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Sample records for biomedical vibrational spectroscopy

  1. Vibrational spectroscopy in biomedical science: bone

    NASA Astrophysics Data System (ADS)

    Gamsjäger, Sonja; Zoehrer, R.; Roschger, P.; Fratzl, P.; Klaushofer, K.; Mendelsohn, R.; Paschalis, E. P.

    2009-02-01

    Fourier transform infrared imaging (FTIR) and Raman Microspectroscopy are powerful tools for characterizing the distribution of different chemical moieties in heterogeneous materials. FTIR and Raman measurements have been adapted to assess the maturity of the mineral and the quality of the organic component (collagen and non-collagenous proteins) of the mineralized tissue in bone. Unique to the FTIRI analysis is the capability to provide the spatial distribution of two of the major collagen cross-links (pyridinoline, and dehydro-dihydroxylysinonorleucine) and through the study of normal and diseased bone, relate them to bone strength. These FTIR parameters have been validated based on analysis of model compounds. It is widely accepted that bone strength is determined by bone mass and bone quality. The latter is a multifactorial term encompassing the material and structural properties of bone, and one important aspect of the bone material properties is the organic matrix. The bone material properties can be defined by parameters of mineral and collagen, as determined by FTIR and Raman analysis. Considerably less attention has been directed at collagen, although there are several publications in the literature reporting altered collagen properties associated with fragile bone, in both animals and humans. Since bone is a heterogeneous tissue due to the remodeling process, microscopic areas may be carefully selected based on quantitative Backscattered Electron Imaging or histological staining, thus ensuring comparison of areas with similar metabolic activity and mineral content. In conclusion, FTIRI and Raman vibrational spectroscopy are proving to be powerful tools in bone-related medical research.

  2. Vibrational spectroscopy

    Treesearch

    Umesh P. Agarwal; Rajai Atalla

    2010-01-01

    Vibrational spectroscopy is an important tool in modern chemistry. In the past two decades, thanks to significant improvements in instrumentation and the development of new interpretive tools, it has become increasingly important for studies of lignin. This chapter presents the three important instrumental methods-Raman spectroscopy, infrared (IR) spectroscopy, and...

  3. 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.

  4. Raman spectroscopy of biomedical polyethylenes.

    PubMed

    Pezzotti, Giuseppe

    2017-06-01

    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. Statement of Significance This review was dedicated to the

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Biomedical applications of laser spectroscopy

    NASA Astrophysics Data System (ADS)

    Svanberg, Sune

    1999-07-01

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

  10. Infrared spectroscopy in biomedical diagnostics

    NASA Astrophysics Data System (ADS)

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

    1998-01-01

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

  11. Usefulness of spectroscopy for biomedical engineering.

    PubMed

    Olsztyńska-Janus, Sylwia; Szymborska, Katarzyna; Komorowska, Malgorzata; Lipiński, Józef

    2008-01-01

    Modifications of phenylalanine amino acid after its exposure to near-infrared (NIR) radiation have been investigated using ATRFTIR (Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy). The process of amino acid aggregation after its exposure to NIR has been observed. A possible mechanism of amino acid dimer formation has been proposed with the help of theoretical calculations of quantum mechanics (MP2 and B3LYP/6-31 G* level) using the GAUSSIAN 03 package. The usefulness of spectroscopy for biomedical engineering is discussed. ATR-FTIR appears to be a powerful tool for measuring tissue damage in aqueous environments.

  12. Soil chemical insights provided through vibrational spectroscopy

    USDA-ARS?s Scientific Manuscript database

    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...

  13. Quantum cascade lasers (QCLs) in biomedical spectroscopy.

    PubMed

    Schwaighofer, Andreas; Brandstetter, Markus; Lendl, Bernhard

    2017-10-02

    Quantum cascade lasers (QCL) are the first room temperature semiconductor laser source for the mid-IR spectral region, triggering substantial development for the advancement of mid-IR spectroscopy. Mid-IR spectroscopy in general provides rapid, label-free and objective analysis, particularly important in the field of biomedical analysis. Due to their unique properties, QCLs offer new possibilities for development of analytical methods to enable quantification of clinically relevant concentration levels and to support medical diagnostics. Compared to FTIR spectroscopy, novel and elaborated measurement techniques can be implemented that allow miniaturized and portable instrumentation. This review illustrates the characteristics of QCLs with a particular focus on their benefits for biomedical analysis. Recent applications of QCL-based spectroscopy for analysis of a variety of clinically relevant samples including breath, urine, blood, interstitial fluid, and biopsy samples are summarized. Further potential for technical advancements is discussed in combination with future prospects for employment of QCL-based devices in routine and point-of-care diagnostics.

  14. 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).

  15. Vibrational spectroscopy of HNS degradation.

    SciTech Connect

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

    2008-07-01

    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 {sigma}-adduct. We have followed these changes as a function of time using various IR sampling techniques including photoacoustic and attenuated total reflectance (ATR).

  16. Vibrational Spectroscopy in Body Fluids Analysis.

    PubMed

    Bunaciu, Andrei A; Fleschin, Şerban; Hoang, Vu Dang; Aboul-Enein, Hassan Y

    2017-01-02

    Vibrational spectroscopy offers a unique opportunity to investigate the composition of unknown substances on a molecular basis. The spectroscopy of molecular vibrations using mid-infrared or Raman techniques has been applied to samples of body fluids. This review presents some applications related to body fluids published in the period 2005-2015.

  17. Vibrational spectroscopy in the electron microscope.

    PubMed

    Krivanek, Ondrej L; Lovejoy, Tracy C; Dellby, Niklas; Aoki, Toshihiro; Carpenter, R W; Rez, Peter; Soignard, Emmanuel; Zhu, Jiangtao; Batson, Philip E; Lagos, Maureen J; Egerton, Ray F; Crozier, Peter A

    2014-10-09

    Vibrational spectroscopies using infrared radiation, Raman scattering, neutrons, low-energy electrons and inelastic electron tunnelling are powerful techniques that can analyse bonding arrangements, identify chemical compounds and probe many other important properties of materials. The spatial resolution of these spectroscopies is typically one micrometre or more, although it can reach a few tens of nanometres or even a few ångströms when enhanced by the presence of a sharp metallic tip. If vibrational spectroscopy could be combined with the spatial resolution and flexibility of the transmission electron microscope, it would open up the study of vibrational modes in many different types of nanostructures. Unfortunately, the energy resolution of electron energy loss spectroscopy performed in the electron microscope has until now been too poor to allow such a combination. Recent developments that have improved the attainable energy resolution of electron energy loss spectroscopy in a scanning transmission electron microscope to around ten millielectronvolts now allow vibrational spectroscopy to be carried out in the electron microscope. Here we describe the innovations responsible for the progress, and present examples of applications in inorganic and organic materials, including the detection of hydrogen. We also demonstrate that the vibrational signal has both high- and low-spatial-resolution components, that the first component can be used to map vibrational features at nanometre-level resolution, and that the second component can be used for analysis carried out with the beam positioned just outside the sample--that is, for 'aloof' spectroscopy that largely avoids radiation damage.

  18. Vibrational spectroscopy in the electron microscope

    NASA Astrophysics Data System (ADS)

    Krivanek, Ondrej L.; Lovejoy, Tracy C.; Dellby, Niklas; Aoki, Toshihiro; Carpenter, R. W.; Rez, Peter; Soignard, Emmanuel; Zhu, Jiangtao; Batson, Philip E.; Lagos, Maureen J.; Egerton, Ray F.; Crozier, Peter A.

    2014-10-01

    Vibrational spectroscopies using infrared radiation, Raman scattering, neutrons, low-energy electrons and inelastic electron tunnelling are powerful techniques that can analyse bonding arrangements, identify chemical compounds and probe many other important properties of materials. The spatial resolution of these spectroscopies is typically one micrometre or more, although it can reach a few tens of nanometres or even a few ångströms when enhanced by the presence of a sharp metallic tip. If vibrational spectroscopy could be combined with the spatial resolution and flexibility of the transmission electron microscope, it would open up the study of vibrational modes in many different types of nanostructures. Unfortunately, the energy resolution of electron energy loss spectroscopy performed in the electron microscope has until now been too poor to allow such a combination. Recent developments that have improved the attainable energy resolution of electron energy loss spectroscopy in a scanning transmission electron microscope to around ten millielectronvolts now allow vibrational spectroscopy to be carried out in the electron microscope. Here we describe the innovations responsible for the progress, and present examples of applications in inorganic and organic materials, including the detection of hydrogen. We also demonstrate that the vibrational signal has both high- and low-spatial-resolution components, that the first component can be used to map vibrational features at nanometre-level resolution, and that the second component can be used for analysis carried out with the beam positioned just outside the sample--that is, for `aloof' spectroscopy that largely avoids radiation damage.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. Vibrational Spectroscopy and Dynamics of Water.

    PubMed

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

    2016-07-13

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

  4. 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

  5. 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.

  6. 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.

  7. Vibrational Spectroscopy and Search for Extraterrestrial Life

    NASA Astrophysics Data System (ADS)

    Girish, T. E.; Sony, K. S.

    2008-11-01

    Vibrational spectroscopy is one of the vital tools in astrobiology. In this paper we have studied the role of IR spectroscopy in the detection of plant and animal life elsewhere in our galaxy. Using relevant astrophysical data of nearby extrasolar planets we have calculated the detection limits of IR spectra of life related chemical compounds from these objects. The probability of detection of methane and plant pigments is found to relatively higher near M type stars compared to G type stars. A list of Jupiter size extrasolar planets discovered around G type stars which are potential objects for possible detection of plant life through IR reflection spectroscopy is also prepared.

  8. Vibrational Spectroscopy in Studies of Atmospheric Corrosion

    PubMed Central

    Hosseinpour, Saman; Johnson, Magnus

    2017-01-01

    Vibrational spectroscopy has been successfully used for decades in studies of the atmospheric corrosion processes, mainly to identify the nature of corrosion products but also to quantify their amounts. In this review article, a summary of the main achievements is presented with focus on how the techniques infrared spectroscopy, Raman spectroscopy, and vibrational sum frequency spectroscopy can be used in the field. Several different studies have been discussed where these instruments have been used to assess both the nature of corrosion products as well as the properties of corrosion inhibitors. Some of these techniques offer the valuable possibility to perform in-situ measurements in real time on ongoing corrosion processes, which allows the kinetics of formation of corrosion products to be studied, and also minimizes the risk of changing the surface properties which may occur during ex-situ experiments. Since corrosion processes often occur heterogeneously over a surface, it is of great importance to obtain a deeper knowledge about atmospheric corrosion phenomena on the nano scale, and this review also discusses novel vibrational microscopy techniques allowing spectra to be acquired with a spatial resolution of 20 nm. PMID:28772781

  9. 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.

  10. 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.

  11. 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.

  12. Heterodyne-Detected Dispersed Vibrational Echo Spectroscopy

    NASA Astrophysics Data System (ADS)

    Jones, Kevin C.; Ganim, Ziad; Tokmakoff, Andrei

    2009-11-01

    We develop heterodyned dispersed vibrational echo spectroscopy (HDVE) and demonstrate the new capabilities in biophysical applications. HDVE is a robust ultrafast technique that provides a characterization of the real and imaginary components of third-order nonlinear signals with high sensitivity and single-laser-shot capability and can be used to extract dispersed pump-probe and dispersed vibrational echo spectra. Four methods for acquiring HDVE phase and amplitude spectra were compared: Fourier transform spectral interferometry, a new phase modulation spectral interferometry technique, and combination schemes. These extraction techniques were demonstrated in the context of protein amide I spectroscopy. Experimental HDVE and heterodyned free induction decay amide I spectra were explicitly compared to conventional dispersed pump-probe, dispersed vibrational echo, and absorption spectra. The new capabilities of HDVE were demonstrated by acquiring single-shot spectra and melting curves of ubiquitin and concentration-dependent spectra of insulin suitable for extracting the binding constant for dimerization. The introduced techniques will prove particularly useful in transient experiments, studying irreversible reactions, and micromolar concentration studies of small proteins.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Raman Plus X: Biomedical Applications of Multimodal Raman Spectroscopy

    PubMed Central

    Das, Nandan K.; Dai, Yichuan; Liu, Peng; Hu, Chuanzhen; Tong, Lieshu; Chen, Xiaoya

    2017-01-01

    Raman spectroscopy is a label-free method of obtaining detailed chemical information about samples. Its compatibility with living tissue makes it an attractive choice for biomedical analysis, yet its translation from a research tool to a clinical tool has been slow, hampered by fundamental Raman scattering issues such as long integration times and limited penetration depth. In this review we detail the how combining Raman spectroscopy with other techniques yields multimodal instruments that can help to surmount the translational barriers faced by Raman alone. We review Raman combined with several optical and non-optical methods, including fluorescence, elastic scattering, OCT, phase imaging, and mass spectrometry. In each section we highlight the power of each combination along with a brief history and presentation of representative results. Finally, we conclude with a perspective detailing both benefits and challenges for multimodal Raman measurements, and give thoughts on future directions in the field. PMID:28686212

  19. Raman Plus X: Biomedical Applications of Multimodal Raman Spectroscopy.

    PubMed

    Das, Nandan K; Dai, Yichuan; Liu, Peng; Hu, Chuanzhen; Tong, Lieshu; Chen, Xiaoya; Smith, Zachary J

    2017-07-07

    Raman spectroscopy is a label-free method of obtaining detailed chemical information about samples. Its compatibility with living tissue makes it an attractive choice for biomedical analysis, yet its translation from a research tool to a clinical tool has been slow, hampered by fundamental Raman scattering issues such as long integration times and limited penetration depth. In this review we detail the how combining Raman spectroscopy with other techniques yields multimodal instruments that can help to surmount the translational barriers faced by Raman alone. We review Raman combined with several optical and non-optical methods, including fluorescence, elastic scattering, OCT, phase imaging, and mass spectrometry. In each section we highlight the power of each combination along with a brief history and presentation of representative results. Finally, we conclude with a perspective detailing both benefits and challenges for multimodal Raman measurements, and give thoughts on future directions in the field.

  20. Vibrational Micro-Spectroscopy of Human Tissues Analysis: Review.

    PubMed

    Bunaciu, Andrei A; Hoang, Vu Dang; Aboul-Enein, Hassan Y

    2017-05-04

    Vibrational spectroscopy (Infrared (IR) and Raman) and, in particular, micro-spectroscopy and micro-spectroscopic imaging have been used to characterize developmental changes in tissues, to monitor these changes in cell cultures and to detect disease and drug-induced modifications. The conventional methods for biochemical and histophatological tissue characterization necessitate complex and "time-consuming" sample manipulations and the results are rarely quantifiable. The spectroscopy of molecular vibrations using mid-IR or Raman techniques has been applied to samples of human tissue. This article reviews the application of these vibrational spectroscopic techniques for analysis of biological tissue published between 2005 and 2015.

  1. Signatures of vibronic coupling in two-dimensional electronic-vibrational and vibrational-electronic spectroscopies.

    PubMed

    Gaynor, James D; Khalil, Munira

    2017-09-07

    Two-Dimensional Electronic-Vibrational (2D EV) spectroscopy and Two-Dimensional Vibrational-Electronic (2D VE) spectroscopy are new coherent four-wave mixing spectroscopies that utilize both electronically resonant and vibrationally resonant field-matter interactions to elucidate couplings between electronic and vibrational degrees of freedom. A system Hamiltonian is developed here to lay a foundation for interpreting the 2D EV and 2D VE signals that arise from a vibronically coupled molecular system in the condensed phase. A molecular system consisting of one anharmonic vibration and two electronic states is modeled. Equilibrium displacement of the vibrational coordinate and vibrational frequency shifts upon excitation to the first electronic excited state are included in our Hamiltonian through linear and quadratic vibronic coupling terms. We explicitly consider the nuclear dependence of the electronic transition dipole moment and demonstrate that these spectroscopies are sensitive to non-Condon effects. A series of simulations of 2D EV and 2D VE spectra obtained by varying parameters of the system, system-bath, and interaction Hamiltonians demonstrate that one of the following conditions must be met to observe signals: (1) non-zero linear and/or quadratic vibronic coupling in the electronic excited state, (2) vibrational-coordinate dependence of the electronic transition dipole moment, or (3) electronic-state-dependent vibrational dephasing dynamics. We explore how these vibronic interactions are manifested in the positions, amplitudes, and line shapes of the peaks in 2D EV and 2D VE spectroscopies.

  2. Signatures of vibronic coupling in two-dimensional electronic-vibrational and vibrational-electronic spectroscopies

    NASA Astrophysics Data System (ADS)

    Gaynor, James D.; Khalil, Munira

    2017-09-01

    Two-Dimensional Electronic-Vibrational (2D EV) spectroscopy and Two-Dimensional Vibrational-Electronic (2D VE) spectroscopy are new coherent four-wave mixing spectroscopies that utilize both electronically resonant and vibrationally resonant field-matter interactions to elucidate couplings between electronic and vibrational degrees of freedom. A system Hamiltonian is developed here to lay a foundation for interpreting the 2D EV and 2D VE signals that arise from a vibronically coupled molecular system in the condensed phase. A molecular system consisting of one anharmonic vibration and two electronic states is modeled. Equilibrium displacement of the vibrational coordinate and vibrational frequency shifts upon excitation to the first electronic excited state are included in our Hamiltonian through linear and quadratic vibronic coupling terms. We explicitly consider the nuclear dependence of the electronic transition dipole moment and demonstrate that these spectroscopies are sensitive to non-Condon effects. A series of simulations of 2D EV and 2D VE spectra obtained by varying parameters of the system, system-bath, and interaction Hamiltonians demonstrate that one of the following conditions must be met to observe signals: (1) non-zero linear and/or quadratic vibronic coupling in the electronic excited state, (2) vibrational-coordinate dependence of the electronic transition dipole moment, or (3) electronic-state-dependent vibrational dephasing dynamics. We explore how these vibronic interactions are manifested in the positions, amplitudes, and line shapes of the peaks in 2D EV and 2D VE spectroscopies.

  3. 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.

  4. 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

  5. Thymine Dimer Formation probed by Time-Resolved Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Schreier, Wolfgang J.; Schrader, Tobias E.; Roller, Florian O.; Gilch, Peter; Zinth, Wolfgang; Kohler, Bern

    Cyclobutane pyrimidine dimers are the major photoproducts formed when DNA is exposed to UV light. Femtosecond time-resolved vibrational spectroscopy reveals that thymine dimers are formed in thymidine oligonucleotides in an ultrafast photoreaction.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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.

  7. 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.

  8. 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

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

    PubMed

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

    2014-05-01

    Vibrational spectroscopy using both infrared and Raman spectroscopies has been used in recent years with the aim to aid clinicians in disease diagnosis. More recently, these techniques have been applied to study stem cell differentiation and to determine stem cell presence in tissues. These studies have demonstrated the potential of these techniques in better characterising stem cell differentiation phenotypes with potential applications in tissue engineering strategies. However, before the translation of vibrational spectroscopy into clinical practice becomes a reality, several issues still need to be addressed. We describe here an overview of the work carried out so far and the problems that might be encountered when using vibrational spectroscopy. Copyright © 2014 Elsevier Ltd. All rights reserved.

  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. Broadband infrared vibrational nano-spectroscopy using thermal blackbody radiation

    DOE PAGES

    O’Callahan, Brian T.; Lewis, William E.; Möbius, Silke; ...

    2015-12-03

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

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

    SciTech Connect

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

    2015-12-03

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

  14. 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.

  15. 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.

  16. 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.

  17. Vibrational Spectroscopy of PTSA—Doped Polyaniline

    NASA Astrophysics Data System (ADS)

    Arora, Manju; Gupta, S. K.

    2008-11-01

    Infrared transmittance spectra of polyaniline emeraldine base (EB) form and its different PTSA (p-toulene sulphonic acid) concentration doped samples were measured in 4000-400 cm-1 region at ambient temperature to reveal the polymeric chain oligomeric unit, interaction of sulphonate ions with these chains and effect of its concentration. The vibrational peaks of benzenoid (B) ring, quinoid (Q) ring, their combination modes and semiquinone units in PTSA doped emeraldine salts (PTSA:ES) are observed and assigned by using Oligomer Compound Approach. The para-substitution of B rings is confirmed by the appearance of B ring C-H out-of-plane deformation mode as a medium intensity band at 827 cm-1 in EB and at 824 cm-1 in ES:PTSA salts. The out-of-plane wagging mode of five adjacent hydrogen in end capped phenyl group due to conformational deformation of rings in polymeric chain is obtained as very weak bands at 712 and 682 cm-1 in EB and PTSA doped salts. These studies showed that B4Q1 is the basic oligomeric unit in polymer chain formation with their ends capped with phenyl rings. The strong and broad sulphonate ion stretching vibration and C-H bending of Q ring is observed at 1120 cm-1 due to the high degree of electron delocalization in PANI polymeric chain. On increasing PTSA concentration minor variations in intensity and position of peaks were observed.

  18. Profiling of counterfeit medicines by vibrational spectroscopy.

    PubMed

    Been, Frederic; Roggo, Yves; Degardin, Klara; Esseiva, Pierre; Margot, Pierre

    2011-09-10

    Counterfeit pharmaceutical products have become a widespread problem in the last decade. Various analytical techniques have been applied to discriminate between genuine and counterfeit products. Among these, Near-infrared (NIR) and Raman spectroscopy provided promising results. The present study offers a methodology allowing to provide more valuable information for organisations engaged in the fight against counterfeiting of medicines. A database was established by analyzing counterfeits of a particular pharmaceutical product using Near-infrared (NIR) and Raman spectroscopy. Unsupervised chemometric techniques (i.e. principal component analysis - PCA and hierarchical cluster analysis - HCA) were implemented to identify the classes within the datasets. Gas Chromatography coupled to Mass Spectrometry (GC-MS) and Fourier Transform Infrared Spectroscopy (FT-IR) were used to determine the number of different chemical profiles within the counterfeits. A comparison with the classes established by NIR and Raman spectroscopy allowed to evaluate the discriminating power provided by these techniques. Supervised classifiers (i.e. k-Nearest Neighbors, Partial Least Squares Discriminant Analysis, Probabilistic Neural Networks and Counterpropagation Artificial Neural Networks) were applied on the acquired NIR and Raman spectra and the results were compared to the ones provided by the unsupervised classifiers. The retained strategy for routine applications, founded on the classes identified by NIR and Raman spectroscopy, uses a classification algorithm based on distance measures and Receiver Operating Characteristics (ROC) curves. The model is able to compare the spectrum of a new counterfeit with that of previously analyzed products and to determine if a new specimen belongs to one of the existing classes, consequently allowing to establish a link with other counterfeits of the database. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  19. Intra-operative optical diagnostics with vibrational spectroscopy.

    PubMed

    Stelling, Allison; Salzer, Reiner; Kirsch, Matthias; Sobottka, Stephan B; Geiger, Kathrin; Koch, Edmund; Schackert, Gabriele; Steiner, Gerald

    2011-07-01

    Established methods for characterization of tissue and diagnostics, for example histochemistry, magnetic resonance imaging (MRI), X-ray tomography, or positron emission tomography (PET), are mostly not suitable for intra-operative use. However, there is a clear need for an intra-operative diagnostics especially to identify the borderline between normal and tumor tissue. Currently, vibrational spectroscopy techniques (both Raman and infrared) complement the standard methods for tissue diagnostics. Vibrational spectroscopy has the potential for intra-operative use, because it can provide a biochemically based profile of tissue in real time and without requiring additional contrast agents, which may perturb the tissue under investigation. In addition, no electric potential needs to be applied, and the measurements are not affected by electromagnetic fields. Currently, promising approaches include Raman fiber techniques and nonlinear Raman spectroscopy. Infrared spectroscopy is also being used to examine freshly resected tissue ex vivo in the operating theater. The immense volume of information contained in Raman and infrared spectra requires multivariate analysis to extract relevant information to distinguish different types of tissue. The promise and limitations of vibrational spectroscopy methods as intra-operative tools are surveyed in this review.

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Monitoring Water Clusters "Melt" Through Vibrational Spectroscopy.

    PubMed

    Brown, Sandra E; Götz, Andreas W; Cheng, Xiaolu; Steele, Ryan P; Mandelshtam, Vladimir A; Paesani, Francesco

    2017-05-24

    Characterizing structural and phase transformations of water at the molecular level is key to understanding a variety of multiphase processes ranging from ice nucleation in the atmosphere to hydration of biomolecules and wetting of solid surfaces. In this study, state-of-the-art quantum simulations with a many-body water potential energy surface, which exhibits chemical and spectroscopic accuracy, are carried out to monitor the microscopic melting of the water hexamer through the analysis of vibrational spectra and appropriate structural order parameters as a function of temperature. The water hexamer is specifically chosen as a case study due to the central role of this cluster in the molecular-level understanding of hydrogen bonding in water. Besides being in agreement with the experimental data available for selected isomers at very low temperature, the present results provide quantitative insights into the interplay between energetic, entropic, and nuclear quantum effects on the evolution of water clusters from "solid-like" to "liquid-like" structures. This study thus demonstrates that computer simulations can now bridge the gap between measurements currently possible for individual isomers at very low temperature and observations of isomer mixtures at ambient conditions.

  9. 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.

  10. Resonance tunneling electron-vibrational spectroscopy of polyoxometalates.

    PubMed

    Dalidchik, F I; Kovalevskii, S A; Balashov, E M

    2017-05-21

    The tunneling spectra of the ordered monolayer films of decamolybdodicobaltate (DMDC) compounds deposited from aqueous solutions on HOPG were measured by scanning tunnel microscopy in air. The DMDC spectra, as well as the tunneling spectra of other polyoxometalates (POMs), exhibit well-defined negative differential resistances (NDRs). The mechanism of formation of these spectral features was established from the collection of revealed NDR dependences on the external varying parameters and found to be common to all systems exhibiting Wannier-Stark localization. A model of biresonance tunneling was developed to provide an explanation for the totality of experimental data, both the literature and original, on the tunneling POM probing. A variant of the tunneling electron-vibrational POM spectroscopy was proposed allowing the determination of the three basic energy parameters-energy gaps between the occupied and unoccupied states, frequencies of the vibrational transitions accompanying biresonance electron-tunneling processes, and electron-vibrational interaction constants on the monomolecular level.

  11. 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.

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

    PubMed

    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. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. Enhanced Vibrational Spectroscopies as Tools for Small Molecule Biosensing.

    PubMed

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

    2015-08-28

    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.

  18. What Can Be Learned from Nuclear Resonance Vibrational Spectroscopy: Vibrational Dynamics and Hemes.

    PubMed

    Scheidt, W Robert; Li, Jianfeng; Sage, J Timothy

    2017-09-18

    Nuclear resonance vibrational spectroscopy (NRVS; also known as nuclear inelastic scattering, NIS) is a synchrotron-based method that reveals the full spectrum of vibrational dynamics for Mössbauer nuclei. Another major advantage, in addition to its completeness (no arbitrary optical selection rules), is the unique selectivity of NRVS. The basics of this recently developed technique are first introduced with descriptions of the experimental requirements and data analysis including the details of mode assignments. We discuss the use of NRVS to probe (57)Fe at the center of heme and heme protein derivatives yielding the vibrational density of states for the iron. The application to derivatives with diatomic ligands (O2, NO, CO, CN(-)) shows the strong capabilities of identifying mode character. The availability of the complete vibrational spectrum of iron allows the identification of modes not available by other techniques. This permits the correlation of frequency with other physical properties. A significant example is the correlation we find between the Fe-Im stretch in six-coordinate Fe(XO) hemes and the trans Fe-N(Im) bond distance, not possible previously. NRVS also provides uniquely quantitative insight into the dynamics of the iron. For example, it provides a model-independent means of characterizing the strength of iron coordination. Prediction of the temperature-dependent mean-squared displacement from NRVS measurements yields a vibrational "baseline" for Fe dynamics that can be compared with results from techniques that probe longer time scales to yield quantitative insights into additional dynamical processes.

  19. Vibrational spectroscopy differentiates between multipotent and pluripotent stem cells.

    PubMed

    Pijanka, Jacek Klaudiusz; Kumar, Deepak; Dale, Tina; Yousef, Ibraheem; Parkes, Gary; Untereiner, Valérie; Yang, Ying; Dumas, Paul; Collins, David; Manfait, Michel; Sockalingum, Ganesh Dhruvananda; Forsyth, Nicholas Robert; Sulé-Suso, Josep

    2010-12-01

    Over the last few years, there has been an increased interest in the study of stem cells in biomedicine for therapeutic use and as a source for healing diseased or injured organs/tissues. More recently, vibrational spectroscopy has been applied to study stem cell differentiation. In this study, we have used both synchrotron based FTIR and Raman microspectroscopies to assess possible differences between human pluripotent (embryonic) and multipotent (adult mesenchymal) stem cells, and how O(2) concentration in cell culture could affect the spectral signatures of these cells. Our work shows that infrared spectroscopy of embryonic (pluripotent) and adult mesenchymal (multipotent) stem cells have different spectral signatures based on the amount of lipids in their cytoplasm (confirmed with cytological staining). Furthermore, O(2) concentration in cell culture causes changes in both the FTIR and Raman spectra of embryonic stem cells. These results show that embryonic stem cells might be more sensitive to O(2) concentration when compared to mesenchymal stem cells. While vibrational spectroscopy could therefore be of potential use in identifying different populations of stem cells further work is required to better understand these differences.

  20. 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.

  1. 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.

  2. 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

  3. 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

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

    SciTech Connect

    Haaland, D.M.

    1996-10-01

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

  5. 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.

  6. [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.

  7. Cryogenic Vibrational Spectroscopy Provides Unique Fingerprints for Glycan Identification

    NASA Astrophysics Data System (ADS)

    Masellis, Chiara; Khanal, Neelam; Kamrath, Michael Z.; Clemmer, David E.; Rizzo, Thomas R.

    2017-06-01

    The structural characterization of glycans by mass spectrometry is particularly challenging. This is because of the high degree of isomerism in which glycans of the same mass can differ in their stereochemistry, attachment points, and degree of branching. Here we show that the addition of cryogenic vibrational spectroscopy to mass and mobility measurements allows one to uniquely identify and characterize these complex biopolymers. We investigate six disaccharide isomers that differ in their stereochemistry, attachment point of the glycosidic bond, and monosaccharide content, and demonstrate that we can identify each one unambiguously. Even disaccharides that differ by a single stereogenic center or in the monosaccharide sequence order show distinct vibrational fingerprints that would clearly allow their identification in a mixture, which is not possible by ion mobility spectrometry/mass spectrometry alone. Moreover, this technique can be applied to larger glycans, which we demonstrate by distinguishing isomeric branched and linear pentasaccharides. The creation of a database containing mass, collision cross section, and vibrational fingerprint measurements for glycan standards should allow unambiguous identification and characterization of these biopolymers in mixtures, providing an enabling technology for all fields of glycoscience.

  8. Cryogenic Vibrational Spectroscopy Provides Unique Fingerprints for Glycan Identification

    NASA Astrophysics Data System (ADS)

    Masellis, Chiara; Khanal, Neelam; Kamrath, Michael Z.; Clemmer, David E.; Rizzo, Thomas R.

    2017-10-01

    The structural characterization of glycans by mass spectrometry is particularly challenging. This is because of the high degree of isomerism in which glycans of the same mass can differ in their stereochemistry, attachment points, and degree of branching. Here we show that the addition of cryogenic vibrational spectroscopy to mass and mobility measurements allows one to uniquely identify and characterize these complex biopolymers. We investigate six disaccharide isomers that differ in their stereochemistry, attachment point of the glycosidic bond, and monosaccharide content, and demonstrate that we can identify each one unambiguously. Even disaccharides that differ by a single stereogenic center or in the monosaccharide sequence order show distinct vibrational fingerprints that would clearly allow their identification in a mixture, which is not possible by ion mobility spectrometry/mass spectrometry alone. Moreover, this technique can be applied to larger glycans, which we demonstrate by distinguishing isomeric branched and linear pentasaccharides. The creation of a database containing mass, collision cross section, and vibrational fingerprint measurements for glycan standards should allow unambiguous identification and characterization of these biopolymers in mixtures, providing an enabling technology for all fields of glycoscience. [Figure not available: see fulltext.

  9. Terahertz mechanical vibrations in lysozyme: Raman spectroscopy vs modal analysis

    NASA Astrophysics Data System (ADS)

    Carpinteri, Alberto; Lacidogna, Giuseppe; Piana, Gianfranco; Bassani, Andrea

    2017-07-01

    The mechanical behaviour of proteins is receiving an increasing attention from the scientific community. Recently it has been suggested that mechanical vibrations play a crucial role in controlling structural configuration changes (folding) which govern proteins biological function. The mechanism behind protein folding is still not completely understood, and many efforts are being made to investigate this phenomenon. Complex molecular dynamics simulations and sophisticated experimental measurements are conducted to investigate protein dynamics and to perform protein structure predictions; however, these are two related, although quite distinct, approaches. Here we investigate mechanical vibrations of lysozyme by Raman spectroscopy and linear normal mode calculations (modal analysis). The input mechanical parameters to the numerical computations are taken from the literature. We first give an estimate of the order of magnitude of protein vibration frequencies by considering both classical wave mechanics and structural dynamics formulas. Afterwards, we perform modal analyses of some relevant chemical groups and of the full lysozyme protein. The numerical results are compared to experimental data, obtained from both in-house and literature Raman measurements. In particular, the attention is focused on a large peak at 0.84 THz (29.3 cm-1) in the Raman spectrum obtained analyzing a lyophilized powder sample.

  10. Cryogenic Vibrational Spectroscopy Provides Unique Fingerprints for Glycan Identification.

    PubMed

    Masellis, Chiara; Khanal, Neelam; Kamrath, Michael Z; Clemmer, David E; Rizzo, Thomas R

    2017-06-22

    The structural characterization of glycans by mass spectrometry is particularly challenging. This is because of the high degree of isomerism in which glycans of the same mass can differ in their stereochemistry, attachment points, and degree of branching. Here we show that the addition of cryogenic vibrational spectroscopy to mass and mobility measurements allows one to uniquely identify and characterize these complex biopolymers. We investigate six disaccharide isomers that differ in their stereochemistry, attachment point of the glycosidic bond, and monosaccharide content, and demonstrate that we can identify each one unambiguously. Even disaccharides that differ by a single stereogenic center or in the monosaccharide sequence order show distinct vibrational fingerprints that would clearly allow their identification in a mixture, which is not possible by ion mobility spectrometry/mass spectrometry alone. Moreover, this technique can be applied to larger glycans, which we demonstrate by distinguishing isomeric branched and linear pentasaccharides. The creation of a database containing mass, collision cross section, and vibrational fingerprint measurements for glycan standards should allow unambiguous identification and characterization of these biopolymers in mixtures, providing an enabling technology for all fields of glycoscience. Graphical Abstract ᅟ.

  11. 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.

  12. 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.

  13. Surface enhanced vibrational spectroscopy for the detection of explosives

    NASA Astrophysics Data System (ADS)

    Büttner, Fritjof; Hagemann, Jan; Wellhausen, Mike; Funke, Sebastian; Lenth, Christoph; Rotter, Frank; Gundrum, Lars; Plachetka, Ulrich; Moormann, Christian; Strube, Moritz; Walte, Andreas; Wackerbarth, Hainer

    2013-10-01

    A detector which can detect a broad range of explosives without false alarms is urgently needed. Vibrational spectroscopy provides specific spectral information about molecules enabling the identification of analytes by their "fingerprint" spectra. The low detection limit caused by the inherent weak Raman process can be increased by the Surface Enhanced Raman (SER) effect. This is particularly attractive because it combines low detection limits with high information content for establishing molecular identity. Based on SER spectroscopy we have constructed a modular detection system. Here, we want to show a combination of SER spectroscopy and chemometrics to distinguish between chemically similar substances. Such an approach will finally reduce the false alarm rate. It is still a challenge to determine the limit of detection of the analyte on a SER substrate or its enhancement factor. For physisorbed molecules we have applied a novel approach. By this approach the performance of plasmonic substrates and Surface Enhanced Raman Scattering (SERS) enhancement of explosives can be evaluated. Moreover, novel nanostructured substrates for surface enhanced IR absorption (SEIRA) spectroscopy will be presented. The enhancement factor and a limit of detection are estimated.

  14. 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.

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

    SciTech Connect

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

    2009-05-21

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

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

    DTIC Science & Technology

    2016-07-01

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

  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. 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.

  19. 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

  20. 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.

  1. 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

  2. Vibrational Spectroscopy of Sympathetically Cooled CaH^+ Molecular Ions

    NASA Astrophysics Data System (ADS)

    Khanyile, Ncamiso B.; Goeders, James E.; Brown, Kenneth R.

    2013-06-01

    The search for time variation in the fundamental constants of nature such as the fine structure constant(α) and the proton/electron mass ratio(μ), is an area of active research. Comparing the vibrational overtones of CaH^+ with electronic transitions in atoms has been proposed as a means to detect possible time variation of μ Before these precision measurements can be realized, the survey spectroscopy needs to be performed. We describe our experiments using a Coulomb crystal of sympathetically cooled CaH^+ and laser-cooled Ca^+ ions to measure the vibrational overtones by resonance-enhanced multiphoton photo-dissociation (REMPD) in a linear Paul trap. The dissociation of CaH^+ is detected by observing the change in the crystal composition by monitoring the Ca^+ fluorescence. Future single ion experiments for the precision measurement are also discussed. J. Uzan, Rev. Mod. Phys. 75, 403 (2003). M. Kajita and Y. Moriwaki, J. Phys. B: At. Mol. Opt. Phys. 42, 154022(2009).

  3. 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.

  4. Spectral modulation observed in artificial photosynthetic complexes by real-time vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Du, Juan; Yuan, Wei; Xing, Xin; Miyatake, Tomohiro; Tamiaki, Hitoshi; Kobayashi, Takayoshi; Leng, Yuxin

    2017-09-01

    By real-time vibrational spectroscopy using 6.8 fs pulses, real-time vibronic coupling in stair-like zinc chlorin aggregates was studied. Besides the observed fast excitonic relaxation, amplitudes of coherent molecular vibrations are found to be linearly dispersed from the resonant peak as a function of their own vibrational frequencies. In addition, the initial phases of the molecular vibrations exhibiting clear π phase jump have been observed. All these results indicate that coherent vibrations in the artificial chlorosome intermediate energy exchange between the laser fields around the resonant peak and those separated from it by photon energy equal to the vibrational frequencies.

  5. 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.

  6. 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

  7. 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).

  8. 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.

  9. Multidimensional vibrational spectroscopy for tunneling processes in a dissipative environment.

    PubMed

    Ishizaki, Akihito; Tanimura, Yoshitaka

    2005-07-01

    Simulating tunneling processes as well as their observation are challenging problems for many areas. In this study, we consider a double-well potential system coupled to a heat bath with a linear-linear (LL) and square-linear (SL) system-bath interactions. The LL interaction leads to longitudinal (T1) and transversal (T2) homogeneous relaxations, whereas the SL interaction leads to the inhomogeneous dephasing (T2*) relaxation in the white noise limit with a rotating wave approximation. We discuss the dynamics of the double-well system under infrared (IR) laser excitations from a Gaussian-Markovian quantum Fokker-Planck equation approach, which was developed by generalizing Kubo's stochastic Liouville equation. Analytical expression of the Green function is obtained for a case of two-state-jump modulation by performing the Fourier-Laplace transformation. We then calculate a two-dimensional infrared signal, which is defined by the four-body correlation function of optical dipole, for various noise correlation time, system-bath coupling parameters, and temperatures. It is shown that the bath-induced vibrational excitation and relaxation dynamics between the tunneling splitting levels can be detected as the isolated off-diagonal peaks in the third-order two-dimensional infrared (2D-IR) spectroscopy for a specific phase matching condition. Furthermore, this spectroscopy also allows us to directly evaluate the rate constants for tunneling reactions, which relates to the coherence between the splitting levels; it can be regarded as a novel technique for measuring chemical reaction rates. We depict the change of reaction rates as a function of system-bath coupling strength and a temperature through the 2D-IR signal.

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. Coherent Multidimensional Vibrational Spectroscopy of Representative N-Alkanes

    NASA Astrophysics Data System (ADS)

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

    2009-08-01

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

  16. Coherent multidimensional vibrational spectroscopy of representative N-alkanes.

    PubMed

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

    2009-09-10

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

  17. 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.

  18. 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.

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

    PubMed Central

    2014-01-01

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

  20. 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.

  1. Vibrational states of atomic hydrogen in bulk and nanocrystalline palladium studied by neutron spectroscopy

    NASA Astrophysics Data System (ADS)

    Kofu, Maiko; Hashimoto, Naoki; Akiba, Hiroshi; Kobayashi, Hirokazu; Kitagawa, Hiroshi; Iida, Kazuki; Nakamura, Mitsutaka; Yamamuro, Osamu

    2017-08-01

    The vibrational states of hydrogen atoms in bulk and nanocrystalline palladium were examined in a wide energy region 0 ≤ℏ ω ≤300 meV using neutron spectroscopy. In bulk PdH0.73, the vibrational excitations of H atoms were roughly reproduced by the quantum harmonic oscillator (QHO) model. In PdH0.42 nanocrystals with a diameter of 8 nm, however, additional vibrational excitations were found at energies above 80 meV. The energies and intensities of the additional states were not explained by the QHO but reasonably described as vibrations in a highly anharmonic trumpetlike potential. The additional excitations are attributed to the vibrations of H atoms at tetrahedral sites in the subsurface region stabilized by surface effects. Thus, this is an experimental work which clearly detects hydrogen vibration inside metal nanoparticles.

  2. Ultrasensitive Ultrafast Vibrational Spectroscopy Employing the Near Field of Gold Nanoantennas

    NASA Astrophysics Data System (ADS)

    Selig, O.; Siffels, R.; Rezus, Y. L. A.

    2015-06-01

    We introduce a novel method to perform nonlinear vibrational spectroscopy on nanoscale volumes. Our technique uses the intense near field of infrared nanoantennas to amplify the nonlinear vibrational signals of molecules located in the vicinity of the antenna surface. We demonstrate the capabilities of the method by performing infrared pump-probe spectroscopy and two-dimensional infrared spectroscopy on 5 nm layers of polymethylmetacrylate. In these experiments we observe enhancement factors of the nonlinear signals of more than 4 orders of magnitude. We discuss the mechanism underlying the amplification process as well as strategies for further increasing the sensitivity of the technique.

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

    NASA Astrophysics Data System (ADS)

    Mandal, Aritra; Tokmakoff, Andrei

    2015-11-01

    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-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.

  4. 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.

  5. 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.

  6. 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.

  7. Plasmonic super-localization using nano-post arrays for biomedical spectroscopy

    NASA Astrophysics Data System (ADS)

    Lee, Hongki; Kim, Donghyun

    2017-02-01

    Plasmonic nanostructures enable field confinement which is locally amplified within sub-diffraction limited volume. The localized near-field can be useful in many biomedical sensing and imaging applications. In this research, we present the near-field characteristics localized by plasmonic nano-post arrays for biomedical spectroscopy. Circular gold nano-post arrays were modeled on gold and chrome films fabricated on a glass substrate whose thickness was 50, 20 and 2 nm, respectively. The nano-post arrays were fabricated with an e-beam lithography and a diameter of the post was 250 nm with periods varied as 500, 700, and 900 nm. The field localization produced by nano-posts was induced by angled illumination with a total internal reflection fluorescence microscope objective lens and measured by a near-field scanning optical microscope (NSOM). The NSOM has a tapered fiber probe with a 70-nm aperture and was a continuous-wave laser whose wavelength is 532 nm as light source. Incident TM-polarized light exhibited field localization on one side of an individual gold nano-post. When the direction of light incidence was changed opposite, localized field was switched to the opposite edge of the circular nano-post. We performed 3D finite difference time domain s for the field calculation and confirmed the localized field distribution at given illumination angles. We also discuss the potential applications of plasmonic field localization for analysis of biomolecules, cells, and tissues.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Vibrational Spectroscopy of Photoreactive Molecules in Atmospheric Chemistry

    NASA Astrophysics Data System (ADS)

    Vaida, Veronica

    2010-06-01

    Vibrational overtone spectra of oxidized atmospheric chromophores are presented and analyzed to energies where chemistry through vibrational overtone pumping is possible. Experimental near infrared and visible spectra complemented by dynamical theory are presented to elucidate the light initiated reaction dynamics of pyruvic and of glyoxilic acid photo-decarboxylation. The role of water is investigated by making use of vibrational spectra of hydrates of the title compounds. Consequences of water and sunlight mediated chemistry to formation of secondary organic aerosol in the atmosphere will be discussed. K. L. Plath, J. L. Axson, G. C. Nelson, K. Takahashi, R. T. Skodje and V. Vaida -- React. Kineti. Catal. Lett. 96, 209 (2009) V. Vaida J. Phys. Chem. A 113, 5 (2009) K. Takahashi, K. L. Plath, R. T. Skodje and V. Vaida J. Phys. Chem A 112 7321 (2008)

  14. 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.

  15. Structure and vibrations of glutathione studied by vibrational spectroscopy and density functional theory.

    PubMed

    Singh, Gurpreet; Dogra, Sukh Dev; Kaur, Sarvpreet; Tripathi, S K; Prakash, Satya; Rai, Bimal; Saini, G S S

    2015-01-01

    The vibrational properties of glutathione have been investigated by infrared absorption and Raman spectroscopic techniques, and density functional theory calculations at the B3LYP/6-31+G(d,p) level. Assignments of all the experimentally observed vibrational bands have been done with the help of simulated vibrational spectra and potential energy distribution calculations of glutathione water cluster, which includes the effect of hydrogen bonding. Optimized molecular parameters of energy minimized structure have been compared with the available experimental values. Calculated molecular parameters of glutathione-water cluster match well with the experimental values. Some of the calculated molecular parameters and vibrational frequencies of vapor phase glutathione-water cluster suggest participation of some atoms of glutathione in hydrogen bonding. Experimentally observed UV-Visible absorption spectrum of glutathione has also been reported. Observed band at 203 nm has been assigned to electronic transitions calculated with time dependent density functional theory. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

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

    PubMed

    Nakamura, Ryosuke; Hamada, Norio

    2015-05-14

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

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

    PubMed

    Gruenbaum, S M; Skinner, J L

    2013-11-07

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

  9. 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.

  10. 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…

  11. 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…

  12. Modulated Surface Vibrational Spectroscopies at Electrode/Electrolyte Interfaces.

    DTIC Science & Technology

    1984-11-28

    Electric Field strength CO C2H4 Napthalene Anthracene TCNQ. 107 4.2 108 4.5 0.056 0.1 1.5 109 7.5 0.6 5.6 11 150 2 x 109 12 2.4 22 44 580 5 x 109 30... sulfuric acid (33). The two bipolar bands clearly visible In Figure BA are from the CO stretch vibrations of two different strongly adsorbed CO poisons

  13. 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.

  14. 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

  15. Vibrational spectroscopy modeling of a drug in molecular solvents and enzymes

    NASA Astrophysics Data System (ADS)

    Devereux, Christian J.; Fulfer, Kristen D.; Zhang, Xiaoliu; Kuroda, Daniel G.

    2017-09-01

    Modeling of drugs in enzymes is of immensurable value to many areas of science. We present a theoretical study on the vibrational spectroscopy of Rilpivirine, a HIV reverse transcriptase inhibitor, in conventional solvents and in clinically relevant enzymes. The study is based on vibrational spectroscopy modeling of the drug using molecular dynamics simulations, DFT frequency maps, and theory. The modeling of the infrared lineshape shows good agreement with experimental data for the drug in molecular solvents where the local environment motions define the vibrational band lineshape. On the other hand, the theoretical description of the drug in the different enzymes does not match previous experimental findings indicating that the utilized methodology might not apply to heterogeneous environments. Our findings show that the lack of reproducibility might be associated with the development of the frequency map which does not contain all of the possible interactions observed in such systems.

  16. 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.

  17. Assignment of vibrational spectral bands of kidney tissue by means of low temperature SERS spectroscopy

    NASA Astrophysics Data System (ADS)

    Velicka, M.; Radzvilaite, M.; Ceponkus, J.; Urboniene, V.; Pucetaite, M.; Jankevicius, F.; Steiner, G.; Sablinskas, V.

    2017-02-01

    Surface enhanced Raman scattering (SERS) spectroscopy is a useful method for detection of trace amounts of molecules. It has already been successfully implemented for detection of explosives, food additives, biomarkers in blood or urine, etc. In the last decade, SERS spectroscopy was introduced into the field of health sciences and has been especially focused on early disease detection. In the recent years, application of SERS spectroscopy for detection of various types of human cancerous tissues emerged. Furthermore, SERS spectroscopy of extracellular fluid shows great potential for the differentiation of normal and cancerous tissues; however, due to high variety of molecules present in such biological samples, the experimental spectrum is a combination of many different overlapping vibrational spectral bands. Thus, precise assignment of these bands to the corresponding molecular vibrations is a difficult task. In most cases, researchers try to avoid this task satisfying just with tentative assignment. In this study, low temperature SERS measurements of extracellular fluid of cancerous and healthy kidney tissue samples were carried out in order to get a deeper understanding of the nature of vibrational spectral bands present in the experimental spectrum. The SERS spectra were measured in temperature range from 300 K down to 100 K. SERS method was implemented using silver nanoparticle colloidal solution. The results of the low temperature SERS experiment were analysed and compared with the results of theoretical calculations. The analysis showed that the SERS spectrum of extracellular fluid of kidney tissue is highly influenced by the vibrational bands of adenine and Lcystine molecules.

  18. 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

  19. 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.

  20. Vibrational Spectroscopy with Angle-Dependent EELS: Acetylene Chemisorption on Pd(111).

    DTIC Science & Technology

    1981-12-28

    STATEMENT (of the .bstel Atered In Block 20, It different fror Report) i𔃽i82 : .. ,0. SUPPLEMENTARY NOTrES... "- To be published in The Journal of Chemical Physics IS...Unlimited To be published in The Journal of Chemical Physics -- -i In -1 it’ .4 .. ’ --- o . | SURFACE VIBRATIONAL SPECTROSCOPY WITH ANGLE-DEPENDENT

  1. Chiral vibrational structures of proteins at interfaces probed by sum frequency generation spectroscopy.

    PubMed

    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.

  2. 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.

  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. 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.

  5. Spectroscopy, reaction, and photodissociation in highly vibrationally excited molecules. Technical progress report

    SciTech Connect

    Not Available

    1991-12-31

    Highly vibrationally excited molecules often control the course of chemical reactions in the atmosphere, combustion, plasmas, and many other environments. The research described in this Progress Report uses laser excitation and interrogation techniques to study and control the dynamics of highly vibrationally excited molecules. In particular, they show that it is possible to unravel the details and influence the course of photodissociation and bimolecular reaction. The experiments use laser excitation of overtone vibrations to prepare highly vibrationally excited molecules, frequently with single quantum state resolution, and laser spectroscopy to monitor the subsequent behavior of the excited molecule. We have studied the vibrationally mediated photodissociation and the bond- and state-selected bimolecular reaction of highly vibrationally excited molecules. In the first process, one photon creates a highly excited molecule, a second photon from another laser dissociates it, and light from a third laser detects the population of individual product quantum states. This approach allows us to explore otherwise inaccessible regions of the ground and excited state potential energy surface and, by exciting to the proper regions of the surface, to control the breaking of a selected chemical bond. In the second process, the highly vibrationally excited molecule reacts with an atom formed either in a microwave discharge or by photolysis and another laser interrogates the products. We have used this approach to demonstrate mode- and bond-selected bimolecular reactions in which the initial excitation controls the subsequent chemistry. 30 refs., 8 figs.

  6. The Microwave Spectroscopy of Aminoacetonitrile in the Vibrational Excited State

    NASA Astrophysics Data System (ADS)

    Fujita, Chiho; Ozeki, Hiroyuki; Kobayashi, Kaori

    2015-06-01

    Aminoacetonitrile (NH_2CH_2CN) is a potential precursor of the simplest amino acid, glycine and was detected toward SgrB2(N). It is expected that the strongest transitions will be found in the terahertz region so that we have extended measurements up to 1.3 THz. This study gave an accurate prediction of aminoacetonitrile up to 2 THz which is useful for astronomically search. This molecule has a few low-lying vibrational excited states and the pure rotational transitions in these vibrational excited states are expected to found. We found a series of transitions with intensity of about 30%. Eighty-eight spectral lines including both a-type and b-type transitions were recorded in the frequency region of 400 - 450 GHz, and centrifugal distortion constants up to the sextic term were determined. Perturbation was recognized. We will report the current status of the 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).

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

    PubMed Central

    Zhuang, Wei; Hayashi, Tomoyuki; Mukamel, Shaul

    2009-01-01

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

  9. Biomedical Imaging

    NASA Astrophysics Data System (ADS)

    MacPherson, Emma

    This chapter builds on the basic principles of THz spectroscopy and explains how they can be applied to biomedical systems as well as the motivation for doing so. Sample preparation techniques and measurement methods for biomedical samples are described in detail. Examples of medical applications investigated hitherto including breast cancer and skin cancer are also presented.

  10. Vibrational spectroscopy for molecular characterisation and diagnosis of benign, premalignant and malignant skin tumours.

    PubMed

    Eikje, Natalja Skrebova; Aizawa, Katsuo; Ozaki, Yukihiro

    2005-01-01

    Understanding the molecular, cellular and tissue changes that occur during skin carcinogenesis is central to cancer research in dermatology. The translational aspects of this field--the development of clinical applications in dermatology from the laboratory findings--aim at improving clinical diagnosis, monitoring and treatment of skin cancer. Vibrational spectroscopy, both infrared (IR) and Raman spectroscopy, would be helpful in achieving those goals, since it has been shown to have potential in characterising and discriminating tumour and dysplastic tissue from normal tissue. Clinically differential diagnosis of skin tumours is often difficult and a histopathologic analysis of skin biopsies remains the standard for diagnostic confirmation. We review and update the literature on the subject, demonstrating that the IR and Raman spectra of skin tissues provide valid and useful diagnostic information about a number of skin tumours. We also include a survey of introduced sampling methods for IR and Raman spectroscopy in dermatology, and additionally describe the differences between microscopic, macroscopic and fibreoptic diagnosis of skin cancer. Although in its early stages, we remain optimistic that vibrational spectroscopy has the potential to be fully accepted as a rapid screening tool with sufficient sensitivity and specificity for non-destructive in vitro, ex vivo and in vivo analyses by the dermatological community. Further progress toward molecular characterisation of skin cancer by vibrational spectroscopy would have important research and clinical benefits in dermatology.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Ultrafast vibrational energy transfer at the water/air interface revealed by two-dimensional surface vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Zhen; Piatkowski, Lukasz; Bakker, Huib J.; Bonn, Mischa

    2011-11-01

    Water is very different from liquids of similar molecular weight, and one of its unique properties is the very efficient transfer of vibrational energy between molecules, which arises as a result of strong dipole-dipole interactions between the O-H oscillators. Although we have a sound understanding of such energy transfer in bulk water, we know less about how, and how quickly, transfer occurs at its interface with a hydrophobic phase, because specifically addressing the outermost monolayer is difficult. Here, we use ultrafast two-dimensional surface-specific vibrational spectroscopy to probe the interfacial energy dynamics of heavy water (D2O) at the water/air interface. The measurements reveal the presence of surprisingly rapid energy transfer, both between hydrogen-bonded interfacial water molecules (intermolecular), and between O-D groups sticking out from the water surface and those located on the same molecule and pointing towards the water bulk (intramolecular). Vibrational energy transfer occurs on sub-picosecond timescales, and its rates and pathways can be quantified directly.

  16. Ultrafast vibrational energy transfer at the water/air interface revealed by two-dimensional surface vibrational spectroscopy.

    PubMed

    Zhang, Zhen; Piatkowski, Lukasz; Bakker, Huib J; Bonn, Mischa

    2011-10-02

    Water is very different from liquids of similar molecular weight, and one of its unique properties is the very efficient transfer of vibrational energy between molecules, which arises as a result of strong dipole-dipole interactions between the O-H oscillators. Although we have a sound understanding of such energy transfer in bulk water, we know less about how, and how quickly, transfer occurs at its interface with a hydrophobic phase, because specifically addressing the outermost monolayer is difficult. Here, we use ultrafast two-dimensional surface-specific vibrational spectroscopy to probe the interfacial energy dynamics of heavy water (D(2)O) at the water/air interface. The measurements reveal the presence of surprisingly rapid energy transfer, both between hydrogen-bonded interfacial water molecules (intermolecular), and between O-D groups sticking out from the water surface and those located on the same molecule and pointing towards the water bulk (intramolecular). Vibrational energy transfer occurs on sub-picosecond timescales, and its rates and pathways can be quantified directly.

  17. 2D-IR spectroscopy of hydrogen-bond-mediated vibrational excitation transfer.

    PubMed

    Chuntonov, Lev

    2016-05-18

    Vibrational excitation transfer along the hydrogen-bond-mediated pathways in the complex of methyl acetate (MA) and 4-cyanophenol (4CP) was studied by dual-frequency femtosecond two-dimensional infrared spectroscopy. We excited the energy-donating ester carbonyl stretching vibrational mode and followed the transfer to the energy-accepting benzene ring and cyano stretching vibrations. The complexes with no, one, and two hydrogen-bonded 4CP molecules were studied. Vibrational relaxation of the carbonyl mode is more efficient in both hydrogen-bonded complexes as compared with free MA molecules. The inter-molecular transport in a hydrogen-bonded complex involving a single 4CP molecule is slower than that in a complex with two 4CP molecules. In the former, vibrational relaxation leads to local heating, as shown by the spectroscopy of the carbonyl mode, whereas the local heating is suppressed in the latter because the excitation redistribution is more efficient. At early times, the transfer to the benzene ring is governed by its direct coupling with the energy-donating carbonyl mode, whereas at later times intermediate states are involved. The transfer to a more distant site of the cyano group in 4CP involves intermediate states at all times, since no direct coupling between the energy-donating and accepting modes was observed. We anticipate that our findings will be of importance for spectroscopic studies of bio-molecular structures and dynamics, and inter- and intra-molecular signaling pathways, and for developing molecular networking applications.

  18. Three-dimensional spectroscopy of vibrational energy in liquids: nitromethane and acetonitrile.

    PubMed

    Sun, Yuxiao; Pein, Brandt C; Dlott, Dana D

    2013-12-12

    We introduce a novel type of three-dimensional (3D) spectroscopy to study vibrational energy transfer, where an IR pulse tunable through the CH-stretching and CD-stretching regions was used to create parent vibrational excitations in liquids and a visible probe pulse was used to generate both Stokes and anti-Stokes Raman spectra as a function of delay time. The Raman spectra determine how much vibrational excitation was present in each probed state. The three dimensions are the wavenumber of the pumped state, the wavenumber of the probed state, and the time interval. The technique was used to study nitromethane (NM) and acetonitrile (ACN) and their deuterated analogues at ambient temperature. The 3D spectra were quite complicated. Three types of artifacts due to nonlinear light scattering were observed. Along the diagonal were two fundamental CH-stretch (or CD-stretch) transitions and several weaker combination bands or overtone transitions. Because Raman spectroscopy allows us to simultaneously probe a wide wavenumber region, for every diagonal peak, there were ∼10 off-diagonal peaks. The cross-peaks at shorter delay times reveal the nature of the initial excitation by showing which lower-wavenumber excitations were produced along with the pumped CH-stretch or CD-stretch. The longer-time spectra characterized vibrational energy relaxation processes, and showed how daughter vibrations were generated by different parent excitations.

  19. Vibrational Spectroscopy of Laser Cooled CaH

    DTIC Science & Technology

    2015-10-28

    Moriwaki have identified halides of alkali metals as ideal candidates for the testing of µ, proton-to-electron mass ratio. 40CaH+ has been proposed...resolved elec- tronic spectra of metal -ion complexes, vanadium oxide-carbonyl cations [19, 84], and IR dip-ultraviolet photodissociation of... metal hydrides [25]. 81 Our experimental setup was intended for high-precision quantum logic spectroscopy [212] experiments on molecular ions. We have

  20. Ultrafast vibrational population transfer dynamics in 2-acetylcyclopentanone studied by 2D IR spectroscopy.

    PubMed

    Park, Sungnam; Ji, Minbiao

    2011-03-14

    2-Acetylcyclopentanone (2-ACP), which is a β-dicarbonyl compound, undergoes keto-enol isomerization, and its enol tautomers are stabilized by a cyclic intramolecular hydrogen bond. 2-ACP (keto form) has symmetric and asymmetric vibrational modes of the two carbonyl groups at 1748 and 1715 cm(-1) , respectively, which are well separated from the carbonyl modes of its enol tautomers in the FTIR spectrum. We have investigated 2-ACP dissolved in carbon tetrachloride by 2D IR spectroscopy and IR pump-probe spectroscopy. Vibrational population transfer dynamics between the two carbonyl modes were observed by 2D IR spectroscopy. To extract the population exchange dynamics (i.e., the down- and uphill population transfer rate constants), we used the normalized volumes of the cross-peaks with respect to the diagonal peaks at the same emission frequency and the survival and conditional probability functions. As expected, the downhill population transfer time constant (3.2 ps) was measured to be smaller than the uphill population transfer time constant (3.8 ps). In addition, the vibrational population relaxation dynamics of the two carbonyl modes were observed to be the same within the experimental error and were found to be much slower than vibrational population transfer between two carbonyl modes. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. 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

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  4. 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.

  5. 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.

  6. Vibrational energy transport in molecules studied by relaxation-assisted two-dimensional infrared spectroscopy.

    PubMed

    Rubtsova, Natalia I; Rubtsov, Igor V

    2015-04-01

    This review presents an overview of the relaxation-assisted two-dimensional infrared (RA 2DIR) spectroscopy method for measuring structures and energy transport dynamics in molecules. The method strongly enhances the range of accessible distances compared to traditional 2DIR and offers new structural reporters, such as the energy transport time, cross-peak amplification factors, and connectivity patterns. The use of the method for assigning vibrational modes with various levels of delocalization is illustrated. RA 2DIR relies on vibrational energy transport in molecules; as such, the transport mechanism can be conveniently studied by the method. Applications to identify diffusive and ballistic energy transport are demonstrated.

  7. 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.

  8. 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

  9. Efficient Vibrational Energy Transfer through Covalent Bond in Indigo Carmine Revealed by Nonlinear IR Spectroscopy.

    PubMed

    He, Xuemei; Yu, Pengyun; Zhao, Juan; Wang, Jianping

    2017-09-28

    Ultrafast vibrational relaxation and structural dynamics of indigo carmine in dimethyl sulfoxide were examined using femtosecond pump-probe infrared and two-dimensional infrared (2D IR) spectroscopies. Using the intramolecularly hydrogen-bonded C═O and delocalized C═C stretching modes as infrared probes, local structural and dynamical variations of this blue dye molecule were observed. Energy relaxation of the vibrationally excited C═O stretching mode was found to occur through covalent bond to the delocalized aromatic vibrational modes on the time scale of a few picoseconds or less. Vibrational quantum beating was observed in magic-angle pump-probe, anisotropy, and 2D IR cross-peak dynamics, showing an oscillation period of ca. 1010 fs, which corresponds to the energy difference between the C═O and C═C transition frequency (33 cm(-1)). This confirms a resonant vibrational energy transfer happened between the two vibrators. However, a more efficient energy-accepting mode of the excited C═O stretching was believed to be a nearby combination and/or overtone mode that is more tightly connected to the C═O species. On the structural aspect, dynamical-time-dependent 2D IR spectra reveal an insignificant inhomogeneous contribution to time-correlation relaxation for both the C═O and C═C stretching modes, which is in agreement with the generally believed structural rigidity of such conjugated molecules.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    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.

  18. 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.

  19. 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.

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

    PubMed

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

    2015-07-28

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

  1. Ultrafast Reorientation of Dangling OH Groups at the Air-Water Interface Using Femtosecond Vibrational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Hsieh, Cho-Shuen; Campen, R. Kramer; Vila Verde, Ana Celia; Bolhuis, Peter; Nienhuys, Han-Kwang; Bonn, Mischa

    2011-09-01

    We report the real-time measurement of the ultrafast reorientational motion of water molecules at the water-air interface, using femtosecond time- and polarization-resolved vibrational sum-frequency spectroscopy. Vibrational excitation of dangling OH bonds along a specific polarization axis induces a transient anisotropy that decays due to the reorientation of vibrationally excited OH groups. The reorientation of interfacial water is shown to occur on subpicosecond time scales, several times faster than in the bulk, which can be attributed to the lower degree of hydrogen bond coordination at the interface. Molecular dynamics simulations of interfacial water dynamics are in quantitative agreement with experimental observations and show that, unlike in bulk, the interfacial reorientation occurs in a largely diffusive manner.

  2. 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.

  3. Advanced Theory of Driven Birdcage Resonator with Losses for Biomedical Magnetic Resonance Imaging and Spectroscopy

    PubMed Central

    Novikov, Alexander

    2010-01-01

    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 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 B1 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 currents losses is the major effect of coil shielding. PMID:20869184

  4. 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

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

    PubMed

    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

    2013-12-01

    We have applied (57)Fe 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.

  6. Identification and Characterization of Skin Biomolecules for Drug Targeting and Monitoring by Vibrational Spectroscopy

    PubMed Central

    Eikje, Natalja Skrebova; Aizawa, Katsuo; Sota, Takayuki; Ozaki, Yukihiro; Arase, Seiji

    2008-01-01

    The article discusses the application of vibrational spectroscopy techniques for in vivo identification and characterization of glucose biomolecules monitored in the skin of healthy, prediabetes and diabetes subjects; for molecular characterization of water and proteins in in vivo monitored patch tested inflamed skin of the patients with contact dermatitis; for description of nucleic acids and proteins at the molecular level with progression to malignancy in skin cancerous lesions. The results of the studies show new possibilities to assess activity levels of glucose metabolism in the skin tissue of healthy, prediabetes and diabetes subjects; activity and severity of inflammation; activity of the processes of carcinogenesis with regard to benign, premalignant and malignant transformation. Based on our findings, we suggest that vibrational spectroscopy might be a rapid screening tool with sufficient sensitivity and specificity to identify and characterize skin biomolecules in described diseases for drug targeting and monitoring by the pharmacological community. PMID:19662142

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  8. 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.

  9. 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

  10. 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. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. 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).

  12. Synthesis, conductivity, and vibrational spectroscopy of tetraphenylphosphonium bis(trifluoromethanesulfonyl)imide

    NASA Astrophysics Data System (ADS)

    Haddad, Boumediene; Paolone, Annalisa; Villemin, Didier; Taqiyeddine, Moumene; Belarbi, El-habib; Bresson, Serge; Rahmouni, Mustapha; Dhumal, Nilesh R.; Kim, Hyung J.; Kiefer, Johannes

    2017-10-01

    The reaction of lithium bis(trifluoromethanesulfonyl)imide with tetraphenylphosphonium bromide in water leads to the formation of tetraphenylphosphonium bis(trifluoromethanesulfonyl)imide ([PPh4+][(CF3SO2)2N-]). The obtained compound was identified by means of 1H, 13C, 19F and 31P NMR spectroscopy. Although it has a structure similar to ionic liquids, it exhibits a melting point above 100 °C. Besides describing the synthesis, a detailed characterization of its conductivity and vibrational spectroscopic properties is presented. For the latter, FT-Raman and FTIR/ATR spectroscopies are used in the wavenumber range from 150 to 3500 cm-1 and from 600 to 3500 cm-1, respectively. Density functional theory calculations reveal a minor influence of the interionic interactions on the vibrational structure. Consequently, the computational vibrational spectra of the isolated ions show a good agreement with the experimental data. A detailed vibrational assignment is presented. Furthermore, the conductivity data indicate a solid-solid phase transition about 130 K below the melting point.

  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. Vibrational spectra of CO on Ni (100) studied by infrared emission spectroscopy

    SciTech Connect

    Not Available

    1984-02-01

    We have developed the technique of infrared emission spectroscopy in order to observe vibrational modes of molecules adsorbed on clean, single crystal metal surfaces. A novel apparatus has been constructed which measures the emission from a single crystal sample in thermal equilibrium at room temperature. The apparatus consists of a liquid helium cooled infrared grating spectrometer coupled to an ultrahigh vacuum system equipped with surface preparation and characterization facilities. 3 references, 3 figures.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  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 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.

  20. 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.

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

    PubMed

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

    2014-12-10

    The mineral sturmanite is a hydrated calcium iron aluminium manganese sulphate tetrahydroxoborate hydroxide of formula Ca6(Fe, Al, Mn)2(SO4)2(B(OH)4)(OH)12·26H2O. We have studied the mineral sturmanite using a number of techniques, including SEM with EPMA and vibrational spectroscopy. Chemical analysis shows a homogeneous phase, composed by Ca, Fe, Mn, S, Al and Si. B is not determined in this EPMA technique. An intense Raman band at 990cm(-1) is assigned to the SO4(2-) symmetric stretching mode. Raman spectroscopy identifies multiple sulphate symmetric stretching modes in line with the three sulphate crystallographically different sites. Raman spectroscopy also identifies a band at 1069cm(-1) which may be attributed to a carbonate symmetric stretching mode, indicating the presence of thaumasite. Infrared spectra display two bands at 1080 and 1107cm(-1) assigned to the SO4(2-) antisymmetric stretching modes. The observation of multiple bands in this ν4 spectral region offers evidence for the reduction in symmetry of the sulphate anion from Td to C2v or even lower symmetry. The Raman band at 3622cm(-1) is assigned to the OH unit stretching vibration and the broad feature at around 3479cm(-1) to water stretching bands. Infrared spectroscopy shows a set of broad overlapping bands in the OH stretching region. Vibrational spectroscopy enables an assessment of the molecular structure of sturmanite to be made. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Laser-induced breakdown spectroscopy (LIBS): an overview of recent progress and future potential for biomedical applications.

    PubMed

    Rehse, S J; Salimnia, H; Miziolek, A W

    2012-02-01

    The recent progress made in developing laser-induced breakdown spectroscopy (LIBS) has transformed LIBS from an elemental analysis technique to one that can be applied for the reagentless analysis of molecularly complex biological materials or clinical specimens. Rapid advances in the LIBS technology have spawned a growing number of recently published articles in peer-reviewed journals which have consistently demonstrated the capability of LIBS to rapidly detect, biochemically characterize and analyse, and/or accurately identify various biological, biomedical or clinical samples. These analyses are inherently real-time, require no sample preparation, and offer high sensitivity and specificity. This overview of the biomedical applications of LIBS is meant to summarize the research that has been performed to date, as well as to suggest to health care providers several possible specific future applications which, if successfully implemented, would be significantly beneficial to humankind.

  3. 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

  4. [The latest development of the research on Chinese medicine by molecular vibrational spectroscopy].

    PubMed

    Sun, S; Zhou, Q; Yu, J; Hu, X

    2000-04-01

    The latest development of the molecular vibrational spectroscopy (Fourier Transform Raman Spectroscopy and Fourier Transform Infraed Spectroscopy) and the latest application of the non-destructive identification, quantitative analysis, thermal-stability monitoring and Chinese medicine optimizing were described in this paper. Some Chinese crude herbs can be directly and quickly identified by Fourier Transform Raman spectroscopy (FT - Raman) and Diffused Reflection Fourier Transform Infrared Spectroscopy (DR-FTIR). The content of Chinese herbs, medicine and medicament can be quantified without destruction by Diffused Reflection Fourier Transform and Near Infrared Spectroscopy (DR-NIR-FTIR). The mechanism of interaction between the Chinese medicine and some cells or bacteria can be in situ monitored by FT-Raman and HATR-FTIR. Best medicine could be selected and medicament could be optimized according to the injury degree of the cell or bacteria. The decomposing and degenerating process of medicines can also be timely monitored by FT-Raman and the temperature controlled FTIR. These are the latest use of molecular spectroscopy in Chinese medicine. The fast indentification, quantitative analysis monitoring, thermal stability predicting and the optimizing of Chinese herbs, medicine and medicament can be guided by the above mentioned methods. It is proved that these methods are nondestructive to samples, fast accurate, and easy to use.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. Proton-bound dimers of 1-methylcytosine and its derivatives: vibrational and NMR spectroscopy.

    PubMed

    Ung, Hou U; Moehlig, Aaron R; Kudla, Ryan A; Mueller, Leonard J; Oomens, Jos; Berden, Giel; Morton, Thomas Hellman

    2013-11-21

    Vibrational spectroscopy and NMR demonstrate that the proton-bound dimer of 1-methylcytosine, 1, has an unsymmetrical structure at room temperature. In the gas phase, investigation of isolated homodimer 1 reveals five fundamental NH vibrations by IR Multiple Photon Dissociation (IRMPD) action spectroscopy. The NH···N stretching vibration between the two ring nitrogens exhibits a frequency of 1570 cm(-1), as confirmed by examination of the proton-bound homodimers of 5-fluoro-1-methycytosine, 2, and of 1,5-dimethylcytosine, 3, which display absorptions in the same region that disappear upon deuterium substitution. (13)C, and (15)N NMR of the solid iodide salt of 1 confirm the nonequivalence of the two rings in the anhydrous proton-bound homodimer at room temperature. IRMPD spectra of the three possible heterodimers also show NH···N stretches in the same domain, and at least one of the heterodimers, the proton-bound dimer of 1,5-dimethylcytosine with 1-methylcytosine, exhibits two bands suggestive of the presence of two tautomers close in energy.

  11. Vibrational Spectroscopy of He-O_2H^+ and O_2H^+

    NASA Astrophysics Data System (ADS)

    Kohguchi, Hiroshi; Yamada, Koichi MT; Jusko, Pavol; Schlemmer, Stephan; Asvany, Oskar

    2017-06-01

    The elusive protonated oxygen, O_2H^+, has been characterized by vibrational action spectroscopy in a cryogenic 22-pole ion trap. On the one hand, the vibrational bands of the tagged He-O_2H^+ have been investigated, using a table-top OPO system for the known OH-stretch^a, whereas the FELIX^b light source has been used to detect the hitherto unknown low-frequency O-O-H bend and O-O stretch. On the other hand, the untagged O_2H^+ has been detected for the first time by high-resolution rovibrational spectroscopy via its ν_1 OH-stretch motion. 38 ro-vibrational fine structure transitions with partly resolved hyperfine satellites were measured (56 resolved lines in total). Spectroscopic parameters were determined by a fit to an asymmetric rotor model with a ^3A'' electronic ground state. The band center is at 3016.73 \\wn, which is in good agreement with experimental^a and ab initio^{c,d} predictions. Based on the spectroscopic parameters, the rotational spectrum is predicted, but not detected yet. ^a S. A. Nizkorodov et al., Chem. Phys. Lett., 278, 26, 1997 ^b D. Oepts et al., Infrared Phys. Technol., 36, 297, 1995 ^c S. L. W. Weaver et al., Astrophys. J., 697, 601, 2009 ^d X. Huang and T. J. Lee, J. Chem. Phys., 129, 044312, 2008

  12. Absolute Configuration of 3-METHYLCYCLOHEXANONE by Chiral Tag Rotational Spectroscopy and Vibrational Circular Dichroism

    NASA Astrophysics Data System (ADS)

    Evangelisti, Luca; Holdren, Martin S.; Mayer, Kevin J.; Smart, Taylor; West, Channing; Pate, Brooks

    2017-06-01

    The absolute configuration of 3-methylcyclohexanone was established by chiral tag rotational spectroscopy measurements using 3-butyn-2-ol as the tag partner. This molecule was chosen because it is a benchmark measurement for vibrational circular dichroism (VCD). A comparison of the analysis approaches of chiral tag rotational spectroscopy and VCD will be presented. One important issue in chiral analysis by both methods is the conformational flexibility of the molecule being analyzed. The analysis of conformational composition of samples will be illustrated. In this case, the high spectral resolution of molecular rotational spectroscopy and potential for spectral simplification by conformational cooling in the pulsed jet expansion are advantages for chiral tag spectroscopy. The computational chemistry requirements for the two methods will also be discussed. In this case, the need to perform conformer searches for weakly bound complexes and to perform reasonably high level quantum chemistry geometry optimizations on these complexes makes the computational time requirements less favorable for chiral tag rotational spectroscopy. Finally, the issue of reliability of the determination of the absolute configuration will be considered. In this case, rotational spectroscopy offers a "gold standard" analysis method through the determination of the ^{13}C-subsitution structure of the complex between 3-methylcyclohexanone and an enantiopure sample of the 3-butyn-2-ol tag.

  13. 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.

  14. A theoretical study of the sum frequency vibrational spectroscopy of the carbon tetrachloride/water interface

    NASA Astrophysics Data System (ADS)

    Green, Anthony J.; Perry, Angela; Moore, Preston B.; Space, Brian

    2012-03-01

    Theoretical approximations to the sum frequency vibrational spectroscopy (SFVS) of the carbon tetrachloride/water interface are constructed using the quantum-corrected time correlation functions (TCF) to aid in interpretation of experimental data and to predict novel vibrational modes. Instantaneous normal mode (INM) methods are used to characterize the observed modes leading to the TCF signal, thus providing molecular resolution of the vibrational lineshapes. Detailed comparisons of the theoretical signals are made with those obtained experimentally and show excellent agreement for the spectral peaks in the O-H stretching region of water. An intermolecular mode, unique to the interface, at 848 cm-1 is also identifiable, similar to the one seen for the water/vapor interface. INM analysis reveals the resonance is due to a wagging mode (hindered rotation) that was previously identified (Perry et al 2005 J. Chem. Phys. 123 144705) as localized on a single water molecule with both hydrogens displaced normal to the interface—generally it is found that the symmetry breaking at the interface leads to hindered translations and rotations at hydrophilic/hydrophobic interfaces that assume finite vibrational frequencies due to anchoring at the aqueous interface. Additionally, examination of the real and imaginary parts of the theoretical SFVS spectra reveal the spectroscopic species attributed the resonances and possible subspecies in the O-H region; these results are consistent with extant experimental data and associated analysis.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. New solid forms of efavirenz: Synthesis, vibrational spectroscopy and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Marques, Marcelo M.; Rezende, Carlos A.; Lima, Gabriel C.; Marques, Andressa C. S.; Prado, Lívia D.; Leal, Kátia Z.; Rocha, Helvécio V. A.; Ferreira, Gláucio B.; Resende, Jackson A. L. C.

    2017-06-01

    Efavirenz,(S)-6-chloro-4-(cyclopropylethynyl)-1,4-dihydro-4-(trifluoromethyl)-2H-3,1-benzoxazin-2-one, is an anti HIV agent from the class of the non-nucleoside inhibitors of the HIV-1 virus reverse transcriptase. This paper describes the synthesis of two new solvatomorphs of efavirenz (EFV). The results through XRPD and DSC/TG indicate that the new forms undergo a solvent loss over the days, and then return to the original polymorph. Structural and spectral characteristics of EFV were studied by vibrational spectroscopy and quantum chemical methods. Density functional theory (DFT) calculations for the potential energy curve, optimized geometries and vibrational spectra were carried out using 6-311 + G** basis sets and CAM-B3LYP functional, solid state calculations were also performed using DFT-XGGA (PBE-D3) exchange-correlation functional with the option of mixtures of Gaussian and plane waves method (GPW). Based on these results, the paper discussed the correlation between the vibrational modes and the crystalline structure of the most stable form of EFV. A complete analysis of the experimental infrared and Raman spectra was reported on the basis of the wavenumbers of the vibrational bands and the potential energy distribution.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Molecular structure of CeI 3 from gas-phase electron diffraction and vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Molnár, Judit; Konings, Rudy J. M.; Kolonits, Mária; Hargittai, Magdolna

    1996-02-01

    CeI 3 was investigated by electron diffraction and infrared spectroscopy, both in the gas phase, at high temperature (around 1270 K). The geometrical parameters are: r g( CeI) 2.948 ± 0.009 Å and r g( I⋯I) 4.943 ± 0.032 Å. One absorption band was detected in the stretching region of the spectrum and we have assigned it to the asymmetric stretch, v3 = 191 ± 10 cm -1. The unusually large uncertainty is due to the large population of excited vibrational and rotational levels. From the very low intensity band at the lower detection limit of the spectrometer, we can conclude that neither v2 nor v4 is above 35 cm -1. From the analysis of electron diffraction data and vibrational spectra we conclude that the molecule is very likely planar or at most slightly pyramidal (quasiplanar).

  7. 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.

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

    PubMed

    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.

  9. Vibrational Spectroscopy for Imaging Single Microbial Cells in Complex Biological Samples

    PubMed Central

    Harrison, Jesse P.; Berry, David

    2017-01-01

    Vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of the samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of single-cell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment. PMID:28450860

  10. Vibrational spectroscopy for imaging single microbial cells in complex biological samples

    DOE PAGES

    Harrison, Jesse P.; Berry, David

    2017-04-13

    Here, vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of themore » samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of singlecell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.« less

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

    NASA Astrophysics Data System (ADS)

    Crane, Nicole J.; Elster, Eric A.

    2012-01-01

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

  12. 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

  13. 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.

  14. First-Principles Vibrational Electron Energy Loss Spectroscopy of β -Guanine

    NASA Astrophysics Data System (ADS)

    Radtke, G.; Taverna, D.; Lazzeri, M.; Balan, E.

    2017-07-01

    A general approach to model vibrational electron energy loss spectra obtained using an electron beam positioned away from the specimen is presented. The energy-loss probability of the fast electron is evaluated using first-principles quantum mechanical calculations (density functional theory) of the dielectric response of the specimen. The validity of the method is assessed using recently measured anhydrous β -guanine, an important molecular solid used by animals to produce structural colors. The good agreement between theory and experiments lays the basis for a quantitative interpretation of this spectroscopy in complex systems.

  15. 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.

  16. 2D THz-THz-Raman Photon-Echo Spectroscopy of Molecular Vibrations in Liquid Bromoform.

    PubMed

    Finneran, Ian A; Welsch, Ralph; Allodi, Marco A; Miller, Thomas F; Blake, Geoffrey A

    2017-09-13

    Fundamental properties of molecular liquids are governed by long-range interactions that most prominently manifest at terahertz (THz) frequencies. Here we report the detection of nonlinear THz photon-echo (rephasing) signals in liquid bromoform using THz-THz-Raman spectroscopy. Together, the many observed signatures span frequencies from 0.5 to 8.5 THz and result from couplings between thermally populated ladders of vibrational states. The strongest peaks in the spectrum are found to be multiquantum dipole and 1-quantum polarizability transitions and may arise from nonlinearities in the intramolecular dipole moment surface driven by intermolecular interactions.

  17. 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.

  18. Orientation determination of protein helical secondary structures using linear and nonlinear vibrational spectroscopy.

    PubMed

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

    2009-09-10

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

  19. 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))).

  20. 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)})

  1. 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)

  2. Vibrational spectroscopy in the monitoring of chilling injury in fruits and vegetables

    NASA Astrophysics Data System (ADS)

    Bertoluzza, Alessandro; Bottura, G.; Filippetti, P.; Tosi, M. R.; Vasina, M.

    1993-06-01

    Vegetable marrows (cv. Seme Bolognese) and peach fruits (cv. Suncrest) were stored at different chilling temperatures in order to evaluate, by vibrational spectroscopy, the unsaturation degree of the total lipidic component and other possible markers of chilling injuries. Capillary Gas Chromatography also has been applied to evaluate the unsaturation degree of the esterified fatty acids. Both methodologies indicate a general increase of the unsaturation degrees with storage time. This can be interpreted as a better adaptation capability of the fruits to low temperatures. Moreover, the FTIR-ATR methodology points out the onset of a hydrolysis reaction of the esteric phosphate group of phospholipids during storage.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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)..

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. Application of vibrational spectroscopy to the structural characterization of monoclonal antibody and its aggregate.

    PubMed

    Li, Cynthia H; Li, Tiansheng

    2009-06-01

    Aggregation is often the major issue during formulation and manufacturing development of therapeutic proteins, in particular human monoclonal antibody. Currently, there is a lack of structural information of aggregates of such large protein as human antibodies, due to the large molecular sizes of the aggregates. In this article, we shall discuss the application of vibrational spectroscopies including FT-IR, Raman and Raman Optical Activity (ROA), to characterize the structures of various types of monoclonal antibody aggregates formed under different stresses. Two different classes of human monoclonal antibodies, namely IgG1 and IgG2, have been subjected to this structural investigation. The common stresses leading to antibody aggregation, mis-folding or unfolding during manufacturing and formulation include exposure to acidic pHs, heat and shear stress. The effect of different types of stresses on the structure and aggregate formation of human monoclonal antibodies has been investigated by employing vibrational spectroscopy. While data present only monoclonal antibody, the same technology can be used for any protein aggregates.

  16. 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.

  17. Vibrational Population Distribution in Formaldehyde Expanding from Chen Pyrolysis Nozzle Measured by Chirped Pulse Millimeter Wave Spectroscopy

    NASA Astrophysics Data System (ADS)

    Kuyanov-Prozument, Kirill; Vasiliou, Angayle; Park, G. Barratt; Muenter, John S.; Stanton, John F.; Ellison, G. Barney; Field, Robert W.

    2011-06-01

    Knowing the vibrational population distribution of unimolecular fragmentation reaction products can reveal the reaction mechanism. Here, we applied Chirped Pulse Millimeter Wave (CPmmW) spectroscopy, invented by Brooks Pate and co-workers, to detect the vibrational population distribution of formaldehyde produced by pyrolysis of methyl nitrite (CH_3ONO) or ethyl nitrite (CH_3CH_2ONO). The pure rotational spectrum contains information about vibrational populations via the known vibration dependence of the rotational constants, which is easily observed in the millimeter-wave spectrum. Only two of six vibrational modes of formaldehyde are significantly populated in both pyrolysis decomposition reactions and in an expansion of pure formaldehyde, suggesting that it is the collisional energy transfer that primarily determines the vibrational population distribution. The non-Boltzmann population distribution among the observed vibrational modes demonstrates non-statistical vibrational energy transfer in formaldehyde. It is in sharp contrast with the equilibrated population distribution measured in OCS and the almost complete vibrational relaxation observed in acetaldehyde. This work is supported by grants from the US Department of Energy and the ACS Petroleum Research Fund, and the National Science Foundation grant "Organic Radicals in Biomass Decomposition: Mechanisms & Dynamics," (CHE-0848606) G. G. Brown, B. C. Dian, K. O. Douglass, S. M. Geyer, S. T. Shipman and B. H. Pate Rev. Sci. Instrum. 79, 053103 (1995).

  18. 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.

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

    PubMed

    Joutsuka, Tatsuya; Ando, Koji

    2011-05-28

    The vibrational spectroscopy and relaxation of an anharmonic oscillator coupled to a harmonic bath are examined to assess the applicability of the time correlation function (TCF), the response function, and the semiclassical frequency modulation (SFM) model to the calculation of infrared (IR) spectra. These three approaches are often used in connection with the molecular dynamics simulations but have not been compared in detail. We also analyze the vibrational energy relaxation (VER), which determines the line shape and is itself a pivotal process in energy transport. The IR spectra and VER are calculated using the generalized Langevin equation (GLE), the Gaussian wavepacket (GWP) method, and the quantum master equation (QME). By calculating the vibrational frequency TCF, a detailed analysis of the frequency fluctuation and correlation time of the model is provided. The peak amplitude and width in the IR spectra calculated by the GLE with the harmonic quantum correction are shown to agree well with those by the QME though the vibrational frequency is generally overestimated. The GWP method improves the peak position by considering the zero-point energy and the anharmonicity although the red-shift slightly overshoots the QME reference. The GWP also yields an extra peak in the higher-frequency region than the fundamental transition arising from the difference frequency of the center and width oscillations of a wavepacket. The SFM approach underestimates the peak amplitude of the IR spectra but well reproduces the peak width. Further, the dependence of the VER rate on the strength of an excitation pulse is discussed. © 2011 American Institute of Physics

  20. 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.

  1. Atomic Force Microscopy-Infrared Spectroscopy of Individual Atmospheric Aerosol Particles: Subdiffraction Limit Vibrational Spectroscopy and Morphological Analysis.

    PubMed

    Bondy, Amy L; Kirpes, Rachel M; Merzel, Rachel L; Pratt, Kerri A; Banaszak Holl, Mark M; Ault, Andrew P

    2017-09-05

    Chemical analysis of atmospheric aerosols is an analytical challenge, as aerosol particles are complex chemical mixtures that can contain hundreds to thousands of species in attoliter volumes at the most abundant sizes in the atmosphere (∼100 nm). These particles have global impacts on climate and health, but there are few methods available that combine imaging and the detailed molecular information from vibrational spectroscopy for individual particles <500 nm. Herein, we show the first application of atomic force microscopy with infrared spectroscopy (AFM-IR) to detect trace organic and inorganic species and probe intraparticle chemical variation in individual particles down to 150 nm. By detecting photothermal expansion at frequencies where particle species absorb IR photons from a tunable laser, AFM-IR can study particles smaller than the optical diffraction limit. Combining strengths of AFM (ambient pressure, height, morphology, and phase measurements) with photothermal IR spectroscopy, the potential of AFM-IR is shown for a diverse set of single-component particles, liquid-liquid phase separated particles (core-shell morphology), and ambient atmospheric particles. The spectra from atmospheric model systems (ammonium sulfate, sodium nitrate, succinic acid, and sucrose) had clearly identifiable features that correlate with absorption frequencies for infrared-active modes. Additionally, molecular information was obtained with <100 nm spatial resolution for phase separated particles with a ∼150 nm shell and 300 nm core. The subdiffraction limit capability of AFM-IR has the potential to advance understanding of particle impacts on climate and health by improving analytical capabilities to study water uptake, heterogeneous reactivity, and viscosity.

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

    PubMed

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

    2016-04-12

    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.

  3. 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

  4. 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

  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 spectroscopy studies of structural changes in lignin under microwave irradiation

    NASA Astrophysics Data System (ADS)

    Arapova, O. V.; Bondarenko, G. N.; Chistyakov, A. V.; Tsodikov, M. V.

    2017-09-01

    Structural changes that occur in lignin surface-modified with nickel nanoparticles during microwave- assisted dry reforming (DR) are studied via vibrational spectroscopy. IR spectroscopy reveals that the nickel deposition has a considerable effect on the structural characteristics of lignin. It is found that nickel deposition from an acetate salt substantially reduces the intensity of absorption bands at 1700 cm-1. This finding suggests that Ni(2+) interacts mostly with formate groups, which are subsequently oxidized to carboxylate groups. It is shown that with the deposition of metallic nickel particles from a colloidal nickel solution in toluene prepared via metal vapor synthesis, the nickel particles do not interact with the surface functional groups of the lignin. Deep conversion of an organic mass of lignin by DR to form synthesis gas reduces the intensity of the absorption bands of the identified functional groups and raises the intensity of the absorption bands of the aromatic rings. Raman spectroscopy shows that during lignin conversion, the aromatic rings condense partially to form amorphized graphite. In operando studies reveal that the DR of nickel-modified lignin heated to 200-400°C results in the isolation of vanillic oxygenates that are probably intermediate products of reforming.

  7. Sample presentation, sources of error and future perspectives on the application of vibrational spectroscopy in the wine industry.

    PubMed

    Cozzolino, Daniel

    2015-03-30

    Vibrational spectroscopy encompasses a number of techniques and methods including ultra-violet, visible, Fourier transform infrared or mid infrared, near infrared and Raman spectroscopy. The use and application of spectroscopy generates spectra containing hundreds of variables (absorbances at each wavenumbers or wavelengths), resulting in the production of large data sets representing the chemical and biochemical wine fingerprint. Multivariate data analysis techniques are then required to handle the large amount of data generated in order to interpret the spectra in a meaningful way in order to develop a specific application. This paper focuses on the developments of sample presentation and main sources of error when vibrational spectroscopy methods are applied in wine analysis. Recent and novel applications will be discussed as examples of these developments. © 2014 Society of Chemical Industry.

  8. 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

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

    PubMed

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

    2014-05-15

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

  10. 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.

  11. 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.

  12. 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.

  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. 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.

  15. 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.

  16. 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

  17. 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.

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

    PubMed

    Frost, Ray L; Xi, Yunfei

    2013-02-15

    Henmilite is a triclinic mineral with the crystal structure consisting of isolated B(OH)(4) tetrahedra, planar Cu(OH)(4) groups and Ca(OH)(3) polyhedra. The structure can also be viewed as having dimers of Ca polyhedra connected to each other through 2B(OH) tetrahedra to form chains parallel to the C axis. The structure of the mineral has been assessed by the combination of Raman and infrared spectra. Raman bands at 902, 922, 951, and 984 cm(-1) and infrared bands at 912, 955 and 998 cm(-1) are assigned to stretching vibrations of tetragonal boron. The Raman band at 758 cm(-1) is assigned to the symmetric stretching mode of tetrahedral boron. The series of bands in the 400-600 cm(-1) region are due to the out-of-plane bending modes of tetrahedral boron. Two very sharp Raman bands are observed at 3559 and 3609 cm(-1). Two infrared bands are found at 3558 and 3607 cm(-1). These bands are assigned to the OH stretching vibrations of the OH units in henmilite. A series of Raman bands are observed at 3195, 3269, 3328, 3396, 3424 and 3501 cm(-1) are assigned to water stretching modes. Infrared spectroscopy also identified water and OH units in the henmilite structure. It is proposed that water is involved in the structure of henmilite. Hydrogen bond distances based upon the OH stretching vibrations using a Libowitzky equation were calculated. The number and variation of water hydrogen bond distances are important for the stability off the mineral. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Excitonic, vibrational, and van der Waals interactions in electron energy loss spectroscopy.

    PubMed

    Mizoguchi, T; Miyata, T; Olovsson, W

    2017-09-01

    The pioneer, Ondrej L. Krivanek, and his collaborators have opened up many frontiers for the electron energy loss spectroscopy (EELS), and they have demonstrated new potentials of the EELS method for investigating materials. Here, inspired by those achievements, we show further potentials of EELS based on the results of theoretical calculations, that is excitonic and van der Waals (vdW) interactions, as well as vibrational information of materials. Concerning the excitonic interactions, we highlight the importance of the two-particle calculation to reproduce the low energy-loss near-edge structure (ELNES), the Na-L2,3 edge of NaI and the Li-K edge of LiCl and LiFePO4. Furthermore, an unusually strong excitonic interaction at the O-K edge of perovskite oxides, SrTiO3 and LaAlO3, is shown. The effect of the vdW interaction in the ELNES is also investigated, and we observe that the magnitude of the vdW effect is approximately 0.1eV in the case of the ELNES from a solid and liquid, whereas its effect is almost negligible in the case of the ELNES from the gaseous phase owing to the long inter-molecular distance. In addition to the "static" information, the influence of the "dynamic" behavior of atoms in materials to EELS is also investigated. We show that measurements of the infrared spectrum are possible by using a modern monochromator system. Furthermore, an estimation of the atomic vibration in core-loss ELNES is also presented. We show the acquisition of vibrational information using the ELNES of liquid methanol and acetic acid, solid Al2O3, and oxygen gas. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. 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.

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

    PubMed

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

    2014-03-14

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

  2. Water induced relaxation of a degenerate vibration of guanidinium using 2D IR echo spectroscopy

    PubMed Central

    Vorobyev, Dmitriy Yu.; Kuo, Chun-Hung; Kuroda, Daniel G.; Scott, J. Nathan; Vanderkooi, Jane M.; Hochstrasser, Robin M.

    2010-01-01

    The nearly degenerate asymmetric stretch vibrations near 1600 cm−1 of the guanidinium cation in D-glycerol/D2O mixtures having different viscosity were studied by 2D IR photon echo spectroscopy. The polarization dependent photon echo signal shows two separate frequency distributions in the 2D spectrum in D2O, even though only one band is evident from inspection of the linear FTIR spectrum. The split components are more clearly seen at higher viscosity. The interactions with solvent induce energy transfer between the degenerate component modes on the time scale of 0.5 ps. The energy transfer between modes is directly observed in 2D IR and distinguished by the waiting time dependence of the cross peaks from the transfers between threefold symmetric configurations of the distorted ion and solvent. The 2D IR analysis carried out for various polarization conditions required specification of frequency-frequency auto- and cross- correlation functions for the degenerate components. PMID:20143800

  3. Microsecond kinetics of photocatalytic oxidation on Pt/TiO 2 traced by vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Yamakata, Akira; Ishibashi, Taka-aki; Onishi, Hiroshi

    2003-07-01

    2-Propanol oxidation to acetone was examined by time-resolved infrared spectroscopy on a Pt/TiO 2 photocatalyst in an aqueous solution. Holes generated by the band-gap excitation were found to attach to the adsorbed reactant within the first 0.5 μs. Subsequent rearrangement of atoms in the hole-attached reactant was observed on a series of time-resolved vibrational spectra. The CO stretching band of a reaction intermediate to be converted to acetone appeared at time delays of 0-20 μs. The observed wavenumber of the intermediate, 1640 cm -1, was compared with theoretically predicted CO stretching frequencies of possible species. An acceptable agreement was obtained with the anion radical of acetone adsorbed on the catalyst.

  4. 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.

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

    PubMed

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

    2015-04-21

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

  6. 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.

  7. 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.

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

    PubMed

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

    2016-10-01

    Understanding the role of water, hydrate and hydroxyl species on nanoparticle surfaces and interfaces is very important in both physical and life sciences. Detecting the presence of oxygen-hydrogen species with nanometer resolution is extremely challenging at present. Here we show that the recently developed vibrational electron energy-loss spectroscopy using subnanometer focused electron beams can be employed to spectroscopically identify the local presence and variation of OH species on nanoscale surfaces. The hydrogen-oxygen fingerprint can be correlated with highly localized structural and morphological information obtained from electron imaging. Moreover, the current approach exploits the aloof beam mode of spectral acquisition which does not require direct electron irradiation of the sample thus greatly reducing beam damage to the OH bond. These findings open the door for using electron microscopy to probe local hydroxyl and hydrate species on nanoscale organic and inorganic structures. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    PubMed

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

    2015-10-14

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

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

    SciTech Connect

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

    2014-03-14

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

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

    NASA Astrophysics Data System (ADS)

    Zhang, Miao; Frei, Heinz

    2017-05-01

    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.

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

    SciTech Connect

    Khachatrian, Ani; Dagdigian, Paul J.

    2010-05-01

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

  13. 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.

  14. 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.

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

    PubMed Central

    Tsen, KT; Dykeman, Eric C; Sankey, Otto F; Lin, Nien-Tsung; Tsen, Shaw-Wei D; Kiang, Juliann G

    2006-01-01

    Background Recently, a technique which departs radically from conventional approaches has been proposed. This novel technique utilizes biological objects such as viruses as nano-templates for the fabrication of nanostructure elements. For example, rod-shaped viruses such as the M13 phage and tobacco mosaic virus have been successfully used as biological templates for the synthesis of semiconductor and metallic nanowires. Results and discussion Low wave number (≤ 20 cm-1) acoustic vibrations of the M13 phage have been studied using Raman spectroscopy. The experimental results are compared with theoretical calculations based on an elastic continuum model and appropriate Raman selection rules derived from a bond polarizability model. The observed Raman mode has been shown to belong to one of the Raman-active axial torsion modes of the M13 phage protein coat. Conclusion It is expected that the detection and characterization of this low frequency vibrational mode can be used for applications in nanotechnology such as for monitoring the process of virus functionalization and self-assembly. For example, the differences in Raman spectra can be used to monitor the coating of virus with some other materials and nano-assembly process, such as attaching a carbon nanotube or quantum dots. PMID:16995944

  16. Photo-vibrational spectroscopy using quantum cascade laser and laser Doppler vibrometer

    NASA Astrophysics Data System (ADS)

    Liu, Huan; Hu, Qi; Xie, Jiecheng; Fu, Yu

    2017-06-01

    Photoacoustic/photothermal spectroscopy is an established technique for detection of chemicals and explosives. However, prior sample preparation is required and the analysis is conducted in a sealed space with a high-sensitivity sensor coupled with a lock-in amplifier, limiting the technique to applications in a controllable laboratory environment. Hence, 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 were excited by an intensity-modulated quantum cascade laser (QCL), while a laser Doppler vibrometer (LDV) 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 in short and long standoff distances demonstrated that the LDV is a capable sensor for chemical detection in an open environment.

  17. 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°.

  18. Thz Spectroscopy and DFT Modeling of Intermolecular Vibrations in Hydrophobic Amino Acids

    NASA Astrophysics Data System (ADS)

    Williams, michael R. C.; Aschaffenburg, Daniel J.; Schmuttenmaer, Charles A.

    2013-06-01

    Vibrations that involve intermolecular displacements occur in molecular crystals at frequencies in the 0.5-5 THz range (˜15-165 cm^{-1}), and these motions are direct indicators of the interaction potential between the molecules. The intermolecular potential energy surface of crystalline hydrophobic amino acids is inherently interesting simply because of the wide variety of forces (electrostatic, dipole-dipole, hydrogen-bonding, van der Waals) that are present. Furthermore, an understanding of these particular interactions is immediately relevant to important topics like protein conformation and pharmaceutical polymorphism. We measured the low-frequency absorption spectra of several polycrystalline hydrophobic amino acids using THz time-domain spectroscopy, and in addition we carried out DFT calculations using periodic boundary conditions and an exchange-correlation functional that accounts for van der Waals dispersion forces. We chose to investigate a series of similar amino acids with closely analogous unit cells (leucine, isoleucine, and allo-isoleucine, in racemic or pseudo-racemic mixtures). This allows us to consider trends in the vibrational spectra as a function of small changes in molecular arrangement and/or crystal geometry. In this way, we gain confidence that peak assignments are not based on serendipitous similarities between calculated and observed features.

  19. 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.

  20. 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

  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. 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.

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

    ERIC Educational Resources Information Center

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

    2004-01-01

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

  4. 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.

  5. 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.

  6. 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

  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. Biomedical Tissue Phantoms with Controlled Geometric and Optical Properties for Raman Spectroscopy and Tomography

    PubMed Central

    Esmonde-White, Francis W.L.; Esmonde-White, Karen A.; Kole, Matthew R.; Goldstein, Steven A.; Roessler, Blake J.; Morris, Michael D.

    2012-01-01

    To support the translation of Raman spectroscopy into clinical applications, synthetic models are needed to accurately test, optimize and validate prototype fiber optic instrumentation. Synthetic models (also called tissue phantoms) are widely used for developing and testing optical instrumentation for diffuse reflectance, fluorescence, and Raman spectroscopies. While existing tissue phantoms accurately model tissue optical scattering and absorption, they do not typically model the anatomic shapes and chemical composition of tissue. Because Raman spectroscopy is sensitive to molecular composition, Raman tissue phantoms should also approximate the bulk tissue composition. We describe the fabrication and characterization of tissue phantoms for Raman tomography and spectroscopy. These phantoms have controlled chemical and optical properties, and also multilayer morphologies which approximate the appropriate anatomic shapes. Tissue phantoms were fabricated to support on-going Raman studies by simulating human wrist and rat leg. Surface meshes (triangle patch models) were generated from computed tomography (CT) images of a human arm and rat leg. Rapid prototyping was used to print mold templates with complex geometric patterns. Plastic casting techniques used for movie special effects were adapted to fabricate molds from the rapid prototypes, and finally to cast multilayer gelatin tissue phantoms. The gelatin base was enriched with additives to model the approximate chemistry and optical properties of individual tissue layers. Additional studies were performed to determine optimal casting conditions, phantom stability, layer delamination and chemical diffusion between layers. Recovery of diffuse reflectance and Raman spectra in tissue phantoms varied with probe placement. These phantoms enable optimization of probe placement for human or rat studies. These multilayer tissue phantoms with complex geometries are shown to be stable, with minimal layer delamination and

  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. 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. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. 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.

  13. Terahertz vibration-rotation-tunneling spectroscopy of the ammonia dimer. II. A-E states of an out-of-plane vibration and an in-plane vibration.

    PubMed

    Lin, Wei; Han, Jia-Xiang; Takahashi, Lynelle K; Loeser, Jennifer G; Saykally, Richard J

    2007-10-04

    Terahertz vibration-rotation-tunneling transitions have been measured between ca. 78.5 and 91.9 cm-1, and assigned to A-E (ortho-para) combinations of NH3 monomer states. The spectrum is complicated by inversion splittings that correlate to E symmetry monomer rovibronic states. Twenty progressions have been assigned to six excited states involving an out-of-plane vibration and an in-plane intermolecular vibration. The quality of the fit was affected by strong Coriolis interactions among these states and possibly an additional K = 2 state that was not explicitly observed in the data.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2006-05-01

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

  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 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.

  20. 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.

  1. Multi-spectral fiber spectroscopy in 0,4-16μm range for biomedical applications(Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Artyushenko, Viacheslav

    2017-02-01

    Various biomedical applications of fiber optics in a broad spectral range 0,4-16μm span from endoscopic imaging and Photo Dynamic Diagnostics (PDD) to laser power delivery for minimal invasive laser surgery, tissue coagulation and welding, Photo Dynamic Therapy (PDT), etc. Present review will highlight the latest results in advanced fiber solutions for a precise tissue diagnostics and control of some therapy methods - for so called "theranostic". Spectral fiber sensing for label free analysis of tissue composition helps to differentiate malignant and normal tissue to secure minimal invasive, but complete tumor removal or treatment. All key methods of Raman, fluorescence, diffuse reflection & MIR-absorption spectroscopy will be compared when used for the same spot of tissue - to select the most specific, sensitive and accurate method or to combine them for the synergy enhanced effect. The most informative spectral features for distinct organs/ tumor can be used to design special fiber sensors to be developed for portable and low cost applications with modern IT-features. Examples of multi-spectral tissue diagnostics promising for the future clinical applications will be presented to enable reduced mortality from cancer in the future. Translation of described methods into clinical practice will be discussed in comparison with the other method of optical diagnostics which should enhance modern medicine by less invasive, more precise and more effective methods of therapy to be fused with in-vivo diagnostics sensors & systems.

  2. Vibrational spectroscopy as a rapid quality control method for Melaleuca alternifolia cheel (tea tree oil).

    PubMed

    Tankeu, Sidonie; Vermaak, Ilze; Kamatou, Guy; Viljoen, Alvaro

    2014-01-01

    Tea tree oil (TTO) is an important commercial oil which has found application in the flavour, fragrance and cosmetic industries. The quality is determined by the relative concentration of its major constituents: 1,8-cineole, terpinen-4-ol, α-terpineol, α-terpinene, terpinolene, γ-terpinene and limonene. Gas chromatography coupled to mass spectrometry (GC-MS) is traditionally used for qualitative and quantitative analyses but is expensive and time consuming. To evaluate the use of vibrational spectroscopy in tandem with chemometric data analysis as a fast and low-cost alternative method for the quality control of TTO. Spectral data were acquired in both the mid-infrared (MIR) and near infrared (NIR) wavelength regions and reference data obtained using GC-MS with flame ionisation detection (FID). Principal component analysis (PCA) was used to investigate the data by observing clustering and identifying outliers. Partial least squares (PLS) multivariate calibration models were constructed for the quantification of the seven major constituents. High correlation coefficients (R(2) ) of ≥ 0.75 were obtained for the seven major compounds and 1,8-cineole showed the best correlation coefficients for both MIR and NIR data (R(2)  = 0.97 and 0.95, respectively). Low values were obtained for the root mean square error of estimation (RMSEE) and root mean square error of prediction (RMSEP) values thereby confirming accuracy. The accurate prediction of the external dataset after introduction into the models confirmed that both MIR and NIR spectroscopy are valuable methods for quantification of the major compounds of TTO when compared with the reference data obtained using GC-MS. Copyright © 2013 John Wiley & Sons, Ltd. Copyright © 2013 John Wiley & Sons, Ltd.

  3. 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.

  4. Applications of resonance ionization spectroscopy for semiconductor, environmental and biomedical analysis, and for DNA sequencing

    NASA Astrophysics Data System (ADS)

    Arlinghaus, Heinrich F.; Spaar, M. T.; Thonnard, N.; McMahon, A. W.; Jacobson, K. Bruce

    1991-07-01

    Resonance Ionization Spectroscopy (RIS), an analytical technique with extremely high element specificity and sensitivity, is becoming recognized as an emerging field with wide applications. The sensitivity and selectivity of the RIS process is especially valuable for ultra-trace element analysis in semiconductor, geological, biological, and environmental samples, where the complexity of the matrix is frequently a serious source of interference. Using either Sputter-Initiated RIS (SIRIS) or Laser Atomization RIS (LARIS), it is possible to localize with high spatial resolution ultra-trace concentrations of a selected element to the sub-parts per billion level. The authors describe the implementation of RIS to solve a number of analysis problems and illustrate its salient characteristic with data from a wide range of applications. Results presented will include (a) concentration plots of ultra- trace elements in semiconductors and biological matrices, (b) characterization of dopants as a function of depth in semiconductors, (c) spatial distribution of natural uranium in bone and bone marrow, and (d) localization of stable isotope-labeled DNA in the development of faster DNA sequencing methods. The practical capabilities of SIRIS/LARIS to determine trace elements as a function of depth and lateral position in semiconductors and biological matrices are discussed.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

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

    PubMed

    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

    2015-08-10

    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 (57)Fe-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)(57)Fe plane was studied using (57)Fe-specific nuclear resonance vibrational spectroscopy and density functional theory (DFT) calculations. On Ni(μ-D)(57)Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe-CO/CN bands. Spectra have been interpreted by comparison with Ni(μ-H/D)(57)Fe enzyme mimics [(dppe)Ni(μ-pdt)(μ-H/D)(57)Fe(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.

  12. 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.

  13. 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

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

    NASA Astrophysics Data System (ADS)

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

    2009-06-01

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

  15. 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.

  16. 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.

  17. 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

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Conboy, John

    2010-03-01

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

  20. 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.

  1. 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.

  2. 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.

  3. Crystal growth, crystal structure, vibrational spectroscopy, linear and nonlinear optical properties of guanidinium phosphates

    NASA Astrophysics Data System (ADS)

    Němec, Ivan; Matulková, Irena; Held, Peter; Kroupa, Jan; Němec, Petr; Li, Dongxu; Bohatý, Ladislav; Becker, Petra

    2017-07-01

    Of the three guanidinium phosphates GuH2PO4 (space group P21/c), Gu2HPO4·H2O (space group P 4 bar 21 c) and Gu3PO4· 3/2 H2O (space group Cc) crystal structures and a vibrational spectroscopy study are presented. Large single crystals of GuH2PO4 and Gu2HPO4·H2O are grown. Refractive indices and their dispersion in the wavelength range 365 nm - 1083 nm are determined and used for the analysis of phase matching conditions for collinear SHG in the case of the non-centrosymmetric crystals of Gu2HPO4·H2O. The crystals are not phase-matchable within their transmission range. Both independent components of the SHG tensor of Gu2HPO4·H2O, determined by the Maker fringe method, are given, with d14 = 0.23 pm/V and d36 = 0.22 pm/V. In addition, the thermal stability and the anisotropy of thermal expansion of GuH2PO4 and Gu2HPO4·H2O is reported.

  4. Structure and Dynamics of Urea/Water Mixtures Investigated by Vibrational Spectroscopy and Molecular Dynamics Simulation

    PubMed Central

    Carr, J. K.; Buchanan, L. E.; Schmidt, J. R.; Zanni, M. T.; Skinner, J. L.

    2013-01-01

    Urea/water is an archetypical “biological” mixture, and is especially well known for its relevance to protein thermodynamics, as urea acts as a protein denaturant at high concentration. This behavior has given rise to an extended debate concerning urea’s influence on water structure. Based on a variety of methods and of definitions of water structure, urea has been variously described as a structure-breaker, a structure-maker, or as remarkably neutral towards water. Because of its sensitivity to microscopic structure and dynamics, vibrational spectroscopy can help resolve these debates. We report experimental and theoretical spectroscopic results for the OD stretch of HOD/H2O/urea mixtures (linear IR, 2DIR, and pump-probe anisotropy decay) and for the CO stretch of urea-D4/D2O mixtures (linear IR only). Theoretical results are obtained using existing approaches for water, and a modification of a frequency map developed for acetamide. All absorption spectra are remarkably insensitive to urea concentration, consistent with the idea that urea only very weakly perturbs water structure. Both this work and experiments by Rezus and Bakker, however, show that water’s rotational dynamics are slowed down by urea. Analysis of the simulations casts doubt on the suggestion that urea immobilizes particular doubly hydrogen bonded water molecules. PMID:23841646

  5. Structure and orientation of interfacial proteins determined by sum frequency generation vibrational spectroscopy: method and application.

    PubMed

    Ye, Shuji; Wei, Feng; Li, Hongchun; Tian, Kangzhen; Luo, Yi

    2013-01-01

    In situ and real-time characterization of molecular structures and orientation of proteins at interfaces is essential to understand the nature of interfacial protein interaction. Such work will undoubtedly provide important clues to control biointerface in a desired manner. Sum frequency generation vibrational spectroscopy (SFG-VS) has been demonstrated to be a powerful technique to study the interfacial structures and interactions at the molecular level. This paper first systematically introduced the methods for the calculation of the Raman polarizability tensor, infrared transition dipole moment, and SFG molecular hyperpolarizability tensor elements of proteins/peptides with the secondary structures of α-helix, 310-helix, antiparallel β-sheet, and parallel β-sheet, as well as the methodology to determine the orientation of interfacial protein secondary structures using SFG amide I spectra. After that, recent progresses on the determination of protein structure and orientation at different interfaces by SFG-VS were then reviewed, which provides a molecular-level understanding of the structures and interactions of interfacial proteins, specially understanding the nature of driving force behind such interactions. Although this review has focused on analysis of amide I spectra, it will be expected to offer a basic idea for the spectral analysis of amide III SFG signals and other complicated molecular systems such as RNA and DNA. Copyright © 2013 Elsevier Inc. All rights reserved.

  6. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

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

    PubMed

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

    2015-09-10

    Since the last decade, more and more Active Pharmaceutical Ingredient (API) candidates have poor water solubility inducing low bioavailability. These molecules belong to the Biopharmaceutical Classification System (BCS) classes II and IV. Thanks to Hot-Melt Extrusion (HME), it is possible to incorporate these candidates in pharmaceutical solid forms. Indeed, HME increases the solubility and the bioavailability of these drugs by encompassing them in a polymeric carrier and by forming solid dispersions. Moreover, in 2004, the FDA's guidance initiative promoted the usefulness of Process Analytical Technology (PAT) tools when developing a manufacturing process. Indeed, the main objective when developing a new pharmaceutical process is the product quality throughout the production chain. The trend is to follow this parameter in real-time in order to react immediately when there is a bias. Vibrational spectroscopic techniques, NIR and Raman, are useful to analyze processes in-line. Moreover, off-line Raman microspectroscopy is more and more used when developing new pharmaceutical processes or when analyzing optimized ones by combining the advantages of Raman spectroscopy and imaging. It is an interesting tool for homogeneity and spatial distribution studies. This review treats about spectroscopic techniques analyzing a HME process, as well off-line as in-line, presenting their advantages and their complementarities. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. Terahertz vibration-rotation-tunneling spectroscopy of the ammonia dimer: characterization of an out of plane vibration.

    PubMed

    Lin, Wei; Han, Jia-Xiang; Takahashi, Lynelle K; Loeser, Jennifer G; Saykally, Richard J

    2006-07-06

    The terahertz vibration-rotation-tunneling (VRT) spectrum of the ammonia dimer (NH(3))(2) has been measured between ca. 78.5 and 91.9 cm(-1). The dipole-allowed transitions are separated into three groups that correspond to the 3-fold internal rotation of the NH(3) subunits. Transitions have been assigned for VRT states of the A-A (ortho-ortho) combinations of NH(3) monomer states. The spectrum is further complicated by strong Coriolis interactions. K = 0 <-- 0, K = 1 <-- 0, K = 0 <-- 1, and K = 1 <-- 1 progressions have been assigned. The band origins, rotational constants, asymmetry doubling, centrifugal distortion, and Coriolis coupling constant have been determined from the fit to an effective Hamiltonian. These VRT transitions are tentatively assigned to an out of plane vibration with a K = 0 state at 89.141305(47) cm(-1), and a K = 1 state at 86.77785(9) cm(-1).

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

    DTIC Science & Technology

    1992-05-29

    excited electronic potential surfaces. Pyrazine , for example, has been studied extensively using rotationally resolved electronic spectroscopy, providing...parameters were varied to optimize the fit of the calculated spectrum to the experimental spectrum. A modified simulated annealing algorithm was employed... simulate vibrational mode coupling from a degenerate bright state to a split dark state in 15 ==..==, .asl lailml t ia m m . M Mi an effort to reproduce

  19. 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.

  20. 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

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

    SciTech Connect

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

    2014-07-14

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

  2. 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.

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

    SciTech Connect

    Zhu, Guo-Zhu; Wang, Lai-Sheng

    2015-12-14

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

  4. 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.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

    Mo, Yuxiang

    2016-06-01

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

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

    NASA Astrophysics Data System (ADS)

    Saurabh, Prasoon; Mukamel, Shaul

    2016-03-01

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

  8. Vibrational spectroscopy--a powerful tool for the rapid identification of microbial cells at the single-cell level.

    PubMed

    Harz, M; Rösch, P; Popp, J

    2009-02-01

    Rapid microbial detection and identification with a high grade of sensitivity and selectivity is a great and challenging issue in many fields, primarily in clinical diagnosis, pharmaceutical, or food processing technology. The tedious and time-consuming processes of current microbiological approaches call for faster ideally on-line identification techniques. The vibrational spectroscopic techniques IR absorption and Raman spectroscopy are noninvasive methods yielding molecular fingerprint information; thus, allowing for a fast and reliable analysis of complex biological systems such as bacterial or yeast cells. In this short review, we discuss recent vibrational spectroscopic advances in microbial identification of yeast and bacterial cells for bulk environment and single-cell analysis. IR absorption spectroscopy enables a bulk analysis whereas micro-Raman-spectroscopy with excitation in the near infrared or visible range has the potential for the analysis of single bacterial and yeast cells. The inherently weak Raman signal can be increased up to several orders of magnitude by applying Raman signal enhancement methods such as UV-resonance Raman spectroscopy with excitation in the deep UV region, surface enhanced Raman scattering, or tip-enhanced Raman scattering. Copyright 2008 International Society for Advancement of Cytometry

  9. 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.

  10. Effect of Ca(2+) to Sphingomyelin Investigated by Sum Frequency Generation Vibrational Spectroscopy.

    PubMed

    Feng, Rong-Juan; Lin, Lu; Li, Yi-Yi; Liu, Ming-Hua; Guo, Yuan; Zhang, Zhen

    2017-05-23

    The interactions between Ca(2+) ions and sphingomyelin play crucial roles in a wide range of cellular activities. However, little is known about the molecular details of the interactions at interfaces. In this work, we investigated the interactions between Ca(2+) ions and egg sphingomyelin (ESM) Langmuir monolayers at the air/water interface by subwavenumber high-resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS). We show that Ca(2+) ions can induce ordering of the acyl chains in the ESM monolayer. An analysis of the one alkyl-chain-deuterated ESM revealed that the Ca(2+) ions do not affect the N-linked saturated fatty acid chain, although they make the sphingosine backbone become ordered. Further analysis of the SFG-VS spectra shows that the interactions between ESM and Ca(2+) ions make the orientation of the methyl group at the end of sphingosine backbone change from pointing downward to pointing upward. Moreover, a large blue shift of the phosphate group at the CaCl2 solution interface indicates, to our knowledge, new cation binding modes. Such binding causes the phosphate moiety to dehydrate, resulting in the conformation change of the phosphate moiety. Based on these results, we propose the molecular mechanism that Ca(2+) ions can bind to the phosphate group and subsequently destroy the intramolecular hydrogen bond between the 3-hydroxyl group and the phosphate oxygen, which results in an ordering change of the sphingosine backbone. These findings illustrate the potential application of HR-BB-SFG-VS to investigate lipid-cation interactions and the calcium channel modulated by lipid domain formation through slight structural changes in the membrane lipid. It will also shed light on the interactions of complex molecules at surfaces and interfaces. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

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

  12. Vibrational spectroscopy of reduced ReI complexes of 1,10-phenanthroline and substituted analogues.

    PubMed

    Howell, Sarah L; Gordon, Keith C

    2006-04-13

    IR spectroscopy in concert with DFT calculations and resonance Raman spectroelectrochemistry has been used to identify the molecular orbital nature of the singly occupied molecular orbital (SOMO) in reduced [Re(CO)(3)Cl(L)] and [Re(CO)(3)(4-Mepy)(L)](+) complexes, where L = 1,10-phenanthroline and its 4,7-diphenyl- and 3,4,7,8-tetramethyl-substituted analogues. The SOMO of each reduced species considered was found to be of b(1) symmetry, rather than the close lying orbital of a(2) symmetry (within a C(2)(v)() symmetry description of the phenanthroline moiety). This was deduced in a number of ways. First, the average carbonyl band force constants (Deltak(av) = k(av){reduced complex} - k(av){parent complex}) range from -57 to -41 N m(-1) for the series of compounds studied. The value of Deltak(av) relates to the extent of orbital overlap between the ligand MO and the metal dpi MO. These values are consistent with population of a b(1) MO because the wave function amplitude at the chelating nitrogens for this MO is significantly greater than that for a(2) MO. Second, calculations on singly reduced [Re(CO)(3)(4-Mepy)(phen)](+) and [Re(CO)(3)(4-Mepy)(tem)](+) predict population of a b(2) SOMO. The spectra predicted for these species are in close agreement with the vibrational spectroscopic data; for the IR data the shifts in the CO bands are predicted to 6 cm(-1) and the mean absolute deviation between calculated and measured Raman bands was found to be 10 cm(-1).

  13. 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.

  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. Vibrations of pyrazine and its ion as studied by threshold ionization spectroscopy

    SciTech Connect

    Zhu, L.; Johnson, P. )

    1993-08-15

    The pump--probe threshold ionization photoelectron spectra of pyrazine have been recorded using nine different vibrations of [ital S][sub 1] as intermediate resonances. The extensive vibrational structure in these spectra of the ionic ground state have enabled the measurement of 12 of its vibrational frequencies and their assignments. Three new vibrational assignments of [ital S][sub 1] are also made. MP2/6-31G* calculations of the vibrational frequencies of the neutral ground, [ital S][sub 1], and the ionic ground state are compared with the experimental values, finding that certain vibrations of [ital S][sub 1] and the ion which engage in extensive vibronic coupling are not properly determined by the calculated force field. Most vibrational frequencies are accurately reproduced, however. Variations in the complexity of the threshold ionization spectra with the level of [ital S][sub 1] excitation indicate that internal vibrational relaxation is taking place at a very low energy in that state, possibly involving vibronic interactions and mixing with the triplet manifold.

  17. Auditory membrane vibrations: measurements at sub-angstrom levels by optical heterodyne spectroscopy.

    PubMed

    Dragsten, P R; Webb, W W; Paton, J A; Capranica, R R

    1974-07-05

    We describe an optical technique for measurement of mechanical vibrations in the auditory organs of living animals. The technique uses light scattered from the vibrating structure and offers several new advantages. Better than 1 angstrom sensitivity, 10 micrometers spatial resolution, and > 70 decibels dynamic range are achieved. Illustrative measurements of the mechanical response of the tympanic membrane of crickets (Gryllidae) are reported.

  18. 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.

  19. Semi-quantitative prediction of a multiple API solid dosage form with a combination of vibrational spectroscopy methods.

    PubMed

    Hertrampf, A; Sousa, R M; Menezes, J C; Herdling, T

    2016-05-30

    Quality control (QC) in the pharmaceutical industry is a key activity in ensuring medicines have the required quality, safety and efficacy for their intended use. QC departments at pharmaceutical companies are responsible for all release testing of final products but also all incoming raw materials. Near-infrared spectroscopy (NIRS) and Raman spectroscopy are important techniques for fast and accurate identification and qualification of pharmaceutical samples. Tablets containing two different active pharmaceutical ingredients (API) [bisoprolol, hydrochlorothiazide] in different commercially available dosages were analysed using Raman- and NIR Spectroscopy. The goal was to define multivariate models based on each vibrational spectroscopy to discriminate between different dosages (identity) and predict their dosage (semi-quantitative). Furthermore the combination of spectroscopic techniques was investigated. Therefore, two different multiblock techniques based on PLS have been applied: multiblock PLS (MB-PLS) and sequential-orthogonalised PLS (SO-PLS). NIRS showed better results compared to Raman spectroscopy for both identification and quantitation. The multiblock techniques investigated showed that each spectroscopy contains information not present or captured with the other spectroscopic technique, thus demonstrating that there is a potential benefit in their combined use for both identification and quantitation purposes. Copyright © 2016 Elsevier B.V. All rights reserved.

  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. 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.

  3. 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.

  4. 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°.

  5. 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.

  6. 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].

  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. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Vibrational spectroscopy of the borate mineral chambersite MnB7O13Cl--implications for the molecular structure.

    PubMed

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

    2014-01-01

    Chambersite is a manganese borate mineral with formula: MnB7O13Cl and occurs as colorless crystals in the monoclinic pyramidal crystal system. Raman bands at 902, 920, 942 and 963 cm(-1) are assigned to the BO stretching vibration of the B7O13 units. Raman bands at 1027, 1045, 1056, 1075 and 1091 cm(-1) are attributed to the BCl in-plane bending modes. The intense infrared band at 866 cm(-1) is assigned to the trigonal borate stretching modes. The Raman band at 660 cm(-1) together with bands at 597, 642 679, 705 and 721 cm(-1) are assigned to the trigonal and tetrahedral borate bending modes. The molecular structure of a natural chambersite has been assessed using vibrational spectroscopy. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. Membrane orientation of MSI-78 measured by sum frequency generation vibrational spectroscopy.

    PubMed

    Yang, Pei; Ramamoorthy, Ayyalusamy; Chen, Zhan

    2011-06-21

    Antimicrobial peptides (AMPs) selectively disrupt bacterial cell membranes to kill bacteria whereas they either do not or weakly interact with mammalian cells. The orientations of AMPs in lipid bilayers mimicking bacterial and mammalian cell membranes are related to their antimicrobial activity and selectivity. To understand the role of AMP-lipid interactions in the functional properties of AMPs better, we determined the membrane orientation of an AMP (MSI-78 or pexiganan) in various model membranes using sum frequency generation (SFG) vibrational spectroscopy. A solid-supported single 1,2-dipalmitoyl-an-glycero-3-[phospho-rac-(1-glycerol)] (DPPG) bilayer or 1-palmitoyl-2-oleoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (POPG) bilayer was used as a model bacterial cell membrane. A supported 1,2-dipalmitoyl-an-glycero-3-phosphocholine (DPPC) bilayer or a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer was used as a model mammalian cell membrane. Our SFG results indicate that the helical MSI-78 molecules are associated with the bilayer surface with ∼70° deviation from the bilayer normal in the negatively charged gel-phase DPPG bilayer at 400 nM peptide concentration. However, when the concentration was increased to 600 nM, MSI-78 molecules changed their orientation to make a 25° tilt from the lipid bilayer normal whereas multiple orientations were observed for an even higher peptide concentration in agreement with toroidal-type pore formation as reported in a previous solid-state NMR study. In contrary, no interaction between MSI-78 and a zwitterionic DPPC bilayer was observed even at a much higher peptide concentration (∼12,000 nM). These results demonstrate that SFG can provide insights into the antibacterial activity and selectivity of MSI-78. Interestingly, the peptide exhibits a concentration-dependent membrane orientation in the lamellar-phase POPG bilayer and was also found to induce toroidal-type pore formation. The deduced lipid flip

  18. 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

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

    PubMed

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

    2002-09-25

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

  20. 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.

  1. A study of the glass transition of polypropylene surfaces by sum-frequency vibrational spectroscopy and scanning force microscopy

    NASA Astrophysics Data System (ADS)

    Gracias, D. H.; Zhang, D.; Lianos, L.; Ibach, W.; Shen, Y. R.; Somorjai, G. A.

    1999-07-01

    Sum-frequency generation (SFG) vibrational spectroscopy and scanning force microscopy (SFM) were used to probe structural changes of atactic polypropylene (APP) and isotactic polypropylene (IPP) surfaces in the glass transition. The results indicate that below the glass transition, the surface polymer chains are better oriented with the CH 2 groups pointing outward and the surface elastic modulus is higher. The SFG and SFM results correlate well in the transition towards the glass phase. No discernible difference between the glass transition temperatures of the bulk and surface was observed.

  2. 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.

  3. 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.

  4. 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.

  5. Vibrational spectroscopy of the basic copper phosphate minerals: pseudomalachite, ludjibaite and reichenbachite.

    PubMed

    Frost, Ray L; Kloprogge, Theo; Williams, Peter A; Martens, Wayde; Johnson, Therese E; Leverett, Peter

    2002-11-01

    The vibrational spectra of pseudomalachite, reichenbachite and ludjibaite have been obtained at 298 K using a combination of FTIR and Raman microscopy. The vibrational spectra of the minerals are different, in line with differences in crystal structure and composition. Some similarity in the Raman spectra of the three polymorphs pseudomalachite, reichenbachite and ludjibaite exists, particularly in the OH stretching region, but characteristic differences in the OH deformation regions are observed. Differences are also observed in the phosphate stretching and deformation regions.

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

    PubMed Central

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

    2010-01-01

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

  7. 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

  8. 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.

  9. 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.

  10. 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.

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

    PubMed

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

    2013-12-12

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

  12. 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.

  13. Ab Initio Vibrational Spectroscopy of cis- and trans-Formic Acid from a Global Potential Energy Surface.

    PubMed

    Tew, David P; Mizukami, Wataru

    2016-12-15

    A global analytic potential energy surface for the ro-vibrational dynamics of cis- and trans-formic acid is presented, constructed using LASSO-based regression to reproduce CCSD(T)(F12*)/cc-pVTZ-F12 energies. The fit is accurate to 0.25% has an RMS deviation from the ab initio data of 9 cm(-1) for the energy range 0-15000 cm(-1). Converged J = 0 vibrational eigenstates are reported, computed using vibrational configuration interaction with an internal coordinate path Hamiltonian for the torsional motion connecting the cis and trans rotamers. Methodological choices concerning the appropriate definitions of the curvilinear and diabatic bath coordinates are discussed. The zero point of the cis rotamer is 1412 cm(-1) above that of the trans, which lies at 7354 cm(-1). The computed fundamentals match the bands recorded from gas-phase IR spectroscopy with an RMSD of only 3 cm(-1). A fresh assignment of the overtone spectra of both the cis and trans rotamers is presented for the energy range 0-4720 cm(-1), where 14 out of the 51 bands are reassigned on the basis of the VCI calculations.

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

    NASA Astrophysics Data System (ADS)

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

    2011-08-01

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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Capturing inhomogeneous broadening of the -CN stretch vibration in a Langmuir monolayer with high-resolution spectra and ultrafast vibrational dynamics in sum-frequency generation vibrational spectroscopy (SFG-VS)

    NASA Astrophysics Data System (ADS)

    Velarde, Luis; Wang, Hong-fei

    2013-08-01

    While in principle the frequency-domain and time-domain spectroscopic measurements should generate identical information for a given molecular system, the inhomogeneous character of surface vibrations in sum-frequency generation vibrational spectroscopy (SFG-VS) studies has only been studied with time-domain SFG-VS by mapping the decay of the vibrational polarization using ultrafast lasers, this due to the lack of SFG vibrational spectra with high enough spectral resolution and accurate enough lineshape. Here, with the recently developed high-resolution broadband SFG-VS (HR-BB-SFG-VS) technique, we show that the inhomogeneous lineshape can be obtained in the frequency-domain for the anchoring CN stretch of the 4-n-octyl-4'-cyanobiphenyl (8CB) Langmuir monolayer at the air-water interface, and that an excellent agreement with the time-domain SFG free-induction-decay can be established. We found that the 8CB CN stretch spectrum consists of a single peak centered at 2234.00 ± 0.01 cm-1 with a total linewidth of 10.9 ± 0.3 cm-1 at half maximum. The Lorentzian contribution accounts only for 4.7 ± 0.4 cm-1 to this width and the Gaussian (inhomogeneous) broadening for as much as 8.1 ± 0.2 cm-1. Polarization analysis of the -CN spectra showed that the -CN group is tilted 57° ± 2° from the surface normal. The large heterogeneity in the -CN spectrum is tentatively attributed to the -CN group interactions with the interfacial water molecules penetrated/accommodated into the 8CB monolayer, a unique phenomenon for the nCB Langmuir monolayers reported previously.

  1. Capturing inhomogeneous broadening of the -CN stretch vibration in a Langmuir monolayer with high-resolution spectra and ultrafast vibrational dynamics in sum-frequency generation vibrational spectroscopy (SFG-VS)

    SciTech Connect

    Velarde Ruiz Esparza, Luis A.; Wang, Hongfei

    2013-08-28

    Even though in principle the frequency-domain and time-domain spectroscopic measurement should generate identical information for a given molecular system, inhomogeneous character of surface vibrations in the sum-frequency generation vibrational spectroscopy (SFG-VS) studies has only been studied with the time-domain SFGVS by mapping the decay of the vibrational polarization using ultrafast lasers, due to the lack of SFG vibrational spectra with high enough spectral resolution and accurate enough line shape. Here with recently developed high-resolution broadband SFG-VS (HR-BB-SFG-VS) we show that the inhomogeneous line shape can be obtained in the frequency-domain, for the anchoring CN stretch of the 4-n-octyl-4'-cyanobiphenyl (8CB) Langmuir monolayer at the air-water interface, and that an excellent agreement with the time-domain SFG free-induction-decay (FID) results can be established. We found that the 8CB CN stretch spectrum consists of a single peak centered at 2234.00 + * 0.01 cm-1 with a total line width of 10.9 + - 0.3 cm-1 at half maximum. The Lorentzian contribution accounts only for 4:7 + -0:4 cm-1 to this width and the Gaussian (inhomogeneous) broadening for as much as 8:1+*0:2 cm-1. Polarization analysis of the -CN spectra showed that the -CN group is tilted 57 + - 2 degrees from the surface normal. The large heterogeneity in the -CN spectrum is tentatively attributed to the -CN group interactions with the interfacial water molecules penetrated/accomodated into the 8CB monolayer, a unique phenomenon for the nCB Langmuir monolayers reported previously.

  2. 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.

  3. 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.

  4. 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.

  5. Two-Dimensional Spectroscopy of Coupled Vibrations with the Optimized Mean-Trajectory Approximation

    PubMed Central

    Gerace, Mallory; Loring, Roger F.

    2013-01-01

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

  6. Overtone spectroscopy of the hydroxyl stretch vibration in hydroxylamine (NH[sub 2]OH)

    SciTech Connect

    Scott, J.L.; Luckhaus, D.; Brown, S.S.; Crim, F.F. )

    1995-01-08

    We present photoacoustic spectra of the second (3[nu][sub OH]), third (4[nu][sub OH]), and fourth (5[nu][sub OH]) overtone bands of the hydroxyl stretch vibration in hydroxylamine. Asymmetric rotor simulations of the rovibrational contours provide rotational constants and an estimate of the homogeneous linewidth. The fourth overtone band appears anomalously broad relative to the two lower bands, reflecting a sharp increase in the rate of intramolecular vibrational energy redistribution (IVR). By contrast, the calculated density of states increases smoothly with energy. The homogeneous linewidth of the fourth overtone transition is similar to that measured by Luo [ital et] [ital al]. [J. Chem. Phys. [bold 93], 9194 (1990)] for the predissociative sixth overtone band, supporting the conclusion that the broadening arises from increased (ro)vibrational coupling at an energy between the third and fourth overtone states.

  7. Comparative study of direct and phase-specific vibrational sum-frequency generation spectroscopy: advantages and limitations.

    PubMed

    Pool, Ruben E; Versluis, Jan; Backus, Ellen H G; Bonn, Mischa

    2011-12-29

    As a surface-specific technique, vibrational sum-frequency generation (SFG) is used in a wide range of applications where soft matter or solid interfaces are to be probed on a molecular level through their vibrational modes. In recent years, phase-specific sum-frequency generation (PS-SFG, also known as heterodyne-detected SFG) spectroscopy has been increasingly replacing its predecessor (direct SFG, also known as homodyne SFG) as the experimental technique of choice for characterizing interfacial structure. The technique enables phase sensitive measurements, allowing for the determination of the real and imaginary parts of the interfacial vibrational response function and thereby the unambiguous identification of molecular orientation. This phase-sensitivity requires, however, a complete understanding of the complex optical properties of the sample and of their effect on the signal. These optical properties significantly influence the raw spectral data from which the real and imaginary parts of the second-order susceptibility are retrieved. We show that it is essential to correct the data appropriately to infer the true molecular response. The current study presents a detailed description of the physical contributions to the phase-resolved spectrum, allowing a direct comparison between the phase-resolved spectrum and that obtained using the well-understood direct detection method in a step-by-step data analysis process. In addition to phase sensitivity, PS-SFG has been shown to increase the sensitivity compared to traditional (direct) SFG spectroscopy. We present a quantitative comparison between theoretical limits of the signal-to-noise ratio of both techniques, which shows that for many systems the signal-to-noise ratio is very similar for direct- and phase-specific SFG signals. © 2011 American Chemical Society

  8. Characterization of a genuin iron(V) - nitrido species by nuclear resonant vibrational spectroscopy coupled to density functional calculations.

    SciTech Connect

    Petrenko, T.; George, S. D.; Aliaga-Alcalde, N.; Bill, E.; Mienert, B.; Xiao, Y.; Guo, Y.; Sturhahn, W.; Cramer, S.P.; Wieghardt, K.; Neese, F.; X-Ray Science Division; Institut of Physikalische und Theoretische Chemie; SSRL; Standford Univ.; Max-Planck Institut fur Bioanogranische Chemie; Univ. of California at Davis; LBNL

    2007-01-01

    The characterization of high-valent iron species is of interest due to their relevance to biological reaction mechanisms. Recently, we have synthesized and characterized an [Fe(V)-nitrido-cyclam-acetato]{sup +} complex, which has been characterized by M{umlt o}ssbauer, magnetic susceptibility data, and XAS spectroscopies combined with DFT calculations . The results of this study indicated that the [Fe(V)-nitrido-cyclam-acetato]+ complex is an unusual d{sup 3} system with a nearly orbitally degenerate S = 1/2 ground state. Although the calculations predicted fairly different Fe-N stretching frequencies for the S = 1/2 and the competing S = 3/2 ground states, a direct experimental determination of this important fingerprint quantity was missing. Here we apply synchrotron-based nuclear resonance vibrational scattering (NRVS) to characterize the Fe-N stretching frequency of an Fe(V)-nitrido complex and its Fe(III)-azide precursor. The NRVS data show a new isolated band at 864 cm{sup -1} in the Fe(V)-nitrido complex that is absent in the precursor. The NRVS spectra are fit and simulated using a DFT approach, and the new feature is unambiguously assigned to a Fe(V)-N stretch. The calculated Fe-N stretching frequency is too high by {approx}75 cm{sup -1}. Anharmonic contributions to the Fe-N stretching frequency have been evaluated and have been found to be small (-5.5 cm{sup -1}). The NRVS data provided a unique opportunity to obtain this vibrational information, which had eluded characterization by more traditional vibrational spectroscopies.

  9. Characterization of a Genuine Lron(V)-Nitrido Species By Nuclear Resonant Vibrational Spectroscopy Coupled to Density Functional Calculations

    SciTech Connect

    Petrenko, T.; George, S.D.; Aliaga-Alcalde, N.; Bill, E.; Mienert, B.; Xiao, Y.; Guo, Y.; Sturhahn, W.; Cramer, S.P.; Wieghardt, K.; Neese, F.; /Bonn U., LTC /SLAC, SSRL /Max Planck Inst., Mulheim /UC, Davis /Argonne /LBL, Berkeley

    2007-10-19

    The characterization of high-valent iron species is of interest due to their relevance to biological reaction mechanisms. Recently, we have synthesized and characterized an [Fe(V)-nitrido-cyclam-acetato]+ complex, which has been characterized by M{umlt o}ssbauer, magnetic susceptibility data, and XAS spectroscopies combined with DFT calculations. The results of this study indicated that the [Fe(V)-nitrido-cyclam-acetato]+ complex is an unusual d3 system with a nearly orbitally degenerate S = 1/2 ground state. Although the calculations predicted fairly different Fe-N stretching frequencies for the S = 1/2 and the competing S = 3/2 ground states, a direct experimental determination of this important fingerprint quantity was missing. Here we apply synchrotron-based nuclear resonance vibrational scattering (NRVS) to characterize the Fe-N stretching frequency of an Fe(V)-nitrido complex and its Fe(III)-azide precursor. The NRVS data show a new isolated band at 864 cm-1 in the Fe(V)-nitrido complex that is absent in the precursor. The NRVS spectra are fit and simulated using a DFT approach, and the new feature is unambiguously assigned to a Fe(V)-N stretch. The calculated Fe-N stretching frequency is too high by {approx}75 cm-1. Anharmonic contributions to the Fe-N stretching frequency have been evaluated and have been found to be small (-5.5 cm-1). The NRVS data provided a unique opportunity to obtain this vibrational information, which had eluded characterization by more traditional vibrational spectroscopies.

  10. Nonequilibrium molecular dynamics simulations with a backward-forward trajectories sampling for multidimensional infrared spectroscopy of molecular vibrational modes

    NASA Astrophysics Data System (ADS)

    Hasegawa, Taisuke; Tanimura, Yoshitaka

    2008-02-01

    A full molecular dynamics (MD) simulation approach to calculate multidimensional third-order infrared (IR) signals of molecular vibrational modes is proposed. Third-order IR spectroscopy involves three-time intervals between three excitation and one probe pulses. The nonequilibrium MD (NEMD) simulation allows us to calculate molecular dipoles from nonequilibrium MD trajectories for different pulse configurations and sequences. While the conventional NEMD approach utilizes MD trajectories started from the initial equilibrium state, our approach does from the intermediate state of the third-order optical process, which leads to the doorway-window decomposition of nonlinear response functions. The decomposition is made before the second pump excitation for a two-dimensional case of IR photon echo measurement, while it is made after the second pump excitation for a three-dimensional case of three-pulse IR photon echo measurement. We show that the three-dimensional IR signals are efficiently calculated by using the MD trajectories backward and forward in time for the doorway and window functions, respectively. We examined the capability of the present approach by evaluating the signals of two- and three-dimensional IR vibrational spectroscopies for liquid hydrogen fluoride. The calculated signals might be explained by anharmonic Brownian model with the linear-linear and square-linear system-bath couplings which was used to discuss the inhomogeneous broadening and dephasing mechanism of vibrational motions. The predicted intermolecular librational spectra clearly reveal the unusually narrow inhomogeneous linewidth due to the one-dimensional character of HF molecule and the strong hydrogen bond network.

  11. 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.

  12. 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.

  13. Orientations of nonlocal vibrational modes from combined experimental and theoretical sum frequency spectroscopy

    NASA Astrophysics Data System (ADS)

    Chase, Hilary M.; Chen, Shunli; Fu, Li; Upshur, Mary Alice; Rudshteyn, Benjamin; Thomson, Regan J.; Wang, Hong-Fei; Batista, Victor S.; Geiger, Franz M.

    2017-09-01

    Inferring molecular orientations from vibrational sum frequency generation (SFG) spectra is challenging in polarization combinations that result in low signal intensities, or when the local point group symmetry approximation fails. While combining experiments with density functional theory (DFT) could overcome this problem, the scope of the combined method has yet to be established. Here, we assess its feasibility of determining the distributions of molecular orientations for one monobasic ester, two epoxides and three alcohols at the vapor/fused silica interface. We find that molecular orientations of nonlocal vibrational modes cannot be determined using polarization-resolved SFG measurements alone.

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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…

  20. 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…

  1. Molecular structure, vibrational spectroscopy, NBO and HOMO, LUMO studies of o-methoxybenzonitrile

    NASA Astrophysics Data System (ADS)

    Elanthiraiyan, M.; Jayasudha, B.; Arivazhagan, M.

    2015-01-01

    In the present study, the FT-IR and FT-Raman spectra of o-methoxybenzonitrile (O-MBN) have been recorded in the region 4000-400 cm-1 and 3500-50 cm-1, respectively. The fundamental modes of vibrational frequencies of O-MBN are assigned. Theoretical information on the optimized geometry, harmonic vibrational frequencies, infrared and Raman intensities were obtained by means of ab initio Hartree-Fock (HF) and density functional theory (DFT) gradient calculations with complete relaxation in the potential energy surface using 6-311++G(d,p) basis set. The vibrational frequencies which were determined experimentally from the spectral data are compared with those obtained theoretically from ab initio and DFT calculations. A close agreement was achieved between the observed and calculated frequencies by refinement of the scale factors. The infrared and Raman spectra were also predicted from the calculated intensities. Thermodynamic properties like entropy, heat capacity, zero point energy, have been calculated for the molecule. The predicted first hyperpolarizability also shows that the molecule might have a reasonably good non-linear optical (NLO) behavior. The calculated HOMO-LUMO energy gap reveals that charge transfer occurs within the molecule. Stability of the molecule arising from hyper conjugative interactions, charge delocalization have been analyzed using natural bond orbitals (NBO) analysis. Unambiguous vibrational assignment of all the fundamentals was made using the total energy distribution (TED).

  2. 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).

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Global Calculations Using Potential Functions and Effective Hamiltonian Models for Vibration-Rotation Spectroscopy and Dynamics of Small Polyatomic Molecules

    NASA Astrophysics Data System (ADS)

    Tuyterev, Vladimir

    2010-06-01

    It has become increasingly common to use accurate potential energy surfaces and dipole moment surfaces for predictions and assignment of high-resolution vibration-rotation molecular spectra. These surfaces are obtained either from high-level ab initio electronic structure calculations or from a direct fit to experimental spectroscopic data. The talk will continue a discussion of some recent advances in the domain of the "potentiology". The role of basis extrapolations, of the Born-Oppenheimer breakdown corrections , in particular for very highly excited vibration states will be considered. As effective polyad Hamiltonians and band transition moment operators are still widely used for data reductions in high-resolutions molecular spectroscopy, experimental spectra analyses invoke a need for accurate methods of building physically meaningful effective models from ab initio surfaces. This involves predictions for various spectroscopic constants, including vibration dependence of rotational and centrifugal distortion and resonance coupling parameters. Topics planned for discussion include: high-order Contact Transformations of rovibrational Hamiltonians and of the dipole moment for small polyatomic molecules; convergence issues; the role of the anharmonicity in a potential energy function and of resonance couplings on the normal mode mixing and on vib-rot assignments with application to high energy vibration levels of SO_2 and to ozone near the dissociation limit; intensity anomalies in H_2S / HDS / D_2S spectra, relation of the shape of ab initio dipole moment surfaces with a "mystery" of nearly vanishing symmetry allowed bands. A full account for symmetry properties requires efficient theoretical tools for transformations of molecular Hamiltonians such as irreducible tensor formalism, applications using phosphine and methane potentials will be discussed. Both potential functions and effective polyad Hamiltonians allow studying changes in quasi-classical vibration

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  12. Reinterpretation of Dynamic Vibrational Spectroscopy to Determine the Molecular Structure and Dynamics of Ferrocene.

    PubMed

    Best, Stephen P; Wang, Feng; Islam, M Tauhidul; Islam, Shawkat; Appadoo, Dominique; Trevorah, Ryan M; Chantler, Christopher T

    2016-12-12

    Molecular distortion of dynamic molecules gives a clear signature in the vibrational spectra, which can be modeled to give estimates of the energy barrier and the sensitivity of the frequencies of the vibrational modes to the reaction coordinate. The reaction coordinate method (RCM) utilizes ab initio-calculated spectra of the molecule in its ground and transition states together with their relative energies to predict the temperature dependence of the vibrational spectra. DFT-calculated spectra of the eclipsed (D5h ) and staggered (D5d ) forms of ferrocene (Fc), and its deuterated analogue, within RCM explain the IR spectra of Fc in gas (350 K), solution (300 K), solid solution (7-300 K), and solid (7-300 K) states. In each case the D5h rotamer is lowest in energy but with the barrier to interconversion between rotamers higher for solution-phase samples (ca. 6 kJ mol(-1) ) than for the gas-phase species (1-3 kJ mol(-1) ). The generality of the approach is demonstrated with application to tricarbonyl(η(4) -norbornadiene)iron(0), Fe(NBD)(CO)3 . The temperature-dependent coalescence of the ν(CO) bands of Fe(NBD)(CO)3 is well explained by the RCM without recourse to NMR-like rapid exchange. The RCM establishes a clear link between the calculated ground and transition states of dynamic molecules and the temperature-dependence of their vibrational spectra. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Modern Raman Imaging: Vibrational Spectroscopy on the Micrometer and Nanometer Scales

    NASA Astrophysics Data System (ADS)

    Opilik, Lothar; Schmid, Thomas; Zenobi, Renato

    2013-06-01

    Raman microscopes are currently used in various fields of research because they allow for label-free sample investigation. Moreover, the inherently low scattering cross section of Raman spectroscopy, as well as its diffraction-limited lateral resolution, has been overcome by new Raman microscopy techniques. Nonlinear methods such as coherent anti-Stokes Raman spectroscopy and stimulated Raman spectroscopy reduce measurement times and improve z resolution, allowing for three-dimensional spectroscopic imaging of biological samples. Moreover, tip-enhanced Raman spectroscopy, a near-field optical technique that combines scanning-probe microscopy with the enhancement offered by surface-enhanced Raman scattering, enables Raman spectroscopic imaging far below the optical diffraction limit. We cover the theoretical and technical aspects of Raman microscopy and related new imaging techniques and review some very recent applications in graphene research and cell biology.

  14. 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.

  15. 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)).

  16. 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.

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

    PubMed

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

    2015-02-26

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

  18. 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.

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

    SciTech Connect

    Lewis, Nicholas H. C.; Fleming, Graham R.

    2016-03-03

    Presented are 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.

  20. 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.

  1. 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.

  2. 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.

  3. To Avoid Chasing Incorrect Chemical Structures of Chiral Compounds: Raman Optical Activity and Vibrational Circular Dichroism Spectroscopies.

    PubMed

    Polavarapu, Prasad L; Covington, Cody L; Raghavan, Vijay

    2017-09-20

    A chemical structure (CS) identifies the connectivities between atoms, and the nature of those connections, for a given elemental composition. For chiral molecules, in addition to the identification of CS, the identification of the correct absolute configuration (AC) is also needed. Several chiral natural products are known whose CSs were initially misidentified and later corrected, and these errors were often discovered during the total synthesis of natural products. In this work, we present a new and convenient approach that can be used with Raman optical activity (ROA) and vibrational circular dichroism (VCD) spectroscopies, to distinguish between the correct and incorrect CSs of chiral compounds. This approach involves analyzing the spectral similarity overlap between experimental spectra and those predicted with advanced quantum chemical theories. Significant labor needed for establishing the correct CSs via chemical syntheses of chiral natural products can thus be avoided. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. In Situ Molecular Level Studies on Membrane Related Peptides and Proteins in Real Time Using Sum Frequency Generation Vibrational Spectroscopy

    PubMed Central

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

    2009-01-01

    Sum frequency generation (SFG) vibrational spectroscopy has been demonstrated to be a powerful technique to study the molecular structures of surfaces and interfaces in different chemical environments. This review summarizes recent SFG studies on hybrid bilayer membranes and substrate-supported lipid monolayers and bilayers, the interaction between peptides/proteins and lipid monolayers/bilayers, and bilayer perturbation induced by peptides/proteins. To demonstrate the ability of SFG to determine the orientations of various secondary structures, studies on the interaction between different peptides/proteins (melittin, G proteins, almethicin, and tachyplesin I) and lipid bilayers are discussed. Molecular level details revealed by SFG in these studies show that SFG can provide a unique understanding on the interactions between a lipid monolayer/bilayer and peptides/proteins in real time, in situ and without any exogenous labeling. PMID:19306928

  11. 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.

  12. 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.

  13. 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.

  14. Tetraplex structure formation in the thrombin-binding DNA aptamer by metal cations measured by vibrational spectroscopy.

    PubMed

    Mondragon-Sanchez, J A; Liquier, J; Shafer, R H; Taillandier, E

    2004-12-01

    Formation of intramolecular tetraplex structures by the thrombin-binding DNA aptamer (TBA) in the presence of K(+), Pb(2+), Ba(2+), Sr(2+) and Mn(2+) has been studied by vibrational spectroscopy. All tetraplex structures contain G-G Hoogsteen type base pairing, both C2'endo/anti and C2'endo/syn deoxyguanosine glycosidic conformations and local B like form DNA phosphate geometries. Addition of Pb(2+) ions modifies the structure by interacting at the level of the guanine carbonyl groups. The very important downshift of the guanine C6=O6 carbonyl vibration mode in the TBA spectrum induced by the addition of one Pb(2+) ion per TBA molecule is in agreement with a localization of the metal ion between both guanine quartets. FTIR melting experiments show an important stabilization of the tetraplex structure upon addition of Pb(2+) ions (DeltaT = 15 degrees C). This strong interaction of lead cations may be correlated with a change in the geometry of the cage formed by the two guanine quartets. A similar but weaker effect is observed for barium and strontium cations.

  15. 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.

  16. 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

  17. 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.

  18. A narrow amide I vibrational band observed by sum frequency generation spectroscopy reveals highly ordered structures of a biofilm protein at the air/water interface.

    PubMed

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

    2016-02-18

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

  19. Vibrational analysis of implants and tissues: Calibration and mechanical spectroscopy of multi-component materials.

    PubMed

    Shah, Ruchit G; DeVore, Dale; Pierce, Mark C; Silver, Frederick H

    2017-06-01

    Several new methods have been used to non-destructively evaluate the mechanical properties of materials and tissues including magnetic resonance elastography, ultrasound elastography, optical coherence elastography, and various forms of vibrational analysis. One of the limitations of using these methods is the need to establish a relationship between the modulus measured using each new technique and moduli measured using well-established