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Sample records for biomedical vibrational spectroscopy

  1. 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.

  2. Raman spectroscopy of biomedical polyethylenes.

    PubMed

    Pezzotti, Giuseppe

    2017-03-27

    With the development of three-dimensional Raman algorithms for local mapping of oxidation and plastic strain, and the ability to resolve molecular orientation patterns with microscopic spatial resolution, there is an opportunity to re-examine many of the foundations on which our understanding of biomedical grade ultra-high molecular weight polyethylenes (UHMWPEs) are based. By implementing polarized Raman spectroscopy into an automatized tool with an improved precision in non-destructively resolving Euler angles, oxidation levels, and microscopic strain, we become capable to make accurate and traceable measurements of the in vitro and in vivo tribological responses of a variety of commercially available UHMWPE bearings for artificial hip and knee joints. In this paper, we first review the foundations and the main algorithms for Raman analyses of oxidation and strain of biomedical polyethylene. Then, we critically re-examine a large body of Raman data previously collected on different polyethylene joint components after in vitro testing or in vivo service, in order to shed new light on an area of particular importance to joint orthopedics: the microscopic nature of UHMWPE surface degradation in the human body. A complex scenario of physical chemistry appears from the Raman analyses, which highlights the importance of molecular-scale phenomena besides mere microstructural changes. The availability of the Raman microscopic probe for visualizing oxidation patterns unveiled striking findings related to the chemical contribution to wear degradation: chain-breaking and subsequent formation of carboxylic acid sites preferentially occur in correspondence of third-phase regions, and they are triggered by emission of dehydroxylated oxygen from ceramic oxide counterparts. These findings profoundly differ from more popular (and simplistic) notions of mechanistic tribology adopted in analyzing joint simulator data.

  3. Vibrational Spectroscopy of Ionic Liquids.

    PubMed

    Paschoal, Vitor H; Faria, Luiz F O; Ribeiro, Mauro C C

    2017-01-04

    Vibrational spectroscopy has continued use as a powerful tool to characterize ionic liquids since the literature on room temperature molten salts experienced the rapid increase in number of publications in the 1990's. In the past years, infrared (IR) and Raman spectroscopies have provided insights on ionic interactions and the resulting liquid structure in ionic liquids. A large body of information is now available concerning vibrational spectra of ionic liquids made of many different combinations of anions and cations, but reviews on this literature are scarce. This review is an attempt at filling this gap. Some basic care needed while recording IR or Raman spectra of ionic liquids is explained. We have reviewed the conceptual basis of theoretical frameworks which have been used to interpret vibrational spectra of ionic liquids, helping the reader to distinguish the scope of application of different methods of calculation. Vibrational frequencies observed in IR and Raman spectra of ionic liquids based on different anions and cations are discussed and eventual disagreements between different sources are critically reviewed. The aim is that the reader can use this information while assigning vibrational spectra of an ionic liquid containing another particular combination of anions and cations. Different applications of IR and Raman spectroscopies are given for both pure ionic liquids and solutions. Further issues addressed in this review are the intermolecular vibrations that are more directly probed by the low-frequency range of IR and Raman spectra and the applications of vibrational spectroscopy in studying phase transitions of ionic liquids.

  4. 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.

  5. Time-resolved vibrational spectroscopy

    SciTech Connect

    Tokmakoff, Andrei; Champion, Paul; Heilweil, Edwin J.; Nelson, Keith A.; Ziegler, Larry

    2009-05-14

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

  6. Vibrational Spectroscopy and Quantum Localization

    NASA Astrophysics Data System (ADS)

    Fillaux, François

    These lecture-notes are meant to provide newcomers with an overview of the impact of vibrational spectroscopy in the field of nonlinear dynamics of atoms and molecules, in the perspective of energy localization. In the introduction, the terminology of nonlinear excitations and tentative experimental evidences are briefly recalled in a brief historical perspective. The basic principles of vibrational spectroscopy are presented in section 11 for infrared, Raman and inelastic neutron scattering. The potentialities for each technique to probing energy localization are discussed. In section 12, nonlinear dynamics in isolated molecules are treated within the framework of normal versus local mode representations. It is shown that these complementary representations are not necessarily distinctive of weak versus strong anharmonicity, in the context of chemical complexity. It is emphasized that local modes and energy localization are totally independent concepts. In section 4, examples of nonlinear dynamics in crystals are reviewed: multiphonon bound states, strong coupling between phonons and electrons probed with resonance Raman, local modes and quantum rotation in one-dimension probed with inelastic neutron scattering, strong coupling in hydrogen-bonded crystals and self-trapping probed with time-resolved vibrational-spectroscopy. The extended character of eigenstates in crystals free of impurities and disorder, the nature of the interaction of periodic lattices with plane waves, the Franck-Condon principle and the particle-wave duality in the quantum regime are key factors preventing observation of energy localization. It is shown that free spatially-localized nondissipative classical waves give rise to free pseudoparticles that behave as planar waves in the quantum regime. In conclusion, a clear demonstration that energy localization corresponds to eigenstates is eagerly expected for further evidencing these states with vibrational spectroscopy.

  7. 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.

  8. 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...

  9. 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).

  10. Vibrational spectroscopy of water interfaces

    SciTech Connect

    Du, Quan

    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.

  11. Surface-Enhanced Impulsive Coherent Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Du, Juan; Harra, Juha; Virkki, Matti; Mäkelä, Jyrki M.; Leng, Yuxin; Kauranen, Martti; Kobayashi, Takayoshi

    2016-11-01

    Surface-enhanced Raman spectroscopy (SERS) has attracted a lot of attention in molecular sensing because of the remarkable ability of plasmonic metal nanostructures to enhance the weak Raman scattering process. On the other hand, coherent vibrational spectroscopy triggered by impulsive excitation using ultrafast laser pulses provides complete information about the temporal evolution of molecular vibrations, allowing dynamical processes in molecular systems to be followed in “real time”. Here, we combine these two concepts and demonstrate surface-enhanced impulsive vibrational spectroscopy. The vibrational modes of the ground and excited states of poly[2-methoxy-5-(2-ethylhexyloxy)‑1,4-phenylenevinylene] (MEH-PPV), spin-coated on a substrate covered with monodisperse silver nanoparticles, are impulsively excited with a sub-10 fs pump pulse and characterized with a delayed broad-band probe pulse. The maximum enhancement in the spectrally and temporally resolved vibrational signatures averaged over the whole sample is about 4.6, while the real-time information about the instantaneous vibrational amplitude together with the initial vibrational phase is preserved. The phase is essential to determine the vibrational contributions from the ground and excited states.

  12. Surface-Enhanced Impulsive Coherent Vibrational Spectroscopy

    PubMed Central

    Du, Juan; Harra, Juha; Virkki, Matti; Mäkelä, Jyrki M.; Leng, Yuxin; Kauranen, Martti; Kobayashi, Takayoshi

    2016-01-01

    Surface-enhanced Raman spectroscopy (SERS) has attracted a lot of attention in molecular sensing because of the remarkable ability of plasmonic metal nanostructures to enhance the weak Raman scattering process. On the other hand, coherent vibrational spectroscopy triggered by impulsive excitation using ultrafast laser pulses provides complete information about the temporal evolution of molecular vibrations, allowing dynamical processes in molecular systems to be followed in “real time”. Here, we combine these two concepts and demonstrate surface-enhanced impulsive vibrational spectroscopy. The vibrational modes of the ground and excited states of poly[2-methoxy-5-(2-ethylhexyloxy)−1,4-phenylenevinylene] (MEH-PPV), spin-coated on a substrate covered with monodisperse silver nanoparticles, are impulsively excited with a sub-10 fs pump pulse and characterized with a delayed broad-band probe pulse. The maximum enhancement in the spectrally and temporally resolved vibrational signatures averaged over the whole sample is about 4.6, while the real-time information about the instantaneous vibrational amplitude together with the initial vibrational phase is preserved. The phase is essential to determine the vibrational contributions from the ground and excited states. PMID:27812020

  13. 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.

  14. 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

  15. Terahertz pulsed imaging and spectroscopy for biomedical and pharmaceutical applications.

    PubMed

    Wallace, Vincent P; Taday, Philip F; Fitzgerald, Anthony J; Woodward, Ruth M; Cluff, Julian; Pye, Richard J; Arnone, Donald D

    2004-01-01

    Terahertz (THz) radiation lies between the infrared and microwave regions of the electromagnetic spectrum. Advances in THz technology have opened up many opportunities in this scientifically and technologically important spectroscopic region. The THz frequency range excites large amplitude vibrational modes of molecules as well as probing the weak interactions between them. Here we describe two techniques that utilize THz radiation, terahertz pulsed imaging (TPI) and terahertz pulsed spectroscopy (TPS). Both have a variety of possible applications in biomedical imaging and pharmaceutical science. TPI, a non-invasive imaging technique, has been used to image epithelial cancer ex vivo and recently in vivo. The diseased tissue showed a change in absorption compared to normal tissue, which was confirmed by histology. To understand the origins of the differences seen between diseased and normal tissue we have developed a TPS system. TPS has also been used to study solids of interest in the pharmaceutical industry. One particularly interesting example is ranitidine hydrochloride, which is used in treatment of stomach ulcers. Crystalline ranitidine has two polymorphic forms known as form 1 and form 2. These polymorphs have the same chemical formula but different crystalline structure that give rise to different physiochemical properties of the material. Using TPS it is possible to rapidly distinguish between the two polymorphic forms.

  16. 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.

  17. 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.

  18. 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.

  19. Anharmonic Vibrational Spectroscopy on Metal Transition Complexes

    NASA Astrophysics Data System (ADS)

    Latouche, Camille; Bloino, Julien; Barone, Vincenzo

    2014-06-01

    Advances in hardware performance and the availability of efficient and reliable computational models have made possible the application of computational spectroscopy to ever larger molecular systems. The systematic interpretation of experimental data and the full characterization of complex molecules can then be facilitated. Focusing on vibrational spectroscopy, several approaches have been proposed to simulate spectra beyond the double harmonic approximation, so that more details become available. However, a routine use of such tools requires the preliminary definition of a valid protocol with the most appropriate combination of electronic structure and nuclear calculation models. Several benchmark of anharmonic calculations frequency have been realized on organic molecules. Nevertheless, benchmarks of organometallics or inorganic metal complexes at this level are strongly lacking despite the interest of these systems due to their strong emission and vibrational properties. Herein we report the benchmark study realized with anharmonic calculations on simple metal complexes, along with some pilot applications on systems of direct technological or biological interest.

  20. Ultrafast time-resolved vibrational spectroscopies of carotenoids in photosynthesis.

    PubMed

    Hashimoto, Hideki; Sugisaki, Mitsuru; Yoshizawa, Masayuki

    2015-01-01

    This review discusses the application of time-resolved vibrational spectroscopies to the studies of carotenoids in photosynthesis. The focus is on the ultrafast time regime and the study of photophysics and photochemistry of carotenoids by femtosecond time-resolved stimulated Raman and four-wave mixing spectroscopies. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.

  1. 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.

  2. 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.

  3. The many facets of Raman spectroscopy for biomedical analysis.

    PubMed

    Krafft, Christoph; Popp, Jürgen

    2015-01-01

    A critical review is presented on the use of linear and nonlinear Raman microspectroscopy in biomedical diagnostics of bacteria, cells, and tissues. This contribution is combined with an overview of the achievements of our research group. Linear Raman spectroscopy offers a wealth of chemical and molecular information. Its routine clinical application poses a challenge due to relatively weak signal intensities and confounding overlapping effects. Nonlinear variants of Raman spectroscopy such as coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS) have been recognized as tools for rapid image acquisition. Imaging applications benefit from the fact that contrast is based on the chemical composition and molecular structures in a label-free and nondestructive manner. Although not label-free, surface enhanced Raman scattering (SERS) has also been recognized as a complementary biomedical tool to increase sensitivity. The current state of the art is evaluated, illustrative examples are given, future developments are pointed out, and important reviews and references from the current literature are selected. The topics are identification of bacteria and single cells, imaging of single cells, Raman activated cell sorting, diagnosis of tissue sections, fiber optic Raman spectroscopy, and progress in coherent Raman scattering in tissue diagnosis. The roles of networks-such as Raman4clinics and CLIRSPEC on a European level-and early adopters in the translation, dissemination, and validation of new methods are discussed.

  4. Mössbauer spectroscopy in biomedical physics research

    NASA Astrophysics Data System (ADS)

    Zhang, Xiufang

    1994-12-01

    Several applications of Mössbauer spectroscopy (MS) as an analytical tool in research on biomedical physics are reviewed: (1) The evaluation of treatments for some diseases such as thalassemia, iron-overload disease, high altitude polycythemia. (2) Medical research on the effects of environmental factors on the human body, for example, the effects of electromagnetic radiation on human red blood cells (RBCs). Some advantages and weaknesses of MS, a new application of the Mössbauer effect, cancer therapy, and some possible applications such as monitoring the RBCs of the patients before, during, and after surgical operation, are discussed.

  5. 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.

  6. 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

  7. 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

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

    PubMed

    Mantsch, Henry H

    2013-07-21

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

  9. 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.

  10. 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.

  11. Broadband nonlinear vibrational spectroscopy by shaping a coherent fiber supercontinuum

    PubMed Central

    Liu, Yuan; King, Matthew D.; Tu, Haohua; Zhao, Youbo; Boppart, Stephen A.

    2013-01-01

    Vibrational spectroscopy has been widely applied in different fields due to its label-free chemical-sensing capability. Coherent anti-Stokes Raman scattering (CARS) provides stronger signal and faster acquisition than spontaneous Raman scattering, making it especially suitable for molecular imaging. Coherently-controlled single-beam CARS simplifies the conventional multi-beam setup, but the vibrational bandwidth and non-trivial spectrum retrieval have been limiting factors. In this work, a coherent supercontinuum generated in an all-normal-dispersion nonlinear fiber is phase-shaped within a narrow bandwidth for broadband vibrational spectroscopy. The Raman spectra can be directly retrieved from the CARS measurements, covering the fingerprint regime up to 1750 cm−1. The retrieved spectra of several chemical species agree with their spontaneous Raman data. The compact fiber supercontinuum source offers broad vibrational bandwidth with high stability and sufficient power, showing the potential for spectroscopic imaging in a wide range of applications. PMID:23571917

  12. 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.

  13. 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.

  14. 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.

  15. 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.; ...

    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

  16. 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.

  17. 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

    2015-05-07

    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.

  18. 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

  19. Nonlinear Vibrational Spectroscopy: a Method to Study Vibrational Self-Trapping

    NASA Astrophysics Data System (ADS)

    Hamm, Peter; Edler, Julian

    We review the capability of nonlinear vibrational spectroscopy to study vibrational self-trapping in hydrogen-bonded molecular crystals. For that purpose, the two relevant coupling mechanisms, excitonic coupling and nonlinear exciton-phonon coupling, are first introduced separately using appropriately chosen molecular systems as examples. Both coupling mechanisms are subsequently combined, yielding vibrational selftrapping. The experiments unambiguously prove that both the N-H and the C=O band of crystalline acetanilide (ACN), a model system for proteins, show vibrational self-trapping. The C=O band is self-trapped only at low enough temperature, while thermally induced disorder destroys the mechanism at room temperature. The binding energy of the N-H band, on the other hand, is considerably larger and self-trapping survives thermal fluctuations even at room temperature.

  20. Thermal degradation of polyketones. Vibrational spectroscopy studies

    NASA Astrophysics Data System (ADS)

    Conti, G.; Sommazzi, A.

    1993-03-01

    Thermal degradation studies of regular alternating polymers of carbon monoxide and olefin have been followed by FT-IR spectroscopy. The I.R spectra of solid samples, performed in inert atmosphere and in high vacuum, were recorded as a function of time at different temperatures. From the I.R. data it is possible to conclude that the reaction process, near the melting point of the polymers, could consist of intra or intermolecular hydrogen transfer yielding an enol and a small quantity of insaturations. The thermal degradation process, at temperatures higher than melting point, involves the scission of the polymer chain and produces fragments with a large number of insaturations.

  1. Vibrational spectroscopy standoff detection of threat chemicals

    NASA Astrophysics Data System (ADS)

    Ortiz-Rivera, William; Pacheco-Londoño, Leonardo C.; Castro-Suarez, John R.; Felix-Rivera, Hilsamar; Hernandez-Rivera, Samuel P.

    2011-06-01

    Spectroscopy based standoff detection systems: Raman and FTIR have been tested for detection of threat chemicals, including highly energetic materials, homemade explosives, explosives formulations and high explosives mixtures. Other threat chemicals studied included toxic industrial compounds (TIC) and chemical agent simulants. Microorganisms and biological threat agent simulants have also been detected at standoff distances. Open Path FTIR has been used to detect vapors and chemicals deposited on metal surfaces at μg/cm2 levels at distances as far as 30 m in active mode and 60 m in passive mode. In the case of Raman telescope, standoff distances for acetonitrile and ammonium nitrate were 140 m.

  2. Vibrational spectroscopy standoff detection of explosives.

    PubMed

    Pacheco-Londoño, Leonardo C; Ortiz-Rivera, William; Primera-Pedrozo, Oliva M; Hernández-Rivera, Samuel P

    2009-09-01

    Standoff infrared and Raman spectroscopy (SIRS and SRS) detection systems were designed from commercial instrumentation and successfully tested in remote detection of high explosives (HE). The SIRS system was configured by coupling a Fourier-transform infrared interferometer to a gold mirror and detector. The SRS instrument was built by fiber coupling a spectrograph to a reflective telescope. HE samples were detected on stainless steel surfaces as thin films (2-30 microg/cm(2)) for SIRS experiments and as particles (3-85 mg) for SRS measurements. Nitroaromatic HEs: TNT, DNT, RDX, C4, and Semtex-H and TATP cyclic peroxide homemade explosive were used as targets. For the SIRS experiments, samples were placed at increasing distances and an infrared beam was reflected from the stainless steel surfaces coated with the target chemicals at an angle of approximately 180 degrees from surface normal. Stainless steel plates containing TNT and RDX were first characterized for coverage distribution and surface concentration by reflection-absorption infrared spectroscopy. Targets were then placed at the standoff distance and SIRS spectra were collected in active reflectance mode. Limits of detection (LOD) were determined for all distances measured for the target HE. LOD values of 18 and 20 microg/cm(2) were obtained for TNT and RDX, respectively, for the SIR longest standoff distance measured. For SRS experiments, as low as 3 mg of TNT and RDX were detected at 7 m source-target distance employing 488 and 514.5 nm excitation wavelengths. The first detection and quantification study of the important formulation C4 is reported. Detection limits as function of laser powers and acquisition times and at a standoff distance of 7 m were obtained.

  3. 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.

  4. Vibrational spectroscopy of microhydrated conjugate base anions.

    PubMed

    Asmis, Knut R; Neumark, Daniel M

    2012-01-17

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

  5. Proteins at interfaces probed by chiral vibrational sum frequency generation spectroscopy.

    PubMed

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

    2015-02-19

    Characterizations of protein structures at interfaces are important in solving an array of fundamental and engineering problems, including understanding transmembrane signal transduction and molecular transport processes and development of biomaterials to meet the needs of biomedical and energy research. However, in situ and real-time characterization of protein secondary structures is challenging because it requires physical methods that are selective to both interface and secondary structures. Here, we summarize recent experimental developments in our laboratory of chiral vibrational sum frequency generation spectroscopy (SFG) for analyzing protein structures at interfaces. We showed that chiral SFG provides vibrational optical signatures of the peptide N-H stretch and amide I modes that can distinguish various protein secondary structures. Using these signatures, we further applied chiral SFG to probe orientations and folding kinetics of proteins at interfaces. Our results show that chiral SFG is a background-free, label-free, in situ, and real-time vibrational method for studying proteins at interfaces. This recent progress demonstrates the potential of chiral SFG in solving problems related to proteins and other chiral biopolymers at interfaces.

  6. Detection of complex formation and determination of intermolecular geometry through electrical anharmonic coupling of molecular vibrations using electron-vibration-vibration two-dimensional infrared spectroscopy.

    PubMed

    Guo, Rui; Fournier, Frederic; Donaldson, Paul M; Gardner, Elizabeth M; Gould, Ian R; Klug, David R

    2009-10-14

    Electrical interactions between molecular vibrations can be non-linear and thereby produce intermolecular coupling even in the absence of a chemical bond. We use this fact to detect the formation of an intermolecular complex using electron-vibration-vibration two-dimensional infrared spectroscopy (EVV 2DIR) and also to determine the distance and angle between the two molecular species.

  7. 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

  8. Application of multivariate data-analysis techniques to biomedical diagnostics based on mid-infrared spectroscopy.

    PubMed

    Wang, Liqun; Mizaikoff, Boris

    2008-07-01

    The objective of this contribution is to review the application of advanced multivariate data-analysis techniques in the field of mid-infrared (MIR) spectroscopic biomedical diagnosis. MIR spectroscopy is a powerful chemical analysis tool for detecting biomedically relevant constituents such as DNA/RNA, proteins, carbohydrates, lipids, etc., and even diseases or disease progression that may induce changes in the chemical composition or structure of biological systems including cells, tissues, and bio-fluids. However, MIR spectra of multiple constituents are usually characterized by strongly overlapping spectral features reflecting the complexity of biological samples. Consequently, MIR spectra of biological samples are frequently difficult to interpret by simple data-analysis techniques. Hence, with increasing complexity of the sample matrix more sophisticated mathematical and statistical data analysis routines are required for deconvoluting spectroscopic data and for providing useful results from information-rich spectroscopic signals. A large body of work relates to the combination of multivariate data-analysis techniques with MIR spectroscopy, and has been applied by a variety of research groups to biomedically relevant areas such as cancer detection and analysis, artery diseases, biomarkers, and other pathologies. The reported results indeed reveal a promising perspective for more widespread application of multivariate data analysis in assisting MIR spectroscopy as a screening or diagnostic tool in biomedical research and clinical studies. While the authors do not mean to ignore any relevant contributions to biomedical analysis across the entire electromagnetic spectrum, they confine the discussion in this contribution to the mid-infrared spectral range as a potentially very useful, yet underutilized frequency region. Selected representative examples without claiming completeness will demonstrate a range of biomedical diagnostic applications with particular

  9. 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

  10. Multinuclear Magnetic Resonance Imaging and NMR Spectroscopy in Biomedical Investigations

    NASA Astrophysics Data System (ADS)

    Pirogov, Yury A.

    Biomedical investigations with small animals using 0.5-T and 7-T MRI scanners adjusted on the Larmor frequencies of different nuclei 1H, 2H, 11B, 13C, 19F, 23Na, 31P, 35Cl are described. Experiments on registration of signals 19F from the fluorocarbons injected in laboratory animals are discussed. They give presentation on the application of fluorocarbon compounds as blood substitutes and contrasting preparations in MRI diagnostics. A blood substitute product fluorocarbon Perfluoranum® has shown effectiveness in oxygen delivery to the tissues of living organisms, and cardioprotective effect which does not depend on the patient's blood group. Inclusion of paramagnetic atoms (gadolinium, iron, etc.) to the Perfluoranum® chemical formula creates a new compounds with high MRI contrast efficiencies at Larmor frequencies of protons so and fluorine-19 nuclei.

  11. Surface sum-frequency vibrational spectroscopy of nonpolar media

    SciTech Connect

    Sun, Shumei; Tian, Chuanshan; Shen, Y. Ron

    2015-04-27

    Sum-frequency generation spectroscopy is surface specific only if the bulk contribution to the signal is negligible. Negligible bulk contribution is, however, not necessarily true, even for media with inversion symmetry. The inevitable challenge is to find the surface spectrum in the presence of bulk contribution, part of which has been believed to be inseparable from the surface contribution. Here, we show that, for nonpolar media, it is possible to separately deduce surface and bulk spectra from combined phase-sensitive sum-frequency vibrational spectroscopic measurements in reflection and transmission. Finally, the study of benzene interfaces is presented as an example.

  12. Vibrational spectroscopy of cinnamaldehyde on graphite and supported Pd islands

    NASA Astrophysics Data System (ADS)

    Grimaud, C.-M.; Radosavkic, D.; Ustaze, S.; Palmer, R. E.

    2001-07-01

    We report the first experimental study of the adsorption of cinnamaldehyde on surfaces under ultra high vacuum (UHV) conditions. Cinnamaldehyde is an α,β-unsaturated aldehyde with important applications in the fine chemicals sector. High-resolution electron energy loss spectroscopy (HREELS) is employed to investigate the vibrational modes of cinnamaldehyde condensed on graphite at 100 K and absorbed on the surface of a Pd islands film (supported on graphite), also at 100 K. In the case of the Pd film, we find strong evidence for a parallel orientation of the phenyl ring consistent with theoretical calculations.

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

    PubMed

    Hiramatsu, Hirotsugu

    2014-01-01

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

  14. 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.

  15. 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.

  16. Exploiting the diagnostic potential of biomolecular fingerprinting with vibrational spectroscopy.

    PubMed

    Kendall, Catherine; Hutchings, Joanne; Barr, Hugh; Shepherd, Neil; Stone, Nicholas

    2011-01-01

    There is immense clinical need for techniques that can detect the biochemical changes associated with pre-malignancy. The ideal diagnostic test would provide rapid, non-invasive diagnosis at the point of care with high throughput and without prior tissue processing. Over the past decade vibrational spectroscopy techniques have demonstrated their ability to provide non-destructive, rapid, clinically relevant diagnostic information. Biochemical fingerprints of tissues measured using Raman and infrared spectroscopy analysed in conjunction with advanced chemometrics have shown great potential in the diagnostic assessment of biological material. Development of Raman probes is enabling the potential of in vivo clinical measurements to be realised. A novel probe design has been evaluated in clinical studies to identify and classify the subtle pre-malignant biochemical changes related to the carcinogenesis process. Exciting recent developments have enabled the probing of tissue samples at depth with huge potential for breast and prostate cancer diagnostics. Furthermore, the potential of vibrational spectroscopy to provide prognostic information is tantalising. Raman spectral data acquired on oesophageal biopsy samples analysed in conjunction with patient outcome data has shown the power of spectral biomolecular fingerprinting in predicting the outcome of patients with high-grade dysplasia in Barrett's oesophagus. Raman mapping can also be used to analyse thin tissue sections on calcium fluoride slides enabling the distribution of tissue constituents to be realised. The spectral data acquired effectively enables multiplexing of digital tissue stains since a whole array of information is gathered simultaneously. Technological developments are bringing the technologies closer to the clinical reality of spectral pathology and high-throughput non-destructive measurement with high resolution.

  17. Isotopic hydration of cellobiose: vibrational spectroscopy and dynamical simulations.

    PubMed

    Pincu, Madeleine; Cocinero, Emilio J; Mayorkas, Nitzan; Brauer, Brina; Davis, Benjamin G; Gerber, R Benny; Simons, John P

    2011-09-01

    The conformation and structural dynamics of cellobiose, one of the fundamental building blocks in nature, its C4' epimer, lactose, and their microhydrated complexes, isolated in the gas phase, have been explored through a combination of experiment and theory. Their structures at low temperature have been determined through double resonance, IR-UV vibrational spectroscopy conducted under molecular beam conditions, substituting D(2)O for H(2)O to separate isotopically, the carbohydrate (OH) bands from the hydration (OD) bands. Car-Parrinello (CP2K) simulations, employing dispersion corrected density functional potentials and conducted "on-the-fly" from ∼20 to ∼300 K, have been used to explore the consequences of raising the temperature. Comparisons between the experimental data, anharmonic vibrational self-consistent field calculations based upon ab initio potentials, and the CP2K simulations have established the role of anharmonicity; the reliability of classical molecular dynamics predictions of the vibrational spectra of carbohydrates and the accuracy of the dispersion corrected (BLYP-D) force fields employed; the structural consequences of increasing hydration; and the dynamical consequences of increasing temperature. The isolated and hydrated cellobiose and lactose units both present remarkably rigid structures: their glycosidic linkages adopt a "cis" (anti-ϕ and syn-ψ) conformation bound by inter-ring hydrogen bonds. This conformation is maintained when the temperature is increased to ∼300 K and it continues to be maintained when the cellobiose (or lactose) unit is hydrated by one or two explicitly bound water molecules. Despite individual fluctuations in the intra- and intermolecular hydrogen bonding pattern and some local structural motions, the water molecules remain locally bound and the isolated carbohydrates remain trapped within the cis potential well. The Car-Parrinello dynamical simulations do not suggest any accessible pathway to the trans

  18. Discovery of Cellulose Surface Layer Conformation by Nonlinear Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Libing; Fu, Li; Wang, Hong-Fei; Yang, Bin

    2017-03-01

    Significant questions remain in respect to cellulose’s structure and polymorphs, particularly the cellulose surface layers and the bulk crystalline core as well as the conformational differences. Total Internal Reflection Sum Frequency Generation Vibrational Spectroscopy (TIR-SFG-VS) combined with conventional SFG-VS (non-TIR) enables selectively characterizing the molecular structures of surface layers and the crystalline core of cellulose, revealing their differences for the first time. From the SFG spectra in the C-H and O-H regions, we found that the surface layers of Avicel are essentially amorphous while the surface layers of Iβ cellulose are crystalline but with different structural and spectroscopic signatures compared with its crystalline core. The differences between hydrogen bonding networks of cellulose surface and crystalline core were also shown by the SFG signal. The discovery here represents yet another instance of the importance of spectroscopic observations in transformative advances to understand the structure of the cellulosic biomass.

  19. Cross-Propagation Sum-Frequency Generation Vibrational Spectroscopy

    SciTech Connect

    Fu, Li; Chen, Shun-li; Gan, Wei; Wang, Hong-fei

    2016-02-27

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

  20. 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

  1. Discovery of Cellulose Surface Layer Conformation by Nonlinear Vibrational Spectroscopy

    PubMed Central

    Zhang, Libing; Fu, Li; Wang, Hong-fei; Yang, Bin

    2017-01-01

    Significant questions remain in respect to cellulose’s structure and polymorphs, particularly the cellulose surface layers and the bulk crystalline core as well as the conformational differences. Total Internal Reflection Sum Frequency Generation Vibrational Spectroscopy (TIR-SFG-VS) combined with conventional SFG-VS (non-TIR) enables selectively characterizing the molecular structures of surface layers and the crystalline core of cellulose, revealing their differences for the first time. From the SFG spectra in the C-H and O-H regions, we found that the surface layers of Avicel are essentially amorphous while the surface layers of Iβ cellulose are crystalline but with different structural and spectroscopic signatures compared with its crystalline core. The differences between hydrogen bonding networks of cellulose surface and crystalline core were also shown by the SFG signal. The discovery here represents yet another instance of the importance of spectroscopic observations in transformative advances to understand the structure of the cellulosic biomass. PMID:28290542

  2. 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.

  3. 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.

  4. 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

  5. Theoretical Study of the Vibrational Spectroscopy of the Ethyl Radical

    NASA Astrophysics Data System (ADS)

    Tabor, Daniel P.; Sibert, Edwin. L. Sibert, Iii

    2013-06-01

    The rich spectroscopy of the ethyl radical has attracted the attention of several experimental and theoretical investigations. The purpose of these studies was to elucidate the signatures of hyperconjugation, torsion, inversion, and Fermi coupling in the molecular spectra. Due to the number of degrees of freedom in the system, previous theoretical studies have implemented reduced-dimensional models. Our ultimate goal is a full-dimensional theoretical treatment of the vibrations using both Van Vleck and variational approaches. The methods will be combined with the potential that we have calculated using the CCSD(T) method on the cc-pVTZ basis set. In this talk we will discuss our initial work, which builds up from these reduced-dimensional models. Our calculations use coordinates that exploit the system's G_{12} PI symmetry in a simple fashion. By systematically adding more degrees of freedom to our model, we can determine the effects of specific couplings on the spectroscopy. T. Häber, A. C. Blair, D. J. Nesbitt and M. D. Schuder J. Chem. Phys. {124}, 054316, (2006). G .E. Douberly, unpublished. R. S. Bhatta, A. Gao and D. S. Perry J. Mol. Struct.: THEOCHEM {941}, 22, (2010).

  6. 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.

  7. 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

  8. 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

  9. Characterizing Anharmonic Vibrational Modes of Quinones with Two-Dimensional Infrared Spectroscopy.

    PubMed

    Cyran, Jenée D; Nite, Jacob M; Krummel, Amber T

    2015-07-23

    Two-dimensional infrared (2D IR) spectroscopy was used to study the vibrational modes of three quinones--benzoquinone, naphthoquinone, and anthraquinone. The vibrations of interest were in the spectral range of 1560-1710 cm(-1), corresponding to the in-plane carbonyl and ring stretching vibrations. Coupling between the vibrational modes is indicated by the cross peaks in the 2D IR spectra. The diagonal and off-diagonal anharmonicities range from 4.6 to 17.4 cm(-1) for the quinone series. In addition, there is significant vibrational coupling between the in-plane carbonyl and ring stretching vibrations. The diagonal anharmonicity, off-diagonal anharmonicity, and vibrational coupling constants are reported for benzoquinone, naphthoquinone, and anthraquinone.

  10. Vibrationally-resolved polyatomic photoelectron spectroscopy: Mode-specific behavior

    NASA Astrophysics Data System (ADS)

    Rathbone, G. J.; Poliakoff, E. D.; Bozek, J. D.; Lucchese, R. R.

    2002-05-01

    We report the first vibrationally-resolved photoelectron spectra for polyatomic molecules performed over a broad spectral range. Such studies elucidate vibrationally mode-specific aspects of the photoelectron scattering dynamics. Three linear triatomic systems (CO_2, N_2O, and CS_2) are studied, and the results exhibit striking differences for alternative modes. For CO_2^+(C^2Σ_g^+), a continuum resonance results in a 15 eV wide dip for the symmetric stretch branching ratio, while strong peaks are observed for vibrational branching ratios associated with the two symmetry forbidden modes. For CS_2^+(B^2Σ_u^+), mode-specific behavior is displayed, as resonance enhancement of a single quantum excitation is weak for the symmetric stretch, but strong for the bending vibration. For N_2O^+(A^2Σ^+), many vibrational excitations are observed and families of vibrational branching ratio spectra emerge.

  11. Vibrational predissociation spectroscopy of Ar-tagged, trisubstituted silyl cations

    NASA Astrophysics Data System (ADS)

    DeBlase, Andrew F.; Scerba, Michael T.; Lectka, Thomas; Johnson, Mark A.

    2013-05-01

    Vibrational predissociation spectra of the (CH3)2RSi+·Arn, (R = H and CH3, n = 1 and 2) ions are compared with harmonic calculations to structurally characterize these putative reactive intermediates. Although the vibrational photofragmentation behavior indicates that the Ar-Si bond is quite strong relative to that found in closed shell ions, formation of the Ar adducts is calculated to cause only minor perturbations to the intrinsic vibrational band patterns of the isolated ions. In both (R = H and CH3) cases, the vibrational spectra are very simple, consisting entirely of sharp features readily assigned to fundamentals anticipated by their harmonic spectra.

  12. 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.

  13. Observation of the Interference Effect in Vibrationally Resolved Electron Momentum Spectroscopy of H2

    NASA Astrophysics Data System (ADS)

    Zhang, Zhe; Shan, Xu; Wang, Tian; Wang, Enliang; Chen, Xiangjun

    2014-01-01

    We report the first measurement on vibrationally resolved electron momentum spectroscopy of H2 by using a high-resolution (e, 2e) spectrometer. The vibrational-specific experimental momentum profiles have been obtained and shown to be in agreement with calculations of (e, 2e) ionization cross sections taking into account the vibrational wave functions. Distinct deviations from Franck-Condon predictions have been observed in vibrational ratios of cross sections, which can readily be ascribed to the Young-type two-center interference. Unlike previous (e, 2e) work, the present observation of an interference effect does not rely on the comparison with the one-center atomic cross section.

  14. Vibrational self-consistent field calculations for spectroscopy of biological molecules: new algorithmic developments and applications.

    PubMed

    Roy, Tapta Kanchan; Gerber, R Benny

    2013-06-28

    This review describes the vibrational self-consistent field (VSCF) method and its other variants for computing anharmonic vibrational spectroscopy of biological molecules. The superiority and limitations of this algorithm are discussed with examples. The spectroscopic accuracy of the VSCF method is compared with experimental results and other available state-of-the-art algorithms for various biologically important systems. For large biological molecules with many vibrational modes, the scaling of computational effort is investigated. The accuracy of the vibrational spectra of biological molecules using the VSCF approach for different electronic structure methods is also assessed. Finally, a few open problems and challenges in this field are discussed.

  15. 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.

  16. Application of THz Vibrational Spectroscopy to Molecular Characterization and the Theoretical Fundamentals: An Illustration Using Saccharide Molecules.

    PubMed

    Zhang, Feng; Wang, Houng-Wei; Tominaga, Keisuke; Hayashi, Michitoshi; Hasunuma, Tomohisa; Kondo, Akihiko

    2017-02-01

    This work illustrates several theoretical fundamentals for the application of THz vibrational spectroscopy to molecular characterization in the solid state using two different types of saccharide systems as examples. Four subjects have been specifically addressed: (1) the qualitative differences in the molecular vibrational signatures monitored by THz and mid-IR vibrational spectroscopy; (2) the selection rules for THz vibrational spectroscopy as applied to crystalline and amorphous systems; (3) a normal mode simulation, using α-l-xylose as an example; and (4) a rigorous mode analysis to quantify the percentage contributions of the intermolecular and intramolecular vibrations to the normal mode of interest.

  17. A specially modified surface-enhanced Raman spectroscopy (SERS) substrate for biomedical applications

    NASA Astrophysics Data System (ADS)

    Yuen, Clement; Zheng, Wei; Huang, Zhiwei

    2008-02-01

    Hierarchically-ordered Au film-coated polystyrene beads have been well-known to be employed as surface enhanced Raman spectroscopy (SERS) substrate. In this study, we propose a novel and facile method to modify the performance of this SERS substrate and investigate the chemical components in saliva. Results have demonstrated that there is at least a 4-fold increase in SERS signals using the modified substrates compared to the non-modified substrates. Besides, the SERS performances of substrates modified by different preparation conditions are examined and compared. These findings show that our fabricated substrates are effective in further enhancing SERS signals and have potential for biomedical applications in trace analytes analysis.

  18. Intermolecular vibrations and vibrational dynamics of a phenol⋯methanol binary complex studied by LIF spectroscopy

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Deb Pratim; Biswas, Souvick; Chakraborty, Tapas

    2017-04-01

    Low-frequency intermolecular vibrations in S0 and S1 states of p-fluorophenol (pFP) methanol binary complex have been studied using laser induced fluorescence (LIF) spectroscopy in a supersonic jet expansion. Vibrational fundamentals of five such modes show up in fluorescence excitation (FE) spectrum, and corresponding ground state frequencies are obtained measuring disperse fluorescence (DF) spectra. Signatures of strong coupling between the hydrogen bond stretching fundamental (σ01) and a ring mode of pFP moiety in S1 state are revealed. In comparison with the analogous pFP-water complex, the present system displays very low threshold (∼170 cm-1) for vibrational energy relaxation in S1 state.

  19. 2012 Gordon Research Conference on Vibrational Spectroscopy - Formal Schedule and Speaker/Poster Program

    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.

  20. Study on pivot-point vibration of molecular bond-rupture events by quartz crystal microbalance for biomedical diagnostics.

    PubMed

    Yuan, Yong J; Jia, Renjie

    2012-01-01

    Bond-rupture scanning for biomedical diagnostics is examined using quartz crystal microbalance (QCM) experiments and microparticle mechanics modeling calculations. Specific and nonspecific interactions between a microparticle and its binding QCM surface can be distinguished by gradually increasing the amplitude of driving voltage applied to QCM and monitoring its frequency changes. This research proposes a mechanical model of interactions between biological molecules and a QCM substrate surface. The mechanical force required to break a biotin-streptavidin bond was calculated through a one-pivot-point bottom-up vibration model. The bond-rupture force increases with an increase of the microparticle radius, the QCM resonant frequency, and the amplitude of driving voltage applied to the QCM. The significance of the research on biological molecular bond rupture is extremely important in characterizing microbial (such as cells and virus) specificity, due to the force magnitude needed to break bonds using a transducer.

  1. 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.

  2. 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.

  3. Vibrational levels of p-xylene cation determined by mass-analyzed threshold ionization spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Bing; Aigner, Udo; Ludwig Selzle, Heinrich; William Schlag, Edward

    2003-10-01

    Mass-analyzed threshold ionization (MATI) spectroscopy and two-color resonant two-photon ionization method were used for the determination of the vibrational levels of the p-xylene cation. The MATI spectrum was recorded via the 0 0 vibrationless level of the S 1 state of p-xylene. The spectrum shows a rich structure and some vibrational frequencies of the cation are determined. The experimental findings are well supported by ab initio calculation.

  4. A practical guide for nuclear resonance vibrational spectroscopy (NRVS) of biochemical samples and model compounds.

    PubMed

    Wang, Hongxin; Alp, Esen Ercan; Yoda, Yoshitaka; Cramer, Stephen P

    2014-01-01

    Nuclear resonance vibrational spectroscopy (NRVS) has been used by physicists for many years. However, it is still a relatively new technique for bioinorganic users. This technique yields a vibrational spectrum for a specific element, which can be easily interpreted. Furthermore, isotopic labeling allows for site-specific experiments. In this chapter, we discuss how to access specific beamlines, what kind of equipment is used in NRVS, and how the sample should be prepared and the data collected and analyzed.

  5. 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.

  6. Vibrational energy dynamics of water studied with ultrafast Stokes and anti-Stokes Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Wang, Zhaohui; Pang, Yoonsoo; Dlott, Dana D.

    2004-10-01

    The transient Stokes Raman spectroscopy method is introduced to study the dynamics of OH-stretching vibrations in water excited by ultrashort infrared pulses. The combination of Stokes and anti-Stokes Raman probing allows the the absorption and emission contributions to be measured separately. Experiments with 3400 cm -1 pumping of OH-stretching of HOD solute in D 2O solvent are reported. The Stokes Raman method is used to study the delay between the excited-state decay and the ground-state recovery, the vibrational Stokes shift, and the generation of weakened hydrogen bonding due to heat released by vibrational relaxation.

  7. Surface Vibrational Spectroscopy on Shear-Aligned Poly(tetrafluoroethylene) Films

    NASA Astrophysics Data System (ADS)

    Ji, Na; Ostroverkhov, Victor; Lagugné-Labarthet, Francois; Shen, Y. R.

    2004-03-01

    Sum-frequency vibrational spectroscopy was used to obtain the first surface vibrational spectra of shear-deposited highly-oriented poly(tetrafluoroethylene) (PTFE) thin films. The analysis of spectra taken with different polarization combinations of the input and output beams allowed us to assess orientation of the polymer chains on the film surface. The surface PTFE chains appeared to lie along the shearing direction. Vibrational modes observed at 1142 and 1204 cm-1 were found to have the E1 symmetry, in support of some earlier analysis in the long-lasting controversy over the assignment of these modes.

  8. Theoretical and experimental vibrational spectroscopy study on rotational isomer of 4-phenylbutylamine

    NASA Astrophysics Data System (ADS)

    Ünal, A.; Okur, M.

    2017-02-01

    The possible four stable rotational isomers of 4-phenylbutylamine (4PBA) molecule were experimentally and theoretically studied by vibrational spectroscopy. The FT-IR (4000-400 cm-1) and Raman (3700-60 cm-1) spectra of 4PBA were recorded at room temperature in liquid phase. The complete vibrational wavenumbers and corresponding vibrational assignments of 4PBA molecule were discussed assisted with B3LYP/6-311++G(d,p) level of theory along with scaled quantum mechanics force field (SQM-FF) method. Results from experimental and theoretical data the most stable form of 4PBA molecule was obtained.

  9. Inversion vibration of PH3+(X~ 2A2'') studied by zero kinetic energy photoelectron spectroscopy

    NASA Astrophysics Data System (ADS)

    Yang, Jie; Li, Juan; Hao, Yusong; Zhou, Chang; Mo, Yuxiang

    2006-08-01

    We report the first rotationally resolved spectroscopic studies on PH3+(X˜A2″2) using zero kinetic energy photoelectron spectroscopy and coherent VUV radiation. The spectra about 8000cm-1 above the ground vibrational state of PH3+(X˜A2″2) have been recorded. We observed the vibrational energy level splittings of PH3+(X˜A2″2) due to the tunneling effect in the inversion (symmetric bending) vibration (ν2+). The energy splitting for the first inversion vibrational state (0+/0-) is 5.8cm-1. The inversion vibrational energy levels, rotational constants, and adiabatic ionization energies (IEs) for ν2+=0-16 have been determined. The bond angles between the neighboring P-H bonds and the P-H bond lengths are also obtained using the experimentally determined rotational constants. With the increasing of the inversion vibrational excitations (ν2+), the bond lengths (P-H) increase a little and the bond angles (H-P-H) decrease a lot. The inversion vibrational energy levels have also been calculated by using one dimensional potential model and the results are in good agreement with the experimental data for the first several vibrational levels. In addition to inversion vibration, we also observed firstly the other two vibrational modes: the symmetric P-H stretching vibration (ν1+) and the degenerate bending vibration (ν4+). The fundamental frequencies for ν1+ and ν4+ are 2461.6 (±2) and 1043.9 (±2)cm-1, respectively. The first IE for PH3 was determined as 79670.9 (±1)cm-1.

  10. Separation of overlapping vibrational peaks in terahertz spectra using two-dimensional correlation spectroscopy

    NASA Astrophysics Data System (ADS)

    Hoshina, Hiromichi; Ishii, Shinya; Otani, Chiko

    2014-07-01

    In this study, the terahertz (THz) absorption spectra of poly(3-hydroxybutyrate) (PHB) were measured during isothermal crystallization at 90-120 °C. The temporal changes in the absorption spectra were analyzed using two-dimensional correlation spectroscopy (2DCOS). In the asynchronous plot, cross peaks were observed around 2.4 THz, suggesting that two vibrational modes overlap in the raw spectrum. By comparing this to the peak at 2.9 THz corresponding to the stretching mode of the helical structure of PHB and the assignment obtained using polarization spectroscopy, we concluded that the high-frequency band could be attributed to the vibration of the helical structure and the low-frequency band to the vibration between the helical structures. The exact frequencies of the overlapping vibrational bands and their assignments provide a new means to inspect the thermal behavior of the intermolecular vibrational modes. The large red-shift of the interhelix vibrational mode suggests a large anharmonicity in the vibrational potential.

  11. Vibrational spectroscopy and the development of new force fields for biological molecules.

    PubMed

    Gerber, R B; Chaban, G M; Gregurick, S K; Brauer, B

    2003-03-01

    The role of vibrational spectroscopy in the testing of force fields of biological molecules and in the determination of improved force fields is discussed. Analysis shows that quantitative testing of potential energy surfaces by comparison with spectroscopic data generally requires calculations that include anharmonic couplings between different vibrational modes. Applications of the vibrational self-consistent field (VSCF) method to calculations of spectroscopy of biological molecules are presented, and comparison with experiment is used to determine the merits and flaws of various types of force fields. The main conclusions include the following: (1) Potential surfaces from ab initio methods at the level of MP2 yield very satisfactory agreement with spectroscopic experimental data. (2) By the test of spectroscopy, ab initio force fields are considerably superior to the standard versions of force fields such as AMBER or OPLS. (3) Much of the spectroscopic weakness of AMBER and OPLS is due to incorrect description of anharmonic coupling between different vibrational modes. (4) Potential surfaces of the QM/MM (Quantum Mechanics/Molecular Mechanics) type, and potentials based on improved versions of semi-empirical electronic structure theory, which are feasible for large biological molecules, yield encouraging results by the test of vibrational spectroscopy.

  12. Vibrational spectroscopy and intramolecular dynamics of 1-butyne.

    PubMed

    Portnov, Alexander; Rosenwaks, Salman; Bar, Ilana

    2004-09-22

    Photodissociation of jet-cooled vibrationally excited 1-butyne, C(2)H(5)C[Triple Bond]C[Single Bond]H, coupled with mass spectrometric detection of H photofragments, facilitated measurements of action spectra and Doppler profiles, expressing the yield of the ensuing fragments versus the vibrational excitation and UV probe lasers, respectively. Both the action spectra and the simultaneously measured room temperature photoacoustic spectra in the 2nu(1), 3nu(1), and 4nu(1) C[Single Bond]H acetylenic stretch regions exhibit unresolved rotational envelopes with significant narrowing of the former due to temperature-related change in the rotational structure. The narrowing of the action spectrum in the 3nu(1) region exposed a resonance splitting, implying intramolecular vibrational energy redistribution (IVR) time of approximately 1 ps. Asymmetric rotor simulation of the band contours provided the rotational constants and estimates for the homogeneous broadening arising from IVR to the bath vibrational states. The homogenous linewidth of 4nu(1) is anomalously narrower than that of 2nu(1) and 3nu(1), indicating a longer lived 4nu(1) state despite the increasing background state density, suggestive of a lack of low-order resonances or of mode-specific coupling with the bath states. The Doppler profiles indicate that the H photofragments are released with low average translational energies, pointing to an indirect dissociation process occurring after internal conversion (IC) to the ground electronic state or after IC and isomerization to butadiene.

  13. 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.

  14. 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.

  15. 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.

  16. Fourier transform spectroscopy in the vibrational fingerprint region with a birefringent interferometer.

    PubMed

    Réhault, J; Borrego-Varillas, R; Oriana, A; Manzoni, C; Hauri, C P; Helbing, J; Cerullo, G

    2017-02-20

    We introduce a birefringent interferometer for Fourier transform (FT) spectroscopy in the mid-infrared, covering the vibrational fingerprint region (5-10 µm, 1000-2000 cm-1), which is crucial for molecular identification. Our interferometer employs the crystal calomel (Hg2Cl2), which combines high birefringence (ne-no≈0.55) with a broad transparency range (0.38-20 µm). We adopt a design based on birefringent wedges, which is simple and compact and guarantees excellent delay accuracy and long-term stability. We demonstrate FTIR spectroscopy, with a frequency resolution of 3 cm-1, as well as two-dimensional IR (2DIR) spectroscopy. Our setup can be extended to other spectroscopic modalities such as vibrational circular dichroism and step-scan FT spectroscopy.

  17. 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…

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

    SciTech Connect

    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 no 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.

  19. 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.

  20. 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

  1. Vibrational Spectroscopy in Ion-Irradiated Carbon-Based Thin Films

    NASA Astrophysics Data System (ADS)

    Compagnini, Giuseppe; Puglisi, Orazio; Baratta, Giuseppe A.; Strazzulla, Giovanni

    In this work we present and discuss some selected experiments on ion-irradiated carbon-based thin films. Vibrational spectroscopy is used to investigate the materials structure and to explore the mechanisms of ion beam-induced modifications in many carbon solids such as crystalline carbon and carbon alloys, hydrocarbon molecules and exotic carbon species.

  2. Chiral Vibrational Structures of Proteins at Interfaces Probed by Sum Frequency Generation Spectroscopy

    PubMed Central

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

    2011-01-01

    We review the recent development of chiral sum frequency generation (SFG) spectroscopy and its applications to study chiral vibrational structures at interfaces. This review summarizes observations of chiral SFG signals from various molecular systems and describes the molecular origins of chiral SFG response. It focuses on the chiral vibrational structures of proteins and presents the chiral SFG spectra of proteins at interfaces in the C-H stretch, amide I, and N-H stretch regions. In particular, a combination of chiral amide I and N-H stretches of the peptide backbone provides highly characteristic vibrational signatures, unique to various secondary structures, which demonstrate the capacity of chiral SFG spectroscopy to distinguish protein secondary structures at interfaces. On the basis of these recent developments, we further discuss the advantages of chiral SFG spectroscopy and its potential application in various fields of science and technology. We conclude that chiral SFG spectroscopy can be a new approach to probe chiral vibrational structures of protein at interfaces, providing structural and dynamic information to study in situ and in real time protein structures and dynamics at interfaces. PMID:22272140

  3. Vibrational sum frequency generation spectroscopy using inverted visible pulses.

    PubMed

    Weeraman, Champika; Mitchell, Steven A; Lausten, Rune; Johnston, Linda J; Stolow, Albert

    2010-05-24

    We present a broadband vibrational sum frequency generation (BB-VSFG) scheme using a novel ps visible pulse shape. We generate the fs IR pulse via standard procedures and simultaneously generate an 'inverted' time-asymmetric narrowband ps visible pulse via second harmonic generation in the pump depletion regime using a very long nonlinear crystal which has high group velocity mismatch (LiNbO3). The 'inverted' ps pulse shape minimally samples the instantaneous nonresonant response but maximally samples the resonant response, maintaining high spectral resolution. We experimentally demonstrate this scheme, presenting SFG spectra of canonical organic monolayer systems in the C-H stretch region (2800-3000 cm(-1)).

  4. Visualization of Vibrational Modes in Real Space by Tip-Enhanced Non-Resonant Raman Spectroscopy.

    PubMed

    Duan, Sai; Tian, Guangjun; Luo, Yi

    2016-01-18

    We present a general theory to model the spatially resolved non-resonant Raman images of molecules. It is predicted that the vibrational motions of different Raman modes can be fully visualized in real space by tip-enhanced non-resonant Raman scattering. As an example, the non-resonant Raman images of water clusters were simulated by combining the new theory and first-principles calculations. Each individual normal mode gives rise its own distinct Raman image, which resembles the expected vibrational motions of the atoms very well. The characteristics of intermolecular vibrations in supermolecules could also be identified. The effects of the spatial distribution of the plasmon as well as nonlinear scattering processes were also addressed. Our study not only suggests a feasible approach to spatially visualize vibrational modes, but also provides new insights in the field of nonlinear plasmonic spectroscopy.

  5. 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.

  6. Anharmonic vibrational modes of nucleic acid bases revealed by 2D IR spectroscopy.

    PubMed

    Peng, Chunte Sam; Jones, Kevin C; Tokmakoff, Andrei

    2011-10-05

    Polarization-dependent two-dimensional infrared (2D IR) spectra of the purine and pyrimadine base vibrations of five nucleotide monophosphates (NMPs) were acquired in D(2)O at neutral pH in the frequency range 1500-1700 cm(-1). The distinctive cross-peaks between the ring deformations and carbonyl stretches of NMPs indicate that these vibrational modes are highly coupled, in contrast with the traditional peak assignment, which is based on a simple local mode picture such as C═O, C═N, and C═C double bond stretches. A model of multiple anharmonically coupled oscillators was employed to characterize the transition energies, vibrational anharmonicities and couplings, and transition dipole strengths and orientations. No simple or intuitive structural correlations are found to readily assign the spectral features, except in the case of guanine and cytosine, which contain a single local CO stretching mode. To help interpret the nature of these vibrational modes, we performed density functional theory (DFT) calculations and found that multiple ring vibrations are coupled and delocalized over the purine and pyrimidine rings. Generally, there is close correspondence between the experimental and computational results, provided that the DFT calculations include explicit waters solvating hydrogen-bonding sites. These results provide direct experimental evidence of the delocalized nature of the nucleotide base vibrations via a nonperturbative fashion and will serve as building blocks for constructing a structure-based model of DNA and RNA vibrational spectroscopy.

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

    PubMed

    Mettu, S; Chaudhury, M K

    2012-10-02

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

  8. Activated vibrational modes and Fermi resonance in tip-enhanced Raman spectroscopy.

    PubMed

    Sun, Mengtao; Fang, Yurui; Zhang, Zhenyu; Xu, Hongxing

    2013-02-01

    Using p-aminothiophenol (PATP) molecules on a gold substrate and high-vacuum tip-enhanced Raman spectroscopy (HV-TERS), we show that the vibrational spectra of these molecules are distinctly different from those in typical surface-enhanced Raman spectroscopy. Detailed first-principles calculations help to assign the Raman peaks in the TERS measurements as Raman-active and IR-active vibrational modes of dimercaptoazobenzene (DMAB), providing strong spectroscopic evidence for the dimerization of PATP molecules to DMAB under the TERS setup. The activation of the IR-active modes is due to enhanced electromagnetic field gradient effects within the gap region of the highly asymmetric tip-surface geometry. Fermi resonances are also observed in HV-TERS. These findings help to broaden the versatility of TERS as a promising technique for ultrasensitive molecular spectroscopy.

  9. 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

  10. Vibrational spectroscopy and density functional theory study of 4-mercaptophenol

    NASA Astrophysics Data System (ADS)

    Li, Ran; Ji, Wei; Chen, Lei; Lv, Haiming; Cheng, Jianbo; Zhao, Bing

    2014-03-01

    In this paper, 4-mercaptophenol (4-MPH) 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. All FTIR and Raman bands of the compound obtained experimentally were assigned based on the modeling results obtained at the B3LYP/6-311 + G** level. 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-MPH has two hydrogen bond donors and three hydrogen bond acceptors. HOMO-LUMO gap was also obtained theoretically at B3LYP/6-311 + G** level.

  11. Nonlinear vibrational spectroscopy of surfactants at liquid interfaces

    SciTech Connect

    Miranda, Paulo B.

    1998-12-14

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

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

    PubMed Central

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

    2014-01-01

    Multidimensional nonlinear spectroscopy, in the electronic and vibrational regimes, has reached maturity. To date, no experimental technique has combined the advantages of 2D electronic spectroscopy and 2D infrared spectroscopy, monitoring the evolution of the electronic and nuclear degrees of freedom simultaneously. The interplay and coupling between the electronic state and vibrational manifold is fundamental to understanding ensuing nonradiative pathways, especially those that involve conical intersections. We have developed a new experimental technique that is capable of correlating the electronic and vibrational degrees of freedom: 2D electronic–vibrational spectroscopy (2D-EV). We apply this new technique to the study of the 4-(di-cyanomethylene)-2-methyl-6-p-(dimethylamino)styryl-4H-pyran (DCM) laser dye in deuterated dimethyl sulfoxide and its excited state relaxation pathways. From 2D-EV spectra, we elucidate a ballistic mechanism on the excited state potential energy surface whereby molecules are almost instantaneously projected uphill in energy toward a transition state between locally excited and charge-transfer states, as evidenced by a rapid blue shift on the electronic axis of our 2D-EV spectra. The change in minimum energy structure in this excited state nonradiative crossing is evident as the central frequency of a specific vibrational mode changes on a many-picoseconds timescale. The underlying electronic dynamics, which occur on the hundreds of femtoseconds timescale, drive the far slower ensuing nuclear motions on the excited state potential surface, and serve as a excellent illustration for the unprecedented detail that 2D-EV will afford to photochemical reaction dynamics. PMID:24927586

  13. Simulating Energy Relaxation in Pump-Probe Vibrational Spectroscopy of Hydrogen-Bonded Liquids.

    PubMed

    Dettori, Riccardo; Ceriotti, Michele; Hunger, Johannes; Melis, Claudio; Colombo, Luciano; Donadio, Davide

    2017-03-14

    We introduce a nonequilibrium molecular dynamics simulation approach, based on the generalized Langevin equation, to study vibrational energy relaxation in pump-probe spectroscopy. A colored noise thermostat is used to selectively excite a set of vibrational modes, leaving the other modes nearly unperturbed, to mimic the effect of a monochromatic laser pump. Energy relaxation is probed by analyzing the evolution of the system after excitation in the microcanonical ensemble, thus providing direct information about the energy redistribution paths at the molecular level and their time scale. The method is applied to hydrogen-bonded molecular liquids, specifically deuterated methanol and water, providing a robust picture of energy relaxation at the molecular scale.

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

    PubMed

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

    2016-04-28

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

  15. Femtosecond time-resolved spectroscopy of coherent vibrational and electronic excitations in solids

    NASA Astrophysics Data System (ADS)

    Williams*, Leah Ruby; Nelson, Keith A.

    1986-08-01

    ``Impulsive'' stimulated scattering (ISS) of femtosecond laser pulses was used to coherently excite and probe a low-lying (61-cm-1) electronic excitation in the cooperative Jahn-Teller crystal, terbium vanadate. Coherent terahertz oscillations and their dephasing were observed in the time domain. ISS is a general aspect of ultrashort-pulse interactions with matter, through which coherent excitations are produced whenever a sufficiently short laser pulse enters a Raman-active medium. Its use for measurement of vibrational and electronic dephasing and lifetimes, and for time-resolved spectroscopy of vibrationally distorted crystals and molecules, is discussed.

  16. Torsional vibrational modes of tryptophan studied by terahertz time-domain spectroscopy.

    PubMed

    Yu, B; Zeng, F; Yang, Y; Xing, Q; Chechin, A; Xin, X; Zeylikovich, I; Alfano, R R

    2004-03-01

    The low-frequency torsional modes, index of refraction, and absorption of a tryptophan film and pressed powders from 0.2 to 2.0 THz (6.6-66 cm(-1)) were measured by terahertz time-domain spectroscopy at room temperature. It was found that there were two dominated torsional vibrational modes at around 1.435 and 1.842 THz. The associated relaxation lifetimes ( approximately 1 ps) for these modes of the tryptophan molecule were measured. Using a density-functional calculation, the origins of the observed torsional vibrations were assigned to the chain and ring of the tryptophan molecule.

  17. Advanced theory of driven birdcage resonator with losses for biomedical magnetic resonance imaging and spectroscopy.

    PubMed

    Novikov, Alexander

    2011-02-01

    A complete time-dependent physics theory of symmetric unperturbed driven hybrid birdcage resonator was developed for general application. In particular, the theory can be applied for radiofrequency (RF) coil engineering, computer simulations of coil-sample interaction, etc. Explicit time dependence is evaluated for different forms of driving voltage. The major steps of the solution development are shown and appropriate explanations are given. Green's functions and spectral density formula were developed for any form of periodic driving voltage. The concept of distributed power losses based on transmission line theory is developed for evaluation of local losses of a coil. Three major types of power losses are estimated as equivalent series resistances in the circuit of the birdcage resonator. Values of generated resistances in legs and end-rings are estimated. An application of the theory is shown for many practical cases. Experimental curve of B(1) field polarization dependence is measured for eight-sections birdcage coil. It was shown that the steady-state driven resonance frequencies do not depend on damping factor unlike the free oscillation (transient) frequencies. An equivalent active resistance is generated due to interaction of RF electromagnetic field with a sample. Resistance of the conductor (enhanced by skin effect), Eddy currents and dielectric losses are the major types of losses which contribute to the values of generated resistances. A biomedical sample for magnetic resonance imaging and spectroscopy is the source of the both Eddy current and dielectric losses of a coil. As demonstrated by the theory, Eddy current loss is the major effect of coil shielding.

  18. Vibrational spectroscopy and DFT calculations of flavonoid derriobtusone A

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

  19. 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.

  20. Vibrational neutron spectroscopy of collagen and model polypeptides.

    PubMed Central

    Middendorf, H D; Hayward, R L; Parker, S F; Bradshaw, J; Miller, A

    1995-01-01

    A pulsed source neutron spectrometer has been used to measure vibrational spectra (20-4000 cm-1) of dry and hydrated type I collagen fibers, and of two model polypeptides, polyproline II and (prolyl-prolyl-glycine)10, at temperatures of 30 and 120 K. the collagen spectra provide the first high resolution neutron views of the proton-dominated modes of a protein over a wide energy range from the low frequency phonon region to the rich spectrum of localized high frequency modes. Several bands show a level of fine structure approaching that of optical data. The principal features of the spectra are assigned. A difference spectrum is obtained for protein associated water, which displays an acoustic peak similar to pure ice and a librational band shifted to lower frequency by the influence of the protein. Hydrogen-weighted densities of states are extracted for collagen and the model polypeptides, and compared with published calculations. Proton mean-square displacements are calculated from Debye-Waller factors measured in parallel quasi-elastic neutron-scattering experiments. Combined with the collagen density of states function, these yield an effective mass of 14.5 a.m.u. for the low frequency harmonic oscillators, indicating that the extended atom approximation, which simplifies analyses of low frequency protein dynamics, is appropriate. PMID:8527680

  1. Investigating Microbial (Micro)colony Heterogeneity by Vibrational Spectroscopy

    PubMed Central

    Choo-Smith, L.-P.; Maquelin, K.; van Vreeswijk, T.; Bruining, H. A.; Puppels, G. J.; Thi, N. A. Ngo; Kirschner, C.; Naumann, D.; Ami, D.; Villa, A. M.; Orsini, F.; Doglia, S. M.; Lamfarraj, H.; Sockalingum, G. D.; Manfait, M.; Allouch, P.; Endtz, H. P.

    2001-01-01

    Fourier transform infrared and Raman microspectroscopy are currently being developed as new methods for the rapid identification of clinically relevant microorganisms. These methods involve measuring spectra from microcolonies which have been cultured for as little as 6 h, followed by the nonsubjective identification of microorganisms through the use of multivariate statistical analyses. To examine the biological heterogeneity of microorganism growth which is reflected in the spectra, measurements were acquired from various positions within (micro)colonies cultured for 6, 12, and 24 h. The studies reveal that there is little spectral variance in 6-h microcolonies. In contrast, the 12- and 24-h cultures exhibited a significant amount of heterogeneity. Hierarchical cluster analysis of the spectra from the various positions and depths reveals the presence of different layers in the colonies. Further analysis indicates that spectra acquired from the surface of the colonies exhibit higher levels of glycogen than do the deeper layers of the colony. Additionally, the spectra from the deeper layers present with higher RNA levels than the surface layers. Therefore, the 6-h colonies with their limited heterogeneity are more suitable for inclusion in a spectral database to be used for classification purposes. These results also demonstrate that vibrational spectroscopic techniques can be useful tools for studying the nature of colony development and biofilm formation. PMID:11282591

  2. 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

  3. OH-stretch vibrational spectroscopy of hydroxymethyl hydroperoxide.

    PubMed

    Fry, Juliane L; Matthews, Jamie; Lane, Joseph R; Roehl, Coleen M; Sinha, Amitabha; Kjaergaard, Henrik G; Wennberg, Paul O

    2006-06-08

    We report measurement and analysis of the photodissociation spectrum of hydroxymethyl hydroperoxide (HOCH(2)OOH) and its partially deuterated analogue, HOCD(2)OOH, in the OH-stretching region. Spectra are obtained by Fourier transform infrared spectroscopy in the 1nu(OH) and 2nu(OH) regions, and by laser induced fluorescence detection of the OH fragment produced from dissociation of HOCH(2)OOH initiated by excitation of the 4nu(OH) and 5nu(OH) overtone regions (action spectroscopy). A one-dimensional local-mode model of each OH chromophore is used with ab initio calculated OH-stretching potential energy and dipole moment curves at the coupled-cluster level of theory. Major features in the observed absorption and photodissociation spectra are explained by our local-mode model. In the 4nu(OH) region, explanation of the photodissocation spectrum requires a nonuniform quantum yield, which is estimated by assuming statistical energy distribution in the excited state. Based on the estimated dissociation threshold, overtone photodissociation is not expected to significantly influence the atmospheric lifetime of hydroxymethyl hydroperoxide.

  4. Vibrational Coupling at the Topmost Surface of Water Revealed by Heterodyne-Detected Sum Frequency Generation Spectroscopy.

    PubMed

    Suzuki, Yudai; Nojima, Yuki; Yamaguchi, Shoichi

    2017-03-15

    Unraveling vibrational coupling is the key to consistently interpret vibrational spectra of complex molecular systems. The vibrational spectrum of the water surface heavily suffers from vibrational coupling, which hinders complete understanding of the molecular structure and dynamics of the water surface. Here we apply heterodyne-detected sum frequency generation spectroscopy to the water surface and accomplish the assignment of a weak vibrational band located at the lower energy side of the free OH stretch. We find that this band is due to a combination mode of the hydrogen-bonded OH stretch and a low-frequency intermolecular vibration, and this combination band appears in the surface vibrational spectrum through anharmonic vibrational coupling that takes place exclusively at the topmost surface.

  5. 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.

  6. Far-infrared vibrational modes of DNA components studied by terahertz time-domain spectroscopy.

    PubMed

    Fischer, B M; Walther, M; Uhd Jepsen, P

    2002-11-07

    The far-infrared dielectric function of a wide range of organic molecules is dominated by vibrations involving a substantial fraction of the atoms forming the molecule and motion associated with intermolecular hydrogen bond vibrations. Due to their collective nature such modes are highly sensitive to the intra- and intermolecular structure and thus provide a unique fingerprint of the conformational state of the molecule and effects of its environment. We demonstrate the use of terahertz time-domain spectroscopy (THz-TDS) for recording the far-infrared (0.5-4.0 THz) dielectric function of the four nucleobases and corresponding nucleosides forming the building blocks of deoxyribose nucleic acid (DNA). We observe numerous distinct spectral features with large differences between the molecules in both frequency-dependent absorption coefficient and index of refraction. Assisted by results from density-functional calculations we interpret the origin of the observed resonances as vibrations of hydrogen bonds between the molecules.

  7. High-resolution vibrational and rotational spectroscopy of CD2H+ in a cryogenic ion trap

    NASA Astrophysics Data System (ADS)

    Jusko, Pavol; Stoffels, Alexander; Thorwirth, Sven; Brünken, Sandra; Schlemmer, Stephan; Asvany, Oskar

    2017-02-01

    The low-lying rotational states (J = 0, … , 5) of CD2H+ have been probed by high-resolution ro-vibrational and pure rotational spectroscopy, applying several action spectroscopic methods in a cryogenic 22-pole ion trap. For this, the ν1 ro-vibrational band has been revisited, detecting 108 transitions, among which 36 are new. The use of a frequency comb system allowed us to measure the ro-vibrational transitions with high precision and accuracy, typically better than 1 MHz. The high precision has been confirmed by comparing equal combination differences in the ground and excited state. Moreover, precise predictions of pure rotational transitions were possible for the ground state. Twenty-five rotational transitions have been detected directly by a novel IR-mm-wave double resonance method, giving rise to highly accurate ground state spectroscopic parameters.

  8. 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.

  9. 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

  10. 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).

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  12. 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

  13. 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.

  14. How fissors works: observing vibrationally adiabatic conformational change through femtosecond stimulated Raman spectroscopy.

    PubMed

    Cina, Jeffrey A; Kovac, Philip A

    2013-07-25

    With the help of a two-dimensional model system comprising a slow conformational degree of freedom and a higher-frequency vibration, we investigate the molecular-level origin and dynamical information content of femtosecond stimulated Raman spectroscopy (fissors) signals. Our treatment avails itself of the time scale separation between conformational and vibrational modes by incorporating a vibrationally adiabatic approximation to the conformational dynamics. We derive an expression for the fissors signal without resort to the macroscopic concepts of light- and phonon-wave propagation employed in prior coupled-wave analyses. Numerical calculations of fissors spectra illustrate the case of relatively small conformational mass (still large enough that conformational motion does not induce any change in the vibrational quantum number) in which conformational sidebands accompany a central peak in the Raman gain at a conformationally averaged vibrational transition frequency, and the case of a larger conformational mass in which the sidebands merge with the central peak and the frequency of the latter tracks the time-evolving conformational coordinate.

  15. 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.

  16. 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; ...

    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

  17. 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.

  18. Vibrational Spectra and Adsorption of Trisiloxane Superspreading Surfactant at Air/Water Interface Studied with Sum Frequency Generation Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Feng, Jun; Wu, Dan; Wen, Jia; Liu, Shi-lin; Wang, Hong-fei

    2008-08-01

    The C-H stretch vibrational spectra of the trisiloxane superspreading surfactant Silwet L-77 ((CH3)3Si-O-Si(CH3)(C3H6)(OCH2CH2)7-8OCH3)-O-Si(CH3)3) at the air/water interface are measured with the surface Sum Frequency Generation Vibrational Spectroscopy (SFG-VS). The spectra are dominated with the features from the -Si-CH3 groups around 2905 cm-1 (symmetric stretch or SS mode) and 2957 cm-1 (mostly the asymmetric stretch or AS mode), and with the weak but apparent contribution from the -O-CH2- groups around 2880 cm-1 (symmetric stretch or SS mode). Comparison of the polarization dependent SFG spectra below and above the critical aggregate or micelle concentration (CAC) indicates that the molecular orientation of the C-H related molecular groups remained unchanged at different surface densities of the Silwet L-77 surfactant. The SFG-VS adsorption isotherm suggested that there was no sign of Silwet L-77 bilayer structure formation at the air/water interface. The Gibbs adsorption free energy of the Silwet surfactant to the air/water interface is -42.2±0.8kcal/mol, indicating the unusually strong adsorption ability of the Silwet L-77 superspreading surfactant.

  19. 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.

  20. Exciton-vibrational coupling in the dynamics and spectroscopy of Frenkel excitons in molecular aggregates

    NASA Astrophysics Data System (ADS)

    Schröter, M.; Ivanov, S. D.; Schulze, J.; Polyutov, S. P.; Yan, Y.; Pullerits, T.; Kühn, O.

    2015-03-01

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

  1. 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.

  2. 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.

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

    DOE PAGES

    Rez, Peter; Aoki, Toshihiro; March, Katia; ...

    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. Femtosecond Broadband Stimulated Raman: A New Approach for High-Performance Vibrational Spectroscopy

    PubMed Central

    McCAMANT, DAVID W.; KUKURA, PHILIPP; MATHIES, RICHARD A.

    2005-01-01

    Femtosecond stimulated Raman spectroscopy (FSRS) is a new technique that produces high-quality vibrational spectra free from background fluorescence. FSRS combines a narrow-bandwidth picosecond Raman pump pulse with an ∼80 fs continuum probe pulse to produce stimulated Raman spectra from the pump-induced gain in the probe spectrum. The high intensity of the Raman pump combined with the broad bandwidth of the probe produces high signal-to-noise vibrational spectra with very short data acquisition times. FSRS spectra of standard solutions and solvents such as aqueous Na2SO4, aqueous KNO3, methanol, isopropanol, and cyclohexane are collected in seconds. Furthermore, stimulated Raman spectra can be obtained using just a single pump–probe pulse pair that illuminates the sample for only ∼1 ps. Fluorescence rejection is demonstrated by collecting FSRS spectra of dyes (rhodamine 6G, chlorophyll a, and DTTCI) with varying degrees of fluorescence background and resonance enhancement. The high signal-to-noise, short data acquisition time, fluorescence rejection, and high spectral and temporal resolution of femtosecond stimulated Raman spectroscopy make it a valuable new vibrational spectroscopic technique. PMID:14658143

  5. 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.

  6. Electron Momentum Spectroscopy Investigation of Molecular Conformations of Ethanol Considering Vibrational Effects.

    PubMed

    Tang, Yaguo; Shan, Xu; Niu, Shanshan; Liu, Zhaohui; Wang, Enliang; Watanabe, Noboru; Yamazaki, Masakazu; Takahashi, Masahiko; Chen, Xiangjun

    2017-01-12

    The interpretation of experimental electron momentum distributions (EMDs) of ethanol, one of the simplest molecules having conformers, has confused researchers for years. High-level calculations of Dyson orbital EMDs by thermally averaging the gauche and trans conformers as well as molecular dynamical simulations failed to quantitatively reproduce the experiments for some of the outer valence orbitals. In this work, the valence shell electron binding energy spectrum and EMDs of ethanol are revisited by the high-sensitivity electron momentum spectrometer employing symmetric noncoplanar geometry at an incident energy of 1200 eV plus binding energy, together with a detailed analysis of the influence of vibrational motions on the EMDs for the two conformers employing a harmonic analytical quantum mechanical (HAQM) approach by taking into account all of the vibrational modes. The significant discrepancies between theories and experiments in previous works have now been interpreted quantitatively, indicating that the vibrational effect plays a significant role in reproducing the experimental results, not only through the low-frequency OH and CH3 torsion modes but also through other high-frequency ones. Rational explanation of experimental momentum profiles provides solid evidence that the trans conformer is slightly more stable than the gauche conformer, in accordance with thermodynamic predictions and other experiments. The case of ethanol demonstrates the significance of considering vibrational effects when performing a conformational study on flexible molecules using electron momentum spectroscopy.

  7. 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.

  8. Experimental and theoretical investigation on the vibrational spectroscopy of L-theanine

    NASA Astrophysics Data System (ADS)

    Chen, Yongjian; Xi, Gangqin; Chen, Rong; Li, Yongzeng; Feng, Shangyuan; Lei, Jinping; Lin, Hongxing

    2011-12-01

    In this work, experimental and theoretical investigations on vibrational spectroscopy of L-theanine were presented. FT-IR and Raman spectra of L-theanine powder sample were recorded and corresponding theoretical calculations were performed based on Density Functional Theory (DFT) at B3LYP level using 6-31++G(d,p) and 6-311++G(d,p) basis sets combined with the Polarized Continuum Model (PCM) with water as the solvent. The experimental vibrational bands were assigned based on the basis of calculations while the predicted geometric parameters were compared with those obtained in experiment, most of the bands measured were well reproduced in the calculations while the discrepancies are significant for the bands mainly related to the vibrations of protonated amino group ( NH3+) and ionized carboxyl group (COO -), which are affected by the intramolecular hydrogen bond interaction. Good agreements between the theoretical and experimental results confirm the feasibility of the DFT method combined with PCM in the study of the molecular structure and vibrational spectra of L-theanine.

  9. 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

  10. 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.

  11. NH stretching vibrations of pyrrole clusters studied by infrared cavity ringdown spectroscopy.

    PubMed

    Matsumoto, Yoshiteru; Honma, Kenji

    2007-11-14

    The IR spectra for various sizes of pyrrole clusters were measured in the NH stretching vibration region by infrared cavity ringdown spectroscopy. The hydrogen-bonded structures and normal modes of the pyrrole clusters were analyzed by a density functional theory calculation of the B3LYP/6-311+G(d,p) level. Two types of pulsed nozzles, a slit and a large pinhole, were used to generate different cluster size distributions in a supersonic jet. A rotational contour analysis of the NH stretching vibration for the monomer revealed that the slit nozzle provides a warmer jet condition than the pinhole one. The IR spectra, measured under the warmer condition, showed the intense bands at 3444, 3392, and 3382 cm(-1), which were assigned to hydrogen-bonded NH stretching vibrations due to the dimer, the trimer, and the tetramer, respectively. On the other hand, the IR spectra measured under a lower temperature condition by a pinhole nozzle showed a broad absorption feature in addition to sharp bands. This broad absorption was reproduced by the sum of two Gaussians peaks at 3400 and 3372 cm(-1) with widths of 30 and 50 cm(-1) (FWHM), respectively. Compared with the spectra of the condensed phase, two bands at 3400 and 3372 cm(-1) were assigned to hydrogen-bonded NH stretching vibrations of larger clusters having liquid-like and solid-like structures, respectively.

  12. 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.

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

    PubMed

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

    2016-11-14

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

  14. 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.

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  17. Resolving fine spectral features in lattice vibrational modes using femtosecond coherent spectroscopy

    NASA Astrophysics Data System (ADS)

    Card, A.; Mokim, M.; Ganikhanov, F.

    2016-02-01

    We show resolution of fine spectral features within several Raman active vibrational modes in potassium titanyl phosphate (KTP) crystal. Measurements are performed using a femtosecond time-domain coherent anti-Stokes Raman scattering spectroscopy technique that is capable of delivering equivalent spectral resolution of 0.1 cm-1. The Raman spectra retrieved from our measurements show several spectral components corresponding to vibrations of different symmetry with distinctly different damping rates. In particular, linewidths for unassigned optical phonon mode triplet centered at around 820 cm-1 are found to be 7.5 ± 0.2 cm-1, 9.1 ± 0.3 cm-1, and 11.2 ± 0.3 cm-1. Results of our experiments will ultimately help to design an all-solid-state source for sub-optical-wavelength waveform generation that is based on stimulated Raman scattering.

  18. Rotational Spectroscopy of Vibrationally Excited N_2H^+ and N_2D^+ up to 2 Thz

    NASA Astrophysics Data System (ADS)

    Yu, Shanshan; Pearson, John; Drouin, Brian; Crawford, Timothy J.; Daly, Adam M.; Elliott, Ben; Amano, Takayoshi

    2015-06-01

    Terahertz absorption spectroscopy was employed to extend the measurements on the pure rotational transitions of N_2H^+, N_2D^+ and their 15N-containing isotopologues in the ground state and first excited vibrational states for the three fundamental vibrational modes. In total 88 new pure rotational transitions were observed in the range of 0.7--2.0~THz. The observed transition frequencies were fit to experimental accuracy, and the improved molecular parameters were obtained. The new measurements and predictions will support the analysis of high-resolution astronomical observations made with facilities such as SOFIA and ALMA where laboratory rest frequencies with uncertainties of 1 MHz or smaller are required for proper analysis of velocity resolved astrophysical components.

  19. 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.

  20. 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

  1. 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.

  2. Communication: Atomic force detection of single-molecule nonlinear optical vibrational spectroscopy

    SciTech Connect

    Saurabh, Prasoon Mukamel, Shaul

    2014-04-28

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

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

    PubMed

    Saurabh, Prasoon; Mukamel, Shaul

    2014-04-28

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

  4. Multipulse polarisation selective spectroscopy of rotational and vibrational responses of molecules in a liquid

    SciTech Connect

    Nikiforov, V G

    2013-02-28

    The amplitude control of time-resolved optical responses in a liquid is theoretically analysed under nonresonant irradiation of the system by a train of femtosecond pulses with parallel and orthogonal polarisations. The control parameters, specifying the excitation scenarios, are the duration of pulses, their relative intensities, polarisation, and the delays between the pulses. It is shown that the choice of specific excitation scenarios transfers the system into a state in which only one response is detected from a set of responses of coherent intramolecular Raman active vibrational modes, coherent molecular librations and orientational rotations. (laser spectroscopy)

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2007-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-05-01

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

    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 UO22 + 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.

  10. Vibrational spectroscopy of O-H and O-D centers in TiO2

    NASA Astrophysics Data System (ADS)

    Bekisli, Figen; Stavola, Michael; Fowler, W. Beall

    2012-02-01

    While the vibrational properties of O-H centers in TiO2 have been studied for many years, recent experiments suggest a new picture of their behavior. In the 1970s, Bates and Perkins found a single, sharp, strongly polarized O-H line in TiO2, and similarly for O-D and O-T [1]. On the contrary, recent studies by Herklotz et al. [2] find three closely spaced O-H (O-D) lines that were assigned to two different charge states of an O-H (O-D) shallow donor. We have in our possession the very TiO2 samples studied many years ago by Bates and Perkins. We have introduced H and D into these samples and also into TiO2 samples obtained recently. High-resolution vibrational spectroscopy performed as a function of temperature at Lehigh provides new insight into the different vibrational properties seen for O-H in TiO2 in the 1970's and in recent studies by Herklotz et al. [1] J.B. Bates and R.A. Perkins, Phys. Rev. B 16, 3713 (1977). [2] F. Herklotz et al., Phys. Rev. B 83, 235202 (2011)..

  11. SEM, EDX and vibrational spectroscopy of the phosphate mineral vauxite from Llallagua, Bolívia.

    PubMed

    Scholz, Ricardo; Frost, Ray L; Frota, Laura; Belotti, Fernanda Maria; López, Andrés

    2015-12-05

    We have undertaken a vibrational spectroscopic study of vauxite from Llallagua, Bolívia. This source is important source for rare and unusual secondary phosphate minerals and is the type locality for a number of rare phosphates such as vauxite, sigloite, metavauxite and for jeanbandyite. The chemical formula was determined as (Fe0.98 Mn0.01)∑0.99(Al2.00)(PO4)∑2.03(OH)1.98·5.95(H2O). The Raman spectrum is dominated by intense Raman bands at 978, 1000, 1009, 1027 cm(-1) assigned to the PO4(3-) and HPO4(2-) stretching modes. Low intensity Raman bands are found at 1046, 1059, 1070, 1105, 1122, 1134 and 1150 cm(-1) and are assigned to the PO4(3-) ν3 antisymmetric stretching vibrations. Raman bands of at 498, 502, 517, 523 and 535 cm(-1) are assigned to the ν4 PO4(3-) bending modes while the Raman bands at 418, 451, 461 and 470 cm(-1) are due to the ν2 PO4(3-) bending modes. The Raman spectral profile of vauxite in the hydroxyl stretching region is broad with component bands resolved at 2918, 3103, 3328, 3402, 3555 and 3648 cm(-1). Vibrational spectroscopy enables the assessment of the molecular structure of vauxite to be undertaken.

  12. 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

    2016-08-24

    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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. Univariate and multivariate analysis of tannin-impregnated wood species using vibrational spectroscopy.

    PubMed

    Schnabel, Thomas; Musso, Maurizio; Tondi, Gianluca

    2014-01-01

    Vibrational spectroscopy is one of the most powerful tools in polymer science. Three main techniques--Fourier transform infrared spectroscopy (FT-IR), FT-Raman spectroscopy, and FT near-infrared (NIR) spectroscopy--can also be applied to wood science. Here, these three techniques were used to investigate the chemical modification occurring in wood after impregnation with tannin-hexamine preservatives. These spectroscopic techniques have the capacity to detect the externally added tannin. FT-IR has very strong sensitivity to the aromatic peak at around 1610 cm(-1) in the tannin-treated samples, whereas FT-Raman reflects the peak at around 1600 cm(-1) for the externally added tannin. This high efficacy in distinguishing chemical features was demonstrated in univariate analysis and confirmed via cluster analysis. Conversely, the results of the NIR measurements show noticeable sensitivity for small differences. For this technique, multivariate analysis is required and with this chemometric tool, it is also possible to predict the concentration of tannin on the surface.

  20. Coherent Vibrational Dynamics and High-Resolution Nonlinear Spectroscopy: A Comparison with the Air/DMSO Liquid Interface

    SciTech Connect

    Velarde Ruiz Esparza, Luis A.; Lu, Zhou; Wang, Hongfei

    2013-12-27

    In this report we present a comparative study on the C-H stretching vibrations at air/DMSO (dimethyl sulfoxide) interface with both the free-induction decay (FID) coherent vibrational dynamics and sub-wavenumber high resolution sum-frequency generation vibrational spectroscopy measurements. In principle the frequency-domain and time-domain spectroscopic measurements should generate identical information for a given molecular system. However, when the molecular systems are with several coupled or overlapping vibrational modes, to obtain detailed spectroscopic and coherent dynamics information is not as straightforward and rather difficult from either the time-domain or the frequency domain measurements. For the case of air/DMSO interface that is with moderately complex vibrational spectra, we show that the frequency-domain measurement with sub-wavenumber high-resolution SFGVS is probably more advantageous than the time-domain measurement in obtaining quantitative understanding of the structure and coherent dynamics of the molecular interface.

  1. Vibrational structure of the S 2 (1B u) excited state of diphenyloctatetraene observed by femtosecond stimulated Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Kukura, Philipp; McCamant, David W.; Davis, Paul H.; Mathies, Richard A.

    2003-11-01

    Femtosecond time-resolved stimulated Raman spectroscopy (FSRS) is used to study the vibrational structure and dynamics of the S 2 state of diphenyloctatetraene. Strong vibrational features at 1184, 1259 and 1578 cm -1 whose linewidths are determined by the S 2 electronic lifetime are observed at early times after photoexcitation at 397 nm. Kinetic analysis of the integrated Raman intensities as well as the transient absorption reveals an exponential decay of the S 2 state on the order of 100 fs. These results demonstrate the ability of FSRS to study the vibrational structure of excited state and chemical reaction dynamics on the femtosecond timescale.

  2. 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

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

    PubMed

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

    2016-04-12

    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.

  4. Vibrational spectroscopy and excited state molecular dynamics of phenylene ethynylene polymers

    NASA Astrophysics Data System (ADS)

    Galindo Cruz, Johan Fabian

    Energy transfer is a vital process because of its critical role in photosynthesis as well as in the development of new technological devices such as biosensors, photovoltaics and light emitting devices. Dendrimeric polymers are one of the most explored light-harvesting molecules. The characterization of the excited states of this group of molecules as well as the study of their energy transfer mechanism is an important step to gain further insight into this process and its application. For this purpose, we have studied a family of two- and three- ring linear poly(phenylene ethynylene) dendrimers which are either meta or ortho substituted. These dendrimers are able to mimic energy transfer that occurs in photosynthetic systems. We have performed IR spectroscopy calculations using linear response theory and analyzed the propagation of the ground state normal modes in the excited state. We identified a band at 2150 cm-1 that is characteristic of S1 in the meta- substituted molecule, for which S1 and S2 have transition densities localized over different regions of the molecule, while the ortho- substituted case, the states are spread over the entire molecule. We find that the coupling between vibrations associated to C≡C triple bonds plays an important role in the nonadiabatic electronic energy transfer. These results are a guide to the experimental characterization of specific electronic excited state vibrations of these molecules. Next, we proceed to study the larger 2G1m-Eper, a Poly(Phenylene Ethynylene) based molecule. We have used Nonadiabatic Excited State Molecular Dynamics to study the energy transfer mechanism after an excitation at 400 nm. We have found that the initial excitation is delocalized between the two monodendrons, evolving to an intermediate state located in one of them. From this state, the system transitions to S1, localized in the perylene trap, and photon emission can take place to return to the ground state. These results are in good

  5. Low-frequency vibration study of amino acids using terahertz spectroscopy and solid-state density functional theory

    NASA Astrophysics Data System (ADS)

    Zhang, Feng; Tominaga, Keisuke; Hayashi, Michitoshi; Wang, Houng-Wei

    2014-11-01

    Understanding the low-frequency normal modes of amino acids, the building blocks of proteins, is crucial to reveal the vibration-function relationship in the macromolecular system. Recent advances in terahertz spectroscopy (THz) and solid-state density functional theory (DFT) have ensured an accurate description of low-frequency modes of amino acids. New knowledge people have learnt so far is that the inter- and intra-molecular vibrations are strongly mixed with each other in the THz region through the vibrational coordinate mixing. Rich information is believed embedded in this phenomenon. We introduce a generalized mode-analysis method that allows for the accurate decomposition of a normal mode of interest into the three intermolecular translations, three principal librations and various intrinsic intramolecular vibrations. This mode-analysis method will be demonstrated in the crystalline C60 systems and then applied to shed light on the nature of low-frequency phonons of glycine, diglycine and triglycine. This method helps reveal new intramolecular vibrational modes on the first hand, and more importantly, illuminate a new phenomenon of the frequency distribution of intramolecular vibrations (FDIV). FDIV describes the possible broad distributions of important intramolecular vibrations in the low-frequency normal modes. The FDIV concept may indicate an additional mechanism for the intramolecular vibrations to become thermally active and participate in various biological functions.

  6. Vibrational sum frequency spectroscopy of surfactants and phospholipid monolayers at liquid-liquid interfaces

    NASA Astrophysics Data System (ADS)

    Smiley, Beth L.; Walker, R. A.; Gragson, D. E.; Hannon, T. E.; Richmond, Geraldine L.

    1998-04-01

    Work from our laboratory on vibrational sum frequency spectroscopic investigations of molecular ordering at the carbon tetrachloride-water interface is reviewed. Simple charged surfactants adsorbed at the liquid-liquid interface are seen to induce alignment of interfacial water molecules to a degree which is dependent on the induced surface potential. Saturation of water molecule alignment occurs at a surfactant surface concentration corresponding to a calculated surface potential of approximately 160 mV. In complementary studies, the relative degree of hydrocarbon chain ordering within monolayers of symmetric phosphatidylcholines of different chain lengths is inferred by the relative signal contributions of the methyl and methylene symmetric stretch modes. The degree of hydrocarbon chain disorder observed depends strongly on the method of monolayer preparation. By one method, a decrease in hydrocarbon chain order is seen with increasing chain length. Another method of monolayer formation yielded very well ordered hydrocarbon chains for the longest chain phosphatidylcholine studied, and showed much greater disorder in shorter chain species which was comparable to the other preparation method. These studies are a foundation for further work with this technique geared towards understanding molecular-level structural features in membrane-like assemblies and surface biochemical interactions of relevance to biomedical research.

  7. Conformations in crystals and solutions of d(CACGTG), d(CCGCGG) and d(GGCGCC) studied by vibrational spectroscopy.

    PubMed Central

    Urpi, L; Ridoux, J P; Liquier, J; Verdaguer, N; Fita, I; Subirana, J A; Iglesias, F; Huynh-Dinh, T; Igolen, J; Taillandier, E

    1989-01-01

    Crystals of self complementary DNA hexamers d(CACGTG), d(CCGCGG) and d(GGCGCC) were grown by vapour diffusion technique and studied by microRaman and microIR spectroscopies. The oligonucleotides were studied in parallel in solution by vibrational spectroscopy. A B- greater than Z transition was detected by Raman spectroscopy during the crystallization process for d(CACGTG). Vibrational spectroscopy shows that the d(GGCGCC) crystals adopt a B geometry. On the contrary the d(CCGCGG) sequence which is shown to be able to undergo in solution or in films quite easily the B- greater than Z transition, remains trapped in crystals in a geometry which may correspond to an intermediate conformation often proposed in models of the B- greater than Z transition. The crystals used in this study were characterized by X-ray diffraction. The unit cell and space group have been determined. PMID:2780292

  8. 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.

  9. Normal mode analysis of Pyrococcus furiosus rubredoxin via nuclear resonance vibrational spectroscopy (NRVS) and resonance raman spectroscopy.

    PubMed

    Xiao, Yuming; Wang, Hongxin; George, Simon J; Smith, Matt C; Adams, Michael W W; Jenney, Francis E; Sturhahn, Wolfgang; Alp, Ercan E; Zhao, Jiyong; Yoda, Y; Dey, Abishek; Solomon, Edward I; Cramer, Stephen P

    2005-10-26

    We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the Fe(S(cys))(4) site in reduced and oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). The oxidized form has also been investigated by resonance Raman spectroscopy. In the oxidized Rd NRVS, strong asymmetric Fe-S stretching modes are observed between 355 and 375 cm(-1); upon reduction these modes shift to 300-320 cm(-1). This is the first observation of Fe-S stretching modes in a reduced Rd. The peak in S-Fe-S bend mode intensity is at approximately 150 cm(-1) for the oxidized protein and only slightly lower in the reduced case. A third band occurs near 70 cm(-1) for both samples; this is assigned primarily as a collective motion of entire cysteine residues with respect to the central Fe. The (57)Fe partial vibrational density of states (PVDOS) were interpreted by normal mode analysis with optimization of Urey-Bradley force fields. The three main bands were qualitatively reproduced using a D(2)(d) Fe(SC)(4) model. A C(1) Fe(SCC)(4) model based on crystallographic coordinates was then used to simulate the splitting of the asymmetric stretching band into at least 3 components. Finally, a model employing complete cysteines and 2 additional neighboring atoms was used to reproduce the detailed structure of the PVDOS in the Fe-S stretch region. These results confirm the delocalization of the dynamic properties of the redox-active Fe site. Depending on the molecular model employed, the force constant K(Fe-S) for Fe-S stretching modes ranged from 1.24 to 1.32 mdyn/A. K(Fe-S) is clearly diminished in reduced Rd; values from approximately 0.89 to 1.00 mdyn/A were derived from different models. In contrast, in the final models the force constants for S-Fe-S bending motion, H(S-Fe-S), were 0.18 mdyn/A for oxidized Rd and 0.15 mdyn/A for reduced Rd. The NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.

  10. Can mid-infrared biomedical spectroscopy of cells, fluids and tissue aid improvements in cancer survival? A patient paradigm.

    PubMed

    Hughes, Caryn; Baker, Matthew J

    2016-01-21

    This review will take a fresh approach from the patient perspective; offering insight into the applications of mid-infrared biomedical spectroscopy in a scenario whereby the patient presents with non-specific symptoms and via an extensive diagnostic process multiple lesions are discovered but no clear sign of the primary tumour; a condition known as cancer of unknown primary (CUP). With very limited options to diagnose the cancer origin, treatment options are likely to be ineffective and prognosis is consequentially very poor. CUP has not yet been targeted by infrared biospectroscopy, however, this timely, concise dissemination will focus on a series of research highlights and breakthroughs from the field for the management of a variety of cancer-related diseases - many examples of which have occurred within this year alone. The case for integration of mid-infrared (MIR) technology into clinical practice will be demonstrated largely via diagnostic, but also therapeutic and prognostic avenues by means of including cytological, bio-fluid and tissue analysis. The review is structured around CUP but is relevant for all cancer diagnoses. Infrared spectroscopy is fast developing a reputation as a valid and powerful tool for the detection and diagnosis of cancer using a variety of sample formats. The technology will produce data and tools that are designed to complement routine clinical practice; enhancing the ability of the clinician to make a reliable and non-subjective decision and enabling decreased levels of mortality and morbidity and gains in patient quality of life.

  11. Structure-dependent vibrational dynamics of Mg(BH 4 ) 2 polymorphs probed with neutron vibrational spectroscopy and first-principles calculations

    DOE PAGES

    Dimitrievska, Mirjana; White, James L.; Zhou, Wei; ...

    2016-08-19

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

  12. Structure-dependent vibrational dynamics of Mg(BH 4 ) 2 polymorphs probed with neutron vibrational spectroscopy and first-principles calculations

    SciTech Connect

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

    2016-01-01

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

  13. Structure-dependent vibrational dynamics of Mg(BH 4 ) 2 polymorphs probed with neutron vibrational spectroscopy and first-principles calculations

    SciTech Connect

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

    2016-08-19

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

  14. 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.

  15. Probing the Structure, Pseudorotation, and Radial Vibrations of Cyclopentane by Femtosecond Rotational Raman Coherence Spectroscopy.

    PubMed

    Kowalewski, Philipp; Frey, Hans-Martin; Infanger, Daniel; Leutwyler, Samuel

    2015-11-12

    Femtosecond time-resolved Raman rotational coherence spectroscopy (RCS) is employed to determine accurate rotational, vibration–rotation coupling constants, and centrifugal distortion constants of cyclopentane (C5H10). Its lowest-frequency vibration is a pseudorotating ring deformation that interconverts 10 permutationally distinct but energetically degenerate "twist" minima interspersed by 10 "bent" conformers. While the individual twist and bent structures are polar asymmetric tops, the pseudorotation is fast on the time scale of external rotation, rendering cyclopentane a fluxionally nonpolar symmetric top molecule. The pseudorotational level pattern corresponds to a one-dimensional internal rotor with a pseudorotation constant Bps ≈ 2.8 cm(-1). The pseudorotational levels are significantly populated up to l = ± 13 at 298 K; <10% of the molecules are in the l = 0 level. The next-higher vibration is the “radial” ν23 ring deformation mode at 273 cm–1, which is far above the pseudorotational fundamental. Femtosecond Raman RCS measurements were performed in a gas cell at T = 293 K and in a pulsed supersonic jet at T ≈ 90 K. The jet cooling reduces the pseudorotational distribution to l < ±8 and eliminates the population of ν23, allowing one to determine the rotational constant as A0 = B0 = 6484.930(11) MHz. This value is ∼300 times more precise than the previous value. The fit of the RCS transients reveals that the rotation–pseudorotation coupling constant αe,psB = −0.00070(1) MHz is diminutive, implying that excitation of the pseudorotation has virtually no effect on the B0 rotational constant of cyclopentane. The smallness of αe,psB can be realized when comparing to the vibration–rotation coupling constant of the ν23 vibration, αe,23B = -9.547(1) MHz, which is about 104 times larger.

  16. Two-Dimensional Electronic-Vibrational Spectroscopy of Chlorophyll a and b.

    PubMed

    Lewis, Nicholas H C; Fleming, Graham R

    2016-03-03

    We present two-dimensional electronic-vibrational (2DEV) spectra of isolated chlorophyll a and b in deuterated ethanol. We excite the Q-band electronic transitions and measure the effects on the carbonyl and C ═ C double-bond stretch region of the infrared spectrum. With the aid of density functional theory calculations, we provide assignments for the major features of the spectrum. We show how the 2DEV spectra can be used to readily distinguish different solvation states of the chlorophyll, with features corresponding to the minority pentacoordinate magnesium (Mg) species being resolved along each dimension of the 2DEV spectra from the dominant hexacoordinate Mg species. These assignments represent a crucial first step toward the application of 2DEV spectroscopy to chlorophyll-containing pigment-protein complexes.

  17. 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.

  18. Collective vibrational modes in biological molecules investigated by terahertz time-domain spectroscopy.

    PubMed

    Walther, M; Plochocka, P; Fischer, B; Helm, H; Uhd Jepsen, P

    2002-01-01

    We present well-resolved absorption spectra of biological molecules in the far-IR (FIR) spectral region recorded by terahertz time-domain spectroscopy (THz-TDS). As an illustrative example we discuss the absorption spectra of benzoic acid, its monosubstitutes salicylic acid (2-hydroxy-benzoic acid), 3- and 4-hydroxybenzoic acid, and aspirin (acetylsalicylic acid) in the spectral region between 18 and 150 cm(-1). The spectra exhibit distinct features originating from low-frequency vibrational modes caused by intra- or intermolecular collective motion and lattice modes. Due to the collective origin of the observed modes the absorption spectra are highly sensitive to the overall structure and configuration of the molecules, as well as their environment. The THz-TDS procedure can provide a direct fingerprint of the molecular structure or conformational state of a compound.

  19. 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.

  20. 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.

  1. Determination of the Rotational Barrier in Ethane by Vibrational Spectroscopy and Statistical Thermodynamics

    NASA Astrophysics Data System (ADS)

    Ercolani, Gianfranco

    2005-11-01

    In a previous article in this Journal ( J. Chem. Educ. 2000 , 77 , 1495 ) we introduced a numerical method, namely, the finite-difference boundary-value method, for the solution of the one-dimensional Schrödinger equation and illustrated its application to the evaluation of energy levels and wave functions for hindered internal rotations. Here the method is used to determine, in combination with vibrational spectroscopy and statistical thermodynamics, the torsional potential in ethane. In particular two distinct approaches have been exploited: the first approach is based on the experimental frequency of torsional mode, and the second, less direct but historically more relevant, approach is based on the experimental heat capacity of ethane at various temperatures and on the frequencies of the other normal modes of vibration. The two approaches provide energy barriers in good agreement with each other, 12.35 and 11.74 kJ mol 1 , respectively, and with the literature values. It is shown that the finite-difference boundary-value method, providing a great number of accurate energy levels, is ideally suited for the calculation of both energy transitions and the partition function for internal rotation. The latter is used to calculate the contribution of torsional mode to thermodynamic functions, such as heat capacity, entropy, and enthalpy. The results are in excellent agreement with those obtained from the tables of Pitzer (Lewis, G. N.; Randall, M.; Pitzer, K. S.; Brewer, L. Thermodynamics , 2nd ed.; McGraw-Hill: New York, 1961; Chapter 27).

  2. Probing the Phosphopantetheine Arm Conformations of Acyl Carrier Proteins Using Vibrational Spectroscopy

    PubMed Central

    2015-01-01

    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. PMID:25080832

  3. Structure and conformations of isoprene by vibrational spectroscopy and gas electron diffraction

    NASA Astrophysics Data System (ADS)

    Traetteberg, M.; Paulen, G.; Cyvin, S. J.; Panchenko, Yu. N.; Mochalov, V. I.

    1984-04-01

    The structure of the isoprene (2-methyl-buta-1,3-diene) molecule has been studied by vibrational spectroscopy and gas electron diffraction techniques. A normal coordinate analysis was used to calculate the vibrational frequencies for the anti ( s-trans), gauche and syn ( s-cis) conformers of the molecule. Assignments of some frequencies of the anti form were revised. The experimental bands at 1255, 635, 555, 419 and 311 cm -1 are assigned as fundamentals of the gauche conformer with a high degree of confidence. Among the structural parameters determined by electron diffraction are the following bond distances (in Å): CC 1.340, CC 1.463, CC methyl 1.512, CH 1.076 and CmethylH 1.110. The abundance of the anti form was determined to be 95.3%, while the rest (4.7%) was interpreted as the gauche form with a dihedral angle of 73.5°.

  4. The determination of the absolute configurations of chiral molecules using vibrational circular dichroism (VCD) spectroscopy.

    PubMed

    Stephens, Philip J; Devlin, Frank J; Pan, Jian-Jung

    2008-05-15

    The vibrational circular dichroism (VCD) spectra of the two enantiomers of a chiral molecule are of equal magnitude and opposite sign: i.e. mirror-image enantiomers give mirror-image VCD spectra. In principle, the absolute configuration (AC) of a chiral molecule can therefore be determined from its VCD spectrum. In practice, the determination of the AC of a chiral molecule from its experimental VCD spectrum requires a methodology which reliably predicts the VCD spectra of its enantiomers. The only reliable methodology developed to date uses the Stephens quantum-mechanical theory of the rotational strengths of fundamental vibrational transitions, developed in the early 1980s, implemented using ab initio density functional theory in the GAUSSIAN program in the mid 1990s. This methodology has by now been widely used in determining ACs from experimental VCD spectra. In this article we discuss the protocol for determining the ACs of chiral molecules with optimum reliability and its implementation for a variety of molecules, including the D3 symmetry perhydrotriphenylene, a thiazino-oxadiazolone recently shown to be a highly active calcium entry channel blocker, the alkaloid natural products schizozygine, iso-schizogaline, and iso-schizogamine, and the iridoid natural products plumericin, iso-plumericin, and prismatomerin. The power of VCD spectroscopy in determining ACs, even for large organic molecules and for substantially conformationally-flexible organic molecules is clearly documented.

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

    NASA Astrophysics Data System (ADS)

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

    2011-08-01

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

  6. 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.

  7. 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.

  8. Gas Phase Vibrational Spectroscopy of Weakly Volatil Safe Taggants Using a Synchrotron Source

    NASA Astrophysics Data System (ADS)

    Cuisset, Arnaud; Hindle, Francis; Mouret, Gael; Gruet, Sebastien; Pirali, Olivier; Roy, Pascale

    2013-06-01

    The high performances of the AILES beamline of SOLEIL allow to study at medium resolution (0.5 cm^{-1}) the gas phase THz vibrational spectra of weakly volatil compounds. Between 2008 and 2010 we recorded and analyzed the THz/Far-IR spectra of phosphorous based nerve agents thanks to sufficient vapour pressures from liquid samples at room temperature. Recently, we extended these experiments towards the vibrational spectroscopy of vapour pressures from solid samples. This project is quite challenging since we target lower volatile compounds, and so requires very high sensitive spectrometers. Moreover a specially designed heated multipass-cell have been developped for the gas phase study of very weak vapor pressures. Thanks to skills acquired during initial studies and recent experiments performed on AILES with solid PAHs, we have recorded and assigned the gas phase vibrational fingerprints from the THz to the NIR spectral domain (10-4000 cm-1) of a set of targeted nitro-derivatives. The study was focused onto the para, ortho-mononitrotoluene (p-NT, o-NT), the 1,4 Dinitrobenzene (1,4 DNB), the 2,3-dimethyl-2,3-dinitrobutane (DMNB), and 2,4 and 2,6-dinitrotoluene (2,4-2,6 DNT), which are safe taggants widely used for the detection of commercial explosives. These taggants are usually added to plastic explosives in order to facilitate their vapour detection. Therefore, there is a continuous interest for their detection and identification in realistic conditions via optical methods. A first step consists in the recording of their gas phase vibrational spectra. These expected spectra focused onto molecules involved into defence and security domains are not yet available to date and will be very useful for the scientific community. This work is supported by the contract ANR-11-ASTR-035-01. A. Cuisset, G. Mouret, O. Pirali, P. Roy, F. Cazier, H. Nouali, J. Demaison, J. Phys. Chem. B, 2008, 112:, 12516-12525 I. Smirnova, A. Cuisset, R. Bocquet, F. Hindle, G. Mouret, O

  9. 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.

  10. 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)

  11. Biomedical Magnetic Resonance Imaging and Spectroscopy with Laser Polarized Noble Gases

    NASA Astrophysics Data System (ADS)

    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 smaller, but the noble gas polarization is thousands of times greater than the proton polarization of order 10-5 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. We 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.

  12. 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.

  13. 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.

  14. 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.

  15. Photodissociation yield spectroscopy of vinyl bromide cation generated by mass-analyzed threshold ionization: Vibrational spectroscopy and decay dynamics in the B ˜ state

    NASA Astrophysics Data System (ADS)

    Lee, Mina; Kim, Myung Soo

    2007-04-01

    A new technique [mass-analyzed threshold ionization (MATI)-photodissociation yield spectroscopy] to probe bound excited states of a cation was developed, which measures photodissociation yield of the cation generated by mass-analyzed threshold ionization. A vibrational spectrum of vinyl bromide cation in the B ˜ state was obtained using this technique. Optical resolution in the low vibrational energy range of the spectrum was far better than in conventional MATI spectra. The origin of the B ˜ state was found at 2.2578±0.0003eV above the first ionization onset. Almost complete vibrational assignment was possible for peaks appearing in the spectrum. Analysis of time-of-flight profiles of C2H3+ product ion obtained with different laser polarization angles suggested that photoexcited vinyl bromide cation remained in the B ˜ state for several hundred picoseconds prior to internal conversion to the ground state and dissociation therein.

  16. Interfacial Processes in Model Lithium Ion Systems Probed with Vibrational Sum Frequency Generation Spectroscopy

    NASA Astrophysics Data System (ADS)

    Nicolau, Bruno G.; Garcia Rey, Natalia; Dlott, Dana

    2014-06-01

    Vibrational sum frequency generation (SFG) spectroscopy was used to probe electrochemical processes taking place at the interface between metal anodes and the liquid phase in model lithium ion systems. Lithium ion batteries have been extensively studied and characterized by numerous techniques. However, the mechanisms behind many properties are still unclear due to the lack of techniques that can directly probe them in situ. The formation of the electrode passivating layer known as solid-electrolyte interphase (SEI) is one such example. During the first charging cycle of a battery, some of the electrolyte undergoes reduction at the electrode surface forming an electrically isolating barrier that prevents the subsequent reduction of more electrolyte molecules. The SFG selection rules suppress signals from molecules in centrosymmetric environments such as electrolyte layers, so SFG is a selective probe of interfacial environments such as the SEI. In this study, ethylene carbonate's (EC) response to potential cycling was observed. EC is commonly used as a high permittivity solvent in batteries and is widely believed to be the main component of the SEI in its reduced form, lithium ethylene dicarbonyl. EC's carbonyl stretch (1850 cm-1) was measured in conjunction with cyclic voltammetry experiments. The SFG intensity showed remarkable agreement with the changing potential, as seen in the figure below. The shoulders on each side of the peaks in (a) are especially interesting, as they correspond to the potentials where lithium metal is oxidized and reduced. Vibrational modes found at 1300-1400 cm-1, usually assigned to the reduced form of EC, are also being studied in order to provide more information on the nature of the SEI.

  17. A study of the eigenvectors of the vibrational modes in crystalline cytidine via high-pressure Raman spectroscopy.

    PubMed

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

    2015-01-01

    Raman spectroscopy has been used to study the eigenvectors and eigenvalues of the vibrational modes of crystalline cytidine at 295 K and high pressures by evaluating the logarithmic derivative of the vibrational frequency ω with respect to pressure P: [Formula: see text]. Crystalline samples of molecular materials have strong intramolecular bonds and weak intermolecular bonds. This hierarchy of bonding strengths causes the vibrational optical modes localized within a molecular unit ("internal" modes) to be relatively high in frequency while the modes in which the molecular units vibrate against each other ("external" modes) have relatively low frequencies. The value of the logarithmic derivative is a useful diagnostic probe of the nature of the eigenvector of the vibrational modes because stretching modes (which are predominantly internal to the molecule) have low logarithmic derivatives while external modes have higher logarithmic derivatives. In crystalline cytidine, the modes at 85.8, 101.4, and 110.6 cm(-1) are external in which the molecules of the unit cell vibrate against each other in either translational or librational motions (or some linear combination thereof). All of the modes above 320 cm(-1) are predominantly internal stretching modes. The remaining modes below 320 cm(-1) include external modes and internal modes, mostly involving either torsional or bending motions of groups of atoms within a molecule.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Vacuum ultraviolet mass-analyzed threshold ionization spectroscopy of vinyl bromide: Franck-Condon analysis and vibrational assignment

    NASA Astrophysics Data System (ADS)

    Lee, Mina; Kim, Myung Soo

    2003-09-01

    Vibrational spectrum of vinyl bromide cation in the ground electronic state was obtained by one-photon mass-analyzed threshold ionization (MATI) spectroscopy using coherent vacuum ultraviolet radiation generated by four-wave difference frequency mixing in Kr. From MATI spectrum, ionization energy to the ground state of the cation was determined to be 9.8171±0.0006 eV (79 180±5 cm-1). Almost complete vibrational assignments for the peaks in the MATI spectrum were possible by utilizing vibrational frequencies and Franck-Condon factors calculated at the Becke three parameter Lee-Yang-Parr (B3LYP)/6-311++G(df,pd) level. Franck-Condon analysis for one-photon MATI spectra is especially useful because calculations of only the ground electronic states are involved while that for two-photon MATI spectra requires excited state calculations.

  3. 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

    2015-03-07

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

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

    PubMed

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

    2014-10-15

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

  5. Drug-Membrane Interactions Studied by Vibrational Sum-Frequency Spectroscopy

    NASA Astrophysics Data System (ADS)

    Wolf, Lauren; Briggman, Kimberly

    2008-03-01

    The activity of a number of drugs depends directly on their interaction with cell membranes and, thus, an understanding of drug-membrane interactions is necessary for improving their pharmacological performance. Drug molecules can interact with membranes by directly binding to membrane-bound proteins or by intercalating into the lipid matrix itself, altering membrane properties such as fluidity, thickness, internal pressure, and phase transition temperature. Here, we focus on the effects of local anesthetics incorporated into the lipid matrix, studying the structural changes induced in supported lipid bilayers by vibrational sum-frequency spectroscopy (VSFS). We find that in addition to depressing the phase transition temperature of the lipid bilayers, most anesthetics also sharpen the gel to liquid- crystalline transition, suggesting an increase in membrane constituent cooperativity. This behavior contrasts the effects of cholesterol on lipid bilayers, which increases membrane rigidity and broadens the phase transition. The structure of the membrane-intercalated anesthetics themselves will also be discussed. This work demonstrates the potential of using supported lipid bilayers and surface-sensitive techniques for future pharmacological studies.

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  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. Water Oxidation Mechanisms of Metal Oxide Catalysts by Vibrational Spectroscopy of Transient Intermediates.

    PubMed

    Zhang, Miao; Frei, Heinz

    2017-02-22

    Water oxidation is an essential reaction of an artificial photosystem for solar fuel generation because it provides electrons needed to reduce carbon dioxide or protons to a fuel. Earth-abundant metal oxides are among the most attractive catalytic materials for this reaction because of their robustness and scalability, but their efficiency poses a challenge. Knowledge of catalytic surface intermediates gained by vibrational spectroscopy under reaction conditions plays a key role in uncovering kinetic bottlenecks and provides a basis for catalyst design improvements. Recent dynamic infrared and Raman studies reveal the molecular identity of transient surface intermediates of water oxidation on metal oxides. Combined with ultrafast infrared observations of how charges are delivered to active sites of the metal oxide catalyst and drive the multielectron reaction, spectroscopic advances are poised to play a key role in accelerating progress toward improved catalysts for artificial photosynthesis. Expected final online publication date for the Annual Review of Physical Chemistry Volume 68 is April 20, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  10. Vibrational and structural investigation of SOUL protein single crystals by using micro-Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Rossi, Barbara; Giarola, Marco; Mariotto, Gino; Ambrosi, Emmanuele; Monaco, Hugo L.

    2010-05-01

    Protein SOUL is a new member of the recently discovered putative heme-binding protein family called SOUL/HEBP and, to date, no structural information exists for this protein. Here, micro-Raman spectroscopy is used to study the vibrational properties of single crystals obtained from recombinant protein SOUL by means of two different optimization routes. This spectroscopic approach offers the valuable advantage of the in-situ collection of experimental data from protein crystals, placed onto a hanging-drop plate, under the same conditions used to grow the crystals. By focusing on the regions of amides I and III bands, some secondary structure characteristic features have been recognized. Moreover, some side-chain marker bands were observed in the Raman spectra of SOUL crystals and the unambiguous assignment of these peaks inferred by comparing the experimental Raman spectra of pure amino acids and their Raman intensities computed using quantum chemical calculations. Our comparative analysis allows to get a deeper understanding of the side-chain environments and of the interactions involving these specific amino acids in the two different SOUL crystals.

  11. 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.

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

    DOE PAGES

    Ogata, Hideaki; Krämer, Tobias; Wang, Hongxin; ...

    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

  13. 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.

  14. 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.

  15. 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

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

    PubMed

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

    2007-05-01

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

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

    PubMed

    Jeništová, Adéla; Dendisová, Marcela; Matějka, Pavel

    2016-12-21

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

  18. Phospholipid monolayers probed by vibrational sum frequency spectroscopy: instability of unsaturated phospholipids.

    PubMed

    Liljeblad, Jonathan F D; Bulone, Vincent; Tyrode, Eric; Rutland, Mark W; Johnson, C Magnus

    2010-05-19

    The surface specific technique vibrational sum frequency spectroscopy has been applied to in situ studies of the degradation of Langmuir monolayers of 1,2-diacyl-phosphocholines with various degrees of unsaturation in the aliphatic chains. To monitor the degradation of the phospholipids, the time-dependent change of the monolayer area at constant surface pressure and the sum frequency intensity of the vinyl CH stretch at the carbon-carbon double bonds were measured. The data show a rapid degradation of monolayers of phospholipids carrying unsaturated aliphatic chains compared to the stable lipids carrying fully saturated chains when exposed to the ambient laboratory air. In addition, the degradation of the phospholipids can be inhibited by purging the ambient air with nitrogen. This instability may be attributed to spontaneous degradation by oxidation mediated by various reactive species in the air. To further elucidate the process of lipid oxidation in biological membranes artificial Langmuir monolayers probed by a surface specific spectroscopic technique as in this study can serve as a model system for studying the degradation/oxidation of cell membrane constituents.

  19. 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.

  20. Vibrational sum-frequency spectroscopy for trace chemical detection on surfaces at stand-off distances.

    PubMed

    Asher, William E; Willard-Schmoe, Ella

    2013-03-01

    Vibrational sum-frequency spectroscopy (VSFS) has been used for some time as a laboratory-based surface chemical analytical tool. Here, theoretical considerations in applying the method as a remote-sensing probe for detecting trace levels of chemicals adsorbed on surfaces are presented. Additionally, a VSFS instrument is configured to operate at a stand-off distance of 2.2 m using near-nadir incidence angles. This system was used to measure VSFS spectra for films of pure 1-amino-4-nitrobenzene (p-nitroaniline, PNA) and pure 2-hydroxy-1,3,5-trinitrobenzene (picric acid, PA) adsorbed on polished T-6061 aluminum alloy. These spectra are used to investigate the effect of optical polarization on the sum-frequency response of these compounds at nadir optical geometries. Detection limits for each compound are also estimated and found to be 0.51 μg cm(2) for PNA and 0.89 μg cm(2) for PA. The implications of these results regarding remote sensing applications of VSFS are discussed.

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

    NASA Astrophysics Data System (ADS)

    Johnson, Mark

    2010-06-01

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

  2. 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

    2016-01-27

    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.

  3. Vibrational spectroscopy and imaging for concurrent cellular trafficking of co-localized doxorubicin and deuterated phospholipid vesicles

    NASA Astrophysics Data System (ADS)

    Misra, S. K.; Mukherjee, P.; Ohoka, A.; Schwartz-Duval, A. S.; Tiwari, S.; Bhargava, R.; Pan, D.

    2016-01-01

    Simultaneous tracking of nanoparticles and encapsulated payload is of great importance and visualizing their activity is arduous. Here we use vibrational spectroscopy to study the in vitro tracking of co-localized lipid nanoparticles and encapsulated drug employing a model system derived from doxorubicin-encapsulated deuterated phospholipid (dodecyl phosphocholine-d38) single tailed phospholipid vesicles.Simultaneous tracking of nanoparticles and encapsulated payload is of great importance and visualizing their activity is arduous. Here we use vibrational spectroscopy to study the in vitro tracking of co-localized lipid nanoparticles and encapsulated drug employing a model system derived from doxorubicin-encapsulated deuterated phospholipid (dodecyl phosphocholine-d38) single tailed phospholipid vesicles. Electronic supplementary information (ESI) available: Raman and confocal images of the Deuto-DOX-NPs in cells, materials and details of methods. See DOI: 10.1039/c5nr07975f

  4. High Resolution Spectroscopy of 1,2-Difluoroethane in a Molecular Beam: A Case Study of Vibrational Mode-Coupling

    DTIC Science & Technology

    1992-05-29

    Spectroscopy of 1,2- Difluoroethane in a Molecular Beam: A Case Study of Vibrational Mode-Coupling by Steven W. Mork, C. Cameron Miller, and Laura A...and sale; its distribution is unlimited. 92-14657 l9lll l l l , II a HIGH RESOLUTION SPECTROSCOPY OF 1,2- DIFLUOROETHANE IN A MOLECULAR BEAM: A CASE...14853-1301 Abstract The high resolution infrared spectrum of 1,2- difluoroethane (DFE) in a molecular beam has been obtained over the 2978-2996 cm-1

  5. 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.

  6. Understanding the vibrational mode-specific polarization effects in femtosecond Raman-induced Kerr-effect spectroscopy.

    PubMed

    McAnally, Michael O; Guo, Yinsheng; Balakrishnan, Gurusamy; Schatz, George C; Van Duyne, Richard P

    2016-11-15

    Optically heterodyne-detected femtosecond Raman-induced Kerr-effect spectroscopy (OHD-FRIKES) was observed in neat cyclohexane. In this Letter, an examination of the effect of the Raman pump ellipticity on the multiplex OHD-FRIKES spectra is discussed. The Raman pump ellipticity scanned OHD-FRIKES results reproduce anomalous observables from previous OHD-FRIKES experiments and suggest new methods of tracking transient vibrational mode polarization in complex systems.

  7. 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

  8. 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.

  9. 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.

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

    PubMed

    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(-) 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.

  11. 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.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2008-11-01

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

  14. Key hydride vibrational modes in [NiFe] hydrogenase model compounds studied by resonance Raman spectroscopy and density functional calculations.

    PubMed

    Shafaat, Hannah S; Weber, Katharina; Petrenko, Taras; Neese, Frank; Lubitz, Wolfgang

    2012-11-05

    Hydrogenase proteins catalyze the reversible conversion of molecular hydrogen to protons and electrons. While many enzymatic states of the [NiFe] hydrogenase have been studied extensively, there are multiple catalytically relevant EPR-silent states that remain poorly characterized. Analysis of model compounds using new spectroscopic techniques can provide a framework for the study of these elusive states within the protein. We obtained optical absorption and resonance Raman (RR) spectra of (dppe)Ni(μ-pdt)Fe(CO)(3) and [(dppe)Ni(μ-pdt)(μ-H)Fe(CO)(3)][BF(4)], which are structural and functional model compounds for the EPR-silent Ni-SI and Ni-R states of the [NiFe] hydrogenase active site. The studies presented here use RR spectroscopy to probe vibrational modes of the active site, including metal-hydride stretching vibrations along with bridging ligand-metal and Fe-CO bending vibrations, with isotopic substitution used to identify key metal-hydride modes. The metal-hydride vibrations are essentially uncoupled and represent isolated, localized stretching modes; the iron-hydride vibration occurs at 1530 cm(-1), while the nickel-hydride vibration is observed at 945 cm(-1). The significant discrepancy between the metal-hydride vibrational frequencies reflects the slight asymmetry in the metal-hydride bond lengths. Additionally, time-dependent density functional theory (TD-DFT) calculations were carried out to obtain theoretical RR spectra of these compounds. On the basis of the detailed comparison of theory and experiment, the dominant electronic transitions and significant normal modes probed in the RR experiments were assigned; the primary transitions in the visible wavelengths represent metal-to-metal and metal-to-ligand charge transfer bands. Inherent properties of metal-hydride vibrational modes in resonance Raman spectra and DFT calculations are discussed together with the prospects of observing such vibrational modes in metal-hydride-containing proteins. Such a

  15. Assignment of the Internal Vibrational Modes of C70 by Inelastic Neutron Scattering Spectroscopy and Periodic-DFT.

    PubMed

    Refson, Keith; Parker, Stewart F

    2015-10-01

    The fullerene C70 may be considered as the shortest possible nanotube capped by a hemisphere of C60 at each end. Vibrational spectroscopy is a key tool in characterising fullerenes, and C70 has been studied several times and spectral assignments proposed. Unfortunately, many of the modes are either forbidden or have very low infrared or Raman intensity, even if allowed. Inelastic neutron scattering (INS) spectroscopy is not subject to selection rules, and all the modes are allowed. We have obtained a new INS spectrum from a large sample recorded at the highest resolution available. An advantage of INS spectroscopy is that it is straightforward to calculate the spectral intensity from a model. We demonstrate that all previous assignments are incorrect in at least some respects and propose a new assignment based on periodic density functional theory (DFT) that successfully reproduces the INS, infrared, and Raman spectra.

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

    NASA Astrophysics Data System (ADS)

    Huang, Zishuai; Allen, Heather C.

    2012-06-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1978-01-01

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

  18. Vibration-rotation interactions and ring-puckering in 3,3-dimethyl oxetane by microwave spectroscopy

    NASA Astrophysics Data System (ADS)

    López, Juan C.; Lesarri, Alberto G.; Villamañán, Rosa M.; Alonso, Josél.

    1990-06-01

    Ring puckering in 3,3-dimethyl oxetane has been investigated using microwave spectroscopy. Microwave spectra of the ground state, the first six ring-puckering excited states, and nine excited states of the methyl groups' deformation vibrations have been observed. The μa electric dipole moment component has been determined as 2.03(3) D from Stark-effect measurements. The vibrational dependence of the rotational constants is consistent with the ring-puckering potential function derived by Duckett et al. ( J. Mol. Spectrosc.69, 159-165 (1978)). Coriolis coupling interactions have been observed and are satisfactorily accounted for with a quartic centrifugal distortion Hamiltonian. The vibrational dependence of the centrifugal distortion constants has been analyzed using the theory developed by Creswell and Mills. In order to reproduce the experimental value of the vibration-rotation interaction parameter, {δμ ab}/{δQ}, a dynamical model allowing the rocking of the CH 3CCH 3 group should be used. The equilibrium ring puckering angle calculated with this model and the ring-puckering potential function is 17.5°.

  19. Effect of impurity molecules on the low-temperature vibrational dynamics of polyisobutylene: Investigation by single-molecule spectroscopy

    NASA Astrophysics Data System (ADS)

    Eremchev, I. Yu.; Naumov, A. V.; Vainer, Yu. G.; Kador, L.

    2009-05-01

    The influence of impurity chromophore molecules—tetra-tert-butylterrylene (TBT) and dibenzo-anthanthrene (DBATT)—on the vibrational dynamics of the amorphous polymer polyisobutylene (PIB) has been studied via single-molecule spectroscopy. The measurements were performed in the temperature region of 7-30 K, where the interaction of the chromophores with quasilocalized low-frequency vibrational modes (LFMs) determines the observed spectral line broadening. The analysis of the individual temperature dependences of the linewidths for a large number of single probe molecules yielded effective frequency values of those LFMs which are located near the respective chromophores. In this way the distributions of the LFM frequencies were measured for the two systems, and they were found to be similar. Moreover, they are in good agreement with the vibrational density of states as measured in pure PIB by inelastic neutron scattering. This allows us to conclude that, at least in the case of PIB, doping with low concentrations of the nonpolar and neutral molecules TBT and DBATT does not affect the vibrational dynamics of the matrix markedly.

  20. Molecular structure and vibrational study of diprotonated guanazolium using DFT calculations and FT-IR and FT-Raman spectroscopies

    NASA Astrophysics Data System (ADS)

    Guennoun, L.; Zaydoun, S.; El jastimi, J.; Marakchi, K.; Komiha, N.; Kabbaj, O. K.; El Hajji, A.; Guédira, F.

    2012-11-01

    The purpose of this manuscript is to discuss our investigations of diprotonated guanazolium chloride using vibrational spectroscopy and quantum chemical methods. The solid phase FT-IR and FT-Raman spectra were recorded in the regions 4000-400 cm-1 and 3600-50 cm-1 respectively, and the band assignments were supported by deuteration effects. Different sites of diprotonation have been theoretically examined at the B3LYP/6-31G∗ level. The results of energy calculations show that the diprotonation process occurs with the two pyridine-like nitrogen N2 and N4 of the triazole ring. The molecular structure, harmonic vibrational wave numbers, infrared intensities and Raman activities were calculated for this form by DFT/B3LYP methods, using a 6-31G∗ basis set. Both the optimized geometries and the theoretical and experimental spectra for diprotonated guanazolium under a stable form are compared with theoretical and experimental data of the neutral molecule reported in our previous work. This comparison reveals that the diprotonation occurs on the triazolic nucleus, and provide information about the hydrogen bonding in the crystal. The scaled vibrational wave number values of the diprotonated form are in close agreement with the experimental data. The normal vibrations were characterized in terms of potential energy distribution (PED) using the VEDA 4 program.

  1. Molecular structure and vibrational study of diprotonated guanazolium using DFT calculations and FT-IR and FT-Raman spectroscopies.

    PubMed

    Guennoun, L; Zaydoun, S; El Jastimi, J; Marakchi, K; Komiha, N; Kabbaj, O K; El Hajji, A; Guédira, F

    2012-11-01

    The purpose of this manuscript is to discuss our investigations of diprotonated guanazolium chloride using vibrational spectroscopy and quantum chemical methods. The solid phase FT-IR and FT-Raman spectra were recorded in the regions 4000-400cm(-1) and 3600-50cm(-1) respectively, and the band assignments were supported by deuteration effects. Different sites of diprotonation have been theoretically examined at the B3LYP/6-31G level. The results of energy calculations show that the diprotonation process occurs with the two pyridine-like nitrogen N2 and N4 of the triazole ring. The molecular structure, harmonic vibrational wave numbers, infrared intensities and Raman activities were calculated for this form by DFT/B3LYP methods, using a 6-31G basis set. Both the optimized geometries and the theoretical and experimental spectra for diprotonated guanazolium under a stable form are compared with theoretical and experimental data of the neutral molecule reported in our previous work. This comparison reveals that the diprotonation occurs on the triazolic nucleus, and provide information about the hydrogen bonding in the crystal. The scaled vibrational wave number values of the diprotonated form are in close agreement with the experimental data. The normal vibrations were characterized in terms of potential energy distribution (PED) using the VEDA 4 program.

  2. Vibration eigenmodes of the Au-(5 ×2 ) /Si(111) surface studied by Raman spectroscopy and first-principles calculations

    NASA Astrophysics Data System (ADS)

    Liebhaber, M.; Halbig, B.; Bass, U.; Geurts, J.; Neufeld, S.; Sanna, S.; Schmidt, W. G.; Speiser, E.; Räthel, J.; Chandola, S.; Esser, N.

    2016-12-01

    Ordered submonolayers of adsorbate atoms on semiconductor surfaces constitute a playground for electronic correlation effects, which are tightly connected to the local atomic arrangement and the corresponding vibration eigenmodes. We report on a study of the vibration eigenmodes of Au-covered Si(111) surfaces with (5 ×2 ) reconstruction using polarized Raman spectroscopy and first-principles calculations. Upon Au coverage, the vibration eigenmodes of the clean reconstructed Si(111)-(7 ×7 ) surface are quenched and replaced by new eigenmodes, determined by the Au-(5 ×2 ) reconstruction. Several polarization-dependent surface eigenmodes emerge in the spectral range from 25 to 120 cm-1 , with the strongest ones at 29, 51, and 106 cm-1. In our first-principles calculations we have determined the vibration frequencies, the corresponding elongation patterns, and the Raman intensities for two different structure models currently discussed in the literature. The best agreement with the experimental results is achieved for a model with 0.7 monolayer coverage and seven Au atoms per unit cell, proposed by S. G. Kwon and M. H. Kang [Phys. Rev. Lett. 113, 086101 (2014), 10.1103/PhysRevLett.113.086101].

  3. Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy.

    PubMed

    Semenov, M A; Blyzniuk, Iu N; Bolbukh, T V; Shestopalova, A V; Evstigneev, M P; Maleev, V Ya

    2012-09-01

    By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (CO and NH(2)) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of Н-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment.

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

    NASA Astrophysics Data System (ADS)

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

    1999-05-01

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

  5. Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Semenov, M. A.; Blyzniuk, Iu. N.; Bolbukh, T. V.; Shestopalova, A. V.; Evstigneev, M. P.; Maleev, V. Ya.

    2012-09-01

    By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (Cdbnd O and NH2) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of Н-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment.

  6. 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.

  7. Rotational spectroscopy of vibrationally excited N2H+ and N2D+ up to 2.7 THz

    NASA Astrophysics Data System (ADS)

    Yu, S.; Pearson, J. C.; Drouin, B. J.; Crawford, T.; Daly, A. M.; Elliott, B.; Amano, T.

    2015-08-01

    Terahertz absorption spectroscopy was employed to extend the measurements on the pure rotational transitions of N2H+, N2D+ and their 15N-containing isotopologues in the ground state and first excited vibrational states for the three fundamental vibrational modes. In total, 91 new pure rotational transitions were observed in the range of 0.7-2.7 THz. The observed transition frequencies were fit to experimental accuracy, and the improved molecular parameters were obtained. The new measurements and predictions reported here will support the analysis of high-resolution astronomical observations made with facilities such as SOFIA and ALMA where laboratory rest frequencies with uncertainties of 1 MHz or smaller are required for proper analysis of velocity resolved astrophysical components.

  8. 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.

  9. 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.

  10. Active vibrations of 1-cyanonaphthalene cation studied by mass-analyzed threshold ionization spectroscopy

    NASA Astrophysics Data System (ADS)

    Shivatare, Vidya; Tzeng, Sheng Yuan; Tzeng, Wen Bih

    2013-02-01

    We apply the two-color resonant two-photon mass-analyzed threshold ionization (MATI) spectroscopic technique to record the cation spectra of 1-cyanonaphthalene via four intermediate vibronic levels. The adiabatic ionization energy is determined to be 69 466 ± 5 cm-1. The distinct bands at 416, 472, 516, 669, and 852 cm-1 result from in-plane ring deformation vibrations of the cation. Analysis of these MATI spectra suggests that the molecular geometry and vibrational coordinates of the observed vibrations of the cation in the ground D0 state resemble those of the neutral in the electronically excited S1 state.

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

    PubMed

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

    2007-09-25

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

  12. 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

  13. Structural and vibrational spectroscopy investigation of the 5-[(diphenyl) amino] isophthalic acid molecule

    NASA Astrophysics Data System (ADS)

    Kurt, M.; Şaş, E. Babur; Can, M.; Okur, S.; Icli, S.; Demic, S.

    2014-10-01

    The molecular structure and vibrations of 5-(diphenyl) amino] isophthalic acid (DPIFA) were investigated by different spectroscopic techniques (such as infrared and Raman). FT-IR, FT-Raman and dispersive Raman spectra were recorded in the solid phase. HOMO-LUMO analyses were performed. The theoretical calculations for the molecular structure and spectroscopic studies were performed with DFT (B3LYP) and 6-311G(d,p) basis set calculations using the Gaussian 09 program. After optimizing the geometry of the molecule, vibration wavenumbers and fundamental vibrations wavenumbers were assigned on the basis of the potential energy distribution (PED) of the vibrational modes calculated with VEDA 4 program. The results of theoretical calculations for the spectra of the title compound were compared with the observed spectra.

  14. From Conventional to Phase-Sensitive Vibrational Sum Frequency Generation Spectroscopy: Probing Water Organization at Aqueous Interfaces.

    PubMed

    Verreault, Dominique; Hua, Wei; Allen, Heather C

    2012-10-18

    Elucidation of water organization at aqueous interfaces has remained a challenging problem. Conventional vibrational sum frequency generation (VSFG) spectroscopy and its most recent extension, phase-sensitive VSFG (PS-VSFG), have emerged as powerful experimental methods for unraveling structural information at various aqueous interfaces. In this Perspective, we briefly describe the two possible VSFG detection modes, and we point out features that make these methods highly suited to address questions about water organization at air/aqueous interfaces. Several important aqueous interfacial systems are discussed to illustrate the versatility of these methods. Remaining challenges and exciting prospective directions are also presented.

  15. Femtosecond stimulated Raman spectroscopy as a tool to detect molecular vibrations in ground and excited electronic states.

    PubMed

    Gelin, Maxim F; Domcke, Wolfgang; Rao, B Jayachander

    2016-05-14

    We give a detailed theoretical analysis of the simplest variant of femtosecond stimulated Raman spectroscopy, where a picosecond Raman pump pulse and a femtosecond Raman probe pulse are applied resonantly to a chromophore in thermal equilibrium in the ground electronic state. We demonstrate that this technique is capable of the detection of dephasing-free Raman-like lines revealing vibrational modes not only in the electronic ground state but also in the excited electronic state of the chromophore. The analytical results obtained with simplifying assumptions for the shape of the laser pulses are substantiated by numerical simulations with realistic laser pulses, employing the equation-of-motion phase-matching approach.

  16. Femtosecond stimulated Raman spectroscopy as a tool to detect molecular vibrations in ground and excited electronic states

    NASA Astrophysics Data System (ADS)

    Gelin, Maxim F.; Domcke, Wolfgang; Rao, B. Jayachander

    2016-05-01

    We give a detailed theoretical analysis of the simplest variant of femtosecond stimulated Raman spectroscopy, where a picosecond Raman pump pulse and a femtosecond Raman probe pulse are applied resonantly to a chromophore in thermal equilibrium in the ground electronic state. We demonstrate that this technique is capable of the detection of dephasing-free Raman-like lines revealing vibrational modes not only in the electronic ground state but also in the excited electronic state of the chromophore. The analytical results obtained with simplifying assumptions for the shape of the laser pulses are substantiated by numerical simulations with realistic laser pulses, employing the equation-of-motion phase-matching approach.

  17. a Study of Vibrational Mode Coupling in 2-FLUOROETHANOL and 1,2-DIFLUOROETHANE Using High-Resolution Infrared Spectroscopy.

    NASA Astrophysics Data System (ADS)

    Mork, Steven Wayne

    High resolution infrared spectroscopy was used to examine intramolecular vibrational interactions in 2 -fluoroethanol (2FE) and 1,2-difluoroethane (DFE). A high resolution infrared spectrophotometer capable of better than 10 MHz spectral resolution was designed and constructed. The excitation source consists of three lasers: an argon-ion pumped dye laser which pumps a color -center laser. The infrared beam from the color-center laser is used to excite sample molecules which are rotationally and vibrationally cooled in a supersonic molecular beam. Rovibrational excitation of the sample molecules is detected by monitoring the kinetic energy of the molecular beam with a bolometer. The high resolution infrared spectrum of 2FE was collected and analyzed over the 2977-2990 cm^ {-1}^ectral region. This region contains the asymmetric CH stretch on the fluorinated carbon. The spectrum revealed extensive perturbations in the rotational fine structure. Analysis of these perturbations has provided a quantitative measure of selective vibrational mode coupling between the C-H stretch and its many neighboring dark vibrational modes. Interestingly, excitation of the C-H stretch is known to induce a photoisomerization reaction between 2FE's Gg^' and Tt conformers. Implications of the role of mode coupling in the reaction mechanism are also addressed. Similarly, the high resolution infrared spectrum of DFE was collected and analyzed over the 2978-2996 cm ^{-1}^ectral region. This region contains the symmetric combination of asymmetric C-H stretches in DFE. Perturbations in the rotational fine structure indicate vibrational mode coupling to a single dark vibrational state. The dark state is split by approximately 19 cm^{-1} due to tunneling between two identical gauche conformers. The coupling mechanism is largely anharmonic with a minor component of B/C-plane Coriolis coupling. Effects of centrifugal distortion along the molecular A-axis are also observed. The coupled vibrational

  18. Vibrational overtone spectroscopy and intramolecular dynamics of C-H stretches in pyrrole

    NASA Astrophysics Data System (ADS)

    Portnov, Alexander; Epshtein, Michael; Rosenwaks, Salman; Bar, Ilana

    2013-05-01

    Room-temperature photoacoustic spectra and jet-cooled action spectra of the regions of the first and second C-H stretch overtones of pyrrole were measured with the goal of gaining new insight on the vibrational patterns and the intramolecular energy flow out of the initially excited vibrational states. The rotational cooling of the action spectra helped in observing hitherto unresolved features, assisting determination of the existing multiple bands and their positions in each region. These bands were analyzed by building vibrational Hamiltonian matrices related to a simplified joint local-mode/normal-mode (LM/NM) model, accounting for two types of C-H stretches and their Fermi resonances with the CCH deformation modes. The diagonalization of the LM/NM vibrational Hamiltonians and the fitting of the eigenvalues to the band positions revealed model parameters, enabling assignment of the observed bands. The time dependences of the survival probabilities of the C-H stretches in the region of the first and second overtones, deduced from the vibrational Hamiltonian, show quantum beats due to the couplings to the deformations and decays driven by weaker interactions to the bath states. The C-H stretches, although somewhat lower in energy, show stronger coupling than the N-H stretches.

  19. Efficient anharmonic vibrational spectroscopy for large molecules using local-mode coordinates.

    PubMed

    Cheng, Xiaolu; Steele, Ryan P

    2014-09-14

    This article presents a general computational approach for efficient simulations of anharmonic vibrational spectra in chemical systems. An automated local-mode vibrational approach is presented, which borrows techniques from localized molecular orbitals in electronic structure theory. This approach generates spatially localized vibrational modes, in contrast to the delocalization exhibited by canonical normal modes. The method is rigorously tested across a series of chemical systems, ranging from small molecules to large water clusters and a protonated dipeptide. It is interfaced with exact, grid-based approaches, as well as vibrational self-consistent field methods. Most significantly, this new set of reference coordinates exhibits a well-behaved spatial decay of mode couplings, which allows for a systematic, a priori truncation of mode couplings and increased computational efficiency. Convergence can typically be reached by including modes within only about 4 Å. The local nature of this truncation suggests particular promise for the ab initio simulation of anharmonic vibrational motion in large systems, where connection to experimental spectra is currently most challenging.

  20. Efficient anharmonic vibrational spectroscopy for large molecules using local-mode coordinates

    NASA Astrophysics Data System (ADS)

    Cheng, Xiaolu; Steele, Ryan P.

    2014-09-01

    This article presents a general computational approach for efficient simulations of anharmonic vibrational spectra in chemical systems. An automated local-mode vibrational approach is presented, which borrows techniques from localized molecular orbitals in electronic structure theory. This approach generates spatially localized vibrational modes, in contrast to the delocalization exhibited by canonical normal modes. The method is rigorously tested across a series of chemical systems, ranging from small molecules to large water clusters and a protonated dipeptide. It is interfaced with exact, grid-based approaches, as well as vibrational self-consistent field methods. Most significantly, this new set of reference coordinates exhibits a well-behaved spatial decay of mode couplings, which allows for a systematic, a priori truncation of mode couplings and increased computational efficiency. Convergence can typically be reached by including modes within only about 4 Å. The local nature of this truncation suggests particular promise for the ab initio simulation of anharmonic vibrational motion in large systems, where connection to experimental spectra is currently most challenging.

  1. Efficient anharmonic vibrational spectroscopy for large molecules using local-mode coordinates

    SciTech Connect

    Cheng, Xiaolu; Steele, Ryan P.

    2014-09-14

    This article presents a general computational approach for efficient simulations of anharmonic vibrational spectra in chemical systems. An automated local-mode vibrational approach is presented, which borrows techniques from localized molecular orbitals in electronic structure theory. This approach generates spatially localized vibrational modes, in contrast to the delocalization exhibited by canonical normal modes. The method is rigorously tested across a series of chemical systems, ranging from small molecules to large water clusters and a protonated dipeptide. It is interfaced with exact, grid-based approaches, as well as vibrational self-consistent field methods. Most significantly, this new set of reference coordinates exhibits a well-behaved spatial decay of mode couplings, which allows for a systematic, a priori truncation of mode couplings and increased computational efficiency. Convergence can typically be reached by including modes within only about 4 Å. The local nature of this truncation suggests particular promise for the ab initio simulation of anharmonic vibrational motion in large systems, where connection to experimental spectra is currently most challenging.

  2. Characterization of compounds derived from copper-oxamate and imidazolium by X-ray absorption and vibrational spectroscopies

    NASA Astrophysics Data System (ADS)

    do Nascimento, Gustavo M.; do Pim, Walace D.; Reis, Daniella O.; Simões, Tatiana R. G.; Pradie, Noriberto A.; Stumpf, Humberto O.

    2015-05-01

    In this work, compounds derived from copper-oxamate anions (ortho, meta, and para)-phenylenebis (oxamate) and imidazolium cations (1-butyl-3-methylimidazolium) were synthesized. The compounds were characterized by Raman and FTIR spectroscopies and the band assignments were supported by DFT calculations. Strong IR bands from 1610 to 1700 cm-1 dominated the spectra of the complex and can be assigned to νCdbnd O vibrations of the [Cu(opba)]2- anions by the comparison with the DFT data. In opposition to the FTIR spectra, the main vibrational bands in the Raman spectra are observed in the 1350-1600 cm-1 range. All bands in this region are associated to the modified benzene vibrations of the copper-phenylenebis(oxamate) anions. X-ray absorption near edge (XANES) at different energies (NK and Cu L2,3 edges) was also used to probe the interionic interactions. XANES data show that anion-cation interaction in the Cu-oxamate-imidazolium changes the electronic structure around the sbnd Cusbnd Nsbnd sites in the oxamate anion.

  3. Characterization of compounds derived from copper-oxamate and imidazolium by X-ray absorption and vibrational spectroscopies.

    PubMed

    do Nascimento, Gustavo M; do Pim, Walace D; Reis, Daniella O; Simões, Tatiana R G; Pradie, Noriberto A; Stumpf, Humberto O

    2015-05-05

    In this work, compounds derived from copper-oxamate anions (ortho, meta, and para)-phenylenebis (oxamate) and imidazolium cations (1-butyl-3-methylimidazolium) were synthesized. The compounds were characterized by Raman and FTIR spectroscopies and the band assignments were supported by DFT calculations. Strong IR bands from 1610 to 1700cm(-1) dominated the spectra of the complex and can be assigned to νCO vibrations of the [Cu(opba)](2-) anions by the comparison with the DFT data. In opposition to the FTIR spectra, the main vibrational bands in the Raman spectra are observed in the 1350-1600cm(-1) range. All bands in this region are associated to the modified benzene vibrations of the copper-phenylenebis(oxamate) anions. X-ray absorption near edge (XANES) at different energies (NK and Cu L2,3 edges) was also used to probe the interionic interactions. XANES data show that anion-cation interaction in the Cu-oxamate-imidazolium changes the electronic structure around the CuN sites in the oxamate anion.

  4. Ultrafast vibrational spectroscopy of water and aqueous N-methylacetamide: Comparison of different electronic structure/molecular dynamics approaches.

    PubMed

    Schmidt, J R; Corcelli, S A; Skinner, J L

    2004-11-08

    Kwac and Cho [J. Chem. Phys. 119, 2247 (2003)] have recently developed a combined electronic structure/molecular dynamics approach to vibrational spectroscopy in liquids. The method involves fitting ab initio vibrational frequencies for a solute in a cluster of solvent molecules to a linear combination of the electrostatic potentials on the solute atoms due to the charges on the solvent molecules. These authors applied their method to the N-methylacetamide-D/D(2)O system. We (S. A. Corcelli, C. P. Lawrence, and J. L. Skinner, [J. Chem. Phys. 120, 8107 (2004)]) have recently explored a closely related method, where instead of the electrostatic potential, the solute vibrational frequencies are fit to the components of the electric fields on the solute atoms due to the solvent molecules. We applied our method to the HOD/D(2)O and HOD/H(2)O systems. In order to make a direct comparison of these two approaches, in this paper we apply their method to the water system, and our method to the N-methylacetamide system. For the water system we find that the electric field method is superior to the potential approach, as judged by comparison with experiments for the absorption line shape. For the N-methylacetamide system the two methods are comparable.

  5. 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.

  6. High-Resolution Spectroscopy with a Free-Electron Laser: Vibrational Lifetimes of Hydrogen-related Defects in Silicon

    NASA Astrophysics Data System (ADS)

    Luepke, Gunter

    2009-03-01

    Gunter Luepke, Department of Applied Science, The College of William and Mary, Williamsburg, VA 23187 Vibrational lifetimes of hydrogen- and deuterium-related bending and stretching modes in crystalline silicon are measured by high-resolution infrared absorption spectroscopy and pump-probe transient bleaching technique using the Jefferson Lab. Free-Electron Laser. We find that the vibrational lifetimes of the bending modes follow a universal frequency-gap law, i.e., the decay time increases exponentially with increasing decay order, with values ranging from 1 ps for a one-phonon process to 265 ps for a four-phonon process. The temperature dependence of the lifetime shows that the bending mode decays by lowest-order multi-phonon process. In contrast, the lifetimes of the stretching modes are found to be extremely dependent on the defect structure, ranging from 2 to 295 ps. Against conventional wisdom, we find that lifetimes of Si-D stretch modes typically are longer than for the corresponding Si-H modes. Our results provide new insights into vibrational decay and the giant isotope effect of hydrogen in semiconductor systems. The potential implications of the results on the physics of electronic device degradation are discussed.

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

    PubMed

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

    2014-04-01

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

  8. Two-Dimensional Infrared Vibrational Echo Spectroscopy Measurements of the Structural Dynamics Occurring in Conducting Polymer Thin Films

    NASA Astrophysics Data System (ADS)

    Eigner, Audrey Ann

    2011-12-01

    The research presented in this thesis is concerned with the elucidation of the origin of structural dynamics and their relationship to charge mobility in conducting polymer systems. In the past thirty years, research in the field of electrically conducting polymers has grown immensely. Interest in such polymers is due mainly to their unique semiconducting properties and thus their potential application in plastic electronics. While it is known that the charge transport of such polymers is linked to their molecular structure, very little is known about the relationship between charge transport and structural dynamics. In particular, this work has focused on the conducting polymers poly(3-hexylthiophene) (P3HT) and polyaniline (PANI). Samples of each polymer were studied using two-dimensional infrared vibrational echo spectroscopy (2D-IR VES), as well as one-dimensional infrared, UV-visible, and fluorescence spectroscopies. Additional characterizations of the polymers were performed, and included transmission electron microscopy (TEM), hole-mobility and resistance measurements. The vibrational echo technique was especially well suited for this study because it removed inhomogeneous broadening and allowed for the monitoring of the time evolution of molecular structure on the picosecond time scale. Viewed together, the studies presented in this work have begun to correlate specific structural dynamics with changes in the film conductivities.

  9. 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.

  10. Infrared overtone spectroscopy and vibrational analysis of a Fermi resonance in nitric acid: Experiment and theory.

    PubMed

    Konen, Ian M; Li, Eunice X J; Lester, Marsha I; Vázquez, Juana; Stanton, John F

    2006-08-21

    High resolution infrared spectra of nitric acid have been recorded in the first OH overtone region under jet-cooled conditions using a sequential IR-UV excitation method. Vibrational bands observed at 6933.39(3), 6938.75(4), and 6951.985(3) cm(-1) (origins) with relative intensities of 0.42(1), 0.38(1), and 0.20(1) are attributed to strongly mixed states involved in a Fermi resonance. A vibrational deperturbation analysis suggests that the optically bright OH overtone stretch (2nu1) at 6939.2(1) cm(-1) is coupled directly to the nu1 + 2nu2 state at 6946.4(1) cm(-1) and indirectly to the 3nu2 + nu3 + nu7 state at 6938.5(1) cm(-1). Both the identity of the zero-order states and the indirect coupling scheme are deduced from complementary CCSD(T) calculations in conjunction with second-order vibrational perturbation theory. The deperturbation analysis also yields the experimental coupling between 2nu1 and nu1 + 2nu2 of -6.9(1) cm(-1), and that between the two dark states of +5.0(1) cm(-1). The calculated vibrational energies and couplings are in near quantitative agreement with experimentally derived values except for a predicted twofold stronger coupling of 2nu1 to nu1 + 2nu2. Weaker coupling of the strongly mixed states to a dense background of vibrational states via intramolecular vibrational energy redistribution is evident from the experimental linewidths of 0.08 and 0.25 cm(-1) for the higher energy and two overlapping lower energy bands, respectively. A comprehensive rotational analysis of the higher energy band yields spectroscopic parameters and the direction of the OH overtone transition dipole moment.

  11. 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.

  12. Water at the Surfaces of Aligned Phospholipid Multi-Bilayer Model Membranes Probed with Ultrafast Vibrational Spectroscopy

    PubMed Central

    Zhao, Wei; Moilanen, David E.; Fenn, Emily E.; Fayer, Michael D.

    2009-01-01

    The dynamics of water at the surface of artificial membranes composed of aligned multibilayers of the phospholipid dilauroyl phosphatidylcholine (DLPC) are probed with ultrafast polarization selective vibrational pump-probe spectroscopy. The experiments are performed at various hydration levels, x = 2 – 16 water molecules per lipid at 37 °C. The water molecules are ~1 nm above or below the membrane surface. The experiments are conducted on the OD stretching mode of dilute HOD in H2O to eliminate vibrational excitation transfer. The FT-IR absorption spectra of the OD stretch in the DLPC bilayer system at low hydration levels shows a red-shift in frequency relative to bulk water, which is in contrast to the blue shift often observed in systems such as water nanopools in reverse micelles. The spectra for x = 4 – 16 can be reproduced by a superposition of the spectra for x = 2 and bulk water. IR Pump-probe measurements reveal that the vibrational population decays (lifetimes) become longer as the hydration level is decreased. The population decays are fit well by biexponential functions. The population decays, measured as a function of the OD stretch frequency, suggest the existence of two major types of water molecules in the interfacial region of the lipid bilayers. One component may be a clathrate-like water cluster near the hydrophobic choline group and the other may be related to the hydration water molecules mainly associated with the phosphate group. As the hydration level increases, the vibrational lifetimes of these two components decrease, suggesting a continuous evolution of the hydration structures in the two components associated with the swelling of the bilayers. The agreement of the magnitudes of the two components obtained from IR spectra with those from vibrational lifetime measurements further supports the two component model. The vibrational population decay fitting also gives an estimation of the number of phosphate-associated water molecules

  13. Vibrational cooling dynamics of a [FeFe]-hydrogenase mimic probed by time-resolved infrared spectroscopy.

    PubMed

    Caplins, Benjamin W; Lomont, Justin P; Nguyen, Son C; Harris, Charles B

    2014-12-11

    Picosecond time-resolved infrared spectroscopy (TRIR) was performed for the first time on a dithiolate bridged binuclear iron(I) hexacarbonyl complex ([Fe₂(μ-bdt)(CO)₆], bdt = benzene-1,2-dithiolate) which is a structural mimic of the active site of the [FeFe]-hydrogenase enzyme. As these model active sites are increasingly being studied for their potential in photocatalytic systems for hydrogen production, understanding their excited and ground state dynamics is critical. In n-heptane, absorption of 400 nm light causes carbonyl loss with low quantum yield (<10%), while the majority (ca. 90%) of the parent complex is regenerated with biexponential kinetics (τ₁ = 21 ps and τ₂ = 134 ps). In order to understand the mechanism of picosecond bleach recovery, a series of UV-pump TRIR experiments were performed in different solvents. The long time decay (τ₂) of the transient spectra is seen to change substantially as a function of solvent, from 95 ps in THF to 262 ps in CCl₄. Broadband IR-pump TRIR experiments were performed for comparison. The measured vibrational lifetimes (T₁(avg)) of the carbonyl stretches were found to be in excellent correspondence to the observed τ₂ decays in the UV-pump experiments, signifying that vibrationally excited carbonyl stretches are responsible for the observed longtime decays. The fast spectral evolution (τ₁) was determined to be due to vibrational cooling of low frequency modes anharmonically coupled to the carbonyl stretches that were excited after electronic internal conversion. The results show that cooling of both low and high frequency vibrational modes on the electronic ground state give rise to the observed picosecond TRIR transient spectra of this compound, without the need to invoke electronically excited states.

  14. Vibrational spectroscopy and dynamics of W(CO)6 in solid methane as a probe of lattice properties

    NASA Astrophysics Data System (ADS)

    Thon, Raphael; Chin, Wutharath; Chamma, Didier; Galaup, Jean-Pierre; Ouvrard, Aimeric; Bourguignon, Bernard; Crépin, Claudine

    2016-12-01

    Methane solids present more than one accessible crystalline phase at low temperature at zero pressure. We trap W(CO)6 in CH4 and CD4 matrices between 8 and 35 K to probe the interaction between an impurity and its surrounding molecular solid under various physical conditions. Linear and nonlinear vibrational spectroscopies of W(CO)6 highlight different kinds of interaction and reveal new and remarkable signatures of the phase transition of methane. The structures in the absorption band of the antisymmetric CO stretching mode exhibit a clear modification at the transition between phase II and phase I in CH4 and motional narrowing is observed upon temperature increase. The vibrational dynamics of this mode is probed in stimulated photon echo experiments performed with a femtosecond IR laser. A short component around 10 ps is detected in the population relaxation lifetime in the high temperature phase of solid CH4 (phase I) and disappears at lower temperatures (phase II) where the vibrational lifetime is in the hundreds of ps. The analysis of the nonlinear time-resolved results suggests that the short component comes from a fast energy transfer between the vibrational excitation of the guest and the lattice in specific families of sites. Such fast transfers are observed in the case of W(CO)6 trapped in CD4 because of an energy overlap of the excitation of W(CO)6 and a lattice vibron. In solid CH4, even when these V-V transfers are not efficient, pure dephasing processes due to the molecular nature of the host occur: they are temperature dependent without a clear modification at the phase transition.

  15. 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; ...

    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

  16. 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…

  17. 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

    2015-06-07

    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.

  18. Precision Spectroscopy on Highly-Excited Vibrational Levels of H_2

    NASA Astrophysics Data System (ADS)

    Niu, Ming Li; Salumbides, Edcel John; Ubachs, Wim

    2015-06-01

    The ground electronic energy levels of H_2 have been used as a benchmark system for the most precise comparisons between ab initio calculations and experimental investigations. Recent examples include the determinations of the ionization energy [1], fundamental vibrational energy splitting [2], and rotational energy progression extending to J=16 [3]. In general, the experimental and theoretical values are in excellent agreement with each other. The energy calculations, however, reduce in accuracy with the increase in rotational and vibrational excitation, limited by the accuracy of non-Born Oppenheimer corrections, as well as the higher-order QED effects. While on the experimental side, it remains difficult to sufficiently populate these excited levels in the ground electronic state. We present here our high-resolution spectroscopic study on the X ^1σ^+_g electronic ground state levels with very high vibrational quanta (ν=10,11,12). Vibrationally-excited H_2 are produced from the photodissociation of H_2S [4], and subsequently probed by a narrowband pulsed dye laser system. The experimental results are consistent with and more accurate than the best theoretical values [5]. These vibrationally-excited level energies are also of interest to studies that extract constraints on the possible new interactions that extend beyond the Standard Model [6]. [1] J. Liu et al., J. Chem. Phys. 130, 174306 (2009). [2] G. Dickenson et al., Phys. Rev. Lett. 110, 193601 (2013). [3] E.J. Salumbides et al., Phys. Rev. Lett. 107, 143005 (2011). [4] J. Steadman and T. Baer, J. Chem. Phys. 91, 6113 (1989). [5] J. Komasa et al., J. Chem. Theory Comp. 7, 3105 (2011). [6] E.J. Salumbides et al., Phys. Rev. D 87, 112008 (2013).

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

    PubMed

    Gruenbaum, S M; Skinner, J L

    2011-08-21

    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 H(2)O. 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

  20. 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

  1. 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.

  2. Tracking a Paternò-Büchi reaction in real time using transient electronic and vibrational spectroscopies.

    PubMed

    Harris, Stephanie J; Murdock, Daniel; Grubb, Michael P; Clark, Ian P; Greetham, Gregory M; Towrie, Michael; Ashfold, Michael N R

    2014-11-06

    A detailed mechanistic investigation of the early stages of the Paternò-Büchi reaction following 267 nm excitation of benzaldehyde in cyclohexene has been completed using ultrafast, broadband transient UV-visible and IR absorption spectroscopies. Absorption due to electronically excited triplet state benzaldehyde decays on a 80 ps time scale via reaction with cyclohexene. The growth and subsequent decay of the biradical intermediate produced following C-O bond formation is followed by transient vibrational spectroscopy. The biradical decays by ring closure to an oxetane or by dissociating, reforming the ground state reactants. Detailed kinetic analysis allowed derivation of quantum yields and rate constants for these competing biradical decay processes, ϕ(oxetane) = 0.53, ϕ(diss) = 0.47, koxetane = 0.27 ± 0.09 ns(-1) and k(diss) = 0.24 ± 0.09 ns(-1). This study provides a striking illustration of the ways in which contemporary ultrafast transient absorption spectroscopy methods can be used to dissect the mechanism and kinetics of a classic photoreaction.

  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. Ensemble of gold-patchy nanoparticles with multiple hot-spots for plasmon-enhanced vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Dao, Thang Duy; Nghiem, Ha Lien Thi; Chen, Kai; Nagao, Tadaaki

    2016-09-01

    Plasmon-enhanced vibrational spectroscopy, including surface-enhanced infrared absorption spectroscopy (SEIRA) and surface-enhanced Raman scattering (SERS), has attracted great attention in molecular sensing and nano-spectroscopy. In this work, we present a facile in situ-controlled method for the chemical synthesis of patchy SiO2@Au core-shell nanoparticles with multiple plasmonic nanogaps. The multiple sizes and shapes of Au nano-islands on patchy Au nanoshells and their plasmonic coupling exhibit broadband resonances ranging from the near infrared (NIR) region to the middle infrared (MIR) region, making patchy Au particles ensemble suitable for both SEIRA and SERS applications. In the SEIRA application, we demonstrate in situ and real-time monitoring of monolayer of reduced glutathione molecules (GSH) adsorbed on the plasmonic Au surface. By using GSH as the molecular linker, we also demonstrate in situ detection of trace amount of mercuric ions in water at nanomolar level. In the SERS application, we show the applicability of patchy Au nanoparticles for SERS at 785 nm excitation.

  5. Intense-field molecular spectroscopy: Vibrational and rotational effects in harmonic generation by H+2

    NASA Astrophysics Data System (ADS)

    Aubanel, E. E.; Zuo, T.; Bandrauk, A. D.

    1994-05-01

    We present results of a complete treatment of electronic, vibrational, and rotational motion in numerical calculation of harmonic generation (HG) of 1064-nm laser radiation by the H+2 molecular ion for intensities 1013<=I<=1014 W/cm2. We show that efficient HG can be enhanced by suppression of photodissociation, a phenomenon which results from vibrational trapping in laser-field-induced potential wells. The HG spectra exhibit peaks clustered around even and odd harmonic orders. All peaks can be assigned to Raman-like transitions between dressed eigenstates of the field-molecule system. Rotational excitation is shown to compete with HG. Thus harmonic generation and photon scattering in molecules holds the promise of a potential diagnostic for molecular stabilization by intense laser fields.

  6. 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.

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

    PubMed

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

    2015-12-10

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

  8. Concepts in bio-molecular spectroscopy: vibrational case studies on metalloenzymes.

    PubMed

    Horch, M; Hildebrandt, P; Zebger, I

    2015-07-28

    Spectroscopic techniques play a major role in the elucidation of structure-function relationships of biological macromolecules. Here we describe an integrated approach for bio-molecular spectroscopy that takes into account the special characteristics of such compounds. The underlying fundamental concepts will be exemplarily illustrated by means of selected case studies on biocatalysts, namely hydrogenase and superoxide reductase. The treatise will be concluded with an overview of challenges and future prospects, laying emphasis on functional dynamics, in vivo studies, and computational spectroscopy.

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

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; Xi, Yunfei

    2013-02-01

    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.

  10. Effect of ethanol on dimyristoylphosphatidylcholine large unilamellar vesicles investigated by quasi-elastic light scattering and vibrational spectroscopy.

    PubMed

    Hantz, E; Cao, A; Taillandier, E

    1988-12-01

    The gel-like liquid phase transition of dimyristoylphosphatidylcholine (DMPC) large unilamellar vesicles prepared by reverse phase evaporation has been investigated in buffers containing ethanol by quasi-elastic light scattering (QLS) and vibrational (infrared and Raman) spectroscopy. With the QLS technique, the relative change in the vesicles area (which is related to the molecular cross-sectional area of lipid molecules) was followed versus both temperature and ethanol concentration. When the latter was low, the depression of the transition point was a linear function of the alcohol concentration, c, but the vesicles area was practically unmodified. At alcohol concentration 10% v/v, an abrupt change of the vesicles area was observed and for c greater than 10% the depression of the transition point was a non-linear function of c. The infrared and Raman spectra showed a perturbation of the hydrophobic regions, including the terminal methyl groups of the acyl tails.

  11. 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

  12. Resolving Vibrational from Electronic Coherences in Two-Dimensional Electronic Spectroscopy: The Role of the Laser Spectrum

    NASA Astrophysics Data System (ADS)

    de A. Camargo, Franco V.; Grimmelsmann, Lena; Anderson, Harry L.; Meech, Stephen R.; Heisler, Ismael A.

    2017-01-01

    The observation of coherent quantum effects in photosynthetic light-harvesting complexes prompted the question whether quantum coherence could be exploited to improve the efficiency in new energy materials. The detailed characterization of coherent effects relies on sensitive methods such as two-dimensional electronic spectroscopy (2D-ES). However, the interpretation of the results produced by 2D-ES is challenging due to the many possible couplings present in complex molecular structures. In this work, we demonstrate how the laser spectral profile can induce electronic coherencelike signals in monomeric chromophores, potentially leading to data misinterpretation. We argue that the laser spectrum acts as a filter for certain coherence pathways and thus propose a general method to differentiate vibrational from electronic coherences.

  13. Femtosecond pump-probe photoionization-photofragmentation spectroscopy: Photoionization-induced twisting and coherent vibrational motion of azobenzene cation

    NASA Astrophysics Data System (ADS)

    Ho-Wei, Jr.; Chen, Wei-Kan; Cheng, Po-Yuan

    2009-10-01

    We report studies of ultrafast dynamics of azobenzene cation using femtosecond photoionization-photofragmentation spectroscopy. In our experiments, a femtosecond pump pulse first produces an ensemble of azobenzene cations via photoionization of the neutrals. A delayed probe pulse then brings the evolving ionic system to excited states that ultimately undergo ion fragmentation. The dynamics is followed by monitoring either the parent-ion depletion or fragment-ion formation as a function of the pump-probe delay time. The observed transients for azobenzene cation are characterized by a constant ion depletion modulated by a rapidly damped oscillatory signal with a period of about 1 ps. Theoretical calculations suggest that the oscillation arises from a vibration motion along the twisting inversion coordinate involving displacements in CNNC and phenyl-ring torsions. The oscillation is damped rapidly with a time constant of about 1.2 ps, suggesting that energy dissipation from the active mode to bath modes takes place in this time scale.

  14. Broadband 308 nm vibrational Raman spectroscopy of gaseous species using a potassium hydrogen phthalate liquid filter and polarization fluorescence suppression.

    PubMed

    Saunders, J E A; Davy, M H

    2010-01-01

    Broadband XeCl excimer lasers operating at 308 nm are not currently used in the field of gas phase vibrational Raman spectroscopy (VRS). An explanation as to why alternative wavelengths, and in particular tuneable, narrowband lasers are currently preferred for gas phase VRS is presented in addition to demonstrating a setup which makes the XeCl laser a viable alternative when considering excitation sources for VRS. A solution of potassium hydrogen phthalate is shown to be a practical low-pass liquid filter and to reduce substantially the effects of Rayleigh scattering on collected Raman spectra. The use of a commercial beam polarizer is also shown to be effective in suppressing background fluorescence that otherwise necessitates the use of expensive tuneable, narrowband lasers when performing VRS with sources of background fluorescence. Finally, an unconventional excitation beam arrangement is shown to produce viable Raman spectra from which species concentrations and distributions can be determined.

  15. Matrix isolation technique for the study of some factors affecting the partitioning of trace elements. [using vibrational spectroscopy

    NASA Technical Reports Server (NTRS)

    Grzybowski, J. M.; Allen, R. O.

    1974-01-01

    The factors that affect the preferred positions of cations in ionic solid solutions were investigated utilizing vibrational spectroscopy. Solid solutions of the sulfate and chromate ions codoped with La(+3) and Ca(+2) in a KBr host lattice were examined as a function of the polyvalent cation concentration. The cation-anion pairing process was found to be random for Ca(+2), whereas the formation of La(+3)-SO4(-2) ion pairs with a C2 sub v bonding geometry is highly preferential to any type of La(+3)-CrO4(-2) ion pair formation. The relative populations of ion pair site configurations are discussed in terms of an energy-entropy competition model which can be applied to the partition of trace elements during magmatic processes.

  16. 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.

  17. Real sample temperature: a critical issue in the experiments of nuclear resonant vibrational spectroscopy on biological samples.

    PubMed

    Wang, Hongxin; Yoda, Yoshitaka; Kamali, Saeed; Zhou, Zhao Hui; Cramer, Stephen P

    2012-03-01

    There are several practical and intertangled issues which make the experiments of nuclear resonant vibrational spectroscopy (NRVS) on biological samples difficult to perform. The sample temperature is one of the most important issues. In NRVS the real sample temperatures can be very different from the readings on the temperature sensors. In this study the following have been performed: (i) citing and analyzing various existing NRVS data to assess the real sample temperatures during the NRVS measurements and to understand their trends with the samples' loading conditions; (ii) designing several NRVS measurements with (Et(4)N)[FeCl(4)] to verify these trends; and (iii) proposing a new sample-loading procedure to achieve significantly lower real sample temperatures and to balance among the intertangled experimental issues in biological NRVS measurements.

  18. Complete assignment of the vibrational modes of C60 by inelastic neutron scattering spectroscopy and periodic-DFT.

    PubMed

    Parker, Stewart F; Bennington, Stephen M; Taylor, Jon W; Herman, Henryk; Silverwood, Ian; Albers, Peter; Refson, Keith

    2011-05-07

    In this paper we exploit the complementarity of inelastic neutron scattering (INS), infrared and Raman spectroscopies with ab initio calculations to generate an updated assignment of the vibrational modes of C(60). We have carried out periodic-DFT calculations of the high temperature face centred cubic phase modelled as the standard structure and also of the low temperature simple cubic phase, the latter for the first time. Our assignment differs from all previous work, however, it is the only one that is able to successfully reproduce the INS spectrum in terms of both transition energies and intensities. In addition to the INS spectrum we are also able to quantitatively simulate the major features of the infrared and Raman spectra in the high temperature phase and the infrared spectrum in the low temperature phase.

  19. Quantification of crystalline cellulose in lignocellulosic biomass using sum frequency generation (SFG) vibration spectroscopy and comparison with other analytical methods.

    PubMed

    Barnette, Anna L; Lee, Christopher; Bradley, Laura C; Schreiner, Edward P; Park, Yong Bum; Shin, Heenae; Cosgrove, Daniel J; Park, Sunkyu; Kim, Seong H

    2012-07-01

    The non-centrosymmetry requirement of sum frequency generation (SFG) vibration spectroscopy allows the detection and quantification of crystalline cellulose in lignocellulose biomass without spectral interferences from hemicelluloses and lignin. This paper shows a correlation between the amount of crystalline cellulose in biomass and the SFG signal intensity. Model biomass samples were prepared by mixing commercially available cellulose, xylan, and lignin to defined concentrations. The SFG signal intensity was found sensitive to a wide range of crystallinity, but varied non-linearly with the mass fraction of cellulose in the samples. This might be due to the matrix effects such as light scattering and absorption by xylan and lignin, as well as the non-linear density dependence of the SFG process itself. Comparison with other techniques such as XRD, FT-Raman, FT-IR and NMR demonstrate that SFG can be a complementary and sensitive tool to assess crystalline cellulose in biomass.

  20. Molecular structure and dynamics of water at the water-air interface studied with surface-specific vibrational spectroscopy.

    PubMed

    Bonn, Mischa; Nagata, Yuki; Backus, Ellen H G

    2015-05-04

    Water interfaces provide the platform for many important biological, chemical, and physical processes. The water-air interface is the most common and simple aqueous interface and serves as a model system for water at a hydrophobic surface. Unveiling the microscopic (<1 nm) structure and dynamics of interfacial water at the water-vapor interface is essential for understanding the processes occurring on the water surface. At the water interface the network of very strong intermolecular interactions, hydrogen-bonds, is interrupted and the density of water is reduced. A central question regarding water at interfaces is the extent to which the structure and dynamics of water molecules are influenced by the interruption of the hydrogen-bonded network and thus differ from those of bulk water. Herein, we discuss recent advances in the study of interfacial water at the water-air interface using laser-based surface-specific vibrational spectroscopy.

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

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

    PubMed

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

    2014-09-01

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

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. Vibrational motions associated with primary processes in bacteriorhodopsin studied by coherent infrared emission spectroscopy.

    PubMed

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

    2011-03-16

    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.

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

    PubMed

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

    2008-08-04

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

  9. 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.

  10. Probing the collective vibrational dynamics of a protein in liquid water by terahertz absorption spectroscopy.

    PubMed

    Xu, Jing; Plaxco, Kevin W; Allen, S James

    2006-05-01

    Biological polymers are expected to exhibit functionally relevant, global, and subglobal collective modes in the terahertz (THz) frequency range (i.e., picosecond timescale). In an effort to monitor these collective motions, we have experimentally determined the absorption spectrum of solvated bovine serum albumin (BSA) from 0.3 to 3.72 THz (10-124 cm(-1)). We successfully extract the terahertz molar absorption of the solvated BSA from the much stronger attenuation of water and observe in the solvated protein a dense, overlapping spectrum of vibrational modes that increases monotonically with increasing frequency. We see no evidence of distinct, strong, spectral features, suggesting that no specific collective vibrations dominate the protein's spectrum of motions, consistent with the predictions of molecular dynamics simulations and normal mode analyses of a range of small proteins. The shape of the observed spectrum resembles the ideal quadratic spectral density expected for a disordered ionic solid, indicating that the terahertz normal mode density of the solvated BSA may be modeled, to first order, as that of a three-dimensional elastic nanoparticle with an aperiodic charge distribution. Nevertheless, there are important detailed departures from that of a disordered inorganic solid or the normal mode densities predicted for several smaller proteins. These departures are presumably the spectral features arising from the unique molecular details of the solvated BSA. The techniques used here and measurements have the potential to experimentally confront theoretical calculations on a frequency scale that is important for macromolecular motions in a biologically relevant water environment.

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

    PubMed

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

    2017-03-01

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

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

    DTIC Science & Technology

    2016-07-01

    TR-1385 Waleed Maswadeh Richard Vanderbeek Raphael Moon RESEARCH AND TECHNOLOGY DIRECTORATE Ashish Tripathi LEIDOS, INC. Gunpowder, MD...0022 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Maswadeh, Waleed; Vanderbeek, Richard; Moon , Raphael (ECBC); Tripathi, Ashish...Chemical Biological Center (ECBC) Spectroscopy Branch RDCB-DRI-S ATTN: Maswadeh, W. Vanderbeek, R. Moon , R

  14. 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.

  15. 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.

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

    PubMed

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

    2014-03-03

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

  17. 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.

  18. 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

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  20. Vibrational spectroscopy and density functional theory 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.

  1. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

  3. Two-Dimensional Vibrational Spectroscopy of a Dissipative System with the Optimized Mean-Trajectory Approximation

    PubMed Central

    2015-01-01

    The optimized mean-trajectory (OMT) approximation is a semiclassical method for computing vibrational response functions from action-quantized classical trajectories connected by discrete transitions representing radiation–matter interactions. Here we apply this method to an anharmonic chromophore coupled to a harmonic bath. A forward–backward trajectory implementation of the OMT method is described that addresses the numerical challenges of applying the OMT to large systems with disparate frequency scales. The OMT is shown to well reproduce line shapes and waiting time dynamics in the pure dephasing limit of weak coupling to an off-resonant bath. The OMT is also shown to describe a case where energy transfer is the predominant source of line broadening. PMID:25275943

  4. Two-dimensional infrared spectroscopy of peptides by phase-controlled femtosecond vibrational photon echoes

    PubMed Central

    Asplund, M. C.; Zanni, M. T.; Hochstrasser, R. M.

    2000-01-01

    Two-dimensional infrared spectra of peptides are introduced that are the direct analogues of two- and three-pulse multiple quantum NMR. Phase matching and heterodyning are used to isolate the phase and amplitudes of the electric fields of vibrational photon echoes as a function of multiple pulse delays. Structural information is made available on the time scale of a few picoseconds. Line narrowed spectra of acyl-proline-NH2 and cross peaks implying the coupling between its amide-I modes are obtained, as are the phases of the various contributions to the signals. Solvent-sensitive structural differences are seen for the dipeptide. The methods show great promise to measure structure changes in biology on a wide range of time scales. PMID:10890905

  5. Adsorption and vibrational spectroscopy of ammonia at mordenite: Ab initio study

    NASA Astrophysics Data System (ADS)

    Bučko, T.; Hafner, J.; Benco, L.

    2004-06-01

    The adsorption of ammonia at various active centers at the outer and inner surfaces of mordenite, involving Brønsted acid (BA) sites, terminal silanol groups, and Lewis sites has been investigated using periodic ab initio density-functional theory. It is shown that ammonia forms an ammonium ion when adsorbed at strong BA sites. The calculated adsorption energies for different BA sites vary in the interval from 111.5 to 174.7 kJ/mol depending on the local environment of the adduct. The lowest adsorption energy is found for a monodentate complex in the main channel, the highest for a tetradentate configuration in the side pocket. At weak BA sites such as terminal silanol groups or a defect with a BA site in a two-membered ring ammonia is H bonded via the N atom. Additional weak H bonds are formed between H atoms of ammonia and O atoms of neighboring terminal silanol groups. The calculated adsorption energies for such adducts range between 61.7 and 70.9 kJ/mol. The interaction of ammonia with different Lewis sites is shown to range between weak (ΔEads=17.8 kJ/mol) and very strong (ΔEads=161.7 kJ/mol), the strongest Lewis site being a tricoordinated Al atom at the outer surface. Our results are in very good agreement with the distribution of desorption energies estimated from temperature-programmed desorption (TPD) and microcalorimetry experiments, the multipeaked structure of the TPD spectra is shown to arise from strong and weak Brønsted and Lewis sites. The vibrational properties of the adsorption complexes are investigated using a force-constant approach. The stretching and bending modes of NH4+ adsorbed to the zeolite are strongly influenced by the local environment. The strongest redshift is calculated for the asymmetric stretching mode involving the NH group hydrogen bonded to the bridging O atom of the BA site, the shift is largest for a monodentate and smallest for a tetradentate adsorption complex. The reduced symmetry of the adsorbate also leads to a

  6. 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

  7. 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

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

    SciTech Connect

    Visser, Hendrik

    2001-01-01

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

  9. 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.

  10. Vanadium doping of LiMnPO4: Vibrational spectroscopy and first-principle studies

    NASA Astrophysics Data System (ADS)

    Kellerman, D.; Medvedeva, N.; Mukhina, N.; Semenova, A.; Baklanova, I.; Perelyaeva, L.; Gorshkov, V.

    2014-01-01

    The samples of pure and 10% vanadium-doped LiMnPO4 have been synthesized by the solid-state reaction technique. The results of Raman and infrared absorption spectroscopy show that the vanadium atoms replace phosphorus giving rise to LiMn(PO4)1-x(VO4)x solid solutions. This conclusion is confirmed by the first-principle studies.

  11. 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.

  12. Molecular interactions of organic molecules at the air/water interface investigated by sum frequency generation vibrational spectroscopy.

    PubMed

    Wang, Wenting; Ye, Shuji

    2017-02-08

    The molecular structure and dynamics of organic molecules at the aqueous interface have attracted a number of investigations owing to their importance and specific nature. However, there are relatively few studies on the direct characterization of the molecular interactions at the air/water interface because they are extremely difficult to measure in experiments. In this study, we use dibutyl ester molecules (R1CO2R2O2CR1) as a model of organic molecules, and investigate their molecular structure and interactions using sum frequency generation vibrational spectroscopy. We demonstrate that the molecular interactions can be estimated by measuring the intensity ratio of the symmetric stretching (ν1) and Fermi resonant bands (2ν2) of methyl groups. Here, dibutyl ester molecules are widely used as plasticizers in polymers to improve the properties of the plastics and polymers. It is found that the orientation angles of the tailed methyl groups at the air/water interface decrease from 34° to 19° when the chain length of R2 increases from 0 to 8. The total intermolecular interactions of the dibutyl ester molecules decrease as the chain length of R2 increases because the van der Waals interactions between the hydrocarbon chains increase, while the hydrogen bond interactions between the carbonyl group and water molecules decrease. Our study demonstrates the stability of ester-based plasticizers in polymers can be well predicted from the intensity ratio of the ν1 and 2ν2 bands of methyl group. Such an intensity ratio can be thus used as an effective vibrational optical ruler for characterizing molecular interactions between plasticizers and polymers.

  13. Structural characterization of (C2H2)1-6+ cluster ions by vibrational predissociation spectroscopy

    NASA Astrophysics Data System (ADS)

    Relph, Rachael A.; Bopp, Joseph C.; Roscioli, Joseph R.; Johnson, Mark A.

    2009-09-01

    Vibrational predissociation spectra are reported for the cationic acetylene clusters, (C2H2)n+, n =1-6, in the region of the C-H stretching fundamentals. For n =1 and 2, predissociation could only be observed for the Ar-tagged clusters. These were prepared by charge-transfer collisions of Ark+ with C2H2 to create C2H2+ṡArm clusters, which were then converted into larger members of the (C2H2)n+ṡAr series by sequential addition of acetylene molecules. The (C2H2)2+ṡAr spectrum indicates that this species is predominantly present as the cyclobutadiene cation. Although mobility measurements on the electron-impact-generated (C2H2)3+ ion indicated that it primarily occurs as the benzene cation, [P. O. Momoh, J. Am. Chem. Soc. 128, 12408 (2006)] photofragmentation of (C2H2)3+ṡAr in the C-H stretching region is dominated by the loss of C2H2 in addition to the weakly bound Ar atom. This suggests that the dominant n =3 species formed by sequential addition of C2H2 is based on a covalently bound C4H4+ core ion. Interestingly, the spectrum of this core C4H4+ species is different from that found for the cyclobutadiene cation, displaying instead a new band pattern that is retained in the higher (C2H2)3-6+ clusters. Multiple isomers are clearly involved, as yet another pattern of bands is recovered when the (C2H2)3+ṡAr action spectrum is recorded in the (minor) Ar loss fragmentation channel. One of these features does appear in the location of the single band characteristic of the Ar-tagged benzene cation reported earlier [Phys. Chem. Chem. Phys. 4, 24 (2002)], supporting a scenario where the benzene cation is one of the isomers present. We then compare the Ar predissociation results with (C2H2)n+ spectra obtained when the ions are prepared by electron impact ionization of neutral acetylene clusters. The photofragmentation behavior and vibrational spectra indicate that the dominant species formed in this way also occur with a covalently bound C4H4+ core. There are

  14. Infrared vibrational spectroscopy of [Ru(bpy)2(bpm)]2+ and [Ru(bpy)3]2+ in the excited triplet state.

    PubMed

    Mukuta, Tatsuhiko; Fukazawa, Naoto; Murata, Kei; Inagaki, Akiko; Akita, Munetaka; Tanaka, Sei'ichi; Koshihara, Shin-ya; Onda, Ken

    2014-03-03

    This work involved a detailed investigation into the infrared vibrational spectra of ruthenium polypyridyl complexes, specifically heteroleptic [Ru(bpy)2(bpm)](2+) (bpy = 2,2'-bipyridine and bpm = 2,2'-bipyrimidine) and homoleptic [Ru(bpy)3](2+), in the excited triplet state. Transient spectra were acquired 500 ps after photoexcitation, corresponding to the vibrational ground state of the excited triplet state, using time-resolved infrared spectroscopy. We assigned the observed bands to specific ligands in [Ru(bpy)2(bpm)](2+) based on the results of deuterium substitution and identified the corresponding normal vibrational modes using quantum-chemical calculations. Through this process, the more complex vibrational bands of [Ru(bpy)3](2+) were assigned to normal vibrational modes. The results are in good agreement with the model in which excited electrons are localized on a single ligand. We also found that the vibrational bands of both complexes associated with the ligands on which electrons are little localized appear at approximately 1317 and 1608 cm(-1). These assignments should allow the study of the reaction dynamics of various photofunctional systems including ruthenium polypyridyl complexes.

  15. Local vibrations in disordered solids studied via single-molecule spectroscopy: Comparison with neutron, nuclear, Raman scattering, and photon echo data

    NASA Astrophysics Data System (ADS)

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

    2008-06-01

    The energy spectrum of low-frequency vibrational modes (LFMs) in three disordered organic solids—amorphous polyisobutylene (PIB), toluene and deuterated toluene glasses, weakly doped with fluorescent chromophore molecules of tetra-tert-butylterrylene (TBT) has been measured via single-molecule (SM) spectroscopy. Analysis of the individual temperature dependences of linewidths of single TBT molecules allowed us to determine the values of the vibrational mode frequencies and the SM-LFM coupling constants for vibrations in the local environment of the molecules. The measured LFM spectra were compared with the “Boson peak” as measured in pure PIB by inelastic neutron scattering, in pure toluene glass by low-frequency Raman scattering, in doped toluene glass by nuclear inelastic scattering, and with photon echo data. The comparative analysis revealed close agreement between the spectra of the local vibrations as measured in the present study and the literature data of the Boson peak in PIB and toluene. The analysis has also the important result that weak doping of the disordered matrices with nonpolar probe molecules whose chemical composition is similar to that of the matrix molecules does not influence the observed vibrational dynamics markedly. The experimental data displaying temporal stability on the time scale of a few hours of vibrational excitation parameters in local surroundings was obtained for the first time both for polymer and molecular glass.

  16. Exploration of molecular orientation in polymers using novel vibrational spectroscopy methods

    NASA Astrophysics Data System (ADS)

    Frisk, Simon

    The knowledge of the structure-processing-property relationships is critical to any application in materials science. This project proposes a multidimensional approach to study the structure of polymer fibers as a function of different processing parameters. The tremendous potential of polarized Raman spectroscopy for the study of oriented polymers was demonstrated using quantitative and spectral analyses. A comparison of three methods to determine the first two coefficients of the orientation distribution function is presented. Based on these results, a graphical representation of the distribution of molecular orientations and its evolution in a series of poly(propylene terephthalate) fibers melt-spun under different processing conditions was attempted. A new method to determine an orientation independent Raman scattered intensity based on various polarized Raman measurements was developed and is introduced. The equivalent term in infrared spectroscopy is the structural absorbance. As with the structural absorbance, the calculated Raman intensity allows one to observe spectral changes that are due uniquely to morphological changes in a set of different samples in the presence of orientation differences. The correlation of the quantitative and spectral analyses yielded valuable information regarding the evolution of the molecular orientation and the structure as a function of spinning speed in the series of melt-spun PPT fibers. A monotonic increase in molecular orientation was observed through the entire spin speed range. Initially, this increase was accompanied by a large increase in density. Due to the absence of a significant increase in crystallinity, it was concluded that an oriented non-crystalline phase was formed. The onset of significant crystallinity was observed for the higher spin speeds. A second objective of this work was to gain a better understanding of the deformation mechanisms in the fibers when subjected to both permanent and reversible

  17. Towards the Limits of Vibrational Circular Dichroism Spectroscopy: VCD Spectra of Some Alkyl Vinylethers.

    PubMed

    Zinna, Francesco; Pescitelli, Gennaro

    2016-02-01

    Three alkyl vinylethers from our collection of chiral samples were investigated through VCD spectroscopy, in combination with Density Functional Theory (DFT) calculations. Despite the simplicity of the compounds, reproducing all the spectral features is an involved task, since the many significantly populated conformers contribute to the total VCD spectrum with bands which often have opposite signatures. Nevertheless, we show that certain bands can be satisfactorily reproduced by calculation and therefore they may be employed for the determination of absolute configuration in these and similar compounds, for which no simple alternative method is available.

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Reppert, Mike; Tokmakoff, Andrei

    2015-08-01

    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-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.

  20. 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.

  1. Gas phase vibrational spectroscopy of cold (TiO2)n(-) (n = 3-8) clusters.

    PubMed

    Weichman, Marissa L; Song, Xiaowei; Fagiani, Matias R; Debnath, Sreekanta; Gewinner, Sandy; Schöllkopf, Wieland; Neumark, Daniel M; Asmis, Knut R

    2016-03-28

    We report infrared photodissociation (IRPD) spectra for the D2-tagged titanium oxide cluster anions (TiO2)n(-) with n = 3-8 in the spectral region from 450 to 1200 cm(-1). The IRPD spectra are interpreted with the aid of harmonic spectra from BP86/6-311+G* density functional theory calculations of energetically low-lying isomers. We conclusively assign the IRPD spectra of the n = 3 and n = 6 clusters to global minimum energy structures with Cs and C2 symmetry, respectively. The vibrational spectra of the n = 4 and n = 7 clusters can be attributed to contributions of at most two low-lying structures. While our calculations indicate that the n = 5 and n = 8 clusters have many more low-lying isomers than the other clusters, the dominant contributions to their spectra can be assigned to the lowest energy structures. Through comparison between the calculated and experimental spectra, we can draw conclusions about the size-dependent evolution of the properties of (TiO2)n(-) clusters, and on their potential utility as model systems for catalysis on a bulk TiO2 surface.

  2. 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

  3. 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.

  4. 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

    2015-01-08

    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.

  5. 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.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1995-05-01

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

  8. [Biomedical informatics].

    PubMed

    Capurro, Daniel; Soto, Mauricio; Vivent, Macarena; Lopetegui, Marcelo; Herskovic, Jorge R

    2011-12-01

    Biomedical Informatics is a new discipline that arose from the need to incorporate information technologies to the generation, storage, distribution and analysis of information in the domain of biomedical sciences. This discipline comprises basic biomedical informatics, and public health informatics. The development of the discipline in Chile has been modest and most projects have originated from the interest of individual people or institutions, without a systematic and coordinated national development. Considering the unique features of health care system of our country, research in the area of biomedical informatics is becoming an imperative.

  9. Biomedical Imaging,

    DTIC Science & Technology

    precision required from the task. This report details the technologies in surface and subsurface imaging systems for research and commercial applications. Biomedical imaging, Anthropometry, Computer imaging.

  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. Solid state vibrational spectroscopy of anhydrous lithium hexafluorophosphate (LiPF6)

    NASA Astrophysics Data System (ADS)

    Kock, L. D.; Lekgoathi, M. D. S.; Crouse, P. L.; Vilakazi, B. M.

    2012-10-01

    Raman and infrared studies of solid anhydrous lithium hexafluorophosphate (LiPF6) have been carried out. The studies were complemented by X-ray powder diffraction (XRD) and Thermogravimetric (TG) analysis techniques. The results indicate that when solid LiPF6 is studied in a strictly anhydrous environment, more consistent thermal stability data can be obtained. TG analysis, using a scan rate of 10 °C min-1, indicate the onset of thermal decomposition of the anhydrous LiPF6 occurring at about 134.84 °C while the partially hydrolysed compound starts at 114.46 °C. The Raman spectra of anhydrous MPF6 (M = Li+, Na+ and K+) are best interpreted in terms of a cubic space group Fm3m(Ohs), (ZB = 1), giving rise to 21 vibrational modes (A1g(R)+Eg(R)+T1g+T2g(R)+3T1u(1R)+T2u) and as such, LiPF6 may be considered isostructural with NaPF6 and KPF6. Crystal symmetry distortions in the anhydrous LiPF6 give rise additional bands in the Raman spectrum due to T1u infrared active modes and the ν1 (A1g) Raman band appears in the infrared spectrum in violation of the mutual exclusion selection rule for centro-symmetric sites. When these observations are considered, the Raman spectrum of LiPF6 is similar to those of NaPF6 and KPF6, with observations of the expected shifts due to cation size and/or electronegativity effects.

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. Variation of exciton-vibrational coupling in photosystem II core complexes from Thermosynechococcus elongatus as revealed by single-molecule spectroscopy.

    PubMed

    Skandary, Sepideh; Hussels, Martin; Konrad, Alexander; Renger, Thomas; Müh, Frank; Bommer, Martin; Zouni, Athina; Meixner, Alfred J; Brecht, Marc

    2015-03-19

    The spectral properties and dynamics of the fluorescence emission of photosystem II core complexes are investigated by single-molecule spectroscopy at 1.6 K. The emission spectra are dominated by sharp zero-phonon lines (ZPLs). The sharp ZPLs are the result of weak to intermediate exciton-vibrational coupling and slow spectral diffusion. For several data sets, it is possible to surpass the effect of spectral diffusion by applying a shifting algorithm. The increased signal-to-noise ratio enables us to determine the exciton-vibrational coupling strength (Huang-Rhys factor) with high precision. The Huang-Rhys factors vary between 0.03 and 0.8. The values of the Huang-Rhys factors show no obvious correlation between coupling strength and wavelength position. From this result, we conclude that electrostatic rather than exchange or dispersive interactions are the main contributors to the exciton-vibrational coupling in this system.

  18. An attempt at a product vibrational analysis of a photo-induced chemical reaction by means of time-resolved (e, 2e) electron momentum spectroscopy

    NASA Astrophysics Data System (ADS)

    Yamazaki, M.; Nakazawa, H.; Zhu, C. Y.; Takahashi, M.

    2015-09-01

    We report on a new attempt at an analysis of the vibrational state distributions in the products of a photo-induced chemical reaction. The experiment was performed by using time- resolved electron momentum spectroscopy (TR-EMS) for the products produced by the three- body photodissociation dynamics of the deuterated acetone molecule at 195 nm. It has been found from a comparison between the experiment and associated theoretical calculations that future TR-EMS measurements with improved statistics could be useful for the vibrational analysis of reaction products, in cases when effects of molecular vibration on their electron momentum densities are large enough so as to be noticeable in the binding energy spectra.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

  1. 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.

  2. Direct Observation of an Iron-Bound Terminal Hydride in [FeFe]-Hydrogenase by Nuclear Resonance Vibrational Spectroscopy.

    PubMed

    Reijerse, Edward J; Pham, Cindy C; Pelmenschikov, Vladimir; Gilbert-Wilson, Ryan; Adamska-Venkatesh, Agnieszka; Siebel, Judith F; Gee, Leland B; Yoda, Yoshitaka; Tamasaku, Kenji; Lubitz, Wolfgang; Rauchfuss, Thomas B; Cramer, Stephen P

    2017-03-29

    [FeFe]-hydrogenases catalyze the reversible reduction of protons to molecular hydrogen with extremely high efficiency. The active site ("H-cluster") consists of a [4Fe-4S]H cluster linked through a bridging cysteine to a [2Fe]H subsite coordinated by CN(-) and CO ligands featuring a dithiol-amine moiety that serves as proton shuttle between the protein proton channel and the catalytic distal iron site (Fed). Although there is broad consensus that an iron-bound terminal hydride species must occur in the catalytic mechanism, such a species has never been directly observed experimentally. Here, we present FTIR and nuclear resonance vibrational spectroscopy (NRVS) experiments in conjunction with density functional theory (DFT) calculations on an [FeFe]-hydrogenase variant lacking the amine proton shuttle which is stabilizing a putative hydride state. The NRVS spectra unequivocally show the bending modes of the terminal Fe-H species fully consistent with widely accepted models of the catalytic cycle.

  3. 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.

  4. 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.

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

    PubMed

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

    2015-01-01

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

  7. Similarities and differences of copper and zinc cations binding to biologically relevant peptides studied by vibrational spectroscopies.

    PubMed

    Schirer, Alicia; El Khoury, Youssef; Faller, Peter; Hellwig, Petra

    2017-03-20

    GHK and DAHK are biological peptides that bind both copper and zinc cations. Here we used infrared and Raman spectroscopies to study the coordination modes of both copper and zinc ions, at pH 6.8 and 8.9, correlating the data with the crystal structures that are only available for the copper-bound form. We found that Cu(II) binds to deprotonated backbone (amidate), the N-terminus and N(π) of the histidine side chain, in both GHK and DAHK, at pH 6.8 and 8.9. The data for the coordination of zinc at pH 6.8 points to two conformers including both nitrogens of a histidine residue. At pH 8.9, vibrational spectra of the ZnGHK complexes show that equilibria between monomers, oligomers exist, where deprotonated histidine residues as well as deprotonated amide nitrogen are involved in the coordination. A common feature is found: zinc cations coordinate to N(τ) and/or N(π) of the His leading to the formation of GHK and DAHK multimers. In contrast, Cu(II) binds His via N(π) regardless of the peptide, in a pH-independent manner.

  8. 2D IR spectroscopy of histidine: probing side-chain structure and dynamics via backbone amide vibrations.

    PubMed

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

    2014-07-17

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

  9. Condensation reaction between carbohydrazide and salicylaldehyde: in-line vibrational spectroscopy monitoring and characterization of the reaction products in solution and solid state.

    PubMed

    Jednačak, Tomislav; Novak, Predrag; Hodzic, Aden; Scheibelhofer, Otto; Khinast, Johannes G; Plavec, Janez; Sket, Primož; Parlov, Vuković Jelena

    2014-01-01

    The condensation reaction between carbohydrazide and salicylaldehyde was monitored in-line by using vibrational NIR and Raman spectroscopies and statistical methods. Prior to in-line data analysis the reaction products were fully characterized in solution and solid state in order to check the potential of the in-line approach as a tool for in-process Schiff bases reaction control. It was demonstrated that a combination of vibrational spectroscopy and principal component analysis made it possible to detect and identify the reaction products, e.g. mono(salicylidene)carbohydrazide (1) and bis(salicylidene)carbohydrazide (2) in different solvents, and to determine the reaction end points in real time. Owing to complexity of the reaction mixtures and band overlapping, it was not possible to determine the relative ratio of the reaction products in-line. The off-line analysis showed that 1 was predominant in methanol while the highest portion of 2 was obtained in ethanol.

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

    PubMed

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

    2010-10-07

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

  11. 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

  12. Copper/oxide interface formation: a vibrational and electronic investigation by electron spectroscopies

    NASA Astrophysics Data System (ADS)

    Conard, T.; Ghijsen, J.; Vohs, J. M.; Thiry, P. A.; Caudano, R.; Johnson, R. L.

    1992-04-01

    In this study, we deposited copper on a MgO(100) surface at room temperature (using a Knudsen cell) and studied the interface formation using electron spectroscopy. The evolution of the AES peak intensities showed that copper grows on MgO(100) in the Stranski-Krastanov mode. In HREELS experiments, the intensity and the position of the energy loss corresponding to the MgO surface optical phonon at 80.7 meV, both decrease with increasing Cu coverage. These results agree with theoretical spectra simulated from the dielectric theory by considering a Cu 2O overlayer on a semi-infinite MgO crystal substrate at the beginning of the growth. From the HREELS data, both the formation of a homogeneous Cu metallic overlayer or a CuO overlayer on MgO can be ruled out. The synchrotron-radiation (SR) photoemission measurements were performed in the vicinity of the Cu3p3d resonance. The positions of the Cu resonance peaks as a function of Cu coverage on MgO show that at low coverage the difference in energy between the main Cu 3d peak and the resonance peak is close to that found in Cu 2O and at higher coverage close to metallic copper indicating the formation of an interacting phase at the beginning followed by the growth of metallic copper.

  13. 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.

  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. 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

  16. 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.

  17. Perspective: Watching low-frequency vibrations of water in biomolecular recognition by THz spectroscopy.

    PubMed

    Xu, Yao; Havenith, Martina

    2015-11-07

    Terahertz (THz) spectroscopy has turned out to be a powerful tool which is able to shed new light on the role of water in biomolecular processes. The low frequency spectrum of the solvated biomolecule in combination with MD simulations provides deep insights into the collective hydrogen bond dynamics on the sub-ps time scale. The absorption spectrum between 1 THz and 10 THz of solvated biomolecules is sensitive to changes in the fast fluctuations of the water network. Systematic studies on mutants of antifreeze proteins indicate a direct correlation between biological activity and a retardation of the (sub)-ps hydration dynamics at the protein binding site, i.e., a "hydration funnel." Kinetic THz absorption studies probe the temporal changes of THz absorption during a biological process, and give access to the kinetics of the coupled protein-hydration dynamics. When combined with simulations, the observed results can be explained in terms of a two-tier model involving a local binding and a long range influence on the hydration bond dynamics of the water around the binding site that highlights the significance of the changes in the hydration dynamics at recognition site for biomolecular recognition. Water is shown to assist molecular recognition processes.

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

    PubMed

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

    2016-03-07

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

  19. 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.

  20. 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)

  1. Vibrational spectroscopy via the Caldeira-Leggett model with anharmonic system potentials

    NASA Astrophysics Data System (ADS)

    Gottwald, Fabian; Ivanov, Sergei D.; Kühn, Oliver

    2016-04-01

    The Caldeira-Leggett (CL) model, which describes a system bi-linearly coupled to a harmonic bath, has enjoyed popularity in condensed phase spectroscopy owing to its utmost simplicity. However, the applicability of the model to cases with anharmonic system potentials, as it is required for the description of realistic systems in solution, is questionable due to the presence of the invertibility problem [F. Gottwald et al., J. Phys. Chem. Lett. 6, 2722 (2015)] unless the system itself resembles the CL model form. This might well be the case at surfaces or in the solid regime, which we here confirm for a particular example of an iodine molecule in the atomic argon environment under high pressure. For this purpose we extend the recently proposed Fourier method for parameterizing linear generalized Langevin dynamics [F. Gottwald et al., J. Chem. Phys. 142, 244110 (2015)] to the non-linear case based on the CL model and perform an extensive error analysis. In order to judge on the applicability of this model in advance, we give practical empirical criteria and discuss the effect of the potential renormalization term. The obtained results provide evidence that the CL model can be used for describing a potentially broad class of systems.

  2. Vibrational spectroscopy study of the oxidation of Hylamer UHMWPE explanted acetabular cups sterilized differently

    NASA Astrophysics Data System (ADS)

    Reggiani, Matteo; Tinti, Anna; Visentin, Manuela; Stea, Susanna; Erani, Paolo; Fagnano, Concezio

    2007-05-01

    Ultra-high-molecular-weight polyethylene (UHMWPE) has been used for over 40 years for acetabular cups in total hip joint prosthesis. Hylamer is a hot isostatically pressed material with high crystallinity. Early loosening due to extensive oxidation and phase transformation has been observed for this material. To analyze the reasons for its high tendency to oxidize, we have examined by FT-IR spectroscopy explanted acetabular cups γ-sterilized in different ways. The oxidation and wear rate observed were: Hylamer cups γ-sterilized in air with a long shelf life > Hylamer cups γ-sterilized in air with short shelf life ⩾ Hylamer cups γ-sterilized in nitrogen. Our data indicate the important role of the shelf life on the oxidation of the cups: the samples γ-sterilized in air characterized by a shelf life greater than 3 years showed severe oxidation, a high wear rate, and marked debris production with delamination and the formation of a brittle zone in the more oxidated regions. In these regions we observed an increase in crystallinity, which was probably due to the decrease in the molecular weight of PE. The high oxidation was probably due to the modifications induced by the material treatment.

  3. Perspective: Watching low-frequency vibrations of water in biomolecular recognition by THz spectroscopy

    NASA Astrophysics Data System (ADS)

    Xu, Yao; Havenith, Martina

    2015-11-01

    Terahertz (THz) spectroscopy has turned out to be a powerful tool which is able to shed new light on the role of water in biomolecular processes. The low frequency spectrum of the solvated biomolecule in combination with MD simulations provides deep insights into the collective hydrogen bond dynamics on the sub-ps time scale. The absorption spectrum between 1 THz and 10 THz of solvated biomolecules is sensitive to changes in the fast fluctuations of the water network. Systematic studies on mutants of antifreeze proteins indicate a direct correlation between biological activity and a retardation of the (sub)-ps hydration dynamics at the protein binding site, i.e., a "hydration funnel." Kinetic THz absorption studies probe the temporal changes of THz absorption during a biological process, and give access to the kinetics of the coupled protein-hydration dynamics. When combined with simulations, the observed results can be explained in terms of a two-tier model involving a local binding and a long range influence on the hydration bond dynamics of the water around the binding site that highlights the significance of the changes in the hydration dynamics at recognition site for biomolecular recognition. Water is shown to assist molecular recognition processes.

  4. Conformational structure of bombesin as studied by vibrational and circular dichroism spectroscopy.

    PubMed

    Carmona, P; Lasagabaster, A; Molina, M

    1995-01-19

    Raman and Fourier transform infrared (FTIR) spectroscopies and circular dichroism (CD) have been applied to investigate the secondary structure of bombesin in the solid state and in phosphate buffer solution (pH 3.8). At concentrations around 10(-5) M, circular dichroism reveals that bombesin exists as an irregular or disordered conformation. However, the secondary structure of the peptide appears to be a mixture of disordered structure and intermolecular beta-sheets in 0.01 M sodium phosphate buffer when the peptide concentrations are higher than around 6.5 mM. The tendency of bombesin to form aggregated beta-sheet species seems to be originated mainly in the sequence of the residues 7-14, as supported by the Raman spectra and beta-sheet propensities (P beta) of the amino-acid residues. It is the hydrophobic force of this amino-acid sequence, and not a salt bridge effect, that is the factor responsible for the formation of peptide aggregates.

  5. Strength by joining methods: combining synthesis with NMR, IR, and vibrational circular dichroism spectroscopy for the determination of the relative configuration in hemicalide.

    PubMed

    De Gussem, Ewoud; Herrebout, Wouter; Specklin, Simon; Meyer, Christophe; Cossy, Janine; Bultinck, Patrick

    2014-12-22

    The relative configuration of a key subunit of hemicalide, a recently isolated, highly bioactive marine natural product having potent antiproliferative activity against a panel of human cancer cell lines, was assigned by combining stereocontrolled synthesis of model substrates with NMR, IR, and vibrational circular dichroism (VCD) spectroscopy. The assignment of the absolute configuration of asymmetric carbon center C42 in two structurally complex epimeric substructures containing six stereocenters by VCD analysis illustrates the power and reliability of combining methods.

  6. 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

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

    PubMed

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

    2006-10-28

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

  8. 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.

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

    PubMed

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

    2014-09-28

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

  10. 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.

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

    PubMed

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

    2011-05-01

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

  12. Coherence Spectroscopy Investigations of the Low-Frequency Vibrations of Heme: Effects of Protein-Specific Perturbations

    PubMed Central

    Gruia, Flaviu; Kubo, Minoru; Ye, Xiong; Ionascu, Dan; Lu, Changyuan; Poole, Robert K.; Yeh, Syun-Ru; Champion, Paul M.

    2009-01-01

    Femtosecond coherence spectroscopy is used to probe the low-frequency (20–200 cm−1) vibrational modes of heme proteins in solution. Horseradish peroxidase (HRP), myoglobin (Mb), and Campylobacter jejuni globin (Cgb) are compared and significant differences in the coherence spectra are revealed. It is concluded that hydrogen bonding and ligand charge do not strongly affect the low-frequency coherence spectra and that protein-specific deformations of the heme group lower its symmetry and control the relative spectral intensities. Such deformations potentially provide a means for proteins to tune heme reaction coordinates, so that they can perform a broad array of specific functions. Native HRP displays complex spectral behavior above ~50 cm−1 and very weak activity below ~50 cm−1. Binding of the substrate analog, benzhydroxamic acid, leads to distinct changes in the coherence and Raman spectra of HRP that are consistent with the stabilization of a heme water ligand. The CN derivatives of the three proteins are studied to make comparisons under conditions of uniform heme coordination and spin-state. MbCN is dominated by a doming mode near 40 cm−1, while HRPCN displays a strong oscillation at higher frequency (96 cm−1) that can be correlated with the saddling distortion observed in the X-ray structure. In contrast, CgbCN displays low-frequency coherence spectra that contain strong modes near 30 and 80 cm−1, probably associated with a combination of heme doming and ruffling. HRPNO displays a strong doming mode near 40 cm−1 that is activated by photolysis. The damping of the coherent motions is significantly reduced when the heme is shielded from solvent fluctuations by the protein material and reduced still further when T ≲ 50 K, as pure dephasing processes due to the protein–solvent phonon bath are frozen out. PMID:18355013

  13. 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.

  14. Effect of solvent polarity on the vibrational dephasing dynamics of the nitrosyl stretch in an Fe(II) complex revealed by 2D IR spectroscopy.

    PubMed

    Brookes, Jennifer F; Slenkamp, Karla M; Lynch, Michael S; Khalil, Munira

    2013-07-25

    The vibrational dephasing dynamics of the nitrosyl stretching vibration (ν(NO)) in sodium nitroprusside (SNP, Na2[Fe(CN)5NO]·2H2O) are investigated using two-dimensional infrared (2D IR) spectroscopy. The ν(NO) in SNP acts as a model system for the nitrosyl ligand found in metalloproteins which play an important role in the transportation and detection of nitric oxide (NO) in biological systems. We perform a 2D IR line shape study of the ν(NO) in the following solvents: water, deuterium oxide, methanol, ethanol, ethylene glycol, formamide, and dimethyl sulfoxide. The frequency of the ν(NO) exhibits a large vibrational solvatochromic shift of 52 cm(-1), ranging from 1884 cm(-1) in dimethyl sulfoxide to 1936 cm(-1) in water. The vibrational anharmonicity of the ν(NO) varies from 21 to 28 cm(-1) in the solvents used in this study. The frequency-frequency correlation functions (FFCFs) of the ν(NO) in SNP in each of the seven solvents are obtained by fitting the experimentally obtained 2D IR spectra using nonlinear response theory. The fits to the 2D IR line shape reveal that the spectral diffusion time scale of the ν(NO) in SNP varies from 0.8 to 4 ps and is negatively correlated with the empirical solvent polarity scales. We compare our results with the experimentally determined FFCFs of other charged vibrational probes in polar solvents and in the active sites of heme proteins. Our results suggest that the vibrational dephasing dynamics of the ν(NO) in SNP reflect the fluctuations of the nonhomogeneous electric field created by the polar solvents around the nitrosyl and cyanide ligands. The solute solvent interactions occurring at the trans-CN ligand are sensed through the π-back-bonding network along the Fe-NO bond in SNP.

  15. 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…

  16. 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.

  17. 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.

  18. Vibrational spectroscopy of synthetic stercorite H(NH 4)Na(PO 4)·4H 2O—A comparison with the natural cave mineral

    NASA Astrophysics Data System (ADS)

    Frost, Ray L.; Xi, Yunfei; Palmer, Sara J.; Millar, Graeme J.; Tan, Keqin; Pogson, Ross E.

    2011-12-01

    In order to mimic the chemical reactions in cave systems, the analogue of the mineral stercorite H(NH 4)Na(PO 4)·4H 2O has been synthesised. X-ray diffraction of the stercorite analogue matches the stercorite reference pattern. A comparison is made with the vibrational spectra of synthetic stercorite analogue and the natural Cave mineral. The mineral in nature is formed by the reaction of bat guano chemicals on calcite substrates. A single Raman band at 920 cm -1 (Cave) and 922 cm -1 (synthesised) defines the presence of hydrogen phosphate in the mineral. In the synthetic stercorite analogue, additional bands are observed and are attributed to the dihydrogen and phosphate anions. The vibrational spectra of synthetic stercorite only partly match that of the natural stercorite. It is suggested that natural stercorite is more pure than that of synthesised stercorite. Antisymmetric stretching bands are observed in the infrared spectrum at 1052, 1097, 1135 and 1173 cm -1. Raman spectroscopy shows the stercorite mineral is based upon the hydrogen phosphate anion and not the phosphate anion. Raman and infrared bands are found and assigned to PO 43-, H 2O, OH and NH stretching vibrations. Raman spectroscopy shows the synthetic analogue is similar to the natural mineral. A mechanism for the formation of stercorite is provided.

  19. Molecular geometry and vibrational studies of 3,5-diamino-1,2,4-triazole using quantum chemical calculations and FT-IR and FT-Raman spectroscopies.

    PubMed

    Guennoun, L; El jastimi, J; Guédira, F; Marakchi, K; Kabbaj, O K; El Hajji, A; Zaydoun, S

    2011-01-01

    The 3,5-diamino-1,2,4-triazole (guanazole) was investigated by vibrational spectroscopy and quantum methods. The solid phase FT-IR and FT-Raman spectra were recorded in the region 4000-400 cm(-1) and 3600-50 cm(-1) respectively, and the band assignments were supported by deuteration effects. The results of energy calculations have shown that the most stable form is 1H-3,5-diamino-1,2,4-triazole under C1 symmetry. For this form, the molecular structure, harmonic vibrational wave numbers, infrared intensities and Raman activities were calculated by the ab initio/HF and DFT/B3LYP methods using 6-31G* basis set. The calculated geometrical parameters of the guanazole molecule using B3LYP methodology are in good agreement with the previously reported X-ray data, and the scaled vibrational wave number values are in good agreement with the experimental data. The normal vibrations were characterized in terms of potential energy distribution (PEDs) using VEDA 4 program.

  20. Molecular geometry and vibrational studies of 3,5-diamino-1,2,4-triazole using quantum chemical calculations and FT-IR and FT-Raman spectroscopies

    NASA Astrophysics Data System (ADS)

    Guennoun, L.; El jastimi, J.; Guédira, F.; Marakchi, K.; Kabbaj, O. K.; El Hajji, A.; Zaydoun, S.

    2011-01-01

    The 3,5-diamino-1,2,4-triazole (guanazole) was investigated by vibrational spectroscopy and quantum methods. The solid phase FT-IR and FT-Raman spectra were recorded in the region 4000-400 cm -1 and 3600-50 cm -1 respectively, and the band assignments were supported by deuteration effects. The results of energy calculations have shown that the most stable form is 1H-3,5-diamino-1,2,4-triazole under C 1 symmetry. For this form, the molecular structure, harmonic vibrational wave numbers, infrared intensities and Raman activities were calculated by the ab initio/HF and DFT/B3LYP methods using 6-31G* basis set. The calculated geometrical parameters of the guanazole molecule using B3LYP methodology are in good agreement with the previously reported X-ray data, and the scaled vibrational wave number values are in good agreement with the experimental data. The normal vibrations were characterized in terms of potential energy distribution (PEDs) using VEDA 4 program.

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  3. 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

  4. 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.

  5. 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.

  6. Interfacial Infrared Vibrational Spectroscopy.

    DTIC Science & Technology

    1986-07-30

    with 0.1 M lithium perchlorate support electrolyte. 2.4.5. Adsorption of Tetracyanoethylene Anion Radical (79) The cyclic voltammetry for TCNE in...utilizing vi~rational spectroscopic techniques. Early efforts to obtain spectroscopic data for species at the electrode solution interface (1,2,3) utilized... calculation of IRRAS-like % % %% spectr: for surface species if an electrode potential is known for which the species is removed from the elecz,-vde

  7. Interfacial Infrared Vibrational Spectroscopy.

    DTIC Science & Technology

    1986-07-30

    Tetracyanoethylene Anion Radical (79) The cyclic voltammetry for TCNE in acetonitrile solutions containing LiClO4 and tetra-n-butylammonium...acetonitrile. Modulation potential 0.0 V to +0.800 V vs. Ag/Ag+ reference. 73 Figure 31 Cyclic voltammetry of TCNE in acetonitrile: (a) 0.1 M TBAF; (b...spectroscopic data for species at the electrode solution interface (1,2,3) utilized infrared transmitting germanium electrodes in an internal reflectance

  8. A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    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.

  9. 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.

  10. Vibrational Coupling Pathways in the CH Stretch Region of CH_3OH and CH_3OD as Revealed by IR and Ftmw-Ir Spectroscopies

    NASA Astrophysics Data System (ADS)

    Twagirayezu, Sylvestre; Wang, Xiaoliang; Perry, David S.; Neill, Justin L.; Muckle, Matt T.; Pate, Brooks H.; Xu, Li-Hong

    2011-06-01

    Infrared spectra of jet-cooled CH_3OD and CH_3OH in the CH stretch region are observed by coherence-converted population transfer Fourier transform microwave-infrared (CCPT-FTMW-IR) spectroscopy (E torsional species only) and by slit-jet single resonance spectroscopy (both A and E torsional species, CH_3OH only). Previously, we reported the analysis of ν_3 symmetric CH stretch region (2750-2900 Cm-1), and the present work extends the analysis to higher frequency (2900-3020 Cm-1). The overall observed spectra contain 17 interacting vibrational bands for CH_3OD and 28 for CH_3OH. The signs and magnitudes of the torsional tunneling splittings are deduced for three CH fundamentals (ν_3, ν_9, ν_2) of both molecules and are compared to a model calculation and to ab initio theory. The number and distribution of observed vibrational bands indicate that the CH stretch bright states couple first to doorway states that are binary combinations of bending modes. In the parts of the spectrum where doorway states are present, the observed density of coupled states is comparable to the total density of vibrational states in the molecule, but where there are no doorway states, only the CH stretch fundamentals are observed. A time-dependent interpretation of the present FTMW-IR spectra indicates a fast (˜ 200 fs) initial decay of the bright state followed by second, slower redistribution (˜ 1-3 ps). The qualitative agreement of the present data with the time-dependent experiments of Iwaki and Dlott provides further support for the similarity of the fastest vibrational relaxation processes in the liquid and gas phases. Twagirayezu, S.; Clasp, T. N.; Perry, D. S.; Neill, J. L.; Muckle, M. T.; Pate, B. H. J. Phys. Chem. A 2010, 114, 6818 Iwaki, L. K.; Dlott, D. D. J. Phys. Chem. A 2000, 104, 9101

  11. 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

  12. Creation and Relaxation of Phospholipid Compositional Asymmetry in Lipid Bilayers Examined by Sum-Frequency Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Anglin, Timothy C.; Brown, Krystal; Conboy, John C.

    2010-08-01

    Eukaryotic cells contain an asymmetric distribution of phospholipids in the two leaflets of the lipid bilayer which is known to contribute to cellular function. In the plasma membrane of eukaryotic cells, the aminophospholipids with phosphatidylserine (PS) and phosphatidylethanolamine (PE) headgroups are predominately located on the cytosolic leaflet while sphingolipids with phosphatidylcholine (PC) headgroups and sphingomeylin are on the extra-cellular leaflet. There have been a 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. It is generally accepted that a significant barrier to native lipid translocation (movement between leaflets of the bilayer) exists which is related to the energetic penalty of moving the hydrophilic headgroup of a phospholipid through the hydrophobic core of the membrane. Overcoming this energetic barrier represents the rate limiting step in the spontaneous flip-flop of phospholipids in biological membranes, yet, while numerous kinetic studies of phospholipid flip-flop have been conducted, few researchers have reported thermodynamic parameters for the process. 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 by exploiting the coherent nature of SFVS. The SFVS intensity arising from the terminal methyl groups of the lipid fatty acid chains is used as an internal probe to directly monitor the compositional asymmetry in planar supported lipid bilayers (PSLBs(. By selectively deuterating a sub

  13. 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.

  14. Detailed structural study of β-artemether: Density functional theory (DFT) calculations of Infrared, Raman spectroscopy, and vibrational circular dichroism

    NASA Astrophysics Data System (ADS)

    Wang, Zhiqiang; Chen, Jianchao; Li, Linwei; Zhou, Zhixu; Geng, Yiding; Sun, Tiemin

    2015-10-01

    In this study, the experimental and theoretical studies on the structure of β-artemether are presented. The optimized molecular structure, Mulliken atomic charges, vibrational spectra (IR, Raman and vibrational circular dichroism), and molecular electrostatic potential have been calculated by density functional theory (DFT) using B3LYP method with the 6-311++G (2d, p) basis set. Reliable vibrational assignments for Artemether have been made on the basis of potential energy distribution (PED). The vibrational circular dichroism (VCD) has been explored by ab initio calculations, and then was used to compare with the experimental VCD. The consistence between them confirmed the absolute configuration of Artemether. In addition, HOMO-LUMO of the title compound as well as thermo-dynamical parameters has illustrated the stability of β-artemether.

  15. Biomedical nanotechnology.

    PubMed

    Hurst, Sarah J

    2011-01-01

    This chapter summarizes the roles of nanomaterials in biomedical applications, focusing on those highlighted in this volume. A brief history of nanoscience and technology and a general introduction to the field are presented. Then, the chemical and physical properties of nanostructures that make them ideal for use in biomedical applications are highlighted. Examples of common applications, including sensing, imaging, and therapeutics, are given. Finally, the challenges associated with translating this field from the research laboratory to the clinic setting, in terms of the larger societal implications, are discussed.

  16. 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.

  17. 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.

  18. Composite vibrational spectroscopy of the group 12 difluorides: ZnF2, CdF2, and HgF2

    NASA Astrophysics Data System (ADS)

    Solomonik, Victor G.; Smirnov, Alexander N.; Navarkin, Ilya S.

    2016-04-01

    The vibrational spectra of group 12 difluorides, MF2 (M = Zn, Cd, Hg), were investigated via coupled cluster singles, doubles, and perturbative triples, CCSD(T), including core correlation, with a series of correlation consistent basis sets ranging in size from triple-zeta through quintuple-zeta quality, which were then extrapolated to the complete basis set (CBS) limit using a variety of extrapolation procedures. The explicitly correlated coupled cluster method, CCSD(T)-F12b, was employed as well. Although exhibiting quite different convergence behavior, the F12b method yielded the CBS limit estimates closely matching more computationally expensive conventional CBS extrapolations. The convergence with respect to basis set size was examined for the contributions entering into composite vibrational spectroscopy, including those from higher-order correlation accounted for through the CCSDT(Q) level of theory, second-order spin-orbit coupling effects assessed within four-component and two-component relativistic formalisms, and vibrational anharmonicity evaluated via a perturbative treatment. Overall, the composite results are in excellent agreement with available experimental values, except for the CdF2 bond-stretching frequencies compared to spectral assignments proposed in a matrix isolation infrared and Raman study of cadmium difluoride vapor species [Loewenschuss et al., J. Chem. Phys. 50, 2502 (1969); Givan and Loewenschuss, J. Chem. Phys. 72, 3809 (1980)]. These assignments are called into question in the light of the composite results.

  19. Vibrational Spectrum of an Excited State and Huang-Rhys Factors by Coherent Wave Packets in Time-Resolved Fluorescence Spectroscopy.

    PubMed

    Lee, Gyeongjin; Kim, Junwoo; Kim, So Young; Kim, Dong Eon; Joo, Taiha

    2017-01-10

    Coherent nuclear wave packet motions in an electronic excited state of a molecule are measured directly by time-resolved spontaneous fluorescence spectroscopy with an unprecedented time resolution by using two-photon absorption excitation and fluorescence upconversion by noncollinear sum frequency generation. With an estimated time resolution of approximately 25 fs, wave packet motions of vibrational modes up to 1600 cm(-1) are recorded for coumarin 153 in ethanol. Two-color transient absorption at 13 fs time resolution are measured to confirm the result. Vibrational displacements between the ground and excited states and Huang-Rhys factors (HRFs) are calculated by quantum mechanical methods and are compared with the experimental results. HRFs calculated by density functional theory (DFT) and time-dependent DFT reproduce the experiment adequately. This fluorescence-based method provides a unique and direct way to obtain the vibrational spectrum of a molecule in an electronic excited state and the HRFs, as well as the dynamics of excited states, and it might provide information on the structure of an excited state through the HRFs.

  20. One-photon mass-analyzed threshold ionization spectroscopy of 2-bromopropene (2-C3H5Br): Analysis of vibration and internal rotation in the cation

    NASA Astrophysics Data System (ADS)

    Lee, Mina; Kim, Myung Soo

    2003-12-01

    Vibrational spectrum of 2-C3H5Br cation in the ground electronic state was obtained by one-photon mass-analyzed threshold ionization (MATI) spectroscopy using coherent vacuum ultraviolet radiation generated by four-wave difference frequency mixing in Kr. From the MATI spectra, ionization energy of 2-C3H5Br to the ionic ground state has been determined to be 9.4377±0.0006 eV. Vibrational assignments have been made by comparing with the vibrational frequencies and Franck-Condon factors calculated at the B3LYP and BP86 levels with the 6-311++G(3df,3pd) basis set. Several low-frequency bands have been assigned to the torsional motion of the methyl group in the cation. Energies of the torsional states and relative transition intensities to these states have been reproduced well by a one-dimensional rotor model. The torsional barrier and internal rotational constant have been determined to be 80.0 and 5.13 cm-1, respectively.

  1. 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.

  2. Overtone spectroscopy of H{sub 2}O clusters in the v{sub OH}=2 manifold: Infrared-ultraviolet vibrationally mediated dissociation studies

    SciTech Connect

    Nizkorodov, Sergey A.; Ziemkiewicz, Michael; Nesbitt, David J.; Knight, Alan E.W.

    2005-05-15

    Spectroscopy and predissociation dynamics of (H{sub 2}O){sub 2} and Ar-H{sub 2}O are investigated with vibrationally mediated dissociation (VMD) techniques, wherein v{sub OH}=2 overtones of the complexes are selectively prepared with direct infrared pumping, followed by 193 nm photolysis of the excited H{sub 2}O molecules. As a function of relative laser timing, the photolysis breaks H{sub 2}O into OH and H fragments either (i) directly inside the complex or (ii) after the complex undergoes vibrational predissociation, with the nascent quantum state distribution of the OH photofragment probed via laser-induced fluorescence. This capability provides the first rotationally resolved spectroscopic analysis of (H{sub 2}O){sub 2} in the first overtone region and vibrational predissociation dynamics of water dimer and Ar-water clusters. The sensitivity of the VMD approach permits several v{sub OH}=2 overtone bands to be observed, the spectroscopic assignment of which is discussed in the context of recent anharmonic theoretical calculations.

  3. Highly vibrationally excited O2 molecules in low-pressure inductively-coupled plasmas detected by high sensitivity ultra-broad-band optical absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Foucher, Mickaël; Marinov, Daniil; Carbone, Emile; Chabert, Pascal; Booth, Jean-Paul

    2015-08-01

    Inductively-coupled plasmas in pure O2 (at pressures of 5-80 mTorr and radiofrequency power up to 500 W) were studied by optical absorption spectroscopy over the spectral range 200-450 nm, showing the presence of highly vibrationally excited O2 molecules (up to vʺ = 18) by Schumann-Runge band absorption. Analysis of the relative band intensities indicates a vibrational temperature up to 10,000 K, but these hot molecules only represent a fraction of the total O2 density. By analysing the (11-0) band at higher spectral resolution the O2 rotational temperature was also determined, and was found to increase with both pressure and power, reaching 900 K at 80 mTorr 500 W. These measurements were achieved using a new high-sensitivity ultra-broad-band absorption spectroscopy setup, based on a laser-plasma light source, achromatic optics and an aberration-corrected spectrograph. This setup allows the measurement of weak broadband absorbances due to a baseline variability lower than 2   ×   10-5 across a spectral range of 250 nm.

  4. 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.

  5. 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.

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

    PubMed

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

    2010-12-01

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

  7. Resolving Two Closely Overlapping -CN Vibrations and Structure in the Langmuir Monolayer of the Long-Chain Nonadecanenitrile by Polarization Sum Frequency Generation Vibrational Spectroscopy

    SciTech Connect

    Zhang, Zhen; Guo, Yuan; Lu, Zhou; Velarde Ruiz Esparza, Luis A.; Wang, Hongfei

    2012-01-10

    Polarization sum frequency generation vibrational spectra (SFG-VS) reveals that there are two distinctively different but closely overlapping -CN vibrations at 2244.5 cm{sup -1} and 2251.1 cm{sup -1}, respectively, in the Langmuir monolayer of the long-chain nonadecanenitrile (C18CN, CH{sub 3}(CH{sub 2}){sub 17}CN, or C18CN)at the air/water interface. The blue shifted -CN groups at 2251.1 cm{sup -1} peak is about 1.8 times broader than that of the 2244.5 cm{sup -1}. Both the spectral shift and spectral width are consistent with the picture that this blue shifted peak corresponds to the solvated -CN group; while the 2244.5 cm{sup -1} peak is the signature of the less solvated -CN group. Polarization dependence of these two peaks further suggest that the -CN group corresponding to the 2251.1 cm{sup -1} peak is tilted with an average angle of 50{sup o} from interface normal, where that to the 2244.5 cm{sup -1} peak is tilted with an angle around 67{sup o}. The relative population for the -CN groups corresponding to the 2251.1 cm{sup -1} peak is about three times of that of the 2244.5 cm{sup -1} peak. These results suggest that the -CN head groups in the C18CN Langmuir monolayer are not aligned uniformly at slightly different depth, in order to avoid the strong repulsive forces between the strong -CN dipoles. The SFG-VS spectra of the O-H stretches at C18CN Langmuir monolayer is similar to those of the 4''-n-pentyl-4-cyano-p-terphenyl (5CT) monolayer, indicating complete exclusion of the water molecules from the C18CN Langmuir monolayer, but significantly different from those of the 4''-n-octyl-4-p-cyanobiphenyl (8CB) monolayer, as well as those of the air/acetonitrile aqueous solution interface. Different from previous held understandings, these results suggest that the structure of the insoluble long-chain C18CN Langmuir monolayer is significantly different from that of the Gibbs adsorption layer of the short chain soluble acetonitrile or propanenitrile aqueous

  8. 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.

  9. Communication: He-tagged vibrational spectra of the SarGlyH+ and H+(H2O)2,3 ions: Quantifying tag effects in cryogenic ion vibrational predissociation (CIVP) spectroscopy

    NASA Astrophysics Data System (ADS)

    Johnson, Christopher J.; Wolk, Arron B.; Fournier, Joseph A.; Sullivan, Erin N.; Weddle, Gary H.; Johnson, Mark A.

    2014-06-01

    To assess the degree to which more perturbative, but widely used "tag" species (Ar, H2, 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+ and the small protonated water clusters: H+(H2O)2,3, including the H5O2+ "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 H2 tag-induced shift (relative to that by He) on the tag-bound NH stretch of the SarGlyH+ spectrum is quite small (12 cm-1), while the effect on the floppy H5O2+ ion is more dramatic (125 cm-1) in going from Ar (or H2) to Ne. The shifts from Ne to He, on the other hand, while quantitatively significant (maximum of 10 cm-1), display the same basic H5O2+ band structure, indicating that the He-tagged H5O2+ spectrum accurately represents the delocalized nature of the vibrational zero-point level. Interestingly, the He-tagged spectrum of H+(H2O)3 reveals the location of the non-bonded OH group on the central H3O+ 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.

  10. 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...

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

    PubMed

    Zhang, Feng; Hayashi, Michitoshi; Wang, Houng-Wei; Tominaga, Keisuke; Kambara, Ohki; Nishizawa, Jun-ichi; Sasaki, Tetsuo

    2014-05-07

    The phonon modes of molecular crystals in the terahertz frequency region often feature delicately coupled inter- and intra-molecular vibrations. Recent advances in density functional theory such as DFT-D(*) have enabled accurate frequency calculation. However, the nature of normal modes has not been quantitatively discussed against experimental criteria such as isotope shift (IS) and correlation field splitting (CFS). Here, we report an analytical mode-decoupling method that allows for the decomposition of a normal mode of interest into intermolecular translation, libration, and intramolecular vibrational motions. We show an application of this method using the crystalline anthracene system as an example. The relationship between the experimentally obtained IS and the IS obtained by PBE-D(*) simulation indicates that two distinctive regions exist. Region I is associated with a pure intermolecular translation, whereas region II features coupled intramolecular vibrations that are further coupled by a weak intermolecular translation. We find that the PBE-D(*) data show excellent agreement with the experimental data in terms of IS and CFS in region II; however, PBE-D(*) produces significant deviations in IS in region I where strong coupling between inter- and intra-molecular vibrations contributes to normal modes. The result of this analysis is expected to facilitate future improvement of DFT-D(*).

  12. Investigations of the Structure and Hydrogen Bonding of Water Molecules at Liquid Surfaces by Vibrational Sum Frequency Spectroscopy

    DTIC Science & Technology

    1998-06-01

    studies conducted for the first time at liquid surfaces are also described. In these studies the intermolecular and intramolecular coupling of vibrational ... modes in the water molecules are diminished. The results of these and above mentioned studies provide valuable information for those interested in developing theoretical descriptions of water at surfaces and interfaces.

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

    NASA Astrophysics Data System (ADS)

    Zhang, Feng; Hayashi, Michitoshi; Wang, Houng-Wei; Tominaga, Keisuke; Kambara, Ohki; Nishizawa, Jun-ichi; Sasaki, Tetsuo

    2014-05-01

    The phonon modes of molecular crystals in the terahertz frequency region often feature delicately coupled inter- and intra-molecular vibrations. Recent advances in density functional theory such as DFT-D* have enabled accurate frequency calculation. However, the nature of normal modes has not been quantitatively discussed against experimental criteria such as isotope shift (IS) and correlation field splitting (CFS). Here, we report an analytical mode-decoupling method that allows for the decomposition of a normal mode of interest into intermolecular translation, libration, and intramolecular vibrational motions. We show an application of this method using the crystalline anthracene system as an example. The relationship between the experimentally obtained IS and the IS obtained by PBE-D* simulation indicates that two distinctive regions exist. Region I is associated with a pure intermolecular translation, whereas region II features coupled intramolecular vibrations that are further coupled by a weak intermolecular translation. We find that the PBE-D* data show excellent agreement with the experimental data in terms of IS and CFS in region II; however, PBE-D* produces significant deviations in IS in region I where strong coupling between inter- and intra-molecular vibrations contributes to normal modes. The result of this analysis is expected to facilitate future improvement of DFT-D*.

  14. Rotational Dependence of Intramolecular Dynamics in Acetylene at Low Vibrational Excitation as Deduced from High Resolution Spectroscopy

    NASA Astrophysics Data System (ADS)

    Perry, David S.; Miller, Anthony; Amyay, B.; Fayt, A.; Herman, M.

    2010-06-01

    The link between energy-resolved spectra and time-resolved dynamics is explored quantitatively for acetylene (12C2H2), X1Σg+ with up to 8,600 wn of vibrational energy. This comparison is based on the extensive knowledge of the vibration-rotation energy levels and on the model Hamiltonian used to fit them to high precision. Simulated intensity borrowing features in high resolution absorption spectra and predicted survival probabilities for intramolecular vibrational redistribution (IVR) are first investigated for the ν4+ν5 and ν3 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 φd, the IVR lifetime τIVR, and the recurrence time τrec. For the two bright states ν3+2ν4 and 7ν4, the collisionless dynamics for thermally averaged rotational distributions at T = 27, 270 and 500 K were calculated from the available spectroscopic data. For the 7ν4 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. 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).

  15. 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

  16. Rotational spectroscopy of pyridazine and its isotopologs from 235-360 GHz: Equilibrium structure and vibrational satellites

    NASA Astrophysics Data System (ADS)

    Esselman, Brian J.; Amberger, Brent K.; Shutter, Joshua D.; Daane, Mitchell A.; Stanton, John F.; Woods, R. Claude; McMahon, Robert J.

    2013-12-01

    The rotational spectrum of pyridazine (o-C4H4N2), the ortho disubstituted nitrogen analog of benzene, has been measured and analyzed in the gas phase. For the ground vibrational state of the normal isotopolog, over 2000 individual rotational transitions have been identified between 238 and 360 GHz and have been fit to 13 parameters of a 6th-order centrifugal distortion Hamiltonian. All transitions in this frequency region can now be predicted from this model to near experimental accuracy, i.e., well enough for the purpose of any future radio-astronomical search for this species. Three isotopologs, [3-13C]-C4H4N2, [4-13C]-C4H4N2, and [1-15N]-C4H4N2, have been detected in natural abundance, and several hundred lines have been measured for each of these species and fit to 6th-order Hamiltonians. Ten additional isotopologs were synthesized with enhanced deuterium substitution and analyzed to allow for a complete structure determination. The equilibrium structure (Re) of pyridazine was obtained by correcting the experimental rotational constants for the effects of vibration-rotation coupling using interaction constants predicted from CCSD(T) calculations with an ANO0 basis set and further correcting for the effect of electron mass. The final Re structural parameters are determined with excellent accuracy, as evidenced by their ability to predict 28 independent moments of inertia (Ia and Ib for 14 isotopologs) very well from 9 structural parameters. The rotational spectra of the six lowest-energy fundamental vibrational satellites of the main isotopolog have been detected. The rotational spectra of the five lowest-energy vibrational satellites have been assigned and fit to yield accurate rotational and distortion constants, while the fit and assignment for the sixth is less complete. The resultant vibration-rotation interaction (α) constants are found to be in excellent agreement with ones predicted from coupled-cluster calculations, which proved to be the key to

  17. Investigation of the terahertz vibrational modes of ZIF-8 and ZIF-90 with terahertz time-domain spectroscopy.

    PubMed

    Tan, Nicholas Y; Ruggiero, Michael T; Orellana-Tavra, Claudia; Tian, Tian; Bond, Andrew D; Korter, Timothy M; Fairen-Jimenez, David; Zeitler, J Axel

    2015-11-18

    We present experimental and computational evidence that gate-opening modes for zeolitic imidazole frameworks can be observed at terahertz frequencies. Our work highlights the critical importance to correctly optimise the crystal structure prior to computational lattice dynamics analysis. The results support the hypothesis that the low energy vibrational modes do indeed play a significant role in host-guest interactions for ZIFs, such as gas loading.

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  19. 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.

  20. 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.

  1. 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.

  2. FT-IR, FT-Raman, UV-visible, and NMR spectroscopy and vibrational properties of the labdane-type diterpene 13-epi-sclareol.

    PubMed

    Chain, Fernando E; Leyton, Patricio; Paipa, Carolina; Fortuna, Mario; Brandán, Silvia A

    2015-03-05

    In this work, FT-IR, FT-Raman, UV-Visible and NMR spectroscopies and density functional theory (DFT) calculations were employed to study the structural and vibrational properties of the labdane-type diterpene 13-epi-sclareol using the hybrid B3LYP method together with the 6-31G(∗) basis set. Three stable structures with minimum energy found on the potential energy curves (PES) were optimized, and the corresponding molecular electrostatic potentials, atomic charges, bond orders, stabilization energies and topological properties were computed at the same approximation level. The complete assignment of the bands observed in the vibrational spectrum of 13-epi-sclareol was performed taking into account the internal symmetry coordinates for the three structures using the scaled quantum mechanical force field (SQMFF) methodology at the same level of theory. In addition, the force constants were calculated and compared with those reported in the literature for similar compounds. The predicted vibrational spectrum and the calculated (1)H NMR and (13)C NMR chemical shifts are in good agreement with the corresponding experimental results. The theoretical UV-Vis spectra for the most stable structure of 13-epi-sclareol demonstrate a better correlation with the corresponding experimental spectrum. The study of the three conformers by means of the theory of atoms in molecules (AIM) revealed different H bond interactions and a strong dependence of the interactions on the distance between the involved atoms. Furthermore, the natural bond orbital (NBO) calculations showed the characteristics of the electronic delocalization for the two six-membered rings with chair conformations.

  3. Combining synchrotron-based X-ray techniques with vibrational spectroscopies for the in situ study of heterogeneous catalysts: a view from a bridge.

    PubMed

    Newton, Mark A; van Beek, Wouter

    2010-12-01

    The advantages, challenges, and future possibilities for combining synchrotron-based X-ray techniques with vibrational spectroscopies are considered in this critical review. Particular emphasis is given to (1) quantifying structure and structural change--on a wide range of length scales--in working heterogeneous catalytic systems; (2) relating that change to chemical speciation occurring at the surface of the catalyst; and (3) determining how such change relates to the overall function of the catalyst material. We will consider those resources that exist today and suggest some possible future directions yet to be ventured into or demonstrated. Lastly, we will consider how the catalysis community interacts with, and uses the resources offered by, modern synchrotron radiation facilities and whether this current relationship provides the best and most inclusive means for the exploitation of these resources in this field of research (83 references).

  4. Conformational change of a chiral Schiff base Ni(II) complex with a binaphthyl moiety: application of vibrational circular dichroism spectroscopy.

    PubMed

    Sato, Hisako; Mori, Yukie; Yamagishi, Akihiko

    2013-05-21

    Vibrational circular dichroism (VCD) spectroscopy was applied to study the structural change of a Ni(II) complex (denoted by [Ni(II)L]) with a chiral Schiff base ligand, (R)- or (S)-2,2'-bis(salicylideneamino)-1,1'-binaphthyl (denoted by H2L), in solution. The major signals in the mid-IR region were assigned on the basis of comparison with the DFT-calculated spectra. The complex transformed reversibly between the square-planar, tetrahedral and octahedral configurations, depending on solvents and temperature. The observed changes in the VCD peaks accompanying the transformation were analyzed in terms of the conformational change of the chiral ligand with a focus on the twisting angle in the Schiff base backbone and the dihedral angle of the binaphthyl group.

  5. 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.

  6. Adsorption and self-assembly of octyl hydroxamic acid at a fluorite surface as revealed by sum-frequency vibrational spectroscopy.

    PubMed

    Wang, Xuming; Liu, Jin; Miller, Jan D

    2008-09-15

    In the study described here, the surface structure of a self-assembly octyl hydroxamic acid at a calcium fluoride (CaF(2)) surface is evaluated using sum-frequency vibrational spectroscopy (SFVS). Of particular significance are the results that show octyl hydroxamic acid adsorbs at the fluorite surface from octanol solution and has more ordering and molecular conformation than the octyl hydroxamic acid adsorbed from solution. At the fluorite/0.1 M octyl hydroxamic acid octanol solution interface a bilayer-like structure consisting of an octyl hydroxamic acid layer in contact with fluorite and a tilted alcohol layer was observed by SFVS. The alcohol molecules are oriented with respect to the hydroxamic acid monolayer with the OH groups directed towards the bulk alcohol phase and the terminal CH(3) group oriented to face the alkyl chains of the hydroxamic acid monolayer.

  7. Sum frequency generation vibrational spectroscopy (SFG-VS) for complex molecular surfaces and interfaces: Spectral lineshape measurement and analysis plus some controversial issues

    SciTech Connect

    Wang, Hong-Fei

    2016-12-01

    Sum-frequency generation vibrational spectroscopy (SFG-VS) was first developed in the 1980s and it has been proven a uniquely sensitive and surface/interface selective spectroscopic probe for characterization of the structure, conformation and dynamics of molecular surfaces and interfaces. In recent years, there has been significant progress in the development of methodology and instrumentation in the SFG-VS toolbox that has significantly broadened the application to complex molecular surfaces and interfaces. In this review, after presenting a unified view on the theory and methodology focusing on the SFG-VS spectral lineshape, as well as the new opportunities in SFG-VS applications with such developments, some of the controversial issues that have been puzzling the community are to be discussed. The aim of this review is to present to the researchers and students interested in molecular surfaces and interfacial sciences up-to-date perspectives complementary to the existing textbooks and reviews on SFG-VS.

  8. Sum frequency generation vibrational spectroscopy (SFG-VS) for complex molecular surfaces and interfaces: Spectral lineshape measurement and analysis plus some controversial issues

    NASA Astrophysics Data System (ADS)

    Wang, Hong-Fei

    2016-12-01

    Sum-frequency generation vibrational spectroscopy (SFG-VS) was first developed in the 1980s and it has been proven a uniquely sensitive and surface/interface selective spectroscopic probe for characterization of the structure, conformation and dynamics of molecular surfaces and interfaces. In recent years, there have been many progresses in the development of methodology and instrumentation in the SFG-VS toolbox that have significantly broadened the application to complex molecular surfaces and interfaces. In this review, after presenting a unified view on the theory and methodology focusing on the SFG-VS spectral lineshape, as well as the new opportunities in SFG-VS applications with such developments, some of the controversial issues that have been puzzling the community are discussed. The aim of this review is to present to the researchers and students interested in molecular surfaces and interfacial sciences up-to-date perspectives complementary to the existing textbooks and reviews on SFG-VS.

  9. 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.

  10. Structural characterization of electron-induced proton transfer in the formic acid dimer anion, (HCOOH)2-, with vibrational and photoelectron spectroscopies

    NASA Astrophysics Data System (ADS)

    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 (FA2), 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), 10.1021/jp980865n; J. H. Hendricks, S. A. Lyapustina, H. L. de Clercq, J. T. Snodgrass, and K. H. Bowen, J. Chem Phys. 104, 7788 (1996), 10.1063/1.471484; C. Desfrancois, H. Abdoul-Carime, and J. P. Schermann, J. Chem Phys. 104, 7792 (1996)]. The FA2 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 FA2 anion was also recorded using velocity-map imaging. The resulting spectroscopic information verifies the equilibrium FA2- 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.

  11. Site-specific vibrational dynamics of the CD3zeta membrane peptide using heterodyned two-dimensional infrared photon echo spectroscopy.

    PubMed

    Mukherjee, Prabuddha; Krummel, Amber T; Fulmer, Eric C; Kass, Itamar; Arkin, Isaiah T; Zanni, Martin T

    2004-06-01

    Heterodyned two-dimensional infrared (2D IR) spectroscopy has been used to study the amide I vibrational dynamics of a 27-residue peptide in lipid vesicles that encompasses the transmembrane domain of the T-cell receptor CD3zeta. Using 1-(13)C[Double Bond](18)O isotope labeling, the amide I mode of the 49-Leucine residue was spectroscopically isolated and the homogeneous and inhomogeneous linewidths of this mode were measured by fitting the 2D IR spectrum collected with a photon echo pulse sequence. The pure dephasing and inhomogeneous linewidths are 2 and 32 cm(-1), respectively. The population relaxation time of the amide I band was measured with a transient grating, and it contributes 9 cm(-1) to the linewidth. Comparison of the 49-Leucine amide I mode and the amide I band of the entire CD3zeta peptide reveals that the vibrational dynamics are not uniform along the length of the peptide. Possible origins for the large amount of inhomogeneity present at the 49-Leucine site are discussed.

  12. Probing electron density of H-bonding between cation-anion of imidazolium-based ionic liquids with different anions by vibrational spectroscopy.

    PubMed

    Gao, Yan; Zhang, Liqun; Wang, Yong; Li, Haoran

    2010-03-04

    Attenuated total reflection infrared spectroscopy and density functional theory calculation have been employed to study the spectral properties of imidazolium-based ionic liquids (ILs) with different anions. ILs based on 1-butyl-3-methylimidazolium cation with different anions, OH(-), CF(3)CO(2)(-), HSO(4)(-), H(2)PO(4)(-), Cl(-), PF(6)(-), and BF(4)(-), are investigated in the present work. It has been shown that the C(2)-H stretching vibration of the imidazolium ring is closely related to the electron density of H-bonding between the two closest cations and anions for pure ILs. The electron density of H-bonding between cation and anion with different anions decreases in the order [OH](-) > [H(2)PO(4)](-) > [HSO(4)](-) > [CF(3)CO(2)](-) > [Cl](-) > [BF(4)](-) > [PF(6)](-). For aqueous ILs, with increasing water content, the aromatic C-H stretching vibration of the imidazolium cation showed systematic blue-shifts. Especially for BmimOH, the nu(C(2))(-H) undergoes a drastic blue-shift by 58 cm(-1), suggesting that the formation of the strong hydrogen bonds O-H...O may greatly weaken the electron density of H-bonding between the cation and anion of ILs.

  13. Observation of multiple vibrational modes in ultrahigh vacuum tip-enhanced Raman spectroscopy combined with molecular-resolution scanning tunneling microscopy.

    PubMed

    Jiang, N; Foley, E T; Klingsporn, J M; Sonntag, M D; Valley, N A; Dieringer, J A; Seideman, T; Schatz, G C; Hersam, M C; Van Duyne, R P

    2012-10-10

    Multiple vibrational modes have been observed for copper phthalocyanine (CuPc) adlayers on Ag(111) using ultrahigh vacuum (UHV) tip-enhanced Raman spectroscopy (TERS). Several important new experimental features are introduced in this work that significantly advance the state-of-the-art in UHV-TERS. These include (1) concurrent sub-nm molecular resolution STM imaging using Ag tips with laser illumination of the tip-sample junction, (2) laser focusing and Raman collection optics that are external to the UHV-STM that has two cryoshrouds for future low temperature experiments, and (3) all sample preparation steps are carried out in UHV to minimize contamination and maximize spatial resolution. Using this apparatus we have been able to demonstrate a TERS enhancement factor of 7.1 × 10(5). Further, density-functional theory calculations have been carried out that allow quantitative identification of eight different vibrational modes in the TER spectra. The combination of molecular-resolution UHV-STM imaging with the detailed chemical information content of UHV-TERS allows the interactions between large polyatomic molecular adsorbates and specific binding sites on solid surfaces to be probed with unprecedented spatial and spectroscopic resolution.

  14. 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.

  15. 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.

  16. On the participation of photoinduced N-H bond fission in aqueous adenine at 266 and 220 nm: a combined ultrafast transient electronic and vibrational absorption spectroscopy study.

    PubMed

    Roberts, Gareth M; Marroux, Hugo J B; Grubb, Michael P; Ashfold, Michael N R; Orr-Ewing, Andrew J

    2014-11-26

    A combination of ultrafast transient electronic absorption spectroscopy (TEAS) and transient vibrational absorption spectroscopy (TVAS) is used to investigate whether photoinduced N–H bond fission, mediated by a dissociative 1πσ(*) state, is active in aqueous adenine (Ade) at 266 and 220 nm. In order to isolate UV/visible and IR spectral signatures of the adeninyl radical (Ade[-H]), formed as a result of N–H bond fission, TEAS and TVAS are performed on Ade in D2O under basic conditions (pD = 12.5), which forms Ade[-H](-) anions via deprotonation at the N7 or N9 sites of Ade's 7H and 9H tautomers. At 220 nm we observe one-photon detachment of an electron from Ade[-H](-), which generates solvated electrons (eaq(-)) together with Ade[-H] radicals, with clear signatures in both TEAS and TVAS. Additional wavelength dependent TEAS measurements between 240–260 nm identify a threshold of 4.9 ± 0.1 eV (∼250 nm) for this photodetachment process in D2O. Analogous TEAS experiments on aqueous Ade at pD = 7.4 generate a similar photoproduct signal together with eaq(-) after excitation at 266 and 220 nm. These eaq(-) are born from ionization of Ade, together with Ade(+) cations, which are indistinguishable from Ade[-H] radicals in TEAS. Ade(+) and Ade[-H] are found to have different signatures in TVAS and we verify that the pD = 7.4 photoproduct signal observed in TEAS following 220 nm excitation is solely due to Ade(+) cations. Based on these observations, we conclude that: (i) N–H bond fission in aqueous Ade is inactive at wavelengths ≥220 nm; and (ii) if such a channel exists in aqueous solution, its threshold is strongly blue-shifted relative to the onset of the same process in gas phase 9H-Ade (≤233 nm). In addition, we extract excited state lifetimes and vibrational cooling dynamics for 9H-Ade and Ade[-H](-). In both cases, excited state lifetimes of <500 fs are identified, while vibrational cooling occurs within a time frame of 4–5 ps. In contrast, 7H

  17. Vibrational spectroscopy, intramolecular CH⋯O interaction and conformational analysis of 2,5-dimethyl-benzyl benzoate

    NASA Astrophysics Data System (ADS)

    Viana, Rommel B.; Ribeiro, Gabriela L. O.; Valencia, Leidy J.; Varela, Jaldyr J. G.; Viana, Anderson B.; da Silva, Albérico B. F.; Moreno-Fuquen, Rodolfo

    2016-12-01

    The aim of this study was to report the spectroscopic and electronic properties of 2,5-dimethyl-benzyl benzoate. FT-IR and Raman vibrational spectral analyses were performed, while a computational approach was used to elucidate the vibrational frequency couplings. The electronic properties were predicted using the Density Functional Theory, while the G3MP2 method was employed in the thermochemical calculation. A conformational analysis, frontier orbitals, partial atomic charge distribution and the molecular electrostatic potential were also estimated. Concerning to the dihedral angles in the ester group, a conformational analysis showed a barrier energy of 10 kcal mol-1, while other small barriers (below 0.6 kcal mol-1) were predicted within the potential surface energy investigation. Insights into the relative stability among the different positions of methyl groups in the phenyl ring demonstrated that the energy gaps were lower than 1 kcal mol-1 among the regioisomers. In addition, the Quantum Theory of Atoms in Molecules (QTAIM) was used to understand the intramolecular CH⋯O interaction in the title compound, while various methodologies were applied in the atomic charge distribution to evaluate the susceptibility to the population method.

  18. High resolution spectroscopy of 1,2-difluoroethane in a molecular beam: A case study of vibrational mode-coupling

    NASA Astrophysics Data System (ADS)

    Mork, Steven W.; Miller, C. Cameron; Philips, Laura A.

    1992-09-01

    The high resolution infrared spectrum of 1,2-difluoroethane (DFE) in a molecular beam has been obtained over the 2978-2996 cm-1 spectral region. This region corresponds to the symmetric combination of asymmetric C-H stretches in DFE. Observed rotational fine structure indicates that this C-H stretch is undergoing vibrational mode coupling to a single dark mode. The dark mode is split by approximately 19 cm-1 due to tunneling between the two identical gauche conformers. The mechanism of the coupling is largely anharmonic with a minor component of B/C plane Coriolis coupling. Effects of centrifugal distortion along the molecular A-axis are also observed. Analysis of the fine structure identifies the dark state as being composed of C-C torsion, CCF bend, and CH2 rock. Coupling between the C-H stretches and the C-C torsion is of particular interest because DFE has been observed to undergo vibrationally induced isomerization from the gauche to trans conformer upon excitation of the C-H stretch.

  19. Synthesis, X-ray structure analysis, thermodynamic and electronic properties of 4-acetamido benzaldehyde using vibrational spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Jeeva Jasmine, N.; Arunagiri, C.; Subashini, A.; Stanley, N.; Thomas Muthiah, P.

    2017-02-01

    Theoretical Spectrograms, namely, FT-Raman (3500-50 cm-1) and FT-Infrared (4000-400 cm-1) spectra have been studied for 4-acetamido benzaldehyde (4ABA) and are assigned to different normal modes of the molecule. Vibrational spectral analysis was compared with the experimental and theoretical, FT-IR and FT-Raman spectra. The effect of polarity on the Harmonic vibrational frequencies, intensities, optimized geometrical parameters and several thermodynamic parameters in the ground state have been computed by the B3LYP method using 6-311 + G(d,p) basis set. The results of the optimized molecular structure is presented and compared with the XRD values. The global chemical reactivity relate to some parameters, such as HOMO, LUMO, gap energy (ΔE) and other parameters, including electronegativity (χ) and global hardness (η). The values of the reactivity descriptors indicated that the interaction between 4ABA molecules reduced its reactivity in comparison with the exhibited in gas phase. In addition, the local reactivity has been analyzed through the Fukui function and condensed softness indices.

  20. Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations

    PubMed Central

    Liu, Yingliang; Guchhait, Biswajit; Siebert, Torsten; Fingerhut, Benjamin P.; Elsaesser, Thomas

    2017-01-01

    Molecular couplings between DNA and water together with the accompanying processes of energy exchange are mapped via the ultrafast response of DNA backbone vibrations after OH stretch excitation of the water shell. Native salmon testes DNA is studied in femtosecond pump-probe experiments under conditions of full hydration and at a reduced hydration level with two water layers around the double helix. Independent of their local hydration patterns, all backbone vibrations in the frequency range from 940 to 1120 cm–1 display a quasi-instantaneous reshaping of the spectral envelopes of their fundamental absorption bands upon excitation of the water shell. The subsequent reshaping kinetics encompass a one-picosecond component, reflecting the formation of a hot ground state of the water shell, and a slower contribution on a time scale of tens of picoseconds. Such results are benchmarked by measurements with resonant excitation of the backbone modes, resulting in distinctly different absorption changes. We assign the fast changes of DNA absorption after OH stretch excitation to structural changes in the water shell which couple to DNA through the local electric fields. The second slower process is attributed to a flow of excess energy from the water shell into DNA, establishing a common heated ground state in the molecular ensemble. This interpretation is supported by theoretical calculations of the electric fields exerted by the water shell at different temperatures.

  1. Phase transition behaviors of the supported DPPC bilayer investigated by sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM).

    PubMed

    Wu, Heng-Liang; Tong, Yujin; Peng, Qiling; Li, Na; Ye, Shen

    2016-01-21

    The phase transition behaviors of a supported bilayer of dipalmitoylphosphatidyl-choline (DPPC) have been systematically evaluated by in situ sum frequency generation (SFG) vibrational spectroscopy and atomic force microscopy (AFM). By using an asymmetric bilayer composed of per-deuterated and per-protonated monolayers, i.e., DPPC-d75/DPPC and a symmetric bilayer of DPPC/DPPC, we were able to probe the molecular structural changes during the phase transition process of the lipid bilayer by SFG spectroscopy. It was found that the DPPC bilayer is sequentially melted from the top (adjacent to the solution) to bottom leaflet (adjacent to the substrate) over a wide temperature range. The conformational ordering of the supported bilayer does not decrease (even slightly increases) during the phase transition process. The conformational defects in the bilayer can be removed after the complete melting process. The phase transition enthalpy for the bottom leaflet was found to be approximately three times greater than that for the top leaflet, indicating a strong interaction of the lipids with the substrate. The present SFG and AFM observations revealed similar temperature dependent profiles. Based on these results, the temperature-induced structural changes in the supported lipid bilayer during its phase transition process are discussed in comparison with previous studies.

  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

    2002-01-01

    Electron based surface probing techniques can provide detailed information about surface structure or chemical composition in vacuum environments. The development of new surface techniques has made possible in situ molecular level studies of solid-gas interfaces and more recently, solid-liquid interfaces. The aim of this dissertation is two-fold. First, by using novel sample preparation, Low Energy Electron Diffraction (LEED) and other traditional ultra high vacuum (UHV) techniques are shown to provide new information on the insulator/vacuum interface. The surface structure of the classic insulator NaCl has been determined using these methods. Second, using sum frequency generation (SFG) surface specific vibrational spectroscopy studies were performed on both the biopolymer/air and electrode/electrolyte interfaces. The surface structure and composition of polyetherurethane-silicone copolymers were determined in air using SFG, atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). SFG studies of the electrode (platinum, gold and copper)/electrolyte interface were performed as a function of applied potential in an electrochemical cell.

  3. Study of NH stretching vibrations in small ammonia clusters by infrared spectroscopy in He droplets and ab initio calculations

    SciTech Connect

    Slipchenko, Mikhail N; Sartakov, Boris G; Vilesov, Andrey F; Xantheas, Sotiris S

    2007-08-09

    Infrared spectra of the NH stretching vibrations of (NH3)n clusters (n=2-4) have been obtained using the helium droplet isolation technique and first principles electronic structure anharmonic calculations. The measured spectra exhibit well-resolved bands, which have been assigned to the v1, v3, and 2v4 modes of the ammonia fragments in the clusters. The formation of a hydrogen bond in ammonia dimers leads to an increase of the infrared intensity by about a factor of four. In the larger clusters the infrared intensity per hydrogen bond is close to the one for dimers and approaches the value in the NH3 crystal. The intensity of the 2v4 overtone band in the trimer and tetramer increases by a factor of 10 relative to that in the monomer and dimer, and is comparable to the intensity of the v1 and v3 fundamental bands in larger clusters. This indicates the onset of the strong anharmonic coupling of the 2v4 and v1 modes in larger clusters. The experimental assignments are compared to the ones obtained from first principles electronic structure anharmonic calculations for the dimer and trimer clusters. The anharmonic calculations were performed at the Møller-Plesset (MP2) level of electronic structure theory and were based on a second-order perturbative evaluation of rovibrational parameters and their effects on the vibrational spectra and average structures. In general there is excellent (<20 cm-1) agreement between the experimentally measured band origins for the N-H stretching frequencies and the calculated anharmonic vibrational frequencies. However, the calculations were found to overestimate the infrared intensities in clusters by about a factor of four. This work was supported by the Office of Basic Energy Sciences of the Department of Energy, in part by the Chemical Sciences program and in part by the Engineering and Geosciences

  4. Vacuum ultraviolet mass-analyzed threshold ionization spectroscopy of hexafluorobenzene: The Jahn-Teller effect and vibrational analysis

    NASA Astrophysics Data System (ADS)

    Kwon, Chan Ho; Kim, Myung Soo

    2004-06-01

    One-photon mass-analyzed threshold ionization (MATI) spectrum of hexafluorobenzene was obtained by using vacuum ultraviolet radiation generated by four-wave difference frequency mixing in Kr. The ionization energy of hexafluorobenzene determined from the position of the 0-0 band was 9.9108±0.0006 eV. To aid the spectral analysis, the Jahn-Teller coupling parameters for four e2g modes of C6F6+ in the ground electronic state were calculated from the topographical data of the potential energy surface obtained at the density functional theory (DFT) level. These were used in the initial calculation of the energies of the Jahn-Teller states and upgraded through the multimode fit to the experimental data. Excellent agreement between the experimental and calculated frequencies was achieved. The vibrations which are not linear Jahn-Teller active were observed and could be assigned by referring to the frequencies obtained at the DFT level.

  5. Terahertz Spectroscopy of the Bending Vibrations of Acetylene 12C2H2 and 12C2D2

    NASA Astrophysics Data System (ADS)

    Yu, Shanshan; Drouin, B.; Pearson, J.

    2009-12-01

    Several fundamental interstellar molecules, e.g., C2H2, CH4 and C3, are completely symmetric molecules and feature no permanent dipole moment and no pure rotation spectrum. As a result they have only previously been observed in the infrared. However, directly observing them with the rest of the molecular column especially when the source is spatially resolved would be very valuable in understanding chemical evolution. Vibrational difference bands provide a means to detect symmetric molecules with microwave precision using terahertz techniques. Herschel, SOFIA and ALMA have the potential to identify a number of vibrational difference bands of light symmetric species. This paper reports laboratory results on 12C2H2 and 12C2D2. Symmetric acetylene isotopologues have two bending modes, the trans bending and the cis bending. Their difference bands are allowed and occur in the microwave, terahertz, and far-infrared wavelengths, with band origins at 3500 GHz for 12C2H2 and 900 GHz for 12C2D2. Twenty 12C2H2 P branch high-J transitions and two hundred and fifty-one 12C2D2 P Q and R branch transitions have been measured in the 0.2 - 1.6 THz region with precision of 50 to 100 kHz. These lines were modeled together with prior data on the pure bending levels. Significantly improved molecular parameters were obtained for 12C2H2 and 12C2D2 with the combined data set, and new frequency and intensity predictions were made to support astrophysics applications. The research was performed at the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration. S. Y. was supported by an appointment to the NASA Postdoctoral Program, administrated by Oak Ridge Associated Universities through a contract with NASA.

  6. Study of conformational stability, structural, electronic and charge transfer properties of cladrin using vibrational spectroscopy and DFT calculations.

    PubMed

    Singh, Swapnil; Singh, Harshita; Srivastava, Anubha; Tandon, Poonam; Sinha, Kirti; Bharti, Purnima; Kumar, Sudhir; Kumar, Padam; Maurya, Rakesh

    2014-11-11

    In the present work, a detailed conformational study of cladrin (3-(3,4-dimethoxy phenyl)-7-hydroxychromen-4-one) has been done by using spectroscopic techniques (FT-IR/FT-Raman/UV-Vis/NMR) and quantum chemical calculations. The optimized geometry, wavenumber and intensity of the vibrational bands of the cladrin in ground state were calculated by density functional theory (DFT) employing 6-311++G(d,p) basis sets. The study has been focused on the two most stable conformers that are selected after the full geometry optimization of the molecule. A detailed assignment of the FT-IR and FT-Raman spectra has been done for both the conformers along with potential energy distribution for each vibrational mode. The observed and scaled wavenumber of most of the bands has been found to be in good agreement. The UV-Vis spectrum has been recorded and compared with calculated spectrum. In addition, 1H and 13C nuclear magnetic resonance spectra have been also recorded and compared with the calculated data that shows the inter or intramolecular hydrogen bonding. The electronic properties such as HOMO-LUMO energies were calculated by using time-dependent density functional theory. Molecular electrostatic potential has been plotted to elucidate the reactive part of the molecule. Natural bond orbital analysis was performed to investigate the molecular stability. Non linear optical property of the molecule have been studied by calculating the electric dipole moment (μ) and the first hyperpolarizability (β) that results in the nonlinearity of the molecule.

  7. Vibrational mid-infrared photothermal spectroscopy using a fiber laser probe: asymptotic limit in signal-to-baseline contrast.

    PubMed

    Totachawattana, Atcha; Liu, Hui; Mertiri, Alket; Hong, Mi K; Erramilli, Shyamsunder; Sander, Michelle Y

    2016-01-01

    We report on a mid-infrared photothermal spectroscopy system with a near-infrared fiber probe laser and a tunable quantum cascade pump laser. Photothermal spectra of a 6 μm-thick 4-octyl-4'-cyanobiphenyl liquid crystal sample are measured with a signal-to-baseline contrast above 103. As both the peak photothermal signal and the corresponding baseline increase linearly with probe power, the signal-to-baseline contrast converges to an asymptotic limit for a given pump power. This limit is independent of the probe power and characterizes the best contrast achievable for the system. This enables sensitive quantitative spectral characterization of linear infrared absorption features directly from photothermal spectroscopy measurements.

  8. Surface-enhanced vibrational spectroscopy of B vitamins: what is the effect of SERS-active metals used?

    PubMed

    Kokaislová, A; Matějka, P

    2012-05-01

    Surface-enhanced Raman scattering (SERS) spectroscopy and surface-enhanced infrared absorption (SEIRA) spectroscopy are analytical tools suitable for the detection of small amounts of various analytes adsorbed on metal surfaces. During recent years, these two spectroscopic methods have become increasingly important in the investigation of adsorption of biomolecules and pharmaceuticals on nanostructured metal surfaces. In this work, the adsorption of B-group vitamins pyridoxine, nicotinic acid, folic acid and riboflavin at electrochemically prepared gold and silver substrates was investigated using Fourier transform SERS spectroscopy at an excitation wavelength of 1,064 nm. Gold and silver substrates were prepared by cathodic reduction on massive platinum targets. In the case of gold substrates, oxidation-reduction cycles were applied to increase the enhancement factor of the gold surface. The SERS spectra of riboflavin, nicotinic acid, folic acid and pyridoxine adsorbed on silver substrates differ significantly from SERS spectra of these B-group vitamins adsorbed on gold substrates. The analysis of near-infrared-excited SERS spectra reveals that each of B-group vitamin investigated interacts with the gold surface via a different mechanism of adsorption to that with the silver surface. In the case of riboflavin adsorbed on silver substrate, the interpretation of surface-enhanced infrared absorption (SEIRA) spectra was also helpful in investigation of the adsorption mechanism.

  9. Vibrational state-selective autodetachment photoelectron spectroscopy from dipole-bound states of cold 2-hydroxyphenoxide: o − HO(C{sub 6}H{sub 4})O{sup −}

    SciTech Connect

    Huang, Dao-Ling; Wang, Lai-Sheng; Liu, Hong-Tao; Ning, Chuan-Gang

    2015-03-28

    We report a photodetachment and high-resolution photoelectron imaging study of cold 2-hydroxyphenoxide anion, o − HO(C{sub 6}H{sub 4})O{sup −}, cooled in a cryogenic ion trap. Photodetachment spectroscopy revealed a dipole-bound state (DBS) of the anion, 25 ± 5 cm{sup −1}, below the detachment threshold of 18784 ± 5 cm{sup −1} (2.3289 ± 0.0006 eV ), i.e., the electron affinity of the 2-hydroxyphenoxy radical o − HO(C{sub 6}H{sub 4})O{sup ⋅}. Twenty-two vibrational levels of the DBS are observed as resonances in the photodetachment spectrum. By tuning the detachment laser to these DBS vibrational levels, we obtain 22 high-resolution resonant photoelectron spectra, which are highly non-Franck-Condon due to mode-selective autodetachment and the Δv = − 1 propensity rule. Numerous Franck-Condon inactive vibrational modes are observed in the resonant photoelectron spectra, significantly expanding the vibrational information that is available in traditional high-resolution photoelectron spectroscopy. A total of 15 fundamental vibrational frequencies are obtained for the o − HO(C{sub 6}H{sub 4})O{sup ⋅}  radical from both the photodetachment spectrum and the resonant photoelectron spectra, including six symmetry-forbidden out-of-plane modes as a result of resonant enhancement.

  10. Vibrational spectroscopy of the electronically excited state. 4. Nanosecond and picosecond time-resolved resonance Raman spectroscopy of carotenoid excited states

    SciTech Connect

    Dallinger, R.F.; Farquharson, S.; Woodruff, W.H.; Rodgers, M.A.J.

    1981-12-16

    Resonance Raman and electronic absorption spectra are reported for the S/sub 0/ and T/sub 1/ states of the carotenoids ..beta..-carotene, zeaxanthin, echinenone, canthaxanthin, dihydroxylycopene, astaxanthin, decapreno(C/sub 50/)-..beta..-carotene, ..beta..-apo-8'-carotenal, and ethyl ..beta..-apo-8'-carotenoate. The results reveal qualitatively similar ground-state spectra and similar frequency shifts in all observed resonance Raman modes between S/sub 0/ and T/sub 1/, regardless of carotenoid structure. Examinations of the relationship of the putative C--C and C==C frequencies in S/sub 0/ and T/sub 1/ reveals anomalous shifts to lower frequency in the ''single-bond'' mode upon electronic excitation. These shifts may be due to molecular distortions in the excited state which force changes in molecular motions comprising the observed modes. However, another possibility requiring no distortion is that the interaction (off-diagonal) force constants connecting the C--C and C==C modes change sign upon electronic excitation. This latter phenomenon may provide a unitary explanation for the ''anomalous'' frequency shifts in the C--C and C==C modes, both in the T/sub 1/ states of carotenoids and in the S/sub 1/ states of simpler polyenes, without postulating large, unpredicted structural changes upon excitation or general errors in existing vibrational or theoretical analyses. Resonance Raman and absorbance studies with 35-ps time resolution suggest that S/sub 1/ lifetime (of the /sup 1/B/sub u/ and/or the /sup 1/A/sub g/* states) of ..beta..-carotene in benzene is less than 1 ps.

  11. 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.

  12. Zepto-mole detection in microfluidics by novel nonlinear multi-photon laser wave-mixing spectroscopy for biomedical and environmental applications

    NASA Astrophysics Data System (ADS)

    Hetu, Marcel; Iwabuchi, Manna; Maxwell, Eric; Wu, Haoli; Ramos, Sashary; Tong, William G.

    2014-09-01

    Laser wave-mixing detectors for microfluidics are presented as compact systems for parts-per-quadrillion-level detection of biomedical and environmental samples. Wave mixing offers unique advantages including absorption-based detection of micrometer-thin samples, generation of coherent laser-like signal beams, and sensitive detection of both fluorescing and non-fluorescing samples. Biomarkers could be detected in their native forms without labels, or if labels are desired, one could use both fluorophores and chromophores as labels. By coupling low-power (mW) solid-state lasers and microfluidics and microarrays, one can design compact optical systems that can be battery powered and used in the field for real-time fingerprinting of chemicals.

  13. Vibrational relaxation and internal conversion in the overlapped optically-allowed 1Bu+ and optically-forbidden 1Bu- or 3Ag- vibronic levels of carotenoids: Effects of diabatic mixing as determined by Kerr-gate fluorescence spectroscopy

    NASA Astrophysics Data System (ADS)

    Kakitani, Yoshinori; Miki, Takeshi; Koyama, Yasushi; Nagae, Hiroyoshi; Nakamura, Ryosuke; Kanematsu, Yasuo

    2009-07-01

    The time constants of the vibrational relaxation, υ = 2 → υ = 1 and υ = 1 → υ = 0, in the 1Bu+ manifold and those of internal conversion from the 1Bu+(0) level, which is isoenergetic (so-called 'diabatic') with the 1Bu- vibronic levels in neurosporene and spheroidene and with the 3Ag- vibronic levels in lycopene and anhydrorhodovibrin, were determined by Kerr-gate fluorescence spectroscopy. The time constants of the vibrational relaxation were in the ˜1:2 ratio, and those of internal conversion agreed with the lifetimes of the diabatic counterparts, i.e., the 1Bu- and 3Ag- electronic states, respectively.

  14. Experimental and theoretical vibrational spectroscopy studies of acetohydroxamic acid and desferrioxamine B in aqueous solution: Effects of pH and iron complexation

    NASA Astrophysics Data System (ADS)

    Edwards, David C.; Nielsen, Steen B.; Jarzęcki, Andrzej A.; Spiro, Thomas G.; Myneni, Satish C. B.

    2005-07-01

    The deprotonation and iron complexation of the hydroxamate siderophore, desferrioxamine B (desB), and a model hydroxamate ligand, acetohydroxamic acid (aHa), were studied using infrared, resonance Raman and UV-vis spectroscopy. The experimental spectra were interpreted by a comparison with DFT calculated spectra of aHa (partly hydrated) and desB (reactive groups of unhydrated molecule) at the B3LYP/6-31G* level of theory. The ab initio models include three water molecules surrounding the deprotonation site of aHa to account for partial hydration. Experiments and calculations were also conducted in D 2O to verify spectral assignments. These studies of aHa suggest that the cis-keto-aHa is the dominant form, and its deprotonation occurs at the oxime oxygen atom in aqueous solutions. The stable form of iron-complexed aHa is identified as Fe(aHa) 3 for a wide range of pH conditions. The spectral information of aHa and an ab initio model of desB were used to interpret the chemical state of different functional groups in desB. Vibrational spectra of desB indicate that the oxime and amide carbonyl groups can be identified unambiguously. Vibrational spectral analysis of the oxime carbonyl after deprotonation and iron complexation of desB indicates that the conformational changes between anion and the iron-complexed anion are small. Enhanced electron delocalization in the oxime group of Fe-desB when compared to that of Fe(aHa) 3 may be responsible for higher stability constant of the former.

  15. Probing the structure and nano-scale mechanical properties of polymer surfaces with scanning force microscopy and sum frequency vibrational spectroscopy

    SciTech Connect

    Gracias, David Hugo

    1999-05-01

    Scanning Force Microscopy (SFM) has been used to quantitatively measure the elastic modulus, friction and hardness of polymer surfaces with special emphasis on polyethylene and polypropylene. In the experiments, tips of different radii of curvature ranging from 20 nm to 1000 nm have been used and the high pressure applied by the SFM have been observed to affect the values obtained in the measurements. The contact of the SFM tip with the polymer surface is explained by fitting the experimental curves to theoretical predictions of contact mechanics. Sum Frequency Generation (SFG) Vibrational Spectroscopy has been used to measure vibrational spectra of polymer surfaces in the vibrational range of 2700 to 3100 cm-1. Strong correlations are established between surface chemistry and surface structure as probed by SFG and mechanical properties measured by SFM on the surfaces. In these studies segregation of low surface energy moieties, from the bulk of the polymer to the surface have been studied. It was found that surface segregation occurs in miscible polymer blends and a small concentration of surface active polymer can be used to totally modify the surface properties of the blend. A novel high vacuum SFM was built to do temperature dependent measurements of mechanical changes occurring at the surface of polypropylene during the glass transition of the polymer. Using this instrument the modulus and friction of polypropylene was measured in the range of room temperature to ˜-60°C. An increase in the ordering of the backbone of the polymer chains below the glass transition measured by SFG correlates well with the increase in modulus measured on the same surface with SFM. Friction measurements have been done on polyethylene with three different instruments by applying loads ranging from nN to sub newton i.e. over eight orders of magnitude. Pressure and contact area effects were observed to play a significant role in determining the frictional response of the polymer

  16. Diffusional and vibrational dynamics of water in NaA zeolites by neutron and Fourier transform infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Crupi, V.; Majolino, D.; Venuti, V.

    2004-11-01

    This paper reports the most recent results of a detailed spectroscopic analysis of water confined in NaA zeolitic matrix, performed, as a function of temperature and hydration level, by means of the simultaneous use of incoherent quasi-elastic neutron scattering (IQENS) and Fourier transform infrared (FT-IR) absorption. The diffusive process reveals a rather wide distribution of relaxation times. Furthermore, we observed a Q-dependence of the mean relaxation time \\langle \\tau \\rangle which does not disagree with the mode coupling theory for associated liquids. As far as vibrational dynamics is concerned, the spectral substructure of the H2O bending (1500-1800 cm-1) andO-H stretching (3000-3800 cm-1) bands has been interpreted in the framework of actual theories for associated liquids and on the basis of previous measurements performed, by Raman scattering, on water confined in a controlled silica glass (GelSil). From a comparison of the results in these two cases, the 'structure-maker' role on confined water, played by the NaA zeolite, and the 'structure-breaker' role, played by the GelSil, have been clearly shown.

  17. Structural study of the zinc and cadmium complexes of a type 2 plant (Quercus suber) metallothionein: insights by vibrational spectroscopy.

    PubMed

    Domènech, Jordi; Tinti, Anna; Capdevila, Mercè; Atrian, Silvia; Torreggiani, Armida

    2007-06-15

    Zn- and Cd-complexes of Quercus suber metallothionein (QsMT) were obtained by in vivo-synthesis, in order to obtain physiologically representative aggregates, and characterized by spectrometric and spectroscopic methods. The secondary structure elements and the coordination environments of the metal binding sites of the two aggregates were determined, as well as the main metal-containing species formed. The results obtained from the analysis of the Raman and IR spectra reveal that these metal-MT complexes predominantly contain beta-sheet elements (about 60%), whereas they lack alpha-helices. These structural features slightly depend on the divalent metal bound. In particular, Cd(II) binding to QsMT induces a slight increase of the beta-sheet percentage, as well as a decrease in beta-turn elements with respect to Zn(II) binding. Conversely, the in vivo capability of QsMT to inglobe metal and sulfide ions is metal-depending. Spectroscopic vibrational data also confirm the presence of sulfide ligands in the metal clusters of both Zn- and Cd-QsMT, while the participation of the spacer His residue in metal coordination was only found in Cd-QsMT, in agreement with the CD results. Overall data suggest different coordination environments for Zn(II) and Cd(II) ions in QsMT.

  18. From light-scattering measurements to polarizability derivatives in vibrational Raman spectroscopy: the 2ν5 overtone of SF6.

    PubMed

    Kremer, D; Rachet, F; Chrysos, M

    2013-05-07

    The room-temperature isotropic spectrum of SF6 was recorded at the frequency of the 2ν5 overtone by running high-sensitivity incoherent Raman experiments for two independent polarizations of the incident beam and for gas densities varying from 2 to 27 amagat. Weak yet observable pressure effects were found. A transparent analysis of the Raman cross-section problem along with the first-ever prediction of the value of the mean polarizability second derivative ∂(2)α/∂q5(2) are made and the hitherto underestimated role of the hot bands of SF6 is brought to the wider public. The emergence of an analytic hotband factor is shown whose magnitude is dramatically increased with the order of the overtone and the gas temperature and all the more so upon considering low-frequency molecular vibrations. Our formulas, which in the harmonic approximation are exact, are still applicable to real situations provided certain conditions are fulfilled. For nondegenerated modes, generalization to higher order overtones is made, an issue addressing the much challenging problem of the IR-allowed second overtone bands. The content of this paper is also an invitation towards ab initio derivative-calculations for sulfur hexafluoride, especially given the today's needs in interpreting spectra of significance for greenhouse atmospheric issues.

  19. 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.

  20. 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

    2013-07-07

    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).