole-phonon excitations in $^{208}$Pb: analysis with multi-reference covariant density functional theory and subbarrier fusion of $^{16}$O+$^{208}$Pb

    CERN Document Server

    Yao, J M

    2016-01-01

    We discuss anharmonicity of the multi-octupole-phonon states in $^{208}$Pb based on a covariant density functional theory, by fully taking into account the interplay between the quadrupole and the octupole degrees of freedom. Our results indicate the existence of a large anharmonicity in the transition strengths, even though the excitation energies are similar to those in the harmonic limit. We also show that the quadrupole-shape fluctuation significantly enhances the fragmentation of the two-octupole-phonon states in $^{208}$Pb. Using those transition strengths as inputs to coupled channels calculations, we then discuss the fusion reaction of $^{16}$O+$^{208}$Pb at energies around the Coulomb barrier. We show that the anharmonicity of the octupole vibrational excitation considerably improves previous coupled-channels calculations in the harmonic oscillator limit, significantly reducing the height of the main peak in the fusion barrier distribution.

  6. 3D Motions of Iron in Six-Coordinate {FeNO}(7) Hemes by Nuclear Resonance Vibration Spectroscopy.

    Science.gov (United States)

    Peng, Qian; Pavlik, Jeffrey W; Silvernail, Nathan J; Alp, E Ercan; Hu, Michael Y; Zhao, Jiyong; Sage, J Timothy; Scheidt, W Robert

    2016-04-25

    The vibrational spectrum of a six-coordinate nitrosyl iron porphyrinate, monoclinic [Fe(TpFPP)(1-MeIm)(NO)] (TpFPP=tetra-para-fluorophenylporphyrin; 1-MeIm=1-methylimidazole), has been studied by oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS). The crystal was oriented to give spectra perpendicular to the porphyrin plane and two in-plane spectra perpendicular or parallel to the projection of the FeNO plane. These enable assignment of the FeNO bending and stretching modes. The measurements reveal that the two in-plane spectra have substantial differences that result from the strongly bonded axial NO ligand. The direction of the in-plane iron motion is found to be largely parallel and perpendicular to the projection of the bent FeNO on the porphyrin plane. The out-of-plane Fe-N-O stretching and bending modes are strongly mixed with each other, as well as with porphyrin ligand modes. The stretch is mixed with v50 as was also observed for dioxygen complexes. The frequency of the assigned stretching mode of eight Fe-X-O (X=N, C, and O) complexes is correlated with the Fe-XO bond lengths. The nature of highest frequency band at ≈560 cm(-1) has also been examined in two additional new derivatives. Previously assigned as the Fe-NO stretch (by resonance Raman), it is better described as the bend, as the motion of the central nitrogen atom of the FeNO group is very large. There is significant mixing of this mode. The results emphasize the importance of mode mixing; the extent of mixing must be related to the peripheral phenyl substituents.

  7. Overtone spectroscopy of benzene derivatives using thermal lensing

    Science.gov (United States)

    Vipin Prasad, J.; Rai, S. B.; Thakur, S. N.

    1989-12-01

    The vibrational overtones of CH stretching oscillators are reported as observed by conventional IR spectroscopy and dual-beam thermal lensing spectroscopy for benzene, fluorobenzene, chlorobenzene, bromobenzene and benzonitrile in the liquid phase at room temperature. The stretching frequency ω e, the anharmonicity constant ω eχ e and the change in CH bond length on substitution in benzene have been determined for all these molecules under the local-mode approximation. Effects of substitution on the change in CH stretching frequency have been discussed in terms of the electronegativity of the substituents as well as the inductive part of the Hammett σ. Variation of thermal lensing signal with chopping frequency and laser power has also been studied.

  8. Communication: Quantitative multi-site frequency maps for amide I vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Reppert, Mike [Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Department of Chemistry, University of Chicago, Chicago, Illinois 60637 (United States); Tokmakoff, Andrei, E-mail: tokmakoff@uchicago.edu [Department of Chemistry, University of Chicago, Chicago, Illinois 60637 (United States)

    2015-08-14

    An accurate method for predicting the amide I vibrational spectrum of a given protein structure has been sought for many years. Significant progress has been made recently by sampling structures from molecular dynamics simulations and mapping local electrostatic variables onto the frequencies of individual amide bonds. Agreement with experiment, however, has remained largely qualitative. Previously, we used dipeptide fragments and isotope-labeled constructs of the protein G mimic NuG2b as experimental standards for developing and testing amide I frequency maps. Here, we combine these datasets to test different frequency-map models and develop a novel method to produce an optimized four-site potential (4P) map based on the CHARMM27 force field. Together with a charge correction for glycine residues, the optimized map accurately describes both experimental datasets, with average frequency errors of 2–3 cm{sup −1}. This 4P map is shown to be convertible to a three-site field map which provides equivalent performance, highlighting the viability of both field- and potential-based maps for amide I spectral modeling. The use of multiple sampling points for local electrostatics is found to be essential for accurate map performance.

  9. Statistical strategies to reveal potential vibrational markers for in vivo analysis by confocal Raman spectroscopy

    Science.gov (United States)

    Oliveira Mendes, Thiago de; Pinto, Liliane Pereira; Santos, Laurita dos; Tippavajhala, Vamshi Krishna; Téllez Soto, Claudio Alberto; Martin, Airton Abrahão

    2016-07-01

    The analysis of biological systems by spectroscopic techniques involves the evaluation of hundreds to thousands of variables. Hence, different statistical approaches are used to elucidate regions that discriminate classes of samples and to propose new vibrational markers for explaining various phenomena like disease monitoring, mechanisms of action of drugs, food, and so on. However, the technical statistics are not always widely discussed in applied sciences. In this context, this work presents a detailed discussion including the various steps necessary for proper statistical analysis. It includes univariate parametric and nonparametric tests, as well as multivariate unsupervised and supervised approaches. The main objective of this study is to promote proper understanding of the application of various statistical tools in these spectroscopic methods used for the analysis of biological samples. The discussion of these methods is performed on a set of in vivo confocal Raman spectra of human skin analysis that aims to identify skin aging markers. In the Appendix, a complete routine of data analysis is executed in a free software that can be used by the scientific community involved in these studies.

  10. Final Technical Report Structural Dynamics in Complex Liquids Studied with Multidimensional Vibrational Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tokmakoff, Andrei [Univ. of Chicago, IL (United States); Fiechtner, Gregory J. [Univ. of Chicago, IL (United States)

    2015-12-10

    This grant supported work in the Tokmakoff lab at the University of Chicago aimed at understanding the fundamental properties of water at a molecular level, and how water participates in proton transport in aqueous media. The physical properties of water and aqueous solutions are inextricably linked with efforts to develop new sustainable energy sources. Energy conversion, storage, and transduction processes, particularly those that occur in biology and soft matter, make use of water for the purpose of storing and moving charge. Water’s unique physical and chemical properties depend on the ability of water molecules to participate in up to four hydrogen bonds, and the rapid fluctuations and ultrafast energy dissipation of its hydrogenbonded networks. Our work during the grant period led to advances in four areas: (1) the generation of short pulses of broadband infrared light (BBIR) for use in time-resolved twodimensional spectroscopy (2D IR), (2) the investigation of the spectroscopy and transport of excess protons in water, (3) the study of aqueous hydroxide to describe the interaction of the ion and water and the dynamics of proton transfer, and (4) the coupled motion of water and its hydrogen-bonding solutes.

  11. Structural study of human growth hormone-releasing factor fragment (1?29) by vibrational spectroscopy

    Science.gov (United States)

    Carmona, P.; Molina, M.; Lasagabaster, A.

    1995-05-01

    The conformational structure of fragment 1-29 of human growth hormone releasing factor, hGHRF (1-29), in aqueous solution and in the solid state is investigated by infrared and Raman spectroscopy. The polypeptide backbone is found to be unordered in the solid state. However, the spectra of the peptide prepared as 5% (w/w) aqueous solutions show that approximately 28% of the peptide is involved in intermolecular β-sheet aggregation. The remainder of the peptide exists largely as disordered and β-sheet conformations with a small portion of α-helices. Tyrosine residues are found to be exposed to the solvent. The secondary structures are quantitatively examined through infrared spectroscopy, the conformational percentages being near those obtained by HONDAet al. [ Biopolymers31, 869 (1991)] using circular dichroism. The fast hydrogen/deuterium exchange in peptide groups and the absence of any NMR sign indicative of ordered structure [ G. M. CLOREet al., J. Molec. Biol.191, 553 (1986)] support that the solution conformations of the non-aggregated peptide interconvert in dynamic equilibrium. Some physiological advantages that may derive from this conformational flexibility are also discussed

  12. Comparison of vibrational dynamics between non-ionic and ionic vibrational probes in water: Experimental study with two-dimensional infrared and infrared pump-probe spectroscopies

    Science.gov (United States)

    Okuda, Masaki; Ohta, Kaoru; Tominaga, Keisuke

    2016-09-01

    Dynamics of the hydration structure around small vibrational probes have been extensively studied over the past few decades. However, we need to gain insight into how vibrational dynamics is affected by the molecular nature of the probe molecules in water. In this study, 2-nitro-5-thiocyanate benzoic acid (NTBA), which has an SCN group attached to an aromatic ring, and thiocyanate ion (SCN-) were used to investigate the vibrational dynamics of two vibrational probes, including vibrational frequency fluctuations and rotational relaxation. By performing two-dimensional infrared spectroscopic measurements, the vibrational frequency fluctuations of the SCN anti-stretching modes of these solutes were compared. The frequency-frequency time correlation function (FFTCF) of these solutes can be modeled by a delta function plus an exponential function and a constant. The FFTCF of NTBA was characterized by a time constant of 1.1 ps, which is similar to that of SCN-. Moreover, no component was longer than this constant. Consequently, the loss of the correlation in frequency fluctuations of the SCN anti-stretching mode of NTBA may be controlled by a mechanism similar to that of the ionic probe, which involves the hydrogen bonding dynamics of water. Polarization-controlled IR pump-probe measurements were performed for these vibrational probes in water to study the vibrational energy relaxation (VER) and reorientational relaxation processes. The VER rate of NTBA is much smaller than that of SCN-, which indicates that the intramolecular relaxation process is significant for VER of NTBA. Based on the rotational relaxation time of NTBA being shorter than that of SCN-, the internal rotational motion of the SCN group around the Cphenyl-S bond axis, where Cphenyl denotes a carbon atom of the aromatic ring to which the SCN group is attached, may play an important role in the anisotropic decay of NTBA in H2O.

  13. Nanoscale chemical and mechanical characterization of thin films:sum frequency generation (SFG) vibrational spectroscopy at buriedinterfaces

    Energy Technology Data Exchange (ETDEWEB)

    Kweskin, Sasha Joseph [Univ. of California, Berkeley, CA (United States)

    2006-01-01

    Sum frequency generation (SFG) surface vibrational spectroscopy was used to characterize interfaces pertinent to current surface engineering applications, such as thin film polymers and novel catalysts. An array of advanced surface science techniques like scanning probe microscopy (SPM), x-ray photoelectron spectroscopy (XPS), gas chromatography (GC) and electron microscopy were used to obtain experimental measurements complementary to SFG data elucidating polymer and catalyst surface composition, surface structure, and surface mechanical behavior. Experiments reported in this dissertation concentrate on three fundamental questions: (1) How does the interfacial molecular structure differ from that of the bulk in real world applications? (2) How do differences in chemical environment affect interface composition or conformation? (3) How do these changes correlate to properties such as mechanical or catalytic performance? The density, surface energy and bonding at a solid interface dramatically alter the polymer configuration, physics and mechanical properties such as surface glass transition, adhesion and hardness. The enhanced sensitivity of SFG at the buried interface is applied to three systems: a series of acrylates under compression, the compositions and segregation behavior of binary polymer polyolefin blends, and the changes in surface structure of a hydrogel as a function of hydration. In addition, a catalytically active thin film of polymer coated nanoparticles is investigated to evaluate the efficacy of SFG to provide in situ information for catalytic reactions involving small mass adsorption and/or product development. Through the use of SFG, in situ total internal reflection (TIR) was used to increase the sensitivity of SFG and provide the necessary specificity to investigate interfaces of thin polymer films and nanostructures previously considered unfeasible. The dynamic nature of thin film surfaces is examined and it is found that the non

  14. Synchrotron FT-FIR spectroscopy of nitro-derivatives vapors: New spectroscopic signatures of explosive taggants and degradation products

    Science.gov (United States)

    Cuisset, Arnaud; Gruet, Sébastien; Pirali, Olivier; Chamaillé, Thierry; Mouret, Gaël

    2014-11-01

    We report on the first successful rovibrational study of gas phase mononitrotoluene and dinitrotoluene in the TeraHertz/Far-Infrared (THz/FIR) spectral domain. Using the AILES beamline of the synchrotron SOLEIL and a Fourier Transform spectrometer connected to multipass cells, the low-energy vibrational cross-sections of the different isomers of mononitrotoluene have been measured and compared to calculated spectra with the density functional theory including the anharmonic contribution. The active FIR modes of 2,4 and 2,6 dinitrotoluene have been assigned to the vibrational bands measured by Fourier Transform FIR spectroscopy of the gas-phase molecular cloud produced in an evaporating/recondensating system. This study highlights the selectivity of gas phase THz/FIR spectroscopy allowing an unambiguous recognition and discrimination of nitro-aromatic compounds used as explosive taggants.

  15. Vibrational spectroscopy and microscopic imaging: novel approaches for comparing barrier physical properties in native and human skin equivalents

    Science.gov (United States)

    Yu, Guo; Zhang, Guojin; Flach, Carol R.; Mendelsohn, Richard

    2013-06-01

    Vibrational spectroscopy and imaging have been used to compare barrier properties in human skin, porcine skin, and two human skin equivalents, Epiderm 200X with an enhanced barrier and Epiderm 200 with a normal barrier. Three structural characterizations were performed. First, chain packing and conformational order were compared in isolated human stratum corneum (SC), isolated porcine SC, and in the Epiderm 200X surface layers. The infrared (IR) spectrum of isolated human SC revealed a large proportion of orthorhombically packed lipid chains at physiological temperatures along with a thermotropic phase transition to a state with hexagonally packed chains. In contrast, the lipid phase at physiological temperatures in both porcine SC and in Epiderm 200X, although dominated by conformationally ordered chains, lacked significant levels of orthorhombic subcell packing. Second, confocal Raman imaging of cholesterol bands showed extensive formation of cholesterol-enriched pockets within the human skin equivalents (HSEs). Finally, IR imaging tracked lipid barrier dimensions as well as the spatial disposition of ordered lipids in human SC and Epiderm 200X. These approaches provide a useful set of experiments for exploring structural differences between excised human skin and HSEs, which in turn may provide a rationale for the functional differences observed among these preparations.

  16. IR and Vibrational Circular Dichroism Spectroscopy of Matrine- and Artemisinin-Type Herbal Products: Stereochemical Characterization and Solvent Effects.

    Science.gov (United States)

    Zhang, Yuefei; Poopari, M Reza; Cai, Xiaoli; Savin, Aliaksandr; Dezhahang, Zahra; Cheramy, Joseph; Xu, Yunjie

    2016-04-22

    Five Chinese herbal medicines--matrine, oxymatrine, sophoridine, artemisinin, and dihydroartemisinin--were investigated using vibrational circular dichroism (VCD) experiments and density functional theory calculations to extract their stereochemical information. The three matrine-type alkaloids are available from the dry roots of Sophora flavescens and have long been used in various traditional Chinese herbal medicines to combat diseases such as cancer and cardiac arrhythmia. Artemisinin and the related dihydroartemisinin, discovered in 1979 by Professor Youyou Tu, a 2015 Nobel laureate in medicine, are effective drugs for the treatment of malaria. The VCD measurements were carried out in CDCl3 and DMSO-d6, two solvents with different dielectric constants and hydrogen-bonding characteristics. A "clusters-in-a-liquid" approach was used to model both explicit and implicit solvent effects. The studies show that effectively accounting for solvent effects is critical to using IR and VCD spectroscopy to provide unique spectroscopic features to differentiate the potential stereoisomers of these Chinese herbal medicines.

  17. Vibrational properties of epitaxial Bi{sub 4}Te{sub 3} films as studied by Raman spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Hao; Pan, Wenwu; Chen, Qimiao; Wu, Xiaoyan [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050 (China); University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049 (China); Song, Yuxin, E-mail: songyuxin@mail.sim.ac.cn, E-mail: shumin@chalmers.se; Gong, Qian [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050 (China); Lu, Pengfei [State Key Laboratory of Information Photonics and Optical Communications, Ministry of Education, Beijing University of Posts and Telecommunications, P.O. Box 72, Beijing 100876 (China); Wang, Shumin, E-mail: songyuxin@mail.sim.ac.cn, E-mail: shumin@chalmers.se [State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050 (China); Department of Microtechnology and Nanoscience, Chalmers University of Technology, 41296 Gothenburg (Sweden)

    2015-08-15

    Bi{sub 4}Te{sub 3}, as one of the phases of the binary Bi–Te system, shares many similarities with Bi{sub 2}Te{sub 3}, which is known as a topological insulator and thermoelectric material. We report the micro-Raman spectroscopy study of 50 nm Bi{sub 4}Te{sub 3} films on Si substrates prepared by molecular beam epitaxy. Raman spectra of Bi{sub 4}Te{sub 3} films completely resolve the six predicted Raman-active phonon modes for the first time. Structural features and Raman tensors of Bi{sub 4}Te{sub 3} films are introduced. According to the wavenumbers and assignments of the six eigenpeaks in the Raman spectra of Bi{sub 4}Te{sub 3} films, it is found that the Raman-active phonon oscillations in Bi{sub 4}Te{sub 3} films exhibit the vibrational properties of those in both Bi and Bi{sub 2}Te{sub 3} films.

  18. Characterization of Alginates by Nuclear Magnetic Resonance (NMR) and Vibrational Spectroscopy (IR, NIR, Raman) in Combination with Chemometrics.

    Science.gov (United States)

    Jensen, Henrik Max; Larsen, Flemming Hofmann; Engelsen, Søren Balling

    2015-01-01

    This chapter describes three different spectroscopic methods for structural characterization of the commercial important hydrocolloid alginate extracted from brown seaweed. The "golden" reference method for characterization of the alginate structure is (1)H liquid-state NMR of depolymerized alginate polymers using a stepwise hydrolysis. Having implemented this method, predictive and rapid non-destructive methods using vibrational spectroscopy and chemometrics can be developed. These methods can predict the M/G-ratio of the intact alginate powder with at least the same precision and accuracy as the reference method in a fraction of the time that is required to measure the alginate using the reference method. The chapter also demonstrates how solid-state (13)C CP/MAS NMR can be used to determine the M/G ratio on the intact sample by the use of multivariate chemometrics and how this method shares the characteristics of the solid-state non-destructive IR method rather than its liquid-state counterpart.

  19. 2D IR spectroscopy of histidine: probing side-chain structure and dynamics via backbone amide vibrations.

    Science.gov (United States)

    Ghosh, Ayanjeet; Tucker, Matthew J; Gai, Feng

    2014-07-17

    It is well known that histidine is involved in many biological functions due to the structural versatility of its side chain. However, probing the conformational transitions of histidine in proteins, especially those occurring on an ultrafast time scale, is difficult. Herein we show, using a histidine dipeptide as a model, that it is possible to probe the tautomer and protonation status of a histidine residue by measuring the two-dimensional infrared (2D IR) spectrum of its amide I vibrational transition. Specifically, for the histidine dipeptide studied, the amide unit of the histidine gives rise to three spectrally resolvable amide I features at approximately 1630, 1644, and 1656 cm(-1), respectively, which, based on measurements at different pH values and frequency calculations, are assigned to a τ tautomer (1630 cm(-1) component) and a π tautomer with a hydrated (1644 cm(-1) component) or dehydrated (1656 cm(-1) component) amide. Because of the intrinsic ultrafast time resolution of 2D IR spectroscopy, we believe that the current approach, when combined with the isotope editing techniques, will be useful in revealing the structural dynamics of key histidine residues in proteins that are important for function.

  20. Characterisation of the membrane affinity of an isoniazide peptide conjugate by tensiometry, atomic force microscopy and sum-frequency vibrational spectroscopy, using a phospholipid Langmuir monolayer model.

    Science.gov (United States)

    Hill, Katalin; Pénzes, Csanád Botond; Schnöller, Donát; Horváti, Kata; Bosze, Szilvia; Hudecz, Ferenc; Keszthelyi, Tamás; Kiss, Eva

    2010-10-07

    Tensiometry, sum-frequency vibrational spectroscopy, and atomic force microscopy were employed to assess the cell penetration ability of a peptide conjugate of the antituberculotic agent isoniazide. Isoniazide was conjugated to peptide (91)SEFAYGSFVRTVSLPV(106), a functional T-cell epitope of the immunodominant 16 kDa protein of Mycobacterium tuberculosis. As a simple but versatile model of the cell membrane a phospholipid Langmuir monolayer at the liquid/air interface was used. Changes induced in the structure of the phospholipid monolayer by injection of the peptide conjugate into the subphase were followed by tensiometry and sum-frequency vibrational spectroscopy. The drug penetrated lipid films were transferred to a solid support by the Langmuir-Blodgett technique, and their structures were characterized by atomic force microscopy. Peptide conjugation was found to strongly enhance the cell penetration ability of isoniazide.

  1. Lattice Vibrations in Chlorobenzenes:

    DEFF Research Database (Denmark)

    Reynolds, P. A.; Kjems, Jørgen; White, J. W.

    1974-01-01

    Lattice vibrational dispersion curves for the ``intermolecular'' modes in the triclinic, one molecule per unit cell β phase of p‐C6D4Cl2 and p‐C6H4Cl2 have been obtained by inelastic neutron scattering. The deuterated sample was investigated at 295 and at 90°K and a linear extrapolation to 0°K...... by consideration of electrostatic forces or by further anisotropy in the dispersion forces not described in the atom‐atom model. Anharmonic effects are shown to be large, but the dominant features in the temperature variation of frequencies are describable by a quasiharmonic model....

  2. Evidence for Tautomerisation of Glutamine in BLUF Blue Light Receptors by Vibrational Spectroscopy and Computational Chemistry

    Science.gov (United States)

    Domratcheva, Tatiana; Hartmann, Elisabeth; Schlichting, Ilme; Kottke, Tilman

    2016-03-01

    BLUF (blue light sensor using flavin) domains regulate the activity of various enzymatic effector domains in bacteria and euglenids. BLUF features a unique photoactivation through restructuring of the hydrogen-bonding network as opposed to a redox reaction or an isomerization of the chromophore. A conserved glutamine residue close to the flavin chromophore plays a central role in the light response, but the underlying modification is still unclear. We labelled this glutamine with 15N in two representative BLUF domains and performed time-resolved infrared double difference spectroscopy. The assignment of the signals was conducted by extensive quantum chemical calculations on large models with 187 atoms reproducing the UV-vis and infrared signatures of BLUF photoactivation. In the dark state, the comparatively low frequency of 1,667 cm-1 is assigned to the glutamine C=O accepting a hydrogen bond from tyrosine. In the light state, the signature of a tautomerised glutamine was extracted with the C=N stretch at ~1,691 cm-1 exhibiting the characteristic strong downshift by 15N labelling. Moreover, an indirect isotope effect on the flavin C4=O stretch was found. We conclude that photoactivation of the BLUF receptor does not only involve a rearrangement of hydrogen bonds but includes a change in covalent bonds of the protein.

  3. Evidence for Tautomerisation of Glutamine in BLUF Blue Light Receptors by Vibrational Spectroscopy and Computational Chemistry.

    Science.gov (United States)

    Domratcheva, Tatiana; Hartmann, Elisabeth; Schlichting, Ilme; Kottke, Tilman

    2016-03-07

    BLUF (blue light sensor using flavin) domains regulate the activity of various enzymatic effector domains in bacteria and euglenids. BLUF features a unique photoactivation through restructuring of the hydrogen-bonding network as opposed to a redox reaction or an isomerization of the chromophore. A conserved glutamine residue close to the flavin chromophore plays a central role in the light response, but the underlying modification is still unclear. We labelled this glutamine with (15)N in two representative BLUF domains and performed time-resolved infrared double difference spectroscopy. The assignment of the signals was conducted by extensive quantum chemical calculations on large models with 187 atoms reproducing the UV-vis and infrared signatures of BLUF photoactivation. In the dark state, the comparatively low frequency of 1,667 cm(-1) is assigned to the glutamine C=O accepting a hydrogen bond from tyrosine. In the light state, the signature of a tautomerised glutamine was extracted with the C=N stretch at ~1,691 cm(-1) exhibiting the characteristic strong downshift by (15)N labelling. Moreover, an indirect isotope effect on the flavin C4=O stretch was found. We conclude that photoactivation of the BLUF receptor does not only involve a rearrangement of hydrogen bonds but includes a change in covalent bonds of the protein.

  4. Evidence for Tautomerisation of Glutamine in BLUF Blue Light Receptors by Vibrational Spectroscopy and Computational Chemistry

    Science.gov (United States)

    Domratcheva, Tatiana; Hartmann, Elisabeth; Schlichting, Ilme; Kottke, Tilman

    2016-01-01

    BLUF (blue light sensor using flavin) domains regulate the activity of various enzymatic effector domains in bacteria and euglenids. BLUF features a unique photoactivation through restructuring of the hydrogen-bonding network as opposed to a redox reaction or an isomerization of the chromophore. A conserved glutamine residue close to the flavin chromophore plays a central role in the light response, but the underlying modification is still unclear. We labelled this glutamine with 15N in two representative BLUF domains and performed time-resolved infrared double difference spectroscopy. The assignment of the signals was conducted by extensive quantum chemical calculations on large models with 187 atoms reproducing the UV-vis and infrared signatures of BLUF photoactivation. In the dark state, the comparatively low frequency of 1,667 cm−1 is assigned to the glutamine C=O accepting a hydrogen bond from tyrosine. In the light state, the signature of a tautomerised glutamine was extracted with the C=N stretch at ~1,691 cm−1 exhibiting the characteristic strong downshift by 15N labelling. Moreover, an indirect isotope effect on the flavin C4=O stretch was found. We conclude that photoactivation of the BLUF receptor does not only involve a rearrangement of hydrogen bonds but includes a change in covalent bonds of the protein. PMID:26947391

  5. In situ vibrational spectroscopy of thin organic films confined at the solid-solid interface

    CERN Document Server

    Haydock, S A

    2002-01-01

    Raman scattering was used to study thin films, of hexadecane, octamethyltetrasiloxane (OMCTS), 1-undecanol and Langmuir-Blodgett (LB) monolayers consisting of zinc stearate, zinc arachidate and zinc behenate, all at the solid-solid interface. This thesis contains the first unenhanced Raman spectrum of an organic monolayer confined in the contact between two solid surfaces. The LB monolayers were also investigated with sum-frequency spectroscopy in order that comparisons could be made between results from the two techniques. Thin films were confined between an optical prism and an optical lens at pressures ranging from 30 MPa to 200 MPa. I have shown that the deposited LB monolayers were conformationally ordered and that this high degree of order was retained at applied pressures of up to 200 MPa. However, the application of pressure caused the hydrocarbon chains to tilt from the surface normal. The changes observed in the overall intensity of the Raman spectra on formation of the solid-solid contact can be ex...

  6. Relations between aliphatics and silicate components in 12 stratospheric particles deduced from vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Merouane, S.; Djouadi, Z.; Le Sergeant d' Hendecourt, L., E-mail: sihane.merouane@ias.u-psud.fr [Institut d' Astrophysique Spatiale, CNRS, UMR-8617, Université Paris Sud, Bâtiment 121, F-91405 Orsay Cedex (France)

    2014-01-10

    Interplanetary dust particles (IDPs) are among the most pristine extraterrestrial samples available in the laboratory for analyses with moderate to high spatial- and spectral-resolution spectroscopic techniques. Their composition can provide precious information on the early stages of the solar nebula as well as on the processes on the surfaces of different small bodies in the solar system from which IDPs originate. In this work, we have analyzed six anhydrous IDPs and six stratospheric particles possibly of cosmic origin through infrared (IR) and Raman micro-spectroscopy to study and investigate their silicate and organic components. We find that the length/ramification of the aliphatic organics given by the CH{sub 2}/CH{sub 3} ratios in the IDPs is closely linked to the silicate family (pyroxene or olivine) present in the samples. Both IR and Raman data suggest that this relation is not correlated with either aqueous (as evidenced by the absence of aqueous related minerals) or thermal processes (as deduced from Raman measurements). Therefore, this observation might be related to the initial path of formation of the organics on the silicate surfaces, thus tracing a possible catalytic role that silicates would play in the formation and/or ramification of organic matter in the primitive nebula.

  7. Infrared vibrational spectroscopy: a rapid and novel diagnostic and monitoring tool for cystinuria

    Science.gov (United States)

    Oliver, Katherine V.; Vilasi, Annalisa; Maréchal, Amandine; Moochhala, Shabbir H.; Unwin, Robert J.; Rich, Peter R.

    2016-01-01

    Cystinuria is the commonest inherited cause of nephrolithiasis (~1% in adults; ~6% in children) and is the result of impaired cystine reabsorption in the renal proximal tubule. Cystine is poorly soluble in urine with a solubility of ~1 mM and can readily form microcrystals that lead to cystine stone formation, especially at low urine pH. Diagnosis of cystinuria is made typically by ion-exchange chromatography (IEC) detection and quantitation, which is slow, laboursome and costly. More rapid and frequent monitoring of urinary cystine concentration would significantly improve the diagnosis and clinical management of cystinuria. We used attenuated total reflection - Fourier transform infrared spectroscopy (ATR-FTIR) to detect and quantitate insoluble cystine in 22 cystinuric and 5 healthy control urine samples. Creatinine concentration was also determined by ATR-FTIR to adjust for urinary concentration/dilution. Urine was centrifuged, the insoluble fraction re-suspended in 5 μL water and dried on the ATR prism. Cystine was quantitated using its 1296 cm−1 absorption band and levels matched with parallel measurements made using IEC. ATR-FTIR afforded a rapid and inexpensive method of detecting and quantitating insoluble urinary cystine. This proof-of-concept study provides a basis for developing a high-throughput, cost-effective diagnostic method for cystinuria, and for point-of-care clinical monitoring PMID:27721432

  8. The effect of calcium and vitamin D supplementation on osteoporotic rabbit bones studied by vibrational spectroscopy.

    Science.gov (United States)

    Lani, Athina; Kourkoumelis, Nikolaos; Baliouskas, Gerasimos; Tzaphlidou, Margaret

    2014-09-01

    Fourier transform infrared spectroscopy is utilized to examine the effects of increased calcium, vitamin D, and combined calcium-vitamin D supplementation on osteoporotic rabbit bones with induced inflammation. The study includes different bone sites (femur, tibia, humerus, vertebral rib) in an effort to explore possible differences among the sites. We evaluate the following parameters: mineral-to-matrix ratio, carbonate content, and non-apatitic species (labile acid phosphate and labile carbonate) contribution to bone mineral. Results show that a relatively high dose of calcium or calcium with vitamin D supplementation increases the bone mineralization index significantly. On the other hand, vitamin D alone is not as effective in promoting mineralization even with high intake. Mature B-type apatite was detected for the group with calcium supplementation similar to that of aged bone. High vitamin D intake led to increased labile species concentration revealing bone formation. This is directly associated with the suppression of pro-inflammatory cytokines linked to induced inflammation. The latter is known to adversely alter bone metabolism, contributing to the aetiopathogenesis of osteoporosis. Thus, a high intake of vitamin D under inflammation-induced osteoporosis does not promote mineralization but suppresses bone resorption and restores metabolic balance.

  9. 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.

  10. Exact and approximate expressions for the period of anharmonic oscillators

    Energy Technology Data Exchange (ETDEWEB)

    Amore, Paolo [Facultad de Ciencias, Universidad de Colima, Bernal DIaz del Castillo 340, Colima (Mexico); Fernandez, Francisco M [INIFTA (Conicet, UNLP), Blvd. 113 y 64 S/N, Sucursal 4, Casilla de Correo 16, 1900 La Plata (Argentina)

    2005-07-01

    In this paper, we present a straightforward systematic method for the exact and approximate calculation of integrals that appear in formulae for the period of anharmonic oscillators and other problems of interest in classical mechanics.

  11. Probing anharmonicity of a quantum oscillator in an optomechanical cavity

    Science.gov (United States)

    Latmiral, Ludovico; Armata, Federico; Genoni, Marco G.; Pikovski, Igor; Kim, M. S.

    2016-05-01

    We present a way of measuring with high precision the anharmonicity of a quantum oscillator coupled to an optical field via radiation pressure. Our protocol uses a sequence of pulsed interactions to perform a loop in the phase space of the mechanical oscillator, which is prepared in a thermal state. We show how the optical field acquires a phase depending on the anharmonicity. Remarkably, one only needs small initial cooling of the mechanical motion to probe even small anharmonicities. Finally, by applying tools from quantum estimation theory, we calculate the ultimate bound on the estimation precision posed by quantum mechanics and compare it with the precision obtainable with feasible measurements such as homodyne and heterodyne detection on the cavity field. In particular we demonstrate that homodyne detection is nearly optimal in the limit of a large number of photons of the field and we discuss the estimation precision of small anharmonicities in terms of its signal-to-noise ratio.

  12. Linear delta expansion technique for the solution of anharmonic oscillations

    Indian Academy of Sciences (India)

    P K Bera; J Datta

    2007-01-01

    The linear delta expansion technique has been developed for solving the differential equation of motion for symmetric and asymmetric anharmonic oscillators. We have also demonstrated the sophistication and simplicity of this new perturbation technique.

  13. 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

  14. Genuine Quantum Signatures in Synchronization of Anharmonic Self-Oscillators

    Science.gov (United States)

    Lörch, Niels; Amitai, Ehud; Nunnenkamp, Andreas; Bruder, Christoph

    2016-08-01

    We study the synchronization of a Van der Pol self-oscillator with Kerr anharmonicity to an external drive. We demonstrate that the anharmonic, discrete energy spectrum of the quantum oscillator leads to multiple resonances in both phase locking and frequency entrainment not present in the corresponding classical system. Strong driving close to these resonances leads to nonclassical steady-state Wigner distributions. Experimental realizations of these genuine quantum signatures can be implemented with current technology.

  15. Vibrational circular dichroism spectroscopy of a spin-triplet bis-(biuretato) cobaltate(III) coordination compound with low-lying electronic transitions.

    Science.gov (United States)

    Johannessen, Christian; Thulstrup, Peter W

    2007-03-14

    Vibrational absorption (VA) and vibrational circular dichroism (VCD) spectroscopy was applied in the analysis of vibrational and low lying electronic transitions of a triplet ground state cobalt(III) coordination compound. The spectroscopic measurements were performed on the tetrabutylammonium salt of (6S,7S)-1,3,5,8,10,12-hexaaza-2,4,9,11-tetraoxo-6,7-diphenyl-dodecanato(4-)cobaltate(III) in DMSO solution and in potassium bromide pellets. The chiral anion exhibits an unusual geometry for cobalt(III), being four-coordinate, planar, and paramagnetic with an intermediate spin state. The spectroscopic results were compared to measurements performed on the free ligand and to theoretical calculations using density functional theory (B3LYP/TZVP). The results of the VCD analysis of the coordination compound identified an electronic, dipole-forbidden, magnetic dipole-allowed low-lying d-d transition located in the mid infrared, as well as several amide stretch transitions located in the fingerprint region (1800-1100 cm(-1)), in both the liquid and solid phase. VCD signals were found to be 5-10 times higher than expected, indicating enhancement of the vibrational CD signals, caused by coupling of the vibrational transitions with the close-lying electronic transition.

  16. Vibrational spectrum of the spin crossover complex [Fe(phen)(2)(NCS)(2)] studied by IR and Raman spectroscopy, nuclear inelastic scattering and DFT calculations.

    Science.gov (United States)

    Ronayne, Kate L; Paulsen, Hauke; Höfer, Andreas; Dennis, Andrew C; Wolny, Juliusz A; Chumakov, Aleksandr I; Schünemann, Volker; Winkler, Heiner; Spiering, Hartmut; Bousseksou, Azzedine; Gütlich, Philipp; Trautwein, Alfred X; McGarvey, John J

    2006-10-28

    The vibrational modes of the low-spin and high-spin isomers of the spin crossover complex [Fe(phen)(2)(NCS)(2)] (phen = 1,10-phenanthroline) have been measured by IR and Raman spectroscopy and by nuclear inelastic scattering. The vibrational frequencies and normal modes and the IR and Raman intensities have been calculated by density functional methods. The vibrational entropy difference between the two isomers, DeltaS(vib), which is--together with the electronic entropy difference DeltaS(el)--the driving force for the spin-transition, has been determined from the measured and from the calculated frequencies. The calculated difference (DeltaS(vib) = 57-70 J mol(-1) K(-1), depending on the method) is in qualitative agreement with experimental values (20-36 J mol(-1) K(-1)). Only the low energy vibrational modes (20% of the 147 modes of the free molecule) contribute to the entropy difference and about three quarters of the vibrational entropy difference are due to the 15 modes of the central FeN(6) octahedron.

  17. Ag clustering investigation in laser irradiated ion-exchanged glasses by optical and vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Trave, E., E-mail: enrico.trave@unive.it [Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venezia, Dorsoduro 2137, I-30123 Venezia (Italy); Cattaruzza, E.; Gonella, F.; Calvelli, P. [Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venezia, Dorsoduro 2137, I-30123 Venezia (Italy); Quaranta, A. [Department of Materials Engineering and Industrial Technologies, University of Trento, via Mesiano 77, I-38050 Povo (Italy); Rahman, A.; Mariotto, G. [Department of Computer Science, University of Verona, Strada le Grazie 15, 37134 Verona (Italy)

    2012-09-15

    Highlights: Black-Right-Pointing-Pointer We modify the properties of Ag{sup +} exchanged glasses by thermal and laser treatment. Black-Right-Pointing-Pointer The induced microstructural changes are analyzed by optical and Raman spectroscopy. Black-Right-Pointing-Pointer Ag-based species in the glass show a peculiar PL activity in the UV-Vis range. Black-Right-Pointing-Pointer Raman and OA analysis allow for determining the Ag cluster size evolution. Black-Right-Pointing-Pointer Laser processing leads to different cluster formation and fragmentation mechanisms. - Abstract: Ion exchange process is widely used to dope silicate glass layers with silver for several applications, ranging from light waveguide to nanostructured composite glass fabrication. The silver-doped structure and its physical properties depend on the preparation parameters as well as on subsequent treatments. In particular, laser irradiation of the ion exchanged glasses has been demonstrated to be an effective tool to control cluster size and size distribution. Nevertheless, a complete comprehension of the basic phenomena and a systematic characterization of these systems are still lacking. In this paper, an extended optical characterization is presented for soda-lime glass slides, doped with silver by Ag{sup +}-Na{sup +} ion exchange, thermally treated and irradiated with a Nd:YAG laser beam at different wavelengths, and for different energy density. The samples were characterized by various spectroscopic techniques, namely, optical absorption, photoluminescence and micro-Raman analysis. The availability of all these characterization techniques allowed pointing out a suitable scenario for the Ag clustering evolution as a function of the ion exchange, annealing and laser irradiation parameters.

  18. High resolution IR diode laser study of collisional energy transfer between highly vibrationally excited monofluorobenzene and CO{sub 2}: The effect of donor fluorination on strong collision energy transfer

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kilyoung; Johnson, Alan M.; Powell, Amber L.; Mitchell, Deborah G.; Sevy, Eric T., E-mail: esevy@byu.edu [Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602 (United States)

    2014-12-21

    Collisional energy transfer between vibrational ground state CO{sub 2} and highly vibrationally excited monofluorobenzene (MFB) was studied using narrow bandwidth (0.0003 cm{sup −1}) IR diode laser absorption spectroscopy. Highly vibrationally excited MFB with E′ = ∼41 000 cm{sup −1} was prepared by 248 nm UV excitation followed by rapid radiationless internal conversion to the electronic ground state (S{sub 1}→S{sub 0}*). The amount of vibrational energy transferred from hot MFB into rotations and translations of CO{sub 2} via collisions was measured by probing the scattered CO{sub 2} using the IR diode laser. The absolute state specific energy transfer rate constants and scattering probabilities for single collisions between hot MFB and CO{sub 2} were measured and used to determine the energy transfer probability distribution function, P(E,E′), in the large ΔE region. P(E,E′) was then fit to a bi-exponential function and extrapolated to the low ΔE region. P(E,E′) and the biexponential fit data were used to determine the partitioning between weak and strong collisions as well as investigate molecular properties responsible for large collisional energy transfer events. Fermi's Golden rule was used to model the shape of P(E,E′) and identify which donor vibrational motions are primarily responsible for energy transfer. In general, the results suggest that low-frequency MFB vibrational modes are primarily responsible for strong collisions, and govern the shape and magnitude of P(E,E′). Where deviations from this general trend occur, vibrational modes with large negative anharmonicity constants are more efficient energy gateways than modes with similar frequency, while vibrational modes with large positive anharmonicity constants are less efficient at energy transfer than modes of similar frequency.

  19. Surface and buried interfacial structures of epoxy resins used as underfills studied by sum frequency generation vibrational spectroscopy.

    Science.gov (United States)

    Vázquez, Anne V; Holden, Brad; Kristalyn, Cornelius; Fuller, Mike; Wilkerson, Brett; Chen, Zhan

    2011-05-01

    Flip chip technology has greatly improved the performance of semiconductor devices, but relies heavily on the performance of epoxy underfill adhesives. Because epoxy underfills are cured in situ in flip chip semiconductor devices, understanding their surface and interfacial structures is critical for understanding their adhesion to various substrates. Here, sum frequency generation (SFG) vibrational spectroscopy was used to study surface and buried interfacial structures of two model epoxy resins used as underfills in flip chip devices, bisphenol A digylcidyl ether (BADGE) and 1,4-butanediol diglycidyl ether (BDDGE). The surface structures of these epoxies were compared before and after cure, and the orientations of their surface functional groups were deduced to understand how surface structural changes during cure may affect adhesion properties. Further, the effect of moisture exposure, a known cause of adhesion failure, on surface structures was studied. It was found that the BADGE surface significantly restructured upon moisture exposure while the BDDGE surface did not, showing that BADGE adhesives may be more prone to moisture-induced delamination. Lastly, although surface structure can give some insight into adhesion, buried interfacial structures more directly correspond to adhesion properties of polymers. SFG was used to study buried interfaces between deuterated polystyrene (d-PS) and the epoxies before and after moisture exposure. It was shown that moisture exposure acted to disorder the buried interfaces, most likely due to swelling. These results correlated with lap shear adhesion testing showing a decrease in adhesion strength after moisture exposure. The presented work showed that surface and interfacial structures can be correlated to adhesive strength and may be helpful in understanding and designing optimized epoxy underfill adhesives.

  20. Living systems as coherent anharmonic oscillators

    Science.gov (United States)

    Molski, M.

    2011-12-01

    A model of living systems considered as coherent, time-dependent anharmonic oscillators is presented. It is based on the concept of space-like coherent states minimizing the time-energy uncertainty relation, adapted to the case of biological systems whose growth is described by the Gompertz or West-Brown-Enquist functions. The coherent states of biological growth evolve coherently in space being localized along the classical time trajectory; hence, the growth is predicted to be coherent in space. It is proven that the Gompertz function is a special solution of the space-like Horodecki-Feinberg equation for the time-dependent Morse oscillator in the dissociation state. Its eigenvalue represents the momentum of biological growth, associated with a space-like component whose properties resemble those attributed by vitalists to the life momentum or vital impulse. The physical characteristics of the life energy and momentum and their connection with the concept of zero-point momentum of vacuum are presented.

  1. The Origin of Ultralow Thermal Conductivity in InTe: Lone-Pair-Induced Anharmonic Rattling.

    Science.gov (United States)

    Jana, Manoj K; Pal, Koushik; Waghmare, Umesh V; Biswas, Kanishka

    2016-06-27

    Understanding the origin of intrinsically low thermal conductivity is fundamentally important to the development of high-performance thermoelectric materials, which can convert waste-heat into electricity. Herein, we report an ultralow lattice thermal conductivity (ca. 0.4 W m(-1)  K(-1) ) in mixed valent InTe (that is, In(+) In(3+) Te2 ), which exhibits an intrinsic bonding asymmetry with coexistent covalent and ionic substructures. The phonon dispersion of InTe exhibits, along with low-energy flat branches, weak instabilities associated with the rattling vibrations of In(+) atoms along the columnar ionic substructure. These weakly unstable phonons originate from the 5s(2) lone pair of the In(+) atom and are strongly anharmonic, which scatter the heat-carrying acoustic phonons through strong anharmonic phonon-phonon interactions, as evident in anomalously high mode Grüneisen parameters. A maximum thermoelectric figure of merit (z T) of about 0.9 is achieved at 600 K for the 0.3 mol % In-deficient sample, making InTe a promising material for mid-temperature thermoelectric applications.

  2. Characterization of the quasi-one-dimensional compounds δ-(EDT-TTF-CONMe{sub 2}){sub 2}X, X=AsF{sub 6} and Br by vibrational spectroscopy and density functional theory calculations

    Energy Technology Data Exchange (ETDEWEB)

    Peterseim, Tobias; Dressel, Martin [1. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart (Germany); Antal, Ágnes [1. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart (Germany); Institute of Condensed Matter Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne (Switzerland); Batail, Patrick [Laboratoire MOLTECH, UMR 6200 CNRS-Université d' Angers, Bt. K, UFR Sciences, 2 Boulevard Lavoisier, F-49045 Angers (France); Drichko, Natalia [1. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart (Germany); Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218 (United States)

    2014-02-14

    We have investigated the infrared spectra of the quarter-filled charge-ordered insulators δ-(EDT-TTF-CONMe{sub 2}){sub 2}X (X= AsF{sub 6}, Br) along all three crystallographic directions in the temperature range from 300 to 10 K. DFT-assisted normal mode analysis of the neutral and ionic EDT-TTF-CONMe{sub 2} molecule allows us to assign the experimentally observed intramolecular modes and to obtain relevant information on the charge ordering and intramolecular interactions. From frequencies of charge-sensitive vibrations we deduce that the charge-ordered state is already present at room temperature and does not change on cooling, in agreement with previous NMR measurements. The spectra taken along the stacking direction clearly show features of vibrational overtones excited due to the anharmonic electronic molecule potential caused by the large charge disproportionation between the molecular sites. The shift of certain vibrational modes indicates the onset of the structural transition below 200 K.

  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. Optimizing Vibrational Coordinates To Modulate Intermode Coupling.

    Science.gov (United States)

    Zimmerman, Paul M; Smereka, Peter

    2016-04-12

    The choice of coordinate system strongly affects the convergence properties of vibrational structure computations. Two methods for efficient generation of improved vibrational coordinates are presented and justified by analysis of a model anharmonic two-mode Hessian and numerical computations on polyatomic molecules. To produce optimal coordinates, metrics which quantify off-diagonal couplings over a grid of Hessian matrices are minimized through unitary rotations of the vibrational basis. The first proposed metric minimizes the total squared off-diagonal coupling, and the second minimizes the total squared change in off-diagonal coupling. In this procedure certain anharmonic modes tend to localize, for example X-H stretches. The proposed methods do not rely on prior fitting of the potential energy, vibrational structure computations, or localization metrics, so they are unique from previous vibrational coordinate generation algorithms and are generally applicable to polyatomic molecules. Fitting the potential to the approximate n-mode representation in the optimized bases for all-trans polyenes shows that off-diagonal anharmonic couplings are substantially reduced by the new choices of coordinate system. Convergence of vibrational energies is examined in detail for ethylene, and it is shown that coupling-optimized modes converge in vibrational configuration interaction computations to within 1 cm(-1) using only 3-mode couplings, where normal modes require 4-mode couplings for convergence. Comparison of the vibrational configuration interaction convergence with respect to excitation level for the two proposed metrics shows that minimization of the total off-diagonal coupling is most effective for low-cost vibrational structure computations.

  5. Vibrational spectroscopy investigation using ab initio and DFT vibrational analysis of 7-chloro-2-methylamino-5-phenyl-3H-1,4-benzodiazepine-4-oxide

    Science.gov (United States)

    Prasath, M.; Muthu, S.; Arun Balaji, R.

    2013-09-01

    The FT-IR and FT-Raman spectrum of 7-chloro-2-methylamino-5-phenyl-3H-1, 4-benzodiazepine-4-oxide (7CMP4BO) has been recorded in the region 4000-400 and 4000-100 cm-1 respectively. The optimized geometry, Thermodynamic properties, NBO, Molecular Electrostatic Potentials, PES, frequency and intensity of the vibrational bands of 7CMP4BO were obtained by the ab initio HF and density functional theory (DFT), B3LYP/6-31G (d,p) basis set. The molecule orbital contributions were studied by using the total (TDOS), partial (PDOS), and overlap population (OPDOS) density of states. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental 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 linear polarizability (α) and the first order hyperpolarizability (β) values of the investigated molecule have been computed using DFT quantum mechanical calculations. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically calculated values.

  6. 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.

  7. Generalized theoretical method for the interaction between arbitrary nonuniform electric field and molecular vibrations: Toward near-field infrared spectroscopy and microscopy.

    Science.gov (United States)

    Iwasa, Takeshi; Takenaka, Masato; Taketsugu, Tetsuya

    2016-03-28

    A theoretical method to compute infrared absorption spectra when a molecule is interacting with an arbitrary nonuniform electric field such as near-fields is developed and numerically applied to simple model systems. The method is based on the multipolar Hamiltonian where the light-matter interaction is described by a spatial integral of the inner product of the molecular polarization and applied electric field. The computation scheme is developed under the harmonic approximation for the molecular vibrations and the framework of modern electronic structure calculations such as the density functional theory. Infrared reflection absorption and near-field infrared absorption are considered as model systems. The obtained IR spectra successfully reflect the spatial structure of the applied electric field and corresponding vibrational modes, demonstrating applicability of the present method to analyze modern nanovibrational spectroscopy using near-fields. The present method can use arbitral electric fields and thus can integrate two fields such as computational chemistry and electromagnetics.

  8. The vibrational structure of (E,E’)-1,4-diphenyl-1,3-butadiene. Linear dichroism FTIR spectroscopy and quantum chemical calculations

    DEFF Research Database (Denmark)

    Hansen, Bjarke Knud Vilster; Møller, Søren; Spanget-Larsen, Jens

    2006-01-01

    The title compound (DPB) was investigated by FTIR spectroscopy in liquid solutions and by FTIR linear dichroism (LD) measurements on samples aligned in stretched polyethylene. The LD data provided experimental assignments of molecular transition moment directions and vibrational symmetries for more...... than 40 vibrational transitions. The observed IR wavenumbers, relative intensities, and polarization directions were generally well reproduced by the results of a harmonic analysis based on B3LYP/cc-pVTZ density functional theory (DFT). The combined experimental and theoretical results led to proposal...... of a nearly complete assignment of the IR active fundamentals of DPB, involving reassignment of a number of transitions. In addition, previously published Raman spectra of DPB were well predicted by the B3LYP/cc-pVTZ calculations....

  9. Analysis of structure and vibrational dynamics of the BeTe(001) surface using X-ray diffraction, Raman spectroscopy, and density functional theory

    DEFF Research Database (Denmark)

    Kumpf, C.; Müller, A.; Weigand, W.;

    2003-01-01

    The atomic structure and lattice dynamics of epitaxial BeTe(001) thin films are derived from surface x-ray diffraction and Raman spectroscopy. On the Te-rich BeTe(001) surface [1 (1) over bar0]-oriented Te dimers are identified. They cause a (2 X 1) superstructure and induce a pronounced buckling...... in the underlying Te layer. The Be-rich surface exhibits a (4 X 1) periodicity with alternating Te dimers and Te-Be-Te trimers. A vibration eigenfrequency of 165 cm(-1) is observed for the Te-rich surface, while eigenmodes at 157 and 188 cm(-1) are found for the Be-rich surface. The experimentally derived atomic...... geometry and the vibration modes are in very good agreement with the results of density functional theory calculations....

  10. Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Hellman, Hal

    1968-01-01

    This booklet discusses spectroscopy, the study of absorption of radiation by matter, including X-ray, gamma-ray, microwave, mass spectroscopy, as well as others. Spectroscopy has produced more fundamental information to the study of the detailed structure of matter than any other tools.

  11. Elastic and anelastic properties of densified vitreous B2O3: Relaxations and anharmonicity

    Science.gov (United States)

    Carini, Giovanni, Jr.; Carini, Giuseppe; Tripodo, Gaspare; di Marco, Gaetano; Gilioli, Edmondo

    2012-03-01

    The elastic and anelastic properties of densified B2O3 glasses, melt quenched under pressures of 2 and 4 GPa, were investigated by measuring the sound velocity and the acoustic attenuation of longitudinal and shear ultrasonic waves in the megahertz range over the temperature interval between 8 and 300 K. Densification from 1826 to 2373 kg/m3 leads to an extraordinarily large growth of both bulk and shear moduli but leaves the Poisson's ratio nearly constant. In the glass compacted at 4 GPa, the elastic moduli become larger by a factor of five than those characterizing normal vitreous B2O3 (v-B2O3) as a consequence of modifications of the chemical bonding in the network. The thermally activated relaxations of intrinsic structural defects, which dominate the acoustic behaviors of normal glass below 150 K, giving rise to an intense attenuation peak and a corresponding steep decrease in sound velocity, are increasingly depressed by growing densification. Above 150 K, the ultrasonic velocity is mainly regulated by the vibrational anharmonicity and shows a nearly linear decrease as the temperature is increased, with a substantially smaller slope with increasing densification. Modeling the relaxation losses and the related velocity variations by an asymmetric double-well potential model that has a distribution of both the barrier potential and the asymmetry, it has been possible to separate the relaxation and the anharmonic contributions to the sound velocity. The former has been ascribed to local motions of boroxol rings formed by connected BO3 planar triangles, the basic units building up the network of v-B2O3, while the latter has been interpreted in terms of the Akhiezer mechanism concerning the “thermal vibration viscosity.”

  12. Spectroscopy

    CERN Document Server

    Walker, S

    1976-01-01

    The three volumes of Spectroscopy constitute the one comprehensive text available on the principles, practice and applications of spectroscopy. By giving full accounts of those spectroscopic techniques only recently introduced into student courses - such as Mössbauer spectroscopy and photoelectron spectroscopy - in addition to those techniques long recognised as being essential in chemistry teaching - sucha as e.s.r. and infrared spectroscopy - the book caters for the complete requirements of undergraduate students and at the same time provides a sound introduction to special topics for graduate students.

  13. The Flux-Flux Correlation Function for Anharmonic Barriers

    CERN Document Server

    Goussev, Arseni; Waalkens, Holger; Wiggins, Stephen

    2010-01-01

    The flux-flux correlation function formalism is a standard and widely used approach for the computation of reaction rates. In this paper we introduce a method to compute the classical and quantum flux-flux correlation functions for anharmonic barriers essentially analytically through the use of the classical and quantum normal forms. In the quantum case we show that the quantum normal form reduces the computation of the flux-flux correlation function to that of an effective one dimensional anharmonic barrier. The example of the computation of the quantum flux-flux correlation function for a fourth order anharmonic barrier is worked out in detail, and we present an analytical expression for the quantum mechanical microcanonical flux-flux correlation function. We then give a discussion of the short-time and harmonic limits.

  14. High-resolution synchrotron infrared spectroscopy of acrolein: The vibrational levels between 850 and 1020 cm-1

    Science.gov (United States)

    McKellar, A. R. W.; Billinghurst, B. E.; Xu, Li-Hong; Lees, R. M.

    2015-11-01

    Using spectra obtained at the Canadian Light Source synchrotron radiation facility, a previously unobserved out-of-plane vibration of trans-acrolein (propenal) is reliably assigned for the first time. Its origin is at 1002.01 cm-1, which is about 20 cm-1 higher than usually quoted in the past. This mode is thus labelled as v14, leaving the label v15 for the known vibration at 992.66 cm-1. Weak combination bands 171182 ← 182, 171131 ← 131, 121182 ← 181, and 171182 ← 181 are studied for the first time, and assignments in the known v11, v16, and v15 fundamental bands are also extended. The seven excited vibrations involved in these bands are analyzed, together with five more unobserved vibrations in the same region (850-1020 cm-1), in a large 12-state simultaneous fit which accounts for most of the many observed perturbations in the spectra.

  15. Structural determination of some uranyl compounds by vibrational spectroscopy; Determinacion estructural de algunos compuestos de uranilo por espectroscopia vibracional

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez S, A.; Martinez Q, E

    1990-07-15

    The vibrational spectra of different uranyl compounds has been studied and of it spectral information has been used the fundamental asymmetric vibrational frequency, to determine the length and constant bond force U=O by means of the combination of the concept of absorbed energy and the mathematical expression of Badger modified by Jones. It is intended a factor that simplifies the mathematical treatment and the results are compared with the values obtained for other methods. (Author)

  16. Exact solutions and ladder operators for a new anharmonic oscillator

    Energy Technology Data Exchange (ETDEWEB)

    Dong Shihai [Programa de Ingenieria Molecular, Instituto Mexicano del Petroleo, Lazaro Cardenas 152, 07730 Mexico DF (Mexico)]. E-mail: dongsh2@yahoo.com; Sun Guohua [Instituto de Investigaciones en Matematicas Aplicadas y en Sistemas, UNAM, A.P. 20-726, Del. Alvaro Obregon, 01000 Mexico DF (Mexico); Lozada-Cassou, M. [Programa de Ingenieria Molecular, Instituto Mexicano del Petroleo, Lazaro Cardenas 152, 07730 Mexico DF (Mexico)

    2005-06-06

    In this Letter, we propose a new anharmonic oscillator and present the exact solutions of the Schrodinger equation with this oscillator. The ladder operators are established directly from the normalized radial wave functions and used to evaluate the closed expressions of matrix elements for some related functions. Some comments are made on the general calculation formula and recurrence relation for off-diagonal matrix elements. Finally, we show that this anharmonic oscillator possesses a hidden symmetry between E(r) and E(ir) by substituting r->ir.

  17. Shocks, Rarefaction Waves, and Current Fluctuations for Anharmonic Chains

    Science.gov (United States)

    Mendl, Christian B.; Spohn, Herbert

    2016-10-01

    The nonequilibrium dynamics of anharmonic chains is studied by imposing an initial domain-wall state, in which the two half lattices are prepared in equilibrium with distinct parameters. We analyse the Riemann problem for the corresponding Euler equations and, in specific cases, compare with molecular dynamics. Additionally, the fluctuations of time-integrated currents are investigated. In analogy with the KPZ equation, their typical fluctuations should be of size t^{1/3} and have a Tracy-Widom GUE distributed amplitude. The proper extension to anharmonic chains is explained and tested through molecular dynamics. Our results are calibrated against the stochastic LeRoux lattice gas.

  18. Vibrational ladder climbing in NO using ultrashort IR laser pulses

    NARCIS (Netherlands)

    Maas, D. J.; Duncan, D. I.; van der Meer, A. F. G.; van der Zande, W. J.; Noordam, L. D.; Lambropoulos, P.; Walther, H.

    1997-01-01

    Chirped excitation of an electronic ladder system has shown complete transfer of the population to the top-level of the ladder system. Similar excitation of vibrational ladders in molecules may provide a tool for state-selective chemistry. Experimental results on the climbing of the anharmonic vibra

  19. Anharmonicity effects in impurity-vacancy centers in diamond revealed by isotopic shifts and optical measurements

    Science.gov (United States)

    Ekimov, E. A.; Krivobok, V. S.; Lyapin, S. G.; Sherin, P. S.; Gavva, V. A.; Kondrin, M. V.

    2017-03-01

    We studied isotopically enriched nano- and microdiamonds with optically active GeV- centers synthesized at high pressures and high temperatures in nonmetallic growth systems. The influence of isotopic composition on optical properties has been thoroughly investigated by photoluminescence-excitation (PLE) and photoluminescence (PL) spectroscopy to get insight into the nature and electronic structure of this color center. We have demonstrated that the large frequency defect (difference between oscillation frequencies in the ground and excited electronic states) does bring about large discrepancy between PLE and PL spectra and comparatively high isotopic shift of the zero phonon line. Both effects seem to be rather common to split-vacancy centers (for example SiV-), where the frequency defect reaches record high values. Isotopic substitution of carbon atoms in the diamond lattice results in even larger shifts, which are only partially accounted for by a redistribution of electron density caused by the volume change of the diamond lattice. It was shown that the vibronic frequency in this case does not depend on the mass of carbon atoms. The greatest part of this isotopic shift is due to anharmonicity effects, which constitute a substantial part of vibronic frequency observed in this center. The exact physical mechanism, which leads to significant enhancement of anharmonicity on substitution of 12C to 13C, is yet to be clarified.

  20. Catalyzed hydrogenation of nitrogen and ethylene on metal (Fe, Pt) single crystal surfaces and effects of coadsorption: A sum frequency generation vibrational spectroscopy study

    Energy Technology Data Exchange (ETDEWEB)

    Westerberg, Staffan Per Gustav [Univ. of California, Berkeley, CA (United States)

    2004-01-01

    High-pressure catalytic reactions and associated processes, such as adsorption have been studied on a molecular level on single crystal surfaces. Sum Frequency Generation (SFG) vibrational spectroscopy together with Auger Electron Spectroscopy (AES), Temperature Programmed Desorption (TPD) and Gas Chromatography (GC) were used to investigate the nature of species on catalytic surfaces and to measure the catalytic reaction rates. Special attention has been directed at studying high-pressure reactions and in particular, ammonia synthesis in order to identify reaction intermediates and the influence of adsorbates on the surface during reaction conditions. The adsorption of gases N2, H2, O2 and NH3 that play a role in ammonia synthesis have been studied on the Fe(111) crystal surface by sum frequency generation vibrational spectroscopy using an integrated Ultra-High Vacuum (UHV)/high-pressure system. SFG spectra are presented for the dissociation intermediates, NH2 (~3325 cm-1) and NH (~3235 cm-1) under high pressure of ammonia (200 Torr) on the clean Fe(111) surface. Addition of 0.5 Torr of oxygen to 200 Torr of ammonia does not significantly change the bonding of dissociation intermediates to the surface. However, it leads to a phase change of nearly 180° between the resonant and non-resonant second order non-linear susceptibility of the surface, demonstrated by the reversal of the SFG spectral features. Heating the surface in the presence of 200 Torr ammonia and 0.5 Torr oxygen reduces the oxygen coverage, which can be seen from the SFG spectra as another relative phase change of 180°. The reduction of the oxide is also supported by Auger electron spectroscopy. The result suggests that the phase change of the spectral features could serve as a sensitive indicator of the chemical environment of the adsorbates.

  1. Catalyzed hydrogenation of nitrogen and ethylene on metal (Fe, Pt) single crystal surfaces and effects of coadsorption: A sum frequency generation vibrational spectroscopy study

    Energy Technology Data Exchange (ETDEWEB)

    Westerberg, Staffan Per Gustav

    2004-12-15

    High-pressure catalytic reactions and associated processes, such as adsorption have been studied on a molecular level on single crystal surfaces. Sum Frequency Generation (SFG) vibrational spectroscopy together with Auger Electron Spectroscopy (AES), Temperature Programmed Desorption (TPD) and Gas Chromatography (GC) were used to investigate the nature of species on catalytic surfaces and to measure the catalytic reaction rates. Special attention has been directed at studying high-pressure reactions and in particular, ammonia synthesis in order to identify reaction intermediates and the influence of adsorbates on the surface during reaction conditions. The adsorption of gases N{sub 2}, H{sub 2}, O{sub 2} and NH{sub 3} that play a role in ammonia synthesis have been studied on the Fe(111) crystal surface by sum frequency generation vibrational spectroscopy using an integrated Ultra-High Vacuum (UHV)/high-pressure system. SFG spectra are presented for the dissociation intermediates, NH{sub 2} ({approx}3325 cm{sup -1}) and NH ({approx}3235 cm{sup -1}) under high pressure of ammonia (200 Torr) on the clean Fe(111) surface. Addition of 0.5 Torr of oxygen to 200 Torr of ammonia does not significantly change the bonding of dissociation intermediates to the surface. However, it leads to a phase change of nearly 180{sup o} between the resonant and non-resonant second order non-linear susceptibility of the surface, demonstrated by the reversal of the SFG spectral features. Heating the surface in the presence of 200 Torr ammonia and 0.5 Torr oxygen reduces the oxygen coverage, which can be seen from the SFG spectra as another relative phase change of 180{sup o}. The reduction of the oxide is also supported by Auger electron spectroscopy. The result suggests that the phase change of the spectral features could serve as a sensitive indicator of the chemical environment of the adsorbates.

  2. Evaluation and differentiation of the Betulaceae birch bark species and their bioactive triterpene content using analytical FT-vibrational spectroscopy and GC-MS

    Directory of Open Access Journals (Sweden)

    Cîntă-Pînzaru Simona

    2012-07-01

    Full Text Available Abstract Background Aiming to obtain the highest triterpene content in the extraction products, nine bark samples from the forest abundant flora of Apuseni Mountains, Romania were Raman spectroscopically evaluated. Three different natural extracts from Betula pendula Roth birch bark have been obtained and characterized using Fourier transform vibrational spectra. Results This study shows that principal components of the birch tree extract can be rapidly recognized and differentiated based on their vibrational fingerprint band shape and intensity. The vibrational spectroscopy results are supported by the GC-MS data. Based on IR and Raman analysis, one can conclude that all the extracts, independent on the solvent(s used, revealed dominant betulin species, followed by lupeol. Conclusions Since Raman measurements could also be performed on fresh plant material, we demonstrated the possibility to apply the present results for the prediction of the highest triterpene content in bark species, for the selection of harvesting time or individual genotypes directly in the field, with appropriate portable Raman equipment.

  3. Vibrational Heat Transport in Molecular Junctions

    Science.gov (United States)

    Segal, Dvira; Agarwalla, Bijay Kumar

    2016-05-01

    We review studies of vibrational energy transfer in a molecular junction geometry, consisting of a molecule bridging two heat reservoirs, solids or large chemical compounds. This setup is of interest for applications in molecular electronics, thermoelectrics, and nanophononics, and for addressing basic questions in the theory of classical and quantum transport. Calculations show that system size, disorder, structure, dimensionality, internal anharmonicities, contact interaction, and quantum coherent effects are factors that combine to determine the predominant mechanism (ballistic/diffusive), effectiveness (poor/good), and functionality (linear/nonlinear) of thermal conduction at the nanoscale. We review recent experiments and relevant calculations of quantum heat transfer in molecular junctions. We recount the Landauer approach, appropriate for the study of elastic (harmonic) phononic transport, and outline techniques that incorporate molecular anharmonicities. Theoretical methods are described along with examples illustrating the challenge of reaching control over vibrational heat conduction in molecules.

  4. Vibrational dynamics of the CN stretching mode of [Ru(CN)6]4- in D2O studied by nonlinear infrared spectroscopy

    Institute of Scientific and Technical Information of China (English)

    Jumpei; TAYAMA; Motohiro; BANNO; Kaoru; OHTA; Keisuke; TOMINAGA

    2010-01-01

    We have studied vibrational dynamics of the T1u mode of the CN stretching mode of [Ru(CN)6 ]4- in D2O by infrared(IR) nonlinear spectroscopy such as an IR three-pulse photon echo experiment and polarization-sensitive IR pump-probe spectroscopy. The isotropic component of the pump-probe signal shows a bi-exponential decay with time constants of 0.8 ps and 20.8 ps. The fast and slow components correspond to the rapid equilibration between the T1u mode and the Raman active modes of the CN stretching mode and the vibrational population relaxation from the v=1 state of the T1u mode,respectively. Anisotropy of the pump-probe signal decays with a time constant of 3.1 ps,which is due to the time evolution of the superposition states of the triply degenerate T1u modes. Three pulse photon echo measurements showed that the time correlation function of the frequency fluctuation decays bi-exponentially with time constants of 80 fs and 1.4 ps. These time constants depend only on the solute and are independent of the solvent,whereas the amplitudes depend on both the solute and solvent.

  5. Studies of Heterogeneously Catalyzed Liquid-Phase Alcohol Oxidation on Platinum bySum-frequency Generation Vibrational Spectroscopy and Reaction Rate Measurements

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Christopher [Univ. of California, Berkeley, CA (United States)

    2014-05-15

    Compared to many branches of chemistry, the molecular level study of catalytically active surfaces is young. Only with the invention of ultrahigh vacuum technology in the past half century has it been possible to carry out experiments that yield useful molecular information about the reactive occurrences at a surface. The reason is two-fold: low pressure is necessary to keep a surface clean for an amount of time long enough to perform an experiment, and most atomic scale techniques that are surface speci c (x-ray photoelectron spectroscopy, electron energy loss spectroscopy, Auger electron spectroscopy, etc.) cannot be used at ambient pressures, because electrons, which act as chemical probes in these techniques, are easily scattered by molecules. Sum-frequency generation (SFG) vibrational spectroscopy is one technique that can provide molecular level information from the surface without the necessity for high vacuum. Since the advent of SFG as a surface spectroscopic tool it has proved its worth in the studies of surface catalyzed reactions in the gas phase, with numerous reactions in the gas phase having been investigated on a multitude of surfaces. However, in situ SFG characterization of catalysis at the solid-liquid interface has yet to be thoroughly pursued despite the broad interest in the use of heterogeneous catalysts in the liquid phase as replacements for homogeneous counterparts. This work describes an attempt to move in that direction, applying SFG to study the solid-liquid interface under conditions of catalytic alcohol oxidation on platinum.

  6. Variational approach to anharmonic collective motion

    CERN Document Server

    Bertsch, George F

    1996-01-01

    We derive large-amplitude collective equations of motion from the variational principle for the time-dependent Schroedinger equation. These equations reduce to the well-known diabatic formulas for vibrational frequencies in the small amplitude limit. The finite amplitude expression allows departures from harmonic behavior of giant resonances to be simply estimated. The relative shift of the second phonon falls with nuclear mass A as A^(-4/3) in the three modes we consider: monopole, dipole, and quadrupole. Numerically the effect is very small in heavy nuclei, as was found with other approaches.

  7. High-resolution synchrotron infrared spectroscopy of acrolein: The vibrational levels between 700 and 820 cm-1

    Science.gov (United States)

    McKellar, A. R. W.; Billinghurst, B. E.

    2015-09-01

    The weak combination bands ν12 + ν18 and ν17 + ν18 of trans-acrolein in the 700-760 cm-1 region are observed at high resolution (facility. A detailed rotational analysis of the 121181 and 171181 upper states is made which includes the nearby perturbing states 185, 132181, and 131183. Taking the results of this 5-state fit, together with earlier results on lower lying vibrations, we now have experimental characterization for all 15 excited vibrational states of acrolein lying below 820 cm-1.

  8. Engineering and Characterization of Peptides and Proteins at Surfaces and Interfaces: A Case Study in Surface-Sensitive Vibrational Spectroscopy.

    Science.gov (United States)

    Ding, Bei; Jasensky, Joshua; Li, Yaoxin; Chen, Zhan

    2016-06-21

    Understanding molecular structures of interfacial peptides and proteins impacts many research fields by guiding the advancement of biocompatible materials, new and improved marine antifouling coatings, ultrasensitive and highly specific biosensors and biochips, therapies for diseases related to protein amyloid formation, and knowledge on mechanisms for various membrane proteins and their interactions with ligands. Developing methods for measuring such unique systems, as well as elucidating the structure and function relationship of such biomolecules, has been the goal of our lab at the University of Michigan. We have made substantial progress to develop sum frequency generation (SFG) vibrational spectroscopy into a powerful technique to study interfacial peptides and proteins, which lays a foundation to obtain unique and valuable insights when using SFG to probe various biologically relevant systems at the solid/liquid interface in situ in real time. One highlighting feature of this Account is the demonstration of the power of combining SFG with other techniques and methods such as ATR-FTIR, surface engineering, MD simulation, liquid crystal sensing, and isotope labeling in order to study peptides and proteins at interfaces. It is necessary to emphasize that SFG plays a major role in these studies, while other techniques and methods are supplemental. The central role of SFG is to provide critical information on interfacial peptide and protein structure (e.g., conformation and orientation) in order to elucidate how surface engineering (e.g., to vary the structure) can ultimately affect surface function (e.g., to optimize the activity). This Account focuses on the most significant recent progress in research on interfacial peptides and proteins carried out by our group including (1) the development of SFG analysis methods to determine orientations of regular as well as disrupted secondary structures, and the successful demonstration and application of an isotope

  9. [The study of dimethoate by means of vibrational and surface enhanced Raman spectroscopy on Au/Ag core-shell nanoparticles].

    Science.gov (United States)

    He, Qiang; Li, Si; Yu, Dan-Ni; Zhou, Gunag-Ming; Ji, Fang-Ying; Subklew, Guenter

    2010-12-01

    The vibrational structure of dimethoate, with its solid state and saturated solutions at acidic and basic conditions, was characterized with combination of means of FTIR and FT-Raman vibrational spectroscopy technology, and the comprehensive information about the dimethoate molecular groups' vibrational features was obtained. The surface enhanced Raman scattering (SERS) spectra of dimethoate at different concentrations with different acidic and basic conditions, and adsorbed on the substrate's surface of the core-shell Au/Ag nanoparticles, were also obtained. The adsorption states of dimethoate's molecule on the substrate's surface of the core-shell Au/Ag nanoparticles and the effects by the different acid-base conditions were investigated, with speculation of the adsorption mechanism. From the results, v(as)(NH), v(as)(CH3), v(O=C-N), tau(O=C-N), v(P-O), v(P=S), v(C-C) and delta(P-O-C) are the characteristic peaks of inner dimethoate structure's vibrations; and the concentration range in which dimethoate could interact with core-shell Au/Ag nanoparticles fully is about 1.0 x 10(-3) mol * L(-1) both in acidic and basic conditions. Dimethoate's molecule interacts with SERS' substrate surface mainly through P-O-C, O=C-C, (S-CH2), P=S, and CH3 structures; and the effects of dimethoate's hydrolysis path in acidic and basic conditions on the adsorption are discussed, which give some good references for the research of organophosphorus pesticides' transformations in different environmental systems.

  10. Structure Sensitivity in Pt Nanoparticle Catalysts for Hydrogenation of 1,3-Butadiene: In Situ Study of Reaction Intermediates Using SFG Vibrational Spectroscopy

    KAUST Repository

    Michalak, William D.

    2013-01-31

    The product selectivity during 1,3-butadiene hydrogenation on monodisperse, colloidally synthesized, Pt nanoparticles was studied under reaction conditions with kinetic measurements and in situ sum frequency generation (SFG) vibrational spectroscopy. SFG was performed with the capping ligands intact in order to maintain nanoparticle size by reduced sintering. Four products are formed at 75 C: 1-butene, cis-2-butene, trans-2-butene, and n-butane. Ensembles of Pt nanoparticles with average diameters of 0.9 and 1.8 nm exhibit a ∼30% and ∼20% increase in the full hydrogenation products, respectively, as compared to Pt nanoparticles with average diameters of 4.6 and 6.7 nm. Methyl and methylene vibrational stretches of reaction intermediates observed under working conditions using SFG were used to correlate the stable reaction intermediates with the product distribution. Kinetic and SFG results correlate with previous DFT predictions for two parallel reaction pathways of 1,3-butadiene hydrogenation. Hydrogenation of 1,3-butadiene can initiate with H-addition at internal or terminal carbons leading to the formation of 1-buten-4-yl radical (metallocycle) and 2-buten-1-yl radical intermediates, respectively. Small (0.9 and 1.8 nm) nanoparticles exhibited vibrational resonances originating from both intermediates, while the large (4.6 and 6.7 nm) particles exhibited vibrational resonances originating predominately from the 2-buten-1-yl radical. This suggests each reaction pathway competes for partial and full hydrogenation and the nanoparticle size affects the kinetic preference for the two pathways. The reaction pathway through the metallocycle intermediate on the small nanoparticles is likely due to the presence of low-coordinated sites. © 2012 American Chemical Society.

  11. A symmetry adapted approach to vibrational excitations in atomic clusters

    CERN Document Server

    Frank, A I; Bijker, R; Lemus, R; Pérez-Bernal, F

    1998-01-01

    An algebraic method especially suited to describe strongly anharmonic vibrational spectra in molecules may be an appropriate framework to study vibrational spectra of Na$^+_n$ clusters, where nearly flat potential energy surfaces and the appearance of close lying isomers have been reported. As an illustration we describe the model and apply it to the Be$_4$, H$_3^+$, Be$_3$ and Na$_3^+$ clusters.

  12. 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.

  13. Simulation of vibrational energy transfer in two-dimensional infrared spectroscopy of amide I and amide II modes in solution

    NARCIS (Netherlands)

    Bloem, Robbert; Dijkstra, Arend G.; Jansen, Thomas La Cour; Knoester, Jasper

    2008-01-01

    Population transfer between vibrational eigenstates is important for many phenomena in chemistry. In solution, this transfer is induced by fluctuations in molecular conformation as well as in the surrounding solvent. We develop a joint electrostatic density functional theory map that allows us to co

  14. Terahertz spectroscopy and solid-state density functional theory calculation of anthracene: Effect of dispersion force on the vibrational modes

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Feng; Tominaga, Keisuke, E-mail: atmyh@ntu.edu.tw, E-mail: tominaga@kobe-u.ca.jp, E-mail: junichi.nishizawa@hanken.jp [Molecular Photoscience Research Center, Kobe University, Nada, Kobe 657-0013 (Japan); Hayashi, Michitoshi, E-mail: atmyh@ntu.edu.tw, E-mail: tominaga@kobe-u.ca.jp, E-mail: junichi.nishizawa@hanken.jp; Wang, Houng-Wei [Center for Condensed Matter Sciences, National Taiwan University, 1 Roosevelt Rd., Sec. 4, Taipei 10617, Taiwan (China); Kambara, Ohki; Sasaki, Tetsuo [Research Institute of Electronics, Shizuoka University, 3-5-1 Jyohoku, Naka-ku, Hamamatsu, Shizuoka 432-8561 (Japan); Nishizawa, Jun-ichi, E-mail: atmyh@ntu.edu.tw, E-mail: tominaga@kobe-u.ca.jp, E-mail: junichi.nishizawa@hanken.jp [Jun-ichi Nishizawa Memorial Research Center, Tohoku University, 519-1176 Aoba, Aramaki, Aoba-ku, Sendai 980-0845 (Japan)

    2014-05-07

    The phonon modes of molecular crystals in the terahertz frequency region often feature delicately coupled inter- and intra-molecular vibrations. Recent advances in density functional theory such as DFT-D{sup *} have enabled accurate frequency calculation. However, the nature of normal modes has not been quantitatively discussed against experimental criteria such as isotope shift (IS) and correlation field splitting (CFS). Here, we report an analytical mode-decoupling method that allows for the decomposition of a normal mode of interest into intermolecular translation, libration, and intramolecular vibrational motions. We show an application of this method using the crystalline anthracene system as an example. The relationship between the experimentally obtained IS and the IS obtained by PBE-D{sup *} simulation indicates that two distinctive regions exist. Region I is associated with a pure intermolecular translation, whereas region II features coupled intramolecular vibrations that are further coupled by a weak intermolecular translation. We find that the PBE-D{sup *} data show excellent agreement with the experimental data in terms of IS and CFS in region II; however, PBE-D{sup *} produces significant deviations in IS in region I where strong coupling between inter- and intra-molecular vibrations contributes to normal modes. The result of this analysis is expected to facilitate future improvement of DFT-D{sup *}.

  15. Insight into structural phase transitions from the decoupled anharmonic mode approximation

    Science.gov (United States)

    Adams, Donat J.; Passerone, Daniele

    2016-08-01

    We develop a formalism (decoupled anharmonic mode approximation, DAMA) that allows calculation of the vibrational free energy using density functional theory even for materials which exhibit negative curvature of the potential energy surface with respect to atomic displacements. We investigate vibrational modes beyond the harmonic approximation and approximate the potential energy surface with the superposition of the accurate potential along each normal mode. We show that the free energy can stabilize crystal structures at finite temperatures which appear dynamically unstable at T  =  0. The DAMA formalism is computationally fast because it avoids statistical sampling through molecular dynamics calculations, and is in principle completely ab initio. It is free of statistical uncertainties and independent of model parameters, but can give insight into the mechanism of a structural phase transition. We apply the formalism to the perovskite cryolite, and investigate the temperature-driven phase transition from the P21/n to the Immm space group. We calculate a phase transition temperature between 710 and 950 K, in fair agreement with the experimental value of 885 K. This can be related to the underestimation of the interaction of the vibrational states. We also calculate the main axes of the thermal ellipsoid and can explain the experimentally observed increase of its volume for the fluorine by 200-300% throughout the phase transition. Our calculations suggest the appearance of tunneling states in the high temperature phase. The convergence of the vibrational DOS and of the critical temperature with respect of reciprocal space sampling is investigated using the polarizable-ion model.

  16. Rotational spectroscopy of pyridazine and its isotopologs from 235-360 GHz: Equilibrium structure and vibrational satellites

    Science.gov (United States)

    Esselman, Brian J.; Amberger, Brent K.; Shutter, Joshua D.; Daane, Mitchell A.; Stanton, John F.; Woods, R. Claude; McMahon, Robert J.

    2013-12-01

    The rotational spectrum of pyridazine (o-C4H4N2), the ortho disubstituted nitrogen analog of benzene, has been measured and analyzed in the gas phase. For the ground vibrational state of the normal isotopolog, over 2000 individual rotational transitions have been identified between 238 and 360 GHz and have been fit to 13 parameters of a 6th-order centrifugal distortion Hamiltonian. All transitions in this frequency region can now be predicted from this model to near experimental accuracy, i.e., well enough for the purpose of any future radio-astronomical search for this species. Three isotopologs, [3-13C]-C4H4N2, [4-13C]-C4H4N2, and [1-15N]-C4H4N2, have been detected in natural abundance, and several hundred lines have been measured for each of these species and fit to 6th-order Hamiltonians. Ten additional isotopologs were synthesized with enhanced deuterium substitution and analyzed to allow for a complete structure determination. The equilibrium structure (Re) of pyridazine was obtained by correcting the experimental rotational constants for the effects of vibration-rotation coupling using interaction constants predicted from CCSD(T) calculations with an ANO0 basis set and further correcting for the effect of electron mass. The final Re structural parameters are determined with excellent accuracy, as evidenced by their ability to predict 28 independent moments of inertia (Ia and Ib for 14 isotopologs) very well from 9 structural parameters. The rotational spectra of the six lowest-energy fundamental vibrational satellites of the main isotopolog have been detected. The rotational spectra of the five lowest-energy vibrational satellites have been assigned and fit to yield accurate rotational and distortion constants, while the fit and assignment for the sixth is less complete. The resultant vibration-rotation interaction (α) constants are found to be in excellent agreement with ones predicted from coupled-cluster calculations, which proved to be the key to

  17. Thermal and magnetic anomalies of α-iron: an exploration by extended x-ray absorption fine structure spectroscopy and synchrotron x-ray diffraction

    Science.gov (United States)

    Boccato, Silvia; Sanson, Andrea; Kantor, Innokenty; Mathon, Olivier; Dyadkin, Vadim; Chernyshov, Dmitry; Carnera, Alberto; Pascarelli, Sakura

    2016-09-01

    The local structure and dynamics of α-iron have been investigated by extended x-ray absorption fine structure (EXAFS) spectroscopy and x-ray diffraction (XRD) in order to shed light on some thermal and magnetic anomalies observed in the last decades. The quantitative EXAFS analysis of the first two coordination shells reveals a peculiar local vibrational dynamics of α-iron: the second neighbor distance exhibits anharmonicity and vibrational anisotropy larger than the first neighbor distance. We search for possible distortions of the bcc structure to justify the unexplained magnetostriction anomalies of α-iron and provide a value for the maximum dislocation of the central Fe atom. No thermal anomalies have been detected from the current XRD data. On the contrary, an intriguing thermal anomaly at about 150 K, ascribed to a stiffening of the Fe-Fe bonds, was found by EXAFS.

  18. Absolute Configuration Assignment of a Paraconic Acid Derivative via Vibrational Circular Dichroism Spectroscopy and Density Functional Theory Calculation.

    Science.gov (United States)

    Meninno, Sara; Rizzo, Paola; Abbate, Sergio; Longhi, Giovanna; Mazzeo, Giuseppe; Monaco, Guglielmo; Lattanzi, Alessandra; Zanasi, Riccardo

    2016-02-01

    Density functional theory calculation of the vibrational circular dichroism spectrum was used to assign the absolute configuration of an all-carbon quaternary β-stereocenter of a γ-butyrolactone recently synthesized through an asymmetric organocatalytic tandem aldol/lactonization sequence. Comparison with the experimental spectrum is satisfactory, on account of the fact that spectroscopic features are weak due to the presence of multiple conformers. As a result, the (R) absolute configuration was assigned to the (+) optical isomer.

  19. Intrinsic chirality and prochirality at Air/R-(+)- and S-(-)-limonene interfaces: spectral signatures with interference chiral sum-frequency generation vibrational spectroscopy.

    Science.gov (United States)

    Fu, Li; Zhang, Yun; Wei, Zhe-Hao; Wang, Hong-Fei

    2014-09-01

    We report in this work detailed measurements of the chiral and achiral sum-frequency vibrational spectra in the C-H stretching vibration region (2800-3050 cm(-1)) of the air/liquid interfaces of R-(+)-limonene and S-(-)-limonene, using the recently developed high-resolution broadband sum-frequency generation vibrational spectroscopy (HR-BB-SFG-VS). The achiral SFG spectra of R-limonene and S-limonene, as well as the RS racemic mixture (50/50 equal amount mixture), show that the corresponding molecular groups of the R and S enantiomers are with the same interfacial orientations. The interference chiral SFG spectra of the limonene enantiomers exhibit a spectral signature from the chiral response of the Cα-H stretching mode, and a spectral signature from the prochiral response of the CH(2) asymmetric stretching mode, respectively. The chiral spectral feature of the Cα-H stretching mode changes sign from R-(+)-limonene to S-(-)-limonene surfaces, and disappears for the RS racemic mixture surface. While the prochiral spectral feature of the CH(2) asymmetric stretching mode is the same for R-(+)-limonene and S-(-)-limonene surfaces, and also surprisingly remains the same for the RS racemic mixture surface. Therefore, the structures of the R-(+)-limonene and the S-(-)-limonene at the liquid interfaces are nevertheless not mirror images to each other, even though the corresponding groups have the same tilt angle from the interfacial normal, i.e., the R-(+)-limonene and the S-(-)-limonene at the surface are diastereomeric instead of enantiomeric. These results provide detailed information in understanding the structure and chirality of molecular interfaces and demonstrate the sensitivity and potential of SFG-VS as a unique spectroscopic tool for chirality characterization and chiral recognition at the molecular interface.

  20. FT-IR, FT-Raman, UV-Visible, and NMR spectroscopy and vibrational properties of the labdane-type diterpene 13-epi-sclareol

    Science.gov (United States)

    Chain, Fernando E.; Leyton, Patricio; Paipa, Carolina; Fortuna, Mario; Brandán, Silvia A.

    2015-03-01

    In this work, FT-IR, FT-Raman, UV-Visible and NMR spectroscopies and density functional theory (DFT) calculations were employed to study the structural and vibrational properties of the labdane-type diterpene 13-epi-sclareol using the hybrid B3LYP method together with the 6-31G∗ basis set. Three stable structures with minimum energy found on the potential energy curves (PES) were optimized, and the corresponding molecular electrostatic potentials, atomic charges, bond orders, stabilization energies and topological properties were computed at the same approximation level. The complete assignment of the bands observed in the vibrational spectrum of 13-epi-sclareol was performed taking into account the internal symmetry coordinates for the three structures using the scaled quantum mechanical force field (SQMFF) methodology at the same level of theory. In addition, the force constants were calculated and compared with those reported in the literature for similar compounds. The predicted vibrational spectrum and the calculated 1H NMR and 13C NMR chemical shifts are in good agreement with the corresponding experimental results. The theoretical UV-Vis spectra for the most stable structure of 13-epi-sclareol demonstrate a better correlation with the corresponding experimental spectrum. The study of the three conformers by means of the theory of atoms in molecules (AIM) revealed different H bond interactions and a strong dependence of the interactions on the distance between the involved atoms. Furthermore, the natural bond orbital (NBO) calculations showed the characteristics of the electronic delocalization for the two six-membered rings with chair conformations.

  1. Excited-state intramolecular hydrogen transfer (ESIHT) of 1,8-Dihydroxy-9,10-anthraquinone (DHAQ) characterized by ultrafast electronic and vibrational spectroscopy and computational modeling

    KAUST Repository

    Mohammed, Omar F.

    2014-05-01

    We combine ultrafast electronic and vibrational spectroscopy and computational modeling to investigate the photoinduced excited-state intramolecular hydrogen-transfer dynamics in 1,8-dihydroxy-9,10-anthraquinone (DHAQ) in tetrachloroethene, acetonitrile, dimethyl sulfoxide, and methanol. We analyze the electronic excited states of DHAQ with various possible hydrogen-bonding schemes and provide a general description of the electronic excited-state dynamics based on a systematic analysis of femtosecond UV/vis and UV/IR pump-probe spectroscopic data. Upon photoabsorption at 400 nm, the S 2 electronic excited state is initially populated, followed by a rapid equilibration within 150 fs through population transfer to the S 1 state where DHAQ exhibits ESIHT dynamics. In this equilibration process, the excited-state population is distributed between the 9,10-quinone (S2) and 1,10-quinone (S1) states while undergoing vibrational energy redistribution, vibrational cooling, and solvation dynamics on the 0.1-50 ps time scale. Transient UV/vis pump-probe data in methanol also suggest additional relaxation dynamics on the subnanosecond time scale, which we tentatively ascribe to hydrogen bond dynamics of DHAQ with the protic solvent, affecting the equilibrium population dynamics within the S2 and S1 electronic excited states. Ultimately, the two excited singlet states decay with a solvent-dependent time constant ranging from 139 to 210 ps. The concomitant electronic ground-state recovery is, however, only partial because a large fraction of the population relaxes to the first triplet state. From the similarity of the time scales involved, we conjecture that the solvent plays a crucial role in breaking the intramolecular hydrogen bond of DHAQ during the S2/S1 relaxation to either the ground or triplet state. © 2014 American Chemical Society.

  2. FT-IR, FT-Raman, UV-visible, and NMR spectroscopy and vibrational properties of the labdane-type diterpene 13-epi-sclareol.

    Science.gov (United States)

    Chain, Fernando E; Leyton, Patricio; Paipa, Carolina; Fortuna, Mario; Brandán, Silvia A

    2015-03-05

    In this work, FT-IR, FT-Raman, UV-Visible and NMR spectroscopies and density functional theory (DFT) calculations were employed to study the structural and vibrational properties of the labdane-type diterpene 13-epi-sclareol using the hybrid B3LYP method together with the 6-31G(∗) basis set. Three stable structures with minimum energy found on the potential energy curves (PES) were optimized, and the corresponding molecular electrostatic potentials, atomic charges, bond orders, stabilization energies and topological properties were computed at the same approximation level. The complete assignment of the bands observed in the vibrational spectrum of 13-epi-sclareol was performed taking into account the internal symmetry coordinates for the three structures using the scaled quantum mechanical force field (SQMFF) methodology at the same level of theory. In addition, the force constants were calculated and compared with those reported in the literature for similar compounds. The predicted vibrational spectrum and the calculated (1)H NMR and (13)C NMR chemical shifts are in good agreement with the corresponding experimental results. The theoretical UV-Vis spectra for the most stable structure of 13-epi-sclareol demonstrate a better correlation with the corresponding experimental spectrum. The study of the three conformers by means of the theory of atoms in molecules (AIM) revealed different H bond interactions and a strong dependence of the interactions on the distance between the involved atoms. Furthermore, the natural bond orbital (NBO) calculations showed the characteristics of the electronic delocalization for the two six-membered rings with chair conformations.

  3. Vibrational spectroscopy of the phosphate mineral lazulite - (Mg, Fe)Al2(PO4)2·(OH)2 found in the Minas Gerais, Brazil

    Science.gov (United States)

    Frost, Ray L.; Xi, Yunfei; Beganovic, Martina; Belotti, Fernanda Maria; Scholz, Ricardo

    2013-04-01

    This research was done on lazulite samples from the Gentil mine, a lithium bearing pegmatite located in the municipality of Mendes Pimentel, Minas Gerais, Brazil. Chemical analysis was carried out by electron microprobe analysis and indicated a magnesium rich phase with partial substitution of iron. Traces of Ca and Mn, (which partially replaced Mg) were found. The calculated chemical formula of the studied sample is: (Mg0.88, Fe0.11)Al1.87(PO4)2.08(OH)2.02. The Raman spectrum of lazulite is dominated by an intense sharp band at 1060 cm-1 assigned to PO stretching vibrations of of tetrahedral [PO4] clusters presents into the HPO42- units. Two Raman bands at 1102 and 1137 cm-1 are attributed to both the HOP and PO antisymmetric stretching vibrations. The two infrared bands at 997 and 1007 cm-1 are attributed to the ν1PO43- symmetric stretching modes. The intense bands at 1035, 1054, 1081, 1118 and 1154 cm-1 are assigned to the ν3PO43- antisymmetric stretching modes from both the HOP and tetrahedral [PO4] clusters. A set of Raman bands at 605, 613, 633 and 648 cm-1 are assigned to the ν4 out of plane bending modes of the PO4, HPO4 and H2PO4 units. Raman bands observed at 414, 425, 460, and 479 cm-1 are attributed to the ν2 tetrahedral PO4 clusters, HPO4 and H2PO4 bending modes. The intense Raman band at 3402 and the infrared band at 3403 cm-1 are assigned to the stretching vibration of the OH units. A combination of Raman and infrared spectroscopy enabled aspects of the molecular structure of the mineral lazulite to be understood.

  4. Sum Frequency Generation Vibrational Spectroscopy and Kinetic Study of 2-Methylfuran and 2,5-Dimethylfuran Hydrogenation over 7 nm Platinum Cubic Nanoparticles

    KAUST Repository

    Aliaga, Cesar

    2011-04-28

    Sum frequency generation vibrational spectroscopy and kinetic measurements obtained from gas chromatography were used to study the adsorption and hydrogenation of 2-methylfuran (MF) and 2,5-dimethylfuran (DMF) over cubic Pt nanoparticles of 7 nm average size, synthesized by colloidal methods and cleaned by ultraviolet light and ozone treatment. Reactions carried out at atmospheric pressure in the temperature range of 20-120 °C produced dihydro and tetrahydro species, as well as ring-opening products (alcohols) and ring-cracking products, showing high selectivity toward ring opening throughout the entire temperature range. The aromatic rings (MF and DMF) adsorbed parallel to the nanoparticle surface. Results yield insight into various surface reaction intermediates and the reason for the significantly lower selectivity for ring cracking in DMF hydrogenation compared to MF hydrogenation. © 2011 American Chemical Society.

  5. Sum frequency generation vibrational spectroscopy (SFG-VS) for complex molecular surfaces and interfaces: Spectral lineshape measurement and analysis plus some controversial issues

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hong-Fei

    2016-12-01

    Sum-frequency generation vibrational spectroscopy (SFG-VS) was first developed in the 1980s and it has been proven a uniquely sensitive and surface/interface selective spectroscopic probe for characterization of the structure, conformation and dynamics of molecular surfaces and interfaces. In recent years, there has been significant progress in the development of methodology and instrumentation in the SFG-VS toolbox that has significantly broadened the application to complex molecular surfaces and interfaces. In this review, after presenting a unified view on the theory and methodology focusing on the SFG-VS spectral lineshape, as well as the new opportunities in SFG-VS applications with such developments, some of the controversial issues that have been puzzling the community are to be discussed. The aim of this review is to present to the researchers and students interested in molecular surfaces and interfacial sciences up-to-date perspectives complementary to the existing textbooks and reviews on SFG-VS.

  6. Interpenetrating polymer network membranes for fuel cells: infrared vibrational spectroscopy; Membranes baseadas dm redes polimericas interpenetrantes para celulas a combustivel: estudo por espectroscopia vibracional no infravermelho

    Energy Technology Data Exchange (ETDEWEB)

    Loureiro, Felipe A.M.; Rocco, Ana Maria [Grupo de Materiais Condutores e Energia, Escola de Quimica, Universidade Federal do Rio de Janeiro, RJ (Brazil)], e-mail: amrocco@eq.ufrj.br; Pereira, Robson Pacheco [Instituto de Ciencias Exatas, Universidade Federal Fluminense (UFF), Volta Redonda, RJ (Brazil)

    2011-07-01

    In the present work, proton conductive membranes based on IPN matrices doped with H{sub 3}PO{sub 4} were developed. The characterization by infrared vibrational spectroscopy evidenced the polymerization of DGEBA and the immobilization of PEI chains, originating a structure containing basic sites suitable for proton coordination and conduction. The FTIR characterization evidenced the polymerization of DGEBA in the presence of PEI thus forming Semi-IPN membranes which, after doped with H{sub 3}PO{sub 4}, exhibited conductivity values of 10{sup -4} W{sup -1}cm{sup -1} at room temperature and 10{sup -3} {omega}{sup -1}cm{sup -1} at 80 degree C, as well as a dependency of conductivity with temperature following the Arrhenius model. The activation energy values (14,33 and 12,96 kJ.mol{sup -1}) indicated a proton conduction mechanism predominantly vehicular in the matrices studied under 100% relative humidity. (author)

  7. Sum frequency generation vibrational spectroscopy (SFG-VS) for complex molecular surfaces and interfaces: Spectral lineshape measurement and analysis plus some controversial issues

    Science.gov (United States)

    Wang, Hong-Fei

    2016-12-01

    Sum-frequency generation vibrational spectroscopy (SFG-VS) was first developed in the 1980s and it has been proven a uniquely sensitive and surface/interface selective spectroscopic probe for characterization of the structure, conformation and dynamics of molecular surfaces and interfaces. In recent years, there have been many progresses in the development of methodology and instrumentation in the SFG-VS toolbox that have significantly broadened the application to complex molecular surfaces and interfaces. In this review, after presenting a unified view on the theory and methodology focusing on the SFG-VS spectral lineshape, as well as the new opportunities in SFG-VS applications with such developments, some of the controversial issues that have been puzzling the community are discussed. The aim of this review is to present to the researchers and students interested in molecular surfaces and interfacial sciences up-to-date perspectives complementary to the existing textbooks and reviews on SFG-VS.

  8. PT-Symmetric Cubic Anharmonic Oscillator as a Physical Model

    CERN Document Server

    Mostafazadeh, A

    2004-01-01

    We perform a perturbative calculation of the physical observables, in particular pseudo-Hermitian position and momentum operators, the equivalent Hermitian Hamiltonian operator, and the classical Hamiltonian for the PT-symmetric cubic anharmonic oscillator, $ H=p^1/(2m)+\\mu^2x^2/2+i\\epsilon x^3 $. Ignoring terms of order $ \\epsilon^4 $ and higher, we show that this system describes an ordinary quartic anharmonic oscillator with a position-dependent mass and real and positive coupling constants. This observation elucidates the classical origin of the reality and positivity of the energy spectrum. We also discuss the quantum-classical correspondence for this PT-symmetric system, compute the associated conserved probability density, and comment on the issue of factor-ordering in the pseudo-Hermitian canonical quantization of the underlying classical system.

  9. Phonon anharmonicity and negative thermal expansion in SnSe

    Science.gov (United States)

    Bansal, Dipanshu; Hong, Jiawang; Li, Chen W.; May, Andrew F.; Porter, Wallace; Hu, Michael Y.; Abernathy, Douglas L.; Delaire, Olivier

    2016-08-01

    The anharmonic phonon properties of SnSe in the P n m a phase were investigated with a combination of experiments and first-principles simulations. Using inelastic neutron scattering (INS) and nuclear resonant inelastic X-ray scattering (NRIXS), we have measured the phonon dispersions and density of states (DOS) and their temperature dependence, which revealed a strong, inhomogeneous shift and broadening of the spectrum on warming. First-principles simulations were performed to rationalize these measurements, and to explain the previously reported anisotropic thermal expansion, in particular the negative thermal expansion within the Sn-Se bilayers. Including the anisotropic strain dependence of the phonon free energy, in addition to the electronic ground state energy, is essential to reproduce the negative thermal expansion. From the phonon DOS obtained with INS and additional calorimetry measurements, we quantify the harmonic, dilational, and anharmonic components of the phonon entropy, heat capacity, and free energy. The origin of the anharmonic phonon thermodynamics is linked to the electronic structure.

  10. Adsorption and Vibrational Study of Folic Acid on Gold Nanopillar Structures Using Surface-enhanced Raman Scattering Spectroscopy

    DEFF Research Database (Denmark)

    Castillo, John J.; Rindzevicius, Tomas; Rozo, Ciro E.;

    2015-01-01

    on the nanopillars within the high electromagnetic field areas. The adsorption behaviour of folic acid and the band assignment of the main vibrations together with the optimized geometry of folic acid and folic acid in the presence of a cluster of 10 gold atoms were assessed using the density functional theory (B3...... that the interaction of folic acid with the Au NP occurred primarily through the nitrogen atoms, from their pteridine ring. Finally, the obtained adsorption isotherm for folic acid was deduced from the analysis of the SERS spectra and it followed a negative cooperative binding model....

  11. Coherent vibrational dynamics

    CERN Document Server

    Lanzani, Guglielmo; De Silvestri, Sandro

    2007-01-01

    Vibrational spectroscopy is a powerful investigation tool for a wide class of materials covering diverse areas in physics, chemistry and biology. The continuous development in the laser field regarding ultrashort pulse generation has led to the possibility of producing light pulses that can follow vibrational motion coupled to the electronic transitions in molecules and solids in real time. Aimed at researchers and graduate students using vibrational spectroscopy, this book provides both introductory chapters as well as more advanced contents reporting on recent progress. It also provides a good starting point for scientists seeking a sound introduction to ultrafast optics and spectroscopic techniques.

  12. Characterization of the primary hydration shell of the hydroxide ion with H2 tagging vibrational spectroscopy of the OH- ṡ (H2O)n=2,3 and OD- ṡ (D2O)n=2,3 clusters

    Science.gov (United States)

    Gorlova, Olga; DePalma, Joseph W.; Wolke, Conrad T.; Brathwaite, Antonio; Odbadrakh, Tuguldur T.; Jordan, Kenneth D.; McCoy, Anne B.; Johnson, Mark A.

    2016-10-01

    We report the isotope-dependent vibrational predissociation spectra of the H2-tagged OH- ṡ (H2O)n=2,3 clusters, from which we determine the strongly coordination-dependent energies of the fundamentals due to the OH groups bound to the ion and the intramolecular bending modes of the water molecules. The HOH bending fundamental is completely missing in the delocalized OH- ṡ (H2O) binary complex but is recovered upon adding the second water molecule, thereby establishing that the dihydrate behaves as a hydroxide ion solvated by two essentially intact water molecules. The energies of the observed OH stretches are in good agreement with the values predicted by Takahashi and co-workers [Phys. Chem. Chem. Phys. 17, 25505 (2015); 15, 114 (2013)] with a theoretical model that treats the strong anharmonicities at play in this system with explicit coupling between the bound OH groups and the O-O stretching modes on an extended potential energy surface. We highlight a surprising similarity between the spectral signatures of OH- ṡ (H2O)3 and the excess proton analogue, H3O+ ṡ (H2O)3, both of which correspond to completed hydration shells around the proton defect. We discuss the origin of the extreme solvatochromicity displayed by both OH- and H+ in the context of the anomalously large "proton polarizabilities" of the H5O2+ and H3O2- binary complexes.

  13. Synthesis, X-ray structure analysis, thermodynamic and electronic properties of 4-acetamido benzaldehyde using vibrational spectroscopy and DFT calculations

    Science.gov (United States)

    Jeeva Jasmine, N.; Arunagiri, C.; Subashini, A.; Stanley, N.; Thomas Muthiah, P.

    2017-02-01

    Theoretical Spectrograms, namely, FT-Raman (3500-50 cm-1) and FT-Infrared (4000-400 cm-1) spectra have been studied for 4-acetamido benzaldehyde (4ABA) and are assigned to different normal modes of the molecule. Vibrational spectral analysis was compared with the experimental and theoretical, FT-IR and FT-Raman spectra. The effect of polarity on the Harmonic vibrational frequencies, intensities, optimized geometrical parameters and several thermodynamic parameters in the ground state have been computed by the B3LYP method using 6-311 + G(d,p) basis set. The results of the optimized molecular structure is presented and compared with the XRD values. The global chemical reactivity relate to some parameters, such as HOMO, LUMO, gap energy (ΔE) and other parameters, including electronegativity (χ) and global hardness (η). The values of the reactivity descriptors indicated that the interaction between 4ABA molecules reduced its reactivity in comparison with the exhibited in gas phase. In addition, the local reactivity has been analyzed through the Fukui function and condensed softness indices.

  14. Vibrational spectroscopy, intramolecular CH⋯O interaction and conformational analysis of 2,5-dimethyl-benzyl benzoate

    Science.gov (United States)

    Viana, Rommel B.; Ribeiro, Gabriela L. O.; Valencia, Leidy J.; Varela, Jaldyr J. G.; Viana, Anderson B.; da Silva, Albérico B. F.; Moreno-Fuquen, Rodolfo

    2016-12-01

    The aim of this study was to report the spectroscopic and electronic properties of 2,5-dimethyl-benzyl benzoate. FT-IR and Raman vibrational spectral analyses were performed, while a computational approach was used to elucidate the vibrational frequency couplings. The electronic properties were predicted using the Density Functional Theory, while the G3MP2 method was employed in the thermochemical calculation. A conformational analysis, frontier orbitals, partial atomic charge distribution and the molecular electrostatic potential were also estimated. Concerning to the dihedral angles in the ester group, a conformational analysis showed a barrier energy of 10 kcal mol-1, while other small barriers (below 0.6 kcal mol-1) were predicted within the potential surface energy investigation. Insights into the relative stability among the different positions of methyl groups in the phenyl ring demonstrated that the energy gaps were lower than 1 kcal mol-1 among the regioisomers. In addition, the Quantum Theory of Atoms in Molecules (QTAIM) was used to understand the intramolecular CH⋯O interaction in the title compound, while various methodologies were applied in the atomic charge distribution to evaluate the susceptibility to the population method.

  15. Low energy electron diffraction (LEED) and sum frequency generation (SFG) vibrational spectroscopy studies of solid-vacuum, solid-air and solid-liquid interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Hoffer, Saskia

    2002-08-19

    Electron based surface probing techniques can provide detailed information about surface structure or chemical composition in vacuum environments. The development of new surface techniques has made possible in situ molecular level studies of solid-gas interfaces and more recently, solid-liquid interfaces. The aim of this dissertation is two-fold. First, by using novel sample preparation, Low Energy Electron Diffraction (LEED) and other traditional ultra high vacuum (UHV) techniques are shown to provide new information on the insulator/vacuum interface. The surface structure of the classic insulator NaCl has been determined using these methods. Second, using sum frequency generation (SFG) surface specific vibrational spectroscopy studies were performed on both the biopolymer/air and electrode/electrolyte interfaces. The surface structure and composition of polyetherurethane-silicone copolymers were determined in air using SFG, atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). SFG studies of the electrode (platinum, gold and copper)/electrolyte interface were performed as a function of applied potential in an electrochemical cell.

  16. Phase transition behaviors of the supported DPPC bilayer investigated by sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM).

    Science.gov (United States)

    Wu, Heng-Liang; Tong, Yujin; Peng, Qiling; Li, Na; Ye, Shen

    2016-01-21

    The phase transition behaviors of a supported bilayer of dipalmitoylphosphatidyl-choline (DPPC) have been systematically evaluated by in situ sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM). By using an asymmetric bilayer composed of per-deuterated and per-protonated monolayers, i.e., DPPC-d75/DPPC and a symmetric bilayer of DPPC/DPPC, we were able to probe the molecular structural changes during the phase transition process of the lipid bilayer by SFG spectroscopy. It was found that the DPPC bilayer is sequentially melted from the top (adjacent to the solution) to bottom leaflet (adjacent to the substrate) over a wide temperature range. The conformational ordering of the supported bilayer does not decrease (even slightly increases) during the phase transition process. The conformational defects in the bilayer can be removed after the complete melting process. The phase transition enthalpy for the bottom leaflet was found to be approximately three times greater than that for the top leaflet, indicating a strong interaction of the lipids with the substrate. The present SFG and AFM observations revealed similar temperature dependent profiles. Based on these results, the temperature-induced structural changes in the supported lipid bilayer during its phase transition process are discussed in comparison with previous studies.

  17. Low energy electron diffraction (LEED) and sum frequency generation (SFG) vibrational spectroscopy studies of solid-vacuum, solid-air and solid-liquid interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Hoffer, Saskia [Univ. of California, Berkeley, CA (United States)

    2002-01-01

    Electron based surface probing techniques can provide detailed information about surface structure or chemical composition in vacuum environments. The development of new surface techniques has made possible in situ molecular level studies of solid-gas interfaces and more recently, solid-liquid interfaces. The aim of this dissertation is two-fold. First, by using novel sample preparation, Low Energy Electron Diffraction (LEED) and other traditional ultra high vacuum (UHV) techniques are shown to provide new information on the insulator/vacuum interface. The surface structure of the classic insulator NaCl has been determined using these methods. Second, using sum frequency generation (SFG) surface specific vibrational spectroscopy studies were performed on both the biopolymer/air and electrode/electrolyte interfaces. The surface structure and composition of polyetherurethane-silicone copolymers were determined in air using SFG, atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). SFG studies of the electrode (platinum, gold and copper)/electrolyte interface were performed as a function of applied potential in an electrochemical cell.

  18. Raman spectroscopic study of phase stability and anharmonicity in Bi{sub 12}TiO{sub 20}

    Energy Technology Data Exchange (ETDEWEB)

    Rao, Rekha, E-mail: rekhar@barc.gov.in [Solid State Physics Division, Bhabha Atomic Research Center, Mumbai 400 085 (India); Salke, Nilesh P. [Solid State Physics Division, Bhabha Atomic Research Center, Mumbai 400 085 (India); Garg, Alka B. [High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Mumbai 400 085 (India)

    2013-05-15

    Raman spectroscopic studies on lead-free piezo-electric compound Bi{sub 12}TiO{sub 20} is reported as a function of pressure upto 25 GPa at room temperature. Results indicate that the compound remains in stable crystalline phase upto 25 GPa. Temperature dependent Raman spectroscopic investigations on Bi{sub 12}TiO{sub 20} indicate that the compound is also stable at high temperatures upto 850 K. From measurements of temperature and pressure dependence of Raman mode frequencies, intrinsic anharmonic parameters are calculated for each of the Raman active modes which are useful in modeling of thermodynamic entities. The results are compared with that of analogous compound Bi{sub 12}SiO{sub 20}. Highlights: ► Raman spectroscopic study of Bi{sub 12}TiO{sub 20} is carried out at high pressure/temperature. ► This study indicates a good structural stability of Bi{sub 12}TiO{sub 20}. ► Bi{sub 12}TiO{sub 20} is an ideal system to evaluate the anharmonicity of vibrational modes.

  19. Airy function approach and Numerov method to study the anharmonic oscillator potentials V(x = Ax2α + Bx2

    Directory of Open Access Journals (Sweden)

    N. Al Sdran

    2016-06-01

    Full Text Available The numerical solutions of the time independent Schrödinger equation of different one-dimensional potentials forms are sometime achieved by the asymptotic iteration method. Its importance appears, for example, on its efficiency to describe vibrational system in quantum mechanics. In this paper, the Airy function approach and the Numerov method have been used and presented to study the oscillator anharmonic potential V(x = Ax2α + Bx2, (A>0, B<0, with (α = 2 for quadratic, (α =3 for sextic and (α =4 for octic anharmonic oscillators. The Airy function approach is based on the replacement of the real potential V(x by a piecewise-linear potential v(x, while, the Numerov method is based on the discretization of the wave function on the x-axis. The first energies levels have been calculated and the wave functions for the sextic system have been evaluated. These specific values are unlimited by the magnitude of A, B and α. It’s found that the obtained results are in good agreement with the previous results obtained by the asymptotic iteration method for α =3.

  20. Understanding Anharmonicity in fcc Materials: From its Origin to ab initio Strategies beyond the Quasiharmonic Approximation.

    Science.gov (United States)

    Glensk, A; Grabowski, B; Hickel, T; Neugebauer, J

    2015-05-15

    We derive the Gibbs energy including the anharmonic contribution due to phonon-phonon interactions for an extensive set of unary fcc metals (Al, Ag, Au, Cu, Ir, Ni, Pb, Pd, Pt, Rh) by combining density-functional-theory (DFT) calculations with efficient statistical sampling approaches. We show that the anharmonicity of the macroscopic system can be traced back to the anharmonicity in local pairwise interactions. Using this insight, we derive and benchmark a highly efficient approach which allows the computation of anharmonic contributions using a few T=0 K DFT calculations only.

  1. Vibrational spectroscopies: a natural ''mesoscope'' for the study of spontaneous ordering in alloys

    Energy Technology Data Exchange (ETDEWEB)

    Chafi, Allal; Souhabi, Jihane; Pages, Olivier; Postnikov, Andrei; Gleize, Jerome [LPMD, Universite Paul Verlaine - Metz, 1 Bd Arago, 57078 Metz (France); Sallet, V. [GEMAC-CNRS, 1 Pl. Briand, 92195 Meudon (France); Li, L.H.; Harmand, J.C. [LPN-CNRS, Route de Nozay, 91460 Marcoussis (France)

    2009-05-15

    The novel paradigm of a 1-bond{yields}2-mode percolation-type behavior for the lattice dynamics at the zone-centre of random semiconductor alloys, that mirrors a lattice relaxation of the similar 1-bond{yields}2-length type, opens an attractive area for a (re-)discussion of spontaneous long-range clustering/anticlustering in terms of purely intrinsic effects. As examples, we show in this work how such antagonist effects as CuPt type spontaneous ordering of InGaP{sub 2} and N-induced In-anticlustering far from N-impurities in (N,In)-dilute InGaAsN can be discussed/evidenced from the transverse optical vibration spectra. The whole discussion is supported by full contour modelling of the TO Raman lineshapes via our percolation model. (copyright 2009 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  2. Study of conformational stability, structural, electronic and charge transfer properties of cladrin using vibrational spectroscopy and DFT calculations.

    Science.gov (United States)

    Singh, Swapnil; Singh, Harshita; Srivastava, Anubha; Tandon, Poonam; Sinha, Kirti; Bharti, Purnima; Kumar, Sudhir; Kumar, Padam; Maurya, Rakesh

    2014-11-11

    In the present work, a detailed conformational study of cladrin (3-(3,4-dimethoxy phenyl)-7-hydroxychromen-4-one) has been done by using spectroscopic techniques (FT-IR/FT-Raman/UV-Vis/NMR) and quantum chemical calculations. The optimized geometry, wavenumber and intensity of the vibrational bands of the cladrin in ground state were calculated by density functional theory (DFT) employing 6-311++G(d,p) basis sets. The study has been focused on the two most stable conformers that are selected after the full geometry optimization of the molecule. A detailed assignment of the FT-IR and FT-Raman spectra has been done for both the conformers along with potential energy distribution for each vibrational mode. The observed and scaled wavenumber of most of the bands has been found to be in good agreement. The UV-Vis spectrum has been recorded and compared with calculated spectrum. In addition, 1H and 13C nuclear magnetic resonance spectra have been also recorded and compared with the calculated data that shows the inter or intramolecular hydrogen bonding. The electronic properties such as HOMO-LUMO energies were calculated by using time-dependent density functional theory. Molecular electrostatic potential has been plotted to elucidate the reactive part of the molecule. Natural bond orbital analysis was performed to investigate the molecular stability. Non linear optical property of the molecule have been studied by calculating the electric dipole moment (μ) and the first hyperpolarizability (β) that results in the nonlinearity of the molecule.

  3. Electronic and vibrational spectroscopy of the cytochrome c:cytochrome c oxidase complexes from bovine and Paracoccus denitrificans.

    OpenAIRE

    Lynch, S. R.; Copeland, R. A.

    1992-01-01

    The 1:1 complex between horse heart cytochrome c and bovine cytochrome c oxidase, and between yeast cytochrome c and Paracoccus denitrificans cytochrome c oxidase have been studied by a combination of second derivative absorption, circular dichroism (CD), and resonance Raman spectroscopy. The second derivative absorption and CD spectra reveal changes in the electronic transitions of cytochrome a upon complex formation. These results could reflect changes in ground state heme structure or chan...

  4. Combined electron microscopy and vibrational spectroscopy study of corroded Magnox sludge from a legacy spent nuclear fuel storage pond

    Science.gov (United States)

    Gregson, Colin R.; Goddard, David T.; Sarsfield, Mark J.; Taylor, Robin J.

    2011-05-01

    Samples of filtered particulates and sludges, formed from corroding magnesium alloy clad uranium metal ("Magnox") fuel elements, collected from one of the legacy nuclear fuel storage ponds located at Sellafield (UK) were investigated by Environmental Scanning Electron Microscopy with Energy Dispersive X-Ray analysis (ESEM/EDX), micro-Raman spectroscopy and Fourier transform infra-red spectroscopy (FT-IR). ESEM imaging confirmed the dominant morphology to be clusters of interlocking platelets typical of brucite (Mg(OH) 2). EDX analysis was suggestive of some conversion to the related phase, hydrotalcite (Mg 6Al 2(CO 3)(OH) 16·4H 2O), due to elevated levels of Al associated with Mg. Other apparent morphologies were less commonly observed including flaky sheets, consistent with earlier stages of Magnox alloy corrosion. In a few specific cases, rods were also observed suggestive of some conversion to Mg-hydroxycarbonate phases. Discrete phases rich in U were also identified. Fluorescence in the Raman spectroscopy also indicated surface coatings of organic macromolecules and iron sulphide on hematite containing particles, attributed to microbial activity within the open air pond. Some specific differences in the solid phases between pond areas with differing conditions were apparent.

  5. Surface-enhanced vibrational spectroscopy of B vitamins: what is the effect of SERS-active metals used?

    Science.gov (United States)

    Kokaislová, A; Matějka, P

    2012-05-01

    Surface-enhanced Raman scattering (SERS) spectroscopy and surface-enhanced infrared absorption (SEIRA) spectroscopy are analytical tools suitable for the detection of small amounts of various analytes adsorbed on metal surfaces. During recent years, these two spectroscopic methods have become increasingly important in the investigation of adsorption of biomolecules and pharmaceuticals on nanostructured metal surfaces. In this work, the adsorption of B-group vitamins pyridoxine, nicotinic acid, folic acid and riboflavin at electrochemically prepared gold and silver substrates was investigated using Fourier transform SERS spectroscopy at an excitation wavelength of 1,064 nm. Gold and silver substrates were prepared by cathodic reduction on massive platinum targets. In the case of gold substrates, oxidation-reduction cycles were applied to increase the enhancement factor of the gold surface. The SERS spectra of riboflavin, nicotinic acid, folic acid and pyridoxine adsorbed on silver substrates differ significantly from SERS spectra of these B-group vitamins adsorbed on gold substrates. The analysis of near-infrared-excited SERS spectra reveals that each of B-group vitamin investigated interacts with the gold surface via a different mechanism of adsorption to that with the silver surface. In the case of riboflavin adsorbed on silver substrate, the interpretation of surface-enhanced infrared absorption (SEIRA) spectra was also helpful in investigation of the adsorption mechanism.

  6. Vibrational state-selective autodetachment photoelectron spectroscopy from dipole-bound states of cold 2-hydroxyphenoxide: o − HO(C{sub 6}H{sub 4})O{sup −}

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Dao-Ling; Wang, Lai-Sheng, E-mail: Lai-Sheng-Wang@brown.edu [Department of Chemistry, Brown University, Providence, Rhode Island 02912 (United States); Liu, Hong-Tao [Department of Chemistry, Brown University, Providence, Rhode Island 02912 (United States); Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Ning, Chuan-Gang [Department of Physics, State Key Laboratory of Low-Dimensional Quantum Physics, Tsinghua University, Beijing 100084 (China)

    2015-03-28

    We report a photodetachment and high-resolution photoelectron imaging study of cold 2-hydroxyphenoxide anion, o − HO(C{sub 6}H{sub 4})O{sup −}, cooled in a cryogenic ion trap. Photodetachment spectroscopy revealed a dipole-bound state (DBS) of the anion, 25 ± 5 cm{sup −1}, below the detachment threshold of 18784 ± 5 cm{sup −1} (2.3289 ± 0.0006 eV ), i.e., the electron affinity of the 2-hydroxyphenoxy radical o − HO(C{sub 6}H{sub 4})O{sup ⋅}. Twenty-two vibrational levels of the DBS are observed as resonances in the photodetachment spectrum. By tuning the detachment laser to these DBS vibrational levels, we obtain 22 high-resolution resonant photoelectron spectra, which are highly non-Franck-Condon due to mode-selective autodetachment and the Δv = − 1 propensity rule. Numerous Franck-Condon inactive vibrational modes are observed in the resonant photoelectron spectra, significantly expanding the vibrational information that is available in traditional high-resolution photoelectron spectroscopy. A total of 15 fundamental vibrational frequencies are obtained for the o − HO(C{sub 6}H{sub 4})O{sup ⋅}  radical from both the photodetachment spectrum and the resonant photoelectron spectra, including six symmetry-forbidden out-of-plane modes as a result of resonant enhancement.

  7. Phonon anharmonicity, lifetimes, and thermal transport in CH3NH3PbI3 from many-body perturbation theory

    Science.gov (United States)

    Whalley, Lucy D.; Skelton, Jonathan M.; Frost, Jarvist M.; Walsh, Aron

    2016-12-01

    Lattice vibrations in CH3NH3PbI3 are strongly interacting, with double-well instabilities present at the Brillouin zone boundary. Analysis within a first-principles lattice-dynamics framework reveals anharmonic potentials with short phonon quasiparticle lifetimes and mean free paths. The phonon behavior is distinct from the inorganic semiconductors GaAs and CdTe where three-phonon interaction strengths are three orders of magnitude smaller. The implications for the applications of hybrid halide perovskites arising from thermal conductivity, band-gap deformation, and charge-carrier scattering through electron-phonon coupling, are presented.

  8. Vibrational spectroscopy of the electronically excited state. 4. Nanosecond and picosecond time-resolved resonance Raman spectroscopy of carotenoid excited states

    Energy Technology Data Exchange (ETDEWEB)

    Dallinger, R.F.; Farquharson, S.; Woodruff, W.H.; Rodgers, M.A.J.

    1981-12-16

    Resonance Raman and electronic absorption spectra are reported for the S/sub 0/ and T/sub 1/ states of the carotenoids ..beta..-carotene, zeaxanthin, echinenone, canthaxanthin, dihydroxylycopene, astaxanthin, decapreno(C/sub 50/)-..beta..-carotene, ..beta..-apo-8'-carotenal, and ethyl ..beta..-apo-8'-carotenoate. The results reveal qualitatively similar ground-state spectra and similar frequency shifts in all observed resonance Raman modes between S/sub 0/ and T/sub 1/, regardless of carotenoid structure. Examinations of the relationship of the putative C--C and C==C frequencies in S/sub 0/ and T/sub 1/ reveals anomalous shifts to lower frequency in the ''single-bond'' mode upon electronic excitation. These shifts may be due to molecular distortions in the excited state which force changes in molecular motions comprising the observed modes. However, another possibility requiring no distortion is that the interaction (off-diagonal) force constants connecting the C--C and C==C modes change sign upon electronic excitation. This latter phenomenon may provide a unitary explanation for the ''anomalous'' frequency shifts in the C--C and C==C modes, both in the T/sub 1/ states of carotenoids and in the S/sub 1/ states of simpler polyenes, without postulating large, unpredicted structural changes upon excitation or general errors in existing vibrational or theoretical analyses. Resonance Raman and absorbance studies with 35-ps time resolution suggest that S/sub 1/ lifetime (of the /sup 1/B/sub u/ and/or the /sup 1/A/sub g/* states) of ..beta..-carotene in benzene is less than 1 ps.

  9. Combined IR/NIR and density functional theory calculations analysis of the solvent effects on frequencies and intensities of the fundamental and overtones of the C ═ O stretching vibrations of acetone and 2-hexanone.

    Science.gov (United States)

    Chen, Yujing; Morisawa, Yusuke; Futami, Yoshisuke; Czarnecki, Mirosław A; Wang, Hai-Shui; Ozaki, Yukihiro

    2014-04-10

    Vibrational overtone studies primarily focus on X-H stretching overtone transitions, where X is an atom like C, O, N, or S. In contrast, the studies on the C ═ O stretching overtones are very scattered. To advance the research in this field, we measured the fundamental, first, and second overtones of the C ═ O stretching vibration of acetone and 2-hexanone in n-hexane, CCl4, and CHCl3, as well as in the vapor phase using FT-IR/FT-NIR spectroscopy. Density functional theory (DFT) calculations have also been performed to help the assignment of the C ═ O stretching bands and to guide interpretation of the experimental results. It was found that the wavenumbers, absorption intensities, and oscillator strengths of the C ═ O stretching bands show marked solvent dependence. In the fundamental and the first overtone regions, the intensities of the C ═ O stretching vibration were found to be pronouncedly more intense than those of the C-H stretching vibration. In the second overtone region, the intensities of the C-H stretching vibration are comparable to those of the C ═ O stretching vibration. The theoretical and observed decrease in integrated intensity upon going from the fundamental to the first overtone of the C ═ O stretching vibration is around 50, which is significantly larger than those of the O-H, C-H, and S-H stretching vibration. Both the calculated and experimental results suggest that excessive weakness in the C ═ O stretching overtone was shown to be a result of both a low anharmonicity and a substantial reduction in the oscillator strength. These results provide new insight into our understanding of the C ═ O stretching vibration.

  10. Airy function approach and Numerov method to study the anharmonic oscillator potentials V(x) = Ax2α + Bx2

    Science.gov (United States)

    Al Sdran, N.; Maiz, F.

    2016-06-01

    The numerical solutions of the time independent Schrödinger equation of different one-dimensional potentials forms are sometime achieved by the asymptotic iteration method. Its importance appears, for example, on its efficiency to describe vibrational system in quantum mechanics. In this paper, the Airy function approach and the Numerov method have been used and presented to study the oscillator anharmonic potential V(x) = Ax2α + Bx2, (A>0, Bdiscretization of the wave function on the x-axis. The first energies levels have been calculated and the wave functions for the sextic system have been evaluated. These specific values are unlimited by the magnitude of A, B and α. It's found that the obtained results are in good agreement with the previous results obtained by the asymptotic iteration method for α =3.

  11. Probing the structure and nano-scale mechanical properties of polymer surfaces with scanning force microscopy and sum frequency vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Gracias, David Hugo [Univ. of California, Berkeley, CA (United States)

    1999-05-01

    Scanning Force Microscopy (SFM) has been used to quantitatively measure the elastic modulus, friction and hardness of polymer surfaces with special emphasis on polyethylene and polypropylene. In the experiments, tips of different radii of curvature ranging from 20 nm to 1000 nm have been used and the high pressure applied by the SFM have been observed to affect the values obtained in the measurements. The contact of the SFM tip with the polymer surface is explained by fitting the experimental curves to theoretical predictions of contact mechanics. Sum Frequency Generation (SFG) Vibrational Spectroscopy has been used to measure vibrational spectra of polymer surfaces in the vibrational range of 2700 to 3100 cm-1. Strong correlations are established between surface chemistry and surface structure as probed by SFG and mechanical properties measured by SFM on the surfaces. In these studies segregation of low surface energy moieties, from the bulk of the polymer to the surface have been studied. It was found that surface segregation occurs in miscible polymer blends and a small concentration of surface active polymer can be used to totally modify the surface properties of the blend. A novel high vacuum SFM was built to do temperature dependent measurements of mechanical changes occurring at the surface of polypropylene during the glass transition of the polymer. Using this instrument the modulus and friction of polypropylene was measured in the range of room temperature to ˜-60°C. An increase in the ordering of the backbone of the polymer chains below the glass transition measured by SFG correlates well with the increase in modulus measured on the same surface with SFM. Friction measurements have been done on polyethylene with three different instruments by applying loads ranging from nN to sub newton i.e. over eight orders of magnitude. Pressure and contact area effects were observed to play a significant role in determining the frictional response of the polymer

  12. Vibrational spectroscopy characterization of low level laser therapy on mammary culture cells: a micro-FTIR study

    Science.gov (United States)

    Magrini, Taciana D.; Villa dos Santos, Nathalia; Pecora Milazzotto, Marcella; Cerchiaro, Giselle; da Silva Martinho, Herculano

    2011-03-01

    Low level laser therapy (LLLT) is an emerging therapeutic approach for several clinical conditions. The clinical effects induced by LLLT presumably go from the photobiostimulation/photobioinibition at cellular level to the molecular level. The detailed mechanism underlying this effect is still obscure. This work is dedicated to quantify some relevant aspects of LLLT related to molecular and cellular variations. This goal was attached by exposing malignant breast cells (MCF7) to spatially filtered light of a He-Ne laser (633 nm) with 28.8 mJ/cm2 of fluency. The cell viability was evaluated by microscopic observation using Trypan Blue viability test. The vibrational spectra of each experimental group (micro- FTIR technique) were used to identify the relevant biochemical alterations occurred due the process. The red light had influence over RNA, phosphate and serine/threonine/tyrosine bands. Light effects on cell number or viability were not detected. However, the irradiation had direct influence on metabolic activity of cells.

  13. Structural study of the zinc and cadmium complexes of a type 2 plant (Quercus suber) metallothionein: insights by vibrational spectroscopy.

    Science.gov (United States)

    Domènech, Jordi; Tinti, Anna; Capdevila, Mercè; Atrian, Silvia; Torreggiani, Armida

    2007-06-15

    Zn- and Cd-complexes of Quercus suber metallothionein (QsMT) were obtained by in vivo-synthesis, in order to obtain physiologically representative aggregates, and characterized by spectrometric and spectroscopic methods. The secondary structure elements and the coordination environments of the metal binding sites of the two aggregates were determined, as well as the main metal-containing species formed. The results obtained from the analysis of the Raman and IR spectra reveal that these metal-MT complexes predominantly contain beta-sheet elements (about 60%), whereas they lack alpha-helices. These structural features slightly depend on the divalent metal bound. In particular, Cd(II) binding to QsMT induces a slight increase of the beta-sheet percentage, as well as a decrease in beta-turn elements with respect to Zn(II) binding. Conversely, the in vivo capability of QsMT to inglobe metal and sulfide ions is metal-depending. Spectroscopic vibrational data also confirm the presence of sulfide ligands in the metal clusters of both Zn- and Cd-QsMT, while the participation of the spacer His residue in metal coordination was only found in Cd-QsMT, in agreement with the CD results. Overall data suggest different coordination environments for Zn(II) and Cd(II) ions in QsMT.

  14. Vibrational spectroscopy of aluminate spinels at 1 atm and of MgAl2O4 to over 200 kbar

    Science.gov (United States)

    Chopelas, A.; Hofmeister, A. M.

    1991-12-01

    Single-crystal Raman and infrared reflectivity data including high pressure results to over 200 kbar on a natural, probably fully ordered MgAl2O4 spinel reveal that many of the reported frequencies from spectra of synthetic spinels are affected by disorder at the cation sites. The spectra are interpreted in terms of factor group analysis and show that the high energy modes are due to the octahedral internal modes, in contrast to the behavior of silicate spinels, but in agreement with previous data based on isotopic and chemical cation substitutions and with new Raman data on gahnite (˜ ZnAl2O4) and new IR reflectivity data on both gahnite and hercynite (˜Fe0.58Mg0.42Al2O4). Therefore, aluminate spinels are inappropriate as elastic or thermodynamic analogs for silicate spinels. Fluorescence sideband spectra yield complementary information on the vibrational modes and provide valuable information on the acoustic modes at high pressure. The transverse acoustic modes are nearly pressure independent, which is similar to the behavior of the shear modes previously measured by ultrasonic techniques. The pressure derivative of all acoustic modes become negative above 110 kbar, indicating a lattice instability, in agreement with previous predictions. This lattice instability lies at approximately the same pressure as the disproportionation of spinel to MgO and Al2O3 reported in high temperature, high pressure work.

  15. Hydrogen local vibrational modes in semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    McCluskey, Matthew D. [Univ. of California, Berkeley, CA (United States). Dept. of Physics

    1997-06-01

    Following, a review of experimental techniques, theory, and previous work, the results of local vibrational mode (LVM) spectroscopy on hydrogen-related complexes in several different semiconductors are discussed. Hydrogen is introduced either by annealing in a hydrogen ambient. exposure to a hydrogen plasma, or during growth. The hydrogen passivates donors and acceptors in semiconductors, forming neutral complexes. When deuterium is substituted for hydrogen. the frequency of the LVM decreases by approximately the square root of two. By varying the temperature and pressure of the samples, the microscopic structures of hydrogen-related complexes are determined. For group II acceptor-hydrogen complexes in GaAs, InP, and GaP, hydrogen binds to the host anion in a bond-centered orientation, along the [111] direction, adjacent to the acceptor. The temperature dependent shift of the LVMs are proportional to the lattice thermal energy U(T), a consequence of anharmonic coupling between the LVM and acoustical phonons. In the wide band gap semiconductor ZnSe, epilayers grown by metalorganic chemical vapor phase epitaxy (MOCVD) and doped with As form As-H complexes. The hydrogen assumes a bond-centered orientation, adjacent to a host Zn. In AlSb, the DX centers Se and Te are passivated by hydrogen. The second, third, and fourth harmonics of the wag modes are observed. Although the Se-D complex has only one stretch mode, the Se-H stretch mode splits into three peaks. The anomalous splitting is explained by a new interaction between the stretch LVM and multi-phonon modes of the lattice. As the temperature or pressure is varied, and anti-crossing is observed between LVM and phonon modes.

  16. Interactions of nitrogen and hydrogen with various 1D and 3D carbon materials probed via in-situ vibrational spectroscopy

    Science.gov (United States)

    Ray, Paramita

    Nanostructured carbon materials are perhaps the most widely studied adsorbents, and cryogenic nitrogen adsorption is likely the most common method to assess textural properties of adsorbents. Yet, in-situ vibrational spectroscopic studies of nitrogen's interactions with three nanostructured carbon materials have provided new insight into carbon-nitrogen interactions. In this dissertation I present the work of 2 projects: (i) Study of the interaction of N2 with different carbon geometries at a molecular level and (ii) exploration of novel C-H interactions on carbon materials via mechano-chemistry. Both of these projects utilize in-situ Raman spectroscopy for exploring gas-surface interactions. Chapters 2 and 3 explore the interaction of molecular Nitrogen on carbon surfaces. With complementary theoretical studies and systematic experimental studies at various temperatures and pressures for different surfaces, I demonstrate how the spectroscopic peak features of N2 gives an indication of gas-surface binding energy, pore structure, and surface chemistry. Using 1D and 3D carbon architectures, spectroscopic perturbation of N2 is probed as a function of adsorption potential and pore dimension, and the spectroscopic response is mapped to the cryogenic volumetric adsorption isotherms. Whereas the latter required multiple days and ˜100 mg of sample, the spectroscopic technique provided similar structural information in the matter of a few hours for a few micrograms of the sample. It is anticipated that the development of the site-specific spectroscopic technique will advance the understanding of adsorbent geometry versus chemical functionality in a way not possible with deconstruction of bulk gas adsorption measurements of pore dimension, surface area, and diffusivity. The second project probed mechanochemical means to polymerize aromatics and hydro-aromatics in the presence of hydrogen in an attempt to form localized carbon cages that trap hydrogen. Interesting aspects of

  17. On the classical dynamics of strongly driven anharmonic oscillators

    Science.gov (United States)

    Breuer, H. P.; Dietz, K.; Holthaus, M.

    1990-12-01

    We investigate the dynamics of periodically driven anharmonic oscillators. In particular, we consider values of the coupling strength which are orders of magnitude higher than those required for the overlap of primary resonances. We observe a division of phase space into a regular and a stochastic region. Both regions are separated by a sharp chaos border which sets an upper limit to the stochastic heating of particles; its dependence on the coupling strength is studied. We construct perpetual adiabatic invariants governing regular motion. A bifurcation mechanism leading to the annihilation of resonances is explained.

  18. Origin of anomalous anharmonic lattice dynamics of lead telluride

    CERN Document Server

    Shiga, Takuma; Hori, Takuma; Delaire, Olivier; Shiomi, Junichiro

    2015-01-01

    The origin of the anomalous anharmonic lattice dynamics of lead telluride is investigated using molecular dynamics simulations with interatomic force constants (IFCs) up to quartic terms obtained from first principles. The calculations reproduce the peak asymmetry of the radial distribution functions and the double peaks of transverse optical phonon previously observed with neutron diffraction and scattering experiments. They are identified to be due to the extremely large nearest-neighbor cubic IFCs in the [100] direction. The outstanding strength of the nearest-neighbor cubic IFCs relative to the longer-range ones explains the reason why the distortion in the radial distribution function is local.

  19. Perfect Lattice Perturbation Theory A Study of the Anharmonic Oscillator

    CERN Document Server

    Bietenholz, W

    1999-01-01

    As an application of perfect lattice perturbation theory, we construct an O(\\lambda) perfect lattice action for the anharmonic oscillator analytically in momentum space. In coordinate space we obtain a set of 2-spin and 4-spin couplings \\propto \\lambda, which we evaluate for various masses. These couplings never involve variables separated by more than two lattice spacings. The O(\\lambda) perfect action is simulated and compared to the standard action. We discuss the improvement for the first two energy gaps \\Delta E_1, \\Delta E_2 and for the scaling quantity \\Delta E_2 / \\Delta E1 in different regimes of the interaction parameter, and of the correlation length.

  20. Fermi-Decay Law of Bose-Einstein Condensate Trapped in an Anharmonic Potential

    Institute of Scientific and Technical Information of China (English)

    LIU Yuan; JIA Ya-Fei; LI Wei-Dong

    2012-01-01

    The Fermi-decay law of Bose-Einstein condensate, which is trapped by a cigar-shaped anharmonic trap and subjected to a weak random perturbation, is investigated by numerically calculating quantum fidelity (Loschmidt echo), to reveal the coherence loss of the condensate. We find that there are three indispensable factors, anharmonic trap, weak random perturbation and nonlinear interaction, in charging of the Fermi-decay law. The anharmonic trap creates anharmonic oscillations, and the weak random perturbation causes coherence loss by disturbing their coherent oscillations, while the nonlinear interaction enhances the loss to the Fermi-decay law. Based on the Fermi-decay law, some suggestions are presented to prolong the coherent time during coherently manipulating condensates.%The Fermi-decay law of Bose Einstein condensate,which is trapped by a cigar-shaped anharmonic trap and subjected to a weak random perturbation,is investigated by numerically calculating quantum fidelity (Loschmidt echo),to reveal the coherence loss of the condensate.We find that there are three indispensable factors,anharmonic trap,weak random perturbation and nonlinear interaction,in charging of the Fermi-decay law.The anharmonic trap creates anharmonic oscillations,and the weak random perturbation causes coherence loss by disturbing their coherent oscillations,while the nonlinear interaction enhances the loss to the Fermi-decay law.Based on the Fermi-decay law,some suggestions are presented to prolong the coherent time during coherently manipulating condensates.

  1. Vibrational spectroscopy and electrophoresis as a "golden means" in monitoring of polysaccharides in medical plant and gels

    Science.gov (United States)

    Pielesz, A.

    In recent years, some bioactive polysaccharides isolated from natural sources have attracted much attention in the field of biochemistry and pharmacology. Of them, polysaccharides or their glycoconjugates were shown to exhibit multiple biological activities including anticarcinogenic, anticoagulant, immunostimulating, antioxidant, etc. Pharmacotherapy using plant-derived substances can be currently regarded as a very promising future alternative to conventional therapy. The advanced biotechnologies available today enable chemical investigation of well-defined bioactive plant components as sources of novel drugs. The need for safer drugs without side effects has led to the use of natural ingredients with proven safety. Special interest is focused on plant polysaccharides. This article attempts to review the current structural and conformational characterization of some importantly bioactive monosaccharides isolated from following plant cell-wall: Symphytum officinale (comfrey), Thymus pulegioides (thyme), Trigonella foenum-graecum L. (fenugreek), Tussilago farfara L. (coltsfoot), Hyssopus officinalis (hyssop), Althaea officinalis L. (marshmallow) and Equisetum arvense L. (horsetail). The chemical structures of monosaccharides were analysed using FTIR and Raman spectroscopies as well as cellulose acetate membrane electrophoresis (CAE). The dried plant samples were gently hydrolysed with sulphuric acid. The presence of glucuronic acid, galacturonic acid, alginic acid, glucose, mannose and xylose in the hydrolysates of reference substances and non-defatted plant films was proved. The possibility of a taxonomic classification of plant cell walls based on infrared and Raman spectroscopies and the use of spectral fingerprinting for authentication and detection of adulteration of products rich in cell-wall materials are discussed. Individual bands were selected to monitor the sugar content in medical plant cell walls and to confirm the identity of the analysed plants.

  2. Liquid/liquid interface layering of 1-butanol and [bmim]PF6 ionic liquid: a nonlinear vibrational spectroscopy and molecular dynamics simulation study.

    Science.gov (United States)

    Iwahashi, Takashi; Ishiyama, Tatsuya; Sakai, Yasunari; Morita, Akihiro; Kim, Doseok; Ouchi, Yukio

    2015-10-14

    IR-visible sum-frequency generation (IV-SFG) vibrational spectroscopy and a molecular dynamics (MD) simulation were used to study the local layering order at the interface of 1-butanol-d9 and 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim]PF6), a room-temperature ionic liquid (RTIL). The presence of a local non-polar layer at the interface of the two polar liquids was successfully demonstrated. In the SFG spectra of 1-butanol-d9, we observed significant reduction and enhancement in the strength of the CD3 symmetric stretching (r(+)) mode and the antisymmetric stretching (r(-)) mode peaks, respectively. The results can be well explained by the presence of an oppositely oriented quasi-bilayer structure of butanol molecules, where the bottom layer is strongly bound by hydrogen-bonding with the PF6(-) anion. MD simulations reveal that the hydrogen-bonding of butanol with the PF6(-) anion causes the preferential orientation of the butanols; the restriction on the rotational distribution of the terminal methyl group along their C3 axis enhances the r(-) mode. As for the [bmim](+) cations, the SFG spectra taken within the CH stretch region indicate that the butyl chain of [bmim](+) points away from the bulk RTIL phase to the butanol phase at the interface. Combining the SFG spectroscopy and MD simulation results, we propose an interfacial model structure of layering, in which the butyl chains of the butanol molecules form a non-polar interfacial layer with the butyl chains of the [bmim](+) cations at the interface.

  3. A combined Raman spectroscopic and theoretical investigation of fundamental vibrational bands of furfuryl alcohol (2-furanmethanol)

    DEFF Research Database (Denmark)

    Barsberg, S.; Berg, Rolf W.

    2006-01-01

    . study of FA in weakly interacting environments. It is the first study of FA vibrational properties based on d. functional theory (DFT/B3LYP), and a recently proposed hybrid approach to the calcn. of fundamental frequencies, which also includes an anharmonic contribution. FA occupies five different...

  4. Anharmonicity in Light Scattering by Optical Phonons in GaAs1-xBix

    Energy Technology Data Exchange (ETDEWEB)

    Joshya, R. S.; Rajaji, V.; Narayana, Chandrabhas; Mascarenhas, Angelo; Kini, R. N.

    2016-05-28

    We present a Raman spectroscopic study of GaAs 1-xBix epilayers grown by molecular beam epitaxy. We have investigated the anharmonic effect on the GaAs-like longitudinal optical phonon mode (LO'GaAs) of GaAs 1-xBix for different Bi concentrations at various temperatures. The results are analyzed in terms of the anharmonic damping effect induced by thermal and compositional disorder. We have observed that the anharmonicity increases with Bi concentration in GaAs 1-xBix as evident from the increase in the anharmonicity constants. In addition, the anharmonic lifetime of the optical phonon decreases with increasing Bi concentration in GaAs 1-xBix.

  5. The theoretical-cum-statistical approach for the investigation of reaction NO2 + O(3P) → NO + O2 using SCTST and a full anharmonic VPT2 model

    Science.gov (United States)

    Shiekh, Bilal Ahmad; Kaur, Damanjit; Seth, Bharti; Mahajan, Shalagha

    2016-10-01

    The study of the titled reaction has been carried out using high-level quantum mechanics in conjugation with SCTST and VPT2 model. The many quantum mechanical methods have been employed in combinatory approach to find out the various properties such as energy, anharmonic vibrational coefficients and ro-vibrational parameters for the stationary points including the transition state of the reaction. Then the thermal rate coefficients were computed over a temperature regime of 150-1500 K and the corresponding results were compared with the available literature. In this temperature regime, our computed results are in excellent contrast with the experiment.

  6. Stochastic Simulation of Chemical Exchange in Two Dimensional Infrared Spectroscopy

    CERN Document Server

    Sanda, F; Sanda, Frantisek; Mukamel, Shaul

    2006-01-01

    The stochastic Liouville equations are employed to investigate the combined signatures of chemical exchange (two-state-jump) and spectral diffusion (coupling to an overdamped Brownian oscillator) in the coherent response of an anharmonic vibration to three femtosecond infrared pulses. Simulations reproduce the main features recently observed in the OD stretch of phenol in benzene.

  7. Exploring the relationship between vibrational mode locality and coupling using constrained optimization

    Science.gov (United States)

    Molina, Andrew; Smereka, Peter; Zimmerman, Paul M.

    2016-03-01

    The use of alternate coordinate systems as a means to improve the efficiency and accuracy of anharmonic vibrational structure analysis has seen renewed interest in recent years. While normal modes (which diagonalize the mass-weighted Hessian matrix) are a typical choice, the delocalized nature of this basis makes it less optimal when anharmonicity is in play. When a set of modes is not designed to treat anharmonicity, anharmonic effects will contribute to inter-mode coupling in an uncontrolled fashion. These effects can be mitigated by introducing locality, but this comes at its own cost of potentially large second-order coupling terms. Herein, a method is described which partially localizes vibrations to connect the fully delocalized and fully localized limits. This allows a balance between the treatment of harmonic and anharmonic coupling, which minimizes the error that arises from neglected coupling terms. Partially localized modes are investigated for a range of model systems including a tetramer of hydrogen fluoride, water dimer, ethene, diphenylethane, and stilbene. Generally, partial localization reaches ˜75% of maximal locality while introducing less than ˜30% of the harmonic coupling of the fully localized system. Furthermore, partial localization produces mode pairs that are spatially separated and thus weakly coupled to one another. It is likely that this property can be exploited in the creation of model Hamiltonians that omit the coupling parameters of the distant (and therefore uncoupled) pairs.

  8. Anharmonic phonons and the isotope effect in superconductivity

    Energy Technology Data Exchange (ETDEWEB)

    Crespi, V.H.; Cohen, M.L. (Department of Physics, University of California at Berkeley, Berkeley, CA (USA) Materials Sciences Division, Lawrence Berkeley Laboratory, Berkeley, CA (USA)); Penn, D.R. (National Institute of Standards and Technology, Gaithersburg, MD (USA))

    1991-06-01

    Anharmonic interionic potentials are examined in an Einstein model to study the unusual isotope-effect exponents for the high-{ital T}{sub {ital c}} oxides. The mass dependences of the electron-phonon coupling constant {lambda} and the average phonon frequency {radical}{l angle}{omega}{sup 2}{r angle} are computed from weighted sums over the oscillator levels. The isotope-effect exponent is depressed below 1/2 by either a double-well potential or a potential with positive quadratic and quartic parts. Numerical solutions of Schroedinger's equation for double-well potentials produce {lambda}'s in the range 1.5--4 for a material with a vanishing isotope-effect parameter {alpha}. However, low phonon frequencies limit {ital T}{sub {ital c}} to roughly 15 K. A negative quartic perturbation to a harmonic well can increase {alpha} above 1/2. In the extreme-strong-coupling limit, {alpha} is 1/2, regardless of anharmonicity.

  9. Vibrational sum-frequency generation spectroscopy of ionic liquid 1-butyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate at the air-water interface

    Science.gov (United States)

    Saha, Ankur; SenGupta, Sumana; Kumar, Awadhesh; Choudhury, Sipra; Naik, Prakash D.

    2016-08-01

    The structure and orientation of room temperature ionic liquid (RTIL) 1-butyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate [PF3(C2F5)3], commonly known as [bmim][fap], have been investigated at the air-[bmim][fap] and air-water interfaces, employing vibrational sum-frequency generation (VSFG) spectroscopy. The VSFG spectra in the CH stretch region suggest presence of the [bmim] cation at the interfaces. Studies reveal that the butyl chain protrudes out into air, and the imidazolium ring lies almost planar to the interface. The CH stretch intensities get enhanced at the air-water interface, mainly because of polar orientation of imidazolium cation induced by interfacial water molecules. The OH stretch intensities are also enhanced at the air-water interface due to polar orientation of interfacial water molecules induced by [bmim][fap]. The Brewster angle microscopy suggests self aggregation of [bmim][fap] in the presence of water, and the aggregation becomes extensive showing dense surface domains with time. However, the surface pressure is almost unaffected due to aggregation.

  10. IR and SFG vibrational spectroscopy of the water bend in the bulk liquid and at the liquid-vapor interface, respectively

    Energy Technology Data Exchange (ETDEWEB)

    Ni, Yicun; Skinner, J. L. [Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706 (United States)

    2015-07-07

    Vibrational spectroscopy of the water bending mode has been investigated experimentally to study the structure of water in condensed phases. In the present work, we calculate the theoretical infrared (IR) and sum-frequency generation (SFG) spectra of the HOH bend in liquid water and at the water liquid/vapor interface using a mixed quantum/classical approach. Classical molecular dynamics simulation is performed by using a recently developed water model that explicitly includes three-body interactions and yields a better description of the water surface. Ab-initio-based transition frequency, dipole, polarizability, and intermolecular coupling maps are developed for the spectral calculations. The calculated IR and SFG spectra show good agreement with the experimental measurements. In the theoretical imaginary part of the SFG susceptibility for the water liquid/vapor interface, we find two features: a negative band centered at 1615 cm{sup −1} and a positive band centered at 1670 cm{sup −1}. We analyze this spectrum in terms of the contributions from molecules in different hydrogen-bond classes to the SFG spectral density and also compare to SFG results for the OH stretch. SFG of the water bending mode provides a complementary picture of the heterogeneous hydrogen-bond configurations at the water surface.

  11. Chemical synthesis, crystal structure, vibrational spectroscopy, non-linear optical properties and DFT calculation of bis (2,6-diaminopyridinium) sulfate monohydrate

    Science.gov (United States)

    Ben Hassen, Chaouki; Dammak, Thameur; Chniba-Boudjada, Nassira; Mhiri, Tahar; Boujelbene, Mohamed

    2017-01-01

    Single crystals of a new organic inorganic hybrid compound "bis (2,6-diaminopyridinium) sulfate monohydrate [C5H8N3]2SO4·H2O ([2,6-HDAP]2SO4·H2O)" was synthesized by slow evaporation method at room temperature and characterized by X-ray single crystal diffraction, infrared spectroscopy and DFT calculation. The new hybrid compound crystallizes in the orthorhombic system with the non-centro symmetric space group Pna21 and the following parameters a = 14.759(2) Å, b = 7.076 (2) Å and c = 28.159 (2) Å. The atomic arrangement can be described as inorganic chains following the b axis connected with the organic groups by means of Nsbnd H⋯O hydrogen bonds to form 3D network. Antiparallelly π-π stacked 2,6-HDAP cations form molecular columns in the spaces between the chains. The optimized molecular structure, vibrational spectra and the optical properties were calculated by the density functional theory (DFT) method using the B3LYP function with the LanL2DV basis set. The wavenumber calculated are in good agreement with the observed frequency values. The calculated hyperpolarizability βtot is about 4.5 times more than that of the reference crystal KDP. Hence, the large β value shows that the title compound is an attractive object for future studies of nonlinear optical properties.

  12. Further understanding of the adsorption mechanism of N719 sensitizer on anatase TiO2 films for DSSC applications using vibrational spectroscopy and confocal Raman imaging.

    Science.gov (United States)

    Lee, Kee Eun; Gomez, Mario A; Elouatik, Samir; Demopoulos, George P

    2010-06-15

    Vibrational spectroscopic studies of N719 dye-adsorbed TiO(2) films have been carried out by using SERRS, ATR-FTIR, and confocal Raman imaging. The high wavenumber region (3000-4000 cm(-1)) of dye adsorbed TiO(2) is analyzed via Raman and IR spectroscopy to investigate the role of surface hydroxyl groups in the anchoring mode. As a complementary technique, confocal Raman imaging is employed to study the distribution features of key dye groups (COO-, bipyridine, and C=O) on the anatase surface. Sensitized TiO(2) films made from two different nanocrystalline anatase powders are investigated: a commercial one (Dyesol) and our synthetic variety produced through aqueous synthesis. It is proposed the binding of the N719 dye to TiO(2) to occur through two neighboring carboxylic acid/carboxylate groups via a combination of bidentate-bridging and H-bonding involving a donating group from the N719 (and/or Ti-OH) units and acceptor from the Ti-OH (and/or N719) groups. The Raman imaging distribution of COO(-)(sym) on TiO(2) was used to show the covalent bonding, while the distribution of C=O mode was applied to observe the electrostatically bonded groups.

  13. Hydrogenation of the alpha,beta-Unsaturated Aldehydes Acrolein, Crotonaldehyde, and Prenal over Pt Single Crystals: A Kinetic and Sum-Frequency Generation Vibrational Spectroscopy Study

    Energy Technology Data Exchange (ETDEWEB)

    Kliewer, C.J.; Somorjai, G.A.

    2008-11-26

    Sum-frequency generation vibrational spectroscopy (SFG-VS) and kinetic measurements using gas chromatography have been used to study the surface reaction intermediates during the hydrogenation of three {alpha},{beta}-unsaturated aldehydes, acrolein, crotonaldehyde, and prenal, over Pt(111) at Torr pressures (1 Torr aldehyde, 100 Torr hydrogen) in the temperature range of 295K to 415K. SFG-VS data showed that acrolein has mixed adsorption species of {eta}{sub 2}-di-{sigma}(CC)-trans, {eta}{sub 2}-di-{sigma}(CC)-cis as well as highly coordinated {eta}{sub 3} or {eta}{sub 4} species. Crotonaldehyde adsorbed to Pt(111) as {eta}{sub 2} surface intermediates. SFG-VS during prenal hydrogenation also suggested the presence of the {eta}{sub 2} adsorption species, and became more highly coordinated as the temperature was raised to 415K, in agreement with its enhanced C=O hydrogenation. The effect of catalyst surface structure was clarified by carrying out the hydrogenation of crotonaldehyde over both Pt(111) and Pt(100) single crystals while acquiring the SFG-VS spectra in situ. Both the kinetics and SFG-VS showed little structure sensitivity. Pt(100) generated more decarbonylation 'cracking' product while Pt(111) had a higher selectivity for the formation of the desired unsaturated alcohol, crotylalcohol.

  14. IR and SFG vibrational spectroscopy of the water bend in the bulk liquid and at the liquid-vapor interface, respectively.

    Science.gov (United States)

    Ni, Yicun; Skinner, J L

    2015-07-07

    Vibrational spectroscopy of the water bending mode has been investigated experimentally to study the structure of water in condensed phases. In the present work, we calculate the theoretical infrared (IR) and sum-frequency generation (SFG) spectra of the HOH bend in liquid water and at the water liquid/vapor interface using a mixed quantum/classical approach. Classical molecular dynamics simulation is performed by using a recently developed water model that explicitly includes three-body interactions and yields a better description of the water surface. Ab-initio-based transition frequency, dipole, polarizability, and intermolecular coupling maps are developed for the spectral calculations. The calculated IR and SFG spectra show good agreement with the experimental measurements. In the theoretical imaginary part of the SFG susceptibility for the water liquid/vapor interface, we find two features: a negative band centered at 1615 cm(-1) and a positive band centered at 1670 cm(-1). We analyze this spectrum in terms of the contributions from molecules in different hydrogen-bond classes to the SFG spectral density and also compare to SFG results for the OH stretch. SFG of the water bending mode provides a complementary picture of the heterogeneous hydrogen-bond configurations at the water surface.

  15. Structure of butanol and hexanol at aqueous, ammonium bisulfate, and sulfuric acid solution surfaces investigated by vibrational sum frequency generation spectroscopy.

    Science.gov (United States)

    Van Loon, Lisa L; Minor, Rena N; Allen, Heather C

    2007-08-09

    The organization of 1-butanol and 1-hexanol at the air-liquid interface of aqueous, aqueous ammonium bisulfate, and sulfuric acid solutions was investigated using vibrational broad bandwidth sum frequency generation spectroscopy. There is spectroscopic evidence supporting the formation of centrosymmetric structures at the surface of pure butanol and pure hexanol. At aqueous, ammonium bisulfate, and at most sulfuric acid solution surfaces, butanol molecules organize in all-trans conformations. This suggests that butanol self-aggregates. The spectrum for the 0.052 M butanol in 59.5 wt % sulfuric acid solution is different from the other butanol solution spectra, that is, the surface butanol molecules are observed to possess a significant number of gauche defects. Relative to surface butanol, surface hexanol chains are more disordered at the surface of their respective solutions. Statistically, an increase in the number of gauche defects is expected for hexanol relative to butanol, a six carbon chain vs a four carbon chain. Yet, self-aggregation of hexanol at its aqueous solution surfaces is not ruled out because the methylene spectral contribution is relatively small. The surface spectra for butanol and hexanol also show evidence for salting out from the ammonium bisulfate solutions.

  16. AKARI near-infrared spectroscopy of the extended green object G318.05+0.09: Detection of CO fundamental ro-vibrational emission

    CERN Document Server

    Onaka, Takashi; Sakon, Itsuki; Ardaseva, Aleksandra

    2016-01-01

    We present the results of near-infrared (2.5--5.4um) long-slit spectroscopy of the extended green object (EGO) G318.05+0.09 with AKARI. Two distinct sources are found in the slit. The brighter source has strong red continuum emission with H2O ice, CO2 ice, and CO gas and ice absorption features at 3.0, 4.25um, 4.67um, respectively, while the other greenish object shows peculiar emission that has double peaks at around 4.5 and 4.7um. The former source is located close to the ultra compact HII region IRAS 14498-5856 and is identified as an embedded massive young stellar object. The spectrum of the latter source can be interpreted by blue-shifted (-3000 ~ -6000km/s) optically-thin emission of the fundamental ro-vibrational transitions (v=1-0) of CO molecules with temperatures of 12000--3700K without noticeable H2 and HI emission. We discuss the nature of this source in terms of outflow associated with the young stellar object and supernova ejecta associated with a supernova remnant.

  17. Synthesis, crystal structure, vibrational and 31P-NMR spectroscopy of the thiophosphate NaMg[PO3S]·9H2O

    Science.gov (United States)

    Höppe, Henning A.; Scharinger, Stefan W.; Heck, Joachim G.; Gross, Peter; Netzsch, Philip; Kazmierczak, Karolina

    2016-12-01

    NaMg[PO3S]·9H2O was obtained as single-phase crystalline powder starting from NaOH, PSCl3 and MgCl2·6H2O. At room temperature NaMg[PO3S]·9H2O crystallises in space group Cmc21 (no. 36) (a=638.58(4) pm, b=1632.31(10) pm, c=1217.16(7) pm, Z = 4; Rint = 0.032, Rσ = 0.034, R1 = 0.036, wR2 = 0.071). The data collection at 100 K reveals an ordering of the PO3S tetrahedra by undergoing a symmetry reduction to P21 (no. 4) and an according formation of twins (C1121, unconv. setting of P21, a=631.41(3) pm, b=1630.00(7) pm, c=1219.24(5) pm, γ=90.00(2)°, Z = 4; Rint = 0.115, Rσ = 0.064, R1 = 0.045, wR2 = 0.070). NaMg[PO3S]·9H2O comprises isolated PO3S tetrahedra, distorted MgO6 octahedra and trigonal NaO6 prisms. 31P NMR spectroscopy showed a chemical shift of 33.7 ppm. The vibrational spectra of NaMg[PO3S]·9H2O were recorded and the relevant bands were assigned.

  18. Hydrogenation of the alpha,beta-unsaturated aldehydes acrolein, crotonaldehyde, and prenal over Pt single crystals: a kinetic and sum-frequency generation vibrational spectroscopy study.

    Science.gov (United States)

    Kliewer, Christopher J; Bieri, Marco; Somorjai, Gabor A

    2009-07-29

    Sum-frequency generation vibrational spectroscopy (SFG-VS) and kinetic measurements using gas chromatography have been used to study the surface reaction intermediates during the hydrogenation of three alpha,beta-unsaturated aldehydes, acrolein, crotonaldehyde, and prenal, over Pt(111) at Torr pressures (1 Torr of aldehyde, 100 Torr of hydrogen) in the temperature range of 295-415 K. SFG-VS data showed that acrolein has mixed adsorption species of eta(2)-di-sigma(CC)-trans, eta(2)-di-sigma(CC)-cis as well as highly coordinated eta(3) or eta(4) species. Crotonaldehyde adsorbed to Pt(111) as eta(2) surface intermediates. SFG-VS during prenal hydrogenation also suggested the presence of the eta(2) adsorption species and became more highly coordinated as the temperature was raised to 415 K, in agreement with its enhanced C=O hydrogenation. The effect of catalyst surface structure was clarified by carrying out the hydrogenation of crotonaldehyde over both Pt(111) and Pt(100) single crystals while acquiring the SFG-VS spectra in situ. Both the kinetics and SFG-VS showed little structure sensitivity. Pt(100) generated more decarbonylation "cracking" product while Pt(111) had a higher selectivity for the formation of the desired unsaturated alcohol, crotyl alcohol.

  19. Aqueous Cu(II)-organic complexation studied in situ using soft X-ray and vibrational spectroscopies.

    Science.gov (United States)

    Phillips, Courtney L; Regier, Tom Z; Peak, Derek

    2013-12-17

    In situ aqueous solutions containing copper-ligand mixtures were measured at the Cu L-edge using X-ray absorption near edge structure (XANES) and with attenuated total reflectance infrared (ATR-FTIR) spectroscopies. Copper complexation with environmentally relevant ligands such as EDTA, citrate, and malate provided a bridge between spectroscopic studies and general environmental behavior and will allow for future study of complex environmental samples. XANES results show that the lowest unoccupied molecular orbital (LUMO) energy is governed by the ligand field strength and is related to Lewis acid/base properties of the ligand functional groups. Complementary ATR-FTIR studies confirmed the importance of water molecules in the structure of these Cu-ligand complexes and provided in-depth structural analysis to support the XANES data. Copper-malate is shown to have a 5/6-O-ring structure, and Cu-ethylenediaminetetraacetate has pentadentate coordination. Cu L-edge XANES also revealed direct Cu-N coordination in these aqueous solutions with amide functional groups.

  20. Characterization of extracellular vesicles by IR spectroscopy: Fast and simple classification based on amide and CH stretching vibrations.

    Science.gov (United States)

    Mihály, Judith; Deák, Róbert; Szigyártó, Imola Csilla; Bóta, Attila; Beke-Somfai, Tamás; Varga, Zoltán

    2017-03-01

    Extracellular vesicles isolated by differential centrifugation from Jurkat T-cell line were investigated by attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR). Amide and CH stretching band intensity ratios calculated from IR bands, characteristic of protein and lipid components, proved to be distinctive for the different extracellular vesicle subpopulations. This proposed 'spectroscopic protein-to-lipid ratio', combined with the outlined spectrum-analysis protocol is valid also for low sample concentrations (0.15-0.05mg/ml total protein content) and can carry information about the presence of other non-vesicular formations such as aggregated proteins, lipoproteins and immune complexes. Detailed analysis of IR data reveals compositional changes of extracellular vesicles subpopulations: second derivative spectra suggest changes in protein composition from parent cell towards exosomes favoring proteins with β-turns and unordered motifs at the expense of intermolecular β-sheet structures. The IR-based protein-to-lipid assessment protocol was tested also for red blood cell derived microvesicles for which similar values were obtained. The potential applicability of this technique for fast and efficient characterization of vesicular components is high as the investigated samples require no further preparations and all the different molecular species can be determined in the same sample. The results indicate that ATR-FTIR measurements provide a simple and reproducible method for the screening of extracellular vesicle preparations. It is hoped that this sophisticated technique will have further impact in extracellular vesicle research.

  1. Vibrational spectroscopy and analytical electron microscopy studies of Fe-V-O and In-V-O thin films

    CERN Document Server

    Vuk, A S; Drazic, G; Colomban, P

    2002-01-01

    Orthovanadate (M sup 3 sup + VO sub 4; M= Fe, In) and vanadate (Fe sub 2 V sub 4 O sub 1 sub 3) thin films were prepared using sol-gel synthesis and dip coating deposition. Using analytical electron microscopy (AEM), the chemical composition and the degree of crystallization of the phases present in the thin Fe-V-O films were investigated. TEM samples were prepared in both orientations: parallel (plan view) and perpendicular (cross section) to the substrate. In the first stages of crystallization, when the particle sizes were in the nanometer range, the classical identification of phases using electron diffraction was not possible. Instead of measuring d values, experimentally selected area electron diffraction (SAED) patterns were compared to calculated (simulated) patterns in order to determine the phase composition. The problems of evaluating the ratio of amorphous and crystalline phases in thin films are reported. Results of TEM and XRD as well as IR and Raman spectroscopy showed that the films made at lo...

  2. 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.

  3. Femtosecond nonlinear spectroscopy at surfaces: Second-harmonic probing of hole burning at the Si(111)7x7 surface and fourier-transform sum-frequency vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    McGuire, John Andrew [Univ. of California, Berkeley, CA (United States)

    2004-11-24

    The high temporal resolution and broad bandwidth of a femtosecond laser system are exploited in a pair of nonlinear optical studies of surfaces. The dephasing dynamics of resonances associated with the adatom dangling bonds of the Si(111)7 x 7 surface are explored by transient second-harmonic hole burning, a process that can be described as a fourth-order nonlinear optical process. Spectral holes produced by a 100 fs pump pulse at about 800 nm are probed by the second harmonic signal of a 100 fs pulse tunable around 800 nm. The measured spectral holes yield homogeneous dephasing times of a few tens of femtoseconds. Fits with a Lorentzian spectral hole centered at zero probe detuning show a linear dependence of the hole width on pump fluence, which suggests that charge carrier-carrier scattering dominates the dephasing dynamics at the measured excitation densities. Extrapolation of the deduced homogeneous dephasing times to zero excitation density yields an intrinsic dephasing time of {approx} 70 fs. The presence of a secondary spectral hole indicates that scattering of the surface electrons with surface optical phonons at 570 cm-1 occurs within the first 200 fs after excitation. The broad bandwidth of femtosecond IR pulses is used to perform IR-visible sum frequency vibrational spectroscopy. By implementing a Fourier-transform technique, we demonstrate the ability to obtain sub-laser-bandwidth spectral resolution. FT-SFG yields a greater signal when implemented with a stretched visible pulse than with a femtosecond visible pulse. However, when compared with multichannel spectroscopy using a femtosecond IR pulse but a narrowband visible pulse, Fourier-transform SFG is found to have an inferior signal-to-noise ratio. A mathematical analysis of the signal-to-noise ratio illustrates the constraints on the Fourier-transform approach.

  4. Hybrid Optimized and Localized Vibrational Coordinates.

    Science.gov (United States)

    Klinting, Emil Lund; König, Carolin; Christiansen, Ove

    2015-11-01

    We present a new type of vibrational coordinates denoted hybrid optimized and localized coordinates (HOLCs) aiming at a good set of rectilinear vibrational coordinates supporting fast convergence in vibrational stucture calculations. The HOLCs are obtained as a compromise between the recently promoted optimized coordinates (OCs) and localized coordinates (LCs). The three sets of coordinates are generally different from each other and differ from standard normal coordinates (NCs) as well. In determining the HOLCs, we optimize the vibrational self-consistent field (VSCF) energy with respect to orthogonal transformation of the coordinates, which is similar to determining OCs but for HOLCs we additionally introduce a penalty for delocalization, by using a measure of localization similar to that employed in determining LCs. The same theory and implementation covers OCs, LCs, and HOLCs. It is shown that varying one penalty parameter allows for connecting OCs and LCs. The HOLCs are compared to NCs, OCs, and LCs in their nature and performance as basis for vibrational coupled cluster (VCC) response calculations of vibrational anharmonic energies for a small set of simple systems comprising water, formaldehyde, and ethylene. It is found that surprisingly good results can be obtained with HOLCs by using potential energy surfaces as simple as quadratic Taylor expansions. Quite similar coordinates are found for the already established OCs but obtaining these OCs requires much more elaborate and expensive potential energy surfaces and localization is generally not guaranteed. The ability to compute HOLCs for somewhat larger systems is demonstrated for coumarin and the alanine quadramer. The good agreement between HOLCs and OCs, together with the much easier applicability of HOLCs for larger systems, suggests that HOLCs may be a pragmatically very interesting option for anharmonic calculations on medium to large molecular systems.

  5. A quantum anharmonic oscillator model for the stock market

    Science.gov (United States)

    Gao, Tingting; Chen, Yu

    2017-02-01

    A financially interpretable quantum model is proposed to study the probability distributions of the stock price return. The dynamics of a quantum particle is considered an analog of the motion of stock price. Then the probability distributions of price return can be computed from the wave functions that evolve according to Schrodinger equation. Instead of a harmonic oscillator in previous studies, a quantum anharmonic oscillator is applied to the stock in liquid market. The leptokurtic distributions of price return can be reproduced by our quantum model with the introduction of mixed-state and multi-potential. The trend following dominant market, in which the price return follows a bimodal distribution, is discussed as a specific case of the illiquid market.

  6. Approximation methods for the partition functions of anharmonic systems

    Energy Technology Data Exchange (ETDEWEB)

    Lew, P.; Ishida, T.

    1979-07-01

    The analytical approximations for the classical, quantum mechanical and reduced partition functions of the diatomic molecule oscillating internally under the influence of the Morse potential have been derived and their convergences have been tested numerically. This successful analytical method is used in the treatment of anharmonic systems. Using Schwinger perturbation method in the framework of second quantization formulism, the reduced partition function of polyatomic systems can be put into an expression which consists separately of contributions from the harmonic terms, Morse potential correction terms and interaction terms due to the off-diagonal potential coefficients. The calculated results of the reduced partition function from the approximation method on the 2-D and 3-D model systems agree well with the numerical exact calculations.

  7. Small perturbation of a disordered harmonic chain by a noise and an anharmonic potential

    CERN Document Server

    Bernardin, Cédric

    2011-01-01

    We study the thermal properties of a pinned disordered harmonic chain weakly perturbed by a noise and an anharmonic potential. The noise is controlled by a parameter $\\lambda \\rightarrow 0$, and the anharmonicity by a parameter $\\lambda' \\le \\lambda$. Let $\\kappa$ be the conductivity of the chain, defined through the Green-Kubo formula. Under suitable hypotheses, we show that $\\kappa = \\mathcal O (\\lambda)$ and, in the absence of anharmonic potential, that $\\kappa \\sim \\lambda$. This is in sharp contrast with the ordered chain for which $\\kappa \\sim 1/\\lambda$, and so shows the persitence of localization effects for a non-integrable dynamics.

  8. 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

  9. Solvent-induced O-H vibration red-shifts of oxygen-acids in hydrogen-bonded O-H···base complexes.

    Science.gov (United States)

    Keinan, Sharon; Pines, Dina; Kiefer, Philip M; Hynes, James T; Pines, Ehud

    2015-01-22

    Infrared spectroscopy has been used to characterize the solvent effect on the OH stretching vibrations νOH of phenol, 1-naphthol, 2-naphthol, 1-hydroxypyrene, and ethanol. We distinguish the dielectric (nonspecific) effect of the solvent on ΔνOH, the observed red-shifts in νOH, from the much larger red-shift caused by direct hydrogen (H)-bonding interactions with the solvents. To isolate the solvent dielectric constant ε effect on νOH, the OH oscillator was also studied when it is already H-bonded with an invariant oxygen base, dimethyl sulfoxide. We find that ΔνOH depends importantly on ΔPA, the difference between the proton affinities of the conjugate base of the proton donor and the proton acceptor. For a given H-bonded complex, νOH tends to vary inversely with ε, exhibiting different slopes for polar and nonpolar solvents, i.e., solvents comprising molecules with and without a permanent dipole moment, respectively. We use a two-state valence-bond-based theory to analyze our experimental data. This demonstrates that the OH oscillator acquires a more ionic-like character in the vibrational excited state, i.e., charge transfer; this results in a stronger H-bond in a more anharmonic potential for the OH vibration. The theory distinguishes between nonpolar and polar solvents and successfully accounts for the observed 1/ε and ΔPA variations.

  10. Synthesis and vibrational spectroscopy of 57Fe-labeled models of [NiFe] hydrogenase: first direct observation of a nickel–iron interaction† †Electronic supplementary information (ESI) available: Experimental procedures, spectral data, computational chemistry details, animated vibrational modes as GIFs. See DOI: 10.1039/c4cc04572f Click here for additional data file. Click here for additional data file.

    Science.gov (United States)

    Pelmenschikov, Vladimir; Wang, Hongxin; Meier, Florian; Gee, Leland B.; Yoda, Yoshitaka; Kaupp, Martin; Rauchfuss, Thomas B.

    2014-01-01

    A new route to iron carbonyls has enabled synthesis of 57Fe-labeled [NiFe] hydrogenase mimic (OC)3 57Fe(pdt)Ni(dppe). Its study by nuclear resonance vibrational spectroscopy revealed Ni–57Fe vibrations, as confirmed by calculations. The modes are absent for [(OC)3 57Fe(pdt)Ni(dppe)]+, which lacks Ni–57Fe bonding, underscoring the utility of the analyses in identifying metal–metal interactions. PMID:25237680

  11. Electrical and mechanical anharmonicities from NIR-VCD spectra of compounds exhibiting axial and planar chirality: the cases of (S)-2,3-pentadiene and methyl-d(3) (R)- and (S)-[2.2]paracyclophane-4-carboxylate.

    Science.gov (United States)

    Abbate, Sergio; Longhi, Giovanna; Gangemi, Fabrizio; Gangemi, Roberto; Superchi, Stefano; Caporusso, Anna Maria; Ruzziconi, Renzo

    2011-10-01

    The IR and Near infrared (NIR) vibrational circular dichroism (VCD) spectra of molecules endowed with noncentral chirality have been investigated. Data for fundamental, first, and second overtone regions of (S)-2,3-pentadiene, exhibiting axial chirality, and methyl-d(3) (R)- and (S)-[2.2]paracyclophane-4-carboxylate, exhibiting planar chirality have been measured and analyzed. The analysis of NIR and IR VCD spectra was based on the local-mode model and the use of density functional theory (DFT), providing mechanical and electrical anharmonic terms for all CH-bonds. The comparison of experimental and calculated spectra is satisfactory and allows one to monitor fine details in the asymmetric charge distribution in the molecules: these details consist in the harmonic frequencies, in the principal anharmonicity constants, in both the atomic polar and axial tensors and in their first and second derivatives with respect to the CH-stretching coordinates.

  12. Electronic and vibrational Raman spectroscopy of Nd0.5Sr0.5MnO3 through the phase transitions

    Indian Academy of Sciences (India)

    Md Motin Seikh; A K Sood; Chandrabhas Narayana

    2005-01-01

    Raman scattering experiments have been carried out on single crystals of Nd0.5Sr0.5MnO3 as a function of temperature in the range of 320–50 K, covering the paramagnetic insulator–ferromagnetic metal transition at 250 K and the charge-ordering antiferromagnetic transition at 150 K. The diffusive electronic Raman scattering response is seen in the paramagnetic phase which continue to exist even in the ferromagnetic phase, eventually disappearing below 150 K. We understand the existence of diffusive response in the ferromagnetic phase to the coexistence of the different electronic phases. The frequency and linewidth of the phonons across the transitions show significant changes, which cannot be accounted for only by anharmonic interactions.

  13. Positron-attachment to small molecules: Vibrational enhancement of positron affinities with configuration interaction level of multi-component molecular orbital approach

    Energy Technology Data Exchange (ETDEWEB)

    Tachikawa, Masanori [Quantum Chemistry Division, Graduate School of NanoBioScience, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama 236-0027 (Japan)

    2015-12-31

    To theoretically demonstrate the binding of a positron to small polarized molecules, we have calculated the vibrational averaged positron affinity (PA) values along the local vibrational contribution with the configuration interaction level of multi-component molecular orbital method. This method can take the electron-positron correlation contribution into account through single electronic - single positronic excitation configurations. The PA values are enhanced by including the local vibrational contribution from vertical PA values due to the anharmonicity of the potential.

  14. 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.

  15. Advanced techniques for actinide spectroscopy (ATAS 2012). Abstract book

    Energy Technology Data Exchange (ETDEWEB)

    Foerstendorf, Harald; Mueller, Katharina; Steudtner, Robin (eds.)

    2012-07-01

    The abstract book of the International workshop on advanced techniques for actinide spectroscopy (ATAS 2012) include contributions concerning the following issues: environmental applications, NMR spectroscopy, vibrational spectroscopy, X-ray spectroscopy and theory, technical application: separation processes, emission spectroscopy.

  16. Application of gas phase cryogenic vibrational spectroscopy to characterize the CO2, CO, N2 and N2O interactions with the open coordination site on a Ni(I) macrocycle using dual cryogenic ion traps

    Science.gov (United States)

    Craig, Stephanie M.; Menges, Fabian S.; Johnson, Mark A.

    2017-02-01

    Recent advances in gas phase ion chemistry, coupled with cryogenic ion vibrational predissociation spectroscopy, provide a powerful way to characterize the structures of small molecules bound to open coordination sites of organometallic compounds. Here we extend our previous measurements on the relatively weakly interacting CO2 molecule with a Ni(I) tetraaza-macrocyclic compound to enable the characterization of more strongly interacting substrates. We first confirm the calculated η2-C,O binding motif of CO2 using isotopic labeling by direct, one photon vibrational predissociation of the Ni(I)-CO2 complex. We then apply this approach to study complexation of N2 at the active site. The generality of the method is then expanded to include application to more strongly bound systems that cannot be photodissociated with one IR photon. This involves implementation of a recently developed scheme (Marsh et al., 2015) involving two temperature-controlled ion traps. The first is optimized to complex the substrate molecule to the active site and the second is cooled to around 10 K to enable condensation of weakly bound "tag" molecules onto the target complex so as to enable its characterization by linear vibrational predissociation spectroscopy. We demonstrate this capability by applying it to the coordination of CO to the active Ni(I) site, as well as to elucidate the nature of the products that are formed upon reaction with N2O.

  17. Quantum thermal transport through anharmonic systems: A self-consistent approach

    Science.gov (United States)

    He, Dahai; Thingna, Juzar; Wang, Jian-Sheng; Li, Baowen

    2016-10-01

    We propose a feasible and effective approach to study quantum thermal transport through anharmonic systems. The main idea is to obtain an effective harmonic Hamiltonian for the anharmonic system by applying the self-consistent phonon theory. By using the effective harmonic Hamiltonian, we study thermal transport within the framework of the nonequilibrium Green's function method using the celebrated Caroli formula. We corroborate our quantum self-consistent approach by using the quantum master equation that can deal with anharmonicity exactly, but is limited to the weak system-bath coupling regime. Finally, in order to demonstrate its strength, we apply the quantum self-consistent approach to study thermal rectification in a weakly coupled two-segment anharmonic system.

  18. Temperature dependence of Raman-active phonons and anharmonic interactions in layered hexagonal BN

    Science.gov (United States)

    Cuscó, Ramon; Gil, Bernard; Cassabois, Guillaume; Artús, Luis

    2016-10-01

    We present a Raman scattering study of optical phonons in hexagonal BN for temperatures ranging from 80 to 600 K. The experiments were performed on high-quality, single-crystalline hexagonal BN platelets. The observed temperature dependence of the frequencies and linewidths of both Raman active E2 g optical phonons is analyzed in the framework of anharmonic decay theory, and possible decay channels are discussed in the light of density-functional theory calculations. With increasing temperature, the E2g high mode displays strong anharmonic interactions, with a linewidth increase that indicates an important contribution of four-phonon processes and a marked frequency downshift that can be attributed to a substantial effect of the four-phonon scattering processes (quartic anharmonicity). In contrast, the E2g low mode displays a very narrow linewidth and weak anharmonic interactions, with a frequency downshift that is primarily accounted for by the thermal expansion of the interlayer spacing.

  19. First-principles study of anharmonic phonon effects in tetrahedral semiconductors via an external electric field

    Science.gov (United States)

    Dabiri, Zohreh; Kazempour, Ali; Sadeghzadeh, Mohammad Ali

    2016-11-01

    The strength of phonon anharmonicity is investigated in the framework of the Density Functional Perturbation Theory via an applied constant electric field. In contrast to routine approaches, we have employed the electric field as an effective probe to quest after the quasi-harmonic and anharmonic effects. Two typical tetrahedral semiconductors (diamond and silicon) have been selected to test the efficiency of this approach. In this scheme the applied field is responsible for establishing the perturbation and also inducing the anharmonicity in systems. The induced polarization is a result of changing the electronic density while ions are located at their ground state coordinates or at a specified strain. Employing this method, physical quantities of the semiconductors are calculated in presence of the electron-phonon interaction directly and, phonon-phonon interaction, indirectly. The present approach, which is in good agreement with previous theoretical and experimental studies, can be introduced as a benchmark to simply investigate the anharmonicity and pertinent consequences in materials.

  20. Ground state properties of a Bose-Einstein condensate confined in an anharmonic external potential

    Institute of Scientific and Technical Information of China (English)

    Wang Deng-Long; Yan Xiao-Hong; Tang Yi

    2004-01-01

    In light of the interference experiment of Bose-Einstein condensates, we present an anharmonic external potential model to study ground state properties of Bose-Einstein condensates. The ground state energy and the chemical potential have been analytically obtained, which are lower than those in harmonic trap. Additionally, it is found that the anharmonic strength of the external potential has an important effect on density and velocity distributions of the ground state for the Thomas-Fermi model.

  1. Communication: Trapping a proton in argon: Spectroscopy and theory of the proton-bound argon dimer and its solvation

    Science.gov (United States)

    McDonald, D. C.; Mauney, D. T.; Leicht, D.; Marks, J. H.; Tan, J. A.; Kuo, J.-L.; Duncan, M. A.

    2016-12-01

    Ion-molecule complexes of the form H+Arn are produced in pulsed-discharge supersonic expansions containing hydrogen and argon. These ions are analyzed and mass-selected in a reflectron spectrometer and studied with infrared laser photodissociation spectroscopy. Infrared spectra for the n = 3-7 complexes are characterized by a series of strong bands in the 900-2200 cm-1 region. Computational studies at the MP2/aug-cc-pVTZ level examine the structures, binding energies, and infrared spectra for these systems. The core ion responsible for the infrared bands is the proton-bound argon dimer, Ar-H+-Ar, which is progressively solvated by the excess argon. Anharmonic vibrational theory is able to reproduce the vibrational structure, identifying it as arising from the asymmetric proton stretch in combination with multiple quanta of the symmetric argon stretch. Successive addition of argon shifts the proton vibration to lower frequencies, as the charge is delocalized over more ligands. The Ar-H+-Ar core ion has a first solvation sphere of five argons.

  2. High-Pressure Vibrational Spectroscopy.

    Science.gov (United States)

    Pogson, Mark

    1987-09-01

    Available from UMI in association with The British Library. Requires signed TDF. The study of solids at high pressure and variable temperature enables development of accurate interatomic potential functions over wide ranges of interatomic distances. A review of the main models used in the determination of these potentials is given in Chapter one. A discussion of phonon frequency as a variable physical parameter reflecting the interatomic potential is given. A high pressure Raman study of inorganic salts of the types MSCN, (M = K,Rb,Cs & NH_4^+ ) and MNO_2, (M = K,Na) has been completed. The studies have revealed two new phases in KNO_2 and one new phase in NaNO _2 at high pressure. The accurate phonon shift data have enabled the determination of the pure and biphasic stability regions of the phases of KNO _2. A discussion of the B1, B2 relationship of univalent nitrites is also given. In the series of thiocyanates studied new phases have been found in all four materials. In both the potassium and rubidium salts two new phases have been detected, and in the ceasium salt one new phase has been detected, all at high pressure, from accurate phonon shift data. These transitions are discussed in terms of second-order mechanisms with space groups suggested for all phases, based on Landau's theory of second-order phase transitions. In the ammonium salt one new phase has been detected. This new phase transition has been interpreted as a second-order transition. The series of molecular crystals CH_3 HgX, (X = Cl,Br & I) has been studied at high pressure and at variable temperature. In Chapter five, their phase behaviour at high pressure is detailed along with the pressure dependencies of their phonon frequencies. In the chloride and the bromide two new phases have been detected. In the bromide one has been detected at high temperature and one at high pressure, and latter being interpreted as the stopping of the methyl rotation. In the chloride one phase has been found at both low temperature as well as high pressure, and the other only at high pressure, the latter again associated with the stopping of methyl rotation. The iodide displays two high pressure transitions. A Raman -active soft-mode has been observed in all three analogues, at both high pressure and variable temperature. For the chloride and bromide analogues there is a discussion of the nature of the soft-mode along with the mechanism associated with the I/II transition. The results of the X-ray crystal structure determination of CH_3HgBr at ambient temperature and pressure are given.

  3. Vibrations of the S{sub 1} state of fluorobenzene-h{sub 5} and fluorobenzene-d{sub 5} via resonance-enhanced multiphoton ionization (REMPI) spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Joe P.; Andrejeva, Anna; Tuttle, William D.; Wright, Timothy G., E-mail: Tim.Wright@nottingham.ac.uk [School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD (United Kingdom); Pugliesi, Igor; Schriever, Christian [Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 München (Germany)

    2014-12-28

    We report resonance-enhanced multiphoton ionization spectra of the isotopologues fluorobenzene-h{sub 5} and fluorobenzene-d{sub 5}. By making use of quantum chemical calculations, the changes in the wavenumber of the vibrational modes upon deuteration are examined. Additionally, the mixing of vibrational modes both between isotopologues and also between the two electronic states is discussed. The isotopic shifts lead to dramatic changes in the appearance of the spectrum as vibrations shift in and out of Fermi resonance. Assignments of the majority of the fluorobenzene-d{sub 5} observed bands are provided, aided by previous results on fluorobenzene-h{sub 5}.

  4. 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.

  5. Overtone spectroscopy of some benzaldehyde derivatives

    Indian Academy of Sciences (India)

    P K Srivastava; D K Rai; S B Rai

    2001-06-01

    Overtone spectrum of , and -nitrobenzaldehydes and -chlorobenzaldehyde has been studied in 2000–12000 cm-1 region. Vibrational frequencies and anharmonicity constants for aryl as well as alkyl CH stretch vibrations have been determined. We have also determined the internuclear distances for the aryl CH bond in the different molecules. The small variation observed in these distances is an indication of the substitution effect. It is observed that in the case of -disubstituted benzenes, the shift in aryl CH bond is proportional to sum of the Hammet of the substituents. However in the case of -disubstituted benzenes it is only 80% of the para-substituted shift.

  6. Reconsidering harmonic and anharmonic coherent states: Partial differential equations approach

    Energy Technology Data Exchange (ETDEWEB)

    Toutounji, Mohamad, E-mail: Mtoutounji@uaeu.ac.ae

    2015-02-15

    This article presents a new approach to dealing with time dependent quantities such as autocorrelation function of harmonic and anharmonic systems using coherent states and partial differential equations. The approach that is normally used to evaluate dynamical quantities involves formidable operator algebra. That operator algebra becomes insurmountable when employing Morse oscillator coherent states. This problem becomes even more complicated in case of Morse oscillator as it tends to exhibit divergent dynamics. This approach employs linear partial differential equations, some of which may be solved exactly and analytically, thereby avoiding the cumbersome noncommutative algebra required to manipulate coherent states of Morse oscillator. Additionally, the arising integrals while using the herein presented method feature stability and high numerical efficiency. The correctness, applicability, and utility of the above approach are tested by reproducing the partition and optical autocorrelation function of the harmonic oscillator. A closed-form expression for the equilibrium canonical partition function of the Morse oscillator is derived using its coherent states and partial differential equations. Also, a nonequilibrium autocorrelation function expression for weak electron–phonon coupling in condensed systems is derived for displaced Morse oscillator in electronic state. Finally, the utility of the method is demonstrated through further simplifying the Morse oscillator partition function or autocorrelation function expressions reported by other researchers in unevaluated form of second-order derivative exponential. Comparison with exact dynamics shows identical results.

  7. Reconsidering harmonic and anharmonic coherent states: Partial differential equations approach

    Science.gov (United States)

    Toutounji, Mohamad

    2015-02-01

    This article presents a new approach to dealing with time dependent quantities such as autocorrelation function of harmonic and anharmonic systems using coherent states and partial differential equations. The approach that is normally used to evaluate dynamical quantities involves formidable operator algebra. That operator algebra becomes insurmountable when employing Morse oscillator coherent states. This problem becomes even more complicated in case of Morse oscillator as it tends to exhibit divergent dynamics. This approach employs linear partial differential equations, some of which may be solved exactly and analytically, thereby avoiding the cumbersome noncommutative algebra required to manipulate coherent states of Morse oscillator. Additionally, the arising integrals while using the herein presented method feature stability and high numerical efficiency. The correctness, applicability, and utility of the above approach are tested by reproducing the partition and optical autocorrelation function of the harmonic oscillator. A closed-form expression for the equilibrium canonical partition function of the Morse oscillator is derived using its coherent states and partial differential equations. Also, a nonequilibrium autocorrelation function expression for weak electron-phonon coupling in condensed systems is derived for displaced Morse oscillator in electronic state. Finally, the utility of the method is demonstrated through further simplifying the Morse oscillator partition function or autocorrelation function expressions reported by other researchers in unevaluated form of second-order derivative exponential. Comparison with exact dynamics shows identical results.

  8. How intermixing and anharmonicity enhances interfacial thermal conductance?

    Science.gov (United States)

    Polanco, Carlos; Zhang, Jingjie; Le, Nam; Rastgarkafshgarkolaei, Rouzbeh; Norris, Pamela; Ghosh, Avik

    2015-03-01

    The thermal conductance at an interface, whether ballistic or diffusive, can be expressed as a product of the number of conducting channels (M) and their average transmission (T). The common expectation is that interfacial defects reduce T and thus hurt the conductance. This is however at odds with recent simulations showing that a thin intermixing layer can in fact enhance the conductance. We argue that such an enhancement occurs when the increase in number of modes outweighs the reduction in their average transmission. The new channels open as a result of (a) the random interfacial structure that relaxes the conservation rules for the transverse momentum and promotes transitions between formerly symmetry disallowed channels; and (b) inelastic scattering through phonon-phonon interactions that allow modes beyond the contact cut-off frequency to contribute to transport. We use these results to build a back of the envelope model for interfacial conductance that depends on the mixing distribution, the anharmonic strength, the phonon polarization and wavelength. Non-Equilibrium Green's Function (NEGF) as well as Molecular Dynamics (MD) simulations on Si/mixed layer/Ge, as well as simpler FCC crystals support our results. NSF-CAREER (QMHP 1028883), NSF-IDR (CBET 1134311), XSEDE (TG-DMR130123).

  9. PREFACE: Vibrations at surfaces Vibrations at surfaces

    Science.gov (United States)

    Rahman, Talat S.

    2011-12-01

    This special issue is dedicated to the phenomenon of vibrations at surfaces—a topic that was indispensible a couple of decades ago, since it was one of the few phenomena capable of revealing the nature of binding at solid surfaces. For clean surfaces, the frequencies of modes with characteristic displacement patterns revealed how surface geometry, as well as the nature of binding between atoms in the surface layers, could be different from that in the bulk solid. Dispersion of the surface phonons provided further measures of interatomic interactions. For chemisorbed molecules on surfaces, frequencies and dispersion of the vibrational modes were also critical for determining adsorption sites. In other words, vibrations at surfaces served as a reliable means of extracting information about surface structure, chemisorption and overlayer formation. Experimental techniques, such as electron energy loss spectroscopy and helium-atom-surface scattering, coupled with infra-red spectroscopy, were continually refined and their resolutions enhanced to capture subtleties in the dynamics of atoms and molecules at surfaces. Theoretical methods, whether based on empirical and semi-empirical interatomic potential or on ab initio electronic structure calculations, helped decipher experimental observations and provide deeper insights into the nature of the bond between atoms and molecules in regions of reduced symmetry, as encountered on solid surfaces. Vibrations at surfaces were thus an integral part of the set of phenomena that characterized surface science. Dedicated workshops and conferences were held to explore the variety of interesting and puzzling features revealed in experimental and theoretical investigations of surface vibrational modes and their dispersion. One such conference, Vibrations at Surfaces, first organized by Harald Ibach in Juelich in 1980, continues to this day. The 13th International Conference on Vibrations at Surfaces was held at the University of

  10. Off-resonant vibrational excitation: Orientational dependence and spatial control of photofragments

    DEFF Research Database (Denmark)

    Machholm, Mette; Henriksen, Niels Engholm

    2000-01-01

    Off-resonant and resonant vibrational excitation with short intense infrared (IR) laser pulses creates localized oscillating wave packets, but differs by the efficiency of the excitation and surprisingly by the orientational dependence. Orientational selectivity of the vibrational excitation......-dependent response to the IR fields is due to the anharmonicity of the potential. A subsequent ultraviolet laser pulse in resonance at the outer turning point of the vibrational motion can then dissociate the oscillating molecules, all with the same orientation, leading to spatial control of the photofragment...

  11. 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.

  12. Determining the structure of Ac-AlanLysH^+ in vacuo: computational spectroscopy using DFT

    Science.gov (United States)

    Rossi, Mariana; Blum, Volker; Kupser, Peter; von Helden, Gert; Bierau, Frauke; Meijer, Gerard; Scheffler, Matthias

    2010-03-01

    Well defined secondary structure motifs (e.g., helices) in polypeptides can be systematically studied in vacuo, offering a unique ``clean room" condition to quantify the stabilizing intramolecular interactions. Here we address theoretically the structure of alanine polypeptides Ac-Alan-LysH^+ (n=5,10,15), for which gas-phase helical structure was indicated in experiment [1]. Using van der Waals (vdW) corrected [2] Density Functional Theory (DFT), we present vibrational spectra and compare to room temperature multiple photon IR spectroscopy data obtained at the FELIX free electron laser. For the longer molecules (n=10,15) α-helical models provide good qualitative agreement (theory vs. experiment) already in the harmonic approximation. For Ac-Ala5LysH^+, the predicted lowest energy conformer (``g-1'') in vdW corrected DFT (PBE, B3LYP, revPBE) is not a simple helix. However, the harmonic free energy suggests that g-1 and the lowest-energy α-helical conformers are energetically close at 300 K, and thus might all coexist in experiment. Consistently, their calculated vibrational spectra agree with experiment, but only if anharmonic effects are included by explicit molecular dynamics simulations. [1] R. Hudgins et al., JACS 120, 12974 (1998) [2] A. Tkatchenko, M. Scheffler, PRL 102, 073005 (2009)

  13. Intermediate vibrational coordinate localization with harmonic coupling constraints

    Science.gov (United States)

    Hanson-Heine, Magnus W. D.

    2016-05-01

    Optimized normal coordinates can significantly improve the speed and accuracy of vibrational frequency calculations. However, over-localization can occur when using unconstrained spatial localization techniques. The unintuitive mixtures of stretching and bending coordinates that result can make interpreting spectra more difficult and also cause artificial increases in mode-coupling during anharmonic calculations. Combining spatial localization with a constraint on the coupling between modes can be used to generate coordinates with properties in-between the normal and fully localized schemes. These modes preserve the diagonal nature of the mass-weighted Hessian matrix to within a specified tolerance and are found to prevent contamination between the stretching and bending vibrations of the molecules studied without a priori classification of the different types of vibration present. Relaxing the constraint can also be used to identify which normal modes form specific groups of localized modes. The new coordinates are found to center on more spatially delocalized functional groups than their fully localized counterparts and can be used to tune the degree of vibrational correlation energy during anharmonic calculations.

  14. 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.

  15. Molecular structure and vibrational analysis of Trifluoperazine by FT-IR, FT-Raman and UV-Vis spectroscopies combined with DFT calculations.

    Science.gov (United States)

    Rajesh, P; Gunasekaran, S; Gnanasambandan, T; Seshadri, S

    2015-02-25

    The complete vibrational assignment and analysis of the fundamental vibrational modes of Trifluoperazine (TFZ) was carried out using the experimental FT-IR, FT-Raman and UV-Vis data and quantum chemical studies. The observed vibrational data were compared with the wavenumbers derived theoretically for the optimized geometry of the compound from the DFT-B3LYP gradient calculations employing 6-31G (d,p) basis set. Thermodynamic properties like entropy, heat capacity and enthalpy have been calculated for the molecule. The HOMO-LUMO energy gap has been calculated. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Important non-linear properties such as first hyperpolarizability of TFZ have been computed using B3LYP quantum chemical calculation.

  16. The anharmonic effect study of coupled Morse oscillators for the unimolecular reaction

    Institute of Scientific and Technical Information of China (English)

    YAO Li; LIN Sheng-Hsien

    2008-01-01

    The importance of anharmonic effect in dissociation of molecular systems especially clusters has been noted. In this paper, we shall study the effect of coupled anharmonic oscillator of the standard bilinear form (SBF) Morse oscillator (MO) potential on unimolecular reaction. We shall use the systematic theoretical approach, YL method, proposed by Yao and Lin (YAO L, et. al. J Phys Chem A, 2007, 111(29): 6722-6729), which can evaluate anharmonic effects on the rate constants based on the transition state theory. In treating the anharmonic effect with the Morse oscillator potential on unimolecular reactions under collision-free conditions by using the RRKM (Rice-Ramsperger-Kassel-Marcus) theory, the in-verse Laplace transformation of the partition functions was used to obtain the total amount of state and density of state by using the first-order and the second-order approximations of the saddle-point method. To demonstrate the anharmonic effect of the SBF Morse model, we choose some model sys-tems and a real reaction as examples.

  17. On anharmonic and pressure corrections to the equilibrium isotopic constants for minerals

    Science.gov (United States)

    Polyakov, Veniamin B.

    1998-09-01

    Specifies of the calculations of the reduced isotopic partition function ratios (β-factor) of minerals are discussed. Comparative calculations in the framework of the fully harmonic, quasi-harmonic, and intrinsic anharmonic approximations show minor anharmonic corrections to the harmonic values of the β-factor. In the case of calcite, the difference between the fully harmonic and intrinsic anharmonic values of 10 3lnβ varies from 0.60 at 300 K to 0.37 at 1200 K and is close to typical values of the anharmonic correction in gas molecules. A new treatment for calculating isotopic effects in molar volumes of minerals and pressure effects on their β-factors is developed on the basis of the Mie-Grüneisen equation of state. There is no significant difference between the quasi-harmonic and intrinsic harmonic values of (∂lnβ/∂ P) T. For calcite, the pressure derivative of the β-factor is positive, decreases monotonically with temperature, and becomes small at T ˜ 1000 K (10 3(∂lnβ/ ∂P) T ≈ 0.1-0.15 GPa -1). These results contradict the large anharmonic and pressure effects to the β-factor of calcite calculated by Gillet et al. (1996) as well as their conclusion that the pressure correction to the β-factor of calcite is negative at higher temperatures and increases in its absolute value with increasing temperature.

  18. The anharmonic effect study of coupled Morse oscillators for the unimolecular reaction

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The importance of anharmonic effect in dissociation of molecular systems especially clusters has been noted. In this paper, we shall study the effect of coupled anharmonic oscillator of the standard bilinear form (SBF) Morse oscillator (MO) potential on unimolecular reaction. We shall use the systematic theoretical approach, YL method, proposed by Yao and Lin (YAO L, et. al. J Phys Chem A, 2007, 111(29): 6722-6729), which can evaluate anharmonic effects on the rate constants based on the transition state theory. In treating the anharmonic effect with the Morse oscillator potential on unimolecular reactions under collision-free conditions by using the RRKM (Rice-Ramsperger-Kassel-Marcus) theory, the in-verse Laplace transformation of the partition functions was used to obtain the total amount of state and density of state by using the first-order and the second-order approximations of the saddle-point method. To demonstrate the anharmonic effect of the SBF Morse model, we choose some model systems and a real reaction as examples.

  19. Vibrational spectroscopy (FT-IR and FT-Raman) investigation, and hybrid computational (HF and DFT) analysis on the structure of 2,3-naphthalenediol.

    Science.gov (United States)

    Shoba, D; Periandy, S; Karabacak, M; Ramalingam, S

    2011-12-01

    The FT-IR and FT-Raman vibrational spectra of 2,3-naphthalenediol (C(10)H(8)O(2)) have been recorded using Bruker IFS 66V spectrometer in the range of 4000-100 cm(-1) in solid phase. A detailed vibrational spectral analysis has been carried out and the 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 by using the ab initio Hartree-Fock (HF) and DFT (LSDA and B3LYP) methods with 6-31+G(d,p) and 6-311+G(d,p) basis sets. There are three conformers, C1, C2 and C3 for this molecule. The computational results diagnose the most stable conformer of title molecule as the C1 form. The isotropic computational analysis showed good agreement with the experimental observations. Comparison of the fundamental vibrational frequencies with calculated results by HF and DFT methods. Comparison of the simulated spectra provides important information about the capability of computational method to describe the vibrational modes. A study on the electronic properties, such as absorption wavelengths, excitation energy, dipole moment and Frontier molecular orbital energies, are performed by time dependent DFT approach. The electronic structure and the assignment of the absorption bands in the electronic spectra of steady compounds are discussed. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. On the basis of the thermodynamic properties of the title compound at different temperatures have been calculated. The statistical thermodynamic properties (standard heat capacities, standard entropies, and standard enthalpy changes) and their correlations with temperature have been obtained from the theoretical vibrations.

  20. Homogeneous and inhomogeneous broadenings and the Voigt line shapes in the phase-resolved and intensity sum-frequency generation vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Shunli; Fu, Li; Gan, Wei; Wang, Hongfei

    2016-01-21

    In this report we show that the ability to measure the sub-1 cm-1 resolution phase-resolved and intensity high-resolution broadband sum frequency generation vibrational spectra (HR-BB-SFG-VS) of the –CN stretch vibration of the Langmuir-Blodgett (LB) monolayer of the 4-n-octyl-4’-cyanobiphenyl (8CB) on the z-cut α-quartz surface allows for the first time the direct comparison and understanding of the homogeneous and inhomogeneous broadenings in the imaginary and intensity SFG vibrational spectral lineshapes in detail. The difference of the full width at half maxima (FWHM) of the imaginary and intensity SFG-VS spectra of the same vibrational mode is the signature of the Voigt lineshape and it measures the relative contribution to the overall lineshape from the homogeneous and inhomogeneous broadenings in SFG vibrational spectra. From the phase-resolved and intensity spectra, we found that the FWHM of the 2238.00 ±0.02 cm-1 peak in the phase-resolved imaginary and intensity spectra is 19.2 ± 0.2 cm-1 and 21.6 ± 0.4 cm-1, respectively, for the –CN group of the 8CB LB monolayer on the z-cut α-quartz crystal surface. The FWHM width difference of 2.4 cm-1 agrees quantitatively with a Voigt lineshape with a homogeneous broadening half width of Γ = 5.29 ± 0.08 cm-1 and a inhomogeneous standard derivation width Δω = 5.42 ± 0.07 cm-1. These results shed new lights on the understanding and interpretation of the lineshapes of both the phase-resolved and the intensity SFG vibrational spectra, as well as other incoherent and coherent spectroscopic techniques in general.

  1. Raman and infrared spectroscopy, DFT calculations, and vibrational assignment of the anticancer agent picoplatin: performance of long-range corrected/hybrid functionals for a platinum(II) complex.

    Science.gov (United States)

    Malik, Magdalena; Wysokiński, Rafał; Zierkiewicz, Wiktor; Helios, Katarzyna; Michalska, Danuta

    2014-08-28

    Picoplatin, cis-[PtCl2(NH3)(2-picoline)], is a new promising anticancer agent undergoing clinical trials, which reveals high efficacy against many tumors and greatly reduced toxicity, in comparison to cisplatin. In this work, we present for the first time the Fourier-transform Raman and infrared spectra of picoplatin, in the region of 3500-50 cm(-1). The comprehensive theoretical studies on the molecular structure, the nature of Pt-ligand bonding, vibrational frequencies, and intensities were performed by employing different DFT methods, including hybrid (PBE0, mPW1PW, and B3LYP) and long-range-corrected hybrid density functionals (LC-ωPBE, CAM-B3LYP). Various effective core potentials (ECP) and basis sets have been used. In the prediction of the molecular structure of picoplatin, the best results have been obtained by LC-ωPBE, followed by PBE0, mPW1PW, and CAM-B3LYP density functionals, while the least accurate is B3LYP. The use of the LanL2TZ(f) ECP/basis set for Pt, in conjunction with all tested DFT methods, improves the calculated geometry of the title complex. The PBE0, mPW1PW, and CAM-B3LYP methods have shown the best performance in the calculations of the frequencies of Pt-ligand vibrations. A clear-cut assignment of all the bands in the IR and Raman spectra have been made on the basis of the calculated potential energy distribution (PED). The nature of the "vibrational signatures" of picoplatin have been determined. These results are indispensable for further investigation on drug-target interactions using vibrational spectroscopy.

  2. Examining the impact of harmonic correlation on vibrational frequencies calculated in localized coordinates

    Energy Technology Data Exchange (ETDEWEB)

    Hanson-Heine, Magnus W. D., E-mail: magnus.hansonheine@nottingham.ac.uk [School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD (United Kingdom)

    2015-10-28

    Carefully choosing a set of optimized coordinates for performing vibrational frequency calculations can significantly reduce the anharmonic correlation energy from the self-consistent field treatment of molecular vibrations. However, moving away from normal coordinates also introduces an additional source of correlation energy arising from mode-coupling at the harmonic level. The impact of this new component of the vibrational energy is examined for a range of molecules, and a method is proposed for correcting the resulting self-consistent field frequencies by adding the full coupling energy from connected pairs of harmonic and pseudoharmonic modes, termed vibrational self-consistent field (harmonic correlation). This approach is found to lift the vibrational degeneracies arising from coordinate optimization and provides better agreement with experimental and benchmark frequencies than uncorrected vibrational self-consistent field theory without relying on traditional correlated methods.

  3. Vibrational Microspectroscopy for Cancer Screening

    Directory of Open Access Journals (Sweden)

    Fiona M. Lyng

    2015-02-01

    Full Text Available Vibrational spectroscopy analyses vibrations within a molecule and can be used to characterise a molecular structure. Raman spectroscopy is one of the vibrational spectroscopic techniques, in which incident radiation is used to induce vibrations in the molecules of a sample, and the scattered radiation may be used to characterise the sample in a rapid and non-destructive manner. Infrared (IR spectroscopy is a complementary vibrational spectroscopic technique based on the absorption of IR radiation by the sample. Molecules absorb specific frequencies of the incident light which are characteristic of their structure. IR and Raman spectroscopy are sensitive to subtle biochemical changes occurring at the molecular level allowing spectral variations corresponding to disease onset to be detected. Over the past 15 years, there have been numerous reports demonstrating the potential of IR and Raman spectroscopy together with multivariate statistical analysis techniques for the detection of a variety of cancers including, breast, lung, brain, colon, oral, oesophageal, prostate and cervical cancer. This paper discusses the recent advances and the future perspectives in relation to cancer screening applications, focussing on cervical and oral cancer.

  4. Vibrational spectroscopy of the double complex salt Pd(NH3)4(ReO4)2, a bimetallic catalyst precursor

    Science.gov (United States)

    Thompson, Simon T.; Lamb, H. Henry; Delley, Bernard; Franzen, Stefan

    2017-02-01

    Tetraamminepalladium(II) perrhenate, a double complex salt, has significant utility in PdRe catalyst preparation; however, the vibrational spectra of this readily prepared compound have not been described in the literature. Herein, we present the infrared (IR) and Raman spectra of tetraamminepalladium(II) perrhenate and several related compounds. The experimental spectra are complemented by an analysis of normal vibrational modes that compares the experimentally obtained spectra with spectra calculated using DFT (DMol3). The spectra are dominated by features due to the ammine groups and the Resbnd O stretch in Td ReO4-; lattice vibrations due to the D4h Pd(NH3)42+ are also observed in the Raman spectrum. Generally, we observe good agreement between ab initio calculations and experimental spectra. The calculated IR spectrum closely matches experimental results for peak positions and their relative intensities. The methods for calculating resonance Raman intensities are implemented using the time correlator formalism using two methods to obtain the excited state displacements and electron-vibration coupling constants, which are the needed inputs in addition to the normal mode wave numbers. Calculated excited state energy surfaces of Raman-active modes correctly predict relative intensities of the peaks and Franck-Condon activity; however, the position of Raman bands are predicted at lower frequencies than observed. Factor group splitting of Raman peaks observed in spectra of pure compounds is not predicted by DFT.

  5. Use of vibrational spectroscopy to study protein and DNA structure, hydration, and binding of biomolecules: A combined theoretical and experimental approach

    DEFF Research Database (Denmark)

    Jalkanen, Karl J.; Jürgensen, Vibeke Würtz; Claussen, Anetta

    2006-01-01

    +disp, RHF, MP2, and DFT methodologies for the modeling studies with the goal of interpreting the experimentally measured vibrational spectra for these molecules to the greatest extent possible and to use this combined approach to understand the structure, function, and electronic properties...

  6. Role of anharmonicities and non-linearities in heavy ion collisions a microscopic approach

    CERN Document Server

    Lanza, E G; Catara, F; Chomaz, P; Volpe, C; Chomaz, Ph.

    1996-01-01

    Using a microscopic approach beyond RPA to treat anharmonicities, we mix two-phonon states among themselves and with one-phonon states. We also introduce non-linear terms in the external field. These non-linear terms and the anharmonicities are not taken into account in the "standard" multiphonon picture. Within this framework we calculate Coulomb excitation of 208Pb and 40Ca by a 208Pb nucleus at 641 and 1000MeV/A. We show with different examples the importance of the non-linearities and anharmonicities for the excitation cross section. We find an increase of 10 % for 208Pb and 20 % for 40Ca of the excitation cross section corresponding to the energy region of the double giant dipole resonance with respect to the "standard" calculation. We also find important effects in the low energy region. The predicted cross section in the DGDR region is found to be rather close to the experimental observation.

  7. Effect of external fields on the energies of hydrogenic donor with the anharmonic confinement potential

    Energy Technology Data Exchange (ETDEWEB)

    Aciksoz, E.; Bayrak, O. [Department of Physics, Akdeniz University, 07058 Antalya (Turkey); Soylu, A., E-mail: asimsoylu@gmail.com [Department of Physics, Nigde University, 51240 Nigde (Turkey)

    2015-01-01

    The impurity binding energy in the GaAs−Ga{sub 1−x}Al{sub x}As system is studied with an anharmonic type confinement potential by taking into account the influence of the external electric and magnetic fields within the framework of the effective mass approximation and asymptotic iteration method (AIM). The influence of the external electromagnetic fields and anharmonicity on a donor binding energy is examined systematically. It is shown that the donor binding energy is highly dependent on the external electric and magnetic fields and the confinement potential shapes. Both the electric and magnetic fields are increased, the binding energies increase for each of them. However, the behaviors of increase in the weak and strong fields’ regimes have different character a bit. Furthermore, when the more anharmonicity is considered, the binding energy of donor slightly increases as well.

  8. In Situ Adsorption Studies at the Solid/Liquid Interface:Characterization of Biological Surfaces and Interfaces Using SumFrequency Generation Vibrational Spectroscopy, Atomic Force Microscopy,and Quartz Crystal Microbalance

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, Diana Christine [Univ. of California, Berkeley, CA (United States)

    2006-01-01

    Sum frequency generation (SFG) vibrational spectroscopy, atomic force microscopy (AFM), and quartz crystal microbalance (QCM) have been used to study the molecular surface structure, surface topography and mechanical properties, and quantitative adsorbed amount of biological molecules at the solid-liquid interface. The molecular-level behavior of designed peptides adsorbed on hydrophobic polystyrene and hydrophilic silica substrates has been examined as a model of protein adsorption on polymeric biomaterial surfaces. Proteins are such large and complex molecules that it is difficult to identify the features in their structure that lead to adsorption and interaction with solid surfaces. Designed peptides which possess secondary structure provide simple model systems for understanding protein adsorption. Depending on the amino acid sequence of a peptide, different secondary structures (α-helix and β-sheet) can be induced at apolar (air/liquid or air/solid) interfaces. Having a well-defined secondary structure allows experiments to be carried out under controlled conditions, where it is possible to investigate the affects of peptide amino acid sequence and chain length, concentration, buffering effects, etc. on adsorbed peptide structure. The experiments presented in this dissertation demonstrate that SFG vibrational spectroscopy can be used to directly probe the interaction of adsorbing biomolecules with a surface or interface. The use of well designed model systems aided in isolation of the SFG signal of the adsorbing species, and showed that surface functional groups of the substrate are sensitive to surface adsorbates. The complementary techniques of AFM and QCM allowed for deconvolution of the effects of surface topography and coverage from the observed SFG spectra. Initial studies of biologically relevant surfaces are also presented: SFG spectroscopy was used to study the surface composition of common soil bacteria for use in bioremediation of nuclear waste.

  9. Equation of State, Nonlinear Elastic Response, and Anharmonic Properties of Diamond-Cubic Silicon and Germanium: First-Principles Investigation

    Science.gov (United States)

    Wang, Chenju; Gu, Jianbing; Kuang, Xiaoyu; Xiang, Shikai

    2015-06-01

    Nonlinear elastic properties of diamond-cubic silicon and germanium have not been investigated sufficiently to date. Knowledge of these properties not only can help us to understand nonlinear mechanical effects but also can assist us to have an insight into the related anharmonic properties, so we investigate the nonlinear elastic behaviour of single silicon and germanium by calculating their second- and third-order elastic constants. All the results of the elastic constants show good agreement with the available experimental data and other theoretical calculations. Such a phenomenon indicates that the present values of the elastic constants are accurate and can be used to further study the related anharmonic properties. Subsequently, the anharmonic properties such as the pressure derivatives of the second-order elastic constants, Grüneisen constants of long-wavelength acoustic modes, and ultrasonic nonlinear parameters are explored. All the anharmonic properties of silicon calculated in the present work also show good agreement with the existing experimental results; this consistency not only reveals that the calculation method of the anharmonic properties is feasible but also illuminates that the anharmonic properties obtained in the present work are reliable. For the anharmonic properties of germanium, since there are no experimental result and other theoretical data till now, we hope that the anharmonic properties of germanium first offered in this work would serve as a reference for future studies.

  10. Equation of state, nonlinear elastic response, and anharmonic properties of diamond-cubic silicon and germanium. First-principles investigation

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Chenju [Sichuan Univ., Chengdu (China). Inst. of Atomic and Molecular Physics; Institute of Fluid Physics, Sichuan (China). National Key Laboratory of Shock Wave and Detonation Physics; Gu, Jianbing [Institute of Fluid Physics, Sichuan (China). National Key Laboratory of Shock Wave and Detonation Physics; Sichuan Univ., Chengdu (China). College of Physical Science and Technology; Kuang, Xiaoyu [Sichuan Univ., Chengdu (China). Inst. of Atomic and Molecular Physics; Xiang, Shikai [Institute of Fluid Physics, Sichuan (China). National Key Laboratory of Shock Wave and Detonation Physics

    2015-10-01

    Nonlinear elastic properties of diamond-cubic silicon and germanium have not been investigated sufficiently to date. Knowledge of these properties not only can help us to understand nonlinear mechanical effects but also can assist us to have an insight into the related anharmonic properties, so we investigate the nonlinear elastic behaviour of single silicon and germanium by calculating their second- and third-order elastic constants. All the results of the elastic constants show good agreement with the available experimental data and other theoretical calculations. Such a phenomenon indicates that the present values of the elastic constants are accurate and can be used to further study the related anharmonic properties. Subsequently, the anharmonic properties such as the pressure derivatives of the second-order elastic constants, Grueneisen constants of long-wavelength acoustic modes, and ultrasonic nonlinear parameters are explored. All the anharmonic properties of silicon calculated in the present work also show good agreement with the existing experimental results; this consistency not only reveals that the calculation method of the anharmonic properties is feasible but also illuminates that the anharmonic properties obtained in the present work are reliable. For the anharmonic properties of germanium, since there are no experimental result and other theoretical data till now, we hope that the anharmonic properties of germanium first offered in this work would serve as a reference for future studies.

  11. Basic molecular spectroscopy

    CERN Document Server

    Gorry, PA

    1985-01-01

    BASIC Molecular Spectroscopy discusses the utilization of the Beginner's All-purpose Symbolic Instruction Code (BASIC) programming language in molecular spectroscopy. The book is comprised of five chapters that provide an introduction to molecular spectroscopy through programs written in BASIC. The coverage of the text includes rotational spectra, vibrational spectra, and Raman and electronic spectra. The book will be of great use to students who are currently taking a course in molecular spectroscopy.

  12. 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.

  13. Design of blade-shaped-electrode linear ion traps with reduced anharmonic contributions

    Energy Technology Data Exchange (ETDEWEB)

    Deng, K.; Che, H.; Ge, Y. P.; Xu, Z. T.; Yuan, W. H.; Zhang, J.; Lu, Z. H., E-mail: zehuanglu@mail.hust.edu.cn [MOE Key Laboratory of Fundamental Physical Quantities Measurement, School of Physics, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074 (China); Lan, Y. [MOE Key Laboratory of Fundamental Physical Quantities Measurement, School of Physics, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074 (China); Department of Physics and Astronomy, University of British Columbia, Vancouver, BC V6T 1Z1 (Canada)

    2015-09-21

    RF quadrupole linear Paul traps are versatile tools in quantum physics experiments. Linear Paul traps with blade-shaped electrodes have the advantages of larger solid angles for fluorescence collection. But with these kinds of traps, the existence of higher-order anharmonic terms of the trap potentials can cause large heating rate for the trapped ions. In this paper, we theoretically investigate the dependence of higher-order terms of trap potentials on the geometry of blade-shaped traps, and offer an optimized design. A modified blade electrodes trap is proposed to further reduce higher-order anharmonic terms while still retaining large fluorescence collection angle.

  14. The influence of anharmonic phonons on the isotope effect in high-{Tc} oxides

    Energy Technology Data Exchange (ETDEWEB)

    Crespi, V.H.; Cohen, M.L.

    1992-01-01

    Anharmonic phonons are examined to study the unusual isotope effect exponents for the high-{Tc} oxides. Within a simple model of anharmonicity, the mass dependences of the electron-phonon coupling constant {lambda} and the phonon frequency determine the isotope effect exponent {alpha} as a function of coupling strength. A model in which the outer wells of a multiple-well potential deepen as the orthorhombic/low temperature tetragonal phase transition in La{sub 2-x}M{sub x}CuO{sub 4} is approached is consistent with some experimentally observed variations in {Tc} and {alpha}. 10 refs.

  15. The influence of anharmonic phonons on the isotope effect in high- Tc oxides

    Energy Technology Data Exchange (ETDEWEB)

    Crespi, V.H.; Cohen, M.L.

    1992-01-01

    Anharmonic phonons are examined to study the unusual isotope effect exponents for the high-{Tc} oxides. Within a simple model of anharmonicity, the mass dependences of the electron-phonon coupling constant {lambda} and the phonon frequency determine the isotope effect exponent {alpha} as a function of coupling strength. A model in which the outer wells of a multiple-well potential deepen as the orthorhombic/low temperature tetragonal phase transition in La{sub 2-x}M{sub x}CuO{sub 4} is approached is consistent with some experimentally observed variations in {Tc} and {alpha}. 10 refs.

  16. Nonlinear optical spectroscopy of diamond surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Chin, R.P.

    1995-04-01

    Second harmonic generation (SHG) and infrared-visible sum frequency generation (SFG) spectroscopies have been shown to be powerful and versatile for studying surfaces with submonolayer sensitivity. They have been used in this work to study bare diamond surfaces and molecular adsorption on them. In particular, infrared-visible SFG as a surface vibrational spectroscopic technique has been employed to identify and monitor in-situ surface bonds and species on the diamond (111) surface. The CH stretch spectra allow us to investigate hydrogen adsorption, desorption, abstraction, and the nature of the hydrogen termination. The C(111) surface dosed with atomic hydrogen was found to be in a monohydride configuration with the hydrogen atoms situated at top-sites. The ratio of the abstraction rate to the adsorption rate was appreciable during atomic hydrogen dosing. Kinetic parameters for thermal desorption of H on C(111) were determined showing a near first-order kinetics. For the fully H-terminated (111) surface, a large (110 cm{sup {minus}1}) anharmonicity and {approximately}19 psec lifetime were measured for the first-excited CH stretch mode. The bare reconstructed C(111)-(2 {times} l) surface showed the presence of CC stretch modes which were consistent with the Pandey {pi}-bonded chain structure. When exposed to the methyl radical, the SFG spectra of the C(111) surface showed features suggesting the presence of adsorbed methyl species. After heating to sufficiently high temperatures, they were converted into the monohydride species. Preliminary results on the hydrogen-terminated diamond (100) surface are also presented.

  17. Resonance-enhanced multiphoton ionization (REMPI) spectroscopy of bromobenzene and its perdeuterated isotopologue: Assignment of the vibrations of the S{sub 0}, S{sub 1}, and D{sub 0}{sup +} states of bromobenzene and the S{sub 0} and D{sub 0}{sup +} states of iodobenzene

    Energy Technology Data Exchange (ETDEWEB)

    Andrejeva, Anna; Tuttle, William D.; Harris, Joe P.; Wright, Timothy G., E-mail: Tim.Wright@nottingham.ac.uk [School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD (United Kingdom)

    2015-12-28

    We report vibrationally resolved spectra of the S{sub 1}←S{sub 0} transition of bromobenzene using resonance-enhanced multiphoton ionization spectroscopy. We study bromobenzene-h{sub 5} as well as its perdeuterated isotopologue, bromobenzene-d{sub 5}. The form of the vibrational modes between the isotopologues and also between the S{sub 0} and S{sub 1} electronic states is discussed for each species, allowing assignment of the bands to be achieved and the activity between states and isotopologues to be established. Vibrational bands are assigned utilizing quantum chemical calculations, previous experimental results, and isotopic shifts. Previous work and assignments of the S{sub 1} spectra are discussed. Additionally, the vibrations in the ground state cation, D{sub 0}{sup +}, are considered, since these have also been used by previous workers in assigning the excited neutral state spectra. We also examine the vibrations of iodobenzene in the S{sub 0} and D{sub 0}{sup +} states and comment on the previous assignments of these. In summary, we have been able to assign the corresponding vibrations across the whole monohalobenzene series of molecules, in the S{sub 0}, S{sub 1}, and D{sub 0}{sup +} states, gaining insight into vibrational activity and vibrational couplings.

  18. Motor effect in electron transport through a molecular junction with torsional vibrations

    OpenAIRE

    Pshenichnyuk, Ivan A.; Čížek, Martin

    2010-01-01

    We propose a model for a molecular junction with internal anharmonic torsional vibrations interacting with an electric current. The Wangsness-Bloch-Redfield master equation approach is used to determine the stationary reduced density matrix of the molecule. The dependence of the current, excitation energy and angular momentum of the junction on the applied voltage is studied. Negative differential conductance is observed in the current-voltage characteristics. It is shown that a model with vi...

  19. Calculations of lattice vibrational mode lifetimes using Jazz: a Python wrapper for LAMMPS

    Science.gov (United States)

    Gao, Y.; Wang, H.; Daw, M. S.

    2015-06-01

    Jazz is a new python wrapper for LAMMPS [1], implemented to calculate the lifetimes of vibrational normal modes based on forces as calculated for any interatomic potential available in that package. The anharmonic character of the normal modes is analyzed via the Monte Carlo-based moments approximation as is described in Gao and Daw [2]. It is distributed as open-source software and can be downloaded from the website http://jazz.sourceforge.net/.

  20. Dynamics of an [Fe4S4(SPh)4]2- cluster explored via IR, Raman, and nuclear resonance vibrational spectroscopy (NRVS)-analysis using 36S substitution, DFT calculations, and empirical force fields.

    Science.gov (United States)

    Xiao, Yuming; Koutmos, Markos; Case, David A; Coucouvanis, Dimitri; Wang, Hongxin; Cramer, Stephen P

    2006-05-14

    We have used four vibrational spectroscopies--FT-IR, FT-Raman, resonance Raman, and 57Fe nuclear resonance vibrational spectroscopy (NRVS)--to study the normal modes of the Fe-S cluster in [(n-Bu)4N]2[Fe4S4(SPh)4]. This [Fe4S4(SR)4]2- complex serves as a model for the clusters in 4Fe ferredoxins and high-potential iron proteins (HiPIPs). The IR spectra exhibited differences above and below the 243 K phase transition. Significant shifts with 36S substitution into the bridging S positions were also observed. The NRVS results were in good agreement with the low temperature data from the conventional spectroscopies. The NRVS spectra were interpreted by normal mode analysis using optimized Urey-Bradley force fields (UBFF) as well as from DFT theory. For the UBFF calculations, the parameters were refined by comparing calculated and observed NRVS frequencies and intensities. The frequency shifts after 36S substitution were used as an additional constraint. A D 2d symmetry Fe4S4S'4 model could explain most of the observed frequencies, but a better match to the observed intensities was obtained when the ligand aromatic rings were included for a D 2d Fe4S4(SPh)4 model. The best results were obtained using the low temperature structure without symmetry constraints. In addition to stretching and bending vibrations, low frequency modes between approximately 50 and 100 cm(-1) were observed. These modes, which have not been seen before, are interpreted as twisting motions with opposing sides of the cube rotating in opposite directions. In contrast with a recent paper on a related Fe4S4 cluster, we find no need to assign a large fraction of the low frequency NRVS intensity to 'rotational lattice modes'. We also reassign the 430 cm(-1) band as primarily an elongation of the thiophenolate ring, with approximately 10% terminal Fe-S stretch character. This study illustrates the benefits of combining NRVS with conventional Raman and IR analysis for characterization of Fe-S centers. DFT

  1. Characterization of 1,5-dimethoxynaphthalene by vibrational spectroscopy (FT-IR and FT-Raman) and density functional theory calculations.

    Science.gov (United States)

    Kandasamy, M; Velraj, G; Kalaichelvan, S; Mariappan, G

    2015-01-05

    In this work, we reported a combined experimental and theoretical study on molecular structure, vibrational spectra and natural bond orbital (NBO) analysis of 1,5-dimethoxynaphthalene. The optimized molecular structure, atomic charges, vibrational frequencies and natural bond orbital analysis of 1,5-dimethoxynaphthalene have been studied by performing DFT/B3LYP/6-31G(d,p) level of theory. The FTIR, FT-Raman spectra were recorded in the region of 4000-400 cm(-1) and 3500-50 cm(-1) respectively. The scaled wavenumbers are compared with the experimental values. The difference between the observed and scaled wavenumber values of the most fundamentals is very small. The formation of hydrogen bond was investigated in terms of the charge density by the NBO analysis. Natural Population Analysis (NPA) was used for charge determination in the title molecule. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis were investigated using theoretical calculations.

  2. Molecular dynamics simulation and vibrational spectroscopy of molecules (Ⅰ)——A method of internal coordinate correlation for band assignment

    Institute of Scientific and Technical Information of China (English)

    杨小震

    1995-01-01

    A method of simulation of vibrational spectra by using the "internal coordinatecorrelation" based on molecular dynamics algorithms and auto-correlation function has been developed.The in-ternal coordinates,such as bond stretching,bond angle bending,out-of-plane bending and torsion,are treatedas the dynamic variables to obtain a density spectrum or the "internal coordinate correlation" spectrum Theadvantages of this method are as follows:i)it is easier to assign vibration modes for the density spectra;ii)itsimply connects the Fourier transformed "internal coordinate correlation" function to the eigenvectors innormal coordinate analysis;iii)it is a basis for simulating IR and Raman active spectra of a large molecularsystem.

  3. Complex vibrational analysis of an antiferroelectric liquid crystal based on solid-state oriented quantum chemical calculations and experimental molecular spectroscopy.

    Science.gov (United States)

    Drużbicki, Kacper; Mikuli, Edward; Kocot, Antoni; Ossowska-Chruściel, Mirosława Danuta; Chruściel, Janusz; Zalewski, Sławomir

    2012-08-02

    The experimental and theoretical vibrational spectroscopic study of one of a novel antiferroelectric liquid crystals (AFLC), known under the MHPSBO10 acronym, have been undertaken. The interpretation of both FT-IR and FT-Raman spectra was focused mainly on the solid-state data. To analyze the experimental results along with the molecular properties, density functional theory (DFT) computations were performed using several modern theoretical approaches. The presented calculations were performed within the isolated molecule model, probing the performance of modern exchange-correlations functionals, as well as going beyond, i.e., within hybrid (ONIOM) and periodic boundary conditions (PBC) methodologies. A detailed band assignment was supported by the normal-mode analysis with SQM ab initio force field scaling. The results are supplemented by the noncovalent interactions analysis (NCI). The relatively noticeable spectral differences observed upon Crystal to AFLC phase transition have also been reported. For the most prominent vibrational modes, the geometries of the transition dipole moments along with the main components of vibrational polarizability were analyzed in terms of the molecular frame. One of the goals of the paper was to optimize the procedure of solid-state calculations to obtain the results comparable with the all electron calculations, performed routinely for isolated molecules, and to test their performance. The presented study delivers a complex insight into the vibrational spectrum with a noticeable improvement of the theoretical results obtained for significantly attracting mesogens using modern molecular modeling approaches. The presented modeling conditions are very promising for further description of similar large molecular crystals.

  4. Waves & vibrations

    OpenAIRE

    Nicolas, Maxime

    2016-01-01

    Engineering school; This course is designed for students of Polytech Marseille, engineering school. It covers first the physics of vibration of the harmonic oscillator with damping and forcing, coupled oscillators. After a presentation of the wave equation, the vibration of strings, beams and membranes are studied.

  5. Characterization of the molecular structure and mechanical properties of polymer surfaces and protein/polymer interfaces by sum frequency generation vibrational spectroscopy and atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Koffas, Telly Stelianos [Univ. of California, Berkeley, CA (United States)

    2004-01-01

    Sum frequency generation (SFG) vibrational spectroscopy, atomic force microscopy (AFM), and other complementary surface-sensitive techniques have been used to study the surface molecular structure and surface mechanical behavior of biologically-relevant polymer systems. SFG and AFM have emerged as powerful analytical tools to deduce structure/property relationships, in situ, for polymers at air, liquid and solid interfaces. The experiments described in this dissertation have been performed to understand how polymer surface properties are linked to polymer bulk composition, substrate hydrophobicity, changes in the ambient environment (e.g., humidity and temperature), or the adsorption of macromolecules. The correlation of spectroscopic and mechanical data by SFG and AFM can become a powerful methodology to study and engineer materials with tailored surface properties. The overarching theme of this research is the interrogation of systems of increasing structural complexity, which allows us to extend conclusions made on simpler model systems. We begin by systematically describing the surface molecular composition and mechanical properties of polymers, copolymers, and blends having simple linear architectures. Subsequent chapters focus on networked hydrogel materials used as soft contact lenses and the adsorption of protein and surfactant at the polymer/liquid interface. The power of SFG is immediately demonstrated in experiments which identify the chemical parameters that influence the molecular composition and ordering of a polymer chain's side groups at the polymer/air and polymer/liquid interfaces. In general, side groups with increasingly greater hydrophobic character will be more surface active in air. Larger side groups impose steric restrictions, thus they will tend to be more randomly ordered than smaller hydrophobic groups. If exposed to a hydrophilic environment, such as water, the polymer chain will attempt to orient more of its hydrophilic groups to

  6. Characterization of the molecular structure and mechanical properties of polymer surfaces and protein/polymer interfaces by sum frequency generation vibrational spectroscopy and atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Koffas, Telly Stelianos

    2004-05-15

    Sum frequency generation (SFG) vibrational spectroscopy, atomic force microscopy (AFM), and other complementary surface-sensitive techniques have been used to study the surface molecular structure and surface mechanical behavior of biologically-relevant polymer systems. SFG and AFM have emerged as powerful analytical tools to deduce structure/property relationships, in situ, for polymers at air, liquid and solid interfaces. The experiments described in this dissertation have been performed to understand how polymer surface properties are linked to polymer bulk composition, substrate hydrophobicity, changes in the ambient environment (e.g., humidity and temperature), or the adsorption of macromolecules. The correlation of spectroscopic and mechanical data by SFG and AFM can become a powerful methodology to study and engineer materials with tailored surface properties. The overarching theme of this research is the interrogation of systems of increasing structural complexity, which allows us to extend conclusions made on simpler model systems. We begin by systematically describing the surface molecular composition and mechanical properties of polymers, copolymers, and blends having simple linear architectures. Subsequent chapters focus on networked hydrogel materials used as soft contact lenses and the adsorption of protein and surfactant at the polymer/liquid interface. The power of SFG is immediately demonstrated in experiments which identify the chemical parameters that influence the molecular composition and ordering of a polymer chain's side groups at the polymer/air and polymer/liquid interfaces. In general, side groups with increasingly greater hydrophobic character will be more surface active in air. Larger side groups impose steric restrictions, thus they will tend to be more randomly ordered than smaller hydrophobic groups. If exposed to a hydrophilic environment, such as water, the polymer chain will attempt to orient more of its hydrophilic groups to

  7. Fourth-Order Vibrational Transition State Theory and Chemical Kinetics

    Science.gov (United States)

    Stanton, John F.; Matthews, Devin A.; Gong, Justin Z.

    2015-06-01

    Second-order vibrational perturbation theory (VPT2) is an enormously successful and well-established theory for treating anharmonic effects on the vibrational levels of semi-rigid molecules. Partially as a consequence of the fact that the theory is exact for the Morse potential (which provides an appropriate qualitative model for stretching anharmonicity), VPT2 calculations for such systems with appropriate ab initio potential functions tend to give fundamental and overtone levels that fall within a handful of wavenumbers of experimentally measured positions. As a consequence, the next non-vanishing level of perturbation theory -- VPT4 -- offers only slight improvements over VPT2 and is not practical for most calculations since it requires information about force constants up through sextic. However, VPT4 (as well as VPT2) can be used for other applications such as the next vibrational correction to rotational constants (the ``gammas'') and other spectroscopic parameters. In addition, the marriage of VPT with the semi-classical transition state theory of Miller (SCTST) has recently proven to be a powerful and accurate treatment for chemical kinetics. In this talk, VPT4-based SCTST tunneling probabilities and cumulative reaction probabilities are give for the first time for selected low-dimensional model systems. The prospects for VPT4, both practical and intrinsic, will also be discussed.

  8. The application of value distribution theory to a doubly anharmonic oscillator

    Energy Technology Data Exchange (ETDEWEB)

    Hu Juan [Department of Applied Mathematics, Zhejiang University of Technology, Hangzhou 310023 (China); Yu Guofu, E-mail: gfyu@sjtu.edu.cn [Department of Mathematics, Shanghai Jiao Tong University, Shanghai 200240 (China)

    2011-07-22

    The model of doubly anharmonic oscillators is first transformed into certain periodic second ordinary differential equations. A class of exact solutions for eigenfunctions and eigenvalues is obtained from Bank and Laine's theory on periodic ordinary differential equations, which is expressed in the form of the products of the polynomial and exponential functions when parameters satisfy some special relations.

  9. Anharmonic resonance absorption of short laser pulses in clusters: A molecular dynamics simulation study

    Science.gov (United States)

    Mahalik, S. S.; Kundu, M.

    2016-12-01

    Linear resonance (LR) absorption of an intense 800 nm laser light in a nano-cluster requires a long laser pulse >100 fs when Mie-plasma frequency ( ω M ) of electrons in the expanding cluster matches the laser frequency (ω). For a short duration of the pulse, the condition for LR is not satisfied. In this case, it was shown by a model and particle-in-cell (PIC) simulations [Phys. Rev. Lett. 96, 123401 (2006)] that electrons absorb laser energy by anharmonic resonance (AHR) when the position-dependent frequency Ω [ r ( t ) ] of an electron in the self-consistent anharmonic potential of the cluster satisfies Ω [ r ( t ) ] = ω . However, AHR remains to be a debate and still obscure in multi-particle plasma simulations. Here, we identify AHR mechanism in a laser driven cluster using molecular dynamics (MD) simulations. By analyzing the trajectory of each MD electron and extracting its Ω [ r ( t ) ] in the self-generated anharmonic plasma potential, it is found that electron is outer ionized only when AHR is met. An anharmonic oscillator model, introduced here, brings out most of the features of MD electrons while passing the AHR. Thus, we not only bridge the gap between PIC simulations, analytical models, and MD calculations for the first time but also unequivocally prove that AHR process is a universal dominant collisionless mechanism of absorption in the short pulse regime or in the early time of longer pulses in clusters.

  10. Generalized Nonanalytic Expansions, PT-Symmetry and Large-Order Formulas for Odd Anharmonic Oscillators

    Directory of Open Access Journals (Sweden)

    Ulrich D. Jentschura

    2009-01-01

    Full Text Available The concept of a generalized nonanalytic expansion which involves nonanalytic combinations of exponentials, logarithms and powers of a coupling is introduced and its use illustrated in various areas of physics. Dispersion relations for the resonance energies of odd anharmonic oscillators are discussed, and higher-order formulas are presented for cubic and quartic potentials.

  11. Application of quasiexactly solvable potential method to the $N$-body problem of anharmonic oscillators

    Indian Academy of Sciences (India)

    PANAHI H; GAVABAR M MOHAMMADKAZEMI

    2016-05-01

    The quasiexactly solvable potential method is used to determine the energies and the corresponding exact eigenfunctions for a system of N particles with equal mass interacting via an anharmonic potential. For systems with five and seven particles, we compute the ground state and the first excited state only, and compare the spectrums with the results obtained by Ritz approximation method.

  12. Unified Treatment of Screening Coulomb and Anharmonic Oscillator Potentials in Arbitrary Dimensions

    Institute of Scientific and Technical Information of China (English)

    Bülent G(o)nül; Okan (O)zer; Mehmet Ko(c)ak

    2006-01-01

    A mapping is obtained relating radial screened Coulomb systems with low screening parameters to radial anharmonic oscillators in N-dimensional space. Using the formalism of supersymmetric quantum mechanics, it is shown that exact solutions of these potentials exist when the parameters satisfy certain constraints.

  13. Periodic permanent waves in an anharmonic chain with nearest-neighbour interaction

    NARCIS (Netherlands)

    Valkering, T.P.

    1978-01-01

    The existence of longitudinal periodic permanent waves in a one-dimensional translationally invariant anharmonic chain with nearest-neighbour interaction is established by means of variational methods. A general expression for the energy is given in terms of the dispersion relation. The interaction

  14. Numerical experiment of anharmonic oscillators by using the symplectic scheme-shooting method

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Symplectic scheme-shooting method (SSSM) is applied to solve the energy eigenvalues of anharmonic oscillators characterized by the potentials V(x)=λx4 and V(x)=(1/2)x2+λx2α with α=2,3,4 and doubly anharmonic oscillators characterized by the potentials V(x)=(1/2)x2+λ1x4+λ2x6, and a high order symplectic scheme tailored to the "time"-dependent Hamiltonian function is presented. The numerical results illustrate that the energy eigenvalues of anharmonic oscillators with the symplectic scheme-shooting method are in good agreement with the numerical accurate ones obtained from the non-perturbative method by using an appropriately scaled basis for the expansion of each eigenfunction; and the energy eigenvalues of doubly anharmonic oscillators with the sympolectic scheme-shooting method are in good agreement with the exact ones and are better than the results obtained from the four-term asymptotic series. Therefore, the symplectic scheme-shooting method, which is very simple and is easy to grasp, is a good numerical algorithm.

  15. Pyrrole Hydrogenation over Rh(111) and Pt(111) Single-Crystal Surfaces and Hydrogenation Promotion Mediated by 1-Methylpyrrole: A Kinetic and Sum-Frequency Generation Vibrational Spectroscopy Study

    Energy Technology Data Exchange (ETDEWEB)

    Kliewer, Christopher J.; Bieri, Marco; Somorjai, Gabor A.

    2008-03-04

    Sum-frequency generation (SFG) surface vibrational spectroscopy and kinetic measurements using gas chromatography have been used to study the adsorption and hydrogenation of pyrrole over both Pt(111) and Rh(111) single-crystal surfaces at Torr pressures (3 Torr pyrrole, 30 Torr H{sub 2}) to form pyrrolidine and the minor product butylamine. Over Pt(111) at 298 K it was found that pyrrole adsorbs in an upright geometry cleaving the N-H bond to bind through the nitrogen evidenced by SFG data. Over Rh(111) at 298 K pyrrole adsorbs in a tilted geometry relative to the surface through the p-aromatic system. A pyrroline surface reaction intermediate, which was not detected in the gas phase, was seen by SFG during the hydrogenation over both surfaces. Significant enhancement of the reaction rate was achieved over both metal surfaces by adsorbing 1-methylpyrrole before reaction. SFG vibrational spectroscopic results indicate that reaction promotion is achieved by weakening the bonding between the N-containing products and the metal surface because of lateral interactions on the surface between 1-methylpyrrole and the reaction species, reducing the desorption energy of the products. It was found that the ring-opening product butylamine was a reaction poison over both surfaces, but this effect can be minimized by treating the catalyst surfaces with 1-methylpyrrole before reaction. The reaction rate was not enhanced with elevated temperatures, and SFG suggests desorption of pyrrole at elevated temperatures.

  16. Sum Frequency Generation Vibrational Spectroscopy of 1,3-Butadiene Hydrogenation on 4 nm Pt@SiO 2 , Pd@SiO 2 , and Rh@SiO 2 Core–Shell Catalysts

    KAUST Repository

    Krier, James M.

    2015-01-14

    © 2014 American Chemical Society. 1,3-Butadiene (1,3-BD) hydrogenation was performed on 4 nm Pt, Pd, and Rh nanoparticles (NPs) encapsulated in SiO2 shells at 20, 60, and 100 °C. The core-shells were grown around polyvinylpyrrolidone (PVP) coated NPs (Stöber encapsulation) prepared by colloidal synthesis. Sum frequency generation (SFG) vibrational spectroscopy was performed to correlate surface intermediates observed in situ with reaction selectivity. It is shown that calcination is effective in removing PVP, and the SFG signal can be generated from the metal surface. Using SFG, it is possible to compare the surface vibrational spectrum of Pt@SiO2 (1,3-BD is hydrogenated through multiple paths and produces butane, 1-butene, and cis/trans-2-butene) to Pd@SiO2 (1,3-BD favors one path and produces 1-butene and cis/trans-2-butene). In contrast to Pt@SiO2 and Pd@SiO2, SFG and kinetic experiments of Rh@SiO2 show a permanent accumulation of organic material.

  17. Anharmonicity and phase stability of antiperovskite Li3OCl

    Science.gov (United States)

    Chen, Min-Hua; Emly, Alexandra; Van der Ven, Anton

    2015-06-01

    A lattice-dynamics study of the cubic Li3OCl antiperovskite, a candidate solid electrolyte in lithium-ion batteries, reveals the presence of dynamical instabilities with respect to rotations of the Li6O octahedra. Calculated energy landscapes in the subspace of unstable octahedral rotational modes are very shallow with at most a 1 meV per formula unit reduction in energy upon breaking the cubic symmetry. While Li3OCl is not stable relative to decomposition into Li2O and LiCl at 0 K, estimates of the vibrational free energy suggest that Li3OCl antiperovskite should become entropically stabilized above approximately 480 K.

  18. Molecular eigenstate spectroscopy: Application to the intramolecular dynamics of some polyatomic molecules in the 3000 to 7000 cm{sup {minus}1} region

    Energy Technology Data Exchange (ETDEWEB)

    Perry, D.S. [Univ. of Akron, OH (United States)

    1993-12-01

    Intramolecular vibrational redistribution (IVR) appears to be a universal property of polyatomic molecules in energy regions where the vibrational density of states is greater than about 5 to 30 states per cm{sup {minus}1}. Interest in IVR stems from its central importance to the spectroscopy, photochemistry, and reaction kinetics of these molecules. A bright state, {var_phi}{sub s}, which may be a C-H stretching vibration, carries the oscillator strength from the ground state. This bright state may mix with bath rotational-vibrational levels to form a clump of molecular eigenstates, each of which carries a portion of the oscillator strength from the ground state. In this work the authors explicitly resolve transitions to each of these molecular eigenstates. Detailed information about the nature of IVR is contained in the frequencies and intensities of the observed discrete transitions. The primary goal of this research is to probe the coupling mechanisms by which IVR takes place. The most fundamental distinction to be made is between anharmonic coupling which is independent of molecular rotation and rotationally-mediated coupling. The authors are also interested in the rate at which IVR takes place. Measurements are strictly in the frequency domain but information is obtained about the decay of the zero order state, {var_phi}{sub s}, which could be prepared in a hypothetical experiment as a coherent excitation of the clump of molecular eigenstates. As the coherent superposition dephases, the energy would flow from the initially prepared mode into nearby overtones and combinations of lower frequency vibrational modes. The decay of the initially prepared mode is related to a pure sequence infrared absorption spectrum by a Fourier transform.

  19. Deducing the molecular properties of zwitterionic, protonated, deprotonated, and double-deprotonated forms of L-cysteine from vibrational spectroscopy (IR, Raman, VCD) and quantum chemical calculations.

    Science.gov (United States)

    Quesada-Moreno, María Mar; Avilés-Moreno, Juan Ramón; Márquez-García, A A; López-González, Juan Jesús

    2014-06-01

    The behavior of L-cysteine (C3H7NO2S, (2R)-2-amino-3-sulfanylpropanoic acid) in water at different pH values was analyzed both experimentally and theoretically. The behavior was studied at pH values of 5.21 (at this pH, L-cysteine is a zwitterionic species), 1.00 (protonated species), 8.84 (monodeprotonated species), and 13.00 (dideprotonated species). We carried out a vibrational study using nonchiroptical (IR-Raman) and chiroptical (VCD) techniques complemented by quantum chemical calculations. We adopted a dual strategy, as follows. (i) The hybrid density functionals B3LYP and M062X and the ab initio MP2 method were employed, with the same 6-311++G (d,p) basis set, in order to characterize the relative energies and structures of an extensive set of conformers of L-cysteine. The presence of water was included by utilizing the IEF-PCM implicit solvation model. (ii) The vibrational analysis was made using a chirality-sensitive using a chirality-sensitive technique (VCD) and chirality-insensitive techniques (IR, including MIR and FIR, and Raman), especially in aqueous solution. The results obtained theoretically and experimentally were compared in order to deduce the most stable structures at each pH. Moreover, for the first time, the monodeprotonated anion of L-cysteine was detected in aqueous solution by means of IR, Raman and vibrational circular dichroism (VCD). Finally, analysis of the low-frequency region using the IR and Raman techniques was shown to be a very important way to understanding the conformational preference of the zwitterionic species.

  20. Direct observation of the cyclic dimer in liquid acetic acid by probing the C=O vibration with ultrafast coherent Raman spectroscopy.

    Science.gov (United States)

    Lütgens, Matthias; Friedriszik, Frank; Lochbrunner, Stefan

    2014-09-01

    We present a comparison of spontaneous Raman and ultrafast coherent anti-Stokes Raman scattering (CARS) spectra of the C=O vibration of liquid acetic acid. The former technique cannot clearly reveal the number of contributions in the spectrum. However, the additional time and spectrally resolved CARS experiment supports strictly the existence of four modes, which proves the coexistence of more than one H-bonded configuration in liquid acetic acid. A comparably slowly dephasing mode which is obscured by a broad band in the linear Raman spectrum is assigned to the cyclic dimer and can be observed freed from all other contributions by ultrafast CARS.

  1. Non-linear vibrational modes in biomolecules: A periodic orbits description

    Energy Technology Data Exchange (ETDEWEB)

    Kampanarakis, Alexandros [Department of Chemistry, University of Crete, and Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas (FORTH), Vasilika Vouton, Heraklion 71110, Crete (Greece); Farantos, Stavros C., E-mail: farantos@iesl.forth.gr [Department of Chemistry, University of Crete, and Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas (FORTH), Vasilika Vouton, Heraklion 71110, Crete (Greece); Daskalakis, Vangelis; Varotsis, Constantinos [Department of Environmental Science and Technology, Cyprus University of Technology, 31 Archbishop Kyprianos St., P.O. Box 50329, 3603 Lemesos (Cyprus)

    2012-05-03

    Graphical abstract: Vibrational frequency shifts in Fe{sup IV} = O species of the active site of cytochrome c oxidase are attributed to changes in the surrounding Coulomb field. Periodic orbits analysis assists to find the most anharmonic modes in model biomolecules. Highlights: Black-Right-Pointing-Pointer Periodic orbits are extended to multidimensional potentials of biomolecules. Black-Right-Pointing-Pointer Highly anharmonic vibrational modes and center-saddle bifurcations are detected. Black-Right-Pointing-Pointer Vibrational frequencies shifts in Oxoferryl species of CcO are observed. - Abstract: The vibrational harmonic normal modes of a molecule, which are valid at energies close to an equilibrium point (a minimum, maximum or saddle of the potential energy surface), are extended by periodic orbits to high energies where anharmonicity and coupling of the degrees of freedom are significant. In this way the assignment of the spectra, and thus the extraction of dynamics in highly excited molecules, can be obtained. New vibrational modes emanating from bifurcations of periodic orbits and long living localized trajectories signal the birth and localization of new quantum states. In this article we review and further study non-linear vibrational modes for model biomolecules such as alanine dipeptide and the active site in the oxoferryl oxidation state of the enzyme cytochrome c oxidase. We locate periodic orbits which exhibit high anhamonicity and lead to center-saddle bifurcations. These modes are associated to an isomerization process in alanine dipeptide and to frequency shifts in the oxoferryl observed by modifying the Coulomb field around the Imidazole-Fe{sup IV} = O species.

  2. Threshold photoelectron spectroscopy of unstable N-containing compounds: Resolution of ΔK subbands in HNCO{sup +} and vibrational resolution in NCO{sup +}

    Energy Technology Data Exchange (ETDEWEB)

    Holzmeier, Fabian; Lang, Melanie; Fischer, Ingo, E-mail: ingo.fischer@uni-wuerzburg.de [Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg (Germany); Tang, Xiaofeng [Synchrotron SOLEIL, l’Orme des Merisiers, Saint Aubin BP 48, F-91192 Gif sur Yvette Cedex (France); Cunha de Miranda, Barbara; Romanzin, Claire; Alcaraz, Christian [Laboratoire de Chimie-Physique, UMR 8000 CNRS and Université Paris-Sud 11, F-91405 Orsay Cedex (France); Hemberger, Patrick [Molecular Dynamics Group, Paul Scherrer Institute (PSI), CH-5232 Villigen (Switzerland)

    2015-05-14

    The threshold photoelectron spectra (TPES) of two unstable nitrogen-containing species, HNCO and NCO, were recorded utilizing vacuum ultraviolet synchrotron radiation. Both are intermediates in combustion processes and play a role in the removal of nitrogen oxides from exhaust gases. The rovibronic structure of the first band in the TPES of HNCO{sup +} was analyzed within the framework of an orbital ionization model, and the resolved structure of the origin band was assigned to ΔK subbands. An ionization energy of 11.602 ± 0.005 eV was determined and the vibrational structure of the cationic ground state was analyzed by a Franck-Condon fit. Low lying electronically excited states of HNCO{sup +} were also observed. In a second series of experiments, the NCO radical was generated by flash pyrolysis from chlorine isocyanate. The ionization energy to the X{sup +} {sup 3}Σ{sup −} ground state was determined to be 11.76 ± 0.02 eV, while for the a{sup +1}Δ state, a value of 12.93 ± 0.02 eV was obtained. Vibrational structure was observed for both states, and bands were assigned by Franck-Condon simulations.

  3. Infrared spectroscopy of OD vibrators in minerals at natural dilution: hydroxyl groups in talc and kaolinite, and structural water in beryl and emerald.

    Science.gov (United States)

    de Donato, Philippe; Cheilletz, Alain; Barres, Odile; Yvon, Jacques

    2004-05-01

    An infrared (IR) study of natural deuteration is conducted on minerals containing hydroxyl groups (talc and kaolinite) and channel-water-bearing minerals (beryl and emerald). In talc, the OD valence vibration is located at 2710 cm(-1), corresponding to OD groups surrounded by 3 Mg atoms. In kaolinite, the OD valence vibrations are located at 2671 cm(-1) (inner OD group), 2712, 2706, and 2700 cm(-1) (three inner-surface OD groups). In beryl and emerald, natural deuteration of channel water is observed for the first time by infrared microspectroscopy. In beryl from Minas Gerais (Brazil), the OD profiles are characterized by four bands at 2735, 2686, 2672, and 2641 cm(-1). In emeralds from Colombia and Brazil, the OD profiles are characterized by five or four bands, respectively, at 2816, 2737, 2685, 2673, and 2641 cm(-1) (Colombia) and 2730, 2684, 2672, and 2640 cm(-1) (Brazil). The band at 2816 cm(-1) can be assigned to -OD or OD(-), and bands at 2686-2684, 2673-2672, and 2641-2640 cm(-1) can be assigned to type-I and type-II HOD molecules. The band at 2737-2730 cm(-1) is partially disturbed by combination bands of the mineral. Such OD profiles are different from those obtained by artificial deuteration at higher OD dilution.

  4. On the limitation of density functional theory (DFT) for the treatment of the anharmonicity in FCC metals

    Science.gov (United States)

    Seifitokaldani, Ali; Gheribi, Aïmen E.; Dollé, Mickael

    2016-12-01

    It has been already shown that the density functional theory (DFT) combined with the quasi-harmonic approximation (QHA) overestimates the specific heat capacity (and in general the thermal properties) of fcc metals. DFT + QHA seemingly shows a large anharmonic contribution to the heat capacity. However, in this article we show that this anharmonicity has no physical origin and it is a consequence of the deviation of the QHA from the Maxwell relations. We show that one can simply avoid this overestimation by enforcing the QHA method to obey the Maxwell relations throughout the thermodynamically self-consistent (TSC) method, instead of considering non-real local anharmonic effects.

  5. Thermodynamics of Anharmonic Systems: Uncoupled Mode Approximations for Molecules.

    Science.gov (United States)

    Li, Yi-Pei; Bell, Alexis T; Head-Gordon, Martin

    2016-06-14

    The partition functions, heat capacities, entropies, and enthalpies of selected molecules were calculated using uncoupled mode (UM) approximations, where the full-dimensional potential energy surface for internal motions was modeled as a sum of independent one-dimensional potentials for each mode. The computational cost of such approaches scales the same with molecular size as standard harmonic oscillator vibrational analysis using harmonic frequencies (HO(hf)). To compute thermodynamic properties, a computational protocol for obtaining the energy levels of each mode was established. The accuracy of the UM approximation depends strongly on how the one-dimensional potentials of each modes are defined. If the potentials are determined by the energy as a function of displacement along each normal mode (UM-N), the accuracies of the calculated thermodynamic properties are not significantly improved versus the HO(hf) model. Significant improvements can be achieved by constructing potentials for internal rotations and vibrations using the energy surfaces along the torsional coordinates and the remaining vibrational normal modes, respectively (UM-VT). For hydrogen peroxide and its isotopologs at 300 K, UM-VT captures more than 70% of the partition functions on average. By contrast, the HO(hf) model and UM-N can capture no more than 50%. For a selected test set of C2 to C8 linear and branched alkanes and species with different moieties, the enthalpies calculated using the HO(hf) model, UM-N, and UM-VT are all quite accurate comparing with reference values though the RMS errors of the HO model and UM-N are slightly higher than UM-VT. However, the accuracies in entropy calculations differ significantly between these three models. For the same test set, the RMS error of the standard entropies calculated by UM-VT is 2.18 cal mol(-1) K(-1) at 1000 K. By contrast, the RMS error obtained using the HO model and UM-N are 6.42 and 5.73 cal mol(-1) K(-1), respectively. For a test set

  6. Computational Studies on the Anharmonic Dynamics of Molecular Clusters

    Science.gov (United States)

    Mancini, John S.

    Molecular nanoclusters present ideal systems to probe the physical forces and dynamics that drive the behavior of larger bulk systems. At the nanocluster limit the first instances of several phenomena can be observed including the breaking of hydrogen and molecular bonds. Advancements in experimental and theoretical techniques have made it possible to explore these phenomena in great detail. The most fruitful of these studies have involved the use of both experimental and theoretical techniques to leverage to strengths of the two approaches. This dissertation seeks to explore several important phenomena of molecular clusters using new and existing theoretical methodologies. Three specific systems are considered, hydrogen chloride clusters, mixed water and hydrogen chloride clusters and the first cluster where hydrogen chloride autoionization occurs. The focus of these studies remain as close as possible to experimentally observable phenomena with the intention of validating, simulating and expanding on experimental work. Specifically, the properties of interested are those related to the vibrational ground and excited state dynamics of these systems. Studies are performed using full and reduced dimensional potential energy surface alongside advanced quantum mechanical methods including diffusion Monte Carlo, vibrational configuration interaction theory and quasi-classical molecular dynamics. The insight gained from these studies are great and varied. A new on-they-fly ab initio method for studying molecular clusters is validated for (HCl)1--6. A landmark study of the dissociation energy and predissociation mechanism of (HCl)3 is reported. The ground states of mixed (HCl)n(H2O)m are found to be highly delocalized across multiple stationary point configurations. Furthermore, it is identified that the consideration of this delocalization is required in vibrational excited state calculations to achieve agreement with experimental measurements. Finally, the theoretical

  7. Mechanical model of carbon dioxide vibrational spectrum

    Science.gov (United States)

    Aldoshin, G. T.; Yakovlev, S. P.

    2016-12-01

    Classical dynamics methods have been used to study the nonlinear vibrations of a CO2 molecule. Consideration includes not only the anharmonicity valence angle, which enables one to explain the Fermi resonance, but also the physical nonlinearity of the force field (stiffness and softness of springs). In the farthest neighbor approximation (with regard to oxygen-oxygen interaction), a set of nonlinear differential equations in the Lagrangian form has been derived. Their analytical solution has been derived using the method of invariant normalization. The occurrence of a strange attractor has been discovered by numerical simulation. Recommendations for the selection of initial conditions are given that take into account the possibility of regular beatings that change into to chaotic beatings.

  8. Good Vibrations

    OpenAIRE

    Panesar, Lucy

    2007-01-01

    Good Vibrations was a market research exercise conducted by Felicity (my alter-ego) and assistants to help develop marketing and packaging for an electro-therapeutic device (vibrator) used to treat hysteria and other female stress related disorders. It was a live art work commissioned by The Live Art Development Agency for East End Collaborations on 6th May 2007 and the South London Gallery for Bonkersfest on 2nd June 2007.

  9. Vibration sensors

    Science.gov (United States)

    Gupta, Amita; Singh, Ranvir; Ahmad, Amir; Kumar, Mahesh

    2003-10-01

    Today, vibration sensors with low and medium sensitivities are in great demand. Their applications include robotics, navigation, machine vibration monitoring, isolation of precision equipment & activation of safety systems e.g. airbags in automobiles. Vibration sensors have been developed at SSPL, using silicon micromachining to sense vibrations in a system in the 30 - 200 Hz frequency band. The sensing element in the silicon vibration sensor is a seismic mass suspended by thin silicon hinges mounted on a metallized glass plate forming a parallel plate capacitor. The movement of the seismic mass along the vertical axis is monitored to sense vibrations. This is obtained by measuring the change in capacitance. The movable plate of the parallel plate capacitor is formed by a block connected to a surrounding frame by four cantilever beams located on sides or corners of the seismic mass. This element is fabricated by silicon micromachining. Several sensors in the chip sizes 1.6 cm x 1.6 cm, 1 cm x 1 cm and 0.7 cm x 0.7 cm have been fabricated. Work done on these sensors, techniques used in processing and silicon to glass bonding are presented in the paper. Performance evaluation of these sensors is also discussed.

  10. Toward feasible and comprehensive computational protocol for simulation of the spectroscopic properties of large molecular systems: the anharmonic infrared spectrum of uracil in the solid state by the reduced dimensionality/hybrid VPT2 approach.

    Science.gov (United States)

    Fornaro, Teresa; Carnimeo, Ivan; Biczysko, Malgorzata

    2015-05-28

    Feasible and comprehensive computational protocols for simulating the spectroscopic properties of large and complex molecular systems are very sought after. Indeed, due to the great variety of intra- and intermolecular interactions that may take place, the interpretation of experimental data becomes more and more difficult as the system under study increases in size or is placed in a complex environment, such as condensed phases. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes, with increasing complexity toward condensed phases and monolayers of biomolecules on solid supports. We have resorted to fully anharmonic quantum mechanical computations within the generalized second-order vibrational perturbation theory (GVPT2) approach, combined with the cost-effective B3LYP-D3 method, in conjunction with basis sets of double-ζ plus polarization quality. Such an approach has been validated in a previous work ( Phys. Chem. Chem. Phys. 2014 , 16 , 10112 - 10128 ) for simulating the IR spectra of the monomers of nucleobases and some of their dimers. In the present contribution we have extended such computational protocol to simulate spectroscopic properties of a molecular solid, namely polycrystalline uracil. First we have selected a realistic molecular model for representing the spectroscopic properties of uracil in the solid state, the uracil heptamer, and then we have computed the relative anharmonic frequencies combining less demanding approaches such as the hybrid B3LYP-D3/DFTBA one, in which the harmonic frequencies are computed at a higher level of theory (B3LYP-D3/N07D) whereas the anharmonic shifts are evaluated at a lower level of theory (DFTBA), and the reduced dimensionality VPT2 (RD-VPT2) approach, where only selected vibrational modes are computed anharmonically along with the couplings with other modes. The good agreement between the

  11. Theoretical investigation on the non-linear optical properties, vibrational spectroscopy and frontier molecular orbital of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide molecule.

    Science.gov (United States)

    Xiao-Hong, Li; Hong-Ling, Cui; Rui-Zhou, Zhang; Xian-Zhou, Zhang

    2015-02-25

    The vibrational frequencies of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide (HB-CA) in the ground state have been calculated using density functional method (B3LYP) with B3LYP/6-311++G(d,p) basis set. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exists C-H⋯O hydrogen bond in the title compound, which is confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as nonlinear optical material. The analysis of frontier molecular orbitals shows that HB-CA has high excitation energies, good stability and high chemical hardness. The analysis of MEP map shows the negative and the positive potential sites.

  12. Theoretical investigation on the non-linear optical properties, vibrational spectroscopy and frontier molecular orbital of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide molecule

    Science.gov (United States)

    Xiao-Hong, Li; Hong-Ling, Cui; Rui-Zhou, Zhang; Xian-Zhou, Zhang

    2015-02-01

    The vibrational frequencies of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide (HB-CA) in the ground state have been calculated using density functional method (B3LYP) with B3LYP/6-311++G(d,p) basis set. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exists Csbnd H⋯O hydrogen bond in the title compound, which is confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as nonlinear optical material. The analysis of frontier molecular orbitals shows that HB-CA has high excitation energies, good stability and high chemical hardness. The analysis of MEP map shows the negative and the positive potential sites.

  13. Contrasting organic aerosol particles from boreal and tropical forests during HUMPPA-COPEC-2010 and AMAZE-08 using coherent vibrational spectroscopy

    Directory of Open Access Journals (Sweden)

    C. J. Ebben

    2011-06-01

    Full Text Available We present the vibrational sum frequency generation spectra of organic particles collected in a boreal forest in Finland and a tropical forest in Brazil. These spectra are compared to those of secondary organic material produced in the Harvard Environmental Chamber. By comparing coherent vibrational spectra of a variety of terpene and olefin reference compounds, along with the secondary organic material synthesized in the environmental chamber, we show that submicron aerosol particles sampled in Southern Finland during HUMPPA-COPEC-2010 are composed to a large degree of material similar in chemical composition to synthetic α-pinene-derived material. For material collected in Brazil as part of AMAZE-08, the organic component is found to be chemically complex in the coarse mode but highly uniform in the fine mode. When combined with histogram analyses of the isoprene and monoterpene abundance recorded during the HUMPPA-COPEC-2010 and AMAZE-08 campaigns, the findings presented here indicate that if air is rich in monoterpenes, submicron-sized secondary aerosol particles that form under normal OH and O3 concentration levels can be described in terms of their hydrocarbon content as being similar to α-pinene-derived model secondary organic aerosol particles. If the isoprene concentration dominates the chemical composition of organic compounds in forest air, then the hydrocarbon component of secondary organic material in the submicron size range is not simply well-represented by that of isoprene-derived model secondary organic aerosol particles but is more complex. Throughout the climate-relevant size range of the fine mode, however, we find that the chemical composition of the secondary organic particle material from such air is invariant with size, suggesting that the particle growth does not change the chemical composition of the hydrocarbon component of the particles in a significant way.

  14. Contrasting organic aerosol particles from boreal and tropical forests during HUMPPA-COPEC-2010 and AMAZE-08 using coherent vibrational spectroscopy

    Directory of Open Access Journals (Sweden)

    C. J. Ebben

    2011-10-01

    Full Text Available We present the vibrational sum frequency generation spectra of organic particles collected in a boreal forest in Finland and a tropical forest in Brazil. These spectra are compared to those of secondary organic material produced in the Harvard Environmental Chamber. By comparing coherent vibrational spectra of a variety of terpene and olefin reference compounds, along with the secondary organic material synthesized in the environmental chamber, we show that submicron aerosol particles sampled in Southern Finland during HUMPPA-COPEC-2010 are composed to a large degree of material similar in chemical composition to synthetic α-pinene-derived material. For material collected in Brazil as part of AMAZE-08, the organic component is found to be chemically complex in the coarse mode but highly uniform in the fine mode. When combined with histogram analyses of the isoprene and monoterpene abundance recorded during the HUMPPA-COPEC-2010 and AMAZE-08 campaigns, the findings presented here indicate that if air is rich in monoterpenes, submicron-sized secondary aerosol particles that form under normal OH and O3 concentration levels can be described in terms of their hydrocarbon content as being similar to α-pinene-derived model secondary organic aerosol particles. If the isoprene concentration dominates the chemical composition of organic compounds in forest air, then the hydrocarbon component of secondary organic material in the submicron size range is not simply well-represented by that of isoprene-derived model secondary organic aerosol particles but is more complex. Throughout the climate-relevant size range of the fine mode, however, we find that the chemical composition of the secondary organic particle material from such air is invariant with size, suggesting that the particle growth does not change the chemical composition of the hydrocarbon component of the particles in a significant way.

  15. Combining gravimetric and vibrational spectroscopy measurements to quantify first- and second-shell hydration layers in polyimides with different molecular architectures.

    Science.gov (United States)

    Musto, Pellegrino; Mensitieri, Giuseppe; Lavorgna, Marino; Scarinzi, Gennaro; Scherillo, Giuseppe

    2012-02-02

    In-situ Fourier transform infrared (FTIR) measurements have been carried out at different relative pressures of water vapor to study the H(2)O diffusion in three polyimides differing in their molecular structure and fluorine substitution. Spectral data have been analyzed by difference spectroscopy, least-squares curve fitting, and two-dimensional (2D) correlation spectroscopy, which provided molecular level information on the diffusion mechanism. In particular, two distinct water species were identified corresponding, respectively, to the first and second-shell hydration layers. The spectroscopic analysis demonstrated that the relative population of these species is a function of the total water content in the system. A method has been devised to quantify the water concentration in the two hydration layers, based on a combination of spectroscopic and gravimetric data. The results have been compared with those from an earlier spectroscopic approach reported in the literature and based on the analysis of the carbonyl region.

  16. A Review on the Role of Vibrational Spectroscopy as An Analytical Method to Measure Starch Biochemical and Biophysical Properties in Cereals and Starchy Foods

    Directory of Open Access Journals (Sweden)

    D. Cozzolino

    2014-12-01

    Full Text Available Starch is the major component of cereal grains and starchy foods, and changes in its biophysical and biochemical properties (e.g., amylose, amylopectin, pasting, gelatinization, viscosity will have a direct effect on its end use properties (e.g., bread, malt, polymers. The use of rapid and non-destructive methods to study and monitor starch properties, such as gelatinization, retrogradation, water absorption in cereals and starchy foods, is of great interest in order to improve and assess their quality. In recent years, near infrared reflectance (NIR and mid infrared (MIR spectroscopy have been explored to predict several quality parameters, such as those generated by instrumental methods commonly used in routine analysis like the rapid visco analyser (RVA or viscometers. In this review, applications of both NIR and MIR spectroscopy to measure and monitor starch biochemical (amylose, amylopectin, starch and biophysical properties (e.g., pasting properties will be presented and discussed.

  17. Mid-infrared upconversion spectroscopy

    DEFF Research Database (Denmark)

    Tidemand-Lichtenberg, Peter; Dam, Jeppe Seidelin; Andersen, H. V.

    2016-01-01

    Mid-infrared (MIR) spectroscopy is emerging as an attractive alternative to near-infrared or visible spectroscopy. MIR spectroscopy offers a unique possibility to probe the fundamental absorption bands of a large number of gases as well as the vibrational spectra of complex molecules. In this paper...

  18. Analysis of red and yellow ochre samples from Clearwell Caves and Çatalhöyük by vibrational spectroscopy and other techniques

    Science.gov (United States)

    Mortimore, Joanne L.; Marshall, Lisa-Jane R.; Almond, Matthew J.; Hollins, Peter; Matthews, Wendy

    2004-04-01

    Ochre samples excavated from the neolithic site at Çatalhöyük, Turkey have been compared with "native" ochres from Clearwell Caves, UK using infrared spectroscopy backed up by Raman spectroscopy, scanning electron microscopy (with energy-dispersive X-rays (EDX) analysis), powder X-ray diffraction, diffuse reflection UV-Vis and atomic absorption spectroscopies. For the Clearwell Caves ochres, which range in colour from yellow-orange to red-brown, it is shown that the colour is related to the nature of the chromophore present and not to any differences in particle size. The darker red ochres contain predominantly haematite while the yellow ochre contains only goethite. The ochres from Çatalhöyük contain only about one-twentieth of the levels of iron found in the Clearwell Caves ochres. The iron oxide pigment (haematite in all cases studied here) has been mixed with a soft lime plaster which also contains calcite and silicate (clay) minerals.

  19. Analysis of red and yellow ochre samples from Clearwell Caves and Catalhöyük by vibrational spectroscopy and other techniques.

    Science.gov (United States)

    Mortimore, Joanne L; Marshall, Lisa-Jane R; Almond, Matthew J; Hollins, Peter; Matthews, Wendy

    2004-04-01

    Ochre samples excavated from the neolithic site at Catalhöyük, Turkey have been compared with "native" ochres from Clearwell Caves, UK using infrared spectroscopy backed up by Raman spectroscopy, scanning electron microscopy (with energy-dispersive X-rays (EDX) analysis), powder X-ray diffraction, diffuse reflection UV-Vis and atomic absorption spectroscopies. For the Clearwell Caves ochres, which range in colour from yellow-orange to red-brown, it is shown that the colour is related to the nature of the chromophore present and not to any differences in particle size. The darker red ochres contain predominantly haematite while the yellow ochre contains only goethite. The ochres from Catalhöyük contain only about one-twentieth of the levels of iron found in the Clearwell Caves ochres. The iron oxide pigment (haematite in all cases studied here) has been mixed with a soft lime plaster which also contains calcite and silicate (clay) minerals.

  20. Mid-Infrared Pulse Shaping and Two-Dimensional Spectroscopy of Open Quantum Systems in Liquid Solution

    Science.gov (United States)

    Ross, Matthew R.

    The primary focus of this work is the development of a mid-infrared pulse shaping system. The primary motivation for this system is for two-dimensional infrared (2DIR) spectroscopy, however, the mid-infrared pulse shaper also allows for more sophisticated spectroscopic experiments not previously attempted in the mid-infrared. Moreover, many can be implemented without changes or realignment of the optical setup. Example spectra are presented along with a discussion of capabilities and diagnostics. A second major project presented is 2DIR spectroscopy of iron pentacarbonyl, Fe(CO)5, a small metal carbonyl. This molecule undergoes Berry pseudorotation, a form of fluxtionality. This fast exchange of ligands mixes axial and equatorial modes and occurs on a timescale of picoseconds, too fast for NMR and other methods of measuring chemical structure and isomerization. Ultrafast chemical exchange spectroscopy, a measurement within 2DIR spectroscopy, is capable of resolving the time scales of this motion. We found that this process is affected by the solvent environment, specifically the solvent viscosity in alkanes and hydrogen bonding environments in alcohols. Lastly, a study is presented in which a series of synthetic metalloenzymes with a metal active site are studied by 2DIR spectroscopy. In this case a carbonyl is ligated to a copper-I atom in the active site, which then serves as our spectroscopic probe. We find, unexpectedly, that the shape of the carbonyl vibrational potential, as measured by the anharmonicity, is time-dependent. We attribute this to a geometrical rearrangement and are able to suggest that this effect is dependent on local site structure and dynamics and not significantly affected by electric potential near the peptide.