Science.gov

Sample records for biomedical vibrational spectroscopy

  1. Vibrational Spectroscopy of Biomembranes

    NASA Astrophysics Data System (ADS)

    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.

  2. 2008 Vibrational Spectroscopy

    SciTech Connect

    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 Echo Correlation Spectroscopy

    NASA Astrophysics Data System (ADS)

    Asbury, John B.; Steinel, Tobias; Fayer, M. D.

    Multidimensional vibrational echo correlation spectroscopy with full phase resolution is used to measure hydrogen bond dynamics in water and methanol. The OD hydroxyl stretches of methanol-OD oligomers in CCl4 and HOD inH2O are studied using the shortest mid-IR pulses (< 45 fs, < 4 cycles of light) produced to date. The pulses have sufficient spectral bandwidth to span the very broad (> 400 cm-1) spectrum of the 0-1 and 1-2 vibrational transitions. Hydrogen bond population dynamics are extricated with exceptional detail in MeOD oligomers because the different hydrogen-bonded species are spectrally distinct. The experimental results along with detailed calculations indicate the strongest hydrogen bonds are selectively broken through a non-equilibrium relaxation pathway following vibrational relaxation of the hydroxyl stretch. Following hydrogen bond breaking, the broken MeOD oligomers retain a detailed structural memory of the prior intact hydrogen bond network. The correlation spectra are also a sensitive probe of the structural fluctuations in water and provide a stringent test of water models that are widely used in simulations of aqueous systems. The analysis of the 2D band shapes demonstrates that different hydrogen-bonded species are subject to distinct (wavelength-dependent) ultrafast (˜ 100 fs) local fluctuations and essentially identical slower (0.4 ps and ˜ 2 ps) structural rearrangements. Observation of wavelength-dependent dynamics demonstrates that standard theoretical approaches assuming Gaussian fluctuations cannot adequately describe water dynamics.

  4. Vibrational spectroscopy of stichtite

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; Erickson, Kristy L.

    2004-11-01

    Raman spectroscopy complimented with infrared spectroscopy has been used to study the mineral stitchtite, a hydrotalcite of formula Mg 6Cr 2(CO 3)(OH) 16·4H 2O. Two bands are observed at 1087 and 1067 cm -1 with an intensity ratio of ˜2.5/1 and are attributed to the symmetric stretching vibrations of the carbonate anion. The observation of two bands is attributed to two species of carbonate in the interlayer, namely weakly hydrogen bonded and strongly hydrogen bonded. Two infrared bands are found at 1457 and 1381 cm -1 and are assigned to the antisymmetric stretching modes. These bands were not observed in the Raman spectrum. Two infrared bands are observed at 744 and 685 cm -1 and are assigned to the ν4 bending modes. Two Raman bands were observed at 539 and 531 cm -1 attributed to the ν2 bending modes. Importantly the band positions of the paragenically related hydrotalcites stitchtite, iowaite, pyroaurite and reevesite all of which contain the carbonate anion occur at different wavenumbers. Consequently, Raman spectroscopy can be used to distinguish these minerals, particularly in the field where many of these hydrotalcites occur simultaneously in ore zones.

  5. Vibrational spectroscopy of resveratrol

    NASA Astrophysics Data System (ADS)

    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.

  6. Biomedical Applications of Terahertz Spectroscopy and Imaging.

    PubMed

    Yang, Xiang; Zhao, Xiang; Yang, Ke; Liu, Yueping; Liu, Yu; Fu, Weiling; Luo, Yang

    2016-10-01

    Terahertz (THz=10(12)Hz) radiation has attracted wide attention for its unprecedented sensing ability and its noninvasive and nonionizing properties. Tremendous strides in THz instrumentation have prompted impressive breakthroughs in THz biomedical research. Here, we review the current state of THz spectroscopy and imaging in various biomedical applications ranging from biomolecules, including DNA/RNA, amino acids/peptides, proteins, and carbohydrates, to cells and tissues. We also address the potential biological effects of THz radiation during its biological applications and propose future prospects for this cutting-edge technology.

  7. TIME-RESOLVED VIBRATIONAL SPECTROSCOPY

    SciTech Connect

    Andrei Tokmakoff, MIT; 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.

  8. Infrared spectroscopy in biomedical diagnostics

    NASA Astrophysics Data System (ADS)

    Afanasyeva, Natalia I.; Kolyakov, Sergei F.; Letokhov, Vladilen S.; Artioushenko, Vjacheslav G.; Golovkina, Viktoriya N.

    1998-01-01

    Fiberoptic evanescent wave Fourier transform infrared (FEW- FTIR) spectroscopy using fiberoptic sensors operated in the attenuated total reflection (ATR) regime in the middle infrared (IR) region of the spectrum (850 - 1850 cm-1) has recently found application in the diagnostics of tissues. The method is suitable for noninvasive and rapid (seconds) direct measurements of the spectra of normal and pathological tissues in vitro, ex vivo and in vivo. The aim of our studies is the express testing of various tumor tissues at the early stages of their development. The method is expected to be further developed for endoscopic and biopsy applications. We measured in vivo the skin normal and malignant tissues on surface (directly on patients) in various cases of basaloma, melanoma and nevus. The experiments were performed in the operating room for measurements of skin in the depth (under/in the layers of epidermis), human breast, stomach, lung, kidney tissues. The breast and skin tissues at different stages of tumor or cancer were distinguished very clearly in spectra of amide, side cyclic and noncyclic hydrogen bonded fragments of amino acid residuals, phosphate groups and sugars. Computer monitoring is being developed for diagnostics.

  9. Biomedical applications of laser spectroscopy

    NASA Astrophysics Data System (ADS)

    Svanberg, Sune

    1999-07-01

    Very soon after the invention of the laser, the use of the thermal effects of the radiation was introduced. Such techniques have been refined and the laser is now routinely used for treatment in many specialities. Photodynamic therapy (PDT) is a non-thermal modality employing the combination of a tumor-seeking agent and activating laser light. During the last 15 years laser spectroscopic techniques have also been developed providing powerful means for non-intrusive medical diagnostics of tissue in real time. At the beginning only few groups were involved in exploratory work, but successively the field has developed now to occupy a large number of research teams, which meet at large specialized conferences. We will here consider three aspects of laser diagnostics: fluorescence, Raman and near-IR, and elastic scattering spectroscopy, and we will also briefly discuss PDT. The activity in the field is very extensive, and rather than trying to give a full overview, illustrations from work performed at the Lund University Medical Laser Center will be given.

  10. Probing zeolites by vibrational spectroscopies.

    PubMed

    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.

  11. Soil chemical insights provided through vibrational spectroscopy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vibrational spectroscopy techniques provide a powerful approach to study environmental materials and processes. These multifunctional analysis tools can be used to probe molecular vibrations of solid, liquid, and gaseous samples for characterizing materials, elucidating reaction mechanisms, and exam...

  12. Vibrational spectroscopy of HNS degradation

    NASA Astrophysics Data System (ADS)

    Alam, M. Kathleen; Martin, Laura; Schmitt, Randal L.; Ten Eyck, Gregory A.; Welle, Eric

    2008-08-01

    Hexanitrostilbene (HNS) is a widely used explosive, due in part to its high thermal stability. Degradation of HNS is known to occur through UV, chemical exposure, and heat exposure, which can lead to reduced performance of the material. Common methods of testing for HNS degradation include wet chemical and surface area testing of the material itself, and performance testing of devices that use HNS. The commonly used chemical tests, such as volatility, conductivity and contaminant trapping provide information on contaminants rather than the chemical stability of the HNS itself. Additionally, these tests are destructive in nature. As an alternative to these methods, we have been exploring the use of vibrational spectroscopy as a means of monitoring HNS degradation non-destructively. In particular, infrared (IR) spectroscopy lends itself well to non-destructive analysis. Molecular variations in the material can be identified and compared to pure samples. The utility of IR spectroscopy was evaluated using pressed pellets of HNS exposed to DETA (diethylaminetriamine). Amines are known to degrade HNS, with the proposed product being a σ-adduct. We have followed these changes as a function of time using various IR sampling techniques including photoacoustic and attenuated total reflectance (ATR).

  13. Vibrational spectroscopy of water interfaces

    SciTech Connect

    Du, Q.

    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.

  14. Probing vibrational anisotropy with nuclear resonance vibrational spectroscopy.

    SciTech Connect

    Pavlik, J. W.; Barabanschikov, A.; Oliver, A. G.; Alp, E. E.; Sturhahn, W.; Zhao, J.; Sage, J. T.; Scheidt, W. R.

    2010-06-14

    A NRVS single-crystal study (NRVS=nuclear resonance vibrational spectroscopy) has provided detailed information on the in-plane modes of nitrosyl iron porphyrinate [Fe(oep)(NO)] (see picture; oep=octaethylporphyrin). The axial nitrosyl ligand controls the direction of the in-plane iron motion.

  15. Vibrational spectroscopy in high temperature dense fluids

    SciTech Connect

    Moore, D.S.; Schmidt, S.C.

    1992-01-01

    Coherent anti-Stokes Raman spectroscopy (CARS) in conjunction with a two-stage light-gas gun has been used to obtain vibrational spectra of shock-compressed liquid N{sub 2}, O{sub 2}, CO, and their mixtures, as well as liquid N{sub 2}O. The experimental spectra are compared to spectra calculated using a semiclassical model for CARS intensities to obtain vibrational frequencies, peak Raman susceptibilities, and linewidths. The derived spectroscopic parameters suggest thermal equilibrium of the vibrational populations is established in less than a few nanoseconds after shock passage. Vibrational temperatures obtained are compared to those derived from equation-of-state calculations. The variation of the vibrational frequency shift at pressure with species concentration in mixtures is investigated.

  16. Vibrational Spectroscopy and Dynamics of Water.

    PubMed

    Perakis, Fivos; Marco, Luigi De; Shalit, Andrey; Tang, Fujie; Kann, Zachary R; Kühne, Thomas D; Torre, Renato; Bonn, Mischa; Nagata, Yuki

    2016-07-13

    We present an overview of recent static and time-resolved vibrational spectroscopic studies of liquid water from ambient conditions to the supercooled state, as well as of crystalline and amorphous ice forms. The structure and dynamics of the complex hydrogen-bond network formed by water molecules in the bulk and interphases are discussed, as well as the dissipation mechanism of vibrational energy throughout this network. A broad range of water investigations are addressed, from conventional infrared and Raman spectroscopy to femtosecond pump-probe, photon-echo, optical Kerr effect, sum-frequency generation, and two-dimensional infrared spectroscopic studies. Additionally, we discuss novel approaches, such as two-dimensional sum-frequency generation, three-dimensional infrared, and two-dimensional Raman terahertz spectroscopy. By comparison of the complementary aspects probed by various linear and nonlinear spectroscopic techniques, a coherent picture of water dynamics and energetics emerges. Furthermore, we outline future perspectives of vibrational spectroscopy for water researches.

  17. Two-dimensional vibrational-electronic spectroscopy

    NASA Astrophysics Data System (ADS)

    Courtney, Trevor L.; Fox, Zachary W.; Slenkamp, Karla M.; Khalil, Munira

    2015-10-01

    Two-dimensional vibrational-electronic (2D VE) spectroscopy is a femtosecond Fourier transform (FT) third-order nonlinear technique that creates a link between existing 2D FT spectroscopies in the vibrational and electronic regions of the spectrum. 2D VE spectroscopy enables a direct measurement of infrared (IR) and electronic dipole moment cross terms by utilizing mid-IR pump and optical probe fields that are resonant with vibrational and electronic transitions, respectively, in a sample of interest. We detail this newly developed 2D VE spectroscopy experiment and outline the information contained in a 2D VE spectrum. We then use this technique and its single-pump counterpart (1D VE) to probe the vibrational-electronic couplings between high frequency cyanide stretching vibrations (νCN) and either a ligand-to-metal charge transfer transition ([FeIII(CN)6]3- dissolved in formamide) or a metal-to-metal charge transfer (MMCT) transition ([(CN)5FeIICNRuIII(NH3)5]- dissolved in formamide). The 2D VE spectra of both molecules reveal peaks resulting from coupled high- and low-frequency vibrational modes to the charge transfer transition. The time-evolving amplitudes and positions of the peaks in the 2D VE spectra report on coherent and incoherent vibrational energy transfer dynamics among the coupled vibrational modes and the charge transfer transition. The selectivity of 2D VE spectroscopy to vibronic processes is evidenced from the selective coupling of specific νCN modes to the MMCT transition in the mixed valence complex. The lineshapes in 2D VE spectra report on the correlation of the frequency fluctuations between the coupled vibrational and electronic frequencies in the mixed valence complex which has a time scale of 1 ps. The details and results of this study confirm the versatility of 2D VE spectroscopy and its applicability to probe how vibrations modulate charge and energy transfer in a wide range of complex molecular, material, and biological systems.

  18. Two-dimensional vibrational-electronic spectroscopy

    SciTech Connect

    Courtney, Trevor L.; Fox, Zachary W.; Slenkamp, Karla M.; Khalil, Munira

    2015-10-21

    Two-dimensional vibrational-electronic (2D VE) spectroscopy is a femtosecond Fourier transform (FT) third-order nonlinear technique that creates a link between existing 2D FT spectroscopies in the vibrational and electronic regions of the spectrum. 2D VE spectroscopy enables a direct measurement of infrared (IR) and electronic dipole moment cross terms by utilizing mid-IR pump and optical probe fields that are resonant with vibrational and electronic transitions, respectively, in a sample of interest. We detail this newly developed 2D VE spectroscopy experiment and outline the information contained in a 2D VE spectrum. We then use this technique and its single-pump counterpart (1D VE) to probe the vibrational-electronic couplings between high frequency cyanide stretching vibrations (ν{sub CN}) and either a ligand-to-metal charge transfer transition ([Fe{sup III}(CN){sub 6}]{sup 3−} dissolved in formamide) or a metal-to-metal charge transfer (MMCT) transition ([(CN){sub 5}Fe{sup II}CNRu{sup III}(NH{sub 3}){sub 5}]{sup −} dissolved in formamide). The 2D VE spectra of both molecules reveal peaks resulting from coupled high- and low-frequency vibrational modes to the charge transfer transition. The time-evolving amplitudes and positions of the peaks in the 2D VE spectra report on coherent and incoherent vibrational energy transfer dynamics among the coupled vibrational modes and the charge transfer transition. The selectivity of 2D VE spectroscopy to vibronic processes is evidenced from the selective coupling of specific ν{sub CN} modes to the MMCT transition in the mixed valence complex. The lineshapes in 2D VE spectra report on the correlation of the frequency fluctuations between the coupled vibrational and electronic frequencies in the mixed valence complex which has a time scale of 1 ps. The details and results of this study confirm the versatility of 2D VE spectroscopy and its applicability to probe how vibrations modulate charge and energy transfer in a

  19. Vibrational Spectroscopy of Chromatographic Interfaces

    SciTech Connect

    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.

  20. Vibrational Spectroscopy on Trapped Cold Molecular Ions

    NASA Astrophysics Data System (ADS)

    Khanyile, Ncamiso B.; Brown, Kenneth R.

    2014-06-01

    We perform vibrational spectroscopy on the V0←10 overtone of a trapped and sympathetically cooled CaH+ molecular ion using a resonance enhanced two photon dissociation scheme. Our experiments are motivated by theoretical work that proposes comparing the vibrational overtones of CaH^+ with electronic transitions in atoms to detect possible time variation of in the mass ratio of the proton to electron. Due to the nonexistence of experimental data of the transition, we start the search with a broadband femtosecond Ti:Saph laser guided by theoretical calculations. Once the vibrational transition has been identified, we will move to CW lasers to perform rotationally resolved spectroscopy. M. Kajita and Y. Moriwaki, J. Phys. B. At. Mol. Opt.Phys., 42,154022(2009) Private communication

  1. Anharmonic Theoretical Vibrational Spectroscopy of Polypeptides.

    PubMed

    Panek, Paweł T; Jacob, Christoph R

    2016-08-18

    Because of the size of polypeptides and proteins, the quantum-chemical prediction of their vibrational spectra presents an exceptionally challenging task. Here, we address one of these challenges, namely, the inclusion of anharmonicities. By performing the expansion of the potential energy surface in localized-mode coordinates instead of the normal-mode coordinates, it becomes possible to calculate anharmonic vibrational spectra of polypeptides efficiently and reliably. We apply this approach to calculate the infrared, Raman, and Raman optical activity spectra of helical alanine polypeptides consisting of up to 20 amino acids. We find that while anharmonicities do not alter the band shapes, simple scaling procedures cannot account for the different shifts found for the individual bands. This closes an important gap in theoretical vibrational spectroscopy by making it possible to quantify the anharmonic contributions and opens the door to a first-principles calculation of multidimensional vibrational spectra. PMID:27472016

  2. Vibrational spectroscopy in shock-compressed liquids

    SciTech Connect

    Schmidt, S.C.; Moore, D.S.

    1992-01-01

    Coherent anti-Stokes Raman spectroscopy is being used to study the structure and energy transfer in simple molecular liquids at the high pressures and temperatures characteristic of explosive detonation. Dense fluids to several thousand degrees temperature and several hundred kilobars pressure are obtained using the shock-compression technique. Vibrational frequencies, third-order susceptibility ratios, and linewidths have been measured for N{sub 2}, O{sub 2}, CO, mixtures of N{sub 2}, O{sub 2}, and CO, and N{sub 2}O. Frequencies are found to increase with pressure. The transition intensity and line-width data suggest that thermal equilibrium of the vibrational levels is attained in less than a few nanoseconds at these high pressures and temperatures. Vibrational temperatures obtained are compared to those derived from equation-of-state calculations.

  3. Vibrational spectroscopy in shock-compressed liquids

    SciTech Connect

    Schmidt, S.C.; Moore, D.S.

    1992-03-01

    Coherent anti-Stokes Raman spectroscopy is being used to study the structure and energy transfer in simple molecular liquids at the high pressures and temperatures characteristic of explosive detonation. Dense fluids to several thousand degrees temperature and several hundred kilobars pressure are obtained using the shock-compression technique. Vibrational frequencies, third-order susceptibility ratios, and linewidths have been measured for N{sub 2}, O{sub 2}, CO, mixtures of N{sub 2}, O{sub 2}, and CO, and N{sub 2}O. Frequencies are found to increase with pressure. The transition intensity and line-width data suggest that thermal equilibrium of the vibrational levels is attained in less than a few nanoseconds at these high pressures and temperatures. Vibrational temperatures obtained are compared to those derived from equation-of-state calculations.

  4. Modeling, calculating, and analyzing multidimensional vibrational spectroscopies.

    PubMed

    Tanimura, Yoshitaka; Ishizaki, Akihito

    2009-09-15

    Spectral line shapes in a condensed phase contain information from various dynamic processes that modulate the transition energy, such as microscopic dynamics, inter- and intramolecular couplings, and solvent dynamics. Because nonlinear response functions are sensitive to the complex dynamics of chemical processes, multidimensional vibrational spectroscopies can separate these processes. In multidimensional vibrational spectroscopy, the nonlinear response functions of a molecular dipole or polarizability are measured using ultrashort pulses to monitor inter- and intramolecular vibrational motions. Because a complex profile of such signals depends on the many dynamic and structural aspects of a molecular system, researchers would like to have a theoretical understanding of these phenomena. In this Account, we explore and describe the roles of different physical phenomena that arise from the peculiarities of the system-bath coupling in multidimensional spectra. We also present simple analytical expressions for a weakly coupled multimode Brownian system, which we use to analyze the results obtained by the experiments and simulations. To calculate the nonlinear optical response, researchers commonly use a particular form of a system Hamiltonian fit to the experimental results. The optical responses of molecular vibrational motions have been studied in either an oscillator model or a vibration energy state model. In principle, both models should give the same results as long as the energy states are chosen to be the eigenstates of the oscillator model. The energy state model can provide a simple description of nonlinear optical processes because the diagrammatic Liouville space theory that developed in the electronically resonant spectroscopies can easily handle three or four energy states involved in high-frequency vibrations. However, the energy state model breaks down if we include the thermal excitation and relaxation processes in the dynamics to put the system in a

  5. Vibrational Spectroscopy and Dynamics of Water.

    PubMed

    Perakis, Fivos; Marco, Luigi De; Shalit, Andrey; Tang, Fujie; Kann, Zachary R; Kühne, Thomas D; Torre, Renato; Bonn, Mischa; Nagata, Yuki

    2016-07-13

    We present an overview of recent static and time-resolved vibrational spectroscopic studies of liquid water from ambient conditions to the supercooled state, as well as of crystalline and amorphous ice forms. The structure and dynamics of the complex hydrogen-bond network formed by water molecules in the bulk and interphases are discussed, as well as the dissipation mechanism of vibrational energy throughout this network. A broad range of water investigations are addressed, from conventional infrared and Raman spectroscopy to femtosecond pump-probe, photon-echo, optical Kerr effect, sum-frequency generation, and two-dimensional infrared spectroscopic studies. Additionally, we discuss novel approaches, such as two-dimensional sum-frequency generation, three-dimensional infrared, and two-dimensional Raman terahertz spectroscopy. By comparison of the complementary aspects probed by various linear and nonlinear spectroscopic techniques, a coherent picture of water dynamics and energetics emerges. Furthermore, we outline future perspectives of vibrational spectroscopy for water researches. PMID:27096701

  6. Analytical methods of laser spectroscopy for biomedical applications

    NASA Astrophysics Data System (ADS)

    Martyshkin, Dmitri V.

    Different aspects of the application of laser spectroscopy in biomedical research have been considered. A growing demand for molecular sensing techniques in biomedical and environmental research has led the introduction of existing spectroscopic techniques, as well as development of new methods. The applications of laser-induced fluorescence, Raman scattering, cavity ring-down spectroscopy, and laser-induced breakdown spectroscopy for the monitoring of superoxide dismutase (SOD) and hemoglobin levels, the study of the characteristics of light-curing dental restorative materials, and the environmental monitoring of levels of toxic metal ion is presented. The development of new solid-state tunable laser sources based on color center crystals for these applications is presented as well.

  7. New developments in IR surface vibrational spectroscopy

    SciTech Connect

    Hirschmugl, C.J.; Lamont, C.L.A.; Williams, G.P.

    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.

  8. Vibrational spectroscopy of N-phenylmaleimide.

    PubMed

    Parker, Stewart F

    2006-03-01

    A combination of infrared, Raman and inelastic neutron scattering (INS) spectroscopies with density functional theory (DFT) calculations is used to provide a complete assignment of the vibrational spectra of N-phenylmaleimide and N-(perdeuterophenyl)maleimide. DFT is shown to give very good results for the frequencies and atomic displacements in the modes. These are used to generate INS spectra which are excellent agreement with the observed. The calculated infrared and Raman spectra are much less reliable, although this may be more of a presentation problem than a real failing. PMID:16157505

  9. Progress towards two-dimensional biomedical imaging with THz spectroscopy

    NASA Astrophysics Data System (ADS)

    Beard, Matthew C.; Turner, Gordon M.; Schmuttenmaer, Charles A.

    2002-11-01

    Terahertz spectroscopy represents a frontier in the field of biomedical imaging. It is possible to image complex objects that are opaque to visible and infrared light. In this paper, we have used THz imaging to reveal the structure inside a sunflower seed. We compare images based on time- and frequency-domain representations of the THz scans, and conclude that for this type of specimen the time-domain THz scans provide more detailed information than their frequency-domain counterparts.

  10. Vibrational spectroscopy of water at interfaces.

    PubMed

    Skinner, J L; Pieniazek, P A; Gruenbaum, S M

    2012-01-17

    Understanding liquid water's behavior at the molecular level is essential to progress in fields as disparate as biology and atmospheric sciences. Moreover, the properties of water in bulk and water at interfaces can be very different, making the study of the hydrogen-bonding networks therein very important. With recent experimental advances in vibrational spectroscopy, such as ultrafast pulses and heterodyne detection, it is now possible to probe the structure and dynamics of bulk and interfacial water in unprecedented detail. We consider here three aqueous interfaces: the water liquid-vapor interface, the interface between water and the surfactant headgroups of reverse micelles, and the interface between water and the lipid headgroups of aligned multi-bilayers. In the first case, sum-frequency spectroscopy is used to probe the interface. In the second and third cases, the confined water pools are sufficiently small that techniques of bulk spectroscopy (such as FTIR, pump-probe, two-dimensional IR, and the like) can be used to probe the interfacial water. In this Account, we discuss our attempts to model these three systems and interpret the existing experiments. For the water liquid-vapor interface, we find that three-body interactions are essential for reproducing the experimental sum-frequency spectrum, and presumably for the structure of the interface as well. The observed spectrum is interpreted as arising from overlapping and canceling positive and negative contributions from molecules in different hydrogen-bonding environments. For the reverse micelles, our theoretical models confirm that the experimentally observed blue shift of the water OD stretch (for dilute HOD in H(2)O) arises from weaker hydrogen bonding to sulfonate oxygens. We interpret the observed slow-down in water rotational dynamics as arising from curvature-induced frustration. For the water confined between lipid bilayers, our theoretical models confirm that the experimentally observed red

  11. Mössbauer Spectroscopy on Compounds of Biomedical Interests

    NASA Astrophysics Data System (ADS)

    Oliver, F.; Ewing, N.; Hoffman, E.; Kinyua, A.; Oladeinde, F.; Murdock, A.

    2006-03-01

    Mössbauer spectroscopy (nuclear gamma resonance spectroscopy)^1 has been used in our laboratory for many biomedical applications. This presentation will demonstrate uses of Mössbauer spectroscopy to obtain qualitative and quantitative information about the electronic and magnetic properties of various systems. Information is obtained related to the electronic spin, electric quadrupole interaction, and magnetic hyperfine interactions. This technique has a very broad spectrum of applications, most of them in solid state physics and chemistry. Experiments may be done using transmission or backscattering geometry. For the past fifteen years we have successfully applied this technique to investigate materials of biomedical interest. Materials investigated include porphyrins containing europium^2, plants, over the counter medicines, hemoglobin, and ion implanted implant materials. Results of these experiments and other possible applications will be reported. 1. Leopold May, An Introduction to Mössbauer Spectroscopy, Plenum Press Z(1971). 2. Oliver, et al., Inorganica Chimica Acta, Vol. 186, 119 (1991). * Partially supported by NIH, ** Partially supported by NSF-SEM program.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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.

  14. Vibrational spectroscopy in stem cell characterisation: is there a niche?

    PubMed

    Sulé-Suso, J; Forsyth, N R; Untereiner, V; Sockalingum, G D

    2014-05-01

    Vibrational spectroscopy using both infrared and Raman spectroscopies has been used in recent years with the aim to aid clinicians in disease diagnosis. More recently, these techniques have been applied to study stem cell differentiation and to determine stem cell presence in tissues. These studies have demonstrated the potential of these techniques in better characterising stem cell differentiation phenotypes with potential applications in tissue engineering strategies. However, before the translation of vibrational spectroscopy into clinical practice becomes a reality, several issues still need to be addressed. We describe here an overview of the work carried out so far and the problems that might be encountered when using vibrational spectroscopy. PMID:24703620

  15. Multireflection sum frequency generation vibrational spectroscopy.

    PubMed

    Zhang, Chi; Jasensky, Joshua; Chen, Zhan

    2015-08-18

    We developed a multireflection data collection method in order to improve the signal-to-noise ratio (SNR) and sensitivity of sum frequency generation (SFG) spectroscopy, which we refer to as multireflection SFG, or MRSFG for short. To achieve MRSFG, a collinear laser beam propagation geometry was adopted and trapezoidal Dove prisms were used as sample substrates. An in-depth discussion on the signal and SNR in MRSFG was performed. We showed experimentally, with "m" total internal reflections in a Dove prism, MRSFG signal is ∼m times that of conventional SFG; SNR of the SFG signal-to-background is improved by a factor of >m(1/2) and vibrational signals. Surface molecular structures of adsorbed ethanol molecules, polymer films, and a lipid monolayer were characterized using both MRSFG and conventional SFG. Molecular orientation information on lipid molecules with a 9% composition in a mixed monolayer was measured using MRSFG, which showed a good agreement with that derived from 100% lipid surface coverage using conventional SFG. MRSFG can both improve the spectral quality and detection limit of SFG spectroscopy and is expected to have important applications in surface science for studying structures of molecules with a low surface coverage or less ordered molecular moieties. PMID:26176565

  16. 2010 GRC VIBRATIONAL SPECTROSCOPY AUGUST 1 - AUGUST 6, 2010

    SciTech Connect

    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.

  17. Vibrational spectroscopy of ion exchange membranes

    NASA Astrophysics Data System (ADS)

    Kumari, Dunesh

    Infrared Spectroscopy (IR) and density functional theory (DFT) calculations were used to study Nafion, a sulfonated tetrafluoroethylene ionomer used as the electrolyte material of choice for polymer electrolyte membrane fuel cells (PEMFCs). A methodology is described for assignment of infrared peaks in terms of mechanically coupled internal coordinates of near neighbor functional groups. This work demonstrates (chapter 2--4) the use of ionomer functional group internal coordinate coupling analysis to assign two key Nafion peaks formerly assigned as the sulfonate symmetric stretch (1056 cm -1) and a COC (A) vibrational mode (971 cm-1). The experiments and theory complement each other to show that the dominate motions of the 1056 cm-1 and 971 cm-1 modes are attributed to the COC (A) and the sulfonate stretch respectively, exactly reverse of the convention used for decades. The salient point is that both peaks result from mechanically coupled internal coordinates of both functional groups. This explains why the 1056 cm-1 and 971 cm -1 peaks shift together with changes in the sulfonate group environment (i.e., ion exchange or membrane dehydration). The assignments, correlated with extensive literature data, and new data showing both peaks vanishing upon rigorous dehydration (i.e. conversion of a C3V deprotonated -SO3- to a C1 -SO3H) of the membrane, were based on the correlation of observed IR peaks with animations of mechanically coupled internal coordinates obtained by DFT calculations. Further, the above methodology was augmented with polarization modulated infrared reflection-adsorption spectroscopy (PM-IRRAS) to elucidate the Nafion ionomers functional groups that participate in self-assembly of Nafion onto Pt surfaces. A model for Nafion adsorption onto Pt shows that the Nafion side-chain sulfonate and CF3 co-adsorbates are structural components of the Nafion-Pt interface. The DFT-spectroscopy method of assigning peaks in terms of mechanically coupled internal

  18. Vibrational spectroscopy at electrolyte/electrode interfaces with graphene gratings

    PubMed Central

    Bie, Ya-Qing; Horng, Jason; Shi, Zhiwen; Ju, Long; Zhou, Qin; Zettl, Alex; Yu, Dapeng; Wang, Feng

    2015-01-01

    Microscopic understanding of physical and electrochemical processes at electrolyte/electrode interfaces is critical for applications ranging from batteries, fuel cells to electrocatalysis. However, probing such buried interfacial processes is experimentally challenging. Infrared spectroscopy is sensitive to molecule vibrational signatures, yet to approach the interface three stringent requirements have to be met: interface specificity, sub-monolayer molecular detection sensitivity, and electrochemically stable and infrared transparent electrodes. Here we show that transparent graphene gratings electrode provide an attractive platform for vibrational spectroscopy at the electrolyte/electrode interfaces: infrared diffraction from graphene gratings offers enhanced detection sensitivity and interface specificity. We demonstrate the vibrational spectroscopy of methylene group of adsorbed sub-monolayer cetrimonium bromide molecules and reveal a reversible field-induced electrochemical deposition of cetrimonium bromide on the electrode controlled by the bias voltage. Such vibrational spectroscopy with graphene gratings is promising for real time and in situ monitoring of different chemical species at the electrolyte/electrode interfaces. PMID:26123807

  19. Chemometric Methods for Biomedical Raman Spectroscopy and Imaging

    NASA Astrophysics Data System (ADS)

    Reddy, Rohith K.; Bhargava, Rohit

    The vibrational spectrum is a quantitative measure of a sample's molecular composition. Hence, classical chemometric methods, especially regression-based, have focused on exact mapping between identity and sample composition. While this approach works well for molecular identifications and scientific investigations, problems of biomedical interest often involve complex mixtures of stochastically varying compositions and complex spatial distributions of molecules contributing to the recorded signals. Hence, the challenge often is not to predict the identity of materials but to determine chemical markers that help rapidly detect species (e.g. impurities, conformations, strains of bacteria) in large areas or indicate changes in function in complex tissue (e.g. cancer or tissue engineering). Hence, the rate of data analysis has to be rapid, has to be robust with respect to stochastic variance and the provided information is usually related to biomedical context and not to molecular compositions. The emergence of imaging techniques and clinical applications are spurring growth in this area. In this chapter, we discuss chemometric methods that are useful in this milieu. We first review methods for data pre-processing with a focus on the key challenges facing a spectroscopist. Next, we survey some of the well known, widely used pattern classification techniques under the framework of supervised and unsupervised classification. We discuss the applicability, advantages and drawbacks of each of these techniques and help the reader not only gain useful insights into the techniques themselves but also acquire an understating of the underlying ideas and principles. We conclude by providing examples of the coupled use of chemometric and statistical tools to develop robust classification protocols for prostate and breast tissue pathology. We specifically focus on the critical factors and pitfalls at each step in converting spectral data sets into hi-fidelity images useful for

  20. Transient Two-Dimensional Infrared Spectroscopy in a Vibrational Ladder.

    PubMed

    Kemlin, Vincent; Bonvalet, Adeline; Daniault, Louis; Joffre, Manuel

    2016-09-01

    We report on transient 2D Fourier transform infrared spectroscopy (2DIR) after vibrational ladder climbing induced in the CO-moiety longitudinal stretch of carboxyhemoglobin. The population distribution, spreading up to seven vibrational levels, results in a nonequilibrium 2DIR spectrum evidencing a large number of peaks that can be easily attributed to individual transitions thanks to the anharmonicity of the vibrational potential. We discuss the physical origin of the observed peaks as well as the qualitative behavior of the subsequent dynamics governed by population relaxation in the vibrational ladder. PMID:27508408

  1. Spectroscopy and reactions of vibrationally excited transient molecules

    SciTech Connect

    Dai, H.L.

    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.

  2. Broadband infrared vibrational nano-spectroscopy using thermal blackbody radiation.

    PubMed

    O'Callahan, Brian T; Lewis, William E; Möbius, Silke; Stanley, Jared C; Muller, Eric A; Raschke, Markus B

    2015-12-14

    Infrared vibrational nano-spectroscopy based on scattering scanning near-field optical microscopy (s-SNOM) provides intrinsic chemical specificity with nanometer spatial resolution. Here we use incoherent infrared radiation from a 1400 K thermal blackbody emitter for broadband infrared (IR) nano-spectroscopy. With optimized interferometric heterodyne signal amplification we achieve few-monolayer sensitivity in phonon polariton spectroscopy and attomolar molecular vibrational spectroscopy. Near-field localization and nanoscale spatial resolution is demonstrated in imaging flakes of hexagonal boron nitride (hBN) and determination of its phonon polariton dispersion relation. The signal-to-noise ratio calculations and analysis for different samples and illumination sources provide a reference for irradiance requirements and the attainable near-field signal levels in s-SNOM in general. The use of a thermal emitter as an IR source thus opens s-SNOM for routine chemical FTIR nano-spectroscopy. PMID:26698997

  3. Seventh international conference on time-resolved vibrational spectroscopy

    SciTech Connect

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

    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.

  4. Vibrational spectroscopy of ferruginous smectite and nontronite.

    PubMed

    Frost, R L; Kloprogge, J T

    2000-10-01

    A comparison is made between the Raman and infrared spectra of ferruginous smectite and a nontronite using both absorption and emission techniques. Raman spectra show hydroxyl stretching bands at 3572, 3434, 3362, 3220 and 3102 cm(-1). The infrared emission spectra of the hydroxyl stretching region are significantly different to the absorption spectrum. These differences are attributed to the loss of water, absent in the emission spectrum, the reduction of the samples in the spectrometer and possible phase changes. Dehydroxylation of the two minerals may be followed by the loss of intensity of the hydroxyl stretching and hydroxyl deformation frequencies. Hydroxyl deformation modes are observed at 873 and 801 cm(-1) for the ferruginous smectite, and at 776 and 792 cm(-1) for the nontronite. Raman hydroxyl deformation vibrations are found at 879 cm(-1). Other Raman bands are observed at 1092 and 1032 cm(-1), assigned to the SiO stretching vibrations, at 675 and 587 cm(-1), assigned to the hydroxyl translation vibrations, at 487 and 450 cm(-1), attributed to OSiO bending type vibrations, and at 363, 287 and 239 cm(-1). The differences in the molecular structure of the two minerals are attributed to the Al/Fe ratio in the minerals. PMID:11058063

  5. Vibrational spectroscopy of shock-compressed liquid CO

    SciTech Connect

    Moore, D.S.; Schmidt, S.C.; Shaw, M.S.; Johnson, J.D.

    1991-01-01

    Single-pulse, multiplex, coherent anti-Stokes Raman spectroscopy (CARS) was used to observe the vibrational spectra of liquid CO shock compressed to several pressures and temperatures up to 9.9 GPa and 2010 K. The experimental spectra were compared to synthetic spectra calculated using a semiclassical model for CARS intensities and estimated vibrational frequencies, peak Raman susceptibilities and Raman line widths. A comparison of these data with result in the isoelectronic and materially very similar N{sub 2} show a significant difference in vibrational frequency shift with pressure. 21 refs., 2 figs.

  6. Biomedical applications of laser-induced breakdown spectroscopy (LIBS)

    NASA Astrophysics Data System (ADS)

    Unnikrishnan, V. K.; Nayak, Rajesh; Bhat, Sujatha; Mathew, Stanley; Kartha, V. B.; Santhosh, C.

    2015-03-01

    LIBS has been proven to be a robust elemental analysis tool attracting interest because of the wide applications. LIBS can be used for analysis of any type of samples i.e. environmental/physiological, regardless of its state of matter. Conventional spectroscopy techniques are good in analytical performance, but their sample preparation method is mostly destructive and time consuming. Also, almost all these methods are incapable of analysing multi elements simaltaneously. On the other hand, LIBS has many potential advantages such as simplicity in the experimental setup, less sample preparation, less destructive analysis of sample etc. In this paper, we report some of the biomedical applications of LIBS. From the experiments carried out on clinical samples (calcified tissues or teeth and gall stones) for trace elemental mapping and detection, it was found that LIBS is a robust tool for such applications. It is seen that the presence and relative concentrations of major elements (calcium, phosphorus and magnesium) in human calcified tissue (tooth) can be easily determined using LIBS technique. The importance of this study comes in anthropology where tooth and bone are main samples from which reliable data can be easily retrieved. Similarly, elemental composition of bile juice and gall stone collected from the same subject using LIBS was found to be similar. The results show interesting prospects for LIBS to study cholelithiasis (the presence of stones in the gall bladder, is a common disease of the gastrointestinal tract) better.

  7. Examining surface and bulk structures using combined nonlinear vibrational spectroscopies.

    PubMed

    Zhang, Chi; Wang, Jie; Khmaladze, Alexander; Liu, Yuwei; Ding, Bei; Jasensky, Joshua; Chen, Zhan

    2011-06-15

    We combined sum-frequency generation (SFG) vibrational spectroscopy with coherent anti-Stokes Raman scattering (CARS) spectroscopy in one system to examine both surface and bulk structures of materials with the same geometry and without the need to move the sample. Poly(methyl methacrylate) (PMMA) and polystyrene (PS) thin films were tested before and after plasma treatment. The sensitivities of SFG and CARS were tested by varying polymer film thickness and using a lipid monolayer. PMID:21685990

  8. Ultrafast time resolved vibrational spectroscopy in liquid systems

    NASA Astrophysics Data System (ADS)

    Seifert, G.; Hofmann, M.; Weidlich, K.; Graener, H.

    1996-04-01

    The ultrafast dynamics of small molecules in the liquid phase can successfully be studied tracing the relaxation pathways of vibrational excess energy. Two complementing experimental techniques, picosecond IR double resonance spectroscopy and time resolved incoherent Anti-Stokes Raman spectroscopy, are very powerful tools for such studies. The capabilities of investigations combining these methods are discussed on the example of new experimental data on liquid dichloromethane (CH2Cl2).

  9. Vibrational photodetachment spectroscopy near the electron affinity of S2

    NASA Astrophysics Data System (ADS)

    Barrick, J. B.; Yukich, J. N.

    2016-02-01

    We have conducted laser photodetachment spectroscopy near the detachment threshold of the electron affinity of S2 in a 1.8-T field. The ions are prepared by dissociative electron attachment to carbonyl sulfide. The experiment is conducted in a Penning ion trap and with a narrow-band, tunable, Ti:sapphire laser. A hybrid model for photodetachment in an ion trap is fit to the data using the appropriate Franck-Condon factors. The observations reveal detachment from and to the first few vibrational levels of the anion and the neutral molecule, respectively. Evaporative cooling of the anion ensemble condenses the thermal distribution to the lowest initial vibrational states. The subsequent detachment spectroscopy yields results consistent with a vibrationally cooled anion population.

  10. Determining the static electronic and vibrational energy correlations via two-dimensional electronic-vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    Changes in the electronic structure of pigments in protein environments and of polar molecules in solution inevitably induce a re-adaption of molecular nuclear structure. Both changes of electronic and vibrational energies can be probed with visible or infrared lasers, such as two-dimensional electronic spectroscopy or vibrational spectroscopy. The extent to which the two changes are correlated remains elusive. The recent demonstration of two-dimensional electronic-vibrational (2DEV) spectroscopy potentially enables a direct measurement of this correlation experimentally. However, it has hitherto been unclear how to characterize the correlation from the spectra. In this paper, we present a theoretical formalism to demonstrate the slope of the nodal line between the excited state absorption and ground state bleach peaks in the spectra as a characterization of the correlation between electronic and vibrational transition energies. We also show the dynamics of the nodal line slope is correlated to the vibrational spectral dynamics. Additionally, we demonstrate the fundamental 2DEV spectral line-shape of a monomer with newly developed response functions.

  11. Determining the static electronic and vibrational energy correlations via two-dimensional electronic-vibrational spectroscopy

    SciTech Connect

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

    2015-05-07

    Changes in the electronic structure of pigments in protein environments and of polar molecules in solution inevitably induce a re-adaption of molecular nuclear structure. Both changes of electronic and vibrational energies can be probed with visible or infrared lasers, such as two-dimensional electronic spectroscopy or vibrational spectroscopy. The extent to which the two changes are correlated remains elusive. The recent demonstration of two-dimensional electronic-vibrational (2DEV) spectroscopy potentially enables a direct measurement of this correlation experimentally. However, it has hitherto been unclear how to characterize the correlation from the spectra. In this report, we present a theoretical formalism to demonstrate the slope of the nodal line between the excited state absorption and ground state bleach peaks in the spectra as a characterization of the correlation between electronic and vibrational transition energies. In conclusion, we also show the dynamics of the nodal line slope is correlated to the vibrational spectral dynamics. Additionally, we demonstrate the fundamental 2DEV spectral line-shape of a monomer with newly developed response functions

  12. Determining the static electronic and vibrational energy correlations via two-dimensional electronic-vibrational spectroscopy

    DOE PAGES

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

    2015-05-07

    Changes in the electronic structure of pigments in protein environments and of polar molecules in solution inevitably induce a re-adaption of molecular nuclear structure. Both changes of electronic and vibrational energies can be probed with visible or infrared lasers, such as two-dimensional electronic spectroscopy or vibrational spectroscopy. The extent to which the two changes are correlated remains elusive. The recent demonstration of two-dimensional electronic-vibrational (2DEV) spectroscopy potentially enables a direct measurement of this correlation experimentally. However, it has hitherto been unclear how to characterize the correlation from the spectra. In this report, we present a theoretical formalism to demonstrate themore » slope of the nodal line between the excited state absorption and ground state bleach peaks in the spectra as a characterization of the correlation between electronic and vibrational transition energies. In conclusion, we also show the dynamics of the nodal line slope is correlated to the vibrational spectral dynamics. Additionally, we demonstrate the fundamental 2DEV spectral line-shape of a monomer with newly developed response functions« less

  13. Determining the static electronic and vibrational energy correlations via two-dimensional electronic-vibrational spectroscopy.

    PubMed

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

    2015-05-01

    Changes in the electronic structure of pigments in protein environments and of polar molecules in solution inevitably induce a re-adaption of molecular nuclear structure. Both changes of electronic and vibrational energies can be probed with visible or infrared lasers, such as two-dimensional electronic spectroscopy or vibrational spectroscopy. The extent to which the two changes are correlated remains elusive. The recent demonstration of two-dimensional electronic-vibrational (2DEV) spectroscopy potentially enables a direct measurement of this correlation experimentally. However, it has hitherto been unclear how to characterize the correlation from the spectra. In this paper, we present a theoretical formalism to demonstrate the slope of the nodal line between the excited state absorption and ground state bleach peaks in the spectra as a characterization of the correlation between electronic and vibrational transition energies. We also show the dynamics of the nodal line slope is correlated to the vibrational spectral dynamics. Additionally, we demonstrate the fundamental 2DEV spectral line-shape of a monomer with newly developed response functions.

  14. Determining the static electronic and vibrational energy correlations via two-dimensional electronic-vibrational spectroscopy

    SciTech Connect

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

    2015-05-07

    Changes in the electronic structure of pigments in protein environments and of polar molecules in solution inevitably induce a re-adaption of molecular nuclear structure. Both changes of electronic and vibrational energies can be probed with visible or infrared lasers, such as two-dimensional electronic spectroscopy or vibrational spectroscopy. The extent to which the two changes are correlated remains elusive. The recent demonstration of two-dimensional electronic-vibrational (2DEV) spectroscopy potentially enables a direct measurement of this correlation experimentally. However, it has hitherto been unclear how to characterize the correlation from the spectra. In this paper, we present a theoretical formalism to demonstrate the slope of the nodal line between the excited state absorption and ground state bleach peaks in the spectra as a characterization of the correlation between electronic and vibrational transition energies. We also show the dynamics of the nodal line slope is correlated to the vibrational spectral dynamics. Additionally, we demonstrate the fundamental 2DEV spectral line-shape of a monomer with newly developed response functions.

  15. FT-IR and FT-NIR Raman spectroscopy in biomedical research

    NASA Astrophysics Data System (ADS)

    Naumann, D.

    1998-06-01

    FT-IR and FT-NIR Raman spectra of intact microbial, plant animal or human cells, tissues, and body fluids are highly specific, fingerprint-like signatures which can be used to discriminate between diverse microbial species and strains, characterize growth-dependent phenomena and cell-drug interactions, and differentiate between various disease states. The spectral information potentially useful for biomedical characterizations may be distributed over the entire infrared region of the electromagnetic spectrum, i.e. over the near-, mid-, and far-infrared. It is therefore a key problem how the characteristic vibrational spectroscopic information can be systematically extracted from the infrared spectra of complex biological samples. In this report these questions are addressed by applying factor and cluster analysis treating the classification problem of microbial infrared spectra as a model task. Particularly interesting applications arise by means of a light microscope coupled to the FT-IR spectrometer. FT-IR spectra of single microcolonies of less than 40 μm in diameter can be obtained from colony replica applying a stamping technique that transfers the different, spatially separated microcolonies from the culture plate to a special IR-sample holder. Using a computer controlled x,y-stage together with mapping and video techniques, the fundamental tasks of microbiological analysis, namely detection, enumeration, and differentiation of micro-organisms can be integrated in one single apparatus. Since high quality, essentially fluorescence free Raman spectra may now be obtained in relatively short time intervals on previously intractable biological specimens, FT-IR and NIR-FT-Raman spectroscopy can be used in tandem to characterize biological samples. This approach seems to open up new horizons for biomedical characterizations of complex biological systems.

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

    NASA Astrophysics Data System (ADS)

    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.

  17. High resolution photoionisation spectroscopy of vibrationally excited Ar · NO

    NASA Astrophysics Data System (ADS)

    Monti, O. L. A.; Cruse, H. A.; Softley, T. P.; Mackenzie, S. R.

    2001-01-01

    Mass-analysed threshold ionisation (MATI) spectra of the Ar · NO complex have been obtained for the first time. These spectra have been used to determine unambiguously the nature of three bands detected by resonance-enhanced multiphoton ionisation (REMPI) spectroscopy via the à state of Ar · NO. The features are shown to originate from vibrationally excited states of Ar · NO in its electronic ground state. The assignment is in agreement with recent theoretical calculations.

  18. Enhanced Vibrational Spectroscopies as Tools for Small Molecule Biosensing

    PubMed Central

    Boujday, Souhir; Lamy de la Chapelle, Marc; Srajer, Johannes; Knoll, Wolfgang

    2015-01-01

    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. PMID:26343666

  19. X-Ray Spectroscopy of Bromine Compounds and Biomedical Applications

    NASA Astrophysics Data System (ADS)

    Nahar, Sultana N.; Luo, Yi; Le, Linh; Pradhan, A. K.; Chowdhury, E.; Pitzer, R.; Montenegro, M.

    2010-06-01

    In conventional biomedical applications intense and broadband high energy X-rays are used in therapy and diagnostics (theranostics) to ensure sufficient tissue penetration for imaging or treatment. To avoid damages incurred by these, our proposed method, Resonant Theranosticsb,c, aims to find narrow energy regions that corresponds to resonant absorption or emission. We show that such energy bands lie below the K-shell ionization energy, contrary to the research focus on the K-shell ionization energy itself. Targeting these energy bands, Auger processes can be initiated to produce a number of photons and electrons from each atomic/molecular species via photon fluorescence and electron ejections. We will report our study on the bromine compound bromodeoxyuridyne (BUdR), widely used as radiological contrast agent in radiation imaging. The active system is Br^o-Br^+ combination, which can emit or absorb X-rays in the relative narrow energy range of 12 to 13.6 keV, through 1s-np transitions. We will present the oscillator strengths and transition probabilities for various Auger or K-shell 1s-np transitions. We will show that the corresponding cross sections and attenuation coefficients per unit mass, are orders of magnitude higher than the background and that at K-shell ionization energy. Employing these attenuation coefficients in the Monte Carlo simulation program Geant4, we study the intensities of photon and electron emission spectra. Acknowledgment: Partially support: Large Interdisciplinary Grant award of the Ohio State University and NASA (SNN). The computational work was carried out at the Ohio Supercomputer Center, Columbus Ohio. "Resonant X-Ray Enhancement of the Auger Effect in High-Z atoms, molecules, and Nanoparticles: Biomedical Applications", A. K. Pradhan, S. N. Nahar, M. Montenegro, Yan Yu, H. L. Zhang, C. Sur, M. Mrozik, R. M. Pitzer, J. of Phys. Chem. A, 113 (2009), 12356. "Monte Carlo Simulations and Atomic Calculations for Auger Processes in

  20. Vibrational Spectroscopy of HD{sup +} with 2-ppb Accuracy

    SciTech Connect

    Koelemeij, J. C. J.; Roth, B.; Wicht, A.; Ernsting, I.; Schiller, S.

    2007-04-27

    By measurement of the frequency of a vibrational overtone transition in the molecular hydrogen ion HD{sup +}, we demonstrate the first optical spectroscopy of trapped molecular ions with submegahertz accuracy. We use a diode laser, locked to a stable frequency comb, to perform resonance-enhanced multiphoton dissociation spectroscopy on sympathetically cooled HD{sup +} ions at 50 mK. The achieved 2-ppb relative accuracy is a factor of 150 higher than previous results for HD{sup +}, and the measured transition frequency agrees well with recent high-accuracy ab initio calculations, which include high-order quantum electrodynamic effects. We also show that our method bears potential for achieving considerably higher accuracy and may, if combined with slightly improved theoretical calculations, lead to a new and improved determination of the electron-proton mass ratio.

  1. Chemometrics applied to vibrational spectroscopy: overview, challenges and pitfalls

    SciTech Connect

    Haaland, D.M.

    1996-10-01

    Chemometric multivariate calibration methods are rapidly impacting quantitative infrared spectroscopy in many positive ways. The combination of vibrational spectroscopy and chemometrics has been used by industry for quality control and process monitoring. The growth of these methods has been phenomenal in the past decade. Yet, as with any new technology, there are growing pains. The methods are so powerful at finding correlations in the data, that when used without great care they can readily yield results that are not valid for the analysis of future unknown samples. In this paper, the power of the multivariate calibration methods is discussed while pointing out common pitfalls and some remaining challenges that may slow the implementation of chemometrics in research and industry.

  2. VLT-CRIRES: ``Good Vibrations'' Rotational-vibrational molecular spectroscopy in astronomy

    NASA Astrophysics Data System (ADS)

    Käufl, H. U.

    2010-05-01

    Near-Infrared high spectral and spatial resolution spectroscopy offers new and innovative observing opportunities for astronomy. The ``traditional'' benefits of IR-astronomy - strongly reduced extinction and availability of adaptive optics - more than offset for many applications the compared to CCD-based astronomy strongly reduced sensitivity. Especially in high resolution spectroscopy interferences by telluric lines can be minimized. Moreover for abundance studies many important atomic lines can be accessed in the NIR. A novel spectral feature available for quantitative spectroscopy are the molecular rotational-vibrational transitions which allow for fundamentally new studies of condensed objects and atmospheres. This is also an important complement to radio-astronomy, especially with ALMA, where molecules are generally only observed in the vibrational ground state. Rot-vib transitions also allow high precision abundance measurements - including isotopic ratios - fundamental to understand the thermo-nuclear processes in stars beyond the main sequence. Quantitative modeling of atmospheres has progressed such that the unambiguous interpretation of IR-spectra is now well established. In combination with adaptive optics spectro-astrometry is even more powerful and with VLT-CRIRES a spatial resolution of better than one milli-arcsecond has been demonstrated. Some highlights and recent results will be presented: our solar system, extrasolar planets, star- and planet formation, stellar evolution and the formation of galactic bulges.

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

    SciTech Connect

    Tokmakoff, Andrei

    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.

  4. Laser spectroscopy applied to environmental, ecological, food safety, and biomedical research.

    PubMed

    Svanberg, Sune; Zhao, Guangyu; Zhang, Hao; Huang, Jing; Lian, Ming; Li, Tianqi; Zhu, Shiming; Li, Yiyun; Duan, Zheng; Lin, Huiying; Svanberg, Katarina

    2016-03-21

    Laser spectroscopy provides many possibilities for multi-disciplinary applications in environmental monitoring, in the ecological field, for food safety investigations, and in biomedicine. The paper gives several examples of the power of multi-disciplinary applications of laser spectroscopy as pursued in our research group. The studies utilize mostly similar and widely applicable spectroscopic approaches. Air pollution and vegetation monitoring by lidar techniques, as well as agricultural pest insect monitoring and classification by elastic scattering and fluorescence spectroscopy are described. Biomedical aspects include food safety applications and medical diagnostics of sinusitis and otitis, with strong connection to the abatement of antibiotics resistance development. PMID:27136872

  5. Vibrational Assignments of Six-Coordinate Ferrous Heme Nitrosyls: New Insight From Nuclear Resonance Vibrational Spectroscopy

    SciTech Connect

    Paulat, F.; Berto, T.C.; George, S.DeBeer; Goodrich, L.; Praneeth, V.K.K.; Sulok, C.D.; Lehnert, N.

    2009-05-21

    This Communication addresses a long-standing problem: the exact vibrational assignments of the low-energy modes of the Fe-N-O subunit in six-coordinate ferrous heme nitrosyl model complexes. This problem is addressed using nuclear resonance vibrational spectroscopy (NRVS) coupled to {sup 15}N{sup 18}O isotope labeling and detailed simulations of the obtained data. Two isotope-sensitive features are identified at 437 and 563 cm{sup -1}. Normal coordinate analysis shows that the 437 cm{sup -1} mode corresponds to the Fe-NO stretch, whereas the 563 cm{sup -1} band is identified with the Fe-N-O bend. The relative NRVS intensities of these features determine the degree of vibrational mixing between the stretch and the bend. The implications of these results are discussed with respect to the trans effect of imidazole on the bound NO. In addition, a comparison to myoglobin-NO (Mb-NO) is made to determine the effect of the Mb active site pocket on the bound NO.

  6. Vibrational and Rotational Spectroscopy of CD_2H^+

    NASA Astrophysics Data System (ADS)

    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

  7. Terahertz vibrational absorption spectroscopy using microstrip-line waveguides

    NASA Astrophysics Data System (ADS)

    Byrne, M. B.; Cunningham, J.; Tych, K.; Burnett, A. D.; Stringer, M. R.; Wood, C. D.; Dazhang, L.; Lachab, M.; Linfield, E. H.; Davies, A. G.

    2008-11-01

    We demonstrate that terahertz microstrip-line waveguides can be used to measure absorption spectra of polycrystalline materials with a high frequency resolution (˜2 GHz) and with a spatial resolution that is determined by the microstrip-line dimensions, rather than the free-space wavelength. The evanescent terahertz-bandwidth electric field extending above the microstrip line interacts with, and is modified by, overlaid dielectric samples, thus enabling the characteristic vibrational absorption resonances in the sample to be probed. As an example, the terahertz absorption spectrum of polycrystalline lactose monohydrate was investigated; the lowest lying mode was observed at 534(±2) GHz, in excellent agreement with free-space measurements. This microstrip technique offers both a higher spatial and frequency resolution than free-space terahertz time-domain spectroscopy and requires no contact between the waveguide and sample.

  8. Neutron Vibrational Spectroscopy and modeling of polymer/dopant interactions

    NASA Astrophysics Data System (ADS)

    Moule, Adam; Harrelson, Thomas; Cheng, Yongqiang; Ramirez-Cuesta, Anibal; Faller, Roland; Huang, David

    Neutron vibrational spectroscopy (VISION and ORNL) is a powerful technique to determine the configurations of organic species in amorphous samples. We apply this technique to samples of the semiconducting polymer regio-regular P3HT to determine the molecular configurations outside of the crystalline domains, which have never been investigated. Application of density functional theory modeling using crystal field theory and for the single molecule approach yield a variety of configurations of the polymer backbone and side chains. These results demonstrate that only 1% of the volume corresponds to the assumed crystal structure solved using x-ray diffraction. In addition we investigate the configurations of P3HT doped with the molecular dopant F4TCNQ and determine that the charging of the polymer backbone leads to increased side chain stiffness. These results have significant implications for design of organic electronic devices based on thiophenes.

  9. Liquid Space Lubricants Examined by Vibrational Micro-Spectroscopy

    NASA Technical Reports Server (NTRS)

    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.

  10. Structural characterization and vibrational spectroscopy of the arsenate mineral wendwilsonite.

    PubMed

    Frost, Ray L; Scholz, Ricardo; López, Andrés; Belotti, Fernanda Maria; Xi, Yunfei

    2014-01-24

    In this paper, we have investigated on the natural wendwilsonite mineral with the formulae Ca2(Mg,Co)(AsO4)2⋅2(H2O). Raman spectroscopy complimented with infrared spectroscopy has been used to determine the molecular structure of the wendwilsonite arsenate mineral. A comparison is made with the roselite mineral group with formula Ca2B(AsO4)2⋅2H2O (where B may be Co, Fe(2+), Mg, Mn, Ni, Zn). The Raman spectra of the arsenate related to tetrahedral arsenate clusters with stretching region shows strong differences between that of wendwilsonite and the roselite arsenate minerals which is attributed to the cation substitution for calcium in the structure. The Raman arsenate (AsO4)(3-) stretching region shows strong differences between that of wendwilsonite and the roselite arsenate minerals which is attributed to the cation substitution for calcium in the structure. In the infrared spectra complexity exists of multiple to tetrahedral (AsO4)(3-) clusters with antisymmetric stretching vibrations observed indicating a reduction of the tetrahedral symmetry. This loss of degeneracy is also reflected in the bending modes. Strong Raman bands around 450 cm(-1) are assigned to ν4 bending modes. Multiple bands in the 350-300 cm(-1) region assigned to ν2 bending modes provide evidence of symmetry reduction of the arsenate anion. Three broad bands for wendwilsonite found at 3332, 3119 and 3001 cm(-1) are assigned to OH stretching bands. By using a Libowitzky empirical equation, hydrogen bond distances of 2.65 and 2.75Å are estimated. Vibrational spectra enable the molecular structure of the wendwilsonite mineral to be determined and whilst similarities exist in the spectral patterns with the roselite mineral group, sufficient differences exist to be able to determine the identification of the minerals.

  11. Vibrationally resolved anion photoelectron spectroscopy of metal clusters

    NASA Astrophysics Data System (ADS)

    Miller, Stephen R.

    Vibrationally resolved anion photoelectron spectroscopy of metal clusters Vibrationally resolved anion photoelectron spectroscopy (APES) and density functional theory (DFT) are applied to the study of structure and reactivity in small metal containing molecules. The studies described fall into two general categories: the study of bare metal clusters and the study of metal/organic ligand reactions. The current lack of spectroscopic data for small, bare gas-phase metal compounds makes the experimental study of such compounds important for understanding structure and bonding in open-shell metallic species. The heteronuclear diatomic anions MCu- (M = Cr, Mo) were prepared in a flowing afterglow ion-molecule reactor, and studied experimentally with APES. Anion and neutral vibrational frequencies and MCu electron affinities were obtained for both systems. The experiments were supplemented by DFT calculations. The combined use of experiment and theory allows for the assignment of both photoelectron spectra, including a reassignment of the CrCu ground state reported in the literature. Similarly, DFT was used to assign the anionic/neutral electronic states observed in the photoelectron spectra of Al3- and Al3O-. The study of partially ligated organometallic complexes offers a means of examining the interactions between metal atoms and individual ligand molecules. DFT was used to assign electronic states observed in the photoelectron spectra of NbC2H2-, NbC4H4 -NbC6H6- and VC6H 6-. Comparison of the NbnHn - (n = 2, 4, 6) spectra (obtained through the reaction of C2 H4 and Nb) with DFT results provides the first direct spectroscopic evidence of the conversion of ethylene to benzene by a gas phase metal atom. Experiments were used to probe the reactivity of Y with C2H 4 in an effort to examine the generality of the metal induced C 2H4 dehydrogenation/cyclization reactions. Some of the key products in the Y reactions were YC2H-, YC 2H2-, and YC6H5 -. However, the results

  12. Vibrational spectroscopy of a transient species through time-resolved Fourier transform infrared emission spectroscopy: The vinyl radical

    SciTech Connect

    Letendre, Laura; Liu, Dean-Kuo; Pibel, Charles D.; Halpern, Joshua B.; Dai, Hai-Lung

    2000-06-01

    An approach for detecting the vibrational spectrum of transient species is demonstrated on the vinyl radical. Photodissociation of carefully chosen precursors at selected photolysis wavelengths produce highly vibrationally excited radicals. Infrared (IR) emission from these radicals is then measured by time-resolved Fourier transform spectroscopy with nanosecond time resolution. All nine vibrational bands of the vinyl radical, generated from four different precursors, are obtained and reported here for the first time. (c) 2000 American Institute of Physics.

  13. Vibrational spectroscopy and ab initio MO study of the molecular structure and vibrational spectra of α- and γ-pyrones

    NASA Astrophysics Data System (ADS)

    Fausto, Rui; Quinteiro, Graciete; Breda, Susana

    2001-12-01

    The molecular structures and vibrational spectra of the monomeric forms of α- and γ-pyrones were investigated by ab initio MO calculations, undertaken at the HF/6-31G ∗ level of theory, and vibrational spectroscopy, including matrix-isolation FTIR spectroscopy. A complete assignment of the vibrational spectra of the studied compounds isolated in an argon matrix, at 8 K, or in the condensed phases, at room temperature, is presented and the vibrational data correlated with some important structural parameters. It is shown that the intermolecular interactions in the room temperature condensed phases do not affect the structure and vibrational properties of the studied molecules strongly, though the vibrational results clearly reveal minor changes induced in the carbonyl groups that indirectly affect the electron distribution in the whole pyrone rings, leading to an increase in their π-electron delocalization. For the isolated monomers, both structural and vibrational results point to a relatively weak π-electron delocalization in both α- and γ-pyrone moieties.

  14. Observation of terahertz vibrations in Pyrococcus furiosus rubredoxin via impulsive coherent vibrational spectroscopy and nuclear resonance vibrational spectroscopy--interpretation by molecular mechanics.

    PubMed

    Tan, Ming-Liang; Bizzarri, Anna Rita; Xiao, Yuming; Cannistraro, Salvatore; Ichiye, Toshiko; Manzoni, Cristian; Cerullo, Giulio; Adams, Michael W W; Jenney, Francis E; Cramer, Stephen P

    2007-03-01

    We have used impulsive coherent vibrational spectroscopy (ICVS) to study the Fe(S-Cys)(4) site in oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). In this experiment, a 15 fs visible laser pulse is used to coherently pump the sample to an excited electronic state, and a second <10 fs pulse is used to probe the change in transmission as a function of the time delay. PfRd was observed to relax to the ground state by a single exponential decay with time constants of approximately 255-275 fs. Superimposed on this relaxation are oscillations caused by coherent excitation of vibrational modes in both excited and ground electronic states. Fourier transformation reveals the frequencies of these modes. The strongest ICV mode with 570 nm excitation is the symmetric Fe-S stretching mode near 310 cm(-1), compared to 313 cm(-1) in the low temperature resonance Raman. If the rubredoxin is pumped at 520 nm, a set of strong bands occurs between 20 and 110 cm(-1). Finally, there is a mode at approximately 500 cm(-1) which is similar to features near 508 cm(-1) in blue Cu proteins that have been attributed to excited state vibrations. Normal mode analysis using 488 protein atoms and 558 waters gave calculated spectra that are in good agreement with previous nuclear resonance vibrational spectra (NRVS) results. The lowest frequency normal modes are identified as collective motions of the entire protein or large segments of polypeptide. Motion in these modes may affect the polar environment of the redox site and thus tune the electron transfer functions in rubredoxins.

  15. Investigating buried polymer interfaces using sum frequency generation vibrational spectroscopy

    PubMed Central

    Chen, Zhan

    2010-01-01

    This paper reviews recent progress in the studies of buried polymer interfaces using sum frequency generation (SFG) vibrational spectroscopy. Both buried solid/liquid and solid/solid interfaces involving polymeric materials are discussed. SFG studies of polymer/water interfaces show that different polymers exhibit varied surface restructuring behavior in water, indicating the importance of probing polymer/water interfaces in situ. SFG has also been applied to the investigation of interfaces between polymers and other liquids. It has been found that molecular interactions at such polymer/liquid interfaces dictate interfacial polymer structures. The molecular structures of silane molecules, which are widely used as adhesion promoters, have been investigated using SFG at buried polymer/silane and polymer/polymer interfaces, providing molecular-level understanding of polymer adhesion promotion. The molecular structures of polymer/solid interfaces have been examined using SFG with several different experimental geometries. These results have provided molecular-level information about polymer friction, adhesion, interfacial chemical reactions, interfacial electronic properties, and the structure of layer-by-layer deposited polymers. Such research has demonstrated that SFG is a powerful tool to probe buried interfaces involving polymeric materials, which are difficult to study by conventional surface sensitive analytical techniques. PMID:21113334

  16. High-Pressure Effects in Benzoic Acid Dimers: Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Tao, Yuchuan; Dreger, Zbigniew; Gupta, Yogendra

    2013-06-01

    To understand pressure effects on dimer structure stability, Raman and FTIR spectroscopy were used to examine changes in hydrogen bonded dimers of benzoic acid crystals up to 31 GPa. Raman measurements indicated a phase transition around 7-8 GPa. It is proposed that this transition is caused by a rearrangement of molecules within the dimer leading to a symmetry change from C2h to likely C2 or Cs. This change was reversible upon pressure release from 15 GPa. Pressures above 15 GPa, induced gradual changes in luminescence and a color change in the crystal from white to brownish. FTIR measurements at 31 GPa revealed the formation of a new broad band centered around 3250 cm-1, which was attributed to the stretching vibrations of the O -H bond. It is proposed that hydrogen bonded dimers of benzoic acid transform partially to a covalently bonded compound composed of benzoic anhydride-like molecules and H2O. This study demonstrates that application of high pressure can lead to significant changes in the H-bonded dimer structure, including formation of chemical bonding. Work supported by DOE/NNSA and ONR/MURI.

  17. Vibrational Spectroscopy of CO2- Radical Anion in Water

    NASA Astrophysics Data System (ADS)

    Janik, Ireneusz; Tripathi, G. N. R.

    2016-06-01

    The reductive conversion of CO2 into industrial products (e.g., oxalic acid, formic acid, and methanol) can occur via aqueous CO2- as a transient intermediate. While the formation, structure and reaction pathways of this radical anion have been modelled for decades using various spectroscopic and theoretical approaches, we present here, for the first time, a vibrational spectroscopic investigation in liquid water, using pulse radiolysis time-resolved resonance Raman spectroscopy for its preparation and observation. Excitation of the radical in resonance with its 235 nm absorption displays a transient Raman band at 1298 wn, attributed to the symmetric CO stretch, which is at 45 wn higher frequency than in inert matrices. Isotopic substitution at C (13CO2-) shifts the frequency downwards by 22 wn which confirms its origin and the assignment. A Raman band of moderate intensity compared to the stronger 1298 wn band also appears at 742 wn, and is assignable to the OCO bending mode. A reasonable resonance enhancement of this mode is possible only in a bent CO2-(C2v/Cs) geometry. These resonance Raman features suggest a strong solute-solvent interaction, the water molecules acting as constituents of the radical structure, rather than exerting a minor solvent perturbation. However, there is no evidence of the non-equivalence (Cs) of the two CO bonds. A surprising resonance Raman feature is the lack of overtones of the symmetric CO stretch, which we interpret due to the detachment of the electron from the CO2- moiety towards the solvation shell. Electron detachment occurs at the energies of 0.28+/-0.03 eV or higher with respect to the zero point energy of the ground electronic state. The issue of acid-base equilibrium of the radical which has been in contention for decades, as reflected in a wide variation in the reported pKa (-0.2 to 3.9), has been resolved. A value of 3.4+/-0.2 measured in this work is consistent with the vibrational properties, bond structure and charge

  18. Coherent Multidimensional Vibrational Spectroscopy of Representative N-Alkanes

    NASA Astrophysics Data System (ADS)

    Mathew, Nathan A.; Rickard, Mark A.; Kornau, Kathryn M.; Pakoulev, Andrei V.; Block, Stephen B.; Yurs, Lena A.; Wright, John C.

    2009-08-01

    Mixed frequency/time domain, two color triply vibrationally enhanced (TRIVE) four wave mixing (FWM) spectroscopy is used to study the methyl and methylene modes in octane and dotriacontane. The experiments involve scanning different combinations of the two excitation frequencies, the monochromator frequency, and the two time delays between the three excitation pulses while the remaining variables are fixed. Two dimensional spectra of the methyl and methylene stretching region have weak, asymmetrical diagonal- and cross-peaks when the excitation pulses are temporally overlapped. As the time delays change, the spectra change as new peaks appear and their peak intensity and position change. Combined two-dimensional scans of the excitation frequency and time delay show the changes are caused by relaxation of the initially excited populations to other states that are coupled to the methyl and methylene stretching modes. Two dimensional time delay scans show that the coherence dephasing rates are very fast so fully coherent TRIVE FWM pathways involving multiple quantum coherences are not possible without shorter excitation pulses. Similar experiments involving the methyl and methylene bend and stretching modes identify cross-peaks between these modes and population transfer processes that create cross-peaks. The asymmetric methylene stretch/Fermi resonance band is observed to contain unresolved states that couple differently with the symmetric methylene stretching and scissor modes as well as with lower lying quantum states that are fed by population transfer. The TRIVE FWM data show that the multidimensional spectra are dominated by rapid population transfer within the methyl and methylene stretching modes and to lower quantum states that are coupled to the stretching modes.

  19. Localized surface plasmon resonances in nanostructures to enhance nonlinear vibrational spectroscopies: towards an astonishing molecular sensitivity

    PubMed Central

    2014-01-01

    Summary Vibrational transitions contain some of the richest fingerprints of molecules and materials, providing considerable physicochemical information. Vibrational transitions can be characterized by different spectroscopies, and alternatively by several imaging techniques enabling to reach sub-microscopic spatial resolution. In a quest to always push forward the detection limit and to lower the number of needed vibrational oscillators to get a reliable signal or imaging contrast, surface plasmon resonances (SPR) are extensively used to increase the local field close to the oscillators. Another approach is based on maximizing the collective response of the excited vibrational oscillators through molecular coherence. Both features are often naturally combined in vibrational nonlinear optical techniques. In this frame, this paper reviews the main achievements of the two most common vibrational nonlinear optical spectroscopies, namely surface-enhanced sum-frequency generation (SE-SFG) and surface-enhanced coherent anti-Stokes Raman scattering (SE-CARS). They can be considered as the nonlinear counterpart and/or combination of the linear surface-enhanced infrared absorption (SEIRA) and surface-enhanced Raman scattering (SERS) techniques, respectively, which are themselves a branching of the conventional IR and spontaneous Raman spectroscopies. Compared to their linear equivalent, those nonlinear vibrational spectroscopies have proved to reach higher sensitivity down to the single molecule level, opening the way to astonishing perspectives for molecular analysis. PMID:25551056

  20. Vibrational Cooling in A Cold Ion Trap: Vibrationally Resolved Photoelectron Spectroscopy of Cold C60- Anions

    SciTech Connect

    Wang, Xue B.; Woo, Hin-koon; Wang, Lai S.

    2005-08-01

    We demonstrate vibrational cooling of anions via collisions with a background gas in an ion trap attached to a cryogenically controlled cold head (10 ? 400 K). Photoelectron spectra of vibrationally cold C60- anions, produced by electrospray ionization and cooled in the cold ion trap, have been obtained. Relative to spectra taken at room temperature, vibrational hot bands are completely eliminated, yielding well resolved vibrational structures and a more accurate electron affinity for neutral C60. The electron affinity of C60 is measured to be 2.683 ? 0.008 eV. The cold spectra reveal complicated vibrational structures for the transition to the C60 ground state due to the Jahn-Teller effect in the ground state of C60-. Vibrational excitations in the two Ag modes and eight Hg modes are observed, providing ideal data to assess the vibronic couplings in C60-.

  1. Prospects for laser-induced breakdown spectroscopy for biomedical applications: a review.

    PubMed

    Singh, Vivek Kumar; Rai, Awadhesh Kumar

    2011-09-01

    We review the different spectroscopic techniques including the most recent laser-induced breakdown spectroscopy (LIBS) for the characterization of materials in any phase (solid, liquid or gas) including biological materials. A brief history of the laser and its application in bioscience is presented. The development of LIBS, its working principle and its instrumentation (different parts of the experimental set up) are briefly summarized. The generation of laser-induced plasma and detection of light emitted from this plasma are also discussed. The merit and demerits of LIBS are discussed in comparison with other conventional analytical techniques. The work done using the laser in the biomedical field is also summarized. The analysis of different tissues, mineral analysis in different organs of the human body, characterization of different types of stone formed in the human body, analysis of biological aerosols using the LIBS technique are also summarized. The unique abilities of LIBS including detection of molecular species and calibration-free LIBS are compared with those of other conventional techniques including atomic absorption spectroscopy, inductively coupled plasma atomic emission spectroscopy and mass spectroscopy, and X-ray fluorescence.

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

    SciTech Connect

    Mandal, Aritra; Tokmakoff, Andrei

    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.

  3. 2012 VIBRATIONAL SPECTROSCOPY GORDON RESEARCH CONFERENCE, AUGUST 5-10, 2012

    SciTech Connect

    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.

  4. Measuring correlated electronic and vibrational spectral dynamics using line shapes in two-dimensional electronic-vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    Two-dimensional electronic-vibrational (2DEV) spectroscopy is an experimental technique that shows great promise in its ability to provide detailed information concerning the interactions between the electronic and vibrational degrees of freedom in molecular systems. The physical quantities 2DEV is particularly suited for measuring have not yet been fully determined, nor how these effects manifest in the spectra. In this work, we investigate the use of the center line slope of a peak in a 2DEV spectrum as a measure of both the dynamic and static correlations between the electronic and vibrational states of a dye molecule in solution. We show how this center line slope is directly related to the solvation correlation function for the vibrational degrees of freedom. We also demonstrate how the strength with which the vibration on the electronic excited state couples to its bath can be extracted from a set of 2DEV spectra. These analytical techniques are then applied to experimental data from the laser dye 3,3'-diethylthiatricarbocyanine iodide in deuterated chloroform, where we determine the lifetime of the correlation between the electronic transition frequency and the transition frequency for the backbone C = C stretch mode to be ˜1.7 ps. Furthermore, we find that on the electronic excited state, this mode couples to the bath ˜1.5 times more strongly than on the electronic ground state.

  5. Measuring correlated electronic and vibrational spectral dynamics using line shapes in two-dimensional electronic-vibrational spectroscopy

    SciTech Connect

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

    2015-05-07

    Two-dimensional electronic-vibrational (2DEV) spectroscopy is an experimental technique that shows great promise in its ability to provide detailed information concerning the interactions between the electronic and vibrational degrees of freedom in molecular systems. The physical quantities 2DEV is particularly suited for measuring have not yet been fully determined, nor how these effects manifest in the spectra. In this work, we investigate the use of the center line slope of a peak in a 2DEV spectrum as a measure of both the dynamic and static correlations between the electronic and vibrational states of a dye molecule in solution. We show how this center line slope is directly related to the solvation correlation function for the vibrational degrees of freedom. We also demonstrate how the strength with which the vibration on the electronic excited state couples to its bath can be extracted from a set of 2DEV spectra. These analytical techniques are then applied to experimental data from the laser dye 3,3′-diethylthiatricarbocyanine iodide in deuterated chloroform, where we determine the lifetime of the correlation between the electronic transition frequency and the transition frequency for the backbone C = C stretch mode to be ∼1.7 ps. Furthermore, we find that on the electronic excited state, this mode couples to the bath ∼1.5 times more strongly than on the electronic ground state.

  6. ULTRAFAST CHEMISTRY: Using Time-Resolved Vibrational Spectroscopy for Interrogation of Structural Dynamics

    NASA Astrophysics Data System (ADS)

    Nibbering, Erik T. J.; Fidder, Henk; Pines, Ehud

    2005-05-01

    Time-resolved infrared (IR) and Raman spectroscopy elucidates molecular structure evolution during ultrafast chemical reactions. Following vibrational marker modes in real time provides direct insight into the structural dynamics, as is evidenced in studies on intramolecular hydrogen transfer, bimolecular proton transfer, electron transfer, hydrogen bonding during solvation dynamics, bond fission in organometallic compounds and heme proteins, cis-trans isomerization in retinal proteins, and transformations in photochromic switch pairs. Femtosecond IR spectroscopy monitors the site-specific interactions in hydrogen bonds. Conversion between excited electronic states can be followed for intramolecular electron transfer by inspection of the fingerprint IR- or Raman-active vibrations in conjunction with quantum chemical calculations. Excess internal vibrational energy, generated either by optical excitation or by internal conversion from the electronic excited state to the ground state, is observable through transient frequency shifts of IR-active vibrations and through nonequilibrium populations as deduced by Raman resonances.

  7. Vibrational spectroscopy of cluster ions: Two novel methods

    SciTech Connect

    Yeh, L.I.; Okumura, M.; Myers, J.D.; Lee, Y.T.

    1987-07-01

    Two sensitive techniques are discussed for obtaining vibrational spectra of cluster ions. The first approach is to attach a H/sub 2/ molecule to the hydrated hydronium ions. Because the original goal was to study the hydrated hydronium ions, the attached H/sub 2/ is hoped to have only a small effect on the spectrum. After an O-H stretch of the cluster ion has been excited, it vibrationally predissociates, losing the H/sub 2/. By monitoring the dissociation product as a function of laser frequency, the absorption spectra of these H/sub 3/O/sup +/ . (H/sub 2/O)/sub n/ . H/sub 2/ (n = 1,2,3) ions have been found. The second approach is to detect the vibrationally excited H/sub 3/O/sup +/ . (H/sub 2/O)/sub n/ (n = 1,2,3) ions using an infrared multiphoton dissociation process. The procedure is to first excite from v = 0 to v = 1 in the O-H stretch using a tunable ir laser. We then make use of the fact that the density of states near v = 0 and v = 1 are very different, and the vibrationally excited ionic clusters, which contain many low frequency vibrations, are likely to be in the quasicontinuum region for the sequential excitation by a fixed frequency laser. This means that one can distinguish between ground state and vibrationally excited H/sub 3/O/sup +/ . (H/sub 2/O)/sub n/ by using a multiphoton dissociation (MPD) process to selectively dissociate the latter using a CO/sub 2/ laser. Once again, we monitor the dissociation product ion signal as a function of the excitation frequency of the first laser to get the absorption spectra of the H/sub 3/O/sup +/ . (H/sub 2/O)/sub n/ ions. 5 refs.

  8. Hydrogen Bonding and Vibrational Spectroscopy: A Theoretical Study

    NASA Technical Reports Server (NTRS)

    Chaban, Galina M.

    2005-01-01

    Effects of hydrogen bonding on vibrational spectra are studied for several hydrogen-bonded complexes, in which hydrogen bonding ranges from weak (<5 kcal/mol) to very strong (>25 kcal/mol). The systems studied include complexes of inorganic acids and salts with water and ammonia, as well as complexes of several organic molecules (nitriles and amino acids) with water. Since anharmonic effects are very strong in hydrogen-bonded systems, anharmonic vibrational frequencies and infrared intensities are computed using the correlation-corrected vibrational self-consistent field (CC-VSCF) method with ab initio potential surfaces at the MP2 and CCSD(T) levels. The most common spectral effects induced by hydrogen bonding are red shifts of stretching vibrational frequencies ranging from approx.200/cm to over 2000/cm and significant increases of infrared intensities for those bonds that participate in hydrogen bonding. However, some systems (e.g. nitrile-water complexes) exhibit shifts in the opposite direction (to the blue) upon formation of hydrogen bonds.

  9. Quantitative Sum-Frequency Generation Vibrational Spectroscopy of Molecular Surfaces and Interfaces: Lineshape, Polarization and Orientation

    SciTech Connect

    Wang, Hongfei; Velarde, Luis; Gan, Wei; Fu, Li

    2015-04-01

    Sum-frequency generation vibrational spectroscopy (SFG) can provide detailed information and understanding of molecular vibrational spectroscopy, orientational and conformational structure, and interactions of molecular surfaces and interfaces, through quantitative measurement and analysis. In this review, we present the current status and discuss the main developments on the measurement of intrinsic SFG spectral lineshape, formulations for polarization measurement and orientation analysis of the SFG-VS spectra. The main focus is to present a coherent formulation and discuss the main concepts or issues that can help to make SFG-VS a quantitative analytical and research tool in revealing the chemistry and physics of complex molecular surface and interface.

  10. Raman spectroscopy of TiO2 thin films formed by hybrid treatment for biomedical applications.

    PubMed

    Lubas, M; Jasinski, J J; Sitarz, M; Kurpaska, L; Podsiad, P; Jasinski, J

    2014-12-10

    The paper presents the results of the investigations of the surface layer obtained after application of the combined hybrid method of oxidation in a fluidized bed (FB) and deposition of the oxide coating by PVD technique. The material used in the study was Ti Grade 2. The process of diffusive saturation was carried out in a fluidized-bed reactor at the temperature of 640°C for 8h in air while the top oxide layer was obtained through PVD method - magnetron sputtering using TiO2 target and argon atmosphere with the pressure of 3×10(-2)mbar and the distance between the substrate to the target of 60mm. In order to determine changes in the properties that occur as a result of modification of the Ti surface, the following examinations were carried out by SEM-EDX, X-ray diffraction methods, Raman spectroscopy, Glow Discharge Optical Spectroscopy (GDOS) and Secondary Ion Mass Spectrometry (SIMS). The coatings obtained were characterized by zonal structure comprising the solution zone of Tiα(O) and oxide zone of TiO2 with modifications of rutile and anatase, depending on the oxidation method. It was found that formation of oxide layers using the hybrid method (FB+PVD) leads to limitation of defects in the oxide layer after fluidized-bed thermal treatment and obtaining a uniform, tight coating with improved corrosion properties which are important from the biomedical standpoint.

  11. Multidimensional infrared spectroscopy reveals the vibrational and solvation dynamics of isoniazid

    NASA Astrophysics Data System (ADS)

    Shaw, Daniel J.; Adamczyk, Katrin; Frederix, Pim W. J. M.; Simpson, Niall; Robb, Kirsty; Greetham, Gregory M.; Towrie, Michael; Parker, Anthony W.; Hoskisson, Paul A.; Hunt, Neil T.

    2015-06-01

    The results of infrared spectroscopic investigations into the band assignments, vibrational relaxation, and solvation dynamics of the common anti-tuberculosis treatment Isoniazid (INH) are reported. INH is known to inhibit InhA, a 2-trans-enoyl-acyl carrier protein reductase enzyme responsible for the maintenance of cell walls in Mycobacterium tuberculosis but as new drug-resistant strains of the bacterium appear, next-generation therapeutics will be essential to combat the rise of the disease. Small molecules such as INH offer the potential for use as a biomolecular marker through which ultrafast multidimensional spectroscopies can probe drug binding and so inform design strategies but a complete characterization of the spectroscopy and dynamics of INH in solution is required to inform such activity. Infrared absorption spectroscopy, in combination with density functional theory calculations, is used to assign the vibrational modes of INH in the 1400-1700 cm-1 region of the infrared spectrum while ultrafast multidimensional spectroscopy measurements determine the vibrational relaxation dynamics and the effects of solvation via spectral diffusion of the carbonyl stretching vibrational mode. These results are discussed in the context of previous linear spectroscopy studies on solid-phase INH and its usefulness as a biomolecular probe.

  12. Vibrational spectroscopy of water in hydrated lipid multi-bilayers. III. Water clustering and vibrational energy transfer.

    PubMed

    Gruenbaum, S M; Skinner, J L

    2013-11-01

    Water clustering and connectivity around lipid bilayers strongly influences the properties of membranes and is important for functions such as proton and ion transport. Vibrational anisotropic pump-probe spectroscopy is a powerful tool for understanding such clustering, as the measured anisotropy depends upon the time-scale and degree of intra- and intermolecular vibrational energy transfer. In this article, we use molecular dynamics simulations and theoretical vibrational spectroscopy to help interpret recent experimental measurements of the anisotropy of water in lipid multi-bilayers as a function of both lipid hydration level and isotopic substitution. Our calculations are in satisfactory agreement with the experiments of Piatkowski, Heij, and Bakker, and from our simulations we can directly probe water clustering and connectivity. We find that at low hydration levels, many water molecules are in fact isolated, although up to 70% of hydration water forms small water clusters or chains. At intermediate hydration levels, water forms a wide range of cluster sizes, while at higher hydration levels, the majority of water molecules are part of a large, percolating water cluster. Therefore, the size, number, and nature of water clusters are strongly dependent on lipid hydration level, and the measured anisotropy reflects this through its dependence on intermolecular energy transfer. PMID:24206336

  13. Microwave spectroscopy of furfural in vibrationally excited states

    NASA Astrophysics Data System (ADS)

    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.

  14. Vibrational energy flow in photoactive yellow protein revealed by infrared pump-visible probe spectroscopy.

    PubMed

    Nakamura, Ryosuke; Hamada, Norio

    2015-05-14

    Vibrational energy flow in the electronic ground state of photoactive yellow protein (PYP) is studied by ultrafast infrared (IR) pump-visible probe spectroscopy. Vibrational modes of the chromophore and the surrounding protein are excited with a femtosecond IR pump pulse, and the subsequent vibrational dynamics in the chromophore are selectively probed with a visible probe pulse through changes in the absorption spectrum of the chromophore. We thus obtain the vibrational energy flow with four characteristic time constants. The vibrational excitation with an IR pulse at 1340, 1420, 1500, or 1670 cm(-1) results in ultrafast intramolecular vibrational redistribution (IVR) with a time constant of 0.2 ps. The vibrational modes excited through the IVR process relax to the initial ground state with a time constant of 6-8 ps in parallel with vibrational cooling with a time constant of 14 ps. In addition, upon excitation with an IR pulse at 1670 cm(-1), we observe the energy flow from the protein backbone to the chromophore that occurs with a time constant of 4.2 ps. PMID:25896223

  15. A vibrational spectroscopy study on anserine and its aqueous solutions.

    PubMed

    Akkaya, Y; Balci, K; Goren, Y; Akyuz, S; Stricker, M C; Stover, D D; Ritzhaupt, G; Collier, W B

    2015-01-01

    In this study based on vibrational spectroscopic measurements and Density Functional Theory (DFT), we aimed for a reliable interpretation of the IR and Raman spectra recorded for anserine in the solid phase and water (H2O) and heavy water (D2O) solutions. Initial DFT calculations at the B3LYP/6-31G(d) searched possible conformers of the anserine zwitterion using a systematic conformational search. The corresponding equilibrium geometrical parameters and vibrational spectral data were determined for each of the stable conformers (in water) by the geometry optimization and hessian calculations performed at the same level of theory using the polarized continuum model (PCM). The same calculations were repeated to determine the most energetically preferred dimer structure for the molecule and the associated geometry, force field and vibrational spectral data. The harmonic force constants obtained from these calculations were scaled by the Scaled Quantum Mechanical Force Field (SQM) method and then used in the calculation of the refined wavenumbers, potential energy distributions, IR and Raman intensities. These refined theoretical data, which confirm the zwitterion structure for anserine in the solid phase or aqueous solvents, revealed the remarkable effects of intermolecular hydrogen bonding on the structural properties and observed IR and Raman spectra of this molecule. PMID:25997178

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

    ERIC Educational Resources Information Center

    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…

  17. Application of vibrational spectroscopy to the study of mineralized tissues (review).

    PubMed

    Carden, A; Morris, M D

    2000-07-01

    The infrared and Raman spectroscopy of bone and teeth tissues are reviewed. Characteristic spectra are obtained for both the mineral and protein components of these tissues. Vibrational spectroscopy is used to study the mineralization process, to define the chemical structure changes accompanying bone diseases, and to characterize interactions between prosthetic implants and tissues. Microspectroscopy allows acquisition of spatially resolved spectra, with micron scale resolution. Recently developed imaging modalities allow tissue imaging with chemical composition contrast.

  18. Expanded Choices for Vibration-Rotation Spectroscopy in the Physical Chemistry Teaching Laboratory

    NASA Astrophysics Data System (ADS)

    Schmitz, Joel R.; Dolson, David A.

    2015-06-01

    Many third-year physical chemistry laboratory students in the US analyze the vibration-rotation spectrum of HCl in support of lecture concepts in quantum theory and molecular spectroscopy. Contemporary students in physical chemistry teaching laboratories increasingly have access to FTIR spectrometers with 1/8th wn resolution, which allows for expanded choices of molecules for vibration-rotation spectroscopy. Here we present the case for choosing HBr/DBr for such a study, where the 1/8th wn resolution enables the bromine isotopic lines to be resolved. Vibration-rotation lines from the fundamental and first-overtone bands of four hydrogen bromide isotopomers are combined in a global analysis to determine molecular spectroscopic constants. Sample production, spectral appearance, analysis and results will be presented for various resolutions commonly available in teaching laboratories.

  19. Damage-free vibrational spectroscopy of biological materials in the electron microscope

    PubMed Central

    Rez, Peter; Aoki, Toshihiro; March, Katia; Gur, Dvir; Krivanek, Ondrej L.; Dellby, Niklas; Lovejoy, Tracy C.; Wolf, Sharon G.; Cohen, Hagai

    2016-01-01

    Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an ‘aloof' electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies <1 eV can be ‘safely' investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C–H, N–H and C=O vibrational signatures with no observable radiation damage. The technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ∼10 nm, simultaneously combined with imaging in the electron microscope. PMID:26961578

  20. Molecular vibrational dynamics in water studied by femtosecond coherent anti-Stokes Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhao, Yang; Zhang, Sheng; Zhou, Boyang; Dong, Zhiwei; Chen, Deying; Zhang, Zhonghua; Xia, Yuanqin

    2014-10-01

    We utilized femtosecond time-resolved coherent anti-Stokes Raman spectroscopy (CARS) to study the ultrafast vibrational dynamics in distilled water at room temperature. The CARS signals from the broad OH-stretching modes between 3100 cm-1 and 3700 cm-1 were obtained and analyzed. The dephasing times of four Raman modes in water were detected and compared.

  1. Coherent Multidimensional Vibrational Spectroscopy of Biomolecules; Concepts, Simulations and Challenges

    PubMed Central

    Zhuang, Wei; Hayashi, Tomoyuki; Mukamel, Shaul

    2009-01-01

    The response of complex molecules to sequences of femtosecond infrared pulses provides a unique window into their structure, dynamics and fluctuating environments, as projected into the vibrational degrees of freedom. In this review we survey the basic principles of these novel two dimensional infrared (2DIR) analogues of multidimensional NMR. The perturbative approach for computing the nonlinear optical response of coupled localized chromophores is introduced and applied to the amide backbone transitions of protein, liquid water, membrane lipids, and amyloid fibrils. The signals are analyzed using classical MD simulations combined with an effective fluctuating Hamiltonian for coupled localized anharmonic vibrations whose dependence on the local electrostatic environment is parameterized by an ab initio map. Several simulation protocols. Including the Cumulant expansion of Gaussian Fluctuation (CGF), a quasiparticle scattering approach (NEE), the Stochastic Liouville Equations (SLE), and Direct Numerical Propagation are surveyed. These are implemented in a code SPECTRON that interfaces with standard electronic structure and molecular mechanisms MD codes. Chirality-induced techniques which dramatically enhance the resolution are demonstrated. Signatures of conformational and hydrogen bonding fluctuations, protein folding, and chemical exchange processes are discussed. PMID:19415637

  2. Vibrational spectroscopy and intramolecular energy transfer in isocyanic acid (HNCO)

    SciTech Connect

    Coffey, M.J.; Berghout, H.L.; Woods, E. III; Crim, F.F.

    1999-06-01

    Room temperature photoacoustic spectra in the region of the first through the fourth overtones (2{nu}{sub 1} to 5{nu}{sub 1}) and free-jet action spectra of the second through the fourth overtones (3{nu}{sub 1} to 5{nu}{sub 1}) of the N{endash}H stretching vibration permit analysis of the vibrational and rotational structure of HNCO. The analysis identifies the strong intramolecular couplings that control the early stages of intramolecular vibrational energy redistribution (IVR) and gives the interaction matrix elements between the zero-order N{endash}H stretching states and the other zero-order states with which they interact. The experimentally determined couplings and zero-order state separations are consistent with {ital ab initio} calculations of East, Johnson, and Allen [J. Chem. Phys. {bold 98}, 1299 (1993)], and comparison with the calculation identifies the coupled states and likely interactions. The states most strongly coupled to the pure N{endash}H stretching zero-order states are ones with a quantum of N{endash}H stretching excitation ({nu}{sub 1}) replaced by different combinations of N{endash}C{endash}O asymmetric or symmetric stretching excitation ({nu}{sub 2} or {nu}{sub 3}) and {ital trans}-bending excitation ({nu}{sub 4}). The two strongest couplings of the n{nu}{sub 1} state are to the states (n{minus}1){nu}{sub 1}+{nu}{sub 2}+{nu}{sub 4} and (n{minus}1){nu}{sub 1}+{nu}{sub 3}+2{nu}{sub 4}, and sequential couplings through a series of low order resonances potentially play a role. The analysis shows that if the pure N{endash}H stretch zero-order state were excited, energy would initially flow out of that mode into the strongly coupled mode in 100 fs to 700 fs, depending on the level of initial excitation. {copyright} {ital 1999 American Institute of Physics.}

  3. Vibrational spectroscopy of the sulphate mineral sturmanite from Kuruman manganese deposits, South Africa.

    PubMed

    Frost, Ray L; Scholz, Ricardo; López, Andrés; Xi, Yunfei; Lana, Cristiano

    2014-12-10

    The mineral sturmanite is a hydrated calcium iron aluminium manganese sulphate tetrahydroxoborate hydroxide of formula Ca6(Fe, Al, Mn)2(SO4)2(B(OH)4)(OH)12·26H2O. We have studied the mineral sturmanite using a number of techniques, including SEM with EPMA and vibrational spectroscopy. Chemical analysis shows a homogeneous phase, composed by Ca, Fe, Mn, S, Al and Si. B is not determined in this EPMA technique. An intense Raman band at 990cm(-1) is assigned to the SO4(2-) symmetric stretching mode. Raman spectroscopy identifies multiple sulphate symmetric stretching modes in line with the three sulphate crystallographically different sites. Raman spectroscopy also identifies a band at 1069cm(-1) which may be attributed to a carbonate symmetric stretching mode, indicating the presence of thaumasite. Infrared spectra display two bands at 1080 and 1107cm(-1) assigned to the SO4(2-) antisymmetric stretching modes. The observation of multiple bands in this ν4 spectral region offers evidence for the reduction in symmetry of the sulphate anion from Td to C2v or even lower symmetry. The Raman band at 3622cm(-1) is assigned to the OH unit stretching vibration and the broad feature at around 3479cm(-1) to water stretching bands. Infrared spectroscopy shows a set of broad overlapping bands in the OH stretching region. Vibrational spectroscopy enables an assessment of the molecular structure of sturmanite to be made.

  4. Vibrational spectroscopy of the sulphate mineral sturmanite from Kuruman manganese deposits, South Africa

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; Scholz, Ricardo; López, Andrés; Xi, Yunfei; Lana, Cristiano

    2014-12-01

    The mineral sturmanite is a hydrated calcium iron aluminium manganese sulphate tetrahydroxoborate hydroxide of formula Ca6(Fe, Al, Mn)2(SO4)2(B(OH)4)(OH)12·26H2O. We have studied the mineral sturmanite using a number of techniques, including SEM with EPMA and vibrational spectroscopy. Chemical analysis shows a homogeneous phase, composed by Ca, Fe, Mn, S, Al and Si. B is not determined in this EPMA technique. An intense Raman band at 990 cm-1 is assigned to the SO42- symmetric stretching mode. Raman spectroscopy identifies multiple sulphate symmetric stretching modes in line with the three sulphate crystallographically different sites. Raman spectroscopy also identifies a band at 1069 cm-1 which may be attributed to a carbonate symmetric stretching mode, indicating the presence of thaumasite. Infrared spectra display two bands at 1080 and 1107 cm-1 assigned to the SO42- antisymmetric stretching modes. The observation of multiple bands in this ν4 spectral region offers evidence for the reduction in symmetry of the sulphate anion from Td to C2v or even lower symmetry. The Raman band at 3622 cm-1 is assigned to the OH unit stretching vibration and the broad feature at around 3479 cm-1 to water stretching bands. Infrared spectroscopy shows a set of broad overlapping bands in the OH stretching region. Vibrational spectroscopy enables an assessment of the molecular structure of sturmanite to be made.

  5. Vibrational spectroscopy of the sulphate mineral sturmanite from Kuruman manganese deposits, South Africa.

    PubMed

    Frost, Ray L; Scholz, Ricardo; López, Andrés; Xi, Yunfei; Lana, Cristiano

    2014-12-10

    The mineral sturmanite is a hydrated calcium iron aluminium manganese sulphate tetrahydroxoborate hydroxide of formula Ca6(Fe, Al, Mn)2(SO4)2(B(OH)4)(OH)12·26H2O. We have studied the mineral sturmanite using a number of techniques, including SEM with EPMA and vibrational spectroscopy. Chemical analysis shows a homogeneous phase, composed by Ca, Fe, Mn, S, Al and Si. B is not determined in this EPMA technique. An intense Raman band at 990cm(-1) is assigned to the SO4(2-) symmetric stretching mode. Raman spectroscopy identifies multiple sulphate symmetric stretching modes in line with the three sulphate crystallographically different sites. Raman spectroscopy also identifies a band at 1069cm(-1) which may be attributed to a carbonate symmetric stretching mode, indicating the presence of thaumasite. Infrared spectra display two bands at 1080 and 1107cm(-1) assigned to the SO4(2-) antisymmetric stretching modes. The observation of multiple bands in this ν4 spectral region offers evidence for the reduction in symmetry of the sulphate anion from Td to C2v or even lower symmetry. The Raman band at 3622cm(-1) is assigned to the OH unit stretching vibration and the broad feature at around 3479cm(-1) to water stretching bands. Infrared spectroscopy shows a set of broad overlapping bands in the OH stretching region. Vibrational spectroscopy enables an assessment of the molecular structure of sturmanite to be made. PMID:24929311

  6. Vibrational spectroscopy and density functional theory study of ninhydrin

    NASA Astrophysics Data System (ADS)

    Li, Ran; Sui, Huimin; Liu, Peipie; Chen, Lei; Cheng, Jianbo; Zhao, Bing

    2015-02-01

    In this paper, ninhydrin was designed as a model molecule for theoretical and experimental studies of the molecule structure. Density functional theory (DFT) calculations have been performed to predict the IR and Raman spectra for the molecule. In addition, Fourier transform infrared (FTIR) and Raman spectra of the compound have been obtained experimentally. Based on the modeling results obtained at the B3LYP/6-311++G** level, all FTIR and Raman bands of the compound obtained experimentally were assigned. Our calculated vibrational frequencies are in good agreement with the experimental values. The molecular electrostatic potential surface calculation was performed and the result suggested that the ninhydrin had two potential hydrogen bond donors and four potential hydrogen bond acceptors. HOMO-LUMO gap was also obtained theoretically at B3LYP/6-311++G** level.

  7. Vibrational spectroscopy and density functional theory study of ninhydrin.

    PubMed

    Li, Ran; Sui, Huimin; Liu, Peipie; Chen, Lei; Cheng, Jianbo; Zhao, Bing

    2015-02-01

    In this paper, ninhydrin was designed as a model molecule for theoretical and experimental studies of the molecule structure. Density functional theory (DFT) calculations have been performed to predict the IR and Raman spectra for the molecule. In addition, Fourier transform infrared (FTIR) and Raman spectra of the compound have been obtained experimentally. Based on the modeling results obtained at the B3LYP/6-311++G** level, all FTIR and Raman bands of the compound obtained experimentally were assigned. Our calculated vibrational frequencies are in good agreement with the experimental values. The molecular electrostatic potential surface calculation was performed and the result suggested that the ninhydrin had two potential hydrogen bond donors and four potential hydrogen bond acceptors. HOMO-LUMO gap was also obtained theoretically at B3LYP/6-311++G** level. PMID:25459727

  8. Broadband spectroscopy of the electromagnetic properties of aqueous ferrofluids for biomedical applications

    NASA Astrophysics Data System (ADS)

    Bellizzi, G.; Bucci, O. M.; Capozzoli, A.

    2010-10-01

    This paper presents the results of a broadband spectroscopy study, over the frequency range 1 MHz-2 GHz, of the electromagnetic properties of a ferrofluid consisting of magnetite nanoparticles, with a mean magnetic size of 10 nm, dispersed in water. An innovative measurement approach and apparatus, allowing an accurate determination of the permeability, even in presence of a large permittivity, have been developed to characterize the suspension. The results obtained show a significant magnetic response over the whole analyzed frequency range, with a good agreement with the theoretical models describing the magnetization dynamics of these systems. Moreover, a strong dielectric response has been detected, which is in satisfactory agreement with the models developed to describe the dielectric behavior of charged nanoparticles suspended in aqueous solution. This result implies that measurement techniques able to determine both the permittivity and permeability become mandatory for a reliable determination of the magnetic properties of aqueous ferrofluids. The accuracy of the determined permeability spectrum is estimated to be of the order of few percent, so these results provide a reliable experimental basis to estimate how fruitful the use of magnetic nanoparticles can be in relevant biomedical applications.

  9. Biomedical and agricultural applications of energy dispersive X-ray spectroscopy in electron microscopy.

    PubMed

    Wyroba, Elżbieta; Suski, Szymon; Miller, Karolina; Bartosiewicz, Rafał

    2015-09-01

    Energy dispersive X-ray spectroscopy (EDS) in electron microscopy has been widely used in many research areas since it provides precise information on the chemical composition of subcellular structures that may be correlated with their high resolution images. In EDS the characteristic X-rays typical of each element are analyzed and the new detectors - an example of which we describe - allow for setting precisely the area of measurements and acquiring signals as a point analysis, as a linescan or in the image format of the desired area. Mapping of the elements requires stringent methods of sample preparation to prevent redistribution/loss of the elements as well as elimination of the risk of overlapping spectra. Both qualitative and quantitative analyses may be performed at a low probe current suitable for thin biological samples. Descriptions of preparation techniques, drawbacks and precautions necessary to obtain reliable results are provided, including data on standards, effects of specimen roughness and quantification. Data on EPMA application in different fields of biomedical and agricultural studies are reviewed. In this review we refer to recent EDS/EPMA applications in medical diagnostics, studies on air pollution and agrochemicals as well as on plant models used to monitor the environment.

  10. Cation Far Infrared Vibrational Spectroscopy of Polycyclic Aromatic Hydrocarbons

    NASA Astrophysics Data System (ADS)

    Kong, W.; Zhang, J.; Han, F.

    2009-06-01

    The far infrared (FIR) region is crucial for spectroscopic investigations because of the existence of skeletal modes of moderately sized molecules. However, our knowledge of FIR modes is significantly lacking, largely due to the limited availability of light sources and detectors in this spectral region. The technique "pulsed field ionization zero kinetic energy electron spectroscopy" (PFI-ZEKE) is ideal for studies of FIR spectroscopy. This is because the low internal energy of the cation associated with the skeletal modes is particularly beneficial for the stability of the corresponding Rydberg states. In this work, we report our effort in studies of FIR spectroscopy of cationic polycyclic aromatic hydrocarbons (PAH). Using laser desorption, we can vaporize the non-volatile PAH for gas phase spectroscopy. To ensure the particle density and therefore the critical ion density in prolonging the lifetime of Rydberg electrons, we have used a "chamber-in-a-chamber" design and significantly shortened the distance between the desorption region and the detection region. From our studies of catacondensed PAHs, we have observed the emergence of the flexible waving modes with the increasing length of the molecular ribbon. Pericondensed PAHs, on the other hand, have shown significant out of plane IR active transitions. The planarity of the molecular frame is therefore a question of debate. The FIR modes are also interesting for another reason: they are also telltales of the precision of modern computational packages. The combination of experimental and theoretical studies will help with the identification of the chemical composition of the interstellar medium. This effort therefore directly serves the missions of the Spitzer Space Observatory and more importantly, the missions of the Herschel Space Observatory.

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

    NASA Astrophysics Data System (ADS)

    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.

  12. Far-red to near infrared emission and scattering spectroscopy for biomedical applications

    NASA Astrophysics Data System (ADS)

    Zhang, Gang

    2001-06-01

    The thesis investigates the far-red and near infrared (NIR) spectral region from biomedical tissue samples for monitoring the state of tissues. The NIR emission wing intensity is weak in comparison to the emission in the visible spectral region. The wing emission from biomedical samples has revealed meaningful information about the state of the tissues. A model is presented to explain the shape of the spectral wing based on a continuum of energy levels. The wing can be used to classify different kinds of tissues; especially it can be used to differentiate cancer part from normal human breast tissues. The research work of the far-red emission from thermal damaged tissue samples shows that the emission intensity in this spectral region is proportional to the extent of the thermal damage of the tissue. Near infrared spectral absorption method is used to investigate blood hemodynamics (perfusion and oxygenation) in brain during sleep-wake transition. The result of the research demonstrates that the continuous wave (CW) type near infrared spectroscopy (NIRS) device can be used to investigate brain blood perfusion and oxygenation with a similar precision with frequency domain (FD) type device. The human subject sleep and wake transition, has been monitored by CW type NIRS instrument with traditional electroencephalograph (EEG) method. Parallel change in oxy-Hb and deoxy-Hb is a discrete event that occurs in the transition from both sleep to wakefulness and wakefulness to sleep. These hemodynamic switches are generally about few seconds delayed from the human decided transition point between sleep and wake on the polygraph EEG recording paper. The combination of NIRS and EEG methods monitor the brain activity, gives more information about the brain activity. The sleep apnea investigation was associated with recurrent apneas, insufficient nasal continuous positive airway pressure (CPAP) and the different response of the peripheral and central compartments to breathing

  13. Gas Phase Spectra and Structural Determination of Glucose 6 Phosphate Using Cryogenic Ion Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Kregel, Steven J.; Voss, Jonathan; Marsh, Brett; Garand, Etienne

    2014-06-01

    Glucose-6-Phosphate (G6P) is one member of a class of simple phosphorylated sugars that are relevant in biological processes. We have acquired a gas phase infrared spectrum of G6P- using cryogenic ion vibrational spectroscopy (CIVS) in a home-built spectrometer. The experimental spectrum was compared with calculated vibrational spectra from a systematic conformer search. For both of the α and β anomers, results show that only the lowest energy conformers are present in the gas phase. If spectral signatures for similar sugars could be cataloged, it would allow for conformer-specific determination of mixture composition, for example, for glycolyzation processes.

  14. Vibrational spectroscopy for online monitoring of extraction solvent degradation products

    SciTech Connect

    Peterson, J.; Robinson, T.; Bryan, S.A.; Levitskaia, T.G.

    2013-07-01

    In our research, we are exploring the potential of online monitoring of the organic solvents for the flowsheets relevant to the used nuclear fuel reprocessing and tributyl phosphate (TBP)- based extraction processes in particular. Utilization of vibrational spectroscopic techniques permits the discrimination of the degradation products from the primary constituents of the loaded extraction solvent. Multivariate analysis of the spectral data facilitates development of the regression models for their quantification in real time and potentially enables online implementation of a monitoring system. Raman and FTIR spectral databases were created and used to develop the regression partial least squares (PLS) chemometric models for the quantitative prediction of HDBP (dibutyl phosphoric acid) degradation product, TBP, and UO{sub 2}{sup 2+} extraction organic product phase. It was demonstrated that both these spectroscopic techniques are suitable for the quantification of the Purex solvent components in the presence of UO{sub 2}(NO{sub 3}){sub 2}. Developed PLS models successfully predicted HDBP and TBP organic concentrations in simulated Purex solutions.

  15. Two-photon vibrational spectroscopy for biosciences based on surface-enhanced hyper-Raman scattering

    PubMed Central

    Kneipp, Janina; Kneipp, Harald; Kneipp, Katrin

    2006-01-01

    Two-photon excitation is gaining rapidly in interest and significance in spectroscopy and microscopy. Here we introduce a new approach that suggests versatile optical labels suitable for both one- and two-photon excitation and also two-photon-excited ultrasensitive, nondestructive chemical probing. The underlying spectroscopic effect is the incoherent inelastic scattering of two photons on the vibrational quantum states called hyper-Raman scattering (HRS). The rather weak effect can be strengthened greatly if HRS takes place in the local optical fields of gold and silver nanostructures. This so-called surface-enhanced HRS (SEHRS) is the two-photon analogue to surface-enhanced Raman scattering (SERS). SEHRS provides structurally sensitive vibrational information complementary to those obtained by SERS. SEHRS combines the advantages of two-photon spectroscopy with the structural information of vibrational spectroscopy and the high-sensitivity and nanometer-scale local confinement of plasmonics-based spectroscopy. We infer effective two-photon cross-sections for SEHRS on the order of 10−46 to 10−45 cm4·s, similar to or higher than the best “action” cross-sections (product of the two-photon absorption cross-section and fluorescence quantum yield) for two-photon fluorescence, and we demonstrate HRS on biological structures such as single cells after incubation with gold nanoparticles. PMID:17088534

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

    NASA Astrophysics Data System (ADS)

    Albert, Julian; Falge, Mirjam; Gomez, Sandra; Sola, Ignacio R.; Hildenbrand, Heiko; Engel, Volker

    2015-07-01

    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.

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

    PubMed

    Albert, Julian; Falge, Mirjam; Gomez, Sandra; Sola, Ignacio R; Hildenbrand, Heiko; Engel, Volker

    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.

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

    PubMed

    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. PMID:27531576

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

    SciTech Connect

    Albert, Julian; Falge, Mirjam; Hildenbrand, Heiko; Engel, Volker; Gomez, Sandra; Sola, Ignacio R.

    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.

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

    NASA Astrophysics Data System (ADS)

    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

  1. Microwave Spectroscopy of the Excited Vibrational States of Methanol

    NASA Astrophysics Data System (ADS)

    Pearson, John; Daly, Adam M.; Bermúdez, Celina

    2015-06-01

    Methanol is the simplest molecule with a three-fold internal rotation and the observation of its νb{8} band served the primary catalyst for the development of internal rotation theory(a,b). The 75 subsequent years of investigation into the νb{8} band region have yielded a large number assignments, numerous high precision energy levels and a great deal of insight into the coupling of νb{t}=3 & 4 with νb{8}, νb{7}, νb{11} and other nearby states(c). In spite of this progress numerous assignment mysteries persist, the origin of almost half the far infrared laser lines remain unknown and all attempts to model the region quantum mechanically have had very limited success. The C3V internal rotation Hamiltonian has successfully modeled the νb{t}=0,1 & 2 states of methanol and other internal rotors(d). However, successful modeling of the coupling between torsional bath states and excited small amplitude motion remains problematic and coupling of multiple interacting excited small amplitude vibrations featuring large amplitude motions remains almost completely unexplored. Before such modeling can be attempted, identifying the remaining low lying levels of νb{7} and νb{11} is necessary. We present an investigation into the microwave spectrum of νb{7}, νb{8} and νb{11} along with the underlying torsional bath states in νb{t}=3 and νb{t}= 4. (a) A. Borden, E.F. Barker J. Chem. Phys., 6, 553 (1938). (b) J. S. Koehler and D. M. Dennison, Phys. Rev. 57, 1006 (1940). (c) R. M. Lees, Li-Hong Xu, J. W. C. Johns, B. P. Winnewisser, and M. Lock, J. Mol. Spectrosc. 243, 168 (2007). (d) L.-H. Xu, J. Fisher, R.M. Lees, H.Y. Shi, J.T. Hougen, J.C. Pearson, B.J. Drouin, G.A. Blake, R. Braakman J. Mol. Spectrosc., 251, 305 (2008).

  2. Nuclear resonance vibrational spectroscopy (NRVS) of rubredoxin and MoFe protein crystals

    PubMed Central

    Guo, Yisong; Brecht, Eric; Aznavour, Kristen; Nix, Jay C.; Xiao, Yuming; Wang, Hongxin; George, Simon J.; Bau, Robert; Keable, Stephen; Peters, John W.; Adams, Michael W.W.; Jenney, Francis; Sturhahn, Wolfgang; Alp, Ercan E.; Zhao, Jiyong; Yoda, Yoshitaka; Cramer, Stephen P.

    2014-01-01

    We have applied 57Fe nuclear resonance vibrational spectroscopy (NRVS) for the first time to study the dynamics of Fe centers in Fe-S protein crystals, including oxidized wild type rubredoxin crystals from Pyrococcus furiosus, and the MoFe protein of nitrogenase from Azotobacter vinelandii. Thanks to the NRVS selection rule, selectively probed vibrational modes have been observed in both oriented rubredoxin and MoFe protein crystals. The NRVS work was complemented by extended X-ray absorption fine structure spectroscopy (EXAFS) measurements on oxidized wild type rubredoxin crystals from Pyrococcus furiosus. The EXAFS spectra revealed the Fe-S bond length difference in oxidized Pf Rd protein, which is qualitatively consistent with the X-ray crystal structure. PMID:26052177

  3. Vibrational spectroscopy of the borate mineral kotoite Mg₃(BO₃)₂.

    PubMed

    Frost, Ray L; Xi, Yunfei

    2013-02-15

    Vibrational spectroscopy has been used to assess the structure of kotoite a borate mineral of magnesium which is isostructural with jimboite. The mineral is orthorhombic with point group: 2/m 2/m 2/m. The mineral has the potential as a new memory insulator material. The mineral has been characterised by a combination of Raman and infrared spectroscopy. The Raman spectrum is dominated by a very intense band at 835 cm(-1), assigned to the symmetric stretching mode of tetrahedral boron. Raman bands at 919, 985 and 1015 cm(-1) are attributed to the antisymmetric stretching modes of tetrahedral boron. Kotoite is strictly an hydrous borate mineral. An intense Raman band observed at 3559 cm(-1) is attributed to the stretching vibration of hydroxyl units, more likely to be associated with the borate mineral hydroxyborate. The lack of observation of water bending modes proves the absence of water in the kotoite structure. PMID:23257343

  4. Nuclear resonance vibrational spectroscopy (NRVS) of rubredoxin and MoFe protein crystals

    NASA Astrophysics Data System (ADS)

    Guo, Yisong; Brecht, Eric; Aznavour, Kristen; Nix, Jay C.; Xiao, Yuming; Wang, Hongxin; George, Simon J.; Bau, Robert; Keable, Stephen; Peters, John W.; Adams, Michael W. W.; , Francis E. Jenney, Jr.; Sturhahn, Wolfgang; Alp, Ercan E.; Zhao, Jiyong; Yoda, Yoshitaka; Cramer, Stephen P.

    2013-12-01

    We have applied 57Fe nuclear resonance vibrational spectroscopy (NRVS) for the first time to study the dynamics of Fe centers in Iron-sulfur protein crystals, including oxidized wild type rubredoxin crystals from Pyrococcus furiosus, and the MoFe protein of nitrogenase from Azotobacter vinelandii. Thanks to the NRVS selection rule, selectively probed vibrational modes have been observed in both oriented rubredoxin and MoFe protein crystals. The NRVS work was complemented by extended X-ray absorption fine structure spectroscopy (EXAFS) measurements on oxidized wild type rubredoxin crystals from Pyrococcus furiosus. The EXAFS spectra revealed the Fe-S bond length difference in oxidized Pf Rd protein, which is qualitatively consistent with the crystal structure.

  5. Observation of Fe-H/D modes by nuclear resonant vibrational spectroscopy.

    PubMed

    Bergmann, Uwe; Sturhahn, Wolfgang; Linn, Donald E; Jenney, Francis E; Adams, Michael W W; Rupnik, Kresimir; Hales, Brian J; Alp, Ercan E; Mayse, Aaron; Cramer, Stephen P

    2003-04-01

    Metal-hydrogen bonding is important in chemistry and catalysis, but H atoms are often difficult to observe, especially in metalloproteins. In this work we show that Fe-H interactions can be probed by nuclear resonance vibrational spectroscopy at the 14.4 keV 57Fe nuclear resonance. An important advantage of this method, compared to Raman and IR spectroscopy, is the selectivity for modes that involve 57Fe motion. We present data on the FeS4 site in rubredoxin and the [FeH(D)6]2- ion. Prospects for studying more complex systems are discussed.

  6. Observation of Fe-H/D Modes by Nuclear Resonant Vibrational Spectroscopy

    SciTech Connect

    Bergman, U B; Sturhahn, W; Linn, D E; Jenny, F E; Adams, M W. W.; Rupnik, K; Hales, B J; Alp, E E; Mayse, A; Cramer, S P; XFD,

    2003-04-01

    Metal-hydrogen bonding is important in chemistry and catalysis, but H atoms are often difficult to observe, especially in metalloproteins. In this work we show that Fe-H interactions can be probed by nuclear resonance vibrational spectroscopy at the 14.4 keV 57Fe nuclear resonance. An important advantage of this method, compared to Raman and IR spectroscopy, is the selectivity for modes that involve {sup 57}Fe motion. We present data on the FeS{sub 4} site in rubredoxin and the [FeH(D){sub 6}]{sup 2-} ion. Prospects for studying more complex systems are discussed.

  7. Surface vibrational modes of alpha-quartz(0001) probed by sum-frequency spectroscopy.

    PubMed

    Liu, Wei-Tao; Shen, Y R

    2008-07-01

    Infrared-visible sum-frequency spectroscopy was used to probe surface vibrations of alpha-quartz(0001) under ambient conditions. Two modes at 880 and 980 cm(-1) were observed and identified as arising from Si-O-Si and Si-OH structures of the surface. Heat treatment and hydroxylation could convert Si-OH to Si-O-Si and vice versa. The technique is generally applicable to studies of surface phonons of other oxides, semiconductors, and insulators. PMID:18764125

  8. Vibrational spectrum of γ-HNIW investigated using terahertz time-domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Guo, Lantao; Hu, Ying; Zhang, Yan; Zhang, Cunlin; Chen, Yunqing; Zhang, X.-C.

    2006-04-01

    Experimental and theoretical investigations of the vibration spectrum of γ-Hexanitrohexaazaisowurtzitane in the region of 0.2-2.5 terahertz are presented for the first time. The refraction index, absorption coefficient, and complex dielectric function of this sample are measured by terahertz time-domain spectroscopy. The simulated spectrum using density functional theory (DFT) is in agreement with the experimental data. The observed spectra features are assigned based on DFT calculation.

  9. Vibrational spectrum of gamma-HNIW investigated using terahertz time-domain spectroscopy.

    PubMed

    Guo, Lantao; Hu, Ying; Zhang, Yan; Zhang, Cunlin; Chen, Yunqing; Zhang, X-C

    2006-04-17

    Experimental and theoretical investigations of the vibration spectrum of gamma-Hexanitrohexaazaisowurtzitane in the region of 0.2-2.5 terahertz are presented for the first time. The refraction index, absorption coefficient, and complex dielectric function of this sample are measured by terahertz time-domain spectroscopy. The simulated spectrum using density functional theory (DFT) is in agreement with the experimental data. The observed spectra features are assigned based on DFT calculation.

  10. Phthalocyanine adsorption to graphene on Ir(111): Evidence for decoupling from vibrational spectroscopy

    SciTech Connect

    Endlich, M. Gozdzik, S.; Néel, N.; Kröger, J.; Rosa, A. L. da; Frauenheim, T.; Wehling, T. O.

    2014-11-14

    Phthalocyanine molecules have been adsorbed to Ir(111) and to graphene on Ir(111). From a comparison of scanning tunneling microscopy images of individual molecules adsorbed to the different surfaces alone it is difficult to discern potential differences in the molecular adsorption geometry. In contrast, vibrational spectroscopy using inelastic electron scattering unequivocally hints at strong molecule deformations on Ir(111) and at a planar adsorption geometry on graphene. The spectroscopic evidence for the different adsorption configurations is supported by density functional calculations.

  11. Nonlinear vibrational spectroscopy of surfactants at liquid interfaces

    NASA Astrophysics Data System (ADS)

    Miranda, Paulo Barbeitas

    Surfactants are widely used to modify physical and chemical properties of interfaces. They play an important role in many technological problems. Surfactant monolayers 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 monolayers at liquid/vapor 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 conformational order of surfactant monolayers. The first part of the Thesis is concerned with surfactant monolayers at the air/water interface (Langmuir films). Surface crystallization of an alcohol Langmuir film and of liquid alkanes are studied and their phase transition behaviors are found to be of different nature, although driven by similar intermolecular interactions. The effect of crystalline order of Langmuir monolayers on the interfacial water structure is also investigated. It is shown that water forms a well-ordered hydrogen-bonded network underneath an alcohol monolayer, in contrast to a fatty acid monolayer which induces a more disordered structure. In the latter case, ionization of the monolayer becomes more significant with increase of the water pH value, leading to an electric-field-induced ordering of interfacial water molecules. We also show that the orientation and conformation of fairly complicated molecules in a Langmuir monolayer can be completely mapped out using a combination of SFG and second harmonic generation (SHG). For a quantitative analysis of molecular orientation at an interface, local-field corrections must be included. The second part is a study of self-assembled surfactant monolayers at the

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

    PubMed

    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.

  13. Vibrational spectral signatures of crystalline cellulose using high resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS)

    SciTech Connect

    Zhang, Libing; Lu, Zhou; Velarde, Luis; Fu, Li; Pu, Yunqiao; Ding, Shi-You; Ragauskas, Arthur; Wang, Hong-Fei; Yang, Bin

    2015-03-03

    Both the C–H and O–H region spectra of crystalline cellulose were studied using the sub-wavenumber high-resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS) for the first time. The resolution of HR-BB-SFG-VS is about 10-times better than conventional scanning SFG-VS and has the capability of measuring the intrinsic spectral lineshape and revealing many more spectral details. With HR-BB-SFG-VS, we found that in cellulose samples from different sources, including Avicel and cellulose crystals isolated from algae Valonia (Iα) and tunicates (Iβ), the spectral signatures in the O–H region were unique for the two 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 spectral signatures of the crystalline cellulose in the O–H and C–H vibrational frequency regions are yet to be correlated to the structure of cellulose, these results lead to new spectroscopic methods and opportunities to classify and to understand the basic crystalline structures, as well as variations in polymorphism of the crystalline cellulose.

  14. Vibrational spectral signatures of crystalline cellulose using high resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS)

    DOE PAGES

    Zhang, Libing; Lu, Zhou; Velarde, Luis; Fu, Li; Pu, Yunqiao; Ding, Shi-You; Ragauskas, Arthur; Wang, Hong-Fei; Yang, Bin

    2015-03-03

    Both the C–H and O–H region spectra of crystalline cellulose were studied using the sub-wavenumber high-resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS) for the first time. The resolution of HR-BB-SFG-VS is about 10-times better than conventional scanning SFG-VS and has the capability of measuring the intrinsic spectral lineshape and revealing many more spectral details. With HR-BB-SFG-VS, we found that in cellulose samples from different sources, including Avicel and cellulose crystals isolated from algae Valonia (Iα) and tunicates (Iβ), the spectral signatures in the O–H region were unique for the two allomorphs, i.e. Iα and Iβ, while the spectral signaturesmore » in the C–H regions varied in all samples examined. Even though the origin of the different spectral signatures of the crystalline cellulose in the O–H and C–H vibrational frequency regions are yet to be correlated to the structure of cellulose, these results lead to new spectroscopic methods and opportunities to classify and to understand the basic crystalline structures, as well as variations in polymorphism of the crystalline cellulose.« less

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

    SciTech Connect

    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. Investigations of the low frequency modes of ferric cytochrome c using vibrational coherence spectroscopy.

    PubMed

    Karunakaran, Venugopal; Sun, Yuhan; Benabbas, Abdelkrim; Champion, Paul M

    2014-06-12

    Femtosecond vibrational coherence spectroscopy is used to investigate the low frequency vibrational dynamics of the electron transfer heme protein, cytochrome c (cyt c). The vibrational coherence spectra of ferric cyt c have been measured as a function of excitation wavelength within the Soret band. Vibrational coherence spectra obtained with excitation between 412 and 421 nm display a strong mode at ~44 cm(-1) that has been assigned to have a significant contribution from heme ruffling motion in the electronic ground state. This assignment is based partially on the presence of a large heme ruffling distortion in the normal coordinate structural decomposition (NSD) analysis of the X-ray crystal structures. When the excitation wavelength is moved into the ~421-435 nm region, the transient absorption increases along with the relative intensity of two modes near ~55 and 30 cm(-1). The intensity of the mode near 44 cm(-1) appears to minimize in this region and then recover (but with an opposite phase compared to the blue excitation) when the laser is tuned to 443 nm. These observations are consistent with the superposition of both ground and excited state coherence in the 421-435 nm region due to the excitation of a weak porphyrin-to-iron charge transfer (CT) state, which has a lifetime long enough to observe vibrational coherence. The mode near 55 cm(-1) is suggested to arise from ruffling in a transient CT state that has a less ruffled heme due to its iron d(6) configuration.

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

    SciTech Connect

    Cahoon, James Francis

    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.

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

    PubMed

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

    2016-06-28

    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, ν1+ν2+ν3+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. PMID:27369508

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

    PubMed

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

    2016-06-28

    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, ν1+ν2+ν3+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.

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

    NASA Astrophysics Data System (ADS)

    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.

  1. Protein dynamics studied with ultrafast two-dimensional infrared vibrational echo spectroscopy.

    PubMed

    Thielges, Megan C; Fayer, Michael D

    2012-11-20

    Proteins, enzymes, and other biological molecules undergo structural dynamics as an intrinsic part of their biological functions. While many biological processes occur on the millisecond, second, and even longer time scales, the fundamental structural dynamics that eventually give rise to such processes occur on much faster time scales. Many decades ago, chemical kineticists focused on the inverse of the reaction rate constant as the important time scale for a chemical reaction. However, through transition state theory and a vast amount of experimental evidence, we now know that the key events in a chemical reaction can involve structural fluctuations that take a system of reactants to its transition state, the crossing of a barrier, and the eventual relaxation to product states. Such dynamics occur on very fast time scales. Today researchers would like to investigate the fast structural fluctuations of biological molecules to gain an understanding of how biological processes proceed from simple structural changes in biomolecules to the final, complex biological function. The study of the fast structural dynamics of biological molecules requires experiments that operate on the appropriate time scales, and in this Account, we discuss the application of ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy to the study of protein dynamics. The 2D IR vibrational echo experiment is akin to 2D NMR, but it operates on time scales many orders of magnitude faster. In the experiments, a particular vibrational oscillator serves as a vibrational dynamics probe. As the structure of the protein evolves in time, the structural changes are manifested as time-dependent changes in the frequency of the vibrational dynamics probe. The 2D IR vibrational echo experiments can track the vibrational frequency evolution, which we then relate to the time evolution of the protein structure. In particular, we measured protein substate interconversion for mutants of

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

    PubMed

    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.

  3. Damage-free vibrational spectroscopy of biological materials in the electron microscope

    DOE PAGES

    Rez, Peter; Aoki, Toshihiro; March, Katia; Gur, Dvir; Krivanek, Ondrej L.; Dellby, Niklas; Lovejoy, Tracy C.; Wolf, Sharon G.; Cohen, Hagai

    2016-03-10

    Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an ‘aloof’ electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies o1 eV can be ‘safely’ investigated. To demonstrate the potential of aloof spectroscopy, we record electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C–H, N–H and C=O vibrational signatures with nomore » observable radiation damage. Furthermore, the technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ~10nm, simultaneously combined with imaging in the electron microscope.« less

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed Central

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

    2009-01-01

    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 104–105. 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. PMID:19880744

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

    PubMed

    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. PMID:19880744

  7. Accurate Lineshapes from Sub-1 cm-1 Resolution Sum Frequency Generation Vibrational Spectroscopy of α-Pinene at Room Temperature

    SciTech Connect

    Mifflin, Amanda L.; Velarde Ruiz Esparza, Luis A.; Ho, Junming; Psciuk, Brian; Negre, Christian; Ebben, Carlena J.; Upshur, Mary Alice; Lu, Zhou; Strick, Benjamin; Thomson, Regan; Batista, Victor; Wang, Hongfei; Geiger, Franz M.

    2015-02-26

    Room temperature sub-wavenumber high-resolution broadband sum frequency generation (HR-BB-SFG) spectra of the common terpene (+)-α-pinene reveal ten peaks in the C–H stretching region. The spectral resolution exceeds that of Fourier transform infrared, femtosecond stimulated Raman, and traditional BB-SFG and scanning SFG spectroscopy of the same molecule. Experiment and simulation show the spectral lineshapes to be accurate. Homogeneous vibrational decoherence lifetimes of up to 1.7 psec are assigned to specific oscillators and compare favorably to lifetimes computed from density functional tight binding molecular dynamics calculations, while phase-resolved spectra yield orientation information for them. We propose the new spectroscopy as an attractive alternative to time-resolved vibrational spectroscopy or heterodyne-detection schemes for studying vibrational energy relaxation and vibrational coherences in molecules.

  8. Dynamics of Functionalized Surface Molecular Monolayers Studied with Ultrafast Infrared Vibrational Spectroscopy

    PubMed Central

    Rosenfeld, Daniel E.; Nishida, Jun; Yan, Chang; Gengeliczki, Zsolt; Smith, Brian J.; Fayer, Michael D.

    2012-01-01

    The structural dynamics of thin films consisting of tricarbonyl (1,10-phenanthroline)rhenium chloride (RePhen(CO)3Cl) linked to an alkyl silane monolayer through a triazole linker synthesized on silica-on-calcium-fluoride substrates are investigated using ultrafast infrared (IR) techniques. Ultrafast 2D IR vibrational echo experiments and polarization selective heterodyne detected transient grating (HDTG) measurements, as well as polarization dependent FT-IR and AFM experiments are employed to study the samples. The vibrational echo experiments measure spectral diffusion, while the HDTG experiments measure the vibrational excited state population relaxation and investigate the vibrational transition dipole orientational anisotropy decay. To investigate the anticipated impact of vibrational excitation transfer, which can be caused by the high concentration of RePhen(CO)3Cl in the monolayer, a concentration dependence of the spectral diffusion is measured. To generate a range of concentrations, mixed monolayers consisting of both hydrogen terminated and triazole/RePhen(CO)3Cl terminated alkyl silanes are synthesized. It is found that the measured rate of spectral diffusion is independent of concentration, with all samples showing spectral diffusion of 37 ± 6 ps. To definitively test for vibrational excitation transfer, polarization selective HDTG experiments are conducted. Excitation transfer will cause anisotropy decay. Polarization resolved heterodyne detected transient grating spectroscopy is sensitive to anisotropy decay (depolarization) caused by excitation transfer and molecular reorientation. The HDTG experiments show no evidence of anisotropy decay on the appropriate time scale, demonstrating the absence of excitation transfer the RePhen(CO)3Cl. Therefore the influence of excitation transfer on spectral diffusion is inconsequential in these samples, and the vibrational echo measurements of spectral diffusion report solely on structural dynamics. A small

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

    NASA Astrophysics Data System (ADS)

    Wang, Xiaowei; Wang, Qiang

    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.

  10. Vibrational Spectra of Cryogenic Peptide Ions Using H_2 Predissociation Spectroscopy

    NASA Astrophysics Data System (ADS)

    Leavitt, Christopher M.; Wolk, Arron B.; Kamrath, Michael Z.; Garand, Etienne; Johnson, Mark A.; Stipdonk, Michael J. Van

    2011-06-01

    H_2 predissociation spectroscopy was used to collect the vibrational spectra of the model protonated peptides, GlyGly, GlySar, SarGly and SarSar (Gly=glycine and Sar=sarcosine). H_2 molecules were condensed onto protonated peptide ions in a quadrupole ion trap cooled to approximately 10 K. The resulting spectra yielded clearly resolved vibrational transitions throughout the mid IR region, 600-4200 Cm-1, with linewidths of approximately 6 Cm-1. Protonation nominally occurred on the amino terminus giving rise to an intramolecular H-bond between the protonated amine and the neighboring amide oxygen. The sarcosine containing peptides incorporate a methyl group onto either the amino group or the amide nitrogen causing the peptide backbone to adopt a different structure, resulting in the shifts in the amide I and II bands and the N-H stretches.

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

    NASA Astrophysics Data System (ADS)

    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.

  12. Detection of simulants and degradation products of chemical warfare agents by vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Ruiz-Pesante, Orlando; Pacheco-Londoño, Leonardo C.; Primera-Pedrozo, Oliva M.; Ortiz, William; Soto-Feliciano, Yadira M.; Nieves, Deborah E.; Ramirez, Michael L.; Hernández-Rivera, Samuel P.

    2007-04-01

    This work was focused in the measurement of spectroscopic signatures of Chemical Warfare Agent Simulants (CWAS) and degradation products of chemical agents using vibrational spectroscopy for the generation of spectroscopic libraries. The chemicals studied were: DMMP, DIMP, 2-CEES, 2-BAET, 1,4-thioxane, thiodiglycol sulfoxide, dihexylamine, cyclohexylamine, among others. Raman microscopy experiments were performed at different excitation wavelengths that spanned from NIR at 1064 and 785 nm to the VIS at 532, 514.5 and 488 nm and even the deep ultraviolet region at 244 nm. For the compounds studied the optimum excitation lines were 488 nm and 532 nm with a laser power of 25 mW. Among the most prominent bands were at these incident wavelengths were located ca. 652 and 1444 cm-1. Fourier Transform Infrared Spectroscopy in liquid and gas phase and Fiber Optics Coupled-Grazing Angle Probe-FTIR (FOCGAP- FTIR) were used to characterize the spectroscopic signature of target threat agents. The surface experiments were performed at detection levels of about 1 μg/cm2 suggest that limits of detection (LOD) achievable could be as low as nanograms/cm2. Remote sensing experiments were performed using a telescope coupled with a Raman spectrophotometer as a function of power and acquisition time. Characterization of compounds by vibrational spectroscopy and the early stages of the transition from the lab based experiments to remote detection experiments will be presented.

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

    SciTech Connect

    Choi, Jun-Ho; Lim, Sohee; Chon, Bonghwan; Cho, Minhaeng; Kim, Heejae; Kim, Seongheun

    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

  14. Investigations of the Low Frequency Modes of Ferric Cytochrome c Using Vibrational Coherence Spectroscopy

    PubMed Central

    2015-01-01

    Femtosecond vibrational coherence spectroscopy is used to investigate the low frequency vibrational dynamics of the electron transfer heme protein, cytochrome c (cyt c). The vibrational coherence spectra of ferric cyt c have been measured as a function of excitation wavelength within the Soret band. Vibrational coherence spectra obtained with excitation between 412 and 421 nm display a strong mode at ∼44 cm–1 that has been assigned to have a significant contribution from heme ruffling motion in the electronic ground state. This assignment is based partially on the presence of a large heme ruffling distortion in the normal coordinate structural decomposition (NSD) analysis of the X-ray crystal structures. When the excitation wavelength is moved into the ∼421–435 nm region, the transient absorption increases along with the relative intensity of two modes near ∼55 and 30 cm–1. The intensity of the mode near 44 cm–1 appears to minimize in this region and then recover (but with an opposite phase compared to the blue excitation) when the laser is tuned to 443 nm. These observations are consistent with the superposition of both ground and excited state coherence in the 421–435 nm region due to the excitation of a weak porphyrin-to-iron charge transfer (CT) state, which has a lifetime long enough to observe vibrational coherence. The mode near 55 cm–1 is suggested to arise from ruffling in a transient CT state that has a less ruffled heme due to its iron d6 configuration. PMID:24823442

  15. Vibrational structure of the polyunsaturated fatty acids eicosapentaenoic acid and arachidonic acid studied by infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Kiefer, Johannes; Noack, Kristina; Bartelmess, Juergen; Walter, Christian; Dörnenburg, Heike; Leipertz, Alfred

    2010-02-01

    The spectroscopic discrimination of the two structurally similar polyunsaturated C 20 fatty acids (PUFAs) 5,8,11,14,17-eicosapentaenoic acid and 5,8,11,14-eicosatetraenoic acid (arachidonic acid) is shown. For this purpose their vibrational structures are studied by means of attenuated total reflection (ATR) Fourier-transform infrared (FT-IR) spectroscopy. The fingerprint regions of the recorded spectra are found to be almost identical, while the C-H stretching mode regions around 3000 cm -1 show such significant differences as results of electronic and molecular structure alterations based on the different degree of saturation that both fatty acids can be clearly distinguished from each other.

  16. A conformational study of hydroxyflavones by vibrational spectroscopy coupled to DFT calculations

    NASA Astrophysics Data System (ADS)

    Machado, N. F. L.; Batista de Carvalho, L. A. E.; Otero, J. C.; Marques, M. P. M.

    2013-05-01

    The conformational preferences of a series of hydroxyflavones were studied by Raman and FTIR spectroscopies, coupled to Density Functional Theory calculations. Special attention was paid to the effect of hydroxyl substitution, due to its importance on the biological activity of these compounds. Their conformational preferences were found to be determined mainly by the orientation of the hydroxylic groups at C7 and within the catechol moiety, leading to the occurrence of distinct conformers in the solid state. A complete assignment of the experimental spectra was carried out for these molecules, in the light of their most stable conformers and the corresponding predicted vibrational pattern.

  17. Vibrational frequencies of anti-diabetic drug studied by terahertz time-domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Du, S. Q.; Li, H.; Xie, L.; Chen, L.; Peng, Y.; Zhu, Y. M.; Li, H.; Dong, P.; Wang, J. T.

    2012-04-01

    By using terahertz time-domain spectroscopy, the absorption spectra of seven anti-diabetic pills have been investigated. For gliquidone, glipizide, gliclazide, and glimepiride, an obvious resonance peak is found at 1.37 THz. Furthermore, to overcome the limit of density functional theory that can analyze the normal mode frequencies of the ground state of organic material, we also present a method that relies on pharmacophore recognition, from which we can obtain the resonance peak at 1.37 THz can be attributed to the vibration of sulfonylurea group. The results indicate that the veracity of density functional theory can be increased by combining pharmacophore recognition.

  18. Orientation Determination of Protein Helical Secondary Structure Using Linear and Nonlinear Vibrational Spectroscopy

    PubMed Central

    Nguyen, Khoi Tan; Le Clair, Stéphanie V.; Ye, Shuji; Chen, Zhan

    2009-01-01

    In this paper, we systematically presented the orientation determination of protein helical secondary structures using vibrational spectroscopic methods, particularly the nonlinear Sum Frequency Generation (SFG) vibrational spectroscopy, along with linear vibrational spectroscopic techniques such as infrared spectroscopy and Raman scattering. SFG amide I signals can be collected using different polarization combinations of the input laser beams and output signal beam to measure the second order nonlinear optical susceptibility components of the helical amide I modes, which are related to their molecular hyperpolarizability elements through the orientation distribution of these helices. The molecular hyperpolarizability elements of amide I modes of a helix can be calculated based on the infrared transition dipole moment and Raman polarizability tensor of the helix; these quantities are determined by using the bond additivity model to sum over the individual infrared dipole transition moments and Raman polarizability tensors, respectively, of the peptide units (or the amino acid residues). The computed overall infrared transition dipole moment and Raman polarizability tensor of a helix can be validated by experimental data using polarized infrared and polarized Raman spectroscopy on samples with well-aligned helical structures. From the deduced SFG hyperpolarizability elements and measured SFG second order nonlinear susceptibility components, orientation information regarding helical structures can be determined. Even though such orientation information can also be measured using polarized infrared or polarized Raman amide I signals, SFG has a much lower detection limit, which can be used to study the orientation of a helix when its surface coverage is much lower than a monolayer. In addition, the combination of different vibrational spectroscopic techniques, e.g., SFG and Attenuated Total Reflectance – Fourier Transform Infrared spectroscopy, provides more

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

    NASA Astrophysics Data System (ADS)

    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

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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 (<50) using small plasmonic noble metal nanoparticles at solid-liquid interfaces. Here, we show that employment of almost continuous noble metal layers results in significantly stronger enhancement factors in 2D ATR IR signals (>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. PMID:27265518

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

    NASA Astrophysics Data System (ADS)

    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.

  3. Vibrational spectroscopy of synthetic analogues of ankoleite, chernikovite and intermediate solid solution.

    PubMed

    Clavier, N; Crétaz, F; Szenknect, S; Mesbah, A; Poinssot, C; Descostes, M; Dacheux, N

    2016-03-01

    Ankoleite (K(UO2)PO4·nH2O), chernikovite (H3O(UO2)PO4·nH2O) and intermediate solid solutions are frequently encountered in the uranium ores that result from the alteration of uranium primary minerals. This paper reports a thorough FTIR and Raman study related to synthetic analogues for these minerals. First, the vibration bands associated to the UO2(2 +) uranyl ion were used to calculate the U = O bond length which appeared in good agreement with the data coming from PXRD. Then, the examination of the phosphate vibration modes in both sets of spectra confirmed the general formulation of the samples and ruled out the presence of hydrogenphosphate groups. Finally, the presence of H2O as well as protonated H3O(+) and/or H5O2(+) species was also pointed out, and could be used to clearly differentiate the various phases prepared. Vibrational spectroscopy then appeared as an efficient method for the investigation of such analogues of natural samples. It should be particularly relevant when identifying these phases in mineral ores or assemblies.

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

    PubMed

    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 (<50) using small plasmonic noble metal nanoparticles at solid-liquid interfaces. Here, we show that employment of almost continuous noble metal layers results in significantly stronger enhancement factors in 2D ATR IR signals (>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.

  5. Vibrational spectroscopy of synthetic analogues of ankoleite, chernikovite and intermediate solid solution.

    PubMed

    Clavier, N; Crétaz, F; Szenknect, S; Mesbah, A; Poinssot, C; Descostes, M; Dacheux, N

    2016-03-01

    Ankoleite (K(UO2)PO4·nH2O), chernikovite (H3O(UO2)PO4·nH2O) and intermediate solid solutions are frequently encountered in the uranium ores that result from the alteration of uranium primary minerals. This paper reports a thorough FTIR and Raman study related to synthetic analogues for these minerals. First, the vibration bands associated to the UO2(2 +) uranyl ion were used to calculate the U = O bond length which appeared in good agreement with the data coming from PXRD. Then, the examination of the phosphate vibration modes in both sets of spectra confirmed the general formulation of the samples and ruled out the presence of hydrogenphosphate groups. Finally, the presence of H2O as well as protonated H3O(+) and/or H5O2(+) species was also pointed out, and could be used to clearly differentiate the various phases prepared. Vibrational spectroscopy then appeared as an efficient method for the investigation of such analogues of natural samples. It should be particularly relevant when identifying these phases in mineral ores or assemblies. PMID:26688205

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

    PubMed

    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

  7. Emission spectroscopy of anharmonic vibrational series for micro-hollow cathode discharge plasmas

    NASA Astrophysics Data System (ADS)

    Lozano F., A.; Juárez, A. M.

    2013-09-01

    The field of micro plasmas is currently very active, due to the useful properties and potential applications of micro-hollow cathode discharges.Our group is currently developing these discharge characterization techniques and, as a first obvious starting point, we are performing emission spectroscopy in normal discharges. The focus of this particular contribution is to present a study of vibrational eigenvalues of Morse potential for diatomic molecules. We performed the experimental measurements of these eigenvalues using a high resolution optical monochromator and a parallel plate nitrogen discharge in the glow regime. In particular we determined using this simple arrangement the ro-vibration transitions in N2, between the electronic states C3Πu -B1Πg . Moreover, we evaluated theoretically the anharmonic eigenvalues of these transitions using Wigner function for a Morse potential. Based on experimental measurements and making use of the calculated Franck-Condon factors it is possible to extract energy potential parameters of these energy states directly from measured transitions. In particular we have calculated the internuclear separation between the excited states associated with the vibrational transitions observed. This work was funded by the grant DGAPA-PAPIIT IT100613.

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

    PubMed Central

    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

  9. Vibrational Sum Frequency Generation Spectroscopy Study of Hydrous Species in Soda Lime Silica Float Glass.

    PubMed

    Luo, Jiawei; Banerjee, Joy; Pantano, Carlo G; Kim, Seong H

    2016-06-21

    It is generally accepted that the mechanical properties of soda lime silica (SLS) glass can be affected by the interaction between sodium ions and hydrous species (silanol groups and water molecules) in its surface region. While the amount of these hydrous species can be estimated from hydrogen profiles and infrared spectroscopy, their chemical environment in the glass network is still not well understood. This work employed vibrational sum frequency generation (SFG) spectroscopy to investigate the chemical environment of hydrous species in the surface region of SLS float glass. SLS float glass shows sharp peaks in the OH stretching vibration region in SFG spectra, while the OH stretch peaks of glasses that do not have leachable sodium ions and the OH peaks of water molecules in condensed phases are normally broad due to fast hydrogen bonding dynamics. The hydrous species responsible for the sharp SFG peaks for the SLS float glass were found to be thermodynamically more stable than physisorbed water molecules, did not exchange with D2O, and were associated with the sodium concentration gradient in the dealkalized subsurface region. These results suggested that the hydrous species reside in static solvation shells defined by the silicate network with relatively slow hydrogen bonding dynamics, compared to physisorbed water layers on top of the glass surface. A putative radial distribution of the hydrous species within the SLS glass network was estimated based on the OH SFG spectral features, which could be compared with theoretical distributions calculated from computational simulations. PMID:27254814

  10. Vibrational Sum Frequency Generation Spectroscopy Study of Hydrous Species in Soda Lime Silica Float Glass.

    PubMed

    Luo, Jiawei; Banerjee, Joy; Pantano, Carlo G; Kim, Seong H

    2016-06-21

    It is generally accepted that the mechanical properties of soda lime silica (SLS) glass can be affected by the interaction between sodium ions and hydrous species (silanol groups and water molecules) in its surface region. While the amount of these hydrous species can be estimated from hydrogen profiles and infrared spectroscopy, their chemical environment in the glass network is still not well understood. This work employed vibrational sum frequency generation (SFG) spectroscopy to investigate the chemical environment of hydrous species in the surface region of SLS float glass. SLS float glass shows sharp peaks in the OH stretching vibration region in SFG spectra, while the OH stretch peaks of glasses that do not have leachable sodium ions and the OH peaks of water molecules in condensed phases are normally broad due to fast hydrogen bonding dynamics. The hydrous species responsible for the sharp SFG peaks for the SLS float glass were found to be thermodynamically more stable than physisorbed water molecules, did not exchange with D2O, and were associated with the sodium concentration gradient in the dealkalized subsurface region. These results suggested that the hydrous species reside in static solvation shells defined by the silicate network with relatively slow hydrogen bonding dynamics, compared to physisorbed water layers on top of the glass surface. A putative radial distribution of the hydrous species within the SLS glass network was estimated based on the OH SFG spectral features, which could be compared with theoretical distributions calculated from computational simulations.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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. PMID:27557194

  13. Dye aggregation identified by vibrational coupling using 2D IR spectroscopy

    SciTech Connect

    Oudenhoven, Tracey A.; Laaser, Jennifer E.; Zanni, Martin T.; Joo, Yongho; Gopalan, Padma

    2015-06-07

    We report that a model dye, Re(CO){sub 3}(bypy)CO{sub 2}H, aggregates into clusters on TiO{sub 2} nanoparticles regardless of our preparation conditions. Using two-dimensional infrared (2D IR) spectroscopy, we have identified characteristic frequencies of monomers, dimers, and trimers. A comparison of 2D IR spectra in solution versus those deposited on TiO{sub 2} shows that the propensity to dimerize in solution leads to higher dimer formation on TiO{sub 2}, but that dimers are formed even if there are only monomers in solution. Aggregates cannot be washed off with standard protocols and are present even at submonolayer coverages. We observe cross peaks between aggregates of different sizes, primarily dimers and trimers, indicating that clusters consist of microdomains in close proximity. 2D IR spectroscopy is used to draw these conclusions from measurements of vibrational couplings, but if molecules are close enough to be vibrationally coupled, then they are also likely to be electronically coupled, which could alter charge transfer.

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

    PubMed Central

    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

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

    PubMed

    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.

  16. Potential biomedical application of the Los Alamos infrared free-electron laser: DNA spectroscopy

    NASA Astrophysics Data System (ADS)

    Lumpkin, A. H.; Trewhella, J.; Garcia, A. E.

    Recently, the Los Alamos Free-Electron Laser has demonstrated optical output at wavelengths from 9 to 45 microns. Potential application of such a laser are proposed for the study of vibrational modes predicted in different conformations of DNA and in DNA complexed with drugs and/or proteins that regulate replication and/or transcription.

  17. Vibrational dynamics of azide-derivatized amino acids studied by nonlinear infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Okuda, Masaki; Ohta, Kaoru; Tominaga, Keisuke

    2015-06-01

    Recently, biomolecules which are labeled by azide or thiocyanate groups in solutions and proteins have been studied to examine microscopic environment around a solute by nonlinear infrared (IR) spectroscopy. In this study, we have performed two-dimensional infrared (2D-IR) spectroscopy to investigate the vibrational frequency fluctuations of two different azide-derivatized amino acids, Ala (N3-Ala) and Pro (N3-Pro), and N3- in water. From the 2D-IR experiments, it was found that the frequency-frequency time correlation function (FFTCF) of solute can be modeled by a delta function plus an exponential function and constant. FFTCF for each probe molecule has a decay component of about 1 ps, and this result suggests that the stretching mode of the covalently bonded azide group is sensitive to the fluctuations of hydrogen bond network system, as found in previous studies of N3- in water. In contrast to FFTCF of N3-, FFTCF of the azide-derivatized amino acids contains static component. This static component may reflect dynamics of water affected by the solutes or the structural fluctuations of the solute itself. We also performed the IR pump-probe measurements for the probe molecules in water in order to investigate vibrational energy relaxation (VER) and reorientational relaxation. It was revealed that the charge fluctuations in the azide group are significant for the VER of this mode in water, reflecting that the VER rate of N3- is faster than those of the azide-derivatized amino acids. While the behaviors of the anisotropy decay of N3-Ala and N3- are similar to each other, the anisotropy decay of N3-Pro contains much slower decaying component. By considering the structural difference around the vibrational probe between N3-Ala and N3-Pro, it is suggested that the structural freedom of the probe molecules can affect the reorientational processes.

  18. Fermi resonance effects in the vibrational spectroscopy of methyl and methoxy groups.

    PubMed

    Sibert, Edwin L; Tabor, Daniel P; Kidwell, Nathanael M; Dean, Jacob C; Zwier, Timothy S

    2014-11-26

    A theoretical model Hamiltonian [J. Chem. Phys. 2013, 138, 064308] for describing vibrational spectra associated with the CH stretch of CH2 groups is extended to molecules containing methyl and methoxy groups. Results are compared to the infrared (IR) spectroscopy of four molecules studied under supersonic expansion cooling in gas phase conditions. The molecules include 1,1-diphenylethane (DPE), 1,1-diphenylpropane (DPP), 2-methoxyphenol (guaiacol), and 1,3-dimethoxy-2-hydroxybenzene (syringol). Transforming the bending normal mode vibrations of CH3 groups to local scissor vibrations leads to model Hamiltonians which share many features present in our model Hamiltonian for the stretching vibrations of CH2 Fermi coupled to scissor modes. The central difference arises from the greater scissor-scissor coupling present in the CH3 case. Comparing anharmonic couplings between these modes and the stretch-bend Fermi coupling for a variety of systems, it is observed that the anharmonic couplings are robust; their values are similar for the four molecules studied as well as for ethane and methanol. Similar results are obtained with both density functional theory and coupled-cluster calculations. This robustness suggests a new parametrization of the model Hamiltonian that reduces the number of fitting parameters. In contrast, the harmonic contributions to the Hamiltonian vary substantially between the molecules leading to important changes in the spectra. The resulting Hamiltonian predicts most of the major spectral features considered in this study and provides insights into mode mixing and the consequences of the mixing on dynamical processes that follow ultrafast CH stretch excitation. PMID:25373009

  19. Vibrational spectroscopy and relaxation of an anharmonic oscillator coupled to harmonic bath.

    PubMed

    Joutsuka, Tatsuya; Ando, Koji

    2011-05-28

    The vibrational spectroscopy and relaxation of an anharmonic oscillator coupled to a harmonic bath are examined to assess the applicability of the time correlation function (TCF), the response function, and the semiclassical frequency modulation (SFM) model to the calculation of infrared (IR) spectra. These three approaches are often used in connection with the molecular dynamics simulations but have not been compared in detail. We also analyze the vibrational energy relaxation (VER), which determines the line shape and is itself a pivotal process in energy transport. The IR spectra and VER are calculated using the generalized Langevin equation (GLE), the Gaussian wavepacket (GWP) method, and the quantum master equation (QME). By calculating the vibrational frequency TCF, a detailed analysis of the frequency fluctuation and correlation time of the model is provided. The peak amplitude and width in the IR spectra calculated by the GLE with the harmonic quantum correction are shown to agree well with those by the QME though the vibrational frequency is generally overestimated. The GWP method improves the peak position by considering the zero-point energy and the anharmonicity although the red-shift slightly overshoots the QME reference. The GWP also yields an extra peak in the higher-frequency region than the fundamental transition arising from the difference frequency of the center and width oscillations of a wavepacket. The SFM approach underestimates the peak amplitude of the IR spectra but well reproduces the peak width. Further, the dependence of the VER rate on the strength of an excitation pulse is discussed. PMID:21639460

  20. Dynamics of Proteins Encapsulated in Silica Sol-gel Glasses Studied with IR Vibrational Echo Spectroscopy

    PubMed Central

    Massari, Aaron M.; Finkelstein, Ilya J.; Fayer, Michael D.

    2008-01-01

    Spectrally-resolved infrared stimulated vibrational echo spectroscopy is used to measure the fast dynamics of heme-bound CO in carbonmonoxy-myoglobin (MbCO) and hemoglobin (HbCO) embedded in silica sol-gel glasses. On the time scale of ~100 fs to several ps, the vibrational dephasing of the heme-bound CO is measurably slower for both MbCO and HbCO relative to aqueous protein solutions. The fast structural dynamics of MbCO, as sensed by the heme-bound CO, are influenced more by the sol-gel environment than those of HbCO. Longer time scale structural dynamics (tens of ps), as measured by the extent of spectral diffusion, are the same for both proteins encapsulated in sol-gel glasses compared to aqueous solutions. A comparison of the sol-gel experimental results to viscosity dependent vibrational echo data taken on various mixtures of water and fructose shows that the sol-gel encapsulated MbCO exhibits dynamics that are the equivalent to the protein in a solution that is nearly 20 times more viscous than bulk water. In contrast, the HbCO dephasing in the sol-gel reflects only a 2-fold increase in viscosity. Attempts to alter the encapsulating pore size by varying the molar ratio of silane precursor to water (R-value) used to prepare the sol-gel glasses were found to have no effect on the fast or steady-state spectroscopic results. The vibrational echo data are discussed in the context of solvent confinement and protein-pore wall interactions to provide insights into the influence of a confined environment on the fast structural dynamics experienced by a biomolecule. PMID:16551107

  1. Laser double-resonance studies of electronic spectroscopy and state-resolved collisional relaxation in highly vibrationally excited acetylene

    SciTech Connect

    Tobiason, J.D.

    1992-01-01

    Vibrational overtone excitation combined with laser-induced fluorescence detection of acetylene molecules permits rotation-selected spectroscopy of the ([tilde A][sup 1]A[sub u]) electronic state and direct, state-resolved measurements of collisional energy transfer in the highly vibrationally excited ground electronic state. The author assigns energies of 1,045 transitions to previously unobserved ungerade vibrational states 2800-4500 cm[sup [minus]1] above the [tilde A] state origin. An analysis yields frequencies of 2856.4 and 3894.3 cm[sup [minus]1] for [nu][sub v][prime] and [nu][sub 3][prime] + [nu][sub 5][prime]. The author performs the first normal coordinate analysis of [tilde A] state acetylene based only on directly observed fundamentals. The spectroscopy measurements enable double-resonance experiments on the collisional dynamics of highly vibrationally excited acetylene. The quenching rate for single rotational states is twice the Lennard-Jones gas kinetic rate and fairly independent of vibrational energy level. Collision-induced detection of vibrational overtone excitation under single collision conditions allows direct measurements of state-of-state rotational and vibrational energy transfer. A collision-induced spectrum obtained by this new technique immediately identifies transfer channels and the [Delta]J and [Delta]E dependence of the transfer rates. The author observes changes of [vert bar][Delta]J[vert bar] and [Delta]E [approx] 3kT in a single collision. Directly measured rates for one set of vibrational relaxation pathways account for [approximately]3% of the total relaxation rate. The author also observes other vibrational relaxation pathways. The available pathways suggest that vibrational relaxation accounts for the rest of the total relaxation. Changes of [vert bar]J[vert bar] = 18 and [vert bar][Delta]E[vert bar] [approximately] 500 cm[sup [minus]1] in a single collision are observed.

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

    PubMed

    Sandasi, Maxleene; Vermaak, Ilze; Chen, Weiyang; Viljoen, Alvaro

    2016-01-01

    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. PMID:27077839

  3. Biomedical Probes Based on Inorganic Nanoparticles for Electrochemical and Optical Spectroscopy Applications

    PubMed Central

    Yakoh, Abdulhadee; Pinyorospathum, Chanika; Siangproh, Weena; Chailapakul, Orawon

    2015-01-01

    Inorganic nanoparticles usually provide novel and unique physical properties as their size approaches nanometer scale dimensions. The unique physical and optical properties of nanoparticles may lead to applications in a variety of areas, including biomedical detection. Therefore, current research is now increasingly focused on the use of the high surface-to-volume ratios of nanoparticles to fabricate superb chemical- or biosensors for various detection applications. This article highlights various kinds of inorganic nanoparticles, including metal nanoparticles, magnetic nanoparticles, nanocomposites, and semiconductor nanoparticles that can be perceived as useful materials for biomedical probes and points to the outstanding results arising from their use in such probes. The progress in the use of inorganic nanoparticle-based electrochemical, colorimetric and spectrophotometric detection in recent applications, especially bioanalysis, and the main functions of inorganic nanoparticles in detection are reviewed. The article begins with a conceptual discussion of nanoparticles according to types, followed by numerous applications to analytes including biomolecules, disease markers, and pharmaceutical substances. Most of the references cited herein, dating from 2010 to 2015, generally mention one or more of the following characteristics: a low detection limit, good signal amplification and simultaneous detection capabilities. PMID:26343676

  4. Vibrational dynamics in dendridic oligoarylamines by Raman spectroscopy and incoherent inelastic neutron scattering.

    PubMed

    Kulszewicz-Bajer, Irena; Louarn, Guy; Djurado, David; Skorka, Lukasz; Szymanski, Marek; Mevellec, Jean Yves; Rols, Stephane; Pron, Adam

    2014-05-15

    Vibrational dynamics in triarylamine dendrimers was studied in a complementary way by Raman and infrared (IR) spectroscopies and incoherent inelastic neutron scattering (IINS). Three molecules were investigated, namely, unsubstituted triarylamine dendrimer of the first generation and two dendrimers of the first and second generation, substituted in the crown with butyl groups. To facilitate the assignment of the observed IR and Raman modes as well as the IINS peaks, vibrational models, based on the general valence force field method (GVFF), were calculated for all three compounds studied. A perfect consistency between the calculated and experimental results was found. Moreover, an important complementarity of the vibrational spectroscopies and IINS was established for the investigated dendrimers. The IINS peaks originating mainly from the C-H motions were not restricted by particular selection rules and only dependent on the IINS cross section. To the contrary, Raman and IR bands were imposed by the selection rules and the local geometry of the dendrimers yielding mainly C-C and C-N deformation modes with those of C-H nature of much lower intensity. Raman spectroscopy was also applied to the studies of the oxidation of dendrimers to their cationic forms. A strong Raman resonance effect was observed, since the spectra of the studied compounds, registered at different levels of their oxidation, strongly depended on the position of the excitation line with respect to their electronic spectrum. In particular, the blue (458 nm) excitation line turned out to be insensitive toward the cationic forms yielding very limited spectral information. To the contrary, the use of the red (647 nm) and infrared (1064 nm) excitation lines allowed for an unambiguous monitoring of the spectral changes in dendrimers oxidized to nominally monocationic and tricationic states. The analysis of oxidation-induced spectral changes in the tricationic state indicated that the charge storage

  5. Investigations of gas/electrode interactions in solid oxide fuel cells using vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Abernathy, Harry Wilson, III

    The goal of current solid oxide fuel cell (SOFC) research is to design electrode materials and other system components that permit the fuel cell to be operated in the 400-700°C range. Cell performance in this lower temperature range is limited by the oxygen reduction process at the SOFC cathode and by multiple contamination processes. The work presented demonstrates that Raman spectroscopy, a form of vibrational spectroscopy, can provide structural and compositional information complementary to that from traditional characterization methods. Initial experiments into the oxygen reduction mechanism on SOFC cathodes were unable to detect surface oxygen species on selected perovksite-based SOFC cathode materials. However, the Raman signal from the cathode surface was able to be enhanced by depositing silver or gold nanoparticles on the cathode, creating the so-called surface-enhanced Raman scattering (SERS) effect. The Raman sample chamber was also used to study two possible electrode contamination processes. First, the deposition of carbon on nickel and copper anodes was observed when exposed to different hydrocarbon fuel gases. Second, the poisoning of an SOFC cathode by chromium-containing vapor (usually generated by stainless steel SOFC system components) was monitored. Overall, Raman spectroscopy was shown to be useful in many areas crucial to the development of practical, cost-effective SOFCs. The techniques developed here could also be applied to other high temperature electrochemical and catalytic systems.

  6. Two-dimensional vibrational spectroscopy of the amide I band of crystalline acetanilide: Fermi resonance, conformational substates, or vibrational self-trapping?

    NASA Astrophysics Data System (ADS)

    Edler, J.; Hamm, P.

    2003-08-01

    Two-dimensional infrared (2D-IR) spectroscopy is applied to investigate acetanilide, a molecular crystal consisting of quasi-one-dimensional hydrogen bonded peptide units. The amide-I band exhibits a double peak structure, which has been attributed to different mechanisms including vibrational self-trapping, a Fermi resonance, or the existence of two conformational substates. The 2D-IR spectrum of crystalline acetanilide is compared with that of two different molecular systems: (i) benzoylchloride, which exhibits a strong symmetric Fermi resonance and (ii) N-methylacetamide dissolved in methanol which occurs in two spectroscopically distinguishable conformations. Both 2D-IR spectra differ significantly from that of crystalline acetanilide, proving that these two alternative mechanisms cannot account for the anomalous spectroscopy of crystalline acetanilide. On the other hand, vibrational self-trapping of the amide-I band can naturally explain the 2D-IR response.

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

    PubMed

    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.

  8. Vibrational spectroscopy of the borate mineral henmilite Ca₂Cu[B(OH)₄]₂(OH)₄.

    PubMed

    Frost, Ray L; Xi, Yunfei

    2013-02-15

    Henmilite is a triclinic mineral with the crystal structure consisting of isolated B(OH)(4) tetrahedra, planar Cu(OH)(4) groups and Ca(OH)(3) polyhedra. The structure can also be viewed as having dimers of Ca polyhedra connected to each other through 2B(OH) tetrahedra to form chains parallel to the C axis. The structure of the mineral has been assessed by the combination of Raman and infrared spectra. Raman bands at 902, 922, 951, and 984 cm(-1) and infrared bands at 912, 955 and 998 cm(-1) are assigned to stretching vibrations of tetragonal boron. The Raman band at 758 cm(-1) is assigned to the symmetric stretching mode of tetrahedral boron. The series of bands in the 400-600 cm(-1) region are due to the out-of-plane bending modes of tetrahedral boron. Two very sharp Raman bands are observed at 3559 and 3609 cm(-1). Two infrared bands are found at 3558 and 3607 cm(-1). These bands are assigned to the OH stretching vibrations of the OH units in henmilite. A series of Raman bands are observed at 3195, 3269, 3328, 3396, 3424 and 3501 cm(-1) are assigned to water stretching modes. Infrared spectroscopy also identified water and OH units in the henmilite structure. It is proposed that water is involved in the structure of henmilite. Hydrogen bond distances based upon the OH stretching vibrations using a Libowitzky equation were calculated. The number and variation of water hydrogen bond distances are important for the stability off the mineral. PMID:23261634

  9. Sum Frequency Generation Vibrational Spectroscopy of Pyridine Hydrogenation on Platinum Nanoparticles

    SciTech Connect

    Bratlie, Kaitlin M.; Komvopoulos, Kyriakos; Somorjai, Gabor A.

    2008-02-22

    Pyridine hydrogenation in the presence of a surface monolayer consisting of cubic Pt nanoparticles stabilized by tetradecyltrimethylammonium bromide (TTAB) was investigated by sum frequency generation (SFG) vibrational spectroscopy using total internal reflection (TIR) geometry. TIR-SFG spectra analysis revealed that a pyridinium cation (C{sub 5}H{sub 5}NH{sup +}) forms during pyridine hydrogenation on the Pt nanoparticle surface, and the NH group in the C{sub 5}H{sub 5}NH{sup +} cation becomes more hydrogen bound with the increase of the temperature. In addition, the surface coverage of the cation decreases with the increase of the temperature. An important contribution of this study is the in situ identification of reaction intermediates adsorbed on the Pt nanoparticle monolayer during pyridine hydrogenation.

  10. Vibrational Sum Frequency Spectroscopy on Polyelectrolyte Multilayers: Effect of Molecular Surface Structure on Macroscopic Wetting Properties.

    PubMed

    Gustafsson, Emil; Hedberg, Jonas; Larsson, Per A; Wågberg, Lars; Johnson, C Magnus

    2015-04-21

    Adsorption of a single layer of molecules on a surface, or even a reorientation of already present molecules, can significantly affect the surface properties of a material. In this study, vibrational sum frequency spectroscopy (VSFS) has been used to study the change in molecular structure at the solid-air interface following thermal curing of polyelectrolyte multilayers of poly(allylamine hydrochloride) and poly(acrylic acid). Significant changes in the VSF spectra were observed after curing. These changes were accompanied by a distinct increase in the static water contact angle, showing how the properties of the layer-by-layer molecular structure are controlled not just by the polyelectrolyte in the outermost layer but ultimately by the orientation of the chemical constituents in the outermost layers. PMID:25859709

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

    NASA Astrophysics Data System (ADS)

    Xu, Hao; Song, Yuxin; Pan, Wenwu; Chen, Qimiao; Wu, Xiaoyan; Lu, Pengfei; Gong, Qian; Wang, Shumin

    2015-08-01

    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.

  12. Two-dimensional ultrafast vibrational spectroscopy of azides in ionic liquids reveals solute-specific solvation.

    PubMed

    Dutta, Samrat; Ren, Zhe; Brinzer, Thomas; Garrett-Roe, Sean

    2015-10-28

    The stereochemistry and the reaction rates of bimolecular nucleophilic substitution reactions involving azides in ionic liquids are governed by solute-solvent interactions. Two-dimensional ultrafast vibrational spectroscopy (2D-IR) shows that the picosecond dynamics of inorganic azides are substantially slower than organic azides in a series of homologous imidazolium ionic liquids. In water, both organic and inorganic azides spectrally diffuse with a ∼2 ps time constant. In the aprotic solvent tetrahydrofuran, both kinds of azides spectrally diffuse on a timescale >5 ps. In ionic liquids, like 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]), organic azides spectrally diffuse with a 2-4 ps time constant, and inorganic azides spectrally diffuse with a >40 ps time constant. Such a striking difference suggests that neutral (organic) and charged (inorganic) azides are incorporated in the ionic liquids with different solvation structures.

  13. Laser-induced breakdown spectroscopy with laser irradiation resonant with vibrational transitions

    SciTech Connect

    Khachatrian, Ani; Dagdigian, Paul J.

    2010-05-01

    An investigation of laser-induced breakdown spectroscopy (LIBS) of polymers, both in bulk form and spin coated on Si wafers, with laser irradiation in the mid-infrared spectral region is presented. Of particular interest is whether the LIBS signals are enhanced when the laser wavelength is resonant with a fundamental vibrational transition of the polymer. Significant increases in the LIBS signals were observed for irradiation on hydride stretch fundamental transitions, and the magnitude of the enhancement showed a strong dependence on the mode excited. The role of the substrate was investigated by comparison of results for bulk and spin-coated samples. The polymers investigated were Nylon 12 and poly(vinyl alcohol-co-ethylene).

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

    PubMed

    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.

  15. Extracting biomarkers of commitment to cancer development: potential role of vibrational spectroscopy in systems biology.

    PubMed

    Theophilou, Georgios; Paraskevaidi, Maria; Lima, Kássio M G; Kyrgiou, Maria; Martin-Hirsch, Pierre L; Martin, Francis L

    2015-05-01

    The complex processes driving cancer have so far impeded the discovery of dichotomous biomarkers associated with its initiation and progression. Reductionist approaches utilizing 'omics' technologies have met some success in identifying molecular alterations associated with carcinogenesis. Systems biology is an emerging science that combines high-throughput investigation techniques to define the dynamic interplay between regulatory biological systems in response to internal and external cues. Vibrational spectroscopy has the potential to play an integral role within systems biology research approaches. It is capable of examining global models of carcinogenesis by scrutinizing chemical bond alterations within molecules. The application of infrared or Raman spectroscopic approaches coupled with computational analysis under the systems biology umbrella can assist the transition of biomarker research from the molecular level to the system level. The comprehensive representation of carcinogenesis as a multilevel biological process will inevitably revolutionize cancer-related healthcare by personalizing risk prediction and prevention.

  16. Detection of water and its derivatives on individual nanoparticles using vibrational electron energy-loss spectroscopy.

    PubMed

    Crozier, Peter A; Aoki, Toshihiro; Liu, Qianlang

    2016-10-01

    Understanding the role of water, hydrate and hydroxyl species on nanoparticle surfaces and interfaces is very important in both physical and life sciences. Detecting the presence of oxygen-hydrogen species with nanometer resolution is extremely challenging at present. Here we show that the recently developed vibrational electron energy-loss spectroscopy using subnanometer focused electron beams can be employed to spectroscopically identify the local presence and variation of OH species on nanoscale surfaces. The hydrogen-oxygen fingerprint can be correlated with highly localized structural and morphological information obtained from electron imaging. Moreover, the current approach exploits the aloof beam mode of spectral acquisition which does not require direct electron irradiation of the sample thus greatly reducing beam damage to the OH bond. These findings open the door for using electron microscopy to probe local hydroxyl and hydrate species on nanoscale organic and inorganic structures. PMID:27423795

  17. Theoretical study of sum-frequency vibrational spectroscopy on limonene surface

    NASA Astrophysics Data System (ADS)

    Zheng, Ren-Hui; Wei, Wen-Mei; Liu, Hao; Jing, Yuan-Yuan; Wang, Bo-Yang; Shi, Qiang

    2014-03-01

    By combining molecule dynamics (MD) simulation and quantum chemistry computation, we calculate the surface sum-frequency vibrational spectroscopy (SFVS) of R-limonene molecules at the gas-liquid interface for SSP, PPP, and SPS polarization combinations. The distributions of the Euler angles are obtained using MD simulation, the ψ-distribution is between isotropic and Gaussian. Instead of the MD distributions, different analytical distributions such as the δ-function, Gaussian and isotropic distributions are applied to simulate surface SFVS. We find that different distributions significantly affect the absolute SFVS intensity and also influence on relative SFVS intensity, and the δ-function distribution should be used with caution when the orientation distribution is broad. Furthermore, the reason that the SPS signal is weak in reflected arrangement is discussed.

  18. Theoretical study of sum-frequency vibrational spectroscopy on limonene surface

    SciTech Connect

    Zheng, Ren-Hui Liu, Hao; Jing, Yuan-Yuan; Wang, Bo-Yang; Shi, Qiang; Wei, Wen-Mei

    2014-03-14

    By combining molecule dynamics (MD) simulation and quantum chemistry computation, we calculate the surface sum-frequency vibrational spectroscopy (SFVS) of R-limonene molecules at the gas-liquid interface for SSP, PPP, and SPS polarization combinations. The distributions of the Euler angles are obtained using MD simulation, the ψ-distribution is between isotropic and Gaussian. Instead of the MD distributions, different analytical distributions such as the δ-function, Gaussian and isotropic distributions are applied to simulate surface SFVS. We find that different distributions significantly affect the absolute SFVS intensity and also influence on relative SFVS intensity, and the δ-function distribution should be used with caution when the orientation distribution is broad. Furthermore, the reason that the SPS signal is weak in reflected arrangement is discussed.

  19. Vibrational spectroscopy and principal component analysis for conformational study of virus nucleic acids

    NASA Astrophysics Data System (ADS)

    Dovbeshko, G. I.; Repnytska, O. P.; Pererva, T.; Miruta, A.; Kosenkov, D.

    2004-07-01

    Conformation analysis of mutated DNA-bacteriophages (PLys-23, P23-2, P47- the numbers have been assigned by T. Pererva) induced by MS2 virus incorporated in Ecoli AB 259 Hfr 3000 has been done. Surface enhanced infrared absorption (SEIRA) spectroscopy and principal component analysis has been applied for solving this problem. The nucleic acids isolated from the mutated phages had a form of double stranded DNA with different modifications. The nucleic acid from phage P47 was undergone the structural rearrangement in the most degree. The shape and position ofthe fine structure of the Phosphate asymmetrical band at 1071cm-1 as well as the stretching OH vibration at 3370-3390 cm-1 has indicated to the appearance ofadditional OH-groups. The Z-form feature has been found in the base vibration region (1694 cm-1) and the sugar region (932 cm-1). A supposition about modification of structure of DNA by Z-fragments for P47 phage has been proposed. The P23-2 and PLys-23 phages have showed the numerous minor structural changes also. On the basis of SEIRA spectra we have determined the characteristic parameters of the marker bands of nucleic acid used for construction of principal components. Contribution of different spectral parameters of nucleic acids to principal components has been estimated.

  20. Probing the phosphopantetheine arm conformations of acyl carrier proteins using vibrational spectroscopy.

    PubMed

    Johnson, Matthew N R; Londergan, Casey H; Charkoudian, Louise K

    2014-08-13

    Acyl carrier proteins (ACPs) are universal and highly conserved domains central to both fatty acid and polyketide biosynthesis. These proteins tether reactive acyl intermediates with a swinging 4'-phosphopantetheine (Ppant) arm and interact with a suite of catalytic partners during chain transport and elongation while stabilizing the growing chain throughout the biosynthetic pathway. The flexible nature of the Ppant arm and the transient nature of ACP-enzyme interactions impose a major obstacle to obtaining structural information relevant to understanding polyketide and fatty acid biosynthesis. To overcome this challenge, we installed a thiocyanate vibrational spectroscopic probe on the terminal thiol of the ACP Ppant arm. This site-specific probe successfully reported on the local environment of the Ppant arm of two ACPs previously characterized by solution NMR, and was used to determine the solution exposure of the Ppant arm of an ACP from 6-deoxyerythronolide B synthase (DEBS). Given the sensitivity of the probe's CN stretching band to conformational distributions resolved on the picosecond time scale, this work lays a foundation for observing the dynamic action-related structural changes of ACPs using vibrational spectroscopy.

  1. Metal-Catalyzed Chemical Reaction of Single Molecules Directly Probed by Vibrational Spectroscopy.

    PubMed

    Choi, Han-Kyu; Park, Won-Hwa; Park, Chan-Gyu; Shin, Hyun-Hang; Lee, Kang Sup; Kim, Zee Hwan

    2016-04-01

    The study of heterogeneous catalytic reactions remains a major challenge because it involves a complex network of reaction steps with various intermediates. If the vibrational spectra of individual molecules could be monitored in real time, one could characterize the structures of the intermediates and the time scales of reaction steps without ensemble averaging. Surface-enhanced Raman scattering (SERS) spectroscopy does provide vibrational spectra with single-molecule sensitivity, but typical single-molecule SERS signals exhibit spatial heterogeneities and temporal fluctuations, making them difficult to be used in single-molecule kinetics studies. Here we show that SERS can monitor the single-molecule catalytic reactions in real time. The surface-immobilized reactants placed at the junctions of well-defined nanoparticle-thin film structures produce time-resolved SERS spectra with discrete, step-transitions of photoproducts. We interpret that such SERS-steps correspond to the reaction events of individual molecules occurring at the SERS hotspot. The analyses of the yield, dynamics, and the magnitude of such SERS steps, along with the associated spectral characteristics, fully support our claim. In addition, a model that is based on plasmonic field enhancement and surface photochemistry reproduces the key features of experimental observation. Overall, the result demonstrates that it is possible, under well-controlled conditions, to differentiate the chemical and physical processes contributing to the single-molecule SERS signals, and thus shows the use of single-molecule SERS as a tool for studying the metal-catalyzed organic reactions.

  2. A new aromatic probe - The ring stretching vibration Raman spectroscopy frequency

    NASA Astrophysics Data System (ADS)

    Guo, Yan-bo; Liu, Zi-zhong; Liu, Hong-xia; Zhang, Feng-ying; Yin, Jun-qing

    2016-07-01

    A new aromatic criterion is presented to determine the aromatic degree of the high symmetric molecules. Group theory is used to explain the correlation between the aromatic degree and the value of Ring Stretching Vibration Raman Spectroscopic Frequency (RSVRSF). The calculations of the geometrical optimization, nucleus-independent chemical shifts (NICS) and values of the Raman Spectroscopy for the aromatic molecules-LnHn (L = C, Si, Ge, n = 3, 5-8) were performed using the Density Functional Theory (DFT) Method, as well as the correlations between the values of their RSVRSF and NICS values by Statistic Package for Social Science (SPSS17.0). There are high positive correlations between the theoretical calculated the NICS values and the value of the RSVRSF (A1g/A1‧) of the LnHn (L = C, Si, Ge, n = 3, 5-8). The bigger the aromatic degree, the bigger the RSVRSF is. The value of the RSVRSF is a new probe of aromaticity. Expectedly, it is predicted that the experimental determination of the aromatic degree can be achieved by the determination of the ring stretching vibration (A1g/A1‧) Raman spectrum frequencies for the aromatic target molecules.

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

    ERIC Educational Resources Information Center

    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.

  4. Early identification of cervical neoplasia with Raman spectroscopy and advanced methods for biomedical applications

    NASA Astrophysics Data System (ADS)

    Jess, Phillip R. T.; Smith, Daniel D. W.; Mazilu, Michael; Cormack, Iain; Riches, Andrew C.; Herrington, C. Simon; Dholakia, Kishan

    2008-02-01

    Early detection of malignant tumours, or their precursor lesions, can dramatically improve patient outcome. High risk human Papillomavirus (HPV), particularly HPV16, infection can lead to the initiation and development of uterine cervical neoplasia. Bearing this in mind the identification of the effects of HPV infection may have clinical value. In this manuscript we investigate the application of Raman microspectroscopy to detect the presence of HPV in cultured cells when compared with normal cells. We also investigate the effect of sample fixation, which is a common clinical practice, on the ability of Raman spectroscopy to detect the presence of HPV. Raman spectra were acquired from Primary Human Keratinocytes (PHK), PHK expressing the E7 gene of HPV 16 (PHK E7) and CaSki cells, an HPV16 containing cervical carcinoma derived cell line. The average Raman spectra display variations, mostly in peaks relating to DNA and proteins, consistent with HPV gene expression and the onset of neoplasia in both live and fixed samples. Principle component analysis was used to objectively discriminate between the cells types giving sensitivities up to 100% for the comparison between PHK and CaSki. These results show that Raman spectroscopy can discriminate between cell lines representing different stages of cervical neoplasia. Furthermore Raman spectroscopy was able to identify cells expressing the HPV 16 E7 gene suggesting the approach may be of value in clinical practice. Finally this technique was also able to detect the effects of the virus in fixed samples demonstrating the compatibility of this technique with current cervical screening methods. However if Raman spectroscopy is to make a significant impact in clinical practice the long acquisition times must be addressed. In this report we examine the potential for beam shaping and advanced to improve the signal to noise ration hence subsequently facilitating a reduction in acquisition time.

  5. Characterization of starch polymorphic structures using vibrational sum frequency generation spectroscopy.

    PubMed

    Kong, Lingyan; Lee, Christopher; Kim, Seong H; Ziegler, Gregory R

    2014-02-20

    The polymorphic structures of starch were characterized with vibrational sum frequency generation (SFG) spectroscopy. The noncentrosymmetry requirement of SFG spectroscopy allows for the detection of the ordered domains without spectral interferences from the amorphous phase and also the distinction of the symmetric elements among crystalline polymorphs. The V-type amylose was SFG-inactive due to the antiparallel packing of single helices in crystal unit cells, whereas the A- and B-type starches showed strong SFG peaks at 2904 cm(-1) and 2952-2968 cm(-1), which were assigned to CH stretching of the axial methine group in the ring and CH2 stretching of the exocyclic CH2OH side group, respectively. The CH2/CH intensity ratios of the A- and B-type starches are significantly different, indicating that the conformation of hydroxymethyl groups in these two polymorphs may be different. Cyclodextrin inclusion complexes were also analyzed as a comparison to the V-type amylose and showed that the head-to-tail and head-to-head stacking patterns of cyclodextrin molecules govern their SFG signals and peak positions. Although the molecular packing is different between V-type amylose and cyclodextrin inclusion complexes, both crystals show the annihilation of SFG signals when the functional group dipoles are arranged pointing in opposite directions. PMID:24432980

  6. Characterization of starch polymorphic structures using vibrational sum frequency generation spectroscopy.

    PubMed

    Kong, Lingyan; Lee, Christopher; Kim, Seong H; Ziegler, Gregory R

    2014-02-20

    The polymorphic structures of starch were characterized with vibrational sum frequency generation (SFG) spectroscopy. The noncentrosymmetry requirement of SFG spectroscopy allows for the detection of the ordered domains without spectral interferences from the amorphous phase and also the distinction of the symmetric elements among crystalline polymorphs. The V-type amylose was SFG-inactive due to the antiparallel packing of single helices in crystal unit cells, whereas the A- and B-type starches showed strong SFG peaks at 2904 cm(-1) and 2952-2968 cm(-1), which were assigned to CH stretching of the axial methine group in the ring and CH2 stretching of the exocyclic CH2OH side group, respectively. The CH2/CH intensity ratios of the A- and B-type starches are significantly different, indicating that the conformation of hydroxymethyl groups in these two polymorphs may be different. Cyclodextrin inclusion complexes were also analyzed as a comparison to the V-type amylose and showed that the head-to-tail and head-to-head stacking patterns of cyclodextrin molecules govern their SFG signals and peak positions. Although the molecular packing is different between V-type amylose and cyclodextrin inclusion complexes, both crystals show the annihilation of SFG signals when the functional group dipoles are arranged pointing in opposite directions.

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

    NASA Astrophysics Data System (ADS)

    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)

  8. Characterizing interstate vibrational coherent dynamics of surface adsorbed catalysts by fourth-order 3D SFG spectroscopy

    NASA Astrophysics Data System (ADS)

    Li, Yingmin; Wang, Jiaxi; Clark, Melissa L.; Kubiak, Clifford P.; Xiong, Wei

    2016-04-01

    We report the first fourth-order 3D SFG spectroscopy of a monolayer of the catalyst Re(diCN-bpy)(CO)3Cl on a gold surface. Besides measuring the vibrational coherences of single vibrational modes, the fourth-order 3D SFG spectrum also measures the dynamics of interstate coherences and vibrational coherences states between two vibrational modes. By comparing the 3D SFG to the corresponding 2D and third-order 3D IR spectroscopy of the same molecules in solution, we found that the interstate coherences exist in both liquid and surface systems, suggesting that the interstate coherence is not disrupted by surface interactions. However, by analyzing the 3D spectral lineshape, we found that the interstate coherences also experience non-negligible homogenous dephasing dynamics that originate from surface interactions. This unique ability of determining interstate vibrational coherence dynamics of the molecular monolayer can help in understanding of how energy flows within surface catalysts and other molecular monolayers.

  9. Vibrational spectroscopy of the phosphate mineral kovdorskite - Mg2PO4(OH)ṡ3H2O

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; López, Andrés; Xi, Yunfei; Granja, Amanda; Scholz, Ricardo; Lima, Rosa Malena Fernandes

    2013-10-01

    The mineral kovdorskite Mg2PO4(OH)ṡ3H2O was studied by electron microscopy, thermal analysis and vibrational spectroscopy. A comparison of the vibrational spectroscopy of kovdorskite is made with other magnesium bearing phosphate minerals and compounds. Electron probe analysis proves the mineral is very pure. The Raman spectrum is characterized by a band at 965 cm-1 attributed to the PO43- ν1 symmetric stretching mode. Raman bands at 1057 and 1089 cm-1 are attributed to the PO43- ν3 antisymmetric stretching modes. Raman bands at 412, 454 and 485 cm-1 are assigned to the PO43- ν2 bending modes. Raman bands at 536, 546 and 574 cm-1 are assigned to the PO43- ν4 bending modes. The Raman spectrum in the OH stretching region is dominated by a very sharp intense band at 3681 cm-1 assigned to the stretching vibration of OH units. Infrared bands observed at 2762, 2977, 3204, 3275 and 3394 cm-1 are attributed to water stretching bands. Vibrational spectroscopy shows that no carbonate bands are observed in the spectra; thus confirming the formula of the mineral as Mg2PO4(OH)ṡ3H2O.

  10. Vibrational spectroscopy of the phosphate mineral kovdorskite-Mg2PO4(OH)·3H2O.

    PubMed

    Frost, Ray L; López, Andrés; Xi, Yunfei; Granja, Amanda; Scholz, Ricardo; Lima, Rosa Malena Fernandes

    2013-10-01

    The mineral kovdorskite Mg2PO4(OH)·3H2O was studied by electron microscopy, thermal analysis and vibrational spectroscopy. A comparison of the vibrational spectroscopy of kovdorskite is made with other magnesium bearing phosphate minerals and compounds. Electron probe analysis proves the mineral is very pure. The Raman spectrum is characterized by a band at 965 cm(-1) attributed to the PO4(3-) ν1 symmetric stretching mode. Raman bands at 1057 and 1089 cm(-1) are attributed to the PO4(3-) ν3 antisymmetric stretching modes. Raman bands at 412, 454 and 485 cm(-1) are assigned to the PO4(3-) ν2 bending modes. Raman bands at 536, 546 and 574 cm(-1) are assigned to the PO4(3-) ν4 bending modes. The Raman spectrum in the OH stretching region is dominated by a very sharp intense band at 3681 cm(-1) assigned to the stretching vibration of OH units. Infrared bands observed at 2762, 2977, 3204, 3275 and 3394 cm(-1) are attributed to water stretching bands. Vibrational spectroscopy shows that no carbonate bands are observed in the spectra; thus confirming the formula of the mineral as Mg2PO4(OH)·3H2O.

  11. Vibrational spectroscopy of the phosphate mineral kovdorskite-Mg2PO4(OH)·3H2O.

    PubMed

    Frost, Ray L; López, Andrés; Xi, Yunfei; Granja, Amanda; Scholz, Ricardo; Lima, Rosa Malena Fernandes

    2013-10-01

    The mineral kovdorskite Mg2PO4(OH)·3H2O was studied by electron microscopy, thermal analysis and vibrational spectroscopy. A comparison of the vibrational spectroscopy of kovdorskite is made with other magnesium bearing phosphate minerals and compounds. Electron probe analysis proves the mineral is very pure. The Raman spectrum is characterized by a band at 965 cm(-1) attributed to the PO4(3-) ν1 symmetric stretching mode. Raman bands at 1057 and 1089 cm(-1) are attributed to the PO4(3-) ν3 antisymmetric stretching modes. Raman bands at 412, 454 and 485 cm(-1) are assigned to the PO4(3-) ν2 bending modes. Raman bands at 536, 546 and 574 cm(-1) are assigned to the PO4(3-) ν4 bending modes. The Raman spectrum in the OH stretching region is dominated by a very sharp intense band at 3681 cm(-1) assigned to the stretching vibration of OH units. Infrared bands observed at 2762, 2977, 3204, 3275 and 3394 cm(-1) are attributed to water stretching bands. Vibrational spectroscopy shows that no carbonate bands are observed in the spectra; thus confirming the formula of the mineral as Mg2PO4(OH)·3H2O. PMID:23778171

  12. Raman and surface-enhanced Raman spectroscopy of amino acids and nucleotide bases for target bacterial vibrational mode identification

    NASA Astrophysics Data System (ADS)

    Guicheteau, Jason; Argue, Leanne; Hyre, Aaron; Jacobson, Michele; Christesen, Steven D.

    2006-05-01

    Raman and surface-enhanced Raman spectroscopy (SERS) studies of bacteria have reported a wide range of vibrational mode assignments associated with biological material. We present Raman and SER spectra of the amino acids phenylalanine, tyrosine, tryptophan, glutamine, cysteine, alanine, proline, methionine, asparagine, threonine, valine, glycine, serine, leucine, isoleucine, aspartic acid and glutamic acid and the nucleic acid bases adenosine, guanosine, thymidine, and uridine to better characterize biological vibrational mode assignments for bacterial target identification. We also report spectra of the bacteria Bacillus globigii, Pantoea agglomerans, and Yersinia rhodei along with band assignments determined from the reference spectra obtained.

  13. A study of the eigenvectors of the low-frequency vibrational modes in crystalline adenosine via high pressure Raman spectroscopy.

    PubMed

    Lee, Scott A; Pinnick, David A; Anderson, A

    2014-12-01

    High-pressure Raman spectroscopy has been used to study the eigenvectors and eigenvalues of the vibrational modes of crystalline adenosine at 295 K by evaluating the logarithmic derivative of the vibrational frequency with respect to pressure: [Formula: see text]. Crystalline samples of molecular materials such as adenosine will have vibrational modes that are localized within a molecular unit ("internal" modes) as well as modes in which the molecular units vibrate against each other ("external" modes). The value of the logarithmic derivative is found to be a diagnostic probe of the nature of the eigenvector of the vibrational modes. Stretching modes which are predominantly internal to the molecule have low logarithmic derivatives while external modes have higher logarithmic derivatives. Particular interest is paid to the low-frequency (≤150 cm(-1)) modes. Based on the pressure dependence of its logarithmic derivative, a mode near 49 cm(-1) is identified as internal mode. The other modes below 400 cm(-1) have pressure dependences of their logarithmic derivatives consistent with being either (1) modes which are mainly external, meaning that the molecules of the unit cell vibrate against each other in translational or librational motions (or linear combinations thereof), or (2) torsional or bending modes involving a large number of atoms, mainly within a molecule. The modes above 400 cm(-1) all have pressure dependences of their logarithmic derivatives consistent with being mainly internal modes. PMID:24127792

  14. Biomedical magnetic resonance imaging and spectroscopy with laser polarized noble gases

    SciTech Connect

    Welsh, R.C.; Rosen, M.S.; Coulter, K.P.; Chupp, T.E.; Swanson, S.D.; Agranoff, B.W.; Prince, M.R.

    1996-05-01

    In the past year, a great deal of attention has been drawn to the use of laser polarized noble gases to produce magnetic resonance images of rodent and human lungs. Initial demonstrations proved the principle that air space images can be produced with noble gases polarized to several percent. (The noble gas density is thousands of times greater than the proton polarization of order 10{sup {minus}5} at 2 Tesla.) The manifold motivations include improvement of pulmonary and circulatory diagnostic radiology techniques as well as study of physiological function including neurological response. The authors have undertaken a program of development and application of MR imaging and spectroscopy using laser polarized gases with several goals including development of techniques and technologies to facilitate research and eventual medical applications. This talk will describe this multi-disciplinary program combining laser and optical physics, magnetic resonance tomography, neurophysiology and medical science.

  15. Time-Resolved Resonance Raman Spectroscopy of Vibrational Populations Monitored after Electronic and Infrared Excitation

    SciTech Connect

    Werncke, W.; Kozich, V.; Dreyer, J.

    2008-11-14

    Pathways of vibrational energy flow in molecules with an intramolecular hydrogen bond are studied after intramolecular proton transfer reactions as well as after infrared excitation of the O-H stretching vibration which is coupled to this hydrogen bond.

  16. Biomedical spectroscopy in clinical applications and implications of liquid crystal filter technologies

    NASA Astrophysics Data System (ADS)

    McMurdy, John W.

    This dissertation discusses two related clinical applications of visible regime diffuse reflectance spectroscopy as well as two new configurations of liquid crystal microspectrometer suitable in these applications. Total hemoglobin concentration can be determined, and thus anemia diagnosed, using diffuse reflectance signals from the inner lining of the eyelid, the palpebral conjunctiva. Alternative technologies for anemia detection are explored, a theoretical model for light diffusion through the conjunctiva is presented, and predictive models are established relating spectral signatures to hemoglobin concentration. Two separate clinical trials were conducted showing accuracy of hemoglobin determination with respect to invasive determination of 5% and 8% of mean hemoglobin concentration, respectively. Local hemoglobin concentration can also be determined in vivo at individual vessels using a single fiber which is directly applicable in endoscopic and laparoscopic surgery. Clinical trials showed signal differentiation of different hemoglobin levels in laparoscopic cases when pressing the single fiber against an individual vessel, and donor/recipient differentiation in fetal endoscopy cases of twin to twin transfusion syndrome. Liquid crystal technologies can be used to create integrated chip-scale microspectrometers. In one configuration, analog tunable ferroelectric liquid crystals are applied to create a tunable filter spectrometer with resolution from 15-30 nm. In a second configuration, stressed liquid crystal polymer composites are used to create large phase modulators, subsequently applied as single panel Fourier transform spectrometers. Proof of concept studies show a 100 microm stressed liquid crystal polymer in double pass mode is capable of 60 nm resolving power.

  17. A new resonance-frequency based electrical impedance spectroscopy and its application in biomedical engineering

    NASA Astrophysics Data System (ADS)

    Dhurjaty, Sreeram; Qiu, Yuchen; Tan, Maxine; Zheng, Bin

    2014-03-01

    Electrical Impedance Spectroscopy (EIS) has shown promising results for differentiating between malignant and benign tumors, which exhibit different dielectric properties. However, the performance of current EIS systems has been inadequate and unacceptable in clinical practice. In the last several years, we have been developing and testing a new EIS approach using resonance frequencies for detection and classification of suspicious tumors. From this experience, we identified several limitations of current technologies and designed a new EIS system with a number of new characteristics that include (1) an increased A/D (analog-to-digital) sampling frequency, 24 bits, and a frequency resolution of 100 Hz, to increase detection sensitivity (2) automated calibration to monitor and correct variations in electronic components within the system, (3) temperature sensing and compensation algorithms to minimize impact of environmental change during testing, and (4) multiple inductor-switching to select optimum resonance frequencies. We performed a theoretical simulation to analyze the impact of adding these new functions for improving performance of the system. This system was also tested using phantoms filled with variety of liquids. The theoretical and experimental test results are consistent with each other. The experimental results demonstrated that this new EIS device possesses the improved sensitivity and/or signal detection resolution for detecting small impedance or capacitance variations. This provides the potential of applying this new EIS technology to different cancer detection and diagnosis tasks in the future.

  18. Vibrational and electronic dynamics of nitrogen-vacancy centres in diamond revealed by two-dimensional ultrafast spectroscopy

    NASA Astrophysics Data System (ADS)

    Huxter, V. M.; Oliver, T. A. A.; Budker, D.; Fleming, G. R.

    2013-11-01

    The optical and material properties of negatively charged nitrogen-vacancy (NV) centres in diamond make them attractive for applications ranging from quantum information to electromagnetic sensing. These properties are strongly dependent on the vibrational manifold associated with the centre, which determines phenomena associated with decoherence, relaxation and spin-orbit coupling. Despite its paramount importance in tuning these properties, the role of the vibrational bath and its effect on the electronic-state dynamics of NV centres in diamond is not fully understood. To elucidate the role of the bath, we present two-dimensional electronic spectroscopic studies of ensembles of negatively charged NV defect centres in diamond (NVD). We observe picosecond non-radiative relaxation within the phonon sideband and find that strongly coupled local modes dominate the vibrational bath. These findings provide a starting point for new insights into dephasing, spin addressing and relaxation in NVD with broad implications for magnetometry, quantum information, nanophotonics, sensing and ultrafast spectroscopy.

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

    PubMed

    Morini, Filippo; Deleuze, Michael S; Watanabe, Noboru; Takahashi, Masahiko

    2015-03-01

    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 A1 symmetry on the 9a1 momentum profile, which can be unravelled from considerations on the symmetry characteristics of orbitals and their energy spacing.

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

    SciTech Connect

    Morini, Filippo; Deleuze, Michael S.; Watanabe, Noboru; Takahashi, Masahiko

    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.

  1. Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy

    SciTech Connect

    Ogata, Hideaki; Krämer, Tobias; Wang, Hongxin; Schilter, David; Pelmenschikov, Vladimir; van Gastel, Maurice; Neese, Frank; Rauchfuss, Thomas B.; Gee, Leland B.; Scott, Aubrey D.; Yoda, Yoshitaka; Lubitz, Wolfgang; Cramer, Stephen P.

    2015-08-10

    The metabolism of many anaerobes relies on [NiFe]-hydrogenases, whose characterization when bound to substrates has proven non-trivial. Presented here is direct evidence for a hydride bridge in the active site of the 57Fe-labelled fully reduced Ni-R form of Desulfovibrio vulgaris Miyazaki F [NiFe]-hydrogenase. A unique ‘wagging’ mode involving H- motion perpendicular to the Ni(μ-H)57Fe plane was studied using 57Fe-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(μ-D)57Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe–CO/CN bands. Spectra have been interpreted by comparison with Ni(μ-H/D)57Fe enzyme mimics [(dppe)Ni(μ-pdt)(μ-H/D)57Fe(CO)3]+ and DFT calculations, which collectively indicate a low-spin Ni(II)(μ-H)Fe(II) core for Ni-R, with H- binding Ni more tightly than Fe. Lastly, the present methodology is also relevant to characterizing Fe–H moieties in other important natural and synthetic catalysts.

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

    SciTech Connect

    Roy, S.; Gruenbaum, S. M.; Skinner, J. L.

    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.

  3. Vibrational spectroscopy and microspectroscopy analyzing qualitatively and quantitatively pharmaceutical hot melt extrudates.

    PubMed

    Netchacovitch, L; Thiry, J; De Bleye, C; Chavez, P-F; Krier, F; Sacré, P-Y; Evrard, B; Hubert, Ph; Ziemons, E

    2015-09-10

    Since the last decade, more and more Active Pharmaceutical Ingredient (API) candidates have poor water solubility inducing low bioavailability. These molecules belong to the Biopharmaceutical Classification System (BCS) classes II and IV. Thanks to Hot-Melt Extrusion (HME), it is possible to incorporate these candidates in pharmaceutical solid forms. Indeed, HME increases the solubility and the bioavailability of these drugs by encompassing them in a polymeric carrier and by forming solid dispersions. Moreover, in 2004, the FDA's guidance initiative promoted the usefulness of Process Analytical Technology (PAT) tools when developing a manufacturing process. Indeed, the main objective when developing a new pharmaceutical process is the product quality throughout the production chain. The trend is to follow this parameter in real-time in order to react immediately when there is a bias. Vibrational spectroscopic techniques, NIR and Raman, are useful to analyze processes in-line. Moreover, off-line Raman microspectroscopy is more and more used when developing new pharmaceutical processes or when analyzing optimized ones by combining the advantages of Raman spectroscopy and imaging. It is an interesting tool for homogeneity and spatial distribution studies. This review treats about spectroscopic techniques analyzing a HME process, as well off-line as in-line, presenting their advantages and their complementarities. PMID:25704954

  4. Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Ogata, Hideaki; Krämer, Tobias; Wang, Hongxin; Schilter, David; Pelmenschikov, Vladimir; van Gastel, Maurice; Neese, Frank; Rauchfuss, Thomas B.; Gee, Leland B.; Scott, Aubrey D.; Yoda, Yoshitaka; Tanaka, Yoshihito; Lubitz, Wolfgang; Cramer, Stephen P.

    2015-08-01

    The metabolism of many anaerobes relies on [NiFe]-hydrogenases, whose characterization when bound to substrates has proven non-trivial. Presented here is direct evidence for a hydride bridge in the active site of the 57Fe-labelled fully reduced Ni-R form of Desulfovibrio vulgaris Miyazaki F [NiFe]-hydrogenase. A unique `wagging' mode involving H- motion perpendicular to the Ni(μ-H)57Fe plane was studied using 57Fe-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(μ-D)57Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe-CO/CN bands. Spectra have been interpreted by comparison with Ni(μ-H/D)57Fe enzyme mimics [(dppe)Ni(μ-pdt)(μ-H/D)57Fe(CO)3]+ and DFT calculations, which collectively indicate a low-spin Ni(II)(μ-H)Fe(II) core for Ni-R, with H- binding Ni more tightly than Fe. The present methodology is also relevant to characterizing Fe-H moieties in other important natural and synthetic catalysts.

  5. Exploring the Underlying Biophysics of Eukaryotic Plasma Membrane Asymmetry by Sum-Frequency Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Conboy, John

    2010-03-01

    A central issue in molecular biology is the movement of lipids across the cellular membrane. The translocation of lipids is involved in cell apoptosis, the viral infection of living cells, the functioning of antibiotics, antiseptics and drugs, and the regulation and growth of cells. There have been a number of studies attempting to find the putative proteins responsive for lipid transbilayer movement in eukaryotic cells. This has led to a large number of theories about the mechanism of transbilayer movement of lipids in cellular systems and the physical process by which lipid compositional asymmetry in the plasma membrane of eukaryotic cells is maintained. Using methods of classical surface chemistry coupled with nonlinear optical methods, we have developed a novel analytical approach, using sum-frequency vibrational spectroscopy (SFVS), to selectively probe lipid compositional asymmetry in a planar supported lipid bilayer. This new method allows for the detection of lipid flip-flop kinetics and compositional asymmetry without the need for a fluorescent or spin-labeled lipid species. The effect of lipid composition, headgroup and fatty acid chemical structure, on the rate and thermodynamics of lipid transbilayer migration and the electrostatic induction of lipid asymmetry will be discussed.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed Central

    Biesheuvel, J.; Karr, J.-Ph.; 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 physical constants and laws. PMID:26815886

  9. Environmental chemistry at vapor/water interfaces: insights from vibrational sum frequency generation spectroscopy.

    PubMed

    Jubb, Aaron M; Hua, Wei; Allen, Heather C

    2012-01-01

    The chemistry that occurs at surfaces has been an intense area of study for many years owing to its complexity and importance in describing a wide range of physical phenomena. The vapor/water interface is particularly interesting from an environmental chemistry perspective as this surface plays host to a wide range of chemistries that influence atmospheric and geochemical interactions. The application of vibrational sum frequency generation (VSFG), an inherently surface-specific, even-order nonlinear optical spectroscopy, enables the direct interrogation of various vapor/aqueous interfaces to elucidate the behavior and reaction of chemical species within the surface regime. In this review we discuss the application of VSFG to the study of a variety of atmospherically important systems at the vapor/aqueous interface. Chemical systems presented include inorganic ionic solutions prevalent in aqueous marine aerosols, small molecular solutes, and long-chain fatty acids relevant to fat-coated aerosols. The ability of VSFG to probe both the organization and reactions that may occur for these systems is highlighted. A future perspective toward the application of VSFG to the study of environmental interfaces is also provided.

  10. Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy

    PubMed Central

    Ogata, Hideaki; Krämer, Tobias; Wang, Hongxin; Schilter, David; Pelmenschikov, Vladimir; van Gastel, Maurice; Neese, Frank; Rauchfuss, Thomas B.; Gee, Leland B.; Scott, Aubrey D.; Yoda, Yoshitaka; Tanaka, Yoshihito; Lubitz, Wolfgang; Cramer, Stephen P.

    2015-01-01

    The metabolism of many anaerobes relies on [NiFe]-hydrogenases, whose characterization when bound to substrates has proven non-trivial. Presented here is direct evidence for a hydride bridge in the active site of the 57Fe-labelled fully reduced Ni-R form of Desulfovibrio vulgaris Miyazaki F [NiFe]-hydrogenase. A unique ‘wagging' mode involving H− motion perpendicular to the Ni(μ-H)57Fe plane was studied using 57Fe-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(μ-D)57Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe–CO/CN bands. Spectra have been interpreted by comparison with Ni(μ-H/D)57Fe enzyme mimics [(dppe)Ni(μ-pdt)(μ-H/D)57Fe(CO)3]+ and DFT calculations, which collectively indicate a low-spin Ni(II)(μ-H)Fe(II) core for Ni-R, with H− binding Ni more tightly than Fe. The present methodology is also relevant to characterizing Fe–H moieties in other important natural and synthetic catalysts. PMID:26259066

  11. Probing Molecular Recognition at the Solid-Gas Interface by Sum-Frequency Vibrational Spectroscopy.

    PubMed

    Aprile, Arianna; Ciuchi, Federica; Pinalli, Roberta; Dalcanale, Enrico; Pagliusi, Pasquale

    2016-08-01

    Molecular recognition is among the most important chemical events in living systems and has been emulated in supramolecular chemistry, driven by chemical and biochemical sensing potential. Identifying host-guest association in situ at the interface, between the substrate-bound receptors and the analyte-containing media, is essential to predict complexation performances in term of the receptor conformation, orientation and organization. Herein, we report the first sum-frequency vibrational spectroscopy study of molecular recognition at the solid-gas interface. The binding capability of tetraquinoxaline cavitands toward volatile aromatic and aliphatic compounds, namely benzonitrile and acetonitrile, is investigated as test system. We prove the selective complexation of the receptors, organized in a solid-supported hybrid bilayer, toward aromatic compounds. Quantitative analysis allows to correlate the average orientations of the guest molecules and the host binding pockets, establishing "on-axis" complexation of benzonitrile within the cavitand cavity. The study is readily applicable to other receptors, molecular architectures, interfaces and analytes. PMID:27438350

  12. Probing QED and fundamental constants through laser spectroscopy of vibrational transitions in HD(.).

    PubMed

    Biesheuvel, J; Karr, J-Ph; 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 physical constants and laws. PMID:26815886

  13. Spatially resolved localized vibrational mode spectroscopy of carbon in liquid encapsulated Czochralski grown gallium arsenide wafers

    SciTech Connect

    Yau, Waifan.

    1988-04-01

    Substitutional carbon on an arsenic lattice site is the shallowest and one of the most dominant acceptors in semi-insulating Liquid Encapsulated Czochralski (LEC) GaAs. However, the role of this acceptor in determining the well known W'' shape spatial variation of neutral EL2 concentration along the diameter of a LEC wafer is not known. In this thesis, we attempt to clarify the issue of the carbon acceptor's effect on this W'' shaped variation by measuring spatial profiles of this acceptor along the radius of three different as-grown LEC GaAs wafers. With localized vibrational mode absorption spectroscopy, we find that the profile of the carbon acceptor is relatively constant along the radius of each wafer. Average values of concentration are 8 {times} 10E15 cm{sup -3}, 1.1 {times} 10E15 cm{sup -3}, and 2.2 {times} 10E15 cm{sup -3}, respectively. In addition, these carbon acceptor LVM measurements indicate that a residual donor with concentration comparable to carbon exists in these wafers and it is a good candidate for the observed neutral EL2 concentration variation. 22 refs., 39 figs.

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

    NASA Astrophysics Data System (ADS)

    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.

  15. Quantitative Surface Chirality Detection with Sum Frequency Generation Vibrational Spectroscopy: Twin Polarization Angle Approach

    SciTech Connect

    Wei, Feng; Xu, Yanyan; Guo, Yuan; Liu, Shi-lin; Wang, Hongfei

    2009-12-27

    Here we report a novel twin polarization angle (TPA) approach in the quantitative chirality detection with the surface sum-frequency generation vibrational spectroscopy (SFG-VS). Generally, the achiral contribution dominates the surface SFG-VS signal, and the pure chiral signal is usually two or three orders of magnitude smaller. Therefore, it has been difficult to make quantitative detection and analysis of the chiral contributions to the surface SFG- VS signal. In the TPA method, by varying together the polarization angles of the incoming visible light and the sum frequency signal at fixed s or p polarization of the incoming infrared beam, the polarization dependent SFG signal can give not only direct signature of the chiral contribution in the total SFG-VS signal, but also the accurate measurement of the chiral and achiral components in the surface SFG signal. The general description of the TPA method is presented and the experiment test of the TPA approach is also presented for the SFG-VS from the S- and R-limonene chiral liquid surfaces. The most accurate degree of chiral excess values thus obtained for the 2878 cm⁻¹ spectral peak of the S- and R-limonene liquid surfaces are (23.7±0.4)% and ({25.4±1.3)%, respectively.

  16. Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy

    DOE PAGES

    Ogata, Hideaki; Krämer, Tobias; Wang, Hongxin; Schilter, David; Pelmenschikov, Vladimir; van Gastel, Maurice; Neese, Frank; Rauchfuss, Thomas B.; Gee, Leland B.; Scott, Aubrey D.; et al

    2015-08-10

    The metabolism of many anaerobes relies on [NiFe]-hydrogenases, whose characterization when bound to substrates has proven non-trivial. Presented here is direct evidence for a hydride bridge in the active site of the 57Fe-labelled fully reduced Ni-R form of Desulfovibrio vulgaris Miyazaki F [NiFe]-hydrogenase. A unique ‘wagging’ mode involving H- motion perpendicular to the Ni(μ-H)57Fe plane was studied using 57Fe-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(μ-D)57Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe–CO/CN bands. Spectra have been interpreted by comparison with Ni(μ-H/D)57Fe enzyme mimics [(dppe)Ni(μ-pdt)(μ-H/D)57Fe(CO)3]+ and DFT calculations, which collectively indicate amore » low-spin Ni(II)(μ-H)Fe(II) core for Ni-R, with H- binding Ni more tightly than Fe. Lastly, the present methodology is also relevant to characterizing Fe–H moieties in other important natural and synthetic catalysts.« less

  17. Ultrafast vibrational spectroscopy of shock compression with molecular resolution: energetic material simulants

    NASA Astrophysics Data System (ADS)

    Dlott, Dana; Lozano, Aaron; Lagutchev, Alexei A.

    2009-06-01

    This project focuses on understanding the properties of molecules immediately behind a shock front using a femtosecond laser to generate a shock wave in a molecular monolayer. In previous work we used nonlinear coherent vibrational spectroscopy to study long chain alkane molecules with a 4 GPa shock. The long-chain molecules have little strength along the long axis, and we found they quickly created gauche defects by rotation around carbon-carbon bonds. We have greatly improved the sensitivity of our laser apparatus. We have also developed the ability to study ``heat shocks'' where large amounts of heat flow ballistically rather than diffusively from a metal surface into the monolayer. We look at energetic molecule simulants, which are monolayers having either nitro or nitramine functionalities. This material is based on work supported by the US Army Research Office under award number UNLV 08-655K-A-00 and the Air Force Office of Scientific Research under award number FA9550-06-1-0235. Aaron Lozano acknowledges the Stewardship Sciences Academic Alliance Program from the Carnegie-DOE Alliance Center under grant number DOE CIW 4-3253-13.

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

    NASA Astrophysics Data System (ADS)

    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.

  19. An experimental and theoretical study of the synthesis and vibrational spectroscopy of triacetone triperoxide (TATP)

    NASA Astrophysics Data System (ADS)

    Pacheco-Londono, Leonardo C.; Pena, Alvaro J.; Primera-Pedrozo, Oliva M.; Hernandez-Rivera, Samuel P.; Mina, Nairmen; Garcia, Rafael; Chamberlain, R. Thomas; Lareau, Richard T.

    2004-09-01

    Non nitrogen containing, organic peroxides explosives Triacetone triperoxide and diacetone diperoxide have been prepared in the laboratory in order to study various aspects of their synthesis and their experimental and theoretical spectroscopic characteristics. By using different proportions of acetone/hydrogen peroxide (Ac/H2O2), sulfuric, hydrochloric and methanosulfuric acids as catalyzers, it was possible to obtain both compounds in a rapid and simple form. Raman, IR spectroscopy, and GC-MS were used in order to determine the precursors, intermediates and final analytes. Experiments and theoretical studies using density functional theory (DFT) have been used in the elucidation step of the mechanism of the synthesis of the so called "transparent" explosives. The B3LYP functional with the 6-31G** basis set was used to carry out the electronic structure calculation of the intermediates and internal rotations and vibrations of TATP. Raman spectra of solid TATP and FTIR spectra of gas TATP, were recorded in order to assign the experimental spectra. Although full agreement with experiment was not obtained, spectral features of the main TATP bands were assigned.

  20. Photoexcitation dynamics of NO-bound ferric myoglobin investigated by femtosecond vibrational spectroscopy.

    PubMed

    Park, Jaeheung; Lee, Taegon; Park, Jaehun; Lim, Manho

    2013-03-14

    Femtosecond vibrational spectroscopy was used to investigate the photoexcitation dynamics of NO-bound ferric myoglobin (Mb(III)NO) in D2O solution at 294 K after excitation with a 575 nm pulse. The stretching mode of NO in Mb(III)NO consists of a major band at 1922 cm(-1) (97.7%) and a minor band at 1902 cm(-1) (2.3%), suggesting that Mb(III)NO in room temperature solution has two conformational substates. The time-resolved spectra show small but significant new absorption features at the lower-energy side of the main band (1920-1800 cm(-1)). One new absorption feature in the region of 1920-1880 cm(-1) exhibits the (15)NO isotope shift (37 cm(-1)) the same as that of the NO band in the ground electronic state of Mb(III)NO. This absorption shifts toward higher energy and narrows with a time constant of 2.4 ps, indicating that it evolves with rapid electronic and thermal relaxation of the photoexcited Mb(III)NO without photodeligation of the NO from the heme. Absorption features assigned to proteins undergoing thermal relaxation without NO deligation add up to 14 ± 1% of the total bleach, implying that the photolysis quantum yield of Mb(III)NO with a Q-band excitation is ≤0.86 ± 0.01. The remaining absorption bands peaked near 1867, 1845, and 1815 cm(-1), each showing the (15)NO isotope shift the same as that of the free NO radical (33 cm(-1)), were assigned to the vibrational band of the photodeligated NO, the NO band of Mb(III)NO in an intermediate electronic state with low-spin Fe(III)-NO(radical) character (denoted as the R state), and the NO band of the vibrationally excited NO in the R state, respectively. A kinetics model successfully reproducing the time-dependent intensity changes of the transient bands suggests that every rebound NO forms the R state that eventually relaxes into the ground electronic state nonexponentially. Most of the photodissociated NO undergoes fast geminate recombination (GR), and the rebinding kinetics depends on the conformation

  1. Hydrogen Bond Lifetimes and Energetics for Solute-Solvent Complexes Studied with 2D-IR Vibrational Echo Spectroscopy

    PubMed Central

    Zheng, Junrong; Fayer, Michael D.

    2008-01-01

    Weak π hydrogen bonded solute-solvent complexes are studied with ultrafast two dimensional infrared (2D-IR) vibrational echo chemical exchange spectroscopy, temperature dependent IR absorption spectroscopy, and density functional theory calculations. Eight solute-solvent complexes composed of a number of phenol derivatives and various benzene derivatives are investigated. The complexes are formed between the phenol derivative (solute) in a mixed solvent of the benzene derivative and CCl4. The time dependence of the 2D-IR vibrational echo spectra of the phenol hydroxyl stretch is used to directly determine the dissociation and formation rates of the hydrogen bonded complexes. The dissociation rates of the weak hydrogen bonds are found to be strongly correlated with their formation enthalpies. The correlation can be described with an equation similar to the Arrhenius equation. The results are discussed in terms of transition state theory. PMID:17373792

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

    NASA Astrophysics Data System (ADS)

    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

  3. Communication: Vibrationally resolved photoelectron spectroscopy of the tetracyanoquinodimethane (TCNQ) anion and accurate determination of the electron affinity of TCNQ

    SciTech Connect

    Zhu, Guo-Zhu; Wang, Lai-Sheng

    2015-12-14

    Tetracyanoquinodimethane (TCNQ) is widely used as an electron acceptor to form highly conducting organic charge-transfer solids. Surprisingly, the electron affinity (EA) of TCNQ is not well known and has never been directly measured. Here, we report vibrationally resolved photoelectron spectroscopy (PES) of the TCNQ{sup −} anion produced using electrospray and cooled in a cryogenic ion trap. Photoelectron spectrum taken at 354.7 nm represents the detachment transition from the ground state of TCNQ{sup −} to that of neutral TCNQ with a short vibrational progression. The EA of TCNQ is measured accurately to be 3.383 ± 0.001 eV (27 289 ± 8 cm{sup −1}), compared to the 2.8 ± 0.1 eV value known in the literature and measured previously using collisional ionization technique. In addition, six vibrational peaks are observed in the photoelectron spectrum, yielding vibrational frequencies for three totally symmetric modes of TCNQ. Two-photon PES via a bound electronic excited state of TCNQ{sup −} at 3.100 eV yields a broad low kinetic energy peak due to fast internal conversion to vibrationally excited levels of the anion ground electronic state. The high EA measured for TCNQ underlies its ability as a good electron acceptor.

  4. Dipole moments of HDO in highly excited vibrational states measured by Stark induced photofragment quantum beat spectroscopy.

    PubMed

    Theulé, Patrice; Callegari, Andrea; Rizzo, Thomas R; Muenter, John S

    2005-03-22

    We report here a measurement of electric dipole moments in highly vibrationally excited HDO molecules. We use photofragment yield detected quantum beat spectroscopy to determine electric field induced splittings of the J=1 rotational levels of HDO excited with 4, 5, and 8 quanta of vibration in the OH stretching mode. The splittings allow us to deduce mua and mub, the projections of dipole moment onto the molecular rotation inertial axes. We compare the measured HDO dipole moment components with the results of quantitative calculations based on Morse oscillator wave functions and an ab initio dipole moment surface. The vibrational dependence of the dipole moment components reflect both structural and electronic changes in HDO upon vibrational excitation; principally the vibrational dependence of the O-H bond length and bond angle, and the resulting change in orientation of the principal inertial coordinate system. The dipole moment data also provide a sensitive test of theoretical dipole moment and potential energy surfaces, particularly for molecular configurations far from equilibrium.

  5. Communication: Vibrationally resolved photoelectron spectroscopy of the tetracyanoquinodimethane (TCNQ) anion and accurate determination of the electron affinity of TCNQ

    NASA Astrophysics Data System (ADS)

    Zhu, Guo-Zhu; Wang, Lai-Sheng

    2015-12-01

    Tetracyanoquinodimethane (TCNQ) is widely used as an electron acceptor to form highly conducting organic charge-transfer solids. Surprisingly, the electron affinity (EA) of TCNQ is not well known and has never been directly measured. Here, we report vibrationally resolved photoelectron spectroscopy (PES) of the TCNQ- anion produced using electrospray and cooled in a cryogenic ion trap. Photoelectron spectrum taken at 354.7 nm represents the detachment transition from the ground state of TCNQ- to that of neutral TCNQ with a short vibrational progression. The EA of TCNQ is measured accurately to be 3.383 ± 0.001 eV (27 289 ± 8 cm-1), compared to the 2.8 ± 0.1 eV value known in the literature and measured previously using collisional ionization technique. In addition, six vibrational peaks are observed in the photoelectron spectrum, yielding vibrational frequencies for three totally symmetric modes of TCNQ. Two-photon PES via a bound electronic excited state of TCNQ- at 3.100 eV yields a broad low kinetic energy peak due to fast internal conversion to vibrationally excited levels of the anion ground electronic state. The high EA measured for TCNQ underlies its ability as a good electron acceptor.

  6. Measurement of vibrational spectrum of liquid using monochromated scanning transmission electron microscopy-electron energy loss spectroscopy.

    PubMed

    Miyata, Tomohiro; Fukuyama, Mao; Hibara, Akihide; Okunishi, Eiji; Mukai, Masaki; Mizoguchi, Teruyasu

    2014-10-01

    Investigations on the dynamic behavior of molecules in liquids at high spatial resolution are greatly desired because localized regions, such as solid-liquid interfaces or sites of reacting molecules, have assumed increasing importance with respect to improving material performance. In application to liquids, electron energy loss spectroscopy (EELS) observed with transmission electron microscopy (TEM) is a promising analytical technique with the appropriate resolutions. In this study, we obtained EELS spectra from an ionic liquid, 1-ethyl-3-methylimidazolium bis (trifluoromethyl-sulfonyl) imide (C2mim-TFSI), chosen as the sampled liquid, using monochromated scanning TEM (STEM). The molecular vibrational spectrum and the highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap of the liquid were investigated. The HOMO-LUMO gap measurement coincided with that obtained from the ultraviolet-visible spectrum. A shoulder in the spectrum observed ∼0.4 eV is believed to originate from the molecular vibration. From a separately performed infrared observation and first-principles calculations, we found that this shoulder coincided with the vibrational peak attributed to the C-H stretching vibration of the [C2mim(+)] cation. This study demonstrates that a vibrational peak for a liquid can be observed using monochromated STEM-EELS, and leads one to expect observations of chemical reactions or aids in the analysis of the dynamic behavior of molecules in liquid.

  7. Light Scattering and Absorption Spectroscopy in Three Dimensions Using Quantitative Low Coherence Interferometry for Biomedical Applications

    NASA Astrophysics Data System (ADS)

    Robles, Francisco E.

    study show that fLCI is able to detect changes in the morphology of tissues undergoing precancerous development. The DW method is also employed to enable a novel form of optical coherence tomography (OCT), an imaging modality that uses coherence gating to obtain micrometer-scale, cross-sectional information of tissues. The novel method, named molecular imaging true color spectroscopic OCT (METRiCS OCT), analyses the depth dependent absorption of light to ascertain quantitative information of chromophore concentration, such as hemoglobin. The molecular information is also processed to yield a true color representation of the sample, a unique capability of this approach. A number of experiments, including hemoglobin absorbing phantoms and in-vivo imaging of a chick embryo model and dorsal skinfold window chamber model, demonstrate the power of the method. The final method presented in this dissertation, consists of a spectroscopic approach that interrogates the dispersive biochemical properties of samples to independently probe the scattering and absorption coefficients. To demonstrate this method, named non-linear phase dispersion spectroscopy (NLDS), a careful analysis of LCI signals is presented. The method is verified using measurements from samples that scatter and absorb light. Lastly, NLDS is combined with phase microscopy to achieve molecular imaging with sub-micron spatial resolution. Imaging of red blood cells (RBCs) shows that the method enables highly sensitive measurements that can quantify hemoglobin content from single RBCs.

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

    SciTech Connect

    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).

  9. Inversion Vibrational Energy Levels of AsH3 + Studied by Zero-Kinetic Photoelectron Spectroscopy

    NASA Astrophysics Data System (ADS)

    Mo, Yuxiang

    2016-06-01

    The rotational-resolved vibrational spectra of AsH3 + have been measured for the first time with vibrational energies up to 6000 wn above the ground state using zero-kinetic energy photoelectron spectroscopic method. The inversion vibrational energy levels (νb{2}) and the corresponding rotational constants for the νb{2} =0-16 have been determined. The tunneling splittings of the inversion vibration energy levels have been observed for the ground and the first excited vibrational states. The geometric parameters of AsH3 + as a function of inversion vibrational quantum states have been determined, indicating that the geometric structure of the cation changes from near planar structure to a pyramidal structure with more vibrational excitations. In addition to the experimental measurement, a two-dimensional theoretical calculation including the two symmetric vibrational modes was performed to determine the energy levels of the symmetric inversion and As-H stretching vibrations. The calculated vibrational energy levels are in good agreement with the experimental results. The first adiabatic ionization energy (IE) for AsH3 was also accurately determined. The result of this work will be compared with our published result on the PH3+.

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

    NASA Astrophysics Data System (ADS)

    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

  11. Photoluminescence spectroscopy of YVO4:Eu3+ nanoparticles with aromatic linker molecules: A precursor to biomedical functionalization

    NASA Astrophysics Data System (ADS)

    Senty, T. R.; Yalamanchi, M.; Zhang, Y.; Cushing, S. K.; Seehra, M. S.; Shi, X.; Bristow, A. D.

    2014-04-01

    Photoluminescence spectra of YVO4:Eu3+ nanoparticles are presented, with and without the attachment of organic molecules that are proposed for linking to biomolecules. YVO4:Eu3+ nanoparticles with 5% dopant concentration were synthesized via wet chemical synthesis. X-ray diffraction and transmission electron microscopy show the expected wakefieldite structure of tetragonal particles with an average size of 17 nm. Fourier-transform infrared spectroscopy determines that metal-carboxylate coordination is successful in replacing native metal-hydroxyl bonds with three organic linkers, namely, benzoic acid, 3-nitro 4-chloro-benzoic acid, and 3,4-dihydroxybenzoic acid, in separate treatments. UV-excitation photoluminescence spectra show that the position and intensity of the dominant 5D0 - 7F2 electric-dipole transition at 619 nm are unaffected by the benzoic acid and 3-nitro 4-chloro-benzoic acid treatments. Attachment of 3,4-dihydroxybenzoic acid produces an order-of-magnitude quenching in the photoluminescence, due to the presence of high-frequency vibrational modes in the linker. Ratios of the dominant electric- and magnetic-dipole transitions confirm infrared measurements, which indicate that the bulk crystal of the nanoparticle is unchanged by all three treatments.

  12. Two-dimensional infrared spectroscopy of vibrational polaritons of molecules in an optical cavity

    NASA Astrophysics Data System (ADS)

    Saurabh, Prasoon; Mukamel, Shaul

    2016-03-01

    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 two-dimensional infrared (2DIR) technique, double quantum coherence. Applications are made to the amide-I (CO) and amide-II (CN) bond vibrations of N-methylacetamide.

  13. Two-dimensional infrared spectroscopy of vibrational polaritons of molecules in an optical cavity.

    PubMed

    Saurabh, Prasoon; Mukamel, Shaul

    2016-03-28

    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 two-dimensional infrared (2DIR) technique, double quantum coherence. Applications are made to the amide-I (CO) and amide-II (CN) bond vibrations of N-methylacetamide. PMID:27036435

  14. Water dynamics in salt solutions studied with ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy.

    PubMed

    Fayer, Michael D; Moilanen, David E; Wong, Daryl; Rosenfeld, Daniel E; Fenn, Emily E; Park, Sungnam

    2009-09-15

    Water is ubiquitous in nature, but it exists as pure water infrequently. From the ocean to biology, water molecules interact with a wide variety of dissolved species. Many of these species are charged. In the ocean, water interacts with dissolved salts. In biological systems, water interacts with dissolved salts as well as charged amino acids, the zwitterionic head groups of membranes, and other biological groups that carry charges. Water plays a central role in a vast number of chemical processes because of its dynamic hydrogen-bond network. A water molecule can form up to four hydrogen bonds in an approximately tetrahedral arrangement. These hydrogen bonds are continually being broken, and new bonds are being formed on a picosecond time scale. The ability of the hydrogen-bond network of water to rapidly reconfigure enables water to accommodate and facilitate chemical processes. Therefore, the influence of charged species on water hydrogen-bond dynamics is important. Recent advances in ultrafast coherent infrared spectroscopy have greatly expanded our understanding of water dynamics. Two-dimensional infrared (2D IR) vibrational echo spectroscopy is providing new observables that yield direct information on the fast dynamics of molecules in their ground electronic state under thermal equilibrium conditions. The 2D IR vibrational echoes are akin to 2D nuclear magnetic resonance (NMR) but operate on time scales that are many orders of magnitude shorter. In a 2D IR vibrational echo experiment (see the Conspectus figure), three IR pulses are tuned to the vibrational frequency of interest, which in this case is the frequency of the hydroxyl stretching mode of water. The first two pulses "label" the initial molecular structures by their vibrational frequencies. The system evolves between pulses two and three, and the third pulse stimulates the emission of the vibrational echo pulse, which is the signal. The vibrational echo pulse is heterodyne, detected by combining it

  15. Polarized vibrational spectroscopy of fiber polymers: hydrogen bonding in cellulose II.

    PubMed

    Sturcová, Adriana; His, Isabelle; Wess, Tim J; Cameron, Graeme; Jarvis, Michael C

    2003-01-01

    Vibrational spectroscopy using polarized incident radiation can be used to determine the orientation of X-H bonds with respect to coordinates such as crystallographic axes. The adaptation of this approach to polymer fibers is described here. It requires spectral intensity to be quantified around a 180 degrees range of polarization angles and not just recorded transversely and longitudinally as is normal in fiber spectroscopy. Mercerized cellulose II is used as an example. The unit cell of the cellulose II lattice contains six distinct hydroxyl groups engaged in a complex network of hydrogen bonds that hold the cellulose chains laterally together. A formalism is described to relate the variation in intensity of each O-H stretching mode to the angle between its transition moment and the chain axis as the polarization axis is rotated with respect to the fiber axis. It was necessary to include the effect of dispersion in chain orientation around the mean and the averaging of all rotational positions of the chains round their axis. The two crystallographically distinct O(2)-H groups, which are each hydrogen-bonded to only one acceptor oxygen, show a close match in orientation between the transition moments of their stretching bands and the O-H bond axis. The two O(3)-H groups each have a three-centered hydrogen bond to O-5 and O-6 of the next residue in the same chain. The transition moments of their stretching modes lay between the acceptor oxygens. Hydrogen bonding from the O(6)-H groups is still more complex but again the transition moment of each O-H bond lay within the cone of orientations described by the acceptor oxygens, provided that one additional acceptor oxygen excluded from the published crystal structure was considered. The transition moments for the O-H stretching modes were approximately aligned with the O-H bond axes, but the alignment was not necessarily exact. This approach is not restricted to hydroxyl groups, but it is particularly useful for the

  16. Phase reference in phase-sensitive sum-frequency vibrational spectroscopy.

    PubMed

    Sun, Shumei; Liang, Rongda; Xu, Xiaofan; Zhu, Heyuan; Shen, Y Ron; Tian, Chuanshan

    2016-06-28

    Phase-sensitive sum-frequency vibrational spectroscopy (PS-SFVS) has been established as a powerful technique for surface characterization, but for it to generate a reliable spectrum, accurate phase measurement with a well-defined phase reference is most important. Incorrect phase measurement can lead to significant distortion of a spectrum, as recently seen in the case for the air/water interface. In this work, we show theoretically and experimentally that a transparent, highly nonlinear crystal, such as quartz and barium borate, can be a good phase reference if the surface is clean and unstrained and the crystal is properly oriented to yield a strong SF output. In such cases, the reflected SF signal is dominated by the bulk electric dipole contribution and its phase is either +90° or -90°. On the other hand, materials with inversion symmetry, such as water, fused quartz, and CaF2 are not good phase references due to the quadrupole contribution and phase dispersion at the interface. Using a proper phase reference in PS-SFVS, we have found the most reliable OH stretching spectrum for the air/water interface. The positive band at low frequencies in the imaginary component of the spectrum, which has garnered much interest and been interpreted by many to be due to strongly hydrogen-bonded water species, is no longer present. A weak positive feature however still exists. Its magnitude approximately equals to that of air/D2O away from resonances, suggesting that this positive feature is unrelated to surface resonance of water. PMID:27369537

  17. Multipodal coordination of a tetracarboxylic crown ether with NH4+: A vibrational spectroscopy and computational study

    NASA Astrophysics Data System (ADS)

    Hurtado, Paola; Gámez, Francisco; Hamad, Said; Martínez-Haya, Bruno; Steill, Jeffrey D.; Oomens, Jos

    2012-03-01

    The elucidation of the structural requirements for molecular recognition by the crown ether (18-crown-6)-2,3,11,12-tetracarboxylic acid (18c6H4) and its cationic complexes constitutes a topic of current fundamental and practical interest in catalysis and analytical sciences. The flexibility of the central ether ring and its four carboxyl side arms poses important challenges to experimental and theoretical approaches. In this study, infrared action vibrational spectroscopy and quantum mechanical computations are employed to characterize the conformational structure of the isolated gas phase complex formed by the 18c6H4 host with NH_4^+ as guest. The results show that the most stable gas-phase structure is a barrel-like conformation sustained by tetrapodal H-bonding of the ammonia cation with two C=O side groups and with four oxygen atoms of the ether ring in a bifurcated arrangement. Interestingly, a similar structure had been proposed in previous crystallographic studies. The experiment also provides evidence for a significant contribution of a higher energy bowl-like conformer with features resembling those adopted by 18c6H4 in the analogous complexes with secondary amines. Such a conformation displays H-bonding between confronted side carboxyl groups and tetrapodal binding of the NH_4^+ with the ether ring and with one C=O group. Structures involving even more extensive intramolecular H-bonding in the 18c6H4 substrate are found to lie higher in energy and are ruled out by the experiment.

  18. Phase reference in phase-sensitive sum-frequency vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Sun, Shumei; Liang, Rongda; Xu, Xiaofan; Zhu, Heyuan; Shen, Y. Ron; Tian, Chuanshan

    2016-06-01

    Phase-sensitive sum-frequency vibrational spectroscopy (PS-SFVS) has been established as a powerful technique for surface characterization, but for it to generate a reliable spectrum, accurate phase measurement with a well-defined phase reference is most important. Incorrect phase measurement can lead to significant distortion of a spectrum, as recently seen in the case for the air/water interface. In this work, we show theoretically and experimentally that a transparent, highly nonlinear crystal, such as quartz and barium borate, can be a good phase reference if the surface is clean and unstrained and the crystal is properly oriented to yield a strong SF output. In such cases, the reflected SF signal is dominated by the bulk electric dipole contribution and its phase is either +90° or -90°. On the other hand, materials with inversion symmetry, such as water, fused quartz, and CaF2 are not good phase references due to the quadrupole contribution and phase dispersion at the interface. Using a proper phase reference in PS-SFVS, we have found the most reliable OH stretching spectrum for the air/water interface. The positive band at low frequencies in the imaginary component of the spectrum, which has garnered much interest and been interpreted by many to be due to strongly hydrogen-bonded water species, is no longer present. A weak positive feature however still exists. Its magnitude approximately equals to that of air/D2O away from resonances, suggesting that this positive feature is unrelated to surface resonance of water.

  19. Identification of vibrational signatures from short chains of interlinked molecule-nanoparticle junctions obtained by inelastic electron tunnelling spectroscopy

    NASA Astrophysics Data System (ADS)

    Jafri, S. H. M.; Löfås, H.; Fransson, J.; Blom, T.; Grigoriev, A.; Wallner, A.; Ahuja, R.; Ottosson, H.; Leifer, K.

    2013-05-01

    Short chains containing a series of metal-molecule-nanoparticle nanojunctions are a nano-material system with the potential to give electrical signatures close to those from single molecule experiments while enabling us to build portable devices on a chip. Inelastic electron tunnelling spectroscopy (IETS) measurements provide one of the most characteristic electrical signals of single and few molecules. In interlinked molecule-nanoparticle (NP) chains containing typically 5-7 molecules in a chain, the spectrum is expected to be a superposition of the vibrational signatures of individual molecules. We have established a stable and reproducible molecule-AuNP multi-junction by placing a few 1,8-octanedithiol (ODT) molecules onto a versatile and portable nanoparticle-nanoelectrode platform and measured for the first time vibrational molecular signatures at complex and coupled few-molecule-NP junctions. From quantum transport calculations, we model the IETS spectra and identify vibrational modes as well as the number of molecules contributing to the electron transport in the measured spectra.Short chains containing a series of metal-molecule-nanoparticle nanojunctions are a nano-material system with the potential to give electrical signatures close to those from single molecule experiments while enabling us to build portable devices on a chip. Inelastic electron tunnelling spectroscopy (IETS) measurements provide one of the most characteristic electrical signals of single and few molecules. In interlinked molecule-nanoparticle (NP) chains containing typically 5-7 molecules in a chain, the spectrum is expected to be a superposition of the vibrational signatures of individual molecules. We have established a stable and reproducible molecule-AuNP multi-junction by placing a few 1,8-octanedithiol (ODT) molecules onto a versatile and portable nanoparticle-nanoelectrode platform and measured for the first time vibrational molecular signatures at complex and coupled few

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

    SciTech Connect

    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.

  1. Computational IR spectroscopy of water: OH stretch frequencies, transition dipoles, and intermolecular vibrational coupling constants

    NASA Astrophysics Data System (ADS)

    Choi, Jun-Ho; Cho, Minhaeng

    2013-05-01

    The Hessian matrix reconstruction method initially developed to extract the basis mode frequencies, vibrational coupling constants, and transition dipoles of the delocalized amide I, II, and III vibrations of polypeptides and proteins from quantum chemistry calculation results is used to obtain those properties of delocalized O-H stretch modes in liquid water. Considering the water symmetric and asymmetric O-H stretch modes as basis modes, we here develop theoretical models relating vibrational frequencies, transition dipoles, and coupling constants of basis modes to local water configuration and solvent electric potential. Molecular dynamics simulation was performed to generate an ensemble of water configurations that was in turn used to construct vibrational Hamiltonian matrices. Obtaining the eigenvalues and eigenvectors of the matrices and using the time-averaging approximation method, which was developed by the Skinner group, to calculating the vibrational spectra of coupled oscillator systems, we could numerically simulate the O-H stretch IR spectrum of liquid water. The asymmetric line shape and weak shoulder bands were quantitatively reproduced by the present computational procedure based on vibrational exciton model, where the polarization effects on basis mode transition dipoles and inter-mode coupling constants were found to be crucial in quantitatively simulating the vibrational spectra of hydrogen-bond networking liquid water.

  2. Surface Structure of Protonated R-Sapphire (1$\\bar{1}$02) Studied by Sum-Frequency Vibrational Spectroscopy

    SciTech Connect

    Sung, Jaeho; Zhang, Luning; Tian, Chuanshan; Waychunas, Glenn A.; Shen, Y. Ron

    2011-03-23

    Sum frequency vibrational spectroscopy was used to study the protonated R-plane (1$\\bar{1}$02 ) sapphire surface. The OH stretch vibrational spectra show that the surface is terminated with three hydroxyl moieties, two from AlOH2 and one from Al2OH functional groups. The observed polarization dependence allows determination of the orientations of the three OH species. The results suggest that the protonated sapphire (1$\\bar{1}$02 ) surface differs from an ideal stoichimetric termination in a manner consistent with previous X-ray surface diffraction (crystal truncation rod) studies. However, in order to best explain the observed hydrogenbonding arrangement, surface oxygen spacing determined from the X-ray diffraction study requires modification.

  3. Vibrational analysis of hydroxyflavylium derivatives by IR, Fourier transform Raman and resonance Raman spectroscopies

    NASA Astrophysics Data System (ADS)

    Merlin, J. C.; Cornard, J. P.; Stastoua, A.; Saidi-Idrissi, M.; Lautie, M. F.; Brouillard, R.

    In order to give a better insight into the vibrational properties of anthocyanins, the synthesis and the vibrational studies of some hydroxyflavylium derivatives with a controlled substitution pattern have been performed. The IR, Raman and resonance Raman spectra of the investigated hydroxyflavylium compounds have been recorded in the solid and solution states. A number of lines have been assigned on the basis of deuterium isotopic shifts, resonance enhancement and previous studies on parent compounds. An attempt has been made to analyze the influence of hydroxy substituents on vibrational properties of the investigated flavylium cations.

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

    PubMed

    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.

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

    SciTech Connect

    Dijkstra, Arend G. E-mail: tanimura@kuchem.kyoto-u.ac.jp; Tanimura, Yoshitaka E-mail: tanimura@kuchem.kyoto-u.ac.jp

    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.

  6. Investigating vibrational anharmonic couplings in cyanide-bridged transition metal mixed valence complexes using two-dimensional infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Slenkamp, Karla M.; Lynch, Michael S.; Van Kuiken, Benjamin E.; Brookes, Jennifer F.; Bannan, Caitlin C.; Daifuku, Stephanie L.; Khalil, Munira

    2014-02-01

    Using polarization-selective two-dimensional infrared (2D IR) spectroscopy, we measure anharmonic couplings and angles between the transition dipole moments of the four cyanide stretching (νCN) vibrations found in [(NH3)5RuIIINCFeII(CN)5]- (FeRu) dissolved in D2O and formamide and [(NC)5FeIICNPtIV(NH3)4NCFeII(CN)5]4- (FePtFe) dissolved in D2O. These cyanide-bridged transition metal complexes serve as model systems for studying the role of high frequency vibrational modes in ultrafast photoinduced charge transfer reactions. Here, we focus on the spectroscopy of the νCN modes in the electronic ground state. The FTIR spectra of the νCN modes of the bimetallic and trimetallic systems are strikingly different in terms of frequencies, amplitudes, and lineshapes. The experimental 2D IR spectra of FeRu and FePtFe and their fits reveal a set of weakly coupled anharmonic νCN modes. The vibrational mode anharmonicities of the individual νCN modes range from 14 to 28 cm-1. The mixed-mode anharmonicities range from 2 to 14 cm-1. In general, the bridging νCN mode is most weakly coupled to the radial νCN mode, which involves the terminal CN ligands. Measurement of the relative transition dipole moments of the four νCN modes reveal that the FeRu molecule is almost linear in solution when dissolved in formamide, but it assumes a bent geometry when dissolved in D2O. The νCN modes are modelled as bilinearly coupled anharmonic oscillators with an average coupling constant of 6 cm-1. This study elucidates the role of the solvent in modulating the molecular geometry and the anharmonic vibrational couplings between the νCN modes in cyanide-bridged transition metal mixed valence complexes.

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

    PubMed

    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

  8. Vibrational spectroscopy in sensing radiobiological effects: analyses of targeted and non-targeted effects in human keratinocytes.

    PubMed

    Meade, Aidan D; Howe, Orla; Unterreiner, Valérie; Sockalingum, Ganesh D; Byrne, Hugh J; Lyng, Fiona M

    2016-06-23

    Modern models of radiobiological effects include mechanisms of damage initiation, sensing and repair, for those cells that directly absorb ionizing radiation as well as those that experience molecular signals from directly irradiated cells. In the former case, the effects are termed targeted effects while, in the latter, non-targeted effects. It has emerged that phenomena occur at low doses below 1 Gy in directly irradiated cells that are associated with cell-cycle-dependent mechanisms of DNA damage sensing and repair. Likewise in non-targeted bystander-irradiated cells the effect saturates at 0.5 Gy. Both effects at these doses challenge the limits of detection of vibrational spectroscopy. In this paper, a study of the sensing of both targeted and non-targeted effects in HaCaT human keratinocytes irradiated with gamma ray photons is conducted with vibrational spectroscopy. In the case of directly irradiated cells, it is shown that the HaCaT cell line does exhibit both hyperradiosensitivity and increased radioresistance at low doses, a transition between the two effects occurring at a dose of 200 mGy, and that cell survival and other physiological effects as a function of dose follow the induced repair model. Both Raman and FTIR signatures are shown to follow a similar model, suggesting that the spectra include signatures of DNA damage sensing and repair. In bystander-irradiated cells, pro- and anti-apoptotic signalling and mechanisms of ROS damage were inhibited in the mitogen-activated protein kinase (MAPK) transduction pathway. It is shown that Raman spectral profiles of bystander-irradiated cells are correlated with markers of bystander signalling and molecular transduction. This work demonstrates for the first time that both targeted and non-targeted effects of ionizing radiation damage are detected by vibrational spectroscopy in vitro.

  9. Environmental effects on phosphoryl group bonding probed by vibrational spectroscopy: implications for understanding phosphoryl transfer and enzymatic catalysis.

    PubMed

    Cheng, Hu; Nikolic-Hughes, Ivana; Wang, Jianghua H; Deng, Hua; O'Brien, Patrick J; Wu, Li; Zhang, Zhong-Yin; Herschlag, Daniel; Callender, Robert

    2002-09-25

    We have used vibrational spectroscopy to study bonding in monosubstituted dianionic phosphates, both to learn more about basic properties intrinsic to this important class of biological substrates and to assess the ability of vibrational spectroscopy to provide a "sensor" or probe of the local environment experienced by the phosphoryl group. We examined the bonding properties of the phosphoryl group via vibrational spectroscopy for a series of compounds in which the phosphoryl substituent was varied systematically and extensively. A broad linear correlation of the bridging P-O(R) bond length and the pK(a) of the substituent alcohol was observed. The results indicate that the P-O(R) bond changes by only approximately 0.04 A with alcohol substituents that vary in pK(a) by approximately 12 units, suggesting that phosphoryl group bonding responds in a subtle but regular manner to changes in the local environment. We also determined the effect on the phosphoryl bonding from changes in the solvent environment. Addition of dimethyl sulfoxide (DMSO) elongates the bridging bond, presumably as a result of lessened solvation to the nonbridging oxygens and conservation of bond order to phosphorus. Finally, we have addressed the relationship between ground-state bonding properties and reactivity, as changing the leaving group substituent and adding DMSO have large rate effects, and it was previously proposed that lengthening of the bond to be broken is the cause of the increased reactivity. The results herein suggest, however, that the change in the bridging bond energy is small compared to the changes in energy that accompany the observed reactivity differences. Further analysis indicates that electrostatic interactions can provide a common driving force underlying both bond lengthening and the observed rate increases. We suggest that ground-state distortions of substrates bound to enzymes can provide a readout of the electrostatic active site environment, an environment that

  10. Vibrational spectroscopy in sensing radiobiological effects: analyses of targeted and non-targeted effects in human keratinocytes.

    PubMed

    Meade, Aidan D; Howe, Orla; Unterreiner, Valérie; Sockalingum, Ganesh D; Byrne, Hugh J; Lyng, Fiona M

    2016-06-23

    Modern models of radiobiological effects include mechanisms of damage initiation, sensing and repair, for those cells that directly absorb ionizing radiation as well as those that experience molecular signals from directly irradiated cells. In the former case, the effects are termed targeted effects while, in the latter, non-targeted effects. It has emerged that phenomena occur at low doses below 1 Gy in directly irradiated cells that are associated with cell-cycle-dependent mechanisms of DNA damage sensing and repair. Likewise in non-targeted bystander-irradiated cells the effect saturates at 0.5 Gy. Both effects at these doses challenge the limits of detection of vibrational spectroscopy. In this paper, a study of the sensing of both targeted and non-targeted effects in HaCaT human keratinocytes irradiated with gamma ray photons is conducted with vibrational spectroscopy. In the case of directly irradiated cells, it is shown that the HaCaT cell line does exhibit both hyperradiosensitivity and increased radioresistance at low doses, a transition between the two effects occurring at a dose of 200 mGy, and that cell survival and other physiological effects as a function of dose follow the induced repair model. Both Raman and FTIR signatures are shown to follow a similar model, suggesting that the spectra include signatures of DNA damage sensing and repair. In bystander-irradiated cells, pro- and anti-apoptotic signalling and mechanisms of ROS damage were inhibited in the mitogen-activated protein kinase (MAPK) transduction pathway. It is shown that Raman spectral profiles of bystander-irradiated cells are correlated with markers of bystander signalling and molecular transduction. This work demonstrates for the first time that both targeted and non-targeted effects of ionizing radiation damage are detected by vibrational spectroscopy in vitro. PMID:27043923

  11. CARS Microscopy: Implementation of Nonlinear Vibrational Spectroscopy for Far-Field and Near-Field Imaging

    NASA Astrophysics Data System (ADS)

    Hashimoto, Mamoru; Ichimura, Taro; Fujita, Katsumasa

    Raman microscopy has been attracting researchers in biology and medicine due to its capability of detecting molecular vibrations that provide information of molecular species, structures, conditions, and environments. Raman scattering can be obtained by simply illuminating molecules with monochromatic light, and providing molecular vibration frequency as wavelengths of scattered light. This does not require labeling of target molecules, such as chemical or biological staining with fluorophore, which may modify the condition of living biological specimens.

  12. Nuclear Resonance Vibrational Spectroscopy applied to [Fe(OEP)(NO)]: The Vibrational Assignments of Five-Coordinate Ferrous Heme Nitrosyls and Implications for Electronic Structure

    PubMed Central

    Lehnert, Nicolai; Galinato, Mary Grace I.; Paulat, Florian; Richter-Addo, George B.; Sturhahn, Wolfgang; Xu, Nan; Zhao, Jiyong

    2010-01-01

    This study presents Nuclear Resonance Vibrational Spectroscopy (NRVS) data on the five-coordinate (5C) ferrous heme nitrosyl complex [Fe(OEP)(NO)] (1, OEP2− = octaethylporphyrinato dianion) and the corresponding 15N18O labeled complex. The obtained spectra identify two isotope sensitive features at 522 and 388 cm−1, which shift to 508 and 381 cm−1, respectively, upon isotope labeling. These features are assigned to the Fe-NO stretch ν(Fe-NO) and the in-plane Fe-N-O bending mode δip(Fe-N-O), the latter has been unambiguously assigned for the first time for 1. The obtained NRVS data were simulated using our quantum chemistry centered normal coordinate analysis (QCC-NCA). Since complex 1 can potentially exist in 12 different conformations involving the FeNO and peripheral ethyl orientations, extended DFT calculations and QCC-NCA simulations were performed to determine how these conformations affect the NRVS properties of [Fe(OEP)NO]. These results show that the properties and force constants of the FeNO unit are hardly affected by the conformational changes involving the ethyl substituents. On the other hand, the NRVS-active porphyrin-based vibrations around 340 – 360, 300 –320, and 250 – 270 cm−1 are sensitive to the conformational changes. The spectroscopic changes observed in these regions are due to selective mechanical couplings of one component of Eu-type (in ideal D4h symmetry) porphyrin-based vibrations with the in-plane Fe-N-O bending mode. This leads to the observed variations in Fe(OEP) core mode energies and NRVS intensities without affecting the properties of the FeNO unit. The QCC-NCA simulated NRVS spectra of 1 show excellent agreement with experiment, and indicate that conformer F is likely present in the samples of this complex investigated here. The observed porphyrin-based vibrations in the NRVS spectra of 1 are also assigned based on the QCC-NCA results. The obtained force constants of the Fe-NO and N-O bonds are 2.83 – 2

  13. Fourier transform two-dimensional electronic-vibrational spectroscopy using an octave-spanning mid-IR probe.

    PubMed

    Gaynor, James D; Courtney, Trevor L; Balasubramanian, Madhumitha; Khalil, Munira

    2016-06-15

    The development of coherent Fourier transform two-dimensional electronic-vibrational (2D EV) spectroscopy with acousto-optic pulse-shaper-generated near-UV pump pulses and an octave-spanning broadband mid-IR probe pulse is detailed. A 2D EV spectrum of a silicon wafer demonstrates the full experimental capability of this experiment, and a 2D EV spectrum of dissolved hexacyanoferrate establishes the viability of our 2D EV experiment for studying condensed phase molecular ensembles. PMID:27304316

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

    PubMed

    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.

  15. Strong intermolecular vibrational coupling through cyclic hydrogen-bonded structures revealed by ultrafast continuum mid-IR spectroscopy.

    PubMed

    Stingel, Ashley M; Calabrese, Carmella; Petersen, Poul B

    2013-12-12

    Cyclic hydrogen-bonded structures are common motifs in biological systems, providing structural stability and mediating proton transfer for redox reactions. The mechanism of proton transfer across hydrogen-bonded interfaces depends on the strength of the intermolecular coupling between bridging OH/NH vibrational modes. Here we present a novel ultrafast continuum mid-IR spectroscopy experiment to study the vibrational dynamics of the 7-azaindole-acetic acid (7AI-Ac) heterodimer as a model system for asymmetric cyclic hydrogen-bonded structures. In addition to spreading of the excitation across the whole OH band within the time resolution of the experiment, excitation of a 300 cm(-1) region of the ∼1000 cm(-1) broad OH stretching mode of the acetic acid monomer leads to a frequency shift in the NH stretching mode of the 7AI monomer. This indicates that the NH and OH stretching modes located on the two monomers are strongly coupled despite being separated by 750 cm(-1). The strong coupling further causes the OH and NH bands to decay with a common decay time of ∼2.5 ps. This intermolecular coupling is mediated through the hydrogen-bonded structure of the 7AI-Ac heterodimer and is likely a general property of cyclic hydrogen-bonded structures. Characterizing the vibrational dynamics of and the coupling between the high-frequency OH/NH modes will be important for understanding proton transfer across such molecular interfaces.

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

    PubMed

    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. PMID:26062639

  17. Frequency-domain time-resolved four wave mixing spectroscopy of vibrational coherence transfer with single-color excitation.

    PubMed

    Pakoulev, Andrei V; Rickard, Mark A; Mathew, Nathan A; Kornau, Kathryn M; Wright, John C

    2008-07-17

    Triply vibrationally enhanced four-wave mixing spectroscopy is employed to observe vibrational coherence transfer between the asymmetric and symmetric CO-stretching modes of rhodium(I) dicarbonyl acetylacetonate (RDC). Coherence transfer is a nonradiative transition of a coherent superposition of quantum states to a different coherent superposition due to coupling of the vibrational modes through the bath. All three excitation pulses in the experiment are resonant with a single quantum coherence, but coherence transfer results in new coherences with different frequencies. The new output frequency is observed with a monochromator that resolves it from the stronger peak at the original excitation frequency. This technique spectrally resolves pathways that include coherence transfer, discriminates against spectral features created solely by radiative transitions, and temporally resolves modulations created by interference between different coherence transfer pathways. Redfield theory simulates the temporal modulations in the impulsive limit, but it is also clear that coherence transfer violates the secular approximation invoked in most Redfield theories. Instead, it requires non-Markovian and bath memory effects. RDC may provide a simple model for the development of theories that incorporate these effects.

  18. Low-frequency vibrational modes of benzoic acid investigated by terahertz time-domain spectroscopy and theoretical simulations

    NASA Astrophysics Data System (ADS)

    Yan, Hui; Fan, Wen-hui; Zheng, Zhuan-ping

    2011-08-01

    In this paper, the low-frequency vibrational modes of crystalline benzoic acid (BA) have been investigated by terahertz time-domain spectroscopy (THz-TDS) and theoretical simulations based on the linearity combination of atomic orbital within the Density Functional Theory (DFT) as well as ab initio molecular orbital method at second-order Moller-Plesset Perturbation Theory (MP2) level for single molecule and dimer. Experimentally, a series of prominent absorption features of pure benzoic acid relevant to intra- and inter-molecular vibrational modes have been obtained below 4 THz at room temperature. For the theoretical simulations, geometry-optimization results of bond lengths and dihedral angles in both BA monomer and dimer are very close to experimental neutron diffraction measurements. Furthermore, the simulation results demonstrate absorption profile centered at 1.89 THz contains low-frequency modes of Ph-COOH twisting due to intramolecular motion and cogwheel owing to intermolecular motion. All the intra- and inter-molecular vibrational modes measured have also been assigned.

  19. Identification of vibrational signatures from short chains of interlinked molecule-nanoparticle junctions obtained by inelastic electron tunnelling spectroscopy.

    PubMed

    Jafri, S H M; Löfås, H; Fransson, J; Blom, T; Grigoriev, A; Wallner, A; Ahuja, R; Ottosson, H; Leifer, K

    2013-06-01

    Short chains containing a series of metal-molecule-nanoparticle nanojunctions are a nano-material system with the potential to give electrical signatures close to those from single molecule experiments while enabling us to build portable devices on a chip. Inelastic electron tunnelling spectroscopy (IETS) measurements provide one of the most characteristic electrical signals of single and few molecules. In interlinked molecule-nanoparticle (NP) chains containing typically 5-7 molecules in a chain, the spectrum is expected to be a superposition of the vibrational signatures of individual molecules. We have established a stable and reproducible molecule-AuNP multi-junction by placing a few 1,8-octanedithiol (ODT) molecules onto a versatile and portable nanoparticle-nanoelectrode platform and measured for the first time vibrational molecular signatures at complex and coupled few-molecule-NP junctions. From quantum transport calculations, we model the IETS spectra and identify vibrational modes as well as the number of molecules contributing to the electron transport in the measured spectra.

  20. Nonlinear vibrational spectroscopy of water structures utilizing laser-induced phase transition phenomena in liquid water

    NASA Astrophysics Data System (ADS)

    Yui, Hiroharu; Sawada, Tsuguo

    2003-01-01

    Anomalous enhancement of the stimulated Raman scattering (SRS) of water molecules in the OH stretching vibrational region is observed when a laser-induced phase transition from liquid to plasma takes place in liquid water. The SRS is emitted before the phase transition and has a duration of several tens of picoseconds full width at half maximum. From the spectroscopic analysis of the SRS, it is suggested that the excess electrons, which are generated in a few picoseconds before the phase transition, play an important role in the transient SRS enhancement through the change of the nonlinear polarizability induced around the electrons in liquid water. Several applications of the enhanced vibrational spectra in the OH stretching vibrational region to the spectroscopic analyses of local water structures in various environments are also described.

  1. Vibrational spectroscopy of triacetone triperoxide (TATP): Anharmonic fundamentals, overtones and combination bands

    NASA Astrophysics Data System (ADS)

    Brauer, Brina; Dubnikova, Faina; Zeiri, Yehuda; Kosloff, Ronnie; Gerber, R. Benny

    2008-12-01

    The vibrational spectrum of triacetone triperoxide (TATP) is studied by the correlation-corrected vibrational self-consistent field (CC-VSCF) method which incorporates anharmonic effects. Fundamental, overtone, and combination band frequencies are obtained by using a potential based on the PM3 method and yielding the same harmonic frequencies as DFT/cc-pVDZ calculations. Fundamentals and overtones are also studied with anharmonic single-mode (without coupling) DFT/cc-pVDZ calculations. Average deviations from experiment are similar for all methods: 2.1-2.5%. Groups of degenerate vibrations form regions of numerous combination bands with low intensity: the 5600-5800 cm -1 region contains ca. 70 overtones and combinations of CH stretches. Anharmonic interactions are analyzed.

  2. Two-dimensional spectroscopy of coupled vibrations with the optimized mean-trajectory approximation.

    PubMed

    Gerace, Mallory; Loring, Roger F

    2013-12-12

    The optimized mean-trajectory (OMT) approximation is a semiclassical representation of the nonlinear vibrational response function used to compute multidimensional infrared spectra. In this method, response functions are calculated from a sequence of classical trajectories linked by discontinuities representing the effects of radiation-matter interactions, thus providing an approximation to quantum dynamics using classical inputs. This approach was previously formulated and assessed numerically for a single anharmonic degree of freedom. Our previous work is generalized here in two respects. First, the derivation of the OMT is extended to any number of coupled anharmonic vibrations by determining semiclassical approximations for pairs of double-sided Feynman diagrams. Second, an efficient numerical procedure is developed for calculating two-dimensional infrared spectra of coupled anharmonic vibrations in the OMT approximation. The OMT approximation is shown to reproduce the fundamental features of the quantum response function including both coherence and population dynamics. PMID:23924378

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

    SciTech Connect

    Holinga IV, George Joseph

    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.

  4. Vibrational spectroscopy of shock-compressed fluid N/sub 2/ and O/sub 2/

    SciTech Connect

    Schmidt, S.C.; Moore, D.S.; Shaw, M.S.; Johnson, J.D.

    1987-01-01

    Single-pulse, multiplex, coherent anti-Stokes Raman scattering (CARS) was used to observe the vibrational spectra of liquid N/sub 2/ shock-compressed to several pressures and temperatures up to 41 GPa and 5200 K and liquid O/sub 2/ shock-compressed to several pressures and temperatures up to 10 GPa and 1000 K. For N/sub 2/, the experimental spectra were compared to synthetic spectra calculated using a semiclassical model for CARS intensities and estimated vibrational frequencies, peak Raman susceptibilities and Raman line widths. The question of excited state populations in the shock-compressed state is addressed.

  5. Vibrational spectroscopy of shock-compressed fluid N/sub 2/ and O/sub 2/

    SciTech Connect

    Schmidt, S.C.; Moore, D.S.; Shaw, M.S.; Johnson, J.D.

    1987-01-01

    Single-pulse multiplex coherent anti-Stokes Raman scattering (CARS) was used to observe the vibrational spectra of liquid N/sub 2/ shock-compressed to several pressures and temperatures up to 41 GPa and 5200 K and liquid O/sub 2/ shock-compressed to several pressures and temperatures up to 10 GPa and 1000 K. For N/sub 2/, the experimental spectra were compared to synthetic spectra calculated using a semiclassical model for CARS intensities and estimated vibrational frequencies, peak Raman susceptibilities, and Raman line widths. The question of excited state populations in the shock-compressed state is addressed.

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

    NASA Astrophysics Data System (ADS)

    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.

  7. Vibrational spectroscopy to study degradation of natural dyes. Assessment of oxygen-free cassette for safe exposition of artefacts.

    PubMed

    Koperska, Monika; Łojewski, Tomasz; Łojewska, Joanna

    2011-03-01

    An important issue connected with conservation chemistry is how to improve the storage and exposure conditions in order to suppress the fading and degradation of dyes and other components of paintings. Although the oxygen-free exposure cassettes are commonly known in museums, there is still lack of information in the literature about the effect of anoxic conditions on the degradation of dyes. This study is an attempt to start a database formation on the dyes degradation. Five commercial dyes (indigo, dragon's blood, curcumin, madder, carminic acid) were submitted to accelerated ageing by exposure to intensive light in the visible range in both oxygen-free (anoxia) and -rich conditions. Degradation of the samples was investigated by several analytical techniques (attenuated total reflectance infrared spectroscopy, Raman spectroscopy, reflectance UV-Vis spectroscopy, X-ray fluorescence spectroscopy and optical microscopy). The conclusions are based on the estimators (derived from the determination of colour differences from Vis spectra and from the changes in FTIR and Raman vibrational bands intensity). According to them, only indigo, dragon's blood and curcumin show greater stability in anoxic conditions in comparison with oxygen-rich ones while madder, carminic acid undergo greater degradation. PMID:21165610

  8. Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O2-tolerant NAD+-reducing [NiFe] hydrogenase

    DOE PAGES

    Lauterbach, Lars; Wang, Hongxin; Horch, Marius; Gee, Leland B.; Yoda, Yoshitaka; Tanaka, Yoshihito; Zebger, Ingo; Lenz, Oliver; Cramer, Stephen P.

    2014-10-30

    Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function of the various metal cofactors present in the enzyme. Here, all iron-containing cofactors of the SH were investigated by 57Fe specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters, whichmore » is consistent with the amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD+-reducing hydrogenases. For the first time, Fe–CO and Fe–CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective 13C labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe–CO modes. The present approach explores the complex vibrational signature of the Fe–S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors.« less

  9. High-Resolution Vibration-Rotation Spectroscopy of CO[subscript 2]: Understanding the Boltzmann Distribution

    ERIC Educational Resources Information Center

    Castle, Karen J.

    2007-01-01

    In this undergraduate physical chemistry laboratory experiment, students acquire a high-resolution infrared absorption spectrum of carbon dioxide and use their data to show that the rotational-vibrational state populations follow a Boltzmann distribution. Data are acquired with a mid-infrared laser source and infrared detector. Appropriate…

  10. VCD spectroscopy as an excellent probe of chiral metal complexes containing a carbon monoxide vibrational chromophore.

    PubMed

    Fusè, Marco; Mazzeo, Giuseppe; Longhi, Giovanna; Abbate, Sergio; Zerla, Daniele; Rimoldi, Isabella; Contini, Alessandro; Cesarotti, Edoardo

    2015-06-01

    Vibrational circular dichroism, VCD, gives evidence that the carbon monoxide chromophore in a heteroleptic cyclopentadienyl Ru(ii)-carbonyl complex is very sensitive to the chirality of the metal centre and becomes an excellent probe to define the configuration of chiral metal complexes.

  11. Vibrational spectroscopy: Can density functional theory cope with highly electronegative atoms?

    NASA Astrophysics Data System (ADS)

    Petković, Milena

    2010-12-01

    Vibrational properties of molecules composed solely of highly electronegative atoms are studied by means of density functional methods. Performance of different combinations of exchange and correlation functionals is tested. It is demonstrated that certain functionals can successfully simulate infrared spectra of systems containing only fluorine, oxygen and nitrogen.

  12. Nonequilibrium vibrational excitation of H2 in radiofrequency discharges: A theoretical approach based on coherent anti-Stokes Raman spectroscopy measurements

    NASA Astrophysics Data System (ADS)

    Hassouni, K.; Lombardi, G.; Gicquel, A.; Capitelli, M.; Shakhatov, V. A.; De Pascale, O.

    2005-07-01

    Vibrational and rotational experimental temperatures of molecular hydrogen obtained by coherent anti-Stokes Raman spectroscopy in radiofrequency inductive plasmas have been analyzed and interpreted in terms of vibration, electron, dissociation-recombination, and attachment kinetics by using a sophisticated kinetic model recently developed. The analysis clarifies the role of atomic hydrogen in affecting the vibrational content of the molecules. Theoretical plasma composition and population and electron energy distributions are presented as a function of the recombination coefficient γH of atomic hydrogen on the surfaces. The agreement between theoretical and experimental results is achieved for recombination coefficients consistent with those found in the literature.

  13. Nonequilibrium vibrational excitation of H{sub 2} in radiofrequency discharges: A theoretical approach based on coherent anti-Stokes Raman spectroscopy measurements

    SciTech Connect

    Hassouni, K.; Lombardi, G.; Gicquel, A.; Capitelli, M.; Shakhatov, V.A.; De Pascale, O.

    2005-07-15

    Vibrational and rotational experimental temperatures of molecular hydrogen obtained by coherent anti-Stokes Raman spectroscopy in radiofrequency inductive plasmas have been analyzed and interpreted in terms of vibration, electron, dissociation-recombination, and attachment kinetics by using a sophisticated kinetic model recently developed. The analysis clarifies the role of atomic hydrogen in affecting the vibrational content of the molecules. Theoretical plasma composition and population and electron energy distributions are presented as a function of the recombination coefficient {gamma}{sub H} of atomic hydrogen on the surfaces. The agreement between theoretical and experimental results is achieved for recombination coefficients consistent with those found in the literature.

  14. Hydrogen bond dynamics of histamine monocation in aqueous solution: Car-Parrinello molecular dynamics and vibrational spectroscopy study.

    PubMed

    Stare, Jernej; Mavri, Janez; Grdadolnik, Jože; Zidar, Jernej; Maksić, Zvonimir B; Vianello, Robert

    2011-05-19

    Hydration of histamine was examined by infrared spectroscopy and Car-Parrinello molecular dynamics simulation. Histamine is a neurotransmitter and inflammation mediator, which at physiological pH conditions is present mainly in monocationic form. Our focus was on the part of vibrational spectra that corresponds to histamine N-H stretching, since these degrees of freedom are essential for its interactions with either water molecules or transporters and receptors. Assignment of the experimental spectra revealed a broad feature between 3350 and 2300 cm(-1), being centered at 2950 cm(-1), which includes a mixed contribution from the ring N-H and the aminoethyl N-H stretching vibrations. Computational analysis was performed in two ways: first, by making Fourier transformation on the autocorrelation function of all four N-H bond distances recorded during CPMD run, and second, and most importantly, by incorporating quantum effects through applying an a posteriori quantization of all N-H stretching motions utilizing our snapshot analysis of the fluctuating proton potential. The one-dimensional vibrational Schrödinger equation was solved numerically for each snapshot, and the N-H stretching envelopes were calculated as a superposition of the 0→1 transitions. The agreement with the experiment was much better in the case of the second approach. Our calculations clearly demonstrated that the ring amino group absorbs at higher frequencies than the remaining three amino N-H protons of the protonated aminoethyl group, implying that the chemical bonding in the former group is stronger than in the three amino N-H bonds, thus forming weaker hydrogen bonding with the surrounding solvent molecules. In this way the results of the simulation complemented the experimental spectrum that cannot distinguish between the two sets of protons. The effects of deuteration were also considered. The resulting N-D absorption is narrower and red-shifted. The presented methodology is of general

  15. Vibrational spectroscopy of water in hydrated lipid multi-bilayers. I. Infrared spectra and ultrafast pump-probe observables

    PubMed Central

    Gruenbaum, S. M.; Skinner, J. L.

    2011-01-01

    The vibrational spectroscopy of hydration water in dilauroylphosphatidylcholine lipid multi-bilayers is investigated using molecular dynamics simulations and a mixed quantum∕classical model for the OD stretch spectroscopy of dilute HDO in H2O. FTIR absorption spectra, and isotropic and anisotropic pump-probe decay curves have been measured experimentally as a function of the hydration level of the lipid multi-bilayer, and our goal is to make connection with these experiments. To this end, we use third-order response functions, which allow us to include non-Gaussian frequency fluctuations, non-Condon effects, molecular rotations, and a fluctuating vibrational lifetime, all of which we believe are important for this system. We calculate the response functions using existing transition frequency and dipole maps. From the experiments it appears that there are two distinct vibrational lifetimes corresponding to HDO molecules in different molecular environments. In order to obtain these lifetimes, we consider a simple two-population model for hydration water hydrogen bonds. Assuming a different lifetime for each population, we then calculate the isotropic pump-probe decay, fitting to experiment to obtain the two lifetimes for each hydration level. With these lifetimes in hand, we then calculate FTIR spectra and pump-probe anisotropy decay as a function of hydration. This approach, therefore, permits a consistent calculation of all observables within a unified computational scheme. Our theoretical results are all in qualitative agreement with experiment. The vibrational lifetime of lipid-associated OD groups is found to be systematically shorter than that of the water-associated population, and the lifetimes of each population increase with decreasing hydration, in agreement with previous analysis. Our theoretical FTIR absorption spectra successfully reproduce the experimentally observed red-shift with decreasing lipid hydration, and we confirm a previous interpretation

  16. Investigating vibrational anharmonic couplings in cyanide-bridged transition metal mixed valence complexes using two-dimensional infrared spectroscopy

    SciTech Connect

    Slenkamp, Karla M.; Lynch, Michael S.; Van Kuiken, Benjamin E.; Brookes, Jennifer F.; Bannan, Caitlin C.; Daifuku, Stephanie L.; Khalil, Munira

    2014-02-28

    Using polarization-selective two-dimensional infrared (2D IR) spectroscopy, we measure anharmonic couplings and angles between the transition dipole moments of the four cyanide stretching (ν{sub CN}) vibrations found in [(NH{sub 3}){sub 5}Ru{sup III}NCFe{sup II}(CN){sub 5}]{sup −} (FeRu) dissolved in D{sub 2}O and formamide and [(NC){sub 5}Fe{sup II}CNPt{sup IV}(NH{sub 3}){sub 4}NCFe{sup II}(CN){sub 5}]{sup 4−} (FePtFe) dissolved in D{sub 2}O. These cyanide-bridged transition metal complexes serve as model systems for studying the role of high frequency vibrational modes in ultrafast photoinduced charge transfer reactions. Here, we focus on the spectroscopy of the ν{sub CN} modes in the electronic ground state. The FTIR spectra of the ν{sub CN} modes of the bimetallic and trimetallic systems are strikingly different in terms of frequencies, amplitudes, and lineshapes. The experimental 2D IR spectra of FeRu and FePtFe and their fits reveal a set of weakly coupled anharmonic ν{sub CN} modes. The vibrational mode anharmonicities of the individual ν{sub CN} modes range from 14 to 28 cm{sup −1}. The mixed-mode anharmonicities range from 2 to 14 cm{sup −1}. In general, the bridging ν{sub CN} mode is most weakly coupled to the radial ν{sub CN} mode, which involves the terminal CN ligands. Measurement of the relative transition dipole moments of the four ν{sub CN} modes reveal that the FeRu molecule is almost linear in solution when dissolved in formamide, but it assumes a bent geometry when dissolved in D{sub 2}O. The ν{sub CN} modes are modelled as bilinearly coupled anharmonic oscillators with an average coupling constant of 6 cm{sup −1}. This study elucidates the role of the solvent in modulating the molecular geometry and the anharmonic vibrational couplings between the ν{sub CN} modes in cyanide-bridged transition metal mixed valence complexes.

  17. Protonated sugars: vibrational spectroscopy and conformational structure of protonated O-methyl α-D-galactopyranoside

    NASA Astrophysics Data System (ADS)

    Rudić, Svemir; Xie, Hong-bin; Gerber, R. Benny; Simons, John P.

    2012-08-01

    'Bridging' protons provide a common structural motif in biological assemblies such as proton wires and proton-bound dimers. Here we present a 'proof-of-principle' computational and vibrational spectroscopic investigation of an 'intra-molecular proton-bound dimer,' O-methyl α-D-galactopyranoside (αMeGal-H+), generated in the gas phase through photo-ionisation of its complex with phenol in a molecular beam. Its vibrational spectrum corresponds well with a classical molecular dynamics simulation conducted 'on-the-fly' and also with the lowest-energy structures predicted by DFT and ab initio calculations. They reveal proton-bound structures that bridge neighbouring pairs of oxygen atoms, preferentially O6 and O4, linked together within the carbohydrate scaffold. Motivated by the possibility of an entry into the microscopic mechanism of its acid (or enzyme)-catalysed hydrolysis, we also report the corresponding predictions for its singly hydrated complex.

  18. Vibrational spectroscopy investigation and density functional theory calculations on (E)-N‧-(4-methoxybenzylidene) benzohydrazide

    NASA Astrophysics Data System (ADS)

    Saleem, H.; Subashchandrabose, S.; Ramesh Babu, N.; Syed Ali Padusha, M.

    2015-05-01

    The FT-IR, FT-Raman and UV-Vis spectra of the Schiff base compound (E)-N‧-(4-methoxybenzylidene) benzohydrazide (MBBH) have been recorded and analyzed. The optimized geometrical parameters were calculated. The complete vibrational assignments were performed on the basis of TED of the vibrational modes, calculated with the help of SQM method. NBO analysis has been carried out to explore the hyperconjugative interactions and their second order stabilization energy within the molecule. The molecular orbitals (MO's) and its energy gap were studied. The first order hyperpolarizability (β0) and related properties (β, α0, Δα) of MBBH are also calculated. All theoretical calculations were performed on the basis of B3LYP/6-311++G(d,p) level of theory.

  19. Vibrational spectroscopy investigation and density functional theory calculations on (E)-N'-(4-methoxybenzylidene) benzohydrazide.

    PubMed

    Saleem, H; Subashchandrabose, S; Ramesh Babu, N; Syed Ali Padusha, M

    2015-05-15

    The FT-IR, FT-Raman and UV-Vis spectra of the Schiff base compound (E)-N'-(4-methoxybenzylidene) benzohydrazide (MBBH) have been recorded and analyzed. The optimized geometrical parameters were calculated. The complete vibrational assignments were performed on the basis of TED of the vibrational modes, calculated with the help of SQM method. NBO analysis has been carried out to explore the hyperconjugative interactions and their second order stabilization energy within the molecule. The molecular orbitals (MO's) and its energy gap were studied. The first order hyperpolarizability (β0) and related properties (β, α0, Δα) of MBBH are also calculated. All theoretical calculations were performed on the basis of B3LYP/6-311++G(d,p) level of theory. PMID:25733250

  20. Ultrafast 2DIR spectroscopy of ferric azide precursors for high-valent iron. Vibrational relaxation, spectral diffusion, and dynamic symmetry breaking.

    PubMed

    Czurlok, Denis; Torres-Alacan, Joel; Vöhringer, Peter

    2015-06-01

    Femtosecond mid-infrared pump-probe and two-dimensional mid-infrared spectroscopy have been used to investigate the dynamics of vibrational relaxation and vibrational spectral diffusion of the asymmetric N3-stretching vibration of pseudo-octahedral azidoiron(III) complexes, [L6-nFe(N3)n](+) with n = 1 or 2 and L being an auxiliary ligand of denticity 6-n, in acetonitrile at room temperature. Compared to the free azide anion in acetonitrile solution, the vibrational relaxation dynamics are considerably accelerated. Vibrational energy transfer to the solvent is accelerated by virtue of a resonance with an overtone transition of the solvent. Intramolecular vibrational redistribution is found to be accelerated by virtue of a coupling between the initial azide stretching vibration and the torsional modes involving the axial ligands. Vibrational spectral diffusion within the asymmetric N3-stretching resonance was found to be insensitive to solvent fluctuations because the axial azide ligands are only partially accessible to the solvent. The particular role of intramolecular structural relaxations of the complex for shaping the linear and nonlinear two-dimensional infrared spectra is discussed in terms of ultrafast symmetry-breaking torsional fluctuations and on the basis of density functional theory calculations.

  1. Does ℏ play a role in multidimensional spectroscopy? Reduced hierarchy equations of motion approach to molecular vibrations.

    PubMed

    Sakurai, Atsunori; Tanimura, Yoshitaka

    2011-04-28

    To investigate the role of quantum effects in vibrational spectroscopies, we have carried out numerically exact calculations of linear and nonlinear response functions for an anharmonic potential system nonlinearly coupled to a harmonic oscillator bath. Although one cannot carry out the quantum calculations of the response functions with full molecular dynamics (MD) simulations for a realistic system which consists of many molecules, it is possible to grasp the essence of the quantum effects on the vibrational spectra by employing a model Hamiltonian that describes an intra- or intermolecular vibrational motion in a condensed phase. The present model fully includes vibrational relaxation, while the stochastic model often used to simulate infrared spectra does not. We have employed the reduced quantum hierarchy equations of motion approach in the Wigner space representation to deal with nonperturbative, non-Markovian, and nonsecular system-bath interactions. Taking the classical limit of the hierarchy equations of motion, we have obtained the classical equations of motion that describe the classical dynamics under the same physical conditions as in the quantum case. By comparing the classical and quantum mechanically calculated linear and multidimensional spectra, we found that the profiles of spectra for a fast modulation case were similar, but different for a slow modulation case. In both the classical and quantum cases, we identified the resonant oscillation peak in the spectra, but the quantum peak shifted to the red compared with the classical one if the potential is anharmonic. The prominent quantum effect is the 1-2 transition peak, which appears only in the quantum mechanically calculated spectra as a result of anharmonicity in the potential or nonlinearity of the system-bath coupling. While the contribution of the 1-2 transition is negligible in the fast modulation case, it becomes important in the slow modulation case as long as the amplitude of the

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

    PubMed

    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.

  3. Vibrational Spectroscopy and Gas-Phase Thermochemistry of the Model Dipeptide N-Acetyl Glycine Methyl Amide

    NASA Astrophysics Data System (ADS)

    Leavitt, Christopher; Raston, Paul; Moody, Grant; Shirley, Caitlyne; Douberly, Gary

    2014-06-01

    The structure-function relationship in proteins is widely recognized, motivating numerous investigations of isolated neutral and ionic polypeptides that generally employ conformation specific, multidimensional UV and IR spectroscopies. This data taken in conjunction with computed harmonic frequencies has provided a snapshot of the underlying molecular physics at play in many polypeptides, but few experiments have been able to probe the energetics of these systems. In this study, we use vibrational spectroscopy to measure the gas-phase enthalpy change for isomerization between two conformations of the dipeptide N-acetyl glycine methyl amide (NAGMA). A two-stage oven source is implemented producing a gas-phase equilibrium distribution of NAGMA molecules that is flash frozen upon pickup by He nanodroplets. Using polarization spectroscopy, the IR spectrum is assigned to a mixture of two conformers having intramolecular hydrogen bonds made up of either five- or seven-membered rings, C5 and C7, respectively. The interconversion enthalpy, obtained from the van't Hoff relation, is 4.52{±}0.12 kJ/mol for isomerization from the C7 to the C5-conformer. This experimental measurement is compared to computations employing a broad range of theoretical methods.

  4. Vibrational Spectroscopy of Au-H and Rh-H Complexes in Silicon

    NASA Astrophysics Data System (ADS)

    Evans, M.; Stavola, Michael; Uftring, S. J.

    1996-03-01

    While the passivation of transition metal impurities in semiconductors by hydrogen has been known for more than a decade, detailed structure-sensitive data is available in only a few cases^1. Here, new hydrogen vibrational bands in Si containing Au or Rh and H are reported. Si containing Au and H shows two hydrogen-stretching bands at 1813.3 and 1827.1 cm-1. The dependence of their relative intensities on Fermi level and secondary illumination suggests that both bands are due to different charge states of the same Au-H complex. Spectra measured under stress show that the center has trigonal symmetry. Additional hydrogen modes are not present in samples containing both H and D which suggests that the Au-H complex contains a single H atom. Vibrational bands in samples containing Pt and H at 1880.7 and 1892.7 cm-1 have similar properties^1, suggesting that this Pt-H defect is similar to the Au-H defect reported here. Samples containing Rh and H show up to 8 new hydrogen vibrational bands between 1814 and 1872 cm-1 which will also be discussed. ^* Supported by NSF Grant No. DMR-9023419. ^1 S. J. Uftring et al, Phys. Rev. B 51, 9612 (1995).

  5. Photoelectron spectroscopy of vibrationally excited H2 (E,F 1Σ+g)

    NASA Astrophysics Data System (ADS)

    Xu, E.; Hickman, A. P.; Kachru, R.; Tsuboi, T.; Helm, H.

    1989-12-01

    Photoelectron energy spectra following (2+1)-multiphoton ionization of H2 via the double-well E,F1Σ+g state have been measured using a magnetic-bottle electron spectrometer. The range of vibrational levels studied, vE,F=3-9, includes states localized at the bottom of the E well, and also states that span both wells. The branching among the vibrational ionization channels is governed by the strong R dependence of the electronic wave function and the degree of localization of the vibrational wave function in the E or the F well. Theoretical analysis confirms that at least two mechanisms contribute to the observations: a direct process involving only the E,F state and the H+2 ionization continuum, and an indirect process involving the 1Σ+u autoionizing state. Mass spectroscopic measurements carried out for vE,F=9, J=1 show that about 25% of the ions produced were H+. Qualitative arguments suggest that most of these protons arise from dissociative ionization to the H+2 continuum.

  6. Molecular vibrations at a liquid-liquid interface observed by fourth-order Raman spectroscopy.

    PubMed

    Fujiyoshi, Satoru; Ishibashi, Taka-aki; Onishi, Hiroshi

    2006-05-18

    Interface-selective, Raman-based observation of molecular vibrations is demonstrated at a liquid-liquid interface. An aqueous solution of oxazine 170 dye interfaced with hexadecane is irradiated with pump and probe light pulses of 630-nm wavelengths in 17-fs width. The ultrashort pulses are broadened due to group velocity dispersion when traveling through the hexadecane layer. The dispersion is optically corrected to give an optimized instrumental response. The pump pulse induces a vibrational coherence of the dye via impulsive stimulated Raman scattering. The probe pulse generates second-harmonic light at the interface. The efficiency of the generation is modulated as a function of the pump-probe delay by the coherently excited molecules. Fourier transformation of the modulated efficiency presents the frequency spectrum of the vibrations. Five bands are recognized at 534, 557, 593, 619, and 683 cm(-1). The pump-and-probe process induces a fourth-order optical response that is forbidden in a centrosymmetric media. The contribution of an undesired, cascaded optical process is quantitatively considered and excluded.

  7. From Ultrafast Structure Determination to Steering Reactions: Mixed IR/Non-IR Multidimensional Vibrational Spectroscopies.

    PubMed

    van Wilderen, Luuk J G W; Bredenbeck, Jens

    2015-09-28

    Ultrafast multidimensional infrared spectroscopy is a powerful method for resolving features of molecular structure and dynamics that are difficult or impossible to address with linear spectroscopy. Augmenting the IR pulse sequences by resonant or nonresonant UV, Vis, or NIR pulses considerably extends the range of application and creates techniques with possibilities far beyond a pure multidimensional IR experiment. These include surface-specific 2D-IR spectroscopy with sub-monolayer sensitivity, ultrafast structure determination in non-equilibrium systems, triggered exchange spectroscopy to correlate reactant and product bands, exploring the interplay of electronic and nuclear degrees of freedom, investigation of interactions between Raman- and IR-active modes, imaging with chemical contrast, sub-ensemble-selective photochemistry, and even steering a reaction by selective IR excitation. We give an overview of useful mixed IR/non-IR pulse sequences, discuss their differences, and illustrate their application potential. PMID:26394274

  8. Direct observation of the fundamental vibration-rotation transitions within the NiD X2Δ ground state by CO-Faraday-L.M.R. spectroscopy and zero field transitions in NiH

    NASA Astrophysics Data System (ADS)

    Lipus, K.; Simon, U.; Bachem, E.; Nelis, Th.; Urban, W.

    We report the first direct observation of the vibration-rotation spectrum of nickel-deuteride in its X2Δ ground state by CO-Faraday-L.M.R. spectroscopy. A set of effective molecular parameters is given. We present first results on the vibration-rotation spectroscopy of NiH, employing a tunable diode laser spectrometer.

  9. Molecular structure and vibrations of NTCDA monolayers on Ag(111) from density-functional theory and infrared absorption spectroscopy.

    PubMed

    Tonner, Ralf; Rosenow, Phil; Jakob, Peter

    2016-02-17

    The structure and vibrational properties of the metal-organic interface of 1,4,5,8-naphthalene-tetracarboxylic dianhydride (NTCDA) on Ag(111) were analysed using Fourier-transform infrared absorption spectroscopy in conjunction with density functional theory calculations including dispersion forces (PBE-D3). Mode assignments and polarizations as well as molecular distortions were determined for four adsorption geometries of NTCDA on top and bridge sites aligned either parallel or perpendicular to the Ag rows and compared to accurate calculations of the free molecule. This enables an in-depth understanding of surface effects on the computed and experimental vibrational spectra of the adsorbed NTCDA molecule. The molecule-substrate interaction comprises two major and equally important contributions: non-directional van der Waals forces between molecule and surface, and covalent bonding of the acyl oxygen atoms with underlying Ag atoms, which is quantified by charge-transfer analysis. Furthermore, adsorption energy calculations showed that the molecular axis of flat-lying NTCDA is oriented preferably in parallel to the Ag rows. The molecule is subject to particular distortions from the planar gas phase structure with covalent bonding leading to downward bending of the acyl oxygen atoms and Pauli repulsion to upward bending of the carbon core. In parallel, strong buckling of the silver surface was identified. As found in previous studies, the lowest unoccupied molecular orbital (LUMO) of the molecule slips below the Fermi level and becomes partially populated upon adsorption. Excitation of totally symmetric vibrational modes then leads to substantial interfacial dynamical charge transfer, which is convincingly reproduced in the calculated IR spectra.

  10. Vibrational spectroscopy of diamond films, Langmuir and Langmuir-Blodgett films and aromatic polyethers

    SciTech Connect

    Yu, L.

    1992-01-01

    This dissertation describes a three part research effort on diamond films, monolayers, and polymers. The first part addresses the surface, interface, and bulk properties of the CVD (chemical vapor deposition) thin films using techniques such as XPS (X-ray photoelectron spectroscopy), SEM (scanning electron microscopy), FTIR-ATR (Fourier transform infrared-attenuated total reflection), spectra subtraction, and Raman spectroscopy. The diamond two phonon mode has been observed in a film microns thick using FTIR spectra subtraction. Second, a method of measuring the optical constant n and the CVD diamond film thickness on a metallic substrate was used without destroying the sample. This method is called FTIR-RAS (reflection absorption spectroscopy). Raman spectroscopy and computer simulations of RAS were used to understand and interpret the RAS spectra. Finally, the effect of planar growth defects (stacking faults) in diamond films on Raman and infrared spectra is examined. The empirical formula for the sp[sup 2]/sp[sup 3] site ratio was experimentally determined by Raman spectroscopy. Preliminary results show a correlation between the Raman band shape and the morphology of the CVD thin films. The second part of this thesis deals with the Raman spectroscopy of monolayers. The first unperturbed Raman spectrum of a Phthalocyanine monolayer at the air water interface was obtained with a satisfactory signal to noise ratio. Raman spectroscopy measured the degree of ordering of the monolayers. The last part concerns the synthesis and characterization of aromatic polyethers. The cation radical polymerization of 1,5-bis(1-naphthoxy)-3-oxapentane is a Scholl reaction. The monomer contains a flexible diethylene oxide unit between the two 1-naphthalene rings. FTIR-DRIFT analysis of the polymers indicates the polymers contain a 1,4-disubstituted naphthalene structure. The polymer is semicrystalline with a melting point of 196[degrees]C, with an inherent viscosity up to 0.53 dl/g.

  11. Accurate line shapes from sub-1 cm(-1) resolution sum frequency generation vibrational spectroscopy of α-pinene at room temperature.

    PubMed

    Mifflin, Amanda L; Velarde, Luis; Ho, Junming; Psciuk, Brian T; Negre, Christian F A; Ebben, Carlena J; Upshur, Mary Alice; Lu, Zhou; Strick, Benjamin L; Thomson, Regan J; Batista, Victor S; Wang, Hong-Fei; Geiger, Franz M

    2015-02-26

    Despite the importance of terpenes in biology, the environment, and catalysis, their vibrational spectra remain unassigned. Here, we present subwavenumber high-resolution broad-band sum frequency generation (HR-BB-SFG) spectra of the common terpene (+)-α-pinene that reveal 10 peaks in the C-H stretching region at room temperature. The high spectral resolution resulted in spectra with more and better resolved spectral features than those of the Fourier transform infrared, femtosecond stimulated Raman spectra in the bulk condensed phase and those of the conventional BB-SFG and scanning SFG spectroscopy of the same molecule on a surface. Experiment and simulation show the spectral line shapes with HR-BB-SFG to be accurate. Homogeneous vibrational decoherence lifetimes of up to 1.7 ps are assigned to specific oscillators and compare favorably to lifetimes computed from density functional tight binding molecular dynamics calculations. Phase-resolved spectra provided their orientational information. We propose the new spectroscopy as an attractive alternative to time domain vibrational spectroscopy or heterodyne detection schemes for studying vibrational energy relaxation and vibrational coherences in molecules at molecular surfaces or interfaces.

  12. Elucidation of molecular structures at buried polymer interfaces and biological interfaces using sum frequency generation vibrational spectroscopy

    PubMed Central

    Zhang, Chi; Myers, John; Chen, Zhan

    2013-01-01

    Sum frequency generation (SFG) vibrational spectroscopy has been developed into an important technique to study surfaces and interfaces. It can probe buried interfaces in situ and provide molecular level structural information such as the presence of various chemical moieties, quantitative molecular functional group orientation, and time dependent kinetics or dynamics at such interfaces. This paper focuses on these three most important advantages of SFG and reviews some of the recent progress in SFG studies on interfaces related to polymer materials and biomolecules. The results discussed here demonstrate that SFG can provide important molecular structural information of buried interfaces in situ and in real time, which is difficult to obtain by other surface sensitive analytical techniques. PMID:23710244

  13. Vibrational spectroscopy of cast Si used to fabricate solar cells: microscopic properties of nitrogen and oxygen impurities

    NASA Astrophysics Data System (ADS)

    Zhang, Haoxiang; Stavola, Michael; Seacrist, Mike

    2012-02-01

    Cast Si with grain sizes from a few mm to a few cm is commonly used for the fabrication of solar cells. Nitrogen impurities are introduced into cast Si by the SiNx coating of the crucible used for casting. Much is known about N and O centers in single-crystal Si used in microelectronics [1]. We have used vibrational; spectroscopy to probe the concentration and defect configurations of nitrogen centers in cast Si used to fabricate solar cells. The interaction of N with O impurities that are present has also been investigated. The dominant N center in cast Si is a N-N interstitial pair. N-O complexes are also formed. Which defect complexes are present depends on the impurity content of the multi-crystalline Si sample, which can vary widely, and its thermal history. [1] H. Ch. Alt and H. E. Wagner, J. Appl. Phys. 106, 103511 (2009) and the references contained therein..

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

    PubMed

    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.

  15. Probing surface and interfacial molecular structures of a rubbery adhesion promoter using sum frequency generation vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Fang, Yong; Li, Bolin; Yu, Jincheng; Zhou, Jie; Xu, Xin; Shao, Wei; Lu, Xiaolin

    2013-09-01

    The molecular structures of an adhesion promoter, polybutadiene-modified epoxy (PBME) rubber at surfaces and buried interfaces with gold (Au) were studied using sum frequency generation (SFG) vibrational spectroscopy. The SFG spectra showed that the soft butadiene part of PBME can segregate to the surfaces and buried interfaces in two base formulations. This is consistent with its application as an adhesion promoter. For the first time, the orientation of the segregated vinyl methylene groups of PBME at the surface and buried interface was evaluated. We found that the vinyl methylene groups at the surface were highly tilted and twisted by quantitative analysis; while the vinyl methylene groups at the buried Au interface were highly tilted by qualitative estimation. Furthermore, this study confirms that the sandwiched-face-down experimental setup can be employed to study the buried interfaces. This could be developed into a standard way to probe the buried interfaces between the commercialized resins and metal substrates.

  16. 2D attenuated total reflectance infrared spectroscopy reveals ultrafast vibrational dynamics of organic monolayers at metal-liquid interfaces

    NASA Astrophysics Data System (ADS)

    Kraack, Jan Philip; Lotti, Davide; Hamm, Peter

    2015-06-01

    We present two-dimensional infrared (2D IR) spectra of organic monolayers immobilized on thin metallic films at the solid liquid interface. The experiments are acquired under Attenuated Total Reflectance (ATR) conditions which allow a surface-sensitive measurement of spectral diffusion, sample inhomogeneity, and vibrational relaxation of the monolayers. Terminal azide functional groups are used as local probes of the environment and structural dynamics of the samples. Specifically, we investigate the influence of different alkyl chain-lengths on the ultrafast dynamics of the monolayer, revealing a smaller initial inhomogeneity and faster spectral diffusion with increasing chain-length. Furthermore, by varying the environment (i.e., in different solvents or as bare sample), we conclude that the most significant contribution to spectral diffusion stems from intra- and intermolecular dynamics within the monolayer. The obtained results demonstrate that 2D ATR IR spectroscopy is a versatile tool for measuring interfacial dynamics of adsorbed molecules.

  17. 2D attenuated total reflectance infrared spectroscopy reveals ultrafast vibrational dynamics of organic monolayers at metal-liquid interfaces.

    PubMed

    Kraack, Jan Philip; Lotti, Davide; Hamm, Peter

    2015-06-01

    We present two-dimensional infrared (2D IR) spectra of organic monolayers immobilized on thin metallic films at the solid liquid interface. The experiments are acquired under Attenuated Total Reflectance (ATR) conditions which allow a surface-sensitive measurement of spectral diffusion, sample inhomogeneity, and vibrational relaxation of the monolayers. Terminal azide functional groups are used as local probes of the environment and structural dynamics of the samples. Specifically, we investigate the influence of different alkyl chain-lengths on the ultrafast dynamics of the monolayer, revealing a smaller initial inhomogeneity and faster spectral diffusion with increasing chain-length. Furthermore, by varying the environment (i.e., in different solvents or as bare sample), we conclude that the most significant contribution to spectral diffusion stems from intra- and intermolecular dynamics within the monolayer. The obtained results demonstrate that 2D ATR IR spectroscopy is a versatile tool for measuring interfacial dynamics of adsorbed molecules.

  18. Vibrational and structural properties of amorphous n-butanol: A complementary Raman spectroscopy and X-ray diffraction study

    NASA Astrophysics Data System (ADS)

    Hédoux, Alain; Guinet, Yannick; Paccou, L.; Derollez, P.; Danède, F.

    2013-06-01

    Raman spectroscopy and X-ray diffraction experiments were performed in the liquid, undercooled liquid, and glassy states of n-butanol. Clear correlated signatures are obtained below the melting temperature, from both temperature dependences of the low-wavenumber vibrational excitations and the intermediate-range order characterized by a prepeak detected in the different amorphous states. It was found that these features are related to molecular associations via strong hydrogen bonds, which preferentially develop at low temperature, and which are not compatible with the long-range order of the crystal. This study provides information on structural heterogeneities developing in hydrogen-bonded liquids, associated to the undercooled regime and the inherent glass transition. The analysis of the isothermal abortive crystallization, 2 K above the glass transition temperature, has given the opportunity to analyze the early stages of the crystallization and to describe the origin of the frustration responsible for an uncompleted crystallization.

  19. Vibrational and electronic spectroscopy of the retro-carotenoid rhodoxanthin in avian plumage, solid-state films, and solution.

    PubMed

    Berg, Christopher J; LaFountain, Amy M; Prum, Richard O; Frank, Harry A; Tauber, Michael J

    2013-11-15

    Rhodoxanthin is one of few retro-carotenoids in nature. These chromophores are defined by a pattern of single and double bond alternation that is reversed relative to most carotenoids. Rhodoxanthin is found in the plumage of several families of birds, including fruit doves (Ptilinopus, Columbidae) and the red cotingas (Phoenicircus, Cotingidae). The coloration associated with the rhodoxanthin-containing plumage of these fruit dove and cotinga species ranges from brilliant red to magenta or purple. In the present study, rhodoxanthin is characterized in situ by UV-Vis reflectance and resonance Raman spectroscopy to gain insights into the mechanisms of color-tuning. The spectra are compared with those of the isolated pigment in solution and in thin solid films. Key vibrational signatures are identified for three isomers of rhodoxanthin, primarily in the fingerprint region. Electronic structure (DFT) calculations are employed to describe the normal modes of vibration, and determine characteristic modes of retro-carotenoids. These results are discussed in the context of various mechanisms that change the electronic absorption, including structural distortion of the chromophore or enhanced delocalization of π-electrons in the ground-state. From the spectroscopic evidence, we suggest that the shift in absorption is likely a consequence of perturbations that primarily affect the excited state of the chromophore. PMID:24055537

  20. Molecular gels in the gas phase? Gelator-gelator and gelator-solvent interactions probed by vibrational spectroscopy.

    PubMed

    Lozada-Garcia, Rolando; Mu, Dan; Plazanet, Marie; Çarçabal, Pierre

    2016-08-10

    Benzylidene glucose (BzGlc) is a member of the benzylidene glycoside family. These molecules have the ability to form molecular physical gels. These materials are formed when gelator molecules create a non-covalently bound frame where solvent molecules are trapped. Since the gel formation process and its properties are determined by the subtle balance between non-covalent forces, it is difficult to anticipate them. Quantitative and qualitative understanding of the gelator-gelator and gelator-solvent interactions is needed to better control these materials for important potential applications. We have used gas phase vibrational spectroscopy and theoretical chemistry to study the conformational choices of BzGlc, its dimer and the complexes it forms with water or toluene. To interpret the vibrational spectra we have used the dispersion corrected functional B97D which we have calibrated for the calculation of OH stretching frequencies. Even at the most basic molecular level, it is possible to interrogate a large range of non-covalent interactions ranging from OH → OH hydrogen bonding, to OH → π, and CH → π, all being at the center of gel properties at the macroscopic level. PMID:27443393

  1. Structure and charging of hydrophobic material/water interfaces studied by phase-sensitive sum-frequency vibrational spectroscopy

    PubMed Central

    Tian, C. S.; Shen, Y. R.

    2009-01-01

    We have studied the hydrophobic water/octadecyltrichlorosilane (OTS) interface by using the phase-sensitive sum-frequency vibrational spectroscopy (PS-SFVS), and we obtained detailed structural information of the interface at the molecular level. Excess ions emerging at the interface were detected by changes of the surface vibrational spectrum induced by the surface field created by the excess ions. Both hydronium (H3O+) and hydroxide (OH−) ions were found to adsorb at the interface, and so did other negative ions such as Cl−. By varying the ion concentrations in the bulk water, their adsorption isotherms were measured. It was seen that among the three, OH− has the highest adsorption energy, and H3O+ has the lowest; OH− also has the highest saturation coverage, and Cl− has the lowest. The result shows that even the neat water/OTS interface is not neutral, but charged with OH− ions. The result also explains the surprising observation that the isoelectric point appeared at ∼3.0 when HCl was used to decrease the pH starting from neat water. PMID:19706483

  2. Vibrational dynamics of hydrogen-bonded complexes in solutions studied with ultrafast infrared pump-probe spectroscopy.

    PubMed

    Banno, Motohiro; Ohta, Kaoru; Yamaguchi, Sayuri; Hirai, Satori; Tominaga, Keisuke

    2009-09-15

    In aqueous solution, the basis of all living processes, hydrogen bonding exerts a powerful effect on chemical reactivity. The vibrational energy relaxation (VER) process in hydrogen-bonded complexes in solution is sensitive to the microscopic environment around the oscillator and to the geometrical configuration of the hydrogen-bonded complexes. In this Account, we describe the use of time-resolved infrared (IR) pump-probe spectroscopy to study the vibrational dynamics of (i) the carbonyl CO stretching modes in protic solvents and (ii) the OH stretching modes of phenol and carboxylic acid. In these cases, the carbonyl group acts as a hydrogen-bond acceptor, whereas the hydroxyl group acts as a hydrogen-bond donor. These vibrational modes have different properties depending on their respective chemical bonds, suggesting that hydrogen bonding may have different mechanisms and effects on the VER of the CO and OH modes than previously understood. The IR pump-probe signals of the CO stretching mode of 9-fluorenone and methyl acetate in alcohol, as well as that of acetic acid in water, include several components with different time constants. Quantum chemical calculations indicate that the dynamical components are the result of various hydrogen-bonded complexes that form between solute and solvent molecules. The acceleration of the VER is due to the increasing vibrational density of states caused by the formation of hydrogen bonds. The vibrational dynamics of the OH stretching mode in hydrogen-bonded complexes were studied in several systems. For phenol-base complexes, the decay time constant of the pump-probe signal decreases as the band peak of the IR absorption spectrum shifts to lower wavenumbers (the result of changing the proton acceptor). For phenol oligomers, the decay time constant of the pump-probe signal decreases as the probe wavenumber decreases. These observations show that the VER time strongly correlates with the strength of hydrogen bonding. This

  3. Vibrational spectroscopy at interfaces by IR-VIS sum-frequency generation using CLIO FEL

    SciTech Connect

    Peremans, A.; Tadjeddine, A.; Wan Quan, Z.

    1995-12-31

    IR-vis sum-frequency generation (SFG) has developed into a versatile technique for probing the vibrational structure of interfaces. To overcome the limited spectral range accessible by benchtop IR lasers, we have developed an SFG spectrometer that makes use of the broad band tuneable infrared beam provided by the CLIO-FEL. We will evaluate the gain in sensitivity of the FEL-SFG spectrometer in comparison to that of benchtop lasers, taking account of the surface damage by laser heating. Thereafter, we review the different research projects undertaken using this facility: (1) The interface selectivity of SFG makes it particularly suitable for probing buried liquid/solid interface. We took advantage of the spectrometer sensitivity to monitor the electrochemical deposition of hydrogen on platinum single crystals at under- and overpotential (2) Because of its sensitivity to the molecular symmetry, SFG allows probing the conformation of self assembled monolayers deposited on metals. We discuss SFG spectra of {omega}(4-nitroanilino)-dodecane adsorbed on polycrystalline gold and silver films; in the 1550 - 900 cm{sup -1} spectral range. (3) We have undertaken a spectroscopic approach for the investigation of polymer films adhesion on glass. Polyurethane/glass interface is investigated in the 2200 - 1600 cin{sup -1} spectral region. (4) The use of the CLIO FEL allows probing of the vibrational dynamics of the prominent IR active vibrations between 1500 and 500 cm{sup -1} of fullerene epitaxial films. These modes are modified upon charge transfer from the substrate to the C{sub 60} molecules. Preliminary SFG spectra of C{sub 60}/Ag interface are presented. (5) Site specific detection of CO adsorption and CO + O coadsorption on Pd(111) are studied.

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

    NASA Astrophysics Data System (ADS)

    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 ∑\

  5. Synchrotron infrared spectroscopy at megabar pressures - Vibrational dynamics of hydrogen to 180 GPa

    NASA Technical Reports Server (NTRS)

    Hanfland, M.; Hemley, R. J.; Mao, H. K.; Williams, G. P.

    1992-01-01

    New techniques for measuring infrared spectra at megabar pressures using synchrotron radiation have been developed and applied to study the Q1(1), Qi(1) + Si(0), and QR(J) vibrational transitions of solid hydrogen to 180 GPa. The frequency difference between the Q1(1) infrared and Raman vibrons increases from 3/cm (zero pressure) to 510/cm (180 GPa), indicating a dramatic increase in intermolecular coupling with pressure. A negative frequency shift is observed for the infrared vibron above 140 GPa. A significant increase in frequency and LO-TO splitting of the lattice phonon is also documented.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2016-09-14

    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. PMID:27634244

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

    PubMed

    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.

  9. A Narrow Amide I Vibrational Band Observed by Sum Frequency Generation Spectroscopy Reveals Highly Ordered Structures of a Biofilm Protein at the Air/Water Interface†

    PubMed Central

    Wang, Zhuguang; Morales-Acosta, M. Daniela; Li, Shanghao; Liu, Wei; Kanai, Tapan; Liu, Yuting; Chen, Ya-Na; Walker, Frederick J.; Ahn, Charles H.; Leblanc, Roger M.

    2016-01-01

    We characterized BslA, a bacterial biofilm protein, at the air/water interface using vibrational sum frequency generation spectroscopy and observed one of the sharpest amide I band ever reported. Combining methods of surface pressure measurements, thin film X-ray reflectivity, and atomic force microscopy, we showed extremely ordered BslA at the interface. PMID:26779572

  10. Isomer selective infrared spectroscopy of supersonically cooled cis- and trans-N-phenylamides in the region from the amide band to NH stretching vibration.

    PubMed

    Miyazaki, Mitsuhiko; Saikawa, Jiro; Ishizuki, Hideki; Taira, Takunori; Fujii, Masaaki

    2009-08-01

    We measured the infrared (IR) spectra of supersonically cooled N-phenylformamide (formanilide) and N-phenylacetamide (acetanilide) in the amide band and X-H stretch vibration regions by using IR-UV depletion spectroscopy combined with a newly developed mid-IR light source based on difference frequency generation in ZnGeP(2). The two rotational isomers, cis- and trans- of the amide group were separately monitored to record the IR spectra. Both of the conformers showed similar features in the amide I and II regions, while major differences of the isomers appeared in the amide III vibration region. The IR spectrum of trans-acetanilide closely resembles that of trans-formanilide, except for vibrations of the methyl group; that is, substitution of the formyl hydrogen to a methyl group has only a minor effect on the amide vibrations. PMID:19606319

  11. Vibrational spectroscopy and chemometrics for rapid, quantitative analysis of bitter acids in hops (Humulus lupulus).

    PubMed

    Killeen, Daniel P; Andersen, David H; Beatson, Ron A; Gordon, Keith C; Perry, Nigel B

    2014-12-31

    Hops, Humulus lupulus, are grown worldwide for use in the brewing industry to impart characteristic flavor and aroma to finished beer. Breeders produce many varietal crosses with the aim of improving and diversifying commercial hops varieties. The large number of crosses critical to a successful breeding program imposes high demands on the supporting chemical analytical laboratories. With the aim of reducing the analysis time associated with hops breeding, quantitative partial least-squares regression (PLS-R) models have been produced, relating reference data acquired by the industrial standard HPLC and UV methods, to vibrational spectra of the same, chemically diverse hops sample set. These models, produced from rapidly acquired infrared (IR), near-infrared (NIR), and Raman spectra, were appraised using standard statistical metrics. Results demonstrated that all three spectroscopic methods could be used for screening hops for α-acid, total bitter acids, and cohumulone concentrations in powdered hops. Models generated from Raman and IR spectra also showed potential for use in screening hops varieties for xanthohumol concentrations. NIR analysis was performed using both a standard benchtop spectrometer and a portable NIR spectrometer, with comparable results obtained by both instruments. Finally, some important vibrational features of cohumulone, colupulone, and xanthohumol were assigned using DFT calculations, which allow more insightful interpretation of PLS-R latent variable plots.

  12. Rotation and Rotation-Vibration Spectroscopy of the 0+-0- Inversion Doublet in Deuterated Cyanamide

    NASA Astrophysics Data System (ADS)

    Kisiel, Zbigniew; Kraśnicki, Adam; Jabs, Wolfgang; Herbst, Eric; Winnewisser, Brenda P.; Winnewisser, Manfred

    2013-10-01

    The pure rotation spectrum of deuterated cyanamide was recorded at frequencies from 118 to 649 GHz, which was complemented by measurement of its high-resolution rotation-vibration spectrum at 8-350 cm-1. For D2NCN the analysis revealed considerable perturbations between the lowest Ka rotational energy levels in the 0+ and 0- substates of the lowest inversion doublet. The final data set for D2NCN exceeded 3000 measured transitions and was successfully fitted with a Hamiltonian accounting for the 0+ - 0- coupling. A smaller data set, consisting only of pure rotation and rotation-vibration lines observed with microwave techniques was obtained for HDNCN, and additional transitions of this type were also measured for H2NCN. The spectroscopic data for all three isotopic species were fitted with a unified, robust Hamiltonian allowing confident prediction of spectra well into the terahertz frequency region, which is of interest to contemporary radioastronomy. The isotopic dependence of the determined inversion splitting, -E = 16.4964789(8), 32.089173(3), and 49.567770(6) cm-1, for D2NCN, HDNCN, and H2NCN, respectively, is found to be in good agreement with estimates from a simple reduced quartic-quadratic double minimum potential.

  13. Vibrational Motions Associated with Primary Processes in Bacteriorhodopsin Studied by Coherent Infrared Emission Spectroscopy

    PubMed Central

    Groma, Géza I.; Colonna, Anne; Martin, Jean-Louis; Vos, Marten H.

    2011-01-01

    The primary energetic processes driving the functional proton pump of bacteriorhodopsin take place in the form of complex molecular dynamic events after excitation of the retinal chromophore into the Franck-Condon state. These early events include a strong electronic polarization, skeletal stretching, and all-trans-to-13-cis isomerization upon formation of the J intermediate. The effectiveness of the photoreaction is ensured by a conical intersection between the electronic excited and ground states, providing highly nonadiabatic coupling to nuclear motions. Here, we study real-time vibrational coherences associated with these motions by analyzing light-induced infrared emission from oriented purple membranes in the 750–1400 cm−1 region. The experimental technique applied is based on second-order femtosecond difference frequency generation on macroscopically ordered samples that also yield information on phase and direction of the underlying motions. Concerted use of several analysis methods resulted in the isolation and characterization of seven different vibrational modes, assigned as C-C stretches, out-of-plane methyl rocks, and hydrogen out-of-plane wags, whereas no in-plane H rock was found. Based on their lifetimes and several other criteria, we deduce that the majority of the observed modes take place on the potential energy surface of the excited electronic state. In particular, the direction sensitivity provides experimental evidence for large intermediate distortions of the retinal plane during the excited-state isomerization process. PMID:21402041

  14. Anharmonic Vibrational Spectroscopy of the F-(H20)n, complexes, n=1,2

    NASA Technical Reports Server (NTRS)

    Chaban, Galina M.; Xantheas, Sotiris; Gerber, R. Benny; Kwak, Dochan (Technical Monitor)

    2003-01-01

    We report anharmonic vibrational spectra (fundamentals, first overtones) for the F-(H(sub 2)O) and F-(H(sub 2)O)2 clusters computed at the MP2 and CCSD(T) levels of theory with basis sets of triple zeta quality. Anharmonic corrections were estimated via the correlation-corrected vibrational self-consistent field (CC-VSCF) method. The CC-VSCF anharmonic spectra obtained on the potential energy surfaces evaluated at the CCSD(T) level of theory are the first ones reported at a correlated level beyond MP2. We have found that the average basis set effect (TZP vs. aug-cc-pVTZ) is on the order of 30-40 cm(exp -1), whereas the effects of different levels of electron correlation [MP2 vs. CCSD(T)] are smaller, 20-30 cm(exp -1). However, the basis set effect is much larger in the case of the H-bonded O-H stretch of the F-(H(sub 2)O) cluster amounting to 100 cm(exp -1) for the fundamentals and 200 cm (exp -1) for the first overtones. Our calculations are in agreement with the limited available set of experimental data for the F-(H(sub 2)O) and F-(H(sub 2)O)2 systems and provide additional information that can guide further experimental studies.

  15. A vibrational spectroscopy study on 3-aminophenylacetic acid by DFT calculations.

    PubMed

    Akkaya, Yasemin; Balci, Kubilay; Goren, Yeliz; Akyuz, Sevim

    2015-08-01

    In this study, in which the group vibrations of 3-aminophenylacetic acid were investigated by electronic structure calculations based on Density Functional Theory (DFT), the possible stable conformers of the molecule were searched through a relaxed "potential energy surface scan" carried out at B3LYP/6-31G(d) level of theory. The corresponding equilibrium geometrical and vibrational spectral data for each of the determined stable conformers and for their possible dimer structures were obtained through "geometry optimisation" and "frequency" calculations carried out at B3LYP/6-31G(d) and B3LYP/6-311G++(d,p) levels of theory. The obtained results confirmed that anharmonic wavenumbers calculated at B3LYP/6-311G++(d,p) level generally quite well agree with the experimental wavenumbers, however, harmonic wavenumbers calculated at both levels of theory need an efficient refinement for a satisfactory agreement with experiment. In particular, the harmonic wavenumbers, IR and Raman intensities refined within Scaled Quantum Mechanical Force Field (SQM FF) methodology constituted the primary data set in the interpretation of the experimental FT-IR, FT-Raman and dispersive Raman spectra of 3-aminophenylacetic acid. By the help of these refined spectral data, the effects of conformation and intermolecular hydrogen bonding on the fundamental bands observed in the experimental spectra could be correctly predicted. PMID:25854610

  16. A vibrational spectroscopy study on 3-aminophenylacetic acid by DFT calculations

    NASA Astrophysics Data System (ADS)

    Akkaya, Yasemin; Balci, Kubilay; Goren, Yeliz; Akyuz, Sevim

    2015-08-01

    In this study, in which the group vibrations of 3-aminophenylacetic acid were investigated by electronic structure calculations based on Density Functional Theory (DFT), the possible stable conformers of the molecule were searched through a relaxed "potential energy surface scan" carried out at B3LYP/6-31G(d) level of theory. The corresponding equilibrium geometrical and vibrational spectral data for each of the determined stable conformers and for their possible dimer structures were obtained through "geometry optimisation" and "frequency" calculations carried out at B3LYP/6-31G(d) and B3LYP/6-311G++(d,p) levels of theory. The obtained results confirmed that anharmonic wavenumbers calculated at B3LYP/6-311G++(d,p) level generally quite well agree with the experimental wavenumbers, however, harmonic wavenumbers calculated at both levels of theory need an efficient refinement for a satisfactory agreement with experiment. In particular, the harmonic wavenumbers, IR and Raman intensities refined within Scaled Quantum Mechanical Force Field (SQM FF) methodology constituted the primary data set in the interpretation of the experimental FT-IR, FT-Raman and dispersive Raman spectra of 3-aminophenylacetic acid. By the help of these refined spectral data, the effects of conformation and intermolecular hydrogen bonding on the fundamental bands observed in the experimental spectra could be correctly predicted.

  17. Nonlinear Spectroscopy Study of Vibrational Self-Trapping in Hydrogen Bonded Crystals

    NASA Astrophysics Data System (ADS)

    Edler, Julian; Hamm, Peter

    Femtosecond pump probe spectroscopy proves that self-trapping occurs in the NH and amide I band of crystalline acetanilide (ACN). The phonon modes that mediate the self-trapping are identified. Comparison between ACN and N-methylacetamide, both model systems for proteins, shows that self-trapping is a common feature in hydrogen bonded systems.

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

    NASA Astrophysics Data System (ADS)

    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.

  19. Vibrational Properties of h-BN and h-BN-Graphene Heterostructures Probed by Inelastic Electron Tunneling Spectroscopy

    NASA Astrophysics Data System (ADS)

    Jung, Suyong; Park, Minkyu; Park, Jaesung; Jeong, Tae-Young; Kim, Ho-Jong; Watanabe, Kenji; Taniguchi, Takashi; Ha, Dong Han; Hwang, Chanyong; Kim, Yong-Sung

    2015-11-01

    Inelastic electron tunneling spectroscopy is a powerful technique for investigating lattice dynamics of nanoscale systems including graphene and small molecules, but establishing a stable tunnel junction is considered as a major hurdle in expanding the scope of tunneling experiments. Hexagonal boron nitride is a pivotal component in two-dimensional Van der Waals heterostructures as a high-quality insulating material due to its large energy gap and chemical-mechanical stability. Here we present planar graphene/h-BN-heterostructure tunneling devices utilizing thin h-BN as a tunneling insulator. With much improved h-BN-tunneling-junction stability, we are able to probe all possible phonon modes of h-BN and graphite/graphene at Γ and K high symmetry points by inelastic tunneling spectroscopy. Additionally, we observe that low-frequency out-of-plane vibrations of h-BN and graphene lattices are significantly modified at heterostructure interfaces. Equipped with an external back gate, we can also detect high-order coupling phenomena between phonons and plasmons, demonstrating that h-BN-based tunneling device is a wonderful playground for investigating electron-phonon couplings in low-dimensional systems.

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

    PubMed

    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

    2010-12-28

    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 Fe(III) 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 Fe(III)BLM and ABLM as (BLM)Fe(III)─OH and (BLM)Fe(III)(η(1)─OOH) species, respectively. The NRVS spectra of Fe(III)BLM 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─N(ax) 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.

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

    SciTech Connect

    Liu, L. V.; Bell, C. B., III; Wong, S. D.; Wilson, S. A.; Kwak, Y.; Chow, M.S.; Zhao, J.; Hodgson, K.O.; Hedman, B.; Solomon, E.I.

    2010-12-28

    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 Fe{sup III} peroxy level species, termed activated bleomycin (ABLM). DNA strand scission is initiated through the abstraction of the C-4{prime} 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 Fe{sup III}BLM and ABLM as (BLM)Fe{sup III}-OH and (BLM)Fe{sup III}({eta}{sup 1}-OOH) species, respectively. The NRVS spectra of Fe{sup III}BLM and ABLM are strikingly different because in ABLM the {delta}Fe-O-O bending mode mixes with, and energetically splits, the doubly degenerate, intense O-Fe-N{sub ax} 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.

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

    PubMed Central

    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

  3. Vibrational Properties of h-BN and h-BN-Graphene Heterostructures Probed by Inelastic Electron Tunneling Spectroscopy

    PubMed Central

    Jung, Suyong; Park, Minkyu; Park, Jaesung; Jeong, Tae-Young; Kim, Ho-Jong; Watanabe, Kenji; Taniguchi, Takashi; Ha, Dong Han; Hwang, Chanyong; Kim, Yong-Sung

    2015-01-01

    Inelastic electron tunneling spectroscopy is a powerful technique for investigating lattice dynamics of nanoscale systems including graphene and small molecules, but establishing a stable tunnel junction is considered as a major hurdle in expanding the scope of tunneling experiments. Hexagonal boron nitride is a pivotal component in two-dimensional Van der Waals heterostructures as a high-quality insulating material due to its large energy gap and chemical-mechanical stability. Here we present planar graphene/h-BN-heterostructure tunneling devices utilizing thin h-BN as a tunneling insulator. With much improved h-BN-tunneling-junction stability, we are able to probe all possible phonon modes of h-BN and graphite/graphene at Γ and K high symmetry points by inelastic tunneling spectroscopy. Additionally, we observe that low-frequency out-of-plane vibrations of h-BN and graphene lattices are significantly modified at heterostructure interfaces. Equipped with an external back gate, we can also detect high-order coupling phenomena between phonons and plasmons, demonstrating that h-BN-based tunneling device is a wonderful playground for investigating electron-phonon couplings in low-dimensional systems. PMID:26563740

  4. Vibrational spectroscopy and density functional theory study of 4-mercaptobenzoic acid

    NASA Astrophysics Data System (ADS)

    Li, Ran; Lv, Haiming; Zhang, Xiaolei; Liu, Peipei; Chen, Lei; Cheng, Jianbo; Zhao, Bing

    2015-09-01

    In this paper, 4-mercaptobenzoic acid (4-MBA/pMBA) was designed as a model molecule for theoretical and experimental studies of the molecule structure. Density functional theory (DFT) calculations have been performed to predict the IR and Raman spectra for the molecule. In addition, Fourier transform infrared (FTIR) and Raman spectra of the compound have been obtained experimentally. Based on the modeling results obtained at the B3LYP/6-311++G∗∗ level, all FTIR and Raman bands of the compound obtained experimentally were assigned. Our calculated vibrational frequencies are in good agreement with the experimental vales. The molecular electrostatic potential surface calculation was performed and the result suggested that the 4-MBA had two hydrogen bond donors and three hydrogen bond acceptors. HOMO-LUMO gap was also obtained theoretically at B3LYP/6-311++G∗∗ level.

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

    PubMed

    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.

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

    SciTech Connect

    Lechaftois, F. Péru, S.; Deloncle, I.

    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.

  7. Hydrocarbon on Carbon: Coherent Vibrational Spectroscopy of Toluene on Graphite (HOPG)

    SciTech Connect

    Achtyl, Jennifer L; Buchbinder, Avram M.; Geiger, Franz M

    2012-01-01

    The ability to study the interactions of hydrocarbons on carbon surfaces is an integral step towards gaining a molecular level understanding of the chemical reactions and physical properties occurring on them. Here, we apply vibrational sum frequency generation (SFG) to determine the tilt angle of toluene, a common organic solvent, on mm-thick highly oriented pyrolytic graphite (HOPG). The combination of a time-delay technique, which results in the successful suppression of the nonresonant SFG response, and a null angle method is shown to overcome the strong optical absorber problem posed by macroscopically thick carbon samples and yields a molecular tilt angle of toluene in the range of 37 to 42 degrees from surface normal. The implications of this approach for determining the orientation of organic species adsorbed on carbon interfaces important for energy relevant processes are discussed.

  8. In vivo molecular labeling of halogenated volatile anesthetics via intrinsic molecular vibrations using nonlinear Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Nagashima, Yu; Suzuki, Takayuki; Terada, Sumio; Tsuji, Shoji; Misawa, Kazuhiko

    2011-01-01

    Halogenated volatile anesthetics are frequently used for inhaled anesthesia in clinical practice. No appropriate biological method has been available for visualizing their localization in action. Therefore, despite their frequent use, the mechanism of action of these drugs has not been fully investigated. We measured coherent anti-Stokes Raman scattering (CARS) spectra of sevoflurane and isoflurane, two of the most representative volatile anesthetics, and determined the low-frequency vibrational modes without nonresonant background disturbance. Molecular dynamics calculations predict that these modes are associated with multiple halogen atoms. Because halogen atoms rarely appear in biological compounds, the entire spectral landscape of these modes is expected to be a good marker for investigating the spatial localization of these drugs within the intracellular environment. Using live squid giant axons, we could detect the unique CARS spectra of sevoflurane for the first time in a biological setting.

  9. Proton Translocation in Cytochrome c Oxidase: Insights from Proton Exchange Kinetics and Vibrational Spectroscopy

    PubMed Central

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

    2014-01-01

    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. PMID:25268561

  10. Dielectric and electric properties of new chitosan-hydroxyapatite materials for biomedical application: Dielectric spectroscopy and corona treatment.

    PubMed

    Petrov, Ivo; Kalinkevich, Oksana; Pogorielov, Maksym; Kalinkevich, Aleksei; Stanislavov, Aleksandr; Sklyar, Anatoly; Danilchenko, Sergei; Yovcheva, Temenuzhka

    2016-10-20

    Chitosan-hydroxyapatite composite materials were synthesized and the possibility to make their surface charged by corona discharge treatment has been evaluated. Dielectric and electric properties of the materials were studied by dielectric spectroscopy, including application of equivalent circuits method and computer simulations. Dielectric spectroscopy shows behavior of the materials quite different from that of both chitosan and HA alone. The obtained dielectric permittivity data are of particular interest in predicting the materials' behavior in electrostimulation after implantation. The ε values observed at physiological temperature in the frequency ranges applied are similar to ε data available for bone tissues.

  11. Application of multivariate analysis and vibrational spectroscopy in classification of biological systems

    NASA Astrophysics Data System (ADS)

    Salman, A.; Shufan, E.; Lapidot, I.; Tsror, L.; Zeiri, L.; Sahu, R. K.; Moreh, R.; Mordechai, S.; Huleihel, M.

    2015-12-01

    Fourier Transform Infrared (FTIR) and Raman spectroscopies have emerged as powerful tools for chemical analysis. This is due to their ability to provide detailed information about the spatial distribution of chemical composition at the molecular level. A biological sample, i.e. bacteria or fungi, has a typical spectrum. This spectral fingerprint, characterizes the sample and can therefore be used for differentiating between biology samples which belong to different groups, i.e., several different isolates of a given fungi. When the spectral differences between the groups are minute, multivariate analysis should be used to provide a good differentiation. We hereby review several results which demonstrate the differentiation success obtained by combining spectroscopy measurements and multivariate analysis.

  12. Photoinduced transformation of UVR8 monitored by vibrational and fluorescence spectroscopy.

    PubMed

    Heilmann, Monika; Christie, John M; Kennis, John T M; Jenkins, Gareth I; Mathes, Tilo

    2015-02-01

    Tryptophan residues at the dimer interface of the plant photoreceptor UVR8 promote monomerisation after UV-B absorption via a so far unknown mechanism. Using FTIR spectroscopy we assign light-induced structural transitions of UVR8 mainly to amino acid side chains without major transformations of the secondary structure of the physiologically relevant C-terminal extension. Additionally, we assign the monomerisation associated increase and red shift of the UVR8 tryptophan emission to a photoinduced rearrangement of tryptophan side chains and a relocation of the aspartic acid residues D96 and D107, respectively. By illumination dependent emission spectroscopy we furthermore determined the quantum yield of photoinduced monomerisation to 20 ± 8%.

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

    SciTech Connect

    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

  14. The Clusters-in-a-Liquid Approach for Solvation: New Insights from the Conformer Specific Gas Phase Spectroscopy and Vibrational Optical Activity Spectroscopy

    PubMed Central

    Perera, Angelo S.; Thomas, Javix; Poopari, Mohammad R.; Xu, Yunjie

    2016-01-01

    Vibrational optical activity spectroscopies, namely vibrational circular dichroism (VCD) and Raman optical activity (ROA), have been emerged in the past decade as powerful spectroscopic tools for stereochemical information of a wide range of chiral compounds in solution directly. More recently, their applications in unveiling solvent effects, especially those associated with water solvent, have been explored. In this review article, we first select a few examples to demonstrate the unique sensitivity of VCD spectral signatures to both bulk solvent effects and explicit hydrogen-bonding interactions in solution. Second, we discuss the induced solvent chirality, or chiral transfer, VCD spectral features observed in the water bending band region in detail. From these chirality transfer spectral data, the related conformer specific gas phase spectroscopic studies of small chiral hydration clusters, and the associated matrix isolation VCD experiments of hydrogen-bonded complexes in cold rare gas matrices, a general picture of solvation in aqueous solution emerges. In such an aqueous solution, some small chiral hydration clusters, rather than the chiral solutes themselves, are the dominant species and are the ones that contribute mainly to the experimentally observed VCD features. We then review a series of VCD studies of amino acids and their derivatives in aqueous solution under different pHs to emphasize the importance of the inclusion of the bulk solvent effects. These experimental data and the associated theoretical analyses are the foundation for the proposed “clusters-in-a-liquid” approach to account for solvent effects effectively. We present several approaches to identify and build such representative chiral hydration clusters. Recent studies which applied molecular dynamics simulations and the subsequent snapshot averaging approach to generate the ROA, VCD, electronic CD, and optical rotatory dispersion spectra are also reviewed. Challenges associated with

  15. The clusters-in-a-liquid approach for solvation: New insights from the conformer specific gas phase spectroscopy and vibrational optical activity spectroscopy

    NASA Astrophysics Data System (ADS)

    Xu, Yunjie; Perera, Angelo; Thomas, Javix; Poopari, Mohammad

    2016-02-01

    Vibrational optical activity spectroscopies, namely vibrational circular dichroism (VCD) and Raman optical activity (ROA), have been emerged in the past decade as a powerful spectroscopic tool for stereochemical information of a wide range of chiral compounds in solution directly. More recently, their applications in unveiling solvent effects, especially those associated with water solvent, have been explored. In this review article, we first select a few examples to demonstrate the unique sensitivity of VCD spectral signatures to both bulk solvent effects and explicit hydrogen-bonding interactions in solution. Second, we discuss the induced solvent chirality, or chiral transfer, VCD spectral features observed at the water bending band region in detail. From these chirality transfer spectral data, the related conformer specific gas phase spectroscopic studies of small chiral hydration clusters, and the associated matrix isolation VCD experiments of hydrogen-bonded complexes in cold rare gas matrices, a general picture of solvation in aqueous solution emerges. In such an aqueous solution, some small chiral hydration clusters, rather than the chiral solutes themselves, are the dominant species and are the ones who contribute mainly to the experimentally observed VCD features. We then review a series of VCD studies of amino acids and their derivatives in aqueous solution under different pHs to emphasize the importance of the inclusion of the bulk solvent effects. These experimental data and the associated theoretical analyses are the foundation for the proposed “clusters-in-a-liquid” approach to account for solvent effects effectively. We present several approaches to identify and build such representative chiral hydration clusters. Recent studies which applied molecular dynamics simulations and the subsequent snapshot averaging approach to generate the ROA, electronic CD, and optical rotatory dispersion spectra are also reviewed. Challenges associated with the

  16. 3D Motions of Iron in Six-Coordinate {FeNO}(7) Hemes by Nuclear Resonance Vibration Spectroscopy.

    PubMed

    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.

  17. Distinguishing gramicidin D conformers through two-dimensional infrared spectroscopy of vibrational excitons

    PubMed Central

    Tokmakoff, Andrei

    2015-01-01

    Gramicidin D is a short peptide which dimerizes to form helical pores, adopting one of two conformations in the process. These conformations differ primarily in number of residues per turn and the hydrogen-bond registry between rungs of the helix. Using amide I 2D infrared (IR) and FTIR, we have demonstrated that it is possible to distinguish between the different conformers of gramicidin D in solution. We show that the spectra observed for this helical peptide bear no resemblance to the spectra of α- or 310-helices and that while the FTIR spectra appear similar to spectra of β-sheets, 2D IR reveals that the observed resonances arise from vibrational modes unlike those observed in β-sheets. We also present an idealized model which reproduces the experimental data with high fidelity. This model is able to explain the polarization-dependence of the experimental 2D IR data. Using this model, we show the coupling between the rungs of the helix dominates the spectra, and as a consequence of this, the number of residues per turn can greatly influence the amide I spectra of gramicidin D. PMID:26049444

  18. Vibrational spectroscopy and mode assignments for an analog of the green fluorescent protein chromophore

    NASA Astrophysics Data System (ADS)

    Esposito, A. P.; Schellenberg, P.; Parson, W. W.; Reid, P. J.

    2001-07-01

    Infrared absorption (IR), Raman, and resonance Raman spectra have been obtained from 500 to 1700 cm -1 for 4-hydroxybenzylidene-2,3-dimethyl-imidazolinone (HBDI), an analog of the green-fluorescent protein (GFP) chromophore. Numerous transitions are evident in both the IR and Raman spectra, with the resonance Raman spectrum of HBDI dominated by a subset of transitions in the 1430-1700 cm -1 region. Assignment of the transitions in this frequency region to the corresponding normal coordinates is accomplished through computational studies employing density functional and Hartree-Fock theory. The computational results indicate that the vibrational transitions in this frequency range are dominated by in-plane stretching modes that are localized to the imidazolinone or tyrosine portions of the chromophore, rather than being delocalized over the entire chromophore. No evidence is obtained for significant excited-state structural evolution along the O-H stretching coordinate. The implications of these findings with respect to the excited-state proton transfer dynamics of GFP are discussed.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  1. Vibrational spectroscopy as a probe to rapidly detect, identify, and characterize micro-organisms

    NASA Astrophysics Data System (ADS)

    Sockalingum, Ganesh D.; Lamfarraj, Hasnae; Beljebbar, Abdelilah; Pina, Patrick; Delavenne, Marc; Witthuhn, Fabienne; Allouch, Pierre; Manfait, Michel

    1999-04-01

    Fast and exact identification of a great number of microorganisms is becoming a serious challenge. Differentiation and identification of microorganisms is today mainly achieved by the use of a variety of distinct techniques based on morphological, serological aspects and a set of biochemical test. Vibrational spectroscopic techniques can be complementary and useful methods in this field due to their rapidity, 'fingerprinting' capabilities, and the molecular information that they can provide. Using SERS at Ag colloids, we have conducted pilot studies to rapidly detect and identify bacterial clinical strains. Using a Raman microspectrometer equipped with a He/Ne laser, a first attempt to record SERS spectra was made on colloidal solutions. Spectra were of good quality but not very reproducible due to the movement of the microorganisms. Strains were then put in presence of Ag colloids and direct on-plate analysis was performed. Spectra were more reproducible, with diminished fluorescence, and reveal characteristic cellular-level information. Different growth conditions and colloid preparations have been tested. Pseudomonas aeruginosa and Escherichia coli clinical strains, responsible for nosocomial infections, have been our first test samples. An attempt has also been made to record SERS data from gold colloids in view of future measurement in the near-IR. Spectroscopic data are compared with ATR-FTIR results.

  2. Full characterization of vibrational coherence in a porphyrin chromophore by two-dimensional electronic spectroscopy.

    PubMed

    Camargo, Franco V A; Anderson, Harry L; Meech, Stephen R; Heisler, Ismael A

    2015-01-01

    In this work we present experimental and calculated two-dimensional electronic spectra for a 5,15-bisalkynyl porphyrin chromophore. The lowest energy electronic Qy transition couples mainly to a single 380 cm(-1) vibrational mode. The two-dimensional electronic spectra reveal diagonal and cross peaks which oscillate as a function of population time. We analyze both the amplitude and phase distribution of this main vibronic transition as a function of excitation and detection frequencies. Even though Feynman diagrams provide a good indication of where the amplitude of the oscillating components are located in the excitation-detection plane, other factors also affect this distribution. Specifically, the oscillation corresponding to each Feynman diagram is expected to have a phase that is a function of excitation and detection frequencies. Therefore, the overall phase of the experimentally observed oscillation will reflect this phase dependence. Another consequence is that the overall oscillation amplitude can show interference patterns resulting from overlapping contributions from neighboring Feynman diagrams. These observations are consistently reproduced through simulations based on third order perturbation theory coupled to a spectral density described by a Brownian oscillator model.

  3. Full characterization of vibrational coherence in a porphyrin chromophore by two-dimensional electronic spectroscopy.

    PubMed

    Camargo, Franco V A; Anderson, Harry L; Meech, Stephen R; Heisler, Ismael A

    2015-01-01

    In this work we present experimental and calculated two-dimensional electronic spectra for a 5,15-bisalkynyl porphyrin chromophore. The lowest energy electronic Qy transition couples mainly to a single 380 cm(-1) vibrational mode. The two-dimensional electronic spectra reveal diagonal and cross peaks which oscillate as a function of population time. We analyze both the amplitude and phase distribution of this main vibronic transition as a function of excitation and detection frequencies. Even though Feynman diagrams provide a good indication of where the amplitude of the oscillating components are located in the excitation-detection plane, other factors also affect this distribution. Specifically, the oscillation corresponding to each Feynman diagram is expected to have a phase that is a function of excitation and detection frequencies. Therefore, the overall phase of the experimentally observed oscillation will reflect this phase dependence. Another consequence is that the overall oscillation amplitude can show interference patterns resulting from overlapping contributions from neighboring Feynman diagrams. These observations are consistently reproduced through simulations based on third order perturbation theory coupled to a spectral density described by a Brownian oscillator model. PMID:25469716

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

    SciTech Connect

    Reppert, Mike; Tokmakoff, Andrei

    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.

  5. Distinguishing gramicidin D conformers through two-dimensional infrared spectroscopy of vibrational excitons.

    PubMed

    Stevenson, Paul; Tokmakoff, Andrei

    2015-06-01

    Gramicidin D is a short peptide which dimerizes to form helical pores, adopting one of two conformations in the process. These conformations differ primarily in number of residues per turn and the hydrogen-bond registry between rungs of the helix. Using amide I 2D infrared (IR) and FTIR, we have demonstrated that it is possible to distinguish between the different conformers of gramicidin D in solution. We show that the spectra observed for this helical peptide bear no resemblance to the spectra of α- or 310-helices and that while the FTIR spectra appear similar to spectra of β-sheets, 2D IR reveals that the observed resonances arise from vibrational modes unlike those observed in β-sheets. We also present an idealized model which reproduces the experimental data with high fidelity. This model is able to explain the polarization-dependence of the experimental 2D IR data. Using this model, we show the coupling between the rungs of the helix dominates the spectra, and as a consequence of this, the number of residues per turn can greatly influence the amide I spectra of gramicidin D.

  6. Distinguishing gramicidin D conformers through two-dimensional infrared spectroscopy of vibrational excitons

    NASA Astrophysics Data System (ADS)

    Stevenson, Paul; Tokmakoff, Andrei

    2015-06-01

    Gramicidin D is a short peptide which dimerizes to form helical pores, adopting one of two conformations in the process. These conformations differ primarily in number of residues per turn and the hydrogen-bond registry between rungs of the helix. Using amide I 2D infrared (IR) and FTIR, we have demonstrated that it is possible to distinguish between the different conformers of gramicidin D in solution. We show that the spectra observed for this helical peptide bear no resemblance to the spectra of α- or 310-helices and that while the FTIR spectra appear similar to spectra of β-sheets, 2D IR reveals that the observed resonances arise from vibrational modes unlike those observed in β-sheets. We also present an idealized model which reproduces the experimental data with high fidelity. This model is able to explain the polarization-dependence of the experimental 2D IR data. Using this model, we show the coupling between the rungs of the helix dominates the spectra, and as a consequence of this, the number of residues per turn can greatly influence the amide I spectra of gramicidin D.

  7. The isomers and conformers of some push pull enamines studied by vibrational and NMR spectroscopy and by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Pigošová, J.; Gatial, A.; Milata, V.; Černuchová, P.; Prónayová, N.; Liptaj, T.; Matějka, P.

    2005-06-01

    The isomers and conformers of six push-pull enamines: 3-dimethylamino-, 3-methylamino- and 3-amino-2-acetyl propenenitrile [(H 3C) 2N-CH dbnd6 C(CN)(COCH 3), H 3C-NH-CH dbnd6 C(CN)(COCH 3) and H 2N-CH dbnd6 C(CN)(COCH 3)] and 3-dimethylamino-, 3-methylamino- and 3-amino-2-methylsulfonyl propenenitrile [(H 3C) 2N-CH dbnd6 C(CN)(SO 2CH 3), H 3C-NH-CH dbnd6 C(CN)(SO 2CH 3) and H 2N-CH dbnd6 C(CN)(SO 2CH 3)] have been studied experimentally by vibrational and NMR spectroscopy and theoretically by the ab initio calculations at MP2 level in 6-31G** basis set. The IR and Raman spectra of all compounds as a solid and solute in various solvents have been recorded in the region 4000-50 cm -1. The NMR spectra were obtained in chloroform and DMSO at room temperature. All six compounds have been prepared by the same way. NMR spectra revealed that both dimethylamino compounds were prepared as a pure E isomers whereas in the case of methylamino compounds the 3-methylamino-2-methylsulfonyl propenenitrile was prepared also as a pure E isomer but 3-methylamino-2-acetyl propenenitrile as a pure Z isomer. Also 3-amino-2-methylsulfonyl propenenitrile was obtained as a pure the E isomer, but 3-amino-2-acetyl propenenitrile as a mixture of both E and Z isomers. Confomational possibilities of studied compounds are given only by the rotation of the acetyl and methylamino groups. Vibrational spectra revealed existence of two conformers with Z and E orientation of acetyl group for 3-dimethylamino-2-acetyl propenenitrile. Two conformers with anti or syn orientation of methylamino group for 3-methylamino-2-methylsulfonyl propenenitrile have been confirmed by vibrational and NMR spectra, but only one conformer with anti orientation of methylamino group for 3-methylamino-2-acetyl propenenitrile in chloroform solution and in solid phase was found. For latter compound the additional isomer/conformer was detected in more polar solvents (acetonitrile/DMSO). These experimental findings have been

  8. Polarized Raman spectroscopy of double-stranded RNA from bacteriophage phi6: local Raman tensors of base and backbone vibrations.

    PubMed Central

    Benevides, J M; Tsuboi, M; Bamford, J K; Thomas, G J

    1997-01-01

    Raman tensors for localized vibrations of base (A, U, G, and C), ribose and phosphate groups of double-stranded RNA have been determined from polarized Raman measurements on oriented fibers of the genomic RNA of bacteriophage phi6. Polarized Raman intensities for which electric vectors of both the incident and scattered light are polarized either perpendicular (I[bb]) or parallel (I[cc]) to the RNA fiber axis have been obtained by Raman microspectroscopy using 514.5-nm excitation. Similarly, the polarized Raman components, I(bc) and I(cb), for which incident and scattered vectors are mutually perpendicular, have been obtained. Spectra collected from fibers maintained at constant relative humidity in both H2O and D2O environments indicate the effects of hydrogen-isotopic shifts on the Raman polarizations and tensors. Novel findings are the following: 1) the intense Raman band at 813 cm(-1), which is assigned to phosphodiester (OPO) symmetrical stretching and represents the key marker of the A conformation of double-stranded RNA, is characterized by a moderately anisotropic Raman tensor; 2) the prominent RNA band at 1101 cm(-1), which is assigned to phosphodioxy (PO2-) symmetrical stretching, also exhibits a moderately anisotropic Raman tensor. Comparison with results obtained previously on A, B, and Z DNA suggests that tensors for localized vibrations of backbone phosphodiester and phosphodioxy groups are sensitive to helix secondary structure and local phosphate group environment; and 3) highly anisotropic Raman tensors have been found for prominent and well-resolved Raman markers of all four bases of the RNA duplex. These enable the use of polarized Raman spectroscopy for the determination of purine and pyrimidine base residue orientations in ribonucleoprotein assemblies. The present determination of Raman tensors for dsRNA is comprehensive and accurate. Unambiguous tensors have been deduced for virtually all local vibrational modes of the 300-1800 cm(-1) spectral

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

    SciTech Connect

    Tokmakoff, Andrei; Fiechtner, Gregory J.

    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.

  10. Determination of omega-3 fatty acids in fish oil supplements using vibrational spectroscopy and chemometric methods.

    PubMed

    Bekhit, Michael Yemane; Grung, Bjørn; Mjøs, Svein Are

    2014-01-01

    The potential of Fourier transform infrared (FT-IR), near-infrared (NIR), and Raman spectroscopic techniques combined with partial least squares (PLS) regression (PLSR) to predict concentrations of eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and total omega-3 fatty acids (n-3 FAs) in fish oil supplements was investigated. FT-IR spectroscopy predicted EPA (coefficient of determination (R(2)) of 0.994, standard error of cross-validation (SECV) of 2.90%, and standard error of prediction (SEP) of 2.49%) and DHA (R(2) = 0.983, SECV = 2.89%, and SEP = 2.55%) with six to seven PLS factors, whereas a simpler PLS model with two factors was obtained for total n-3 FAs (R(2) = 0.985, SECV = 2.73%, and SEP = 2.75%). Selected regions in the NIR spectra gave models with good performances and predicted EPA (R(2) = 0.979, SECV = 2.43%, and SEP = 3.11%) and DHA (R(2) = 0.972, SECV = 2.34%, and SEP = 2.60%) with four to six PLS factors. Both the whole and selected NIR regions gave simple models (two PLS factors) with similar results (R(2) = 0.997, SECV = 2.18%, and SEP = 1.60%) for total n-3 FAs. The whole and selected regions of Raman spectra provided models with comparable results and predicted EPA (R(2) = 0.977, SECV = 3.18%, and SEP = 2.73%) and DHA (R(2) = 0.966, SECV = 3.31%, and SEP = 2.56%) with seven to eight PLS factors, whereas a simpler model (three PLS factors) with R(2) = 0.993, SECV = 2.82%, and SEP = 3.27% was obtained for total n-3 FAs. The results demonstrated that FT-IR, NIR, and Raman spectroscopy combined with PLSR can be used as simple, fast, and nondestructive methods for quantitative analysis of EPA, DHA, and total n-3 FAs. FT-IR and NIR spectroscopy, in particular, have the potential to be applied in process industries during production of fish oil supplements.

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

    NASA Astrophysics Data System (ADS)

    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.

  12. A vibrational spectroscopy study of the orientational ordering in CH 3 Cl monolayers physisorbed on graphite

    NASA Astrophysics Data System (ADS)

    Nalezinski, R.; Bradshaw, A. M.; Knorr, K.

    1997-12-01

    Methylchloride physisorbed on highly ordered pyrolytic graphite (HOPG) has been investigated by infrared reflection-absorption spectroscopy (IRAS). The results confirm the change in orientation of the molecules from flat to inclined between the two 2D crystalline monolayer phases and the up-down staggering in the inclined phase as suggested by previous diffraction studies. At lower coverages the molecules are found to be oriented perpendicular to the substrate, in disagreement with calculations for single, isolated molecules physisorbed on a smooth graphite surface. Measurements of the transient growth behaviour show that this latter state is long-lived and gives rise to complex growth laws. The results show that IRAS is a valuable tool for the study of physisorbed molecular layers.

  13. Interactions of ibuprofen with hybrid lipid bilayers probed by complementary surface-enhanced vibrational spectroscopies

    PubMed Central

    Levin, Carly S.; Kundu, Janardan; Janesko, Benjamin G.; Scuseria, Gustavo E.; Raphael, Robert M.; Halas, Naomi J.

    2016-01-01

    The incorporation of small molecules into lipid bilayers is a process of biological importance and clinical relevance that can change the material properties of cell membranes and cause deleterious side effects for certain drugs. Here we report the direct observation, using surface enhanced Raman and IR spectroscopies (SERS, SEIRA), of the insertion of ibuprofen molecules into hybrid lipid bilayers. The alkanethiol-phospholipid hybrid bilayers were formed onto gold nanoshells by self-assembly, where the underlying nanoshell substrates provided the necessary enhancements for SERS and SEIRA. The spectroscopic data reveal specific interactions between ibuprofen and phospholipid moieties and indicate that the overall hydrophobicity of ibuprofen plays an important role in its intercalation in these membrane mimics. PMID:18942873

  14. Do vibrational spectroscopies uniquely describe protein dynamics? The case for myoglobin.

    PubMed Central

    Bialek, W; Goldstein, R F

    1985-01-01

    We develop a quasi-harmonic description of protein dynamics and apply this description to the anomalous Mössbauer, infrared, x-ray diffraction, and EXAFS (extended x-ray absorption fine structure spectroscopy) data that are available for myoglobin (Mb) and its interactions with carbon monoxide (CO). In the quasi-harmonic approximation the dynamical parameters derived from these spectroscopic data are relevant in the calculation of reaction rates, and we give a quantitative description of the nonexponential kinetics of Mb-CO binding observed at low temperatures. All these data have previously been interpreted in terms of the more complex conformational substates model for protein dynamics. We point out several problems with this model and propose experiments that can provide detailed tests of the quasi-harmonic theory proposed here. PMID:4092066

  15. Quantification of blockiness in pectins-A comparative study using vibrational spectroscopy and chemometrics.

    PubMed

    Winning, Hanne; Viereck, Nanna; Salomonsen, Tina; Larsen, Jan; Engelsen, Søren B

    2009-09-28

    The gelling properties of pectins are related not only to the degree of esterification (DE), but also to the distribution of the ester groups. In this study, we have examined an experimentally designed series of 31 pectins originating from the same mother pectin and de-esterified using combinations of two different enzymatic mechanisms. The potential of using infrared (IR), Raman, and near infrared (NIR) spectroscopies combined with chemometrics for reliable and rapid determination of the DE and distribution patterns of methyl ester groups in a designed set of pectin powders was investigated. Quantitative calibration models using partial least squares (PLS) regression were developed and compared. The calibration models for prediction of DE obtained on extended inverse signal correction (EISC)-treated spectra of all three spectroscopic methods yielded models with cross-validated prediction errors (RMSECV) between 1.1%p and 1.6%p DE and correlation coefficients of 0.99. A calibration model predicting degree of random de-esterification (R) and block de-esterification (B) was developed for each spectroscopic method, yielding RMSECV values between 4.4 and 6.7 and correlation coefficients (r) between 0.79 and 0.92. Variable selection using interval PLS (iPLS) significantly improved the prediction of R for IR spectroscopy, yielding RMSECV of 3.5 and correlation coefficients of 0.95. All three spectroscopic methods were able to distinguish the spectral patterns of pectins with different enzyme treatments in simple classification models by principal component analysis (PCA). Extended canonical variate analysis revealed one specific signal in the Raman (1045cm(-1)) spectrum and one significant area (1250-1400cm(-1)) in the IR spectrum which are able to classify the pectin samples according to the four different enzyme treatments. In both Raman and IR spectra, the signal intensity decreased in the sequence R-B>B>B-R>R>re-methylated pectin. PMID:19101665

  16. Fourier-Transform Microwave and Millimeterwave Spectroscopy of CH2IBr in its Ground Vibrational State

    NASA Astrophysics Data System (ADS)

    Taniguchi, Kotomi; Sakai, Shohei; Ozeki, Hiroyuki; Okabayashi, Toshiaki; Bailey, William C.; Duflot, Denis; Bailleux, Stephane

    2014-06-01

    Halo-substituted methanes constitute a class of molecules that are important in various fields, from spectroscopy to quantum-chemical calculations. They are also gaining interest due to their potential adverse impact on the atmospheric chemistry. In the series of the CH_2IX iodomethanes where X = {F, Cl, Br}, only the rotational spectra of CH_2IF and CH_2ICl have been published. We present our investigations on the high-resolution rotational spectroscopy of the two bromine isotopologues of bromoiodomethane, CH_2I79Br and CH_2I81Br. Due to the lack of spectroscopic information available for this compound, high-level quantum-chemical calculations were essential to guide the microwave and millimeterwave spectral assignments of both μ_a- and μ_b-type transitions. They provided rotational and centrifugal distortion constants (quartic and sextic), as well as the quadrupole-coupling tensor of the iodine (II = 5/2) and bromine (IBr = 3/2) nuclei. More than 1900 lines have been analyzed, leading to an accurate determination of molecular constants for both isotopologues. The experimental structure (r_0) of the title species has been derived from the two sets of rotational constants. S.B. acknowledges support from the Laboratoire d'Excellence CaPPA (Chemical and Physical Properties of the Atmosphere) through contract ANR-10-LABX-005 of the Programme d'Investissement d'Avenir. C. Puzzarini, G. Cazzoli, J. C. López, J. L. Alonso, A. Baldacci, A. Baldan, S. Stopkowicz, L. Cheng and J. Gauss, J. Chem. Phy. 62, 174312 (2011). S. Bailleux, H. Ozeki, S. Sakai, T. Okabayashi, P. Kania and D. Duflot, J. Mol. Spectrosc. 270, 51 (2011).

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

    SciTech Connect

    Kweskin, Sasha Joseph

    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

  18. Vibrational spectroscopy of the borate mineral tunellite SrB6O9(OH)2·3(H2O) - Implications for the molecular structure

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; López, Andrés; Scholz, Ricardo; Xi, Yunfei

    2014-02-01

    Tunellite is a strontium borate mineral with formula: SrB6O9(OH)2·3(H2O) and occurs as colorless crystals in the monoclinic pyramidal crystal system. An intense Raman band at 994 cm-1 was assigned to the BO stretching vibration of the B2O3 units. Raman bands at 1043, 1063, 1082 and 1113 cm-1 are attributed to the in-plane bending vibrations of trigonal boron. Sharp Raman bands observed at 464, 480, 523, 568 and 639 cm-1 are simply defined as trigonal and tetrahedral borate bending modes. The Raman spectrum clearly shows intense Raman bands at 3567 and 3614 cm-1, attributed to OH units. The molecular structure of a natural tunellite has been assessed by using vibrational spectroscopy.

  19. Ultrafast absorption spectroscopy of photodissociated CF2Br2: Details of the reaction mechanism and evidence for anomalously slow intramolecular vibrational redistribution within the CF2Br intermediate

    NASA Astrophysics Data System (ADS)

    Gosnell, T. R.; Taylor, A. J.; Lyman, J. L.

    1991-05-01

    Ultrafast time-resolved absorption spectroscopy in the hard ultraviolet has been used to investigate the photodissociation of gas-phase CF2Br2 photolyzed at 248 nm. The broadband spectra obtained in the 250-265 nm region have shown that absorption of a single photon activates a two-step sequential elimination of the molecule's two bromine atoms, leaving the product CF2 radical in the ground or first-excited vibrational state of its ν2 bending mode. The spectra also demonstrate the direct detection of the vibrationally hot CF2Br intermediate species itself. We interpret the ˜6 ps time scale over which the diffuse CF2Br spectrum evolves as evidence for slow intramolecular vibrational redistribution within this molecule.

  20. Effect of surface structure on catalytic reactions: A sum frequency generation surface vibrational spectroscopy study

    SciTech Connect

    McCrea, Keith R.

    2001-09-07

    In the results discussed above, it is clear that Sum Frequency Generation (SFG) is a unique tool that allows the detection of vibrational spectra of adsorbed molecules present on single crystal surfaces under catalytic reaction conditions. Not only is it possible to detect active surface intermediates, it is also possible to detect spectator species which are not responsible for the measured turnover rates. By correlating high-pressure SFG spectra under reaction conditions and gas chromatography (GC) kinetic data, it is possible to determine which species are important under reaction intermediates. Because of the flexibility of this technique for studying surface intermediates, it is possible to determine how the structures of single crystal surfaces affect the observed rates of catalytic reactions. As an example of a structure insensitive reaction, ethylene hydrogenation was explored on both Pt(111) and Pt(100). The rates were determined to be essentially the same. It was observed that both ethylidyne and di-{sigma} bonded ethylene were present on the surface under reaction conditions on both crystals, although in different concentrations. This result shows that these two species are not responsible for the measured turnover rate, as it would be expected that one of the two crystals would be more active than the other, since the concentration of the surface intermediate would be different on the two crystals. The most likely active intermediates are weakly adsorbed molecules such as {pi}-bonded ethylene and ethyl. These species are not easily detected because their concentration lies at the detection limit of SFG. The SFG spectra and GC data essentially show that ethylene hydrogenation is structure insensitive for Pt(111) and Pt(100). SFG has proven to be a unique and excellent technique for studying adsorbed species on single crystal surfaces under high-pressure catalytic reactions. Coupled with kinetic data obtained from gas chromatography measurements, it can

  1. Rotational and vibrational Raman spectroscopy for thermochemistry measurements in supersonic flames

    NASA Astrophysics Data System (ADS)

    Bayeh, Alexander Christian

    High speed chemically reacting flows are important in a variety of aerospace applications, namely ramjets, scramjets, afterburners, and rocket exhausts. To study flame extinction under similar high Mach number conditions, we need access to thermochemistry measurements in supersonic environments. In the current work a two-stage miniaturized combustor has been designed that can produce open supersonic methane-air flames amenable to laser diagnostics. The first stage is a vitiation burner, and was inspired by well-known principles of jet combustors. We explored the salient parameters of operation experimentally, and verified flame holding computationally using a well-stirred reactor model. The second stage of the burner generates an external supersonic flame, operating in premixed and partially premixed modes. The very high Mach numbers present in the supersonic flames should provide a useful test bed for the examination of flame suppression and extinction using laser diagnostics. We also present the development of new line imaging diagnostics for thermochemistry measurements in high speed flows. A novel combination of vibrational and rotational Raman scattering is used to measure major species densities (O 2, N2, CH4, H2O,CO2, CO, & H2) and temperature. Temperature is determined by the rotational Raman technique by comparing measured rotational spectra to simulated spectra based on the measured chemical composition. Pressure is calculated from density and temperature measurements through the ideal gas law. The independent assessment of density and temperature allows for measurements in environments where the pressure is not known a priori. In the present study we applied the diagnostics to laboratory scale supersonic air and vitiation jets, and examine the feasibility of such measurements in reacting supersonic flames. Results of full thermochemistry were obtained for the air and vitiation jets that reveal the expected structure of an under-expanded jet. Centerline

  2. Towards a non-invasive quantitative analysis of the organic components in museum objects varnishes by vibrational spectroscopies: methodological approach.

    PubMed

    Daher, Céline; Pimenta, Vanessa; Bellot-Gurlet, Ludovic

    2014-11-01

    The compositions of ancient varnishes are mainly determined destructively by separation methods coupled to mass spectrometry. In this study, a methodology for non-invasive quantitative analyses of varnishes by vibrational spectroscopies is proposed. For that, experimental simplified varnishes of colophony and linseed oil were prepared according to 18th century traditional recipes with an increasing mass concentration ratio of colophony/linseed oil. FT-Raman and IR analyses using ATR and non-invasive reflectance modes were done on the "pure" materials and on the different mixtures. Then, a new approach involving spectral decomposition calculation was developed considering the mixture spectra as a linear combination of the pure materials ones, and giving a relative amount of each component. Specific spectral regions were treated and the obtained results show a good accuracy between the prepared and calculated amounts of the two compounds. We were thus able to detect and quantify from 10% to 50% of colophony in linseed oil using non-invasive techniques that can also be conducted in situ with portable instruments when it comes to museum varnished objects and artifacts.

  3. Electron beam exposure mechanisms in hydrogen silsesquioxane investigated by vibrational spectroscopy and in-situ electron beam induced desorption

    SciTech Connect

    Olynick, D.L.; Cord, B.; Schipotinin, A.; Ogletree, D.F.; Schuck, P.J.

    2009-11-13

    Hydrogen Silsesquioxane (HSQ) is used as a high-resolution resist with resolution down below 10nm half-pitch. This material or materials with related functionalities could have widespread impact in nanolithography and nanoscience applications if the exposure mechanism was understood and instabilities controlled. Here we have directly investigated the exposure mechanism using vibrational spectroscopy (both Raman and Fourier transform Infrared) and electron beam desorption spectrocscopy (EBDS). In the non-networked HSQ system, silicon atoms sit at the corners of a cubic structure. Each silicon is bonded to a hydrogen atom and bridges 3 oxygen atoms (formula: HSiO3/2). For the first time, we have shown, via changes in the Si-H2 peak at ~;;2200 cm -1 in the Raman spectra and the release of SiHx products in EBID, that electron-bam exposed materials crosslinks via a redistribution reaction. In addition, we observe the release of significantly more H2 than SiH2 during EBID, which is indicative of additional reaction mechanisms. Additionally, we compare the behavior of HSQ in response to both thermal and electron-beam induced reactions.

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

    PubMed

    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. PMID:27070079

  5. Rapid vibrational and rotational energy-transfer rates in heated carbon dioxide collisions by double-resonance laser spectroscopy

    SciTech Connect

    Thomason, M.D.

    1982-07-01

    Rates for resonant vibrational and rotational energy transfer from the 001 state by CO/sub 2/ + CO/sub 2/ collisions have been measured. All data were obtained by double resonance spectroscopy with CO/sub 2/ lasers in a 2.5 meter absorption cell at 700/sup 0/K. Results for rotation transfer include pumped-level relaxation and the response of other 001 levels with ..delta..J up to 18. These data are compared to four relevant collision models via a 35-level rate equation analysis. Sequence-band (002 ..-->.. 101) and hot-band (011 ..-->.. 110) lasting have been used to observe resonant nu/sub 3/-transfer relaxation involving 001 + 001 reversible 002 + 000, 001 + 100 reversible 101 + 000, and 001 + 010 reversible 011 + 000. A multilevel rate analysis has been utilized to determine the rate coefficients for 001 going to the 002, the 101, and the 011 levels. Part of the hot-band data has been interpreted as due to 110 + 000 reversible 100 + 010, and the associated rate constant has been estimated. The results of the study are compared to the theory and to other experiments.

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

    SciTech Connect

    Xu, Hao; Pan, Wenwu; Chen, Qimiao; Wu, Xiaoyan; Song, Yuxin E-mail: shumin@chalmers.se; Gong, Qian; Lu, Pengfei; Wang, Shumin E-mail: shumin@chalmers.se

    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.

  7. Sub-Doppler Resolution Spectroscopy of the Fundamental Vibration Band of HCl with a Comb-Referenced Spectrometer

    NASA Astrophysics Data System (ADS)

    Iwakuni, Kana; Sera, Hideyuki; Abe, Masashi; Sasada, Hiroyuki

    2015-06-01

    Sub-Doppler resolution spectroscopy of the fundamental bands of H35Cl and H37Cl has been carried out from 87 to 90 THz using a comb-referenced difference-frequency-generation (DFG) spectrometer. While the frequencies of the pump and signal waves are locked to that of the individual nearest comb mode, the repetition rate of the comb is varied for sweeping the idler frequency. Therefore, the relative uncertainty of the frequency scale is 10-11, and the spectral resolution remains about 250 kHz even when the spectrum is accumulated for a long time. The hyperfine structures caused by chlorine nucleus are resolved for the R(0) to R(4) transitions. The figure depicts wavelength-modulation spectrum of the R(0) transition of H35Cl. Three Lamb dips correspond to the F= 0, 1, and -1 components left to right, and the others with arrows are cross-over resonances which are useful for determining the weak F=-1 component frequencies for the R(1) to R(3) transitions. We have determined 49 and 44 transition frequencies of H35Cl and H37Cl with an uncertainty of 10 kHz. Six molecular constants of the vibrational excited state for each isotopomer are determined. They reproduce the determined frequencies with a standard deviation of about 10 kHz.

  8. Vibrationally resolved photoelectron spectroscopy of electronic excited states of DNA bases: application to the ã state of thymine cation.

    PubMed

    Hochlaf, Majdi; Pan, Yi; Lau, Kai-Chung; Majdi, Youssef; Poisson, Lionel; Garcia, Gustavo A; Nahon, Laurent; Al Mogren, Muneerah Mogren; Schwell, Martin

    2015-02-19

    For fully understanding the light-molecule interaction dynamics at short time scales, recent theoretical and experimental studies proved the importance of accurate characterizations not only of the ground (D0) but also of the electronic excited states (e.g., D1) of molecules. While ground state investigations are currently straightforward, those of electronic excited states are not. Here, we characterized the à electronic state of ionic thymine (T(+)) DNA base using explicitly correlated coupled cluster ab initio methods and state-of-the-art synchrotron-based electron/ion coincidence techniques. The experimental spectrum is composed of rich and long vibrational progressions corresponding to the population of the low frequency modes of T(+)(Ã). This work challenges previous numerous works carried out on DNA bases using common synchrotron and VUV-based photoelectron spectroscopies. We provide hence a powerful theoretical and experimental framework to study the electronic structure of ionized DNA bases that could be generalized to other medium-sized biologically relevant systems.

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

    PubMed

    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.

  10. Time-resolved spectroscopic fluorescence imaging, transient absorption and vibrational spectroscopy of intact and photo-inhibited photosynthetic tissue.

    PubMed

    Lukins, Philip B; Rehman, Shakil; Stevens, Gregory B; George, Doaa

    2005-01-01

    Fluorescence, absorption and vibrational spectroscopic techniques were used to study spinach at the photosystem II (PS II), chloroplast and cellular levels and to determine the effects and mechanisms of ultraviolet-B (UV-B) photoinhibition of these structures. Two-photon fluorescence spectroscopic imaging of intact chloroplasts shows significant spatial variations in the component fluorescence spectra in the range 640-740 nm, indicating that the type and distribution of chlorophylls vary markedly with position in the chloroplast. The chlorophyll distributions and excitonic behaviour in chloroplasts and whole plant tissue were studied using picosecond time-gated fluorescence imaging, which also showed UV-induced kinetic changes that clearly indicate that UV-B induces both structural and excitonic uncoupling of chlorophylls within the light-harvesting complexes. Transient absorption measurements and low-frequency infrared and Raman spectroscopy show that the predominant sites of UV-B damage in PS II are at the oxygen-evolving centre (OEC) itself, as well as at specific locations near the OEC-binding sites.

  11. New Insights from Sum Frequency Generation Vibrational Spectroscopy into the Interactions of Islet Amyloid Polypeptides with Lipid Membranes

    PubMed Central

    Wang, Zhuguang; Batista, Victor S.; Yan, Elsa C. Y.

    2016-01-01

    Studies of amyloid polypeptides on membrane surfaces have gained increasing attention in recent years. Several studies have revealed that membranes can catalyze protein aggregation and that the early products of amyloid aggregation can disrupt membrane integrity, increasing water permeability and inducing ion cytotoxicity. Nonetheless, probing aggregation of amyloid proteins on membrane surfaces is challenging. Surface-specific methods are required to discriminate contributions of aggregates at the membrane interface from those in the bulk phase and to characterize protein secondary structures in situ and in real time without the use of perturbing spectroscopic labels. Here, we review the most recent applications of sum frequency generation (SFG) vibrational spectroscopy applied in conjunction with computational modeling techniques, a joint experimental and computational methodology that has provided valuable insights into the aggregation of islet amyloid polypeptide (IAPP) on membrane surfaces. These applications show that SFG can provide detailed information about structures, kinetics, and orientation of IAPP during interfacial aggregation, relevant to the molecular mechanisms of type II diabetes. These recent advances demonstrate the promise of SFG as a new approach for studying amyloid diseases at the molecular level and for the rational drug design targeting early aggregation products on membrane surfaces. PMID:26697504

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed Central

    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

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

    PubMed

    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.

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

    SciTech Connect

    Merouane, S.; Djouadi, Z.; Le Sergeant d'Hendecourt, L.

    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.

  16. XRD, Electron Microscopy and Vibrational Spectroscopy Characterization of Simulated SB6 HLW Glasses - 13028

    SciTech Connect

    Stefanovsky, S.V.; Nikonov, B.S.; Omelianenko, B.I.; Choi, A.; Marra, J.C.

    2013-07-01

    Sample glasses have been made using SB6 high level waste (HLW) simulant (high in both Al and Fe) with 12 different frit compositions at a constant waste loading of 36 wt.%. As follows from X-ray diffraction (XRD) and optical and scanning electron microscopy (SEM) data, all the samples are composed of primarily glass and minor concentration of spinel phases which form both isometric grains and fine cubic (∼1 μm) crystals. Infrared spectroscopy (IR) spectra of all the glasses within the range of 400-1600 cm{sup -1} consist of the bands due to stretching and bending modes in silicon-oxygen, boron-oxygen, aluminum-oxygen and iron-oxygen structural groups. Raman spectra showed that for the spectra of all the glasses within the range of 850-1200 cm{sup -1} the best fit is achieved by suggestion of overlapping of three major components with maxima at 911-936 cm{sup -1}, 988-996 cm{sup -1} and 1020-1045 cm{sup -1}. The structural network is primarily composed of metasilicate chains and rings with embedded AlO{sub 4} and FeO{sub 4} tetrahedra. Major BO{sub 4} tetrahedra and BO{sub 3} triangles form complex borate units and are present as separate constituents. (authors)

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

    PubMed Central

    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

  18. Vibrational Spectroscopy after OSU - From C2- to Interstellar Polycyclic Aromatic Hydrocarbons

    NASA Technical Reports Server (NTRS)

    Allamandola, Louis J.

    2006-01-01

    The composition of interstellar ice and dust provides insight into the chemical history of the interstellar medium and early solar system. It is now possible to probe this unique and unusual chemistry and determine the composition of these microscopic interstellar particles which are hundreds to many thousands of light years away thanks to substantial progress in two areas: astronomical spectroscopic techniques in the middle-infrared, the spectral region most diagnostic of chemical composition, and laboratory simulations which realistically reproduce the critical conditions in various interstellar environments. High quality infrared spectra of many different astronomical sources, some associated with giant, dark molecular clouds -the birthplace of stars and planets- and others in more tenuous, UV radiation rich regions are now available. The fundamentals of IR spectroscopy and what comparisons of astronomical IR spectra with laboratory spectra of materials prepared under realistic simulated interstellar conditions tell us about the components of these materials is the subject of this talk. These observations have shown that mixed molecular ices comprised of H2O, CH3OH, CO, NH3 and H2CO contain most of the molecular material in molecular clouds and that gas phase, ionized polycyclic aromatic hydrocarbons (PAHs) are widespread and surprisingly abundant throughout most of the interstellar medium.

  19. Vibrational spectroscopy of bacteriorhodopsin mutants: Evidence for the interaction of proline-186 with the retinylidene chromophore

    SciTech Connect

    Rothschild, K.J.; He, Y.W.; Mogi, T.; Marti, T.; Stern, L.J.; Khorana, H.G. )

    1990-06-26

    Fourier-transform infrared difference spectroscopy has been used to study the role of the three membrane-embedded proline residues, Pro-50, Pro-91, and Pro-186, in the structure and function of bacteriorhodopsin. All three prolines were replaced by alanine and glycine; in addition, Pro-186 was changed to valine. Difference spectra were recorded for the bR----K and bR----M photoreactions of each of these mutants and compared to those of wild-type bacteriorhodopsin. Only substitutions of Pro-186 caused significant perturbations in the frequency of the C = C and C - C stretching modes of the retinylidene chromophore. In addition, these substitutions reduced bands in the amide I and II region associated with secondary structural changes and altered signals assigned to the adjacent Tyr-185. Pro-186----Val caused the largest alterations, producing a second species similar to bR548 and nearly blocking chromophore isomerization at 78 K but not at 250 K. These results are consistent with a model of the retinal binding site in which Pro-186 and Tyr-185 are located in direct proximity to the chromophore and may be involved in linking chromophore isomerization to protein structural changes. Evidence is also found that Pro-50 may be structurally active during the bR----K transition and that substitution of this residue by glycine preserves the normal protein structural changes during the photocycle.

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

    SciTech Connect

    Pincu, Madeleine; Gerber, Robert Benny

    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. Vibrational Spectroscopy of Parent Volatiles in Comets: Spectral Frontiers and Critical Needs for Relevant Molecular Parameters

    NASA Astrophysics Data System (ADS)

    Mumma, Michael J.

    2009-05-01

    Today, as many as ten parent volatile species are measured simultaneously in infrared spectra of comets, but their interpretation is sometimes challenged by inaccurate or unavailable molecular parameters. These are essential for identifying a specific molecular emitter and for quantifying its abundance by comparing the observed line intensities with excitation models. This difficulty will become more severe in the near future, as cross-dispersed echelle spectrometers with very high resolving power come on line (e.g., iSHELL at the NASA IRTF). Somewhat farther downstream, future large telescopes (30-meter class) will provide a ten-fold increase in collecting area and the potential for important advances in cometary and planetary science. With such new facilities, major advances are expected in three areas of cometary science: 1. The suite of detected parent volatiles will be extended to less abundant species (e.g., C2H4, the hypothesized intermediate in hydrogenating C2H2 to C2H6). 2. The accuracy of nuclear spin temperatures will be greatly improved, providing a sensitive measure of this cosmogonic parameter for diverse parent volatiles (H2O, NH3, CH4, H2CO, etc.) in many comets, and further constraining the origin and subsequent evolution of these primitive materials. 3. The extension of compositional measurements to isotopologues of the more abundant parent volatiles will provide key insights into their origins by comparing isotopic ratios (D/H, 14N/15N, 12C/13C, etc.) in comets with predictions based on models for interstellar and nebular processing. An expanded and vigorous laboratory program in fundamental molecular spectroscopy and structure is needed, to ensure full exploitation of these new frontiers.

  2. Semifluorinated thiols in Langmuir monolayers - a study by nonlinear and linear vibrational spectroscopies.

    PubMed

    Volpati, Diogo; Chachaj-Brekiesz, Anna; Souza, Adriano L; Rimoli, Caio Vaz; Miranda, Paulo B; Oliveira, Osvaldo N; Dynarowicz-Łątka, Patrycja

    2015-12-15

    A series of semifluorinated thiols of the general formula CmF2m+1CnH2nSH (abbr. FmHnSH) have been synthesized and characterized in Langmuir monolayers with surface pressure-area isotherms, complemented with polarization-modulated reflection absorption spectroscopy (PM-IRRAS) and sum-frequency generation (SFG) techniques. A comparative analysis was performed for compounds having the same length of fluorinated segment (F10) and variable length of the hydrogenated part (H6, H10, H12), and having identical hydrogenated segment (H12) connected to a fluorinated moiety of different lengths (F6, F8, F10). For the sake of comparison, an alkanethiol (H18SH) was also examined, and F10H10COOH and F10H10OH molecules were used for helping the assignment of SFG spectra of CH stretches. SFG was applied to investigate the hydrocarbon chain and the terminal CF3 group, while PM-IRRAS was used to probe CF2 groups. The number of gauche defects in the hydrocarbon chain increased with the increasing length of the molecule, either by elongation of the hydrogenated or perfluorinated part. SFG measurements recorded at three polarization combinations (ppp, ssp, sps) enabled us to estimate the tilt angle of the terminal CF3 group in semifluorinated thiol molecules as ranging from 35° to 45°, which is consistent with nearly vertical fluorinated segments. Upon increasing the surface pressure, the fluorinated segment gets slightly more upright, but the hydrocarbon chain tilt increases while keeping the same average number of gauche defects. The extent of disorder in the hydrogenated segment may be controlled by varying the size of the fluorinated segment, and this could be exploited for designing functionalized surfaces with insertion of other molecules in the defect region.

  3. Homogeneous and inhomogeneous broadenings and the Voigt line shapes in the phase-resolved and intensity sum-frequency generation vibrational spectroscopy.

    PubMed

    Chen, Shun-Li; Fu, Li; Gan, Wei; Wang, Hong-Fei

    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 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 the direct comparison and understanding of the homogeneous and inhomogeneous broadenings in the imaginary and intensity SFG vibrational spectral line shapes in detail. The difference of the full width at half maximum (FWHM) of the imaginary and intensity sum-frequency generation vibrational spectroscopy spectra of the same vibrational mode is the signature of the Voigt line shape and it measures the relative contribution to the overall line shape 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 line shape with a homogeneous broadening half width of Γ = 5.29 ± 0.08 cm(-1) and an inhomogeneous standard derivation width Δω = 5.42 ± 0.07 cm(-1). These results shed new lights on the understanding and interpretation of the line shapes of both the phase-resolved and the intensity SFG vibrational spectra, as well as other incoherent and coherent spectroscopic techniques in general. PMID:26801040

  4. Homogeneous and inhomogeneous broadenings and the Voigt line shapes in the phase-resolved and intensity sum-frequency generation vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Chen, Shun-Li; Fu, Li; Gan, Wei; Wang, Hong-Fei

    2016-01-01

    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 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 the direct comparison and understanding of the homogeneous and inhomogeneous broadenings in the imaginary and intensity SFG vibrational spectral line shapes in detail. The difference of the full width at half maximum (FWHM) of the imaginary and intensity sum-frequency generation vibrational spectroscopy spectra of the same vibrational mode is the signature of the Voigt line shape and it measures the relative contribution to the overall line shape 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 line shape with a homogeneous broadening half width of Γ = 5.29 ± 0.08 cm-1 and an inhomogeneous standard derivation width Δω = 5.42 ± 0.07 cm-1. These results shed new lights on the understanding and interpretation of the line shapes of both the phase-resolved and the intensity SFG vibrational spectra, as well as other incoherent and coherent spectroscopic techniques in general.

  5. Quantitative determination of molecular structure in multilayered thin films of biaxial and lower symmetry from photon spectroscopies. I. Reflection infrared vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Parikh, Atul N.; Allara, David L.

    1992-01-01

    A semitheoretical formalism based on classical electromagnetic wave theory has been developed for application to the quantitative treatment of reflection spectra from multilayered anisotropic films on both metallic and nonmetallic substrates. Both internal and external reflection experiments as well as transmission can be handled. The theory is valid for all wavelengths and is appropriate, therefore, for such experiments as x-ray reflectivity, uv-visible spectroscopic ellipsometry, and infrared reflection spectroscopy. Further, the theory is applicable to multilayered film structures of variable number of layers, each with any degree of anisotropy up to and including full biaxial symmetry. The reflectivities (and transmissivities) are obtained at each frequency by solving the wave propagation equations using a rigorous 4×4 transfer matrix method developed by Yeh in which the optical functions of each medium are described in the form of second rank (3×3) tensors. In order to obtain optical tensors for materials not readily available in single crystal form, a method has been developed to evaluate tensor elements from the complex scalar optical functions (n̂) obtained from the isotropic material with the limitations that the molecular excitations are well characterized and obey photon-dipole selection rules. This method is intended primarily for infrared vibrational spectroscopy and involves quantitative decomposition of the isotropic imaginary optical function (k) spectrum into a sum of contributions from fundamental modes, the assignment of a direction in molecular coordinates to the transition dipole matrix elements for each mode, the appropriate scaling of each k vector component in surface coordinates according to a selected surface orientation of the molecule to give a diagonal im(n̂) tensor, and the calculation of the real(n̂) spectrum tensor elements by the Kramers-Kronig transformation. Tensors for other surface orientations are generated by an

  6. Isomers and conformers of two push pull hydrazines studied by NMR and vibrational spectroscopy and by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Gróf, M.; Polovková, J.; Gatial, A.; Milata, V.; Černuchová, P.; Prónayová, N.; Matějka, P.

    2007-05-01

    The isomers and conformers of two push-pull hydrazines: 3- N, N-dimethylhydrazino-2-acetyl propenenitrile [(H 3C) 2N sbnd NH sbnd CH dbnd C(CN)(COCH 3)] (DMHAP) and 3- N, N-dimethylhydrazino-2-methylsulfonyl propenenitrile [(H 3C) 2N sbnd NH sbnd CH dbnd C(CN)(SO 2CH 3)] (DMHSP) have been studied experimentally by NMR and vibrational spectroscopy and theoretically by the ab initio calculations at MP2 level in 6-31G** basis set. The IR and Raman spectra of both compounds as a solid and solute in various solvents have been recorded. The NMR spectra were obtained in chloroform and DMSO at room temperature. Both compounds have been prepared by the same way. NMR spectra revealed that DMHAP was prepared as a pure Z-isomer whereas in the case of DMHSP a pure E-isomer was obtained. Due to the low barrier for both compounds practically free isomerisation process occurred in the solutions but in opposite directions. Whereas DMHAP exists in the solid state and in the less polar solvent as Z-isomer, in more polar solvents the appearance of next two conformers of E-isomer was observed. On the contrary DMHSP exists in the solid state and in the more polar solvent as E-isomer only but in less polar solvent the presence of Z-isomer was observed as well. Conformational possibilities of both studied compounds are given by the rotation of dimethylhydrazino group with its anti- or syn-orientation towards the olefinic double bond. Moreover, by the rotation of the acetyl group with Z- and E-orientation of carbonyl bond towards olefinic double bond can occur in DMHAP. Vibrational and NMR spectra revealed the existence of single conformer with intramolecular hydrogen bond for Z-isomer in less polar solvent and next two conformers for E-isomer of DMHAP with Z-orientation of acetyl group and anti and syn orientation of dimethylhydrazine group in more polar solvents. For E-isomer of DMHSP two conformers with anti or syn orientations of dimethylhydrazino group have been also confirmed by NMR

  7. Observation of the Fe—CN and Fe—CO Vibrations in the Active Site of [NiFe] Hydrogenase by Nuclear Resonance Vibrational Spectroscopy**

    PubMed Central

    Kamali, Saeed; Wang, Hongxin; Mitra, Devrani; Ogata, Hideaki; Manor, Brian C.; Rauchfuss, Thomas B.; Byrne, Deborah; Bonnefoy, Violaine; Jenney, Francis E.; Adams, Michael W. W.; Yoda, Yoshitaka; Alp, Ercan; Zhao, Jiyong; Cramer, Stephen P.

    2012-01-01

    Nuclear inelastic scattering of 57Fe labeled [NiFe] hydrogenase is shown to give information on different states of the enzyme. It was thus possible to detect and assign Fe–CO and Fe–CN bending and stretching vibrations of the active site outside the spectral range of the Fe–S cluster normal modes. PMID:23136119

  8. Vibration-rotation alchemy in acetylene (12C2H2), ? at low vibrational excitation: from high resolution spectroscopy to fast intramolecular dynamics

    NASA Astrophysics Data System (ADS)

    Perry, David S.; Miller, Anthony; Amyay, Badr; Fayt, André; Herman, Michel

    2010-04-01

    The link between energy-resolved spectra and time-resolved dynamics is explored quantitatively for acetylene (12C2H2), ? with up to 8600 cm-1 of vibrational energy. This comparison is based on the extensive and reliable knowledge of the vibration-rotation energy levels and on the model Hamiltonian used to fit them to high precision [B. Amyay, S. Robert, M. Herman, A. Fayt, B. Raghavendra, A. Moudens, J. Thiévin, B. Rowe, and R. Georges, J. Chem. Phys. 131, 114301 (2009)]. Simulated intensity borrowing features in high resolution absorption spectra and predicted survival probabilities in intramolecular vibrational redistribution (IVR) are first investigated for the v 4 + v 5 and v 3 bright states, for J = 2, 30 and 100. The dependence of the results on the rotational quantum number and on the choice of vibrational bright state reflects the interplay of three kinds of off-diagonal resonances: anharmonic, rotational l-type, and Coriolis. The dynamical quantities used to characterize the calculated time-dependent dynamics are the dilution factor φ d, the IVR lifetime τ IVR , and the recurrence time τ rec. For the two bright states v 3 + 2v 4 and 7v 4, the collisionless dynamics for thermally averaged rotational distributions at T = 27, 270 and 500 K were calculated from the available spectroscopic data. For the 7v 4 bright state, an apparent irreversible decay of is found. In all cases, the model Hamiltonian allows a detailed calculation of the energy flow among all of the coupled zeroth-order vibration-rotation states.

  9. Time Correlation Function Modeling of Third-Order Sum Frequency Vibrational Spectroscopy of a Charged Surface/Water Interface.

    PubMed

    Green, Anthony J; Space, Brian

    2015-07-23

    Sum frequency vibrational spectroscopy (SFVS), a second-order optical process, is interface-specific in the dipole approximation [Perry, A.; Neipert, C.; Moore, P.; Space, B. Chem. Rev. 2006, 106, 1234-1258; Richmond, G. L. Chem. Rev. 2002, 102, 2693-2724; Byrnes, S. J.; Geissler, P. L.; Shen, Y. R. Chem. Phys. Lett. 2011, 516, 115-124]. At charged interfaces, the experimentally detected signal is a combination of enhanced second-order and static-field-induced third-order contributions due to the existence of a static field. Evidence of the importance/relative magnitude of this third-order contribution is seen in the literature [Ong, S.; Zhao, X.; Eisenthal, K. B. Chem. Phys. Lett. 1992, 191, 327-335; Zhao, X.; Ong, S.; Eisenthal, K. B. Chem. Phys. Lett. 1993, 202, 513-520; Shen, Y. R. Appl. Phys. B: Laser Opt. 1999, 68, 295-300], but a molecularly detailed approach to separately calculating the second- and third-order contributions is difficult to construct. Recent work presented a novel molecular dynamics (MD)-based theory that provides a direct means to calculate the third-order contributions to SFVS spectra at charged interfaces [Neipert, C.; Space, B. J. Chem. Phys. 2006, 125, 224706], and a hyperpolarizability model for water was developed as a prerequisite to practical implementation [Neipert, C.; Space, B. Comput. Lett. 2007, 3, 431-440]. Here, these methods are applied to a highly abstracted/idealized silica/water interface, and the results are compared to experimental data for water at a fused quartz surface. The results suggest that such spectra have some quite general spectral features.

  10. Electronic and vibrational spectroscopy of the cytochrome c:cytochrome c oxidase complexes from bovine and Paracoccus denitrificans.

    PubMed Central

    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 changes in the protein environment surrounding the chromophore that affect either the ground or excited electronic states. The resonance Raman spectrum, on the other hand, reflects the heme structure in the ground electronic state only and shows no significant difference between cytochrome a vibrations in the complex or free enzyme. The only major difference between the Raman spectra of the free enzyme and complex is a broadening of the cytochrome a3 formyl band of the complex that is relieved upon complex dissociation at high ionic strength. These data suggest that the differences observed in the second derivative and CD spectra are the result of changes in the protein environment around cytochrome a that affect the electronic excited state. By analogy to other protein-chromophore systems, we suggest that the energy of the Soret pi* state of cytochrome a may be affected by (1) changes in the local dielectric, possibly brought about by movement of a charged amino acid side chain in proximity to the heme group, or (2) pi-pi interactions between the heme and aromatic amino acid residues. PMID:1338946

  11. I. Hydrophobic nanoporous silica particles for biomedical applications II. Novel approaches to two-dimensional correlation spectroscopy

    NASA Astrophysics Data System (ADS)

    Brumaru, Claudiu Stelian

    of adsorption sites. One of them corresponds to the polarity of surface silanol groups while the other sites have a polarity consistent with the environment inside the C18 organic layer. We also discover an additional adsorption mode situated at a polarity higher than exposed silanol surface that could presumably be linked to a different ionization state of the silanol groups. We are developing a method for resolving spectra of complex samples using two-dimensional hetero-correlation spectroscopy by correlating the intensity fluctuations in optical spectra to those of completely separated peaks in analytical separations. We demonstrate this methodology for fluorescence spectra and electrophoregrams of mixtures anthracene-pyrene. All the individual vibronic features that overlap in mixtures are cleanly extracted in cross-sections of the two-dimensional asynchronous spectrum.

  12. Use of Molecular Symmetry to Describe Pauli Principle Effects on the Vibration-Rotation Spectroscopy of Co2(g)

    ERIC Educational Resources Information Center

    Myrick, M. L.; Colavita, P. E.; Greer, A. E.; Long, B.; Andreatta, D.

    2004-01-01

    The measurement of the infrared rotation-vibration spectrum of HCl(g) is a common experiment in the physical chemistry laboratory, which allows students the opportunity to explore quantization of rotational states in diatomic molecules. It is found that the CO2 vibration-rotation spectrum if used as an addition to the HCl experiment would give the…

  13. Photoluminescence spectroscopy of YVO{sub 4}:Eu{sup 3+} nanoparticles with aromatic linker molecules: A precursor to biomedical functionalization

    SciTech Connect

    Senty, T. R.; Yalamanchi, M.; Cushing, S. K.; Seehra, M. S.; Bristow, A. D.; Zhang, Y.; Shi, X.

    2014-04-28

    Photoluminescence spectra of YVO{sub 4}:Eu{sup 3+} nanoparticles are presented, with and without the attachment of organic molecules that are proposed for linking to biomolecules. YVO{sub 4}:Eu{sup 3+} nanoparticles with 5% dopant concentration were synthesized via wet chemical synthesis. X-ray diffraction and transmission electron microscopy show the expected wakefieldite structure of tetragonal particles with an average size of 17 nm. Fourier-transform infrared spectroscopy determines that metal-carboxylate coordination is successful in replacing native metal-hydroxyl bonds with three organic linkers, namely, benzoic acid, 3-nitro 4-chloro-benzoic acid, and 3,4-dihydroxybenzoic acid, in separate treatments. UV-excitation photoluminescence spectra show that the position and intensity of the dominant {sup 5}D{sub 0} – {sup 7}F{sub 2} electric-dipole transition at 619 nm are unaffected by the benzoic acid and 3-nitro 4-chloro-benzoic acid treatments. Attachment of 3,4-dihydroxybenzoic acid produces an order-of-magnitude quenching in the photoluminescence, due to the presence of high-frequency vibrational modes in the linker. Ratios of the dominant electric- and magnetic-dipole transitions confirm infrared measurements, which indicate that the bulk crystal of the nanoparticle is unchanged by all three treatments.

  14. Unified treatment and measurement of the spectral resolution and temporal effects in frequency-resolved sum-frequency generation vibrational spectroscopy (SFG-VS)

    SciTech Connect

    Velarde Ruiz Esparza, Luis A.; Wang, Hongfei

    2013-12-14

    The emergence of sub-wavenumber high-resolution broadband sum-frequency generation vibrational spectroscopy (HR-BBSFG-VS) [Velarde et al., J. Chem. Phys., 2011, 135, 241102] has offered new opportunities in obtaining and understanding the spectral lineshape and temporal effects on the surface vibrational spectroscopy. Particularly, the high accuracy in the HR-BBSFG-VS spectral lineshape measurement provides detailed information on the complex coherent vibrational dynamics through spectral measurement. Here we present a unified formalism of the theoretical and experimental approaches for obtaining the accurate lineshape of the SFG response, and then present a analysis on the higher and lower spectral resolution SFG spectra as well as their temporal effects of the cholesterol molecules at the air/water interface. With the high spectral resolution and accurate lineshape, it is shown that the parameters from the sub-wavenumber resolution SFG spectra can be used not only to understand but also to quantitatively reproduce the temporal effects in the lower resolution SFG measurement. These not only provide a unified picture in understanding both the frequency-domain and the time-domain SFG response of the complex molecular interface, but also provide novel experimental approaches that can directly measure them.

  15. Application of high-resolution photoelectron spectroscopy: Vibrational resolved C 1s and O 1s spectra of CO adsorbed on Ni(100)

    SciTech Connect

    Foehlisch, A.; Nilsson, A.; Martensson, N.

    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.

  16. Biomedical Telectrodes

    NASA Technical Reports Server (NTRS)

    Shepherd, C. K.

    1989-01-01

    Compact transmitters eliminate need for wires to monitors. Biomedical telectrode is small electronic package that attaches to patient in manner similar to small adhesive bandage. Patient wearing biomedical telectrodes moves freely, without risk of breaking or entangling wire connections. Especially beneficial to patients undergoing electrocardiographic monitoring in intensive-care units in hospitals. Eliminates nuisance of coping with wire connections while dressing and going to toilet.

  17. Study on vibrational relaxation dynamics of phenol-water complex by picosecond time-resolved IR-UV pump-probe spectroscopy in a supersonic molecular beam

    NASA Astrophysics Data System (ADS)

    Miyazaki, Yasunori; Inokuchi, Yoshiya; Ebata, Takayuki; Petković, Milena

    2013-06-01

    A comparative study of vibrational energy relaxation (VER) between the monohydrated complexes of phenol-d0 and phenol-d1 is investigated in a supersonic molecular beam. The direct time-resolved measurement of energy redistribution from the phenolic OH/OD stretching mode of the phenol-d0-H2O/phenol-d1-D2O is performed by picosecond IR-UV pump-probe spectroscopy. Two complexes follow the same relaxation process that begins with the intramolecular vibrational energy redistribution (IVR) and the intermolecular vibrational energy redistribution (IVR), which is followed by the vibrational predissociation (VP). The difference in the relaxation lifetimes between them is discussed by anharmonic force field and RRKM calculations. Anharmonic analysis implies that intra- (IVR) and intermolecular (IVR) relaxations occur in parallel in the complexes. The RRKM-predicted dissociation (VP) lifetimes show qualitative agreement with the observed results, suggesting that VP takes place after the statistical energy distribution in the complexes.

  18. Infrared micro-spectroscopy of human tissue: principles and future promises.

    PubMed

    Diem, Max; Ergin, Ayşegül; Remiszewski, Stan; Mu, Xinying; Akalin, Ali; Raz, Dan

    2016-06-23

    This article summarizes the methods employed, and the progress achieved over the past two decades in applying vibrational (Raman and IR) micro-spectroscopy to problems of medical diagnostics and cellular biology. During this time, several research groups have verified the enormous information contained in vibrational spectra; in fact, information on protein, lipid and metabolic composition of cells and tissues can be deduced by decoding the observed vibrational spectra. This decoding process is aided by the availability of computer workstations and advanced algorithms for data analysis. Furthermore, commercial instrumentation for the fast collection of both Raman and infrared micro-spectral data has enabled the collection of images of cells and tissues based solely on vibrational spectroscopic data. The progress in the field has been manifested by a steady increase in the number and quality of publications submitted by established and new research groups in vibrational spectroscopy in the biological and biomedical arenas. PMID:27075634

  19. Infrared micro-spectroscopy of human tissue: principles and future promises.

    PubMed

    Diem, Max; Ergin, Ayşegül; Remiszewski, Stan; Mu, Xinying; Akalin, Ali; Raz, Dan

    2016-06-23

    This article summarizes the methods employed, and the progress achieved over the past two decades in applying vibrational (Raman and IR) micro-spectroscopy to problems of medical diagnostics and cellular biology. During this time, several research groups have verified the enormous information contained in vibrational spectra; in fact, information on protein, lipid and metabolic composition of cells and tissues can be deduced by decoding the observed vibrational spectra. This decoding process is aided by the availability of computer workstations and advanced algorithms for data analysis. Furthermore, commercial instrumentation for the fast collection of both Raman and infrared micro-spectral data has enabled the collection of images of cells and tissues based solely on vibrational spectroscopic data. The progress in the field has been manifested by a steady increase in the number and quality of publications submitted by established and new research groups in vibrational spectroscopy in the biological and biomedical arenas.

  20. Investigating vibrational relaxation in cyanide-bridged transition metal mixed-valence complexes using two-dimensional infrared and infrared pump-probe spectroscopies

    PubMed Central

    Slenkamp, Karla M.; Lynch, Michael S.; Brookes, Jennifer F.; Bannan, Caitlin C.; Daifuku, Stephanie L.; Khalil, Munira

    2016-01-01

    Using polarization-selective two-dimensional infrared (2D IR) and infrared pump-probe spectroscopies, we study vibrational relaxation of the four cyanide stretching (νCN) vibrations found in [(NH3)5RuIIINCFeII(CN)5]− (FeRu) dissolved in D2O or formamide and [(NC)5FeIICNPtIV(NH3)4NCFeII(CN)5]4− (FePtFe) dissolved in D2O. These cyanide-bridged transition metal complexes serve as models for understanding the role high frequency vibrational modes play in metal-to-metal charge transfers over a bridging ligand. However, there is currently little information about vibrational relaxation and dephasing dynamics of the anharmonically coupled νCN modes in the electronic ground state of these complexes. IR pump-probe experiments reveal that the vibrational lifetimes of the νCN modes are ∼2 times faster when FeRu is dissolved in D2O versus formamide. They also reveal that the vibrational lifetimes of the νCN modes of FePtFe in D2O are almost four times as long as for FeRu in D2O. Combined with mode-specific relaxation dynamics measured from the 2D IR experiments, the IR pump-probe experiments also reveal that intramolecular vibrational relaxation is occurring in all three systems on ∼1 ps timescale. Center line slope dynamics, which have been shown to be a measure of the frequency-frequency correlation function, reveal that the radial, axial, and trans νCN modes exhibit a ∼3 ps timescale for frequency fluctuations. This timescale is attributed to the forming and breaking of hydrogen bonds between each mode and the solvent. The results presented here along with our previous work on FeRu and FePtFe reveal a picture of coupled anharmonic νCN modes where the spectral diffusion and vibrational relaxation dynamics depend on the spatial localization of the mode on the molecular complex and its specific interaction with the solvent. PMID:27158634

  1. Far-infrared VRT spectroscopy of the water dimer: Characterization of the 20 μm out-of-plane librational vibration

    SciTech Connect

    Cole, William T. S.; Fellers, Ray S.; Viant, Mark R.; Saykally, Richard J.; Leforestier, Claude

    2015-10-21

    We report the first high-resolution spectra for the out-of-plane librational vibration in the water dimer. Three vibrational subbands comprising a total of 188 transitions have been measured by diode laser spectroscopy near 500 cm{sup −1} and assigned to (H{sub 2}O){sub 2} libration-rotation-tunneling eigenstates. The band origin for the K{sub a} = 1 subband is ~524 cm{sup −1}. Librational excitation increases the interchange and bifurcation hydrogen bond rearrangement tunneling splittings by factors of 3-5 and 4-40, respectively. Analysis of the rotational constants obtained from a nonlinear least squares fit indicates that additional external perturbations to the energy levels are likely.

  2. Systematic Vibration Studies on a Cryogen-Free ^3He/^4He Dilution Refrigerator for X-ray Spectroscopy at Storage Rings

    NASA Astrophysics Data System (ADS)

    Scholz, P. A.; Kraft-Bermuth, S.; Andrianov, V.

    2016-08-01

    High-precision X-ray spectroscopy of highly charged ions at storage rings provides a sensitive test of quantum electrodynamics in strong Coulomb fields. To increase the precision of such experiments, silicon microcalorimeters have already been applied successfully. To minimize the interruption of beam times due to maintenance, a new cryogen-free ^3He/^4He dilution refrigerator has been designed and is under commissioning. However, in cryogen-free systems microphonic noise due to vibrations contributes considerably to the overall noise and may limit the detector energy resolution. Therefore, we report on systematic vibration studies on a cryogen-free ^3He/^4He dilution refrigerator which is specially adapted for experiments at storage rings.

  3. A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

    SciTech Connect

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

    2015-09-28

    Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derive response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.

  4. A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy.

    PubMed

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

    2015-09-28

    Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derive response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.

  5. Low frequency dynamics of the nitrogenase MoFe protein via femtosecond pump probe spectroscopy - Observation of a candidate promoting vibration.

    PubMed

    Maiuri, Margherita; Delfino, Ines; Cerullo, Giulio; Manzoni, Cristian; Pelmenschikov, Vladimir; Guo, Yisong; Wang, Hongxin; Gee, Leland B; Dapper, Christie H; Newton, William E; Cramer, Stephen P

    2015-12-01

    We have used femtosecond pump-probe spectroscopy (FPPS) to study the FeMo-cofactor within the nitrogenase (N2ase) MoFe protein from Azotobacter vinelandii. A sub-20-fs visible laser pulse was used to pump the sample to an excited electronic state, and a second sub-10-fs pulse was used to probe changes in transmission as a function of probe wavelength and delay time. The excited protein relaxes to the ground state with a ~1.2ps time constant. With the short laser pulse we coherently excited the vibrational modes associated with the FeMo-cofactor active site, which are then observed in the time domain. Superimposed on the relaxation dynamics, we distinguished a variety of oscillation frequencies with the strongest band peaks at ~84, 116, 189, and 226cm(-1). Comparison with data from nuclear resonance vibrational spectroscopy (NRVS) shows that the latter pair of signals comes predominantly from the FeMo-cofactor. The frequencies obtained from the FPPS experiment were interpreted with normal mode calculations using both an empirical force field (EFF) and density functional theory (DFT). The FPPS data were also compared with the first reported resonance Raman (RR) spectrum of the N2ase MoFe protein. This approach allows us to outline and assign vibrational modes having relevance to the catalytic activity of N2ase. In particular, the 226cm(-1) band is assigned as a potential 'promoting vibration' in the H-atom transfer (or proton-coupled electron transfer) processes that are an essential feature of N2ase catalysis. The results demonstrate that high-quality room-temperature solution data can be obtained on the MoFe protein by the FPPS technique and that these data provide added insight to the motions and possible operation of this protein and its catalytic prosthetic group. PMID:26343576

  6. Low frequency dynamics of the nitrogenase MoFe protein via femtosecond pump probe spectroscopy - Observation of a candidate promoting vibration.

    PubMed

    Maiuri, Margherita; Delfino, Ines; Cerullo, Giulio; Manzoni, Cristian; Pelmenschikov, Vladimir; Guo, Yisong; Wang, Hongxin; Gee, Leland B; Dapper, Christie H; Newton, William E; Cramer, Stephen P

    2015-12-01

    We have used femtosecond pump-probe spectroscopy (FPPS) to study the FeMo-cofactor within the nitrogenase (N2ase) MoFe protein from Azotobacter vinelandii. A sub-20-fs visible laser pulse was used to pump the sample to an excited electronic state, and a second sub-10-fs pulse was used to probe changes in transmission as a function of probe wavelength and delay time. The excited protein relaxes to the ground state with a ~1.2ps time constant. With the short laser pulse we coherently excited the vibrational modes associated with the FeMo-cofactor active site, which are then observed in the time domain. Superimposed on the relaxation dynamics, we distinguished a variety of oscillation frequencies with the strongest band peaks at ~84, 116, 189, and 226cm(-1). Comparison with data from nuclear resonance vibrational spectroscopy (NRVS) shows that the latter pair of signals comes predominantly from the FeMo-cofactor. The frequencies obtained from the FPPS experiment were interpreted with normal mode calculations using both an empirical force field (EFF) and density functional theory (DFT). The FPPS data were also compared with the first reported resonance Raman (RR) spectrum of the N2ase MoFe protein. This approach allows us to outline and assign vibrational modes having relevance to the catalytic activity of N2ase. In particular, the 226cm(-1) band is assigned as a potential 'promoting vibration' in the H-atom transfer (or proton-coupled electron transfer) processes that are an essential feature of N2ase catalysis. The results demonstrate that high-quality room-temperature solution data can be obtained on the MoFe protein by the FPPS technique and that these data provide added insight to the motions and possible operation of this protein and its catalytic prosthetic group.

  7. Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, II: Fluorescence and Vibrational Spectroscopy Using a Cyanophenylalanine Probe

    SciTech Connect

    Liu, J.; Strzalka, J; Tronin, A; Johansson, J; Blasie, J

    2009-01-01

    We demonstrate that cyano-phenylalanine (PheCN) can be utilized to probe the binding of the inhalational anesthetic halothane to an anesthetic-binding, model ion channel protein hbAP-PheCN. The Trp to PheCN mutation alters neither the a-helical conformation nor the 4-helix bundle structure. The halothane binding properties of this PheCN mutant hbAP-PheCN, based on fluorescence quenching, are consistent with those of the prototype, hbAP1. The dependence of fluorescence lifetime as a function of halothane concentration implies that the diffusion of halothane in the nonpolar core of the protein bundle is one-dimensional. As a consequence, at low halothane concentrations, the quenching of the fluorescence is dynamic, whereas at high concentrations the quenching becomes static. The 4-helix bundle structure present in aqueous detergent solution and at the air-water interface, is preserved in multilayer films of hbAP-PheCN, enabling vibrational spectroscopy of both the protein and its nitrile label (-CN). The nitrile groups' stretching vibration band shifts to higher frequency in the presence of halothane, and this blue-shift is largely reversible. Due to the complexity of this amphiphilic 4-helix bundle model membrane protein, where four PheCN probes are present adjacent to the designed cavity forming the binding site within each bundle, all contributing to the infrared absorption, molecular dynamics (MD) simulation is required to interpret the infrared results. The MD simulations indicate that the blue-shift of -CN stretching vibration induced by halothane arises from an indirect effect, namely an induced change in the electrostatic protein environment averaged over the four probe oscillators, rather than a direct interaction with the oscillators. hbAP-PheCN therefore provides a successful template for extending these investigations of the interactions of halothane with the model membrane protein via vibrational spectroscopy, using cyano-alanine residues to form the

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

    NASA Astrophysics Data System (ADS)

    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.

  9. Biomedical research

    NASA Technical Reports Server (NTRS)

    1981-01-01

    Biomedical problems encountered by man in space which have been identified as a result of previous experience in simulated or actual spaceflight include cardiovascular deconditioning, motion sickness, bone loss, muscle atrophy, red cell alterations, fluid and electrolyte loss, radiation effects, radiation protection, behavior, and performance. The investigations and the findings in each of these areas were reviewed. A description of how biomedical research is organized within NASA, how it is funded, and how it is being reoriented to meet the needs of future manned space missions is also provided.

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

    SciTech Connect

    Westerberg, Staffan Per Gustav

    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.

  11. Vibrational Conical Intersections in CH3SH: Implications for Spectroscopy and Dynamics in the CH Stretch Region

    NASA Astrophysics Data System (ADS)

    Perry, David S.; Thapaliya, Bishnu P.; Dawadi, Mahesh B.; Bhatta, Ram

    2016-06-01

    The adiabatic separation in methyl mercaptan of the high-frequency asymmetric CH stretch vibrations from the low-frequency torsional (γ) and CSH bend (ρ) coordinates yields a set of 7 vibrational conical intersections (CIs). The three CIs in the staggered conformation at ρ = 79° are close to the global minimum energy geometries (ρe = 83.3°), accounting for the observed near-degeneracy of the two asymmetric CH stretch vibrations. The vibrational frequencies were computed at the CCSD(T)/aug-cc-pVTZ level. A new high-order Exe Jahn-Teller model, which involves a spherical harmonic expansion in ρ and γ, fits the calculated electronic and vibrational energies over the whole range of γ and for ρ between 0° and 100° to within a standard deviation of 0.2 wn. The pattern of the CIs contrasts with that in methanol where the CIs occur only in the eclipsed conformation near the top of the torsional barrier. An examination of three alternative diabatization schemes for the two molecules points to rather different nuclear dynamics. In CH_3SH crossings between the upper and lower adiabatic surfaces are predicted to occur predominantly with motion along the CSH bending coordinate; whereas in CH_3OH, such crossings are predicted to occur predominantly with torsional motion.

  12. Hydrogen-bonding and vibrational coupling of water in a hydrophobic hydration shell as observed by Raman-MCR and isotopic dilution spectroscopy.

    PubMed

    Ahmed, Mohammed; Singh, Ajay K; Mondal, Jahur A

    2016-01-28

    Hydrogen-bonding and intra/intermolecular vibrational coupling of water next to a hydrophobic molecule (tert-butyl alcohol, TBA) have been studied by Raman multivariate curve resolution (Raman-MCR) and isotopic dilution spectroscopy. Raman-MCR provides the vibrational spectrum of water pertinent to the hydration shell of TBA, which shows a distinct Raman band at around 3660 cm(-1) corresponding to the dangling OH in the hydration shell. The presence of positive charge on the hydrophobe decreases the propensity of dangling OH in the hydration shell, presumably due to unfavorable electrostatic interaction. Analysis of the dangling OH band with isotopic dilution reveals that the 'dangling OH' is intramolecularly coupled with the 'H-bonded OH' of the same water molecule. The hydration water spectrum in the H-bonded OH stretch region (3000-3600 cm(-1)) shows a depletion of weakly H-bonded water (∼3580 cm(-1)) and an increase of strongly H-bonded water (∼3250 cm(-1)), making the average H-bonding stronger in a hydrophobic hydration shell than that in bulk. This strongly H-bonded hydration water exhibits weaker intra- and intermolecular vibrational coupling than that of bulk water. PMID:26725484

  13. Intrinsic Chirality and Prochirality at Air/R-(+)- and S-(-)-Limonene Interfaces: Spectral Signatures with Interference Chiral Sum-Frequency Generation Vibrational Spectroscopy

    SciTech Connect

    Fu, Li; Zhang, Yun; Wei, Zhehao; Wang, Hongfei

    2014-06-04

    We report in this work detailed measurements on the chiral and achiral sum-frequency vibrational spectra in the C-H stretching vibration region (2800-3050cm-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 equal amount (50/50) racemic mixture show that the enantiomers are with the same interfacial orientations. The interference chiral SFG spectra of the limonene enantiomers exhibit spectral signature from chiral response of the Cα-H stretching mode, and spectral signature from prochiral response of the CH2 asymmetric stretching mode, respectively. The chiral spectral feature of the Cα-H stretching mode changes sign from R-limonene to S-limonene, and disappears for the 50/50 racemic mixture. While the prochiral spectral feature of the CH2 asymmetric stretching mode is the same for R-limonene and S-limonene, and also surprisingly remains the same for the 50/50 racemic mixture. These results provided detail information in understanding the structure and chirality of molecular interfaces, and demonstrated the sensitivity and potential of SFG-VS as unique spectroscopic tool for chirality characterization and chiral recognition at the molecular interface.

  14. Partially Hydrated Electrons at the Air/Water Interface Observed by UV-Excited Time-Resolved Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy.

    PubMed

    Matsuzaki, Korenobu; Kusaka, Ryoji; Nihonyanagi, Satoshi; Yamaguchi, Shoichi; Nagata, Takashi; Tahara, Tahei

    2016-06-22

    Hydrated electrons are the most fundamental anion species, consisting only of electrons and surrounding water molecules. Although hydrated electrons have been extensively studied in the bulk aqueous solutions, even their existence is still controversial at the water surface. Here, we report the observation and characterization of hydrated electrons at the air/water interface using new time-resolved interface-selective nonlinear vibrational spectroscopy. With the generation of electrons at the air/water interface by ultraviolet photoirradiation, we observed the appearance of a strong transient band in the OH stretch region by heterodyne-detected vibrational sum-frequency generation. Through the comparison with the time-resolved spectra at the air/indole solution interface, the transient band was assigned to the vibration of water molecules that solvate electrons at the interface. The analysis of the frequency and decay of the observed transient band indicated that the electrons are only partially hydrated at the water surface, and that they escape into the bulk within 100 ps. PMID:27281547

  15. The molecular structures, vibrational spectroscopies (FT-IR and Raman) and quantum chemical calculations of n-alkyltrimethylammonium bromides

    NASA Astrophysics Data System (ADS)

    Gökce, Halil; Bahçeli, Semiha

    2013-11-01

    The FT-IR and micro-Raman spectra of three n-alkyltrimethylammonium bromides (dodecyltrimethylammonium bromide (DTAB), tetradecyltrimethylammonium bromide (TTAB) and hexadecyl(cetyl)trimethylammonium bromide (CTAB)) in powder form were recorded in the regions 4000-550 cm-1 and 3200-300 cm-1, respectively. The optimized geometries and vibrational frequencies of DTAB, TTAB and CTAB have been carried out with ab initio Hartree-Fock (HF) and density functional theory method B3LYP calculations with the 6-31 G (d, p) basis set in the ground state. The comparison of the observed fundamental vibrational frequencies and calculated results for the fundamental vibrational frequencies of DTAB, TTAB and CTAB indicate that the scaled B3LYP method is superior compared to the scaled HF method.

  16. Isolated Ground-State Vibrational Coherence Measured by Fifth-Order Single-Shot Two-Dimensional Electronic Spectroscopy.

    PubMed

    Hutson, William O; Spencer, Austin P; Harel, Elad

    2016-09-15

    Vibrations play a critical role in many photochemical and photophysical processes in which excitations reside on the electronically excited state. However, difficulty in assigning signals from spectroscopic measurements uniquely to a specific electronic state, ground or otherwise, has exposed limitations to their physical interpretation. Here, we demonstrate the selective excitation of vibrational coherences on the ground electronic state through impulsive Raman scattering, whose weak fifth-order signal is resonantly enhanced by coupling to strong electronic transitions. The six-wave mixing signals measured using this technique are free of lower-order cascades and represent correlations between zero-quantum vibrational coherences in the ground state and single-quantum coherences between the ground and electronic states. We believe that this technique has the potential to shed much-needed insight onto some of the mysteries regarding the origin of long-lived coherences observed in photosynthetic and other coupled chromophore systems. PMID:27574915

  17. Fe-H/D stretching and bending modes in nuclear resonant vibrational, Raman and infrared spectroscopies: Comparisons of density functional theory and experiment

    PubMed Central

    Pelmenschikov, Vladimir; Guo, Yisong; Wang, Hongxin; Cramer, Stephen P.; Case, David A.

    2010-01-01

    Infrared, Raman, and nuclear resonant vibrational (NRVS) spectroscopies have been used to address the Fe-H bonding in trans-Fe(H)(CO) iron hydride compound, Fe(H)(CO)(dppe)2, dppe = 1,2-bis(diphenylphosphino)ethane. H and D isotopomers of the compound, with the selective substitution at the metal-coordinated hydrogen, have been considered in order to address the Fe-H/D stretching and bending modes. Experimental results are compared to the normal mode analysis by the density functional theory (DFT). The results are that (i) the IR spectrum does not clearly show Fe–H stretching or bending modes; (ii) Fe–H stretching modes are clear but weak in the Raman spectrum, and Fe–H bending modes are weak; (iii) NRVS 57Fe spectroscopy resolves Fe-H bending clearly, but Fe–H or Fe–D stretching is above its experimentally resolved frequency range. DFT caclulations (with no scaling of frequencies) show intensities and peak locations that allow unambigous correlations between observed and calculated features, with frequency errors generally less than 15 cm−1. Prospects for using these techniques to unravel vibrational modes of protein active sites are discussed. PMID:21322496

  18. Adsorption of 4-picoline and piperidine to the hydrated SiO2 surface: probing the surface acidity with vibrational sum frequency generation spectroscopy.

    PubMed

    Liu, Dingfang; Ma, Gang; Allen, Heather C

    2005-04-01

    Vapor adsorption is an important process influencing the migration and the fate of many organic pollutants in the environment. In this study, vibrational sum frequency generation (SFG) spectroscopy was used to study the adsorption of two surface acidity probe molecules, 4-picoline (pKa = 5.94) and piperidine (pKa = 11.24), onto the amorphous SiO2 surface. The adsorption of 4-picoline onto the silica surface occurs by forming weak hydrogen bonds between the nitrogen atoms of 4-picoline molecules and the hydrogen atoms of surface silanol OH groups. Piperidine molecules are strongly chemisorbed onto the SiO2 surface through the protonation of piperidine molecules by surface silanol OH groups. The SFG results indicate that the surface acidity constant of silanol OH groups (pKa-(HOSi triple bond)) is in the range of 5.94-11.24 at the air/solid interface. Although this range of surface acidity constants is quite wide, it is possible to narrow it by choosing probe molecules with a smaller pKa range. Together with theoretical prediction methods, adsorption studies using vibrational SFG spectroscopy are capable of quantifying the surface acidity of mineral oxides by carefully choosing the acidity probe molecules.

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

    NASA Astrophysics Data System (ADS)

    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 (<0.001 cm-1) using spectra obtained at the Canadian Light Source synchrotron radiation 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.

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

    SciTech Connect

    Thompson, Christopher

    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.

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

    PubMed

    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

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

    PubMed

    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

  3. 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

    SciTech Connect

    Johnson, Christopher J.; Wolk, Arron B.; Fournier, Joseph A.; Johnson, Mark A.; Sullivan, Erin N.; Weddle, Gary H.

    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.

  4. ROLE OF VIBRATIONAL SPECTROSCOPY AT THE U.S. ENVIRONMENTAL PROTECTION AGENCY'S ENVIRONMENTAL RESEARCH LABORATORY IN ATHENS, GEORGIA

    EPA Science Inventory

    The Environmental Research Laboratory, U.S. Environmental Protection Agency, Athens GA, is best known by vibrational spectroscopists as the laboratory where much of the pioneering work on the development of a sensitive, real-time gas chromatograph/Fourier transform infrared syste...

  5. Measurement of vibrational, gas, and rotational temperatures of H2 (X1 Σg+) in radio frequency inductive discharge plasma by multiplex coherent anti-Stokes Raman scattering spectroscopy technique

    NASA Astrophysics Data System (ADS)

    Shakhatov, V. A.; De Pascale, O.; Capitelli, M.; Hassouni, K.; Lombardi, G.; Gicquel, A.

    2005-02-01

    Translational, rotational, and vibrational temperatures of H2 in radio frequency inductive discharge plasmas at pressures and power release ranges, respectively, of 0.5-8 torr and 0.5-2W/cm3 have been measured by using multiplex coherent anti-Stokes Raman scattering (CARS) spectroscopy. Computational codes have been developed to determine the rotational and vibrational temperatures and to analyze H2 CARS spectrum for nonequilibrium conditions. The results show a decrease of the vibrational temperature from 4250 to 2800 K by increasing the pressure from 0.5 to 8 torr and a corresponding increase of the rotational temperature from 525 to 750 K.

  6. Biomedical Conferences

    NASA Technical Reports Server (NTRS)

    1976-01-01

    As a result of Biomedical Conferences, Vivo Metric Systems Co. has produced cardiac electrodes based on NASA technology. Frequently in science, one highly specialized discipline is unaware of relevant advances made in other areas. In an attempt to familiarize researchers in a variety of disciplines with medical problems and needs, NASA has sponsored conferences that bring together university scientists, practicing physicians and manufacturers of medical instruments.

  7. Rotational spectroscopy of pyridazine and its isotopologs from 235-360 GHz: equilibrium structure and vibrational satellites.

    PubMed

    Esselman, Brian J; Amberger, Brent K; Shutter, Joshua D; Daane, Mitchell A; Stanton, John F; Woods, R Claude; McMahon, Robert J

    2013-12-14

    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-(13)C]-C4H4N2, [4-(13)C]-C4H4N2, and [1-(15)N]-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

  8. Rotational spectroscopy of pyridazine and its isotopologs from 235–360 GHz: Equilibrium structure and vibrational satellites

    SciTech Connect

    Esselman, Brian J.; Amberger, Brent K.; Shutter, Joshua D.; Daane, Mitchell A.; Woods, R. Claude; McMahon, Robert J.; Stanton, John F.

    2013-12-14

    The rotational spectrum of pyridazine (o-C{sub 4}H{sub 4}N{sub 2}), 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-{sup 13}C]-C{sub 4}H{sub 4}N{sub 2}, [4-{sup 13}C]-C{sub 4}H{sub 4}N{sub 2}, and [1-{sup 15}N]-C{sub 4}H{sub 4}N{sub 2}, 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 (R{sub e}) 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 R{sub e} structural parameters are determined with excellent accuracy, as evidenced by their ability to predict 28 independent moments of inertia (I{sub a} and I{sub b} 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

  9. Flexibility of the saturated five-membered ring in 2,5-pyrrolidinedione (succinimide): electron diffraction and quantum-chemical studies with use of vibrational spectroscopy data.

    PubMed

    Vogt, Natalja; Khaikin, Leonid S; Grikina, Olga E; Karasev, Nikolai M; Vogt, Jürgen; Vilkov, Lev V

    2009-02-01

    The flexibility of succinimide molecule has been studied for the first time by quantum-chemical (at the MP2 level with up to the 6-311G(3df,2p) basis sets) and gas-phase electron diffraction (GED) methods using vibrational spectroscopy data from literature. The analysis of vibrational spectra, performed for the molecular model of C(2v) symmetry (predicted by high-level ab initio calculations) using the scaling procedure, has shown that the two out-of-plane ring motions, that is, ring-bending and ring-twisting, are practically pure modes of different symmetry types and can be considered separately. The one-dimensional potential curves for the ring-bending and ring-twisting vibrations calculated at the MP2(full)/6-311G(3df,2p) level could be approximated by harmonic and anharmonic functions, respectively. The diverged energy levels for the ring-twisting vibration and the constant transition frequencies for the bending motion, obtained by the solution of the direct one-dimensional problem for the nonrigid model, demonstrate this statement. In the GED analysis, the succinimide molecule with a large-amplitude ring-twisting motion was described by a dynamic model with the distribution of pseudoconformers according to the calculated potential function taking into account structural relaxation effects from the MP2(full)/6-311G(3df,2p) calculations. This model greatly improved the fit of the GED intensities (R factor decreased from 4.6% for static model to 2.8%). The equilibrium molecular parameters r(e) determined in the dynamic approximation are very close to the corresponding values from the ab initio calculations. At the same time, the parameters of the -CH(2)-CH(2)- fragment involved in the ring-twisting motion deviate considerably from those obtained for the static model (C-C bond length by 0.027 A, =C-C-H, C-C-H, and H-C-C-N angles by up to 7 degrees). The flexibility influence on the C-C bond length is several times larger than the calculated vibrational correction

  10. Sum Frequency Generation Vibrational Spectroscopy Studies on ModelPeptide Adsorption at the Hydrophobic Solid-Water and HydrophilicSolid-Water Interfaces

    SciTech Connect

    York, Roger L.

    2007-01-01

    Sum frequency generation (SFG) vibrational spectroscopy has been used to study the interfacial structure of several polypeptides and amino acids adsorbed to hydrophobic and hydrophilic surfaces under a variety of experimental conditions. Peptide sequence, peptide chain length, peptide hydrophobicity, peptide side-chain type, surface hydrophobicity, and solution ionic strength all affect an adsorbed peptide's interfacial structure. Herein, it is demonstrated that with the choice of simple, model peptides and amino acids, surface specific SFG vibrational spectroscopy can be a powerful tool to elucidate the interfacial structure of these adsorbates. Herein, four experiments are described. In one, a series of isosequential amphiphilic peptides are synthesized and studied when adsorbed to both hydrophobic and hydrophilic surfaces. On hydrophobic surfaces of deuterated polystyrene, it was determined that the hydrophobic part of the peptide is ordered at the solid-liquid interface, while the hydrophilic part of the peptide appears to have a random orientation at this interface. On a hydrophilic surface of silica, it was determined that an ordered peptide was only observed if a peptide had stable secondary structure in solution. In another experiment, the interfacial structure of a model amphiphilic peptide was studied as a function of the ionic strength of the solution, a parameter that could change the peptide's secondary structure in solution. It was determined that on a hydrophobic surface, the peptide's interfacial structure was independent of its structure in solution. This was in contrast to the adsorbed structure on a hydrophilic surface, where the peptide's interfacial structure showed a strong dependence on its solution secondary structure. In a third experiment, the SFG spectra of lysine and proline amino acids on both hydrophobic and hydrophilic surfaces were obtained by using a different experimental geometry that increases the SFG signal. Upon comparison of

  11. Jet spectroscopy of buckybowl: electronic and vibrational structures in the S0 and S1 states of triphenylene and sumanene.

    PubMed

    Kunishige, Sachi; Kawabata, Megumi; Baba, Masaaki; Yamanaka, Takaya; Morita, Yuki; Higashibayashi, Shuhei; Sakurai, Hidehiro

    2013-07-28

    Sumanene is a typical buckybowl molecule with C3v symmetry. We observed a fluorescence excitation spectrum and a dispersed fluorescence spectrum of sumanene in a supersonic jet. Bowl effects were clarified by comparing the spectra with those of triphenylene (D3h symmetry), which is a planar prototype of nonplanar sumanene. The S1 (1)A1 ← S0 (1)A1 transition is symmetry allowed. We found the 0(0)(0) band in the fluorescence excitation spectrum at 357.78 nm; this band was missing in the forbidden S1 (1)A1(') ← S0 (1)A1(') transition of triphenylene. The transition moment was shown to be along the oblate symmetric top axis (out of plane) by the observed rotational contour. A large number of vibronic bands were observed, unlike in triphenylene. Some were considered to be out-of-plane vibrational modes, which lead to a bowl-to-bowl inversion reaction assisted by in-plane vibrations. We found that the vibronic bands were markedly weak in the high energy region of triphenylene-d12. This indicates that the fluorescence quantum yield is very low at the high vibrational levels in the S1 state due to the rapid radiationless transition. The main process is considered to be internal conversion to the S0 state. The nonplanar structural distortion may also enhance radiationless transitions. We could not, however, observe weakening of the vibronic bands in the fluorescence excitation spectrum of sumanene. PMID:23901986

  12. Vibrational Spectroscopy of Ions and Radicals Present in the Interstellar Medium and in Planetary Atmospheres: A Theoretical Study

    NASA Technical Reports Server (NTRS)

    Chaban, Galina M.

    2004-01-01

    Anharmonic vibrational frequencies and intensities are calculated for OH(H2O)n and H(H2O)n radicals (that form on icy particles of the interstellar medium), HCO radical (the main intermediate in the synthesis of organic molecules in space), NH2(-) and C2H(-) anions, H5(+) cation, and other systems relevant to interstellar chemistry. In addition to pure ions and radicals, their complexes with water are studied to assess the effects of water environment on infrared spectra. The calculations are performed using the correlation-corrected vibrational self-consistent field (CC-VSCF) method with ab initio potential surfaces at the MP2 and CCSD(T) levels. Fundamental, overtone, and combination excitations are computed. The results are in good agreement with available experimental data and provide reliable predictions for vibrational excitations not yet measured in laboratory experiments. The data should be useful for interpretation of astronomically observed spectra and identification of ions and radicals present in the interstellar medium and in planetary atmospheres.

  13. Vibrational biospectroscopy: from plants to animals to humans. A historical perspective

    NASA Astrophysics Data System (ADS)

    Shaw, R. Anthony; Mantsch, Henry H.

    1999-05-01

    Today, more than ever, vibrational spectroscopy means different things to different people. From their roots as molecular fingerprinting techniques, both infrared and Raman spectroscopy have evolved to the point where they play roles in a staggering variety of scientific endeavors. This survey focuses upon biological and medical applications. The past 40 years have witnessed enormous advances in our understanding of the building blocks of life, and vibrational spectroscopy has played an important role. That role is reviewed briefly here. In parallel with these efforts, the near-IR community developed powerful 'chemometric' methods to extract a wealth of information from spectra that appeared superficially featureless. As vibrational spectroscopy is finding new niches in the medical and clinical realms, these chemometric methods are proving to be a valuable (but not infallible!) adjunct to conventional spectral interpretation. This survey includes a brief outline of biomedical vibrational spectroscopy and imaging, including several representative examples to illustrate the strengths and pitfalls of a growing reliance upon multivariate quantitation and classification methods.

  14. Vibrational spectroscopy of the phosphate mineral lazulite--(Mg, Fe)Al2(PO4)2·(OH)2 found in the Minas Gerais, Brazil.

    PubMed

    Frost, Ray L; Xi, Yunfei; Beganovic, Martina; Belotti, Fernanda Maria; Scholz, Ricardo

    2013-04-15

    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 HPO4(2-) 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 ν1PO4(3-) symmetric stretching modes. The intense bands at 1035, 1054, 1081, 1118 and 1154 cm(-1) are assigned to the ν3PO4(3-) 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.

  15. FT-IR, FT-Raman, UV-Visible, and NMR spectroscopy and vibrational properties of the labdane-type diterpene 13-epi-sclareol

    NASA Astrophysics Data System (ADS)

    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.

  16. Vibrational spectroscopy of the phosphate mineral lazulite - (Mg, Fe)Al2(PO4)2·(OH)2 found in the Minas Gerais, Brazil

    NASA Astrophysics Data System (ADS)

    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.

  17. Excited-state intramolecular hydrogen transfer (ESIHT) of 1,8-dihydroxy-9,10-anthraquinone (DHAQ) characterized by ultrafast electronic and vibrational spectroscopy and computational modeling.

    PubMed

    Mohammed, Omar F; Xiao, Dequan; Batista, Victor S; Nibbering, Erik T J

    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 S2 electronic excited state is initially populated, followed by a rapid equilibration within 150 fs through population transfer to the S1 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. PMID:24684387

  18. Vibrational spectroscopy of the phosphate mineral lazulite--(Mg, Fe)Al2(PO4)2·(OH)2 found in the Minas Gerais, Brazil.

    PubMed

    Frost, Ray L; Xi, Yunfei; Beganovic, Martina; Belotti, Fernanda Maria; Scholz, Ricardo

    2013-04-15

    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 HPO4(2-) 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 ν1PO4(3-) symmetric stretching modes. The intense bands at 1035, 1054, 1081, 1118 and 1154 cm(-1) are assigned to the ν3PO4(3-) 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. PMID:23434550

  19. Intrinsic chirality and prochirality at Air/R-(+)- and S-(-)-limonene interfaces: spectral signatures with interference chiral sum-frequency generation vibrational spectroscopy.

    PubMed

    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. Laser excitation spectroscopy of the B 1Sigma + u(O + u) <-- a 3Pi g(O + g) transition of Cd2: Vibrational analysis and rotational structure

    NASA Astrophysics Data System (ADS)

    Tran, H. C.; Eden, J. G.

    1996-10-01

    The B 1Σ+u←a 3Πg transition of Cd2 (natural abundance) and 114Cd2 has been observed by laser excitation spectroscopy and analyzed. By exciting the Cd2 B←a transition in the visible (560≤λ≤730 nm) while monitoring B 1Σ+u→X 1Σ+g (bound→free) emission in the ultraviolet (˜270-310 nm), more than 40 red-degraded vibrational bands were recorded. Analysis of the spectrum has yielded vibrational constants for both the a 3Πg and B 1Σ+u states: ωe″=153.6±4.0 cm-1, ωe″xe″=0.52±0.06 cm-1, ωe'=105.3±1.0 cm-1, and ωe'xe'=0.44±0.03 cm-1. In addition, ΔRe≡ReB-Rea was determined to be 0.31±0.03 Å. Rotational structure has been partially resolved for 114Cd2 bands in the 620-655 nm and 719-723 nm regions, and the spontaneous emission lifetime of the a 3Πg state and the rate constant for quenching of Cd2 (a 3Πg) by collisions with background Cd atoms have been determined to be 8.6±2.5 μs and (2.2±0.3)×10-13 cm3 s-1, respectively. Also, analysis of the B→X emission (Condon internal diffraction) spectra produced when specific B 1Σ+u vibrational levels are populated has yielded ReX-ReB=0.95±0.02 Å.

  1. Synthesis, vibrational spectroscopy and crystal structure of zinc and sodium tricarboxylate coordination polymers with the flexible ligand tricarballylate anion (TCA 3-)

    NASA Astrophysics Data System (ADS)

    Williams, Patricia A. M.; Naso, Luciana G.; Echeverría, Gustavo A.; Ferrer, Evelina G.

    2010-08-01

    A new 3D coordination polymer of general formula [NaZn(C 6H 5O 6)(H 2O) 3] n has been hydrothermally synthesized and characterized by vibrational spectroscopy (Raman and Infrared), X-ray diffraction and thermal analysis. The compound crystallizes in the centrosymmetric monoclinic group C2/ c with a = 10.885(2), b = 13.219(3), c = 15.299(5) Å, β = 102.23(2)°, V = 2151(1) (Å 3), Z = 8. The crystal structure consists in an open framework where the arrangement of tetrahedral zinc and octahedral sodium cations, coordinated by water and carboxylate oxygens atoms, are linked by tricarballylate anions developing channels parallel to the [0 1-1] crystallographic direction. Thermogravimetric analysis indicates that the complex is thermally stable up to 200 °C.

  2. Absolute configuration and predominant conformations of a chiral crown ether-based colorimetric sensor: a vibrational circular dichroism spectroscopy and DFT study of chiral recognition.

    PubMed

    Merten, Christian; Hyun, Myung Ho; Xu, Yunjie

    2013-05-01

    In the present work, we report a comprehensive vibrational circular dichroism (VCD) spectroscopic study of a chiral crown ether which features an axial chiral 3.3'-diphenyl-1,1'-binaphthyl group as chiral moiety. By comparing the experimental and calculated VCD spectra, we show that the presumably very flexible crown ether preferably adopts only one ring conformation. Conformational flexibility is observed in the 2,4-dinitrophenyl-diazophenol group, which was previously introduced for colorimetric detection of primary amines and amino alcohols (Cho et al., Chirality 2011;23:349-353). The VCD spectra of the host-guest complexes with phenyl glycinol (PG) and phenyl alaninol have been studied as well. Based on the spectra calculated, it is shown that the diastereomeric complexes in general can be differentiated using VCD spectroscopy. Furthermore, the experimental VCD spectra of the complexes of the host molecule with PG support the above finding.

  3. Polymorphism of resorcinol explored by complementary vibrational spectroscopy (FT-RS, THz-TDS, INS) and first-principles solid-state computations (plane-wave DFT).

    PubMed

    Drużbicki, Kacper; Mikuli, Edward; Pałka, Norbert; Zalewski, Sławomir; Ossowska-Chruściel, Mirosława D

    2015-01-29

    The polymorphism of resorcinol has been complementary studied by combining Raman, time-domain terahertz, and inelastic neutron scattering spectroscopy with modern solid-state density functional theory (DFT) calculations. The spectral differences, emerging from the temperature-induced structural phase transition, have been successfully interpreted with an emphasis on the low-wavenumber range. The given interpretation is based on the plane-wave DFT computations, providing an excellent overall reproduction of both wavenumbers and intensities and revealing the source of the observed spectral differences. The performance of the generalized gradient approximation (GGA) functionals in prediction of the structural parameters and the vibrational spectra of the normal-pressure polymorphs of resorcinol has been extensively examined. The results show that the standard Perdew, Burke, and Ernzerhof (PBE) approach along with its "hard" revised form tends to be superior if compared to the "soft" GGA approximation.

  4. Microsolvation of the Mg2SO42+ Cation: Cryogenic Vibrational Spectroscopy of (Mg2+)2SO42-(H2O)n=4-11

    NASA Astrophysics Data System (ADS)

    Kelleher, Patrick J.; DePalma, Joseph W.; Johnson, Christopher J.; Fournier, Joseph; Johnson, Mark

    2015-06-01

    Cryogenic ion vibrational predissociation (CIVP) spectroscopy was used to examine the onset of solvation upon the incremental addition of water molecules to the Mg2SO42+(H2O)n cation (n = 4 - 11). D2 predissociation spectra are reported for each cluster over the range 1000-3800 cm-1. Initially, the Mg2+ atoms each interact with two oxygen atoms on the sulfate anion in a bifurcated arrangement. The breaking of this motif occurs upon addition of the eighth water molecule as evidenced by splitting of the water bend, and broad absorption in the 3000-3400 cm-1 range indicative of hydrogen bonding between the water molecules and sulfate ion.

  5. Molecular ordering in layer-by-layer polyelectrolyte films studied by sum-frequency vibrational spectroscopy: the effects of drying procedures.

    PubMed

    Silva, Heurison S; Uehara, Thiers M; Bergamaski, Kleber; Miranda, Paulo B

    2008-07-01

    Sum-Frequency Vibrational Spectroscopy (SFVS) has been used to investigate the effect of nitrogen-flow drying on the molecular ordering of Layer-by-Layer (LbL) films of poly(allylamine hydrochloride) (PAH) alternated with poly(styrene sulfonate) (PSS). We find that films dried by spontaneous water evaporation are more ordered and homogeneous than films dried by nitrogen flow. The latter are quite inhomogeneous and may have regions with highly disordered polymer conformation. We propose that drying by spontaneous water evaporation reduces the effect of drag by the drying front, while during nitrogen-flow drying the fast evaporation of water "freezes" the disordered conformation of adsorbed polyelectrolyte molecules. These findings are important for many applications of LbL films, since device performance usually depends on film morphology and its molecular structure.

  6. Polymorphism of resorcinol explored by complementary vibrational spectroscopy (FT-RS, THz-TDS, INS) and first-principles solid-state computations (plane-wave DFT).

    PubMed

    Drużbicki, Kacper; Mikuli, Edward; Pałka, Norbert; Zalewski, Sławomir; Ossowska-Chruściel, Mirosława D

    2015-01-29

    The polymorphism of resorcinol has been complementary studied by combining Raman, time-domain terahertz, and inelastic neutron scattering spectroscopy with modern solid-state density functional theory (DFT) calculations. The spectral differences, emerging from the temperature-induced structural phase transition, have been successfully interpreted with an emphasis on the low-wavenumber range. The given interpretation is based on the plane-wave DFT computations, providing an excellent overall reproduction of both wavenumbers and intensities and revealing the source of the observed spectral differences. The performance of the generalized gradient approximation (GGA) functionals in prediction of the structural parameters and the vibrational spectra of the normal-pressure polymorphs of resorcinol has been extensively examined. The results show that the standard Perdew, Burke, and Ernzerhof (PBE) approach along with its "hard" revised form tends to be superior if compared to the "soft" GGA approximation. PMID:25564699

  7. Amine Chemistry at Aqueous Interfaces: The Study of Organic Amines in Neutralizing Acidic Gases at an Air/Water Surface Using Vibrational Sum Frequency Spectroscopy

    NASA Astrophysics Data System (ADS)

    McWilliams, L.; Wren, S. N.; Valley, N. A.; Richmond, G.

    2014-12-01

    Small organic bases have been measured in atmospheric samples, with their sources ranging from industrial processing to animal husbandry. These small organic amines are often highly soluble, being found in atmospheric condensed phases such as fogwater and rainwater. Additionally, they display acid-neutralization ability often greater than ammonia, yet little is known regarding their kinetic and thermodynamic properties. This presentation will describe the molecular level details of a model amine system at the vapor/liquid interface in the presence of acidic gas. We find that this amine system shows very unique properties in terms of its bonding, structure, and orientation at aqueous surfaces. The results of our studies using a combination of computation, vibrational sum frequency spectroscopy, and surface tension will report the properties inherent to these atmospherically relevant species at aqueous surfaces.

  8. Evidence for a High-Pressure Phase Transition of ε-2,4,6,8,10,12-hexanitrohexaazaisowurtzitane (CL-20) Using Vibrational Spectroscopy

    SciTech Connect

    Ciezak, J.; Jenkins, T; Liu, Z

    2007-01-01

    The high-pressure response of {epsilon}-2,4,6,8,10,12-hexanitrohexaazaisowurtizane (CL-20) has been examined to 27 GPa in diamond anvil cells using vibrational spectroscopy. The results reveal evidence of an {epsilon}{yields}{Upsilon} pressure-induced phase transition between 4.1 and 6.4 GPa and suggest the existence of a {Upsilon}{yields}{zeta} transition near 18.7 GPa. Several Raman and infrared frequencies were found to decrease in intensity as the phase boundaries are approached. An anomalous intensity increase was noted in the C-N-C infrared mode that is believed to result from an increase in the Raman cross-section due to a stronger interlayer coupling under pressure.

  9. Absolute configuration and predominant conformations of a chiral crown ether-based colorimetric sensor: a vibrational circular dichroism spectroscopy and DFT study of chiral recognition.

    PubMed

    Merten, Christian; Hyun, Myung Ho; Xu, Yunjie

    2013-05-01

    In the present work, we report a comprehensive vibrational circular dichroism (VCD) spectroscopic study of a chiral crown ether which features an axial chiral 3.3'-diphenyl-1,1'-binaphthyl group as chiral moiety. By comparing the experimental and calculated VCD spectra, we show that the presumably very flexible crown ether preferably adopts only one ring conformation. Conformational flexibility is observed in the 2,4-dinitrophenyl-diazophenol group, which was previously introduced for colorimetric detection of primary amines and amino alcohols (Cho et al., Chirality 2011;23:349-353). The VCD spectra of the host-guest complexes with phenyl glycinol (PG) and phenyl alaninol have been studied as well. Based on the spectra calculated, it is shown that the diastereomeric complexes in general can be differentiated using VCD spectroscopy. Furthermore, the experimental VCD spectra of the complexes of the host molecule with PG support the above finding. PMID:23620265

  10. Study of the adsorption of sodium dodecyl sulfate (SDS) at the air/water interface: targeting the sulfate headgroup using vibrational sum frequency spectroscopy.

    PubMed

    Johnson, C Magnus; Tyrode, Eric

    2005-07-01

    The surface sensitive technique vibrational sum frequency spectroscopy (VSFS), has been used to study the adsorption behaviour of SDS to the liquid/vapour interface of aqueous solutions, specifically targeting the sulfate headgroup stretches. In the spectral region extending from 980 to 1850 cm(-1), only the vibrations due to the SO(3) group were detectable. The fitted amplitudes for the symmetric SO(3) stretch observed at 1070 cm(-1) for the polarization combinations ssp and ppp, were seen to follow the adsorption isotherm calculated from surface tension measurements. The orientation of the sulfate headgroup in the concentration range spanning from 1.0 mM to above the critical micellar concentration (c.m.c.) was observed to remain constant within experimental error, with the pseudo-C(3) axis close to the surface normal. Furthermore, the effect of increasing amounts of sodium chloride at SDS concentrations above c.m.c. was also studied, showing an increase of approximately 12% in the fitted amplitude for the symmetric SO(3) stretch when increasing the ionic strength from 0 to 300 mM NaCl. Interestingly, the orientation of the SDS headgroup was also observed to remain constant within this concentration range and identical to the case without NaCl.

  11. Vibrational spectroscopy and conformation of S-ethyl thioacetate: CH3COSCH2CH3 and comparison with -C(O)S- and -C(O)O- compounds.

    PubMed

    Defonsi Lestard, María Eliana; Tuttolomondo, María Eugenia; Ben Altabef, Aida

    2015-01-25

    The molecular structure and conformational properties of S-ethyl thioacetate, CH3COSCH2CH3, were determined in the gas phase by electron diffraction and vibrational spectroscopy (IR and Raman). The experimental investigations were supplemented by ab initio (MP2) and DFT quantum chemical calculations at different levels of theory. Theoretical methods reveal two structures with Cs (anti, anti) and C1 (anti, gauche) symmetries. The infrared and Raman spectra for different phases were also recorded and the bands observed assigned to the vibrational normal modes. Liquid Raman and infrared spectra in liquid and gaseous state measurements revealed the presence of two conformations anti, anti (Cs symmetry) and anti, gauche (C1 symmetry). The study was completed using natural bond orbital (NBO) analysis. We have also analyzed the internal rotation barrier about the C(O)SCC dihedral angle using a variety of computational approaches and natural bond orbital (NBO) analyses to understand the nature of the potential function and to explain the preferred conformation of the molecule.

  12. Using AN Organic Scaffold to Modulate the Quantum Structure of AN Intramolecular Proton Bond: Cryogenic Vibrational Predissociation Spectroscopy of H2 on Protonated 8-NAPHTHALENE-1-AMINE

    NASA Astrophysics Data System (ADS)

    Deblase, Andrew F.; Guasco, Timothy L.; Leavitt, Christopher M.; Johnson, Mark A.; Lectka, Thomas

    2011-06-01

    The quantum structure of the intermolecular proton bond is a key aspect in understanding proton transfer events that govern the efficiency of fuel cells and various biological membranes. Previously, we have constructed a soft binding motif, that consists of a "point contact" between the lone pairs of two small molecules (combinations of ethers, alcohols, ammonia, and water) that are linked by a shared proton [Science 2007, 613, 249]. Although the frequency of the shared proton vibration has been correlated with effects of acid and base structure, such as proton affinities and dipole moments, the spatial arrangement of the proton donor and acceptor remains unexplored. Towards this aim, we have obtained a molecule of rigid topology that contains a proton donor and acceptor capable of intramolecular proton-bonding (protonated 8-flouronaphthalene-1-amine). Using electrospray ionization coupled with a novel cryogenic mass spectrometry scheme, we employ vibrational predissociation spectroscopy of H2 tagged ions to elucidate how a forced spatial configuration of the acid and base perturbs the energetics of the proton bond.

  13. Structural characterization of electron-induced proton transfer in the formic acid dimer anion, (HCOOH)2-, with vibrational and photoelectron spectroscopies.

    PubMed

    Gerardi, Helen K; DeBlase, Andrew F; Leavitt, Christopher M; Su, Xiaoge; Jordan, Kenneth D; McCoy, Anne B; Johnson, Mark A

    2012-04-01

    The (HCOOH)(2) anion, formed by electron attachment to the formic acid dimer (FA(2)), is an archetypal system for exploring the mechanics of the electron-induced proton transfer motif that is purported to occur when neutral nucleic acid base-pairs accommodate an excess electron [K. Aflatooni, G. A. Gallup, and P. D. Burrow, J. Phys. Chem. A 102, 6205 (1998); J. H. Hendricks, S. A. Lyapustina, H. L. de Clercq, J. T. Snodgrass, and K. H. Bowen, J. Chem Phys. 104, 7788 (1996); C. Desfrancois, H. Abdoul-Carime, and J. P. Schermann, ibid. 104, 7792 (1996)]. The FA(2) anion and several of its H∕D isotopologues were isolated in the gas phase and characterized using Ar-tagged vibrational predissociation and electron autodetachment spectroscopies. The photoelectron spectrum of the FA(2) anion was also recorded using velocity-map imaging. The resulting spectroscopic information verifies the equilibrium FA(2)(-) geometry predicted by theory which features a symmetrical, double H-bonded bridge effectively linking together constituents that most closely resemble the formate ion and a dihydroxymethyl radical. The spectroscopic signatures of this ion were analyzed with the aid of calculated anharmonic vibrational band patterns. PMID:22482563

  14. Structural characterization of electron-induced proton transfer in the formic acid dimer anion, (HCOOH)2-, with vibrational and photoelectron spectroscopies.

    PubMed

    Gerardi, Helen K; DeBlase, Andrew F; Leavitt, Christopher M; Su, Xiaoge; Jordan, Kenneth D; McCoy, Anne B; Johnson, Mark A

    2012-04-01

    The (HCOOH)(2) anion, formed by electron attachment to the formic acid dimer (FA(2)), is an archetypal system for exploring the mechanics of the electron-induced proton transfer motif that is purported to occur when neutral nucleic acid base-pairs accommodate an excess electron [K. Aflatooni, G. A. Gallup, and P. D. Burrow, J. Phys. Chem. A 102, 6205 (1998); J. H. Hendricks, S. A. Lyapustina, H. L. de Clercq, J. T. Snodgrass, and K. H. Bowen, J. Chem Phys. 104, 7788 (1996); C. Desfrancois, H. Abdoul-Carime, and J. P. Schermann, ibid. 104, 7792 (1996)]. The FA(2) anion and several of its H∕D isotopologues were isolated in the gas phase and characterized using Ar-tagged vibrational predissociation and electron autodetachment spectroscopies. The photoelectron spectrum of the FA(2) anion was also recorded using velocity-map imaging. The resulting spectroscopic information verifies the equilibrium FA(2)(-) geometry predicted by theory which features a symmetrical, double H-bonded bridge effectively linking together constituents that most closely resemble the formate ion and a dihydroxymethyl radical. The spectroscopic signatures of this ion were analyzed with the aid of calculated anharmonic vibrational band patterns.

  15. Efficient Spectral Diffusion at the Air/Water Interface Revealed by Femtosecond Time-Resolved Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy.

    PubMed

    Inoue, Ken-Ichi; Ishiyama, Tatsuya; Nihonyanagi, Satoshi; Yamaguchi, Shoichi; Morita, Akihiro; Tahara, Tahei

    2016-05-19

    Femtosecond vibrational dynamics at the air/water interface is investigated by time-resolved heterodyne-detected vibrational sum frequency generation (TR-HD-VSFG) spectroscopy and molecular dynamics (MD) simulation. The low- and high-frequency sides of the hydrogen-bonded (HB) OH stretch band at the interface are selectively excited with special attention to the bandwidth and energy of the pump pulses. Narrow bleach is observed immediately after excitation of the high-frequency side of the HB OH band at ∼3500 cm(-1), compared to the broad bleach observed with excitation of the low-frequency side at ∼3300 cm(-1). However, the time-resolved spectra observed with the two different excitations become very similar at 0.5 ps and almost indistinguishable by 1.0 ps. This reveals that efficient spectral diffusion occurs regardless of the difference of the pump frequency. The experimental observations are well-reproduced by complementary MD simulation. There is no experimental and theoretical evidence that supports extraordinary slow dynamics in the high-frequency side of the HB OH band, which was reported before. PMID:27120559

  16. Millimeter-wave spectroscopy of the FeCO radical in the ν2 and ν3 vibrationally excited states.

    PubMed

    Tanaka, Keiichi; Nakamura, Mitsuhiro; Shirasaka, Mitsuaki; Sakamoto, Ai; Harada, Kensuke; Tanaka, Takehiko

    2015-07-01

    The pure rotational spectra of the FeCO radical in the ν2 (bending) and ν3 (Fe-C stretching) vibrational states of the ground X̃(3)Σ(-) electronic state were observed in the millimeter-wave region. The equilibrium rotational and centrifugal distortion constants were determined to be Be = 4374.631 (58) MHz and De = 1.1666 (20) kHz together with the spin-spin coupling constant λe = 691.89 (37) GHz and spin-rotation coupling constant γe = - 1079.4 (55) MHz with use of the millimeter-wave results and the ν1 IR data. The equilibrium bond length for Fe-C was derived to be 1.725 Å assuming that for C-O to be 1.159 Å. Since the vibronic symmetry of the excited state of bending vibration is (3)Π, the analysis of spectrum in the ν2 state required an effective spin-orbit interaction constant of A2 = 6.0219 (61) GHz together with three parity doubling constants of o2 = 36.168 (10) GHz, p2 = 85.18 (34) MHz, and q2 = 4.7024 (17) MHz. The effective spin-orbit interaction constant A2 is attributed to the vibronic mixing of the (3)Π excited electronic states. The vibronic mixing also cause the parity doubling constants o2 and p2, but the main contribution to q2 is given by the vibrational l-type doubling.

  17. Microanalysis of Ar and He bombarded biomedical polymer films

    NASA Astrophysics Data System (ADS)

    Manso Silvan, M.; Gago, R.; Valsesia, A.; Climent Font, A.; Duart, J. M. Martínez; Rossi, F.

    2007-04-01

    Implantations onto polyethyleneglycol, polycaprolactone and polymethylmethacrylate, carried out with Ar and He ions at 25 and 100 KeV with fluences of 5 × 1013 cm-2, have been made with identical ion currents (20 μA) but different sweep areas in order to take into account the effect of the ion flux on the composition and structure of these biopolymers. Vibrational (Fourier transformed infrared spectroscopy), microanalytical (Rutherford backscattering and energy recoil detection) and microscopic techniques (atomic force microscopy) confirm that, even in this low fluence regime, the ion flux effect is responsible of scaled modifications. More interestingly, these techniques indicate that the damage seems to be higher for He. All these factors suggest that He could be preferentially used to engineer biomedical polymers exploiting the tailoring opportunities offered by ion flux effects.

  18. Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O2-tolerant NAD+-reducing [NiFe] hydrogenase

    SciTech Connect

    Lauterbach, Lars; Wang, Hongxin; Horch, Marius; Gee, Leland B.; Yoda, Yoshitaka; Tanaka, Yoshihito; Zebger, Ingo; Lenz, Oliver; Cramer, Stephen P.

    2014-10-30

    Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function of the various metal cofactors present in the enzyme. Here, all iron-containing cofactors of the SH were investigated by 57Fe specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters, which is consistent with the amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD+-reducing hydrogenases. For the first time, Fe–CO and Fe–CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective 13C labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe–CO modes. The present approach explores the complex vibrational signature of the Fe–S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors.

  19. Terahertz Spectroscopy and Global Analysis of the Bending Vibrations of ^{12}C_2H_2 and ^{12}C_2D_2

    NASA Astrophysics Data System (ADS)

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

    2009-06-01

    Symmetric molecules have no permanent dipole moment and are undetectable by rotational spectroscopy. Their interstellar observations have previously been limited to mid-infrared vibration-rotation spectroscopy. Although relatively weak, vibrational difference bands provide a means for detection of non polar molecules by terahertz techniques with microwave precision. Herschel, SOFIA, and ALMA have the potential to identify a number of difference bands of light symmetric species, e.g., C_2H_2, CH_4 and C_3. This paper reports the results of the laboratory study on ^{12}C_2H_2 and ^{12}C_2D_2. The symmetric isotopomers of acetylene have two bending modes, the trans bending ν_4 (^1{π}_g), and the cis bending ν_5 (^1{π}_u). For ^{12}C_2H_2, the two bending modes occur at 612 and 729 cm^{-1}, respectively. For ^{12}C_2D_2, the two bending modes occur at 511 and 538 cm^{-1}. The ν_5-ν_4 difference bands are allowed and occur in the microwave, terahertz, and far-infrared wavelengths, with band origins at 117 cm^{-1} (3500 GHz) for ^{12}C_2H_2 and 27 cm^{-1} (900 GHz) for ^{12}C_2D_2. Two hundred and fifty-one ^{12}C_2D_2 transitions, which are from ν_5-ν_4, (ν_5+ν_4)-2ν_4 and 2ν_5-(ν_5+ν_4) bands, have been measured in the 0.2-1.6 THz region, and 202 of them were observed for the first time. The precision of these measurements is estimated to be from 50 kHz to 100 kHz. A multistate analysis was carried out for the bending vibrational modes ν_4 and ν_5 of ^{12}C_2D_2, 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 ^{12}C_2D_2 by adding the new measurements to the old data set which had only 10 lines with microwave measurement precision. The experiments on ^{12}C_2H_2 are in progress and ten P branch lines have been observed. We will present the ^{12}C_2H_2 results to date.

  20. Mefenamic acid anti-inflammatory drug: probing its polymorphs by vibrational (IR and Raman) and solid-state NMR spectroscopies.

    PubMed

    Cunha, Vanessa R R; Izumi, Celly M S; Petersen, Philippe A D; Magalhães, Alviclér; Temperini, Marcia L A; Petrilli, Helena M; Constantino, Vera R L

    2014-04-24

    This work deals with the spectroscopic (supported by quantum chemistry calculations), structural, and morphological characterization of mefenamic acid (2-[(2,3-(dimethylphenyl)amino] benzoic acid) polymorphs, known as forms I and II. Polymorph I was obtained by recrystallization in ethanol, while form II was reached by heating form I up to 175 °C, to promote the solid phase transition. Experimental and theoretical vibrational band assignments were performed considering the presence of centrosymmetric dimers. Besides band shifts in the 3345-3310 cm(-1) range, important vibrational modes to distinguish the polymorphs are related to out-of-phase and in-phase N-H bending at 1582 (Raman)/1577 (IR) cm(-1) and 1575 (Raman)/1568 (IR) cm(-1) for forms I and II, respectively. In IR spectra, bands assigned to N-H bending out of plane are observed at 626 and 575 cm(-1) for polymorphs I and II, respectively. Solid-state (13)C NMR spectra pointed out distinct chemical shifts for the dimethylphenyl group: 135.8 to 127.6 ppm (carbon bonded to N) and 139.4 to 143.3 ppm (carbon bonded to methyl group) for forms I and II, respectively. PMID:24654805

  1. Vibrational mode deactivation rates for gaseous discharge-excited nitrogen(2) on selected surfaces measured with coherent anti-Stokes Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Parish, John Walter, Jr.

    2000-09-01

    The disposal rate of nitrogen molecule internal-mode energy, kv , by deactivation in the presence of various surfaces was studied at low pressure and at approximately room temperature using coherent anti-Stokes Raman spectroscopy (CARS). Deactivation is the process whereby vibrational energy is lost one quantum or a few quanta at a time rather than all at once as in quenching. Deactivation coefficients, γv, or loss probabilities, of vibrationally-excited N2(X1Σg +,v) on gold, Pyrex, Teflon and alloys of aluminum, stainless steel and titanium, were calculated from the wall deactivation rate coefficients for the hot band quantum numbers v = 1 to 4 or 5. Vibration states were populated with a 1.5 cm diameter water-cooled-in- glass positive column discharge where the residence time was estimated to be about 60 ms in the tube. The flow rate and pressure were adjusted to optimize the populations and the observed decay. Subsequently, the excited gas was presented via a source tube to a tubular reactor. For precisely controlled residence times, the excited nitrogen would communicate with the reactor interior surface. Only the gas that had been exposed to the surface was measured upon exit from the reactor by a CARS system in the 3-D BOXCARS configuration. Extensive measurements on Pyrex gave γ 1 values between 2.4 × 10-4 and 6.7 × 10-4 depending on the treatment history of the surface. The values for γ4 ranged from 2.9 × 10-4 for the AMS 4943D alloy of titanium to approximately unity for the AMS 312 stainless steel alloy. The low value for titanium can be attributed to the oxide layer. The variation of kv with v was linear or nearly linear in all cases with slopes lower in most cases than the rate of increase of the vibration-translation V-T exchange rate with v. Direct measurement of rates, in this way, detects losses due to homogeneous gas collisions as well as heterogeneous collisions with the surface. An attempt to extract the true value of γv from the data was

  2. Low energy electron diffraction (LEED) and sum frequency generation (SFG) vibrational spectroscopy studies of solid-vacuum, solid-air and solid-liquid interfaces

    SciTech Connect

    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.

  3. Biosensing with T-ray spectroscopy

    NASA Astrophysics Data System (ADS)

    Fischer, Bernd M.; Helm, Hanspeter; Abbott, Derek

    2007-07-01

    In the recent years, it has been shown that terahertz (or T-ray) spectroscopy is a versatile tool for biosensing and safety applications. This is due to the fact that the THz-spectra of many biomolecules show very characteristic, distinct spectroscopic features. Furthermore, most non-metallic packaging materials are nearly transparent in this frequency range (0.1 - 6 THz, 3 cm -1 - 200 cm -1), so that it is possible to non-invasively identify even sealed substances like pharmaceuticals, illicit drugs or explosives by their spectroscopic signatures. This opens a significant potential for a wide range of applications from quality control of pharmaceutical substances via safety applications through to biomedical applications. The individual spectroscopic features below approximately 5 THz that spurred the increased world wide interest in T-ray spectroscopy are mainly due to intermolecular rather than intramolecular vibrations in the polycrystalline samples. The spectra of more complex biomolecules, like proteins and nucleotides, typically show less or even no sharp features, due to the lack of long- range intermolecular order. Furthermore, due to the typically significantly smaller sample amount, the signal to noise ratio is strongly increased. Water shows a strong absorption in this frequency range, which all together makes real biomedical applications of T-ray spectroscopy rather difficult. Yet, by combining a careful sample preparation, novel experimental techniques and an advanced signal processing of the experimental data we can still clearly distinguish between even complex biomolecules and therefore demonstrate the potential the technique holds for biomedical applications.

  4. Identification of the 0+ proton pairing vibration state in the doubly magic nucleus 208Pb by particle spectroscopy

    NASA Astrophysics Data System (ADS)

    Heusler, A.; Faestermann, T.; Hertenberger, R.; Wirth, H.-F.; von Brentano, P.

    2015-04-01

    Among about 150 levels below Ex=5.86 MeV in 208Pb listed by the Nuclear Data Sheets as of 2007, most levels were recently identified as particle-hole states. All natural parity states excited by the 208Pb(α ,α') reaction are identified, two of them are newly identified. The state at Ex=5667 keV is identified as the 0+ proton pairing vibration state. Based on the analysis of data from the Pb 206 ,207 ,208 (d ,p ) ,208Pb(d ,d') , and 208Pb(p ,p') reactions obtained with the Q3D magnetic spectrograph of the Maier-Leibnitz-Laboratorium at Garching (Germany) at scattering angles 15° ≤Θ ≤138° and bombarding energies Ed=22 ,24 MeV and 14.8 vibration state at Ex=4868 keV and the 0+ member of the double-octupole multiplet at Ex=5241 keV are verified by the nonresonant 208Pb(p ,p') and 208Pb(d ,d') reactions with cross sections of around 3 μ b /sr .

  5. Conformation-Specific Electronic and Vibrational Spectroscopy of DIBENZO-15-CROWN-5 Ether in a Supersonic Jet.

    NASA Astrophysics Data System (ADS)

    Buchanan, Evan G.; Rodrigo, Chirantha P.; James, William H. James, III; Newby, Josh J.; Zwier, Timothy S.

    2009-06-01

    Crown ethers are oxygen containing cyclic structures noted for their ability to preferentially bind substrates such as ions and water. Despite the high symmetry inherent to the chemical structure, crown ethers are remarkably flexible, adapting their conformation to the substrate to which they are bound. As such, it is valuable to study the conformational preferences of the isolated crown ethers in the absence of any substrate. Here, we present the electronic and infrared spectroscopy of jet-cooled, isolated dibenzo-15-crown-5 ether (DB15C). By incorporating two phenyl rings into the crown, we are afforded the opportunity to explore the ultraviolet spectroscopy of both groups and the coupling between them. One-color resonant two-photon ionization, laser induced fluorescence, UV-UV holeburning, and resonant ion-dip infrared spectroscopies are used to provide conformation-specific electronic and infrared spectra of the three conformers. Additionally, single vibronic level dispersed fluorescence spectra provide evidence for the existence of close lying S_2 states in the two major conformers, located about 527 cm^{-1} above their S_1 counterparts. Based on a comparison with benzo-15-crown-5 ether, we surmise that the local conformation of the ethoxy groups about the two phenyl rings are different. Electronic energy transfer appears to be slow between these phenyl rings on the timescale of the excited state fluorescence. Finally, DFT and MP2 calculations will be presented as a basis for tentative structural assignments and provide insight into the excitonic coupling of the two chromophores.

  6. Combined electron microscopy and vibrational spectroscopy study of corroded Magnox sludge from a legacy spent nuclear fuel storage pond

    NASA Astrophysics Data System (ADS)

    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.

  7. Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm(-1) studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations.

    PubMed

    Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Pietropolli Charmet, Andrea; Gambi, Alberto

    2012-06-01

    Difluoromethane (CH(2)F(2), HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH(2)F(2), providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm(-1). Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm(-1) while intensities are predicted within few km mol(-1) from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν(1)>, |2ν(8)>, |2ν(2)> three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm(-1

  8. Ultraviolet Raman spectroscopy of catalysts: Adsorption and coke formation in zeolites and vibrational spectra of supported metal oxides

    NASA Astrophysics Data System (ADS)

    Chua, Yek Tann

    2001-10-01

    The primary goal of this dissertation is to study the physicochemical and catalytic properties of zeolites and supported metal oxide catalysts using UV Raman spectroscopy. In order to reduce the thermal degradation and possible photodecomposition of adsorbates by UV radiation, we have developed a novel fluidized bed method for measuring the UV Raman spectra of catalysts and adsorbates. The UV Raman spectra of various organic compounds adsorbed in zeolites H-USY and H-ZSM-5 are recorded. When measurements are performed on stationary and spinning samples, the Raman spectra show the presence of coke, a typical end product of heat and photochemistry. In contrast, the Raman peaks of the unreacted adsorbates dominate the spectra measured using the fluidized bed method. These results indicate that the fluidized bed technique is a good method for measuring UV Raman spectra of catalysts and adsorbates. The formation of coke in the methanol-to-gasoline conversion over zeolite H-ZSM-5 causes deactivation of the catalyst. To gain insight into the formation of coke, we have studied this reaction using UV Raman spectroscopy. The Raman spectral changes suggest coke is produced from conjugated olefins via cyclopentadiene intermediates. Aromatic compounds in gasoline may also be produced from cyclopentadienes. The adsorbate-induced structural changes of zeolites may alter the molecular sieving characteristics of these materials which ultimately affect their performance as catalysts and adsorbents. We have quantified the adsorbate-induced structural changes of zeolite H-RHO using UV Raman spectroscopy. The Raman spectra of the zeolite after the adsorption of water, methanol or acetonitrile are consistent with an increase in the average T-O-T angle of the zeolite of 5-8°. The adsorption of ammonia, on the other hand, decreases the average T-O-T angle by 5°. Because of certain advantages of UV Raman spectroscopy over visible Raman spectroscopy, recently there is a strong interest in

  9. Conformational manifold of alpha-aminoisobutyric acid (Aib) containing alanine-based tripeptides in aqueous solution explored by vibrational spectroscopy, electronic circular dichroism spectroscopy, and molecular dynamics simulations.

    PubMed

    Schweitzer-Stenner, Reinhard; Gonzales, Widalys; Bourne, Gregory T; Feng, Jianwen A; Marshall, Garland R

    2007-10-31

    Replacement of the alpha-proton of an alanine residue to generate alpha-aminoisobutyric acid (Aib) in alanine-based oligopeptides favors the formation of a 3(10) helix when the length of the oligopeptide is about four to six residues. This research was aimed at experimentally identifying the structural impact of an individual Aib residue in an alanine context of short peptides in water and Aib's influence on the conformation of nearest-neighbor residues. The amide I band profile of the IR, isotropic and anisotropic Raman, and vibrational circular dichroism (VCD) spectra of Ac-Ala-Ala-Aib-OMe, Ac-Ala-Aib-Ala-OMe, and Ac-Aib-Ala-Ala-OMe were measured and analyzed in terms of different structural models by utilizing an algorithm that exploits the excitonic coupling between amide I' modes. The conformational search was guided by the respective 1H NMR and electronic circular dichroism spectra of the respective peptides, which were also recorded. From these analyses, all peptides adopted multiple conformations. Aib predominantly sampled the right-handed and left-handed 3(10)-helix region and to a minor extent the bridge region between the polyproline (PPII) and the helical regions of the Ramachandran plot. Generally, alanine showed the anticipated PPII propensity, but its conformational equilibrium was shifted towards helical conformations in Ac-Aib-Ala-Ala-OMe, indicating that Aib can induce helical conformations of neighboring residues positioned towards the C-terminal direction of the peptide. An energy landscape exploration by molecular dynamics simulations corroborated the results of the spectroscopic studies. They also revealed the dynamics and pathways of potential conformational transitions of the corresponding Aib residues.

  10. Characterization of Structural Motifs for CO_{2} Accommodation by Ionic Species Relevant to Photoelectrocatalysis Using Cryogenic Vibrational Predissociation Spectroscopy

    NASA Astrophysics Data System (ADS)

    Fournier, Joseph A.; Johnson, Christopher J.; Wolke, Conrad T.; Wolk, Arron B.; Leavitt, Christopher M.; Breen, Kristen J.; Johnson, Mark A.

    2013-06-01

    Two aspects of catalytic CO_{2} conversion to transportable fuels involve understanding the local interactions between CO_{2} and the solvent mediating the reduction and the coordination of CO_{2} onto the organometallic framework that executes the chemical transformation. To address why ionic liquids are emerging as the solvents of choice for the catalysis, we first explore how CO_{2} attaches to two archetypal ionic liquid components: imidazole (Im) and acetate (Ac^{-}). Im was seeded in a CO_{2} pulsed free jet expansion forming Im(CO_{2}^{-})(CO_{2})_{m} (m=1-2) clusters. Previous studies with pyridine revealed C-N bond formation between CO_{2}^{-} and pyridine with m=5 or 7, evidenced by the observation of a C-N stretch in the vibrational spectra. No such C-N bond formation is observed with Im; the CO_{2}^{-} appears to be hydrogen bonded to the Im N-H in an ion-molecule complex. Attachment to Ac^{-} was studied by predissociation of the Ac^{-}(CO_{2})_{m} (m=1-4) clusters and, for m=1-3, a single peak assigned to the CO_{2} asymmetric stretch is observed near that of bare CO_{2}, suggesting that the CO_{2} molecules are weakly bound adducts. However, the combination bands 2νb{2} + νb{3} and νb{1} + νb{3} in the 3600-3750wn region reveal two distinct binding sites: a neutral site and a red-shifted, more perturbed site. For m=4, a red-shifted CO_{2} asymmetric stretch is observed, perhaps indicating the beginning of solvent mediated activation of a CO_{2} adduct. Finally, the CO_{2} reduction catalyst Ni(cyclam)^{2+} has been investigated using an electrospray ionization source coupled to a cryogenically cooled ion trap. By adding CO_{2} to the He buffer gas used to collisionally cool the ions in the trap, we have been able to condense up to five CO_{2} molecules onto Ni(cyclam)^{2+} at a trap temperature of 100K. The cryogenic ion vibrational predissociation (CIVP) spectra show the CO_{2} molecules to be acting as neutral adducts. We are now working to

  11. Characterization of the Fe Site in Iron-Sulfur-Cluster-Free Hydrogenase (Hmd) and of a Model Compound via Nuclear Resonance Vibrational Spectroscopy (NRVS)

    PubMed Central

    Guo, Yisong; Wang, Hongxin; Xiao, Yuming; vogt, Sonja; Shima, Seigo; Volkers, Phillip I.; Pelmentschikov, Vladimir; Alp, Ercan E.; Sturhahn, Wolfgang; Yada, Yoshitaka

    2009-01-01

    We have used 57Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur-cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO)2-ligated Fe model compound, Fe(S2C2H4)(CO)2(PMe3)2, as well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey-Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results. Previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm−1, interpreted as evidence for cis-Fe(CO)2 ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm−1, consistent with the proposed cis-Fe(CO)2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at ~311 cm−1, and another reproducible feature at ~380 cm−1. The 57Fe partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey-Bradley force field for a 5-coordinate cis-(CO)2-ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a 3-dimensional structure for the active site. PMID:18407624

  12. Hydration of Sulphobetaine (SB) and Tetra(ethylene glycol) (EG4)-Terminated Self-Assembled Monolayers Studied by Sum Frequency Generation (SFG) Vibrational Spectroscopy

    PubMed Central

    Stein, M. Jeanette; Weidner, Tobias; McCrea, Keith; Castner, David G.; Ratner, Buddy D.

    2010-01-01

    Sum frequency generation (SFG) vibrational spectroscopy is used to study the surface and the underlying substrate of both homogeneous and mixed self-assembled monolayers (SAMs) of 11-mercaptoundecyl-1-sulphobetainethiol (HS(CH2)11N+(CH3)2(CH2)3SO3−, SB) and 1-mercapto-11-undecyl tetra(ethylene glycol) (HS(CH2)11O(CH2CH2O)4OH, EG4) with an 11-mercapto-1-undecanol (HS(CH2)11OH, MCU) diluent. SFG results on the C–H region of the dry and hydrated SAMs gave an in situ look into the molecular orientation and suggested an approach to maximize signal-to-noise ratio on these difficult to analyze hydrophilic SAMs. Vibrational fingerprint studies in the 3000–3600 cm−1 spectral range for the SAMs exposed serially to air, water, and deuterated water revealed that a layer of tightly-bound structured water was associated with the surface of a non-fouling monolayer but was not present on a hydrophobic N-undecylmercaptan (HS(CH2)10CH3, UnD) control. The percentage of water retained upon submersion in D2O correlated well with the relative amount of protein that was previously shown to absorb onto the monolayers. These results provide evidence supporting the current theory regarding the role of a tightly-bound vicinal water layer in the protein resistance of a non-fouling group. PMID:19639981

  13. Application of vibrational spectroscopy supported by theoretical calculations in identification of amorphous and crystalline forms of cefuroxime axetil.

    PubMed

    Talaczyńska, Alicja; Lewandowska, Kornelia; Jelińska, Anna; Garbacki, Piotr; Podborska, Agnieszka; Zalewski, Przemysław; Oszczapowicz, Irena; Sikora, Adam; Kozak, Maciej; Cielecka-Piontek, Judyta

    2015-01-01

    FT-IR and Raman scattering spectra of cefuroxime axetil were proposed for identification studies of its crystalline and amorphous forms. An analysis of experimental spectra was supported by quantum-chemical calculations performed with the use of B3LYP functional and 6-31G(d,p) as a basis set. The geometric structure of a cefuroxime axetil molecule, HOMO and LUMO orbitals, and molecular electrostatic potential were also determined by using DFT (density functional theory). The benefits of applying FT-IR and Raman scattering spectroscopy for characterization of drug subjected to degradation were discussed.

  14. Vibrational spectroscopy characterization of low level laser therapy on mammary culture cells: a micro-FTIR study

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  16. Overtone vibrational spectroscopy in H2-H2O complexes: A combined high level theoretical ab initio, dynamical and experimental study

    NASA Astrophysics Data System (ADS)

    Ziemkiewicz, Michael P.; Pluetzer, Christian; Nesbitt, David J.; Scribano, Yohann; Faure, Alexandre; van der Avoird, Ad

    2012-08-01

    First results are reported on overtone (vOH = 2 ← 0) spectroscopy of weakly bound H2-H2O complexes in a slit supersonic jet, based on a novel combination of (i) vibrationally mediated predissociation of H2-H2O, followed by (ii) UV photodissociation of the resulting H2O, and (iii) UV laser induced fluorescence on the nascent OH radical. In addition, intermolecular dynamical calculations are performed in full 5D on the recent ab initio intermolecular potential of Valiron et al. [J. Chem. Phys. 129, 134306 (2008), 10.1063/1.2988314] in order to further elucidate the identity of the infrared transitions detected. Excellent agreement is achieved between experimental and theoretical spectral predictions for the most strongly bound van der Waals complex consisting of ortho (I = 1) H2 and ortho (I = 1) H2O (oH2-oH2O). Specifically, two distinct bands are seen in the oH2-oH2O spectrum, corresponding to internal rotor states in the upper vibrational manifold of Σ and Π rotational character. However, none of the three other possible nuclear spin modifications (pH2-oH2O, pH2-pH2O, or oH2-pH2O) are observed above current signal to noise level, which for the pH2 complexes is argued to arise from displacement by oH2 in the expansion mixture to preferentially form the more strongly bound species. Direct measurement of oH2-oH2O vibrational predissociation in the time domain reveals lifetimes of 15(2) ns and <5(2) ns for the Σ and Π states, respectively. Theoretical calculations permit the results to be interpreted in terms of near resonant energy levels and intermolecular alignment of the H2 and H2O wavefunctions, providing insight into predissociation dynamical pathways from these metastable levels.

  17. Biomedical ultrasonoscope

    NASA Technical Reports Server (NTRS)

    Lee, R. D. (Inventor)

    1979-01-01

    The combination of a "C" mode scan electronics in a portable, battery powered biomedical ultrasonoscope having "A" and "M" mode scan electronics, the latter including a clock generator for generating clock pulses, a cathode ray tube having X, Y and Z axis inputs, a sweep generator connected between the clock generator and the X axis input of the cathode ray tube for generating a cathode ray sweep signal synchronized by the clock pulses, and a receiver adapted to be connected to the Z axis input of the cathode ray tube. The "C" mode scan electronics comprises a plurality of transducer elements arranged in a row and adapted to be positioned on the skin of the patient's body for converting a pulsed electrical signal to a pulsed ultrasonic signal, radiating the ultrasonic signal into the patient's body, picking up the echoes reflected from interfaces in the patient's body and converting the echoes to electrical signals; a plurality of transmitters, each transmitter being coupled to a respective transducer for transmitting a pulsed electrical signal thereto and for transmitting the converted electrical echo signals directly to the receiver, a sequencer connected between the clock generator and the plurality of transmitters and responsive to the clock pulses for firing the transmitters in cyclic order; and a staircase voltage generator connected between the clock generator and the Y axis input of the cathode ray tube for generating a staircase voltage having steps synchronized by the clock pulses.

  18. The vacuum UV photoabsorption spectroscopy of vinyl fluoride (C 2H 3F): The vibrational fine structure and its analysis

    NASA Astrophysics Data System (ADS)

    Locht, R.; Leyh, B.; Dehareng, D.; Jochims, H. W.; Baumgärtel, H.

    2009-08-01

    The vacuum UV photoabsorption spectrum of C 2H 3F has been examined in detail between 6 eV and 25 eV photon energy by using synchrotron radiation. The analysis of the data is supported by ab initio quantum mechanical calculations applied to valence and Rydberg excited states of C 2H 3F. At 7.6 eV the π → π ∗ and the 2a″ → 3s transitions are observed. An analysis is proposed and applied to the mixed fine structure belonging to these transitions. For the π → π ∗ transition one single long vibrational progression is observed with hcω e = 95 ± 7 meV (766 ± 56 cm -1) and its adiabatic excitation energy is 6.892 eV (55 588 cm -1). The 2a″ → 3s transition is characterized by a single short progression with hcω e = 167 ± 10 meV (1350 ± 80 cm -1) starting at 6.974 eV (56 249 cm -1). From the present ab initio calculations these two wavenumbers best correspond to the vibrational modes v9 (CH 2 rock in-plane, FCC-bend) and v6 (CH 2 rock in-plane, CF stretch) calculated at 615 cm -1 in the π ∗ state and 1315 cm -1 in the ( 2A″)3s Rydberg state respectively. The C dbnd C stretching could not be excluded. The dense structured spectrum observed between 8.0 eV and 10.5 eV has been analyzed in terms of vibronic transitions to Rydberg states all converging to the CHF(X˜A) ionic ground state. An analysis of the associated complex fine structure of the individual Rydberg states has been attempted providing average values of the wavenumbers, e.g., for the ( 2A″)3p Rydberg state hcω9 = 60 ± 1 meV (or 484 ± 8 cm -1), hcω7 = 151 ± 7 meV (or 1218 ± 60 cm -1), hcω4 = 191 ± 3 meV (or 1540 ± 24 cm -1). The assignment of hcω = 105 ± 5 meV (or 823 ± 40 cm -1) is discussed. These experimental values are in good agreement with the theoretical predictions for C 2H 3F + [R. Locht, B. Leyh, D. Dehareng, K. Hottmann, H. Baumgärtel, Chem. Phys. (in press)]. Above 10.5 eV and up to 25 eV several broad and strong bands are tentatively assigned to

  19. Fundamental and overtone vibrational spectroscopy, enthalpy of hydrogen bond formation and equilibrium constant determination of the methanol-dimethylamine complex.

    PubMed

    Du, Lin; Mackeprang, Kasper; Kjaergaard, Henrik G

    2013-07-01

    We have measured gas phase vibrational spectra of the bimolecular complex formed between methanol (MeOH) and dimethylamine (DMA) up to about 9800 cm(-1). In addition to the strong fundamental OH-stretching transition we have also detected the weak second overtone NH-stretching transition. The spectra of the complex are obtained by spectral subtraction of the monomer spectra from spectra recorded for the mixture. For comparison, we also measured the fundamental OH-stretching transition in the bimolecular complex between MeOH and trimethylamine (TMA). The enthalpies of hydrogen bond formation (ΔH) for the MeOH-DMA and MeOH-TMA complexes have been determined by measurements of the fundamental OH-stretching transition in the temperature range from 298 to 358 K. The enthalpy of formation is found to be -35.8 ± 3.9 and -38.2 ± 3.3 kJ mol(-1) for MeOH-DMA and MeOH-TMA, respectively, in the 298 to 358 K region. The equilibrium constant (Kp) for the formation of the MeOH-DMA complex has been determined from the measured and calculated transition intensities of the OH-stretching fundamental transition and the NH-stretching second overtone transition. The transition intensities were calculated using an anharmonic oscillator local mode model with dipole moment and potential energy curves calculated using explicitly correlated coupled cluster methods. The equilibrium constant for formation of the MeOH-DMA complex was determined to be 0.2 ± 0.1 atm(-1), corresponding to a ΔG value of about 4.0 kJ mol(-1).

  20. Ultrafast vibrational dynamics of the DNA backbone at different hydration levels mapped by two-dimensional infrared spectroscopy

    PubMed Central

    Guchhait, Biswajit; Liu, Yingliang; Siebert, Torsten; Elsaesser, Thomas

    2015-01-01

    DNA oligomers are studied at 0% and 92% relative humidity, corresponding to N < 2 and N > 20 water molecules per base pair. Two-dimensional (2D) infrared spectroscopy of DNA backbone modes between 920 and 1120 cm−1 maps fluctuating interactions at the DNA surface. At both hydration levels, a frequency fluctuation correlation function with a 300 fs decay and a slow decay beyond 10 ps is derived from the 2D lineshapes. The fast component reflects motions of DNA helix, counterions, and water shell. Its higher amplitude at high hydration level reveals a significant contribution of water to the fluctuating forces. The slow component reflects disorder-induced inhomogeneous broadening. PMID:26798841