WorldWideScience

Sample records for biology vibrational spectroscopy

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

    Science.gov (United States)

    2016-07-01

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

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

    Science.gov (United States)

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

    2016-12-01

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

  3. Vibrational Spectroscopy of Biomembranes

    Science.gov (United States)

    Schultz, Zachary D.; Levin, Ira W.

    2011-07-01

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

  4. 2008 Vibrational Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Philip J. Reid

    2009-09-21

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

  5. TIME-RESOLVED VIBRATIONAL SPECTROSCOPY

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-05-14

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

  6. Time-resolved vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-05-14

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

  7. Vibrational spectroscopy of resveratrol

    Science.gov (United States)

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

    2007-11-01

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

  8. Ultrafast infrared vibrational spectroscopy

    CERN Document Server

    Fayer, Michael D

    2013-01-01

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

  9. Vibrational spectroscopy at electrified interfaces

    CERN Document Server

    Wieckowski, Andrzej; Braunschweig, Björn

    2013-01-01

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

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

    Science.gov (United States)

    Buckup, Tiago; Motzkus, Marcus

    2014-04-01

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

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

    Science.gov (United States)

    Buckup, Tiago; Motzkus, Marcus

    2014-01-01

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

  12. Probing zeolites by vibrational spectroscopies.

    Science.gov (United States)

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

    2015-10-21

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

  13. Vibrations, Quanta and Biology

    CERN Document Server

    Huelga, S F

    2013-01-01

    Quantum biology is an emerging field of research that concerns itself with the experimental and theoretical exploration of non-trivial quantum phenomena in biological systems. In this tutorial overview we aim to bring out fundamental assumptions and questions in the field, identify basic design principles and develop a key underlying theme -- the dynamics of quantum dynamical networks in the presence of an environment and the fruitful interplay that the two may enter. At the hand of three biological phenomena whose understanding is held to require quantum mechanical processes, namely excitation and charge transfer in photosynthetic complexes, magneto-reception in birds and the olfactory sense, we demonstrate that this underlying theme encompasses them all, thus suggesting its wider relevance as an archetypical framework for quantum biology.

  14. Vibrational Spectroscopy of Chromatographic Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Jeanne E. Pemberton

    2011-03-10

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

  15. 2010 GRC VIBRATIONAL SPECTROSCOPY AUGUST 1 - AUGUST 6, 2010

    Energy Technology Data Exchange (ETDEWEB)

    Brooks Pate

    2010-08-06

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

  16. Vibrational spectroscopy of water interfaces

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-12-01

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

  17. Vibrational Spectroscopy of Methyl benzoate

    CERN Document Server

    Maiti, Kiran Sankar

    2014-01-01

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

  18. Seventh international conference on time-resolved vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-04-01

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

  19. Submillimeter wave spectroscopy of biological macromolecules

    Science.gov (United States)

    Globus, Tatiana

    2005-03-01

    The recently emergence of submillimeter-wave or terahertz (THz) spectroscopy of biological molecules has demonstrated the capability to detect low-frequency internal molecular vibrations involving the weakest hydrogen bonds of the DNA base pairs and/or non-bonded interactions. These multiple bonds, although having only ˜ 5% of the strength of covalent bonds, stabilize the structure of bio-polymers, by holding the two strands of the DNA double helix together, or polypeptides together in different secondary structure conformations. There will be a review of THz-frequency transmission (absorption) results for biological materials obtained from Fourier Transform Infrared (FTIR) spectroscopy during the last few years^1,2. Multiple resonances, due to low frequency vibrational modes within biological macromolecules, have been unambiguously demonstrated in qualitative agreement with theoretical prediction, thereby confirming the fundamental physical nature of observed resonance features. The discovery of resonance character of interaction between THz radiation and biological materials opens many possible applications for THz spectroscopy technique in biological sensing and biomedicine using multiple resonances as distinctive spectral fingerprints. However, many issues still require investigation. Kinetics of interactions with radiation at THz has not been studied and vibrational lifetimes have not been measured directly as a function of frequency. The strength of resonant modes of bio-molecules in aqueous environment and strong dependence of spectra on molecular orientation need explanation. Vibrational modes have not been assigned to specific motions within molecules. THz spectroscopy of bio-polymers makes it only in first steps. 1. T. Globus, D. Woolard, M. Bykhovskaia, B. Gelmont, L. Werbos, A. Samuels. International Journal of High Speed Electronics and Systems (IJHSES), 13, No. 4, 903-936 (2003). 2. T. Globus, T. Khromova, D. Woolard and B. Gelmont. Proceedings of

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

    DEFF Research Database (Denmark)

    Lassen, Peter Rygaard

    2006-01-01

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

  1. New developments in IR surface vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

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

    1995-12-31

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

  2. Vibrational spectroscopy in diagnosis and screening

    CERN Document Server

    Severcan, F

    2012-01-01

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

  3. In Situ Adsorption Studies at the Solid/Liquid Interface:Characterization of Biological Surfaces and Interfaces Using SumFrequency Generation Vibrational Spectroscopy, Atomic Force Microscopy,and Quartz Crystal Microbalance

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, Diana Christine [Univ. of California, Berkeley, CA (United States)

    2006-01-01

    Sum frequency generation (SFG) vibrational spectroscopy, atomic force microscopy (AFM), and quartz crystal microbalance (QCM) have been used to study the molecular surface structure, surface topography and mechanical properties, and quantitative adsorbed amount of biological molecules at the solid-liquid interface. The molecular-level behavior of designed peptides adsorbed on hydrophobic polystyrene and hydrophilic silica substrates has been examined as a model of protein adsorption on polymeric biomaterial surfaces. Proteins are such large and complex molecules that it is difficult to identify the features in their structure that lead to adsorption and interaction with solid surfaces. Designed peptides which possess secondary structure provide simple model systems for understanding protein adsorption. Depending on the amino acid sequence of a peptide, different secondary structures (α-helix and β-sheet) can be induced at apolar (air/liquid or air/solid) interfaces. Having a well-defined secondary structure allows experiments to be carried out under controlled conditions, where it is possible to investigate the affects of peptide amino acid sequence and chain length, concentration, buffering effects, etc. on adsorbed peptide structure. The experiments presented in this dissertation demonstrate that SFG vibrational spectroscopy can be used to directly probe the interaction of adsorbing biomolecules with a surface or interface. The use of well designed model systems aided in isolation of the SFG signal of the adsorbing species, and showed that surface functional groups of the substrate are sensitive to surface adsorbates. The complementary techniques of AFM and QCM allowed for deconvolution of the effects of surface topography and coverage from the observed SFG spectra. Initial studies of biologically relevant surfaces are also presented: SFG spectroscopy was used to study the surface composition of common soil bacteria for use in bioremediation of nuclear waste.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-08-31

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

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

    Science.gov (United States)

    Mantsch, Henry H

    2013-07-21

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

  6. Spectroscopy and reactions of vibrationally excited transient molecules

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-12-01

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

  7. 2012 VIBRATIONAL SPECTROSCOPY GORDON RESEARCH CONFERENCE, AUGUST 5-10, 2012

    Energy Technology Data Exchange (ETDEWEB)

    Geiger, Franz

    2012-08-10

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

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

    NARCIS (Netherlands)

    Nissink, Johannes Wilhelmus Maria

    2001-01-01

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

  9. Ultrafast spectroscopy of model biological membranes

    NARCIS (Netherlands)

    Ghosh, Avishek

    2009-01-01

    In this PhD thesis, I have described the novel time-resolved sum-frequency generation (TR-SFG) spectroscopic technique that I developed during the course of my PhD research and used it study the ultrafast vibrational, structural and orientational dynamics of water molecules at model biological membr

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

    CERN Document Server

    Ferraro, John R

    1984-01-01

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

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

    Science.gov (United States)

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

    2013-06-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Zoppi Marco

    2015-01-01

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

  14. Vibrational spectroscopy of microhydrated conjugate base anions.

    Science.gov (United States)

    Asmis, Knut R; Neumark, Daniel M

    2012-01-17

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

  15. Nanomechanical Infrared Spectroscopy with Vibrating Filters for Pharmaceutical Analysis

    DEFF Research Database (Denmark)

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

    2017-01-01

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

  16. Enhanced Vibrational Spectroscopies as Tools for Small Molecule Biosensing

    Directory of Open Access Journals (Sweden)

    Souhir Boujday

    2015-08-01

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

  17. Sub-terahertz resonance spectroscopy of biological macromolecules and cells

    Science.gov (United States)

    Globus, Tatiana; Moyer, Aaron; Gelmont, Boris; Khromova, Tatyana; Sizov, Igor; Ferrance, Jerome

    2013-05-01

    Recently we introduced a Sub-THz spectroscopic system for characterizing vibrational resonance features from biological materials. This new, continuous-wave, frequency-domain spectroscopic sensor operates at room temperature between 315 and 480 GHz with spectral resolution of at least 1 GHz and utilizes the source and detector components from Virginia Diode, Inc. In this work we present experimental results and interpretation of spectroscopic signatures from bacterial cells and their biological macromolecule structural components. Transmission and absorption spectra of the bacterial protein thioredoxin, DNA and lyophilized cells of Escherichia coli (E. coli), as well as spores of Bacillus subtillis and B. atrophaeus have been characterized. Experimental results for biomolecules are compared with absorption spectra calculated using molecular dynamics simulation, and confirm the underlying physics for resonance spectroscopy based on interactions between THz radiation and vibrational modes or groups of modes of atomic motions. Such interactions result in multiple intense and narrow specific resonances in transmission/absorption spectra from nano-gram samples with spectral line widths as small as 3 GHz. The results of this study indicate diverse relaxation dynamic mechanisms relevant to sub-THz vibrational spectroscopy, including long-lasting processes. We demonstrate that high sensitivity in resolved specific absorption fingerprints provides conditions for reliable detection, identification and discrimination capability, to the level of strains of the same bacteria, and for monitoring interactions between biomaterials and reagents in near real-time. Additionally, it creates the basis for the development of new types of advanced biological sensors through integrating the developed system with a microfluidic platform for biomaterial samples.

  18. Transient grating spectroscopy of SF6 molecular vibrations

    CERN Document Server

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

    2014-01-01

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

  19. Terahertz spectroscopy for chemicals and biological sensing applications

    Science.gov (United States)

    Liu, Hai-Bo

    Terahertz (THz) radiation offers innovative sensing and imaging technologies that can provide information unavailable through other conventional electromagnetic techniques. With the advancement of THz technologies, THz sensing will impact a broad range of areas. This thesis focuses on the use of THz spectroscopy for sensing applications including explosives detection, pharmaceutical identification and biological characterization. Using both a THz time-domain spectroscopy (THz-TDS) system and a Fourier transform far-infrared spectrometer (FT-FIR), a THz spectral database of explosives and related compounds (ERCs) in the range of 0.1-20 THz was established. The transmission measurements show good agreement with the diffuse reflectance measurements, which are more feasible for practical applications. Density Functional Theory was employed to calculate structures and vibrational modes of several important ERCs and the calculated spectra are in good accordance with the experimental data in the 3-20 THz range. The detection and identification of the explosive RDX using diffusely reflected THz waves were also demonstrated. THz-TDS was applied successfully for pharmaceutical study, such as investigating drug interactions, as well as identifying hydrated and anhydrous drugs, based upon the intermolecular vibrational modes of drug substances. Dehydrations and complex solid state reactions of pharmaceutical materials were studied with THz-TDS and the reaction kinetics was successfully probed. These investigations have opened new avenues for using THz technologies in pharmaceutical science and industry. THz spectra of amino acids, purines and other biomolecules were recorded. Most of these solid-state biocompounds have THz spectral features in the 0.1-3.0 THz range. THz spectroscopy of solid-state proteins and bioactive protein micro suspensions in organic media was studied and their THz absorption features may reflect their collective vibrational modes which could be used to

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

    Science.gov (United States)

    Hiramatsu, Hirotsugu

    2014-01-01

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

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

    Science.gov (United States)

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

    2007-05-01

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

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

    Science.gov (United States)

    Hu, Yongjun; Bernstein, Elliot R

    2008-04-28

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

  3. Vibrational and Rotational Spectroscopy of CD_2H^+

    Science.gov (United States)

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

    2016-06-01

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

  4. Cross-Propagation Sum-Frequency Generation Vibrational Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-02-01

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

  5. Liquid Space Lubricants Examined by Vibrational Micro-Spectroscopy

    Science.gov (United States)

    Street, Kenneth W., Jr.

    2008-01-01

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

  6. Nonlinear vibrational spectroscopy of surfactants at liquid interfaces

    Energy Technology Data Exchange (ETDEWEB)

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

    1998-12-14

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

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

    Science.gov (United States)

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

    2016-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Tsen Shaw-Wei D

    2006-09-01

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

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

    Science.gov (United States)

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

    2012-11-29

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

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

    Science.gov (United States)

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

    2014-10-15

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

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

    OpenAIRE

    1995-01-01

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

  12. Terahertz spectroscopy of dry, hydrated, and thermally denatured biological macromolecules

    Science.gov (United States)

    Lipscomb, Dawn; Echchgadda, Ibtissam; Ibey, Bennett L.; Beier, Hope; Thomas, Robert J.; Peralta, Xomalin; Wilmink, Gerald J.

    2012-03-01

    Terahertz time-domain spectroscopy (THz-TDS) is an effective technique to probe the intermolecular and collective vibrational modes of biological macromolecules at THz frequencies. To date, the vast majority of spectroscopic studies have been performed on dehydrated biomolecular samples. Given the fact that all biochemical processes occur in aqueous environments and water is required for proper protein folding and function, we hypothesize that valuable information can be gained from spectroscopic studies performed on hydrated biomolecules in their native conformation. In this study, we used a THz-TDS system that exploits photoconductive techniques for THz pulse generation and freespace electro-optical sampling approaches for detection. We used the THz spectrometer to measure the time-dependent electric field of THz waves upon interaction with water, phosphate buffered saline (PBS), and collagen gels. By comparing these waveforms with references, we simultaneously determined each sample's index of refraction (n) and absorption coefficients (μa) as a function of frequency. Our data show that the properties we measure for the water, PBS and collagen are comparable to those reported in the literature. In the future, we plan to examine the effect that both temperature and pH have on the optical properties of other biological macromolecules. Studies will also be performed to compare our results to those generated using molecular dynamics simulations.

  13. APD detectors for biological fluorescence spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Mazeres, S. [Institut de Pharmacologie et de Biologie Structurale, IPBS-CNRS, 205 route de Narbonne 31077 Toulouse Cedex 4 (France)]. E-mail: serge.mazeres@ipbs.fr; Borrel, V. [GIATHE/CESR, 9 avenue du Colonel Roche BP 4346, 31029 Toulouse Cedex (France); Magenc, C. [GIATHE/CESR, 9 avenue du Colonel Roche BP 4346, 31029 Toulouse Cedex (France); Courrech, J.L. [GIATHE/CESR, 9 avenue du Colonel Roche BP 4346, 31029 Toulouse Cedex (France); Bazer-Bachi, R. [GIATHE/CESR, 9 avenue du Colonel Roche BP 4346, 31029 Toulouse Cedex (France)

    2006-11-01

    Fluorescence spectroscopy is a very convenient and widely used method for studying the molecular background of biological processes [L. Salome, J.L. Cazeil, A. Lopez, J.F. Tocanne, Eur. Biophys. J. 27 (1998) 391-402]. Chromophores are included in the structure under study and a flash of laser light induces fluorescence (Fluorescence Recovery After Photo-bleaching), the decay of which yields information on the polarity, the speed of rotation, and the speed of diffusion as well as on the temporal and spatial evolution of interactions between molecular species. The method can even be used to study living cells [J.F. Tocanne, L. Cezanne, A. Lopez, Prog. Lipid Res. 33 (1994) 203-237, L. Cezanne, A. Lopez, F. Loste, G. Parnaud, O. Saurel, P. Demange, J.F. Tocanne, Biochemistry 38 (1999) 2779-2786]. This is classically performed with a PM-based system. For biological reasons a decrease of the excitation of the cells is highly desirable. Because the fluorescence response then becomes fainter a significant improvement in detector capability would be welcome. We present here results obtained with an Avalanche Photo Diode (APD)-based system. The small sensitive area of detection allows a very significant improvement in signal/noise ratio, improvement in gain, and the opening-up of a new parameter space. With these new detectors we can begin the study of information transmission between cells through morphine receptors. This work involves both electronics engineers and biophysicists, so results and techniques in both fields will be presented here.

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

    Science.gov (United States)

    Huang, Zishuai; Allen, Heather C.

    2012-06-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-11-21

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

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

    Indian Academy of Sciences (India)

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

    2010-01-01

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

  17. Microwave spectroscopy of furfural in vibrationally excited states

    Science.gov (United States)

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

    2007-07-01

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

  18. Carbon-13 NMR spectroscopy of biological systems

    CERN Document Server

    Beckmann, Nicolau

    1995-01-01

    This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-15

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

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

    DEFF Research Database (Denmark)

    Schrøder, Sidsel Dahl

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

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

    Science.gov (United States)

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

    2016-11-01

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

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

    CERN Document Server

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

    2016-01-01

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

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

    Science.gov (United States)

    Mettu, S; Chaudhury, M K

    2012-10-02

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

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

    Science.gov (United States)

    Viana, Rommel B.

    2017-01-01

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

  6. Measurement of Mechatronic Property of Biological Gel with Micro-Vibrating Electrode at Ultrasonic Frequency

    Directory of Open Access Journals (Sweden)

    Shigehiro Hashimoto

    2008-10-01

    Full Text Available A measurement system has been designed with a micro-vibrating electrode at ultrasonic frequency to measure local impedance of biological gel in vitro. The designed system consists of two electrodes, where one of the electrodes vibrates with a piezoelectric actuator. The component of variation at impedance between two electrodes with vibration of one electrode is analyzed at the corresponding spectrum. The manufactured system was applied to measure impedance of a physiological saline solution, a potassium chloride solution, a dextran aqueous solution, and an egg. The experimental results show that the designed system is effective to measure local mechatronic property of biological gel.

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

    DEFF Research Database (Denmark)

    Eskildsen, Carl Emil Aae

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-10-15

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

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

    Science.gov (United States)

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

    2005-06-01

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

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

    Science.gov (United States)

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

    2014-07-15

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

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

    Science.gov (United States)

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

    2016-04-28

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

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

    CERN Document Server

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

    2016-01-01

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

  13. Vibrational spectroscopy and DFT calculations of flavonoid derriobtusone A

    Science.gov (United States)

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

    2017-02-01

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

  14. Computational Laser Spectroscopy in a Biological Tissue

    Directory of Open Access Journals (Sweden)

    M. Gantri

    2010-01-01

    Full Text Available We present a numerical spectroscopic study of visible and infrared laser radiation in a biological tissue. We derive a solution of a general two-dimensional time dependent radiative transfer equation in a tissue-like medium. The used model is suitable for many situations especially when the external source is time-dependent or continuous. We use a control volume-discrete ordinate method associated with an implicit three-level second-order time differencing scheme. We consider a very thin rectangular biological-tissue-like medium submitted to a visible or a near infrared light sources. The RTE is solved for a set of different wavelength source. All sources are assumed to be monochromatic and collimated. The energetic fluence rate is computed at a set of detector points on the boundaries. According to the source type, we investigate either the steady-state or transient response of the medium. The used model is validated in the case of a heterogeneous tissue-like medium using referencing experimental results from the literature. Also, the developed model is used to study changes on transmitted light in a rat-liver tissue-like medium. Optical properties depend on the source wavelength and they are taken from the literature. In particular, light-transmission in the medium is studied for continuous wave and for short pulse.

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

    DEFF Research Database (Denmark)

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

    2002-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-09-01

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

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

    Science.gov (United States)

    Kerssens, Marleen Maartje

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

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

    Science.gov (United States)

    Ritchie, Andrew W; Webb, Lauren J

    2015-11-05

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

  19. A Biological Model for Directional Sensing of Seismic Vibration

    Science.gov (United States)

    2007-11-02

    186: 695-705. Cokl, A., Otto, C. and Kalmring, K. 1985. The processing of directional vibratory signals in the ventral nerve cord of Locusta ... migratoria . J. Comp. Physiol. A 156:45-52. Cokl, A., M. Virant-Doberlet, and A. McDowell. 1999. Vibrational directionality in the southern green stink bug

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

    Science.gov (United States)

    Kraack, Jan Philip; Hamm, Peter

    2016-06-28

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-28

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

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

    Science.gov (United States)

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

    2016-09-21

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

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

    Science.gov (United States)

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

    2014-06-01

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

  4. Spectroscopy

    DEFF Research Database (Denmark)

    Berg, Rolf W.

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

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

    Science.gov (United States)

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

    2007-02-15

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-03

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-18

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-12-01

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

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

    Science.gov (United States)

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

    2016-06-01

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

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

    Science.gov (United States)

    Barani, Hossein; Haji, Aminoddin

    2015-01-01

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

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

    Science.gov (United States)

    Noid, W G; Loring, Roger F

    2004-10-15

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

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

    Science.gov (United States)

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

    2009-11-17

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

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

    Science.gov (United States)

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

    2016-06-01

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

  14. Coherent vibrational dynamics

    CERN Document Server

    Lanzani, Guglielmo; De Silvestri, Sandro

    2007-01-01

    Vibrational spectroscopy is a powerful investigation tool for a wide class of materials covering diverse areas in physics, chemistry and biology. The continuous development in the laser field regarding ultrashort pulse generation has led to the possibility of producing light pulses that can follow vibrational motion coupled to the electronic transitions in molecules and solids in real time. Aimed at researchers and graduate students using vibrational spectroscopy, this book provides both introductory chapters as well as more advanced contents reporting on recent progress. It also provides a good starting point for scientists seeking a sound introduction to ultrafast optics and spectroscopic techniques.

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

    CERN Document Server

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-11-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-02-01

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

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

    Science.gov (United States)

    Crane, Nicole J.; Elster, Eric A.

    2012-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-05-28

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

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

    Science.gov (United States)

    Saurabh, Prasoon; Mukamel, Shaul

    2014-04-28

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

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

    Science.gov (United States)

    Paarmann, Alexander

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

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

    Science.gov (United States)

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

    2009-05-01

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

  3. Vibration-induced coherence enhances the performance of a biological quantum heat engine

    CERN Document Server

    Chen, Hong-Bin; Chen, Yueh-Nan

    2016-01-01

    Photosynthesis has been the long-standing research interest due to its fundamental importance. Recently, studies on photosynthesis processes also inspire attention from thermodynamical aspect when considering photosynthetic apparatuses as biological quantum heat engines. Quantum coherence is shown to play a crucial role in enhancing the performance of these quantum heat engines. Based on the experimentally reported structure, we propose a quantum heat engine model with a non-Markovian vibrational mode. We show that one can obtain a performance enhancement easily for a wide range of parameters in the presence of the vibrational mode. Our results suggest new insights into the photosynthetic processes and a design principle mimicking natural organisms.

  4. Vibration-induced coherence enhancement of the performance of a biological quantum heat engine

    Science.gov (United States)

    Chen, Hong-Bin; Chiu, Pin-Yi; Chen, Yueh-Nan

    2016-11-01

    Photosynthesis has been a long-standing research interest due to its fundamental importance. Recently, studies on photosynthesis processes also have inspired attention from a thermodynamical aspect when considering photosynthetic apparatuses as biological quantum heat engines. Quantum coherence is shown to play a crucial role in enhancing the performance of these quantum heat engines. Based on the experimentally reported structure, we propose a quantum heat engine model with a non-Markovian vibrational mode. We show that one can obtain a performance enhancement easily for a wide range of parameters in the presence of the vibrational mode. Our results provide insights into the photosynthetic processes and a design principle mimicking natural organisms.

  5. Nanophotonic waveguide enhanced Raman spectroscopy of biological submonolayers

    CERN Document Server

    Dhakal, Ashim; Peyskens, Frédéric; Jans, Karolien; Thomas, Nicolas Le; Baets, Roel

    2016-01-01

    Characterizing a monolayer of biological molecules has been a major challenge. We demonstrate nanophotonic wave-guide enhanced Raman spectroscopy (NWERS) of monolayers in the near-infrared region, enabling real-time measurements of the hybridization of DNA strands and the density of sub-monolayers of biotin-streptavidin complex immobilized on top of a photonics chip. NWERS is based on enhanced evanescent excitation and collection of spontaneous Raman scattering near nanophotonic waveguides, which for a one centimeter silicon nitride waveguide delivers a signal that is more than four orders of magnitude higher in comparison to a confocal Raman microscope. The reduced acquisition time and specificity of the signal allows for a quantitative and real-time characterization of surface species, hitherto not possible using Raman spectroscopy. NWERS provides a direct analytic tool for monolayer research and also opens a route to compact microscope-less lab-on-a-chip devices with integrated sources, spectrometers and d...

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-08-01

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

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

    KAUST Repository

    Krier, James M.

    2012-08-23

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

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

    Science.gov (United States)

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

    2016-07-01

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

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

    Directory of Open Access Journals (Sweden)

    Kirill O. Bugaev

    2012-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-08-22

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

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

    Directory of Open Access Journals (Sweden)

    Maxleene Sandasi

    2016-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Diethelm Johannsmann

    2016-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2001-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Visser, Hendrik

    2001-05-16

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-09-28

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2015-10-14

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

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

    Directory of Open Access Journals (Sweden)

    Hao Xu

    2015-08-01

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

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

    Science.gov (United States)

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

    2011-08-01

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

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

    Science.gov (United States)

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

    2004-01-01

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

  3. 2D IR spectroscopy of histidine: probing side-chain structure and dynamics via backbone amide vibrations.

    Science.gov (United States)

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

    2014-07-17

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

  4. Optical multi-frequency swept sensing for wide-field vibration measurement of interior surfaces in biological tissue

    Science.gov (United States)

    Choi, S.; Nin, F.; Hibino, H.; Suzuki, T.

    2015-12-01

    Multifrequency sensing technique adopting the wide field heterodyne detection technique is demonstrated for interior surface vibration measurements in thick biological tissue. These arrangements allow obtaining not only 3D tomographic images but also various vibration parameters such as spatial amplitude, phase, and frequency, with high temporal and transverse resolutions over a wide field. The axial resolution and the accuracy of vibration amplitude measurement were estimated to be 2.5 μm and 3 nm, respectively. This wide-field tomographic sensing method can be applied for measuring microdynamics of a variety of biological samples, thus contributing to the progress in life sciences research.

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

    Science.gov (United States)

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

    2016-06-01

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

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

    CERN Document Server

    Dijkstra, Arend G

    2015-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    张贞; 郭源

    2012-01-01

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

  8. Steady-state spectroscopy of new biological probes

    Science.gov (United States)

    Abou-Zied, Osama K.

    2007-02-01

    The steady state absorption and fluorescence spectroscopy of 2-(2'-hydroxyphenyl)benzoxazole (HBO) and (2,2'-bipyridine)-3,3'-diol (BP(OH) II) were studied here free in solution and in human serum albumin (HSA) in order to test their applicability as new biological probes. HBO and BP(OH) II are known to undergo intramolecular proton transfers in the excited state. Their absorption and fluorescence spectra are sensitive to environmental change from hydrophilic to hydrophobic, thus allowing the opportunity to use them as environment-sensitive probes. The effect of water on the steady state spectra of the two molecules also shows unique features which may position them as water sensors in biological systems. For HBO in buffer, fluorescence is only due to the syn-keto tautomer, whereas in HSA the fluorescence is due to four species in equilibrium in the excited state (the syn-keto tautomer, the anti-enol tautomer, the solvated syn-enol tautomer, and the anion species of HBO). Analysis of the fluorescence spectra of HBO in HSA indicates that HBO is exposed to less water in the HBO:HSA complex. For the BP(OH) II molecule, unique absorption due to water was observed in the spectral region of 400-450 nm. This absorption decreases in the presence of HSA due to less accessibility to water as a result of binding to HSA. Fluorescence of BP(OH) II is due solely to the di-keto tautomer after double proton transfer in the excited state. The fluorescence peak of BP(OH) II shows a red-shift upon HSA recognition which is attributed to the hydrophobic environment inside the binding site of HSA. We discuss also the effect of probe-inclusion inside well-defined hydrophobic cavities of cyclodextrins.

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

    Science.gov (United States)

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

    2016-07-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-07

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

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

    Science.gov (United States)

    Johnson, Mark

    2010-06-01

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

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

    Science.gov (United States)

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

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

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

    Science.gov (United States)

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

    2013-08-01

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

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

    CERN Document Server

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

    2016-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-07-28

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

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

    Science.gov (United States)

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

    2013-09-01

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

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

    Science.gov (United States)

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

    2007-05-01

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

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

    Science.gov (United States)

    Jeništová, Adéla; Dendisová, Marcela; Matějka, Pavel

    2016-12-21

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

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

    Science.gov (United States)

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

    2009-06-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-11-14

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

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

    Science.gov (United States)

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

    2001-03-01

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

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

    Science.gov (United States)

    Frost, Ray L; Xi, Yunfei

    2012-06-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-07-14

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

  4. Detection of Biological Materials Using Ion Mobility Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Rodacy, P.J.; Sterling, J.P.; Butler, M.A.

    1999-03-01

    Traditionally, Ion Mobility Spectroscopy has been used to examine ions of relatively low molecular weight and high ion mobility. In recent years, however, biomolecules such as bradykinin, cytochrome c, bovine pancreatic trypsin inhibitor (BPTI), apomyoglobin, and lysozyme, have been successfully analyzed, but studies of whole bio-organisms have not been performed. In this study an attempt was made to detect and measure the mobility of two bacteriophages, {lambda}-phage and MS2 using electrospray methods to inject the viruses into the ion mobility spectrometer. Using data from Yeh, et al., which makes a comparison between the diameter of non-biologic particles and the specific particle mobility, the particle mobility for the MS2 virus was estimated to be 10{sup {minus}2} cm{sup 2}/volt-sec. From this mobility the drift time of these particles in our spectrometer was calculated to be approximately 65 msec. The particle mobility for the {lambda}-phage virus was estimated to be 10{sup {minus}3} cm{sup 2}/volt-sec. which would result in a drift time of 0.7 sec. Spectra showing the presence of a viral peak at the expected drift time were not observed. However, changes in the reactant ion peak that could be directly attributed to the presence of the viruses were observed. Virus clustering, excessive collisions, and the electrospray injection method limited the performance of this IMS. However, we believe that an instrument specifically designed to analyze such bioagents and utilizing other injection and ionization methods will succeed in directly detecting viruses and bacteria.

  5. Fluorescence correlation spectroscopy: Statistical analysis and biological applications

    Science.gov (United States)

    Saffarian, Saveez

    2002-01-01

    The experimental design and realization of an apparatus which can be used both for single molecule fluorescence detection and also fluorescence correlation and cross correlation spectroscopy is presented. A thorough statistical analysis of the fluorescence correlation functions including the analysis of bias and errors based on analytical derivations has been carried out. Using the methods developed here, the mechanism of binding and cleavage site recognition of matrix metalloproteinases (MMP) for their substrates has been studied. We demonstrate that two of the MMP family members, Collagenase (MMP-1) and Gelatinase A (MMP-2) exhibit diffusion along their substrates, the importance of this diffusion process and its biological implications are discussed. We show through truncation mutants that the hemopexin domain of the MMP-2 plays and important role in the substrate diffusion of this enzyme. Single molecule diffusion of the collagenase MMP-1 has been observed on collagen fibrils and shown to be biased. The discovered biased diffusion would make the MMP-1 molecule an active motor, thus making it the first active motor that is not coupled to ATP hydrolysis. The possible sources of energy for this enzyme and their implications are discussed. We propose that a possible source of energy for the enzyme can be in the rearrangement of the structure of collagen fibrils. In a separate application, using the methods developed here, we have observed an intermediate in the intestinal fatty acid binding protein folding process through the changes in its hydrodynamic radius also the fluctuations in the structure of the IFABP in solution were measured using FCS.

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

    Science.gov (United States)

    Maley, Nagendranath

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-12-10

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

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

    CERN Document Server

    Saurabh, Prasoon

    2016-01-01

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

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

    Science.gov (United States)

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

    2008-11-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-06-18

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

  11. Single Molecule Spectroscopy in Chemistry, Physics and Biology Nobel Symposium

    CERN Document Server

    Gräslund, Astrid; Widengren, Jerker

    2010-01-01

    Written by the leading experts in the field, this book describes the development and current state-of-the-art in single molecule spectroscopy. The application of this technique, which started 1989, in physics, chemistry and biosciences is displayed.

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

    Science.gov (United States)

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

    1999-05-01

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

  13. Feasibility Study of Using Short Wave Infrared Cavity Ringdown Spectroscopy (SWIR-CRDS) for Biological Agent Detection

    Energy Technology Data Exchange (ETDEWEB)

    Aker, Pam M.; Johnson, Timothy J.; Williams, Richard M.; Valentine, Nancy B.

    2007-10-01

    This project focused on determining the feasibility of using short wave infrared (SWIR) cavity ring down spectroscopy (CRDS) as a means for real-time detection of biological aerosols. The first part of the project involved identifying biological agent signatures that could be detected with SWIR CRDS. After an exhaustive search of the open literature it was determined that whole biological spores and/or cells would not be good candidates for direct SWIR CRDS probing because they have no unique SWIR signatures. It was postulated that while whole cells or spores are not good candidates for SWIR CRDS detection, their pyrolysis break-down products might be. A literature search was then conducted to find biological pyrolysis products with low molecular weights and high symmetry since these species most likely would have overtone and combination vibrational bands that can be detected in the SWIR. It was determined that pyrrole, pyridine and picolinamide were good candidates for evaluation. These molecules are formed when proteins and porphyrins, proteins and dipicolinic acid, and dipicolinic acid are pyrolyzed, respectively. The second part of the project involved measuring quantitative SWIR spectra of pyrrole, pyridine and picolinamide in PNNL’s FTIR Spectroscopy Laboratory. Spectral information about these molecules, in the vapor phase is sparse – there were only a few prior studies that measured line positions and no information on absorption cross sections. Absorption cross sections are needed in order to estimate the SWIR CRDS detection sensitivity, and line position determines what type of laser will be needed for the sensor. The results of the spectroscopy studies allowed us to estimate the SWIR CRDS detection sensitivity for pyrrole to be 3 x 1012 molec cm-3 or 0.1 ppmv, and for pyridine it was 1.5 x 1015 molec cm-3 or 0.6 ppmv. These detection sensitivity limits are close what we have measured for ammonia. Given these detection limits we then estimated the

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-06-07

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

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

    Science.gov (United States)

    Dijkstra, Arend G; Tanimura, Yoshitaka

    2015-06-01

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

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

    Science.gov (United States)

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

    2009-05-15

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

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

    Science.gov (United States)

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

    2007-09-25

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

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

    Science.gov (United States)

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

    2015-10-14

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

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

    DEFF Research Database (Denmark)

    Lassen, Peter Rygaard

    2005-01-01

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

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

    Science.gov (United States)

    2010-02-03

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

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

    Indian Academy of Sciences (India)

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

    2008-09-01

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

  2. Terahertz time-domain spectroscopy in physics, chemistry, and biology

    DEFF Research Database (Denmark)

    Jepsen, Peter Uhd

    are investigating a wide range of applications of THz spectroscopy in medicine, gene analysis, safety and security, and pharmacy. In this presentation I will give an overview of THz research conducted in the recent years at the University of Freiburg. We have investigated fundamental interactions in ionic...

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

    CERN Document Server

    Maiti, Kiran Sankar; Scheurer, Christoph

    2016-01-01

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

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

    Science.gov (United States)

    Wang, Liang; Liu, Weimin; Fang, Chong

    2015-07-14

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

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

    Science.gov (United States)

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

    2014-04-01

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

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

    Science.gov (United States)

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

    2016-02-01

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

  7. CMOS based sensor for dielectric spectroscopy of biological cell suspension

    Science.gov (United States)

    Guha, S.; Schmalz, K.; Meliani, C.; Wenger, Ch

    2013-04-01

    In this work we investigate the use of microwave frequency range to measure the concentration of cells in a biological cell suspension. A theoretical model is discussed and the advantage of high frequency, which is to avoid dispersion mechanisms due to the cell parameters at lower frequencies (for example membrane capacitance), has been described. Interdigitated capacitor (IDC) has been proposed as the sensor for analysing the concentration of a cell species in the suspension. The read-out circuit is a VCO using the IDC and a pair of inductors as resonator. The capacitance of the IDC which is the function of the permittivity of the biological cell suspension determines the resonant frequency of the LC tank oscillator. Thus the concentration of cells in a solution, affecting its permittivity, is read out as the frequency of the oscillator.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2009-01-01

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

  10. Random matrix theory in biological nuclear magnetic resonance spectroscopy.

    Science.gov (United States)

    Lacelle, S

    1984-01-01

    The statistical theory of energy levels or random matrix theory is presented in the context of the analysis of chemical shifts of nuclear magnetic resonance (NMR) spectra of large biological systems. Distribution functions for the spacing between nearest-neighbor energy levels are discussed for uncorrelated, correlated, and random superposition of correlated energy levels. Application of this approach to the NMR spectra of a vitamin, an antibiotic, and a protein demonstrates the state of correlation of an ensemble of energy levels that characterizes each system. The detection of coherent and dissipative structures in proteins becomes feasible with this statistical spectroscopic technique. PMID:6478032

  11. Spectroscopy of Multilayered Biological Tissues for Diabetes Care

    Science.gov (United States)

    Yudovsky, Dmitry

    Neurological and vascular complications of diabetes mellitus are known to cause foot ulceration in diabetic patients. Present clinical screening techniques enable the diabetes care provider to triage treatment by identifying diabetic patients at risk of foot ulceration. However, these techniques cannot effectively identify specific areas of the foot at risk of ulceration. This study aims to develop non-invasive optical techniques for accurate assessment of tissue health and viability with spatial resolution on the order of 1 mm². The thesis can be divided into three parts: (1) the use of hyperspectral tissue oximetry to detect microcirculatory changes prior to ulcer formation, (2) development of a two-layer tissue spectroscopy algorithm and its application to detection of callus formation or epidermal degradation prior to ulceration, and (3) multi-layered tissue fluorescence modeling for identification of bacterial growth in existing diabetic foot wounds. The first part of the dissertation describes a clinical study in which hyperspectral tissue oximetry was performed on multiple diabetic subjects at risk of ulceration. Tissue oxyhemoglobin and deoxyhemoglobin concentrations were estimated using the Modified Beer-Lambert law. Then, an ulcer prediction algorithm was developed based on retrospective analysis of oxyhemoglobin and deoxyhemoglobin concentrations in sites that were known to ulcerate. The ulcer prediction algorithm exhibited a large sensitivity but low specificity of 95 and 80%, respectively. The second part of the dissertation revisited the hyperspectral data presented in part one with a new and novel two-layer tissue spectroscopy algorithm. This algorithm was able to detect not only oxyhemoglobin and deoxyhemoglobin concentrations, but also the thickness of the epidermis, and the tissue's scattering coefficient. Specifically, change in epidermal thickness provided insight into the formation of diabetic foot ulcers over time. Indeed, callus formation or

  12. Fluorescence correlation spectroscopy in biology, chemistry, and medicine.

    Science.gov (United States)

    Perevoshchikova, I V; Kotova, E A; Antonenko, Y N

    2011-05-01

    This review describes the method of fluorescence correlation spectroscopy (FCS) and its applications. FCS is used for investigating processes associated with changes in the mobility of molecules and complexes and allows researchers to study aggregation of particles, binding of fluorescent molecules with supramolecular complexes, lipid vesicles, etc. The size of objects under study varies from a few angstroms for dye molecules to hundreds of nanometers for nanoparticles. The described applications of FCS comprise various fields from simple chemical systems of solution/micelle to sophisticated regulations on the level of living cells. Both the methodical bases and the theoretical principles of FCS are simple and available. The present review is concentrated preferentially on FCS applications for studies on artificial and natural membranes. At present, in contrast to the related approach of dynamic light scattering, FCS is poorly known in Russia, although it is widely employed in laboratories of other countries. The goal of this review is to promote the development of FCS in Russia so that this technique could occupy the position it deserves in modern Russian science.

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

    Science.gov (United States)

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

    2016-04-28

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

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

    Science.gov (United States)

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

    2015-12-10

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

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

    Science.gov (United States)

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

    2004-12-01

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

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

    Science.gov (United States)

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

    2012-08-16

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

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

    Science.gov (United States)

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

    2014-04-01

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

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

    Science.gov (United States)

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

    2014-09-01

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

  19. Research of biological liquid albumin based on terahertz time domain spectroscopy

    Science.gov (United States)

    Yang, Shuai; Liu, Shang-jian; Zuo, Jian; Zhang, Cun-lin

    2016-11-01

    There is no corresponding fingerprint characteristic spectrum detecting complex ensemble biological samples in liquid, in the paper, such urine of kidney disease patients as samples of the research, using terahertz time-domain spectroscopy emphatically explores response characteristics of the urine albumin in the terahertz spectrum characteristics, and combined with stoichiometric method, we find a certain kind of relationship between terahertz spectrum data and the content of urine albumin, which offsets the defects of other spectroscopy in measuring liquid protein, and in accordance with hospital clinical data. This study established a semi-qualitative method of using terahertz spectroscopy in detecting non-purification of biological liquid sample, which provides a simple, nondestructive, cheap and fast reference method in identifying the early nephropathy for medical test.

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

    Science.gov (United States)

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

    2016-06-21

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Kobayashi Takayoshi.

    2013-03-01

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

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

    Science.gov (United States)

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

    2013-04-01

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

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

    Science.gov (United States)

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

    2016-09-01

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

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

    Science.gov (United States)

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

    2009-11-01

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

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

    Science.gov (United States)

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

    2006-08-01

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

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

    Science.gov (United States)

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

    2008-08-04

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

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

    Science.gov (United States)

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

    2017-03-01

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

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

    Science.gov (United States)

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

    2015-05-01

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

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

    Science.gov (United States)

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

    2010-01-01

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

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

    Science.gov (United States)

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

    2014-03-03

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

  12. Social inclusion enhances biological motion processing: a functional near-infrared spectroscopy study.

    Science.gov (United States)

    Bolling, Danielle Z; Pelphrey, Kevin A; Kaiser, Martha D

    2013-04-01

    Humans are especially tuned to the movements of other people. Neural correlates of this social attunement have been proposed to lie in and around the right posterior superior temporal sulcus (STS) region, which robustly responds to biological motion in contrast to a variety of non-biological motions. This response persists even when no form information is provided, as in point-light displays (PLDs). The aim of the current study was to assess the ability of functional near-infrared spectroscopy (fNIRS) to reliably measure brain responses to PLDs of biological motion, and determine the sensitivity of these responses to interpersonal contextual factors. To establish reliability, we measured brain activation to biological motion with fNIRS and functional magnetic resonance imaging (fMRI) during two separate sessions in an identical group of 12 participants. To establish sensitivity, brain responses to biological motion measured with fNIRS were subjected to an additional social manipulation where participants were either socially included or excluded before viewing PLDs of biological motion. Results revealed comparable brain responses to biological motion using fMRI and fNIRS in the right supramarginal gyrus. Further, social inclusion increased brain responses to biological motion in right supramarginal gyrus and posterior STS. Thus, fNIRS can reliably measure brain responses to biological motion and can detect social experience-dependent modulations of these brain responses.

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

    Science.gov (United States)

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

    2017-03-01

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

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

    Science.gov (United States)

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

    2013-03-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-10-15

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

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

    Science.gov (United States)

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

    2017-02-15

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

  17. 3D Motions of Iron in Six-Coordinate {FeNO}(7) Hemes by Nuclear Resonance Vibration Spectroscopy.

    Science.gov (United States)

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

    2016-04-25

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

  18. Oxygen chemistry in biology: Vibrational spectroscopy, stable isotopes, and future applications

    Energy Technology Data Exchange (ETDEWEB)

    Babcock, G.T. [Michigan State Univ., East Lansing, MI (United States)

    1994-12-01

    Dioxygen is an ideally suited substrate for enzymatic manipulation in oxidation-reduction chemistry and in substrate transformation. It is a powerful oxidant with a midpoint potential of 0.815 at neutral pH; at the same time, however, it exists in a triplet state in its most stable electronic configuration. This latter property confers kinetic inertness as a result of spin-conservation restrictions on reaction chemistry. If these restrictions can be overcome and controlled, dioxygen`s high redox potential can be used to maximize efficiency in free-energy conversion processes and to effect activation of relatively inert substrates.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-05-04

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-08-14

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

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

    Science.gov (United States)

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

    1994-02-01

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

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

    Science.gov (United States)

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

    1995-05-01

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

  3. Quantifying Carbon-14 for Biology Using Cavity Ring-Down Spectroscopy

    OpenAIRE

    McCartt, A. Daniel; Ognibene, Ted J.; Bench, Graham; Turteltaub, Kenneth W.

    2016-01-01

    A cavity ring-down spectroscopy (CRDS) instrument was developed using mature, robust hardware for the measurement of carbon-14 in biological studies. The system was characterized using carbon-14 elevated glucose samples and returned a linear response up to 387 times contemporary carbon-14 concentrations. Carbon-14 free and contemporary carbon-14 samples with varying carbon-13 concentrations were used to assess the method detection limit of approximately one-third contemporary carbon-14 levels...

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

    Science.gov (United States)

    Okuda, Masaki; Ohta, Kaoru; Tominaga, Keisuke

    2016-09-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-01-01

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

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

    Science.gov (United States)

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

    2013-06-01

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

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

    Science.gov (United States)

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

    2016-04-22

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-08-15

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2010-10-07

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

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

    Science.gov (United States)

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

    2016-03-01

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

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

    Science.gov (United States)

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

    2016-03-07

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    CERN Document Server

    Haydock, S A

    2002-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-01-10

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2014-09-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-07-17

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

  19. Spectral pre and post processing for infrared and Raman spectroscopy of biological tissues and cells.

    Science.gov (United States)

    Byrne, Hugh J; Knief, Peter; Keating, Mark E; Bonnier, Franck

    2016-04-07

    Vibrational spectroscopy, both infrared absorption and Raman spectroscopy, have attracted increasing attention for biomedical applications, from in vivo and ex vivo disease diagnostics and screening, to in vitro screening of therapeutics. There remain, however, many challenges related to the accuracy of analysis of physically and chemically inhomogeneous samples, across heterogeneous sample sets. Data preprocessing is required to deal with variations in instrumental responses and intrinsic spectral backgrounds and distortions in order to extract reliable spectral data. Data postprocessing is required to extract the most reliable information from the sample sets, based on often very subtle changes in spectra associated with the targeted pathology or biochemical process. This review presents the current understanding of the factors influencing the quality of spectra recorded and the pre-processing steps commonly employed to improve on spectral quality. It further explores some of the most common techniques which have emerged for classification and analysis of the spectral data for biomedical applications. The importance of sample presentation and measurement conditions to yield the highest quality spectra in the first place is emphasised, as is the potential of model simulated datasets to validate both pre- and post-processing protocols.

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

    Science.gov (United States)

    Johannessen, Christian; Thulstrup, Peter W

    2007-03-14

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

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

    Science.gov (United States)

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

    2006-10-28

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-09-15

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

  3. Spectroscopy of scattered light for the characterization of micro and nanoscale objects in biology and medicine.

    Science.gov (United States)

    Turzhitsky, Vladimir; Qiu, Le; Itzkan, Irving; Novikov, Andrei A; Kotelev, Mikhail S; Getmanskiy, Michael; Vinokurov, Vladimir A; Muradov, Alexander V; Perelman, Lev T

    2014-01-01

    The biomedical uses for the spectroscopy of scattered light by micro and nanoscale objects can broadly be classified into two areas. The first, often called light scattering spectroscopy (LSS), deals with light scattered by dielectric particles, such as cellular and sub-cellular organelles, and is employed to measure their size or other physical characteristics. Examples include the use of LSS to measure the size distributions of nuclei or mitochondria. The native contrast that is achieved with LSS can serve as a non-invasive diagnostic and scientific tool. The other area for the use of the spectroscopy of scattered light in biology and medicine involves using conducting metal nanoparticles to obtain either contrast or electric field enhancement through the effect of the surface plasmon resonance (SPR). Gold and silver metal nanoparticles are non-toxic, they do not photobleach, are relatively inexpensive, are wavelength-tunable, and can be labeled with antibodies. This makes them very promising candidates for spectrally encoded molecular imaging. Metal nanoparticles can also serve as electric field enhancers of Raman signals. Surface enhanced Raman spectroscopy (SERS) is a powerful method for detecting and identifying molecules down to single molecule concentrations. In this review, we will concentrate on the common physical principles, which allow one to understand these apparently different areas using similar physical and mathematical approaches. We will also describe the major advancements in each of these areas, as well as some of the exciting recent developments.

  4. A rapid screening method for heavy metals in biological materials by emission spectroscopy.

    Science.gov (United States)

    Blacklock, E C; Sadler, P A

    1981-06-02

    A semi-quantitative screening method for heavy metals in biological material is described. The metals are complexed with ammonium pyrrolidine dithiocarbamate, sodium diethyl dithiocarbamate and potassium sodium tartrate. The solutions are adjusted to pH 4 and then extracted into chloroform. The chloroform phase is evaporated onto a matrix mixture of lithium fluoride and graphite. The sample is analysed by direct current arc emission spectroscopy using a 3 metre grating spectrograph. The spectra are recorded on a photographic plate. The method is developed on aqueous and spiked samples and then applied to in vivo samples containing toxic levels of heavy metals. Atomic absorption spectroscopy is used to check standard concentrations and to monitor the efficiency of the extraction procedure.

  5. Application of terahertz spectroscopy for characterization of biologically active organic molecules in natural environment

    Science.gov (United States)

    Karaliūnas, Mindaugas; Jakštas, Vytautas; Nasser, Kinan E.; Venckevičius, Rimvydas; Urbanowicz, Andrzej; Kašalynas, Irmantas; Valušis, Gintaras

    2016-09-01

    In this work, a comparative research of biologically active organic molecules in its natural environment using the terahertz (THz) time domain spectroscopy (TDS) and Fourier transform spectroscopy (FTS) systems is carried out. Absorption coefficient and refractive index of Nicotiana tabacum L. leaves containing nicotine, Cannabis sativa L. leaves containing tetrahydrocannabinol, and Humulu lupulus L. leaves containing α-acids, active organic molecules that obtain in natural environment, were measured in broad frequency range from 0.1 to 13 THz at room temperature. In the spectra of absorption coefficient the features were found to be unique for N. tabacum, C. sativa and H. lupulus. Moreover, those features can be exploited for identification of C. sativa sex and N. tabacum origin. The refractive index can be also used to characterize different species.

  6. Surface-enhanced Raman spectroscopy at single-molecule scale and its implications in biology.

    Science.gov (United States)

    Wang, Yuling; Irudayaraj, Joseph

    2013-02-05

    Single-molecule (SM) spectroscopy has been an exciting area of research offering significant promise and hope in the field of sensor development to detect targets at ultra-low levels down to SM resolution. To the experts and developers in the field of surface-enhanced Raman spectroscopy (SERS), this has often been a challenge and a significant opportunity for exploration. Needless to say, the opportunities and excitement of this multidisciplinary area impacts span the fields of physics, chemistry and engineering, along with a significant thrust in applications constituting areas in medicine, biology, environment and agriculture among others. In this review, we will attempt to provide a quick snapshot of the basics of SM-SERS, nanostructures and devices that can enable SM Raman measurement. We will conclude with a discussion on SERS implications in biomedical sciences.

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

    Science.gov (United States)

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

    2014-09-28

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

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

    Science.gov (United States)

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

    2011-05-01

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

  9. Quantifying Carbon-14 for Biology Using Cavity Ring-Down Spectroscopy.

    Science.gov (United States)

    McCartt, A Daniel; Ognibene, Ted J; Bench, Graham; Turteltaub, Kenneth W

    2016-09-06

    A cavity ring-down spectroscopy (CRDS) instrument was developed using mature, robust hardware for the measurement of carbon-14 in biological studies. The system was characterized using carbon-14 elevated glucose samples and returned a linear response up to 387 times contemporary carbon-14 concentrations. Carbon-14 free and contemporary carbon-14 samples with varying carbon-13 concentrations were used to assess the method detection limit of approximately one-third contemporary carbon-14 levels. Sources of inaccuracies are presented and discussed, and the capability to measure carbon-14 in biological samples is demonstrated by comparing pharmacokinetics from carbon-14 dosed guinea pigs analyzed by both CRDS and accelerator mass spectrometry. The CRDS approach presented affords easy access to powerful carbon-14 tracer techniques that can characterize complex biochemical systems.

  10. 2D-Cosy NMR Spectroscopy as a Quantitative Tool in Biological Matrix: Application to Cyclodextrins.

    Science.gov (United States)

    Dufour, Gilles; Evrard, Brigitte; de Tullio, Pascal

    2015-11-01

    Classical analytical quantifications in biological matrices require time-consuming sample pre-treatments and extractions. Nuclear magnetic resonance (NMR) analysis does not require heavy sample treatments or extractions which therefore increases its accuracy in quantification. In this study, even if quantitative (q)NMR could not be applied to 2D spectra, we demonstrated that cross-correlations and diagonal peak intensities have a linear relationship with the analyzed pharmaceutical compound concentration. This work presents the validation process of a 2D-correlation spectroscopy (COSY) NMR quantification of 2-hydroxypropyl-β-cyclodextrin in plasma. Specificity, linearity, precision (repeatability and intermediate precision), trueness, limits of quantification (LOQs), and accuracy were used as validation criteria. 2D-NMR could therefore be used as a valuable and accurate analytical technique for the quantification of pharmaceutical compounds, including hardly detectable compounds such as cyclodextrins or poloxamers, in complex biological matrices based on a calibration curve approach.

  11. Magnetic nanoparticles in different biological environments analyzed by magnetic particle spectroscopy

    Science.gov (United States)

    Löwa, Norbert; Seidel, Maria; Radon, Patricia; Wiekhorst, Frank

    2017-04-01

    Quantification of magnetic iron oxide nanoparticles (MNP) in biological systems like cells, tissue, or organs is of vital importance for development of novel biomedical applications, e.g. magnetofection, drug targeting or hyperthermia. Among others, the recently developed magnetic measurement technique magnetic particle spectroscopy (MPS) provides signals that are specific for MNP. MPS is based on the non-linear magnetic response of MNP exposed to a strong sinusoidal excitation field of up to 25 mT amplitude and 25 kHz frequency. So far, it has been proven a powerful tool for quantification of MNP in biological systems. In this study we investigated in detail the influence of typical biological media on the magnetic behavior of different MNP systems by MPS. The results reveal that amplitude and shape (ratio of harmonics) of the MPS spectra allow for perceptively monitoring changes in MNP magnetism caused by different physiological media. Additionally, the observed linear correlation between MPS amplitude and shape alterations can be used to reduce the quantification uncertainty for MNP suspended in a biological environment.

  12. Application of high-resolution photoelectron spectroscopy: Vibrational resolved C 1s and O 1s spectra of CO adsorbed on Ni(100)

    Energy Technology Data Exchange (ETDEWEB)

    Foehlisch, A.; Nilsson, A.; Martensson, N. [Uppsala Univ. (Sweden)] [and others

    1997-04-01

    There are various effects which determine the line shape of a core-level electron spectrum. These are due to the finite life-time of the core hole, inelastic scattering of the outgoing photoelectron, electronic shake-up and shake-off processes and vibrational excitations. For free atoms and molecules the different contributions to the observed line shapes can often be well separated. For solids, surfaces and adsorbates the line shapes are in general much broader and it has in the past been assumed that no separation of the various contributions can be made. In the present report the authors will show that this is indeed not the case. Surprisingly, the vibrational fine structure of CO adsorbed on Ni(100) can be resolved in the C 1s and O 1s electron spectra. This was achieved by the combination of highly monochromatized soft X-rays from B18.0 with a high resolution Scienta 200 mm photoelectron spectrometer. X-ray photoelectron spectroscopy (XPS) with tunable excitation energy yields as a core level spectroscopy atomic and site-specific information. The presented measurements allow for a determination of internuclear distances and potential energy curves in corehole ionized adsorbed molecules. The authors analysis of the c(2x2) phase CO/Ni(100) on {open_quotes}top{close_quotes} yielded a vibrational splitting of 217 +/- 2 meV for C 1s ionization. For O 1s ionization a splitting of 173 +/- 8 meV was found.

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

    Science.gov (United States)

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

    2013-09-01

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

  14. Vibrational spectroscopy and electrophoresis as a "golden means" in monitoring of polysaccharides in medical plant and gels

    Science.gov (United States)

    Pielesz, A.

    In recent years, some bioactive polysaccharides isolated from natural sources have attracted much attention in the field of biochemistry and pharmacology. Of them, polysaccharides or their glycoconjugates were shown to exhibit multiple biological activities including anticarcinogenic, anticoagulant, immunostimulating, antioxidant, etc. Pharmacotherapy using plant-derived substances can be currently regarded as a very promising future alternative to conventional therapy. The advanced biotechnologies available today enable chemical investigation of well-defined bioactive plant components as sources of novel drugs. The need for safer drugs without side effects has led to the use of natural ingredients with proven safety. Special interest is focused on plant polysaccharides. This article attempts to review the current structural and conformational characterization of some importantly bioactive monosaccharides isolated from following plant cell-wall: Symphytum officinale (comfrey), Thymus pulegioides (thyme), Trigonella foenum-graecum L. (fenugreek), Tussilago farfara L. (coltsfoot), Hyssopus officinalis (hyssop), Althaea officinalis L. (marshmallow) and Equisetum arvense L. (horsetail). The chemical structures of monosaccharides were analysed using FTIR and Raman spectroscopies as well as cellulose acetate membrane electrophoresis (CAE). The dried plant samples were gently hydrolysed with sulphuric acid. The presence of glucuronic acid, galacturonic acid, alginic acid, glucose, mannose and xylose in the hydrolysates of reference substances and non-defatted plant films was proved. The possibility of a taxonomic classification of plant cell walls based on infrared and Raman spectroscopies and the use of spectral fingerprinting for authentication and detection of adulteration of products rich in cell-wall materials are discussed. Individual bands were selected to monitor the sugar content in medical plant cell walls and to confirm the identity of the analysed plants.

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

    Science.gov (United States)

    Iwasa, Takeshi; Takenaka, Masato; Taketsugu, Tetsuya

    2016-03-28

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

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

    DEFF Research Database (Denmark)

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

    2006-01-01

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

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

    DEFF Research Database (Denmark)

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

    2003-01-01

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

  18. Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Hellman, Hal

    1968-01-01

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

  19. Spectroscopy

    CERN Document Server

    Walker, S

    1976-01-01

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

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

    Science.gov (United States)

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

    2015-11-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez S, A.; Martinez Q, E

    1990-07-15

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

  2. X-ray absorption spectroscopy in biological systems. Opportunities and limitations

    Energy Technology Data Exchange (ETDEWEB)

    Bovenkamp, Gudrun Lisa

    2013-05-15

    X-ray absorption spectroscopy has become more important for applications in the material sciences, geology, environmental science and biology, specifically in the field of molecular biology. The scope of this thesis is to add more experimental evidence in order to show how applicable X-ray absorption near edge structure (XANES) is to biology. Two biological systems were investigated, at the molecular level, lead uptake in plants and the effect of silver on bacteria. This investigation also included an analysis of the sensitivity of Pb L{sub 3}- and Ag L{sub 3}-XANES spectra with regard to their chemical environment. It was shown that Pb L{sub 3}- and Ag L{sub 3}-XANES spectra are sensitive to an environment with at least differences in the second coordination shell. The non-destructive and element specific properties of XANES are the key advantages that were very important for this investigation. However, in both projects the adequate selection of reference compounds, which required in some cases a chemical synthesis, was the critical factor to determine the chemical speciation and, finally, possible uptake and storage mechanisms for plants and antibacterial mechanisms of silver. The chemical environment of Pb in roots and leaves of plants from four different plant families and a lichen from a former lead mining site in the Eifel mountains in Germany was determined using both solid compounds and aqueous solutions of different ionic strength, which simulate the plant environment. The results can be interpreted in such a way that lead is sorbed on the surface of cell walls. Silver bonding as reaction with Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli bacteria was determined using inorganic silver compounds and synthesized silver amino acids. Silver binds to sulfur, amine and carboxyl groups in amino acids.

  3. 3D Imaging of Nanoparticle Distribution in Biological Tissue by Laser-Induced Breakdown Spectroscopy

    Science.gov (United States)

    Gimenez, Y.; Busser, B.; Trichard, F.; Kulesza, A.; Laurent, J. M.; Zaun, V.; Lux, F.; Benoit, J. M.; Panczer, G.; Dugourd, P.; Tillement, O.; Pelascini, F.; Sancey, L.; Motto-Ros, V.

    2016-07-01

    Nanomaterials represent a rapidly expanding area of research with huge potential for future medical applications. Nanotechnology indeed promises to revolutionize diagnostics, drug delivery, gene therapy, and many other areas of research. For any biological investigation involving nanomaterials, it is crucial to study the behavior of such nano-objects within tissues to evaluate both their efficacy and their toxicity. Here, we provide the first account of 3D label-free nanoparticle imaging at the entire-organ scale. The technology used is known as laser-induced breakdown spectroscopy (LIBS) and possesses several advantages such as speed of operation, ease of use and full compatibility with optical microscopy. We then used two different but complementary approaches to achieve 3D elemental imaging with LIBS: a volume reconstruction of a sliced organ and in-depth analysis. This proof-of-concept study demonstrates the quantitative imaging of both endogenous and exogenous elements within entire organs and paves the way for innumerable applications.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Westerberg, Staffan Per Gustav

    2004-12-15

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

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

    Directory of Open Access Journals (Sweden)

    Cîntă-Pînzaru Simona

    2012-07-01

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

  7. Improved preparation of small biological samples for mercury analysis using cold vapor atomic absorption spectroscopy.

    Science.gov (United States)

    Adair, B M; Cobb, G P

    1999-05-01

    Concentrations of mercury in biological samples collected for environmental studies are often less than 0.1 microgram/g. Low mercury concentrations and small organ sizes in many wildlife species (approximately 0.1 g) increase the difficulty of mercury determination at environmentally relevant concentrations. We have developed a digestion technique to extract mercury from small (0.1 g), biological samples at these relevant concentrations. Mean recoveries (+/- standard error) from validation trials of mercury fortified tissue samples using cold vapor atomic absorption spectroscopy for analysis ranged from 102 +/- 4.3% (2.5 micrograms/L, n = 15) to 108 +/- 1.4% (25 micrograms/L, n = 15). Recoveries of inorganic mercury were 99 +/- 5 (n = 19) for quality assurance samples analyzed during environmental evaluations conducted during a 24 month period. This technique can be used to determine total mercury concentrations of 60 ng Hg/g sample. Samples can be analyzed in standard laboratories in a short time, at minimal cost. The technique is versatile and can be used to determine mercury concentrations in several different matrices, limiting the time and expense of method development and validation.

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

    Institute of Scientific and Technical Information of China (English)

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

    2010-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-05-15

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

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

    Science.gov (United States)

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

    2015-09-01

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

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

    Science.gov (United States)

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

    2010-12-01

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

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

    KAUST Repository

    Michalak, William D.

    2013-01-31

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

  13. Communication: He-tagged vibrational spectra of the SarGlyH{sup +} and H{sup +}(H{sub 2}O){sub 2,3} ions: Quantifying tag effects in cryogenic ion vibrational predissociation (CIVP) spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Christopher J.; Wolk, Arron B.; Fournier, Joseph A.; Johnson, Mark A. [Sterling Chemistry Laboratory, Yale University, 225 Prospect St., New Haven, Connecticut 06520 (United States); Sullivan, Erin N. [Department of Chemistry and Biochemistry, Fairfield University, 1073 North Benson Rd., Fairfield, Connecticut 06824 (United States); Weddle, Gary H. [Sterling Chemistry Laboratory, Yale University, 225 Prospect St., New Haven, Connecticut 06520 (United States); Department of Chemistry and Biochemistry, Fairfield University, 1073 North Benson Rd., Fairfield, Connecticut 06824 (United States)

    2014-06-14

    To assess the degree to which more perturbative, but widely used “tag” species (Ar, H{sub 2}, Ne) affect the intrinsic band patterns of the isolated ions, we describe the extension of mass-selective, cryogenic ion vibrational spectroscopy to the very weakly interacting helium complexes of three archetypal ions: the dipeptide SarGlyH{sup +} and the small protonated water clusters: H{sup +}(H{sub 2}O){sub 2,3}, including the H{sub 5}O{sub 2}{sup +} “Zundel” ion. He adducts were generated in a 4.5 K octopole ion trap interfaced to a double-focusing, tandem time-of-flight photofragmentation mass spectrometer to record mass-selected vibrational predissociation spectra. The H{sub 2} tag-induced shift (relative to that by He) on the tag-bound NH stretch of the SarGlyH{sup +} spectrum is quite small (12 cm{sup −1}), while the effect on the floppy H{sub 5}O{sub 2}{sup +} ion is more dramatic (125 cm{sup −1}) in going from Ar (or H{sub 2}) to Ne. The shifts from Ne to He, on the other hand, while quantitatively significant (maximum of 10 cm{sup −1}), display the same basic H{sub 5}O{sub 2}{sup +} band structure, indicating that the He-tagged H{sub 5}O{sub 2}{sup +} spectrum accurately represents the delocalized nature of the vibrational zero-point level. Interestingly, the He-tagged spectrum of H{sup +}(H{sub 2}O){sub 3} reveals the location of the non-bonded OH group on the central H{sub 3}O{sup +} ion to fall between the collective non-bonded OH stretches on the flanking water molecules in a position typically associated with a neutral OH group.

  14. Introduction: Andrew Thomson and the Centre for Metalloprotein Spectroscopy and Biology at the University of East Anglia.

    Science.gov (United States)

    Wilson, Michael T

    2008-12-01

    The present article briefly relates the early history and growth of the Centre for Metalloprotein Spectroscopy and Biology at UEA (University of East Anglia) under the joint directorship of A.J. Thomson and C. Greenwood, and charts the exceptional success that this centre has had in fostering bioinorganic chemistry in the U.K. and the impact that it has had internationally.

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

    NARCIS (Netherlands)

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

    2008-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-05-07

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

  17. Lanthanide tris(β-diketonates) as useful probes for chirality determination of biological amino alcohols in vibrational circular dichroism: ligand to ligand chirality transfer in lanthanide coordination sphere.

    Science.gov (United States)

    Miyake, Hiroyuki; Terada, Keiko; Tsukube, Hiroshi

    2014-06-01

    A series of lanthanide tris(β-diketonates) functioned as useful chirality probes in the vibrational circular dichroism (VCD) characterization of biological amino alcohols. Various chiral amino alcohols induced intense VCD signals upon ternary complexation with racemic lanthanide tris(β-diketonates). The VCD signals observed around 1500 cm(-1) (β-diketonate IR absorption region) correlated well with the stereochemistry and enantiomeric purity of the targeted amino alcohol, while the corresponding monoalcohol, monoamine, and diol substrates induced very weak VCD signals. The high-coordination number and dynamic property of the lanthanide complex offer an effective chirality VCD probing of biological substrates.

  18. Spectroscopic characterization of biological agents using FTIR, normal Raman and surface-enhanced Raman spectroscopies

    Science.gov (United States)

    Luna-Pineda, Tatiana; Soto-Feliciano, Kristina; De La Cruz-Montoya, Edwin; Pacheco Londoño, Leonardo C.; Ríos-Velázquez, Carlos; Hernández-Rivera, Samuel P.

    2007-04-01

    FTIR, Raman spectroscopy and Surface Enhanced Raman Scattering (SERS) requires a minimum of sample allows fast identification of microorganisms. The use of this technique for characterizing the spectroscopic signatures of these agents and their stimulants has recently gained considerable attention due to the fact that these techniques can be easily adapted for standoff detection from considerable distances. The techniques also show high sensitivity and selectivity and offer near real time detection duty cycles. This research focuses in laying the grounds for the spectroscopic differentiation of Staphylococcus spp., Pseudomonas spp., Bacillus spp., Salmonella spp., Enterobacter aerogenes, Proteus mirabilis, Klebsiella pneumoniae, and E. coli, together with identification of their subspecies. In order to achieve the proponed objective, protocols to handle, cultivate and analyze the strains have been developed. Spectroscopic similarities and marked differences have been found for Spontaneous or Normal Raman spectra and for SERS using silver nanoparticles have been found. The use of principal component analysis (PCA), discriminate factor analysis (DFA) and a cluster analysis were used to evaluate the efficacy of identifying potential threat bacterial from their spectra collected on single bacteria. The DFA from the bacteria Raman spectra show a little discrimination between the diverse bacterial species however the results obtained from the SERS demonstrate to be high discrimination technique. The spectroscopic study will be extended to examine the spores produced by selected strains since these are more prone to be used as Biological Warfare Agents due to their increased mobility and possibility of airborne transport. Micro infrared spectroscopy as well as fiber coupled FTIR will also be used as possible sensors of target compounds.

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

    Science.gov (United States)

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

    2013-12-01

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

  20. IRMPD spectroscopy of protonated S-nitrosocaptopril, a biologically active, synthetic amino acid.

    Science.gov (United States)

    Coletti, Cecilia; Re, Nazzareno; Scuderi, Debora; Maître, Philippe; Chiavarino, Barbara; Fornarini, Simonetta; Lanucara, Francesco; Sinha, Rajeev K; Crestoni, Maria Elisa

    2010-11-07

    S-Nitrosocaptopril, a biologically active S-nitrosothiol, is generated as protonated species and isolated in the gas phase by electrospray ionization coupled to Fourier Transform Ion Cyclotron Resonance (FT-ICR) or ion-trap mass spectrometry. The structural and IR spectroscopic characterization of protonated S-nitrosocaptopril (SNOcapH(+)) is aided by the comparative study of the parent species lacking the NO feature, namely protonated captopril. The study is accomplished by methodologies based on tandem mass spectrometry, namely by energy resolved collision-induced dissociation and infrared multiple-photon dissociation (IRMPD) spectroscopy, backed by density functional theory calculations. IRMPD spectra have been obtained both in the 1000-1900 cm(-1) fingerprint range, using a beamline of the infrared free electron laser (IR-FEL) at the Centre Laser Infrarouge d'Orsay (CLIO), and in the O-H and N-H stretching region (2900-3700 cm(-1)) using the tunable IR radiation of a tabletop parametric oscillator/amplifier (OPO/OPA) laser source. The structural features of the ion have been ascertained by comparison of the experimental IRMPD spectra with the IR transitions calculated for the lowest energy isomers. Evidence is obtained that protonation occurs at the amide carbonyl oxygen which is found to be the thermodynamically most basic site. However, SNOcapH(+) is present as a thermally equilibrated mixture of low-energy structures, with a major contribution of the most stable isomer characterized by a trans relationship of the positively charged OH group with respect to the carboxylic acid functionality on the adjacent proline ring and by an anti conformation at the S-N (partial) double bond, though the energy difference with the analogous trans-syn isomer is less than 1 kJ mol(-1). The highly diagnostic N-O stretching mode has been unambiguously identified, which may be regarded as an informative probe for S-nitrosation features in more complex, biologically active

  1. Absolute Configuration Assignment of a Paraconic Acid Derivative via Vibrational Circular Dichroism Spectroscopy and Density Functional Theory Calculation.

    Science.gov (United States)

    Meninno, Sara; Rizzo, Paola; Abbate, Sergio; Longhi, Giovanna; Mazzeo, Giuseppe; Monaco, Guglielmo; Lattanzi, Alessandra; Zanasi, Riccardo

    2016-02-01

    Density functional theory calculation of the vibrational circular dichroism spectrum was used to assign the absolute configuration of an all-carbon quaternary β-stereocenter of a γ-butyrolactone recently synthesized through an asymmetric organocatalytic tandem aldol/lactonization sequence. Comparison with the experimental spectrum is satisfactory, on account of the fact that spectroscopic features are weak due to the presence of multiple conformers. As a result, the (R) absolute configuration was assigned to the (+) optical isomer.

  2. Technique for examining biological materials using diffuse reflectance spectroscopy and the kubelka-munk function

    Energy Technology Data Exchange (ETDEWEB)

    Alfano, Robert R.; Yang, Yuanlong

    2003-09-02

    Method and apparatus for examining biological materials using diffuse reflectance spectroscopy and the Kubelka-Munk function. In one aspect, the method is used to determine whether a tissue sample is cancerous or not and comprises the steps of (a) measuring the diffuse reflectance from the tissue sample at a first wavelength and at a second wavelength, wherein the first wavelength is a wavelength selected from the group consisting of 255-265 nm and wherein the second wavelength is a wavelength selected from the group consisting of 275-285 nm; (b) using the Kubelka-Munk function to transform the diffuse reflectance measurement obtained at the first and second wavelengths; and (c) comparing a ratio or a difference of the transformed Kubelka-Munk measurements at the first and second wavelengths to appropriate standards determine whether or not the tissue sample is cancerous. One can use the spectral profile of KMF between 250 nm to 300 nm to determine whether or not the tissue sample is cancerous or precancerous. According to the value at the first and second wavelengths determine whether or not the malignant tissue is invasive or mixed invasive and in situ or carcinoma in situ.

  3. Biological effects and physical safety aspects of NMR imaging and in vivo spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tenforde, T.S.; Budinger, T.F.

    1985-08-01

    An assessment is made of the biological effects and physical hazards of static and time-varying fields associated with the NMR devices that are being used for clinical imaging and in vivo spectroscopy. A summary is given of the current state of knowledge concerning the mechanisms of interaction and the bioeffects of these fields. Additional topics that are discussed include: (1) physical effects on pacemakers and metallic implants such as aneurysm clips, (2) human health studies related to the effects of exposure to nonionizing electromagnetic radiation, and (3) extant guidelines for limiting exposure of patients and medical personnel to the fields produced by NMR devices. On the basis of information available at the present time, it is concluded that the fields associated with the current generation of NMR devices do not pose a significant health risk in themselves. However, rigorous guidelines must be followed to avoid the physical interaction of these fields with metallic implants and medical electronic devices. 476 refs., 5 figs., 2 tabs.

  4. Diffuse reflectance spectroscopy and optical polarization imaging of in-vivo biological tissue

    Science.gov (United States)

    Mora-Núñez, A.; Castillejos, Y.; García-Torales, G.; Martínez-Ponce, G.

    2013-11-01

    A number of optical techniques have been reported in the scientific literature as accomplishable methodologies to diagnose diseases in biological tissue, for instance, diffuse reflectance spectroscopy (DRS) and optical polarization imaging (OPI). The skin is the largest organ in the body and consists of three primary layers, namely, the epidermis (the outermost layer exposed to the world), the dermis, and the hypodermis. The epidermis changes from to site to site, mainly because of difference in hydration. A lower water content increase light scattering and reduce the penetration depth of radiation. In this work, two hairless mice have been selected to evaluate their skin features by using DRS and OPI. Four areas of the specimen body were chosen to realize the comparison: back, abdomen, tail, and head. From DRS, it was possible to distinguish the skin nature because of different blood irrigation at dermis. In the other hand, OPI shows pseudo-depolarizing regions in the measured Mueller images related to a spatially varying propagation of the scattered light. This provides information about the cell size in the irradiated skin.

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

    Science.gov (United States)

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

    2017-01-01

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

  6. Intrinsic chirality and prochirality at Air/R-(+)- and S-(-)-limonene interfaces: spectral signatures with interference chiral sum-frequency generation vibrational spectroscopy.

    Science.gov (United States)

    Fu, Li; Zhang, Yun; Wei, Zhe-Hao; Wang, Hong-Fei

    2014-09-01

    We report in this work detailed measurements of the chiral and achiral sum-frequency vibrational spectra in the C-H stretching vibration region (2800-3050 cm(-1)) of the air/liquid interfaces of R-(+)-limonene and S-(-)-limonene, using the recently developed high-resolution broadband sum-frequency generation vibrational spectroscopy (HR-BB-SFG-VS). The achiral SFG spectra of R-limonene and S-limonene, as well as the RS racemic mixture (50/50 equal amount mixture), show that the corresponding molecular groups of the R and S enantiomers are with the same interfacial orientations. The interference chiral SFG spectra of the limonene enantiomers exhibit a spectral signature from the chiral response of the Cα-H stretching mode, and a spectral signature from the prochiral response of the CH(2) asymmetric stretching mode, respectively. The chiral spectral feature of the Cα-H stretching mode changes sign from R-(+)-limonene to S-(-)-limonene surfaces, and disappears for the RS racemic mixture surface. While the prochiral spectral feature of the CH(2) asymmetric stretching mode is the same for R-(+)-limonene and S-(-)-limonene surfaces, and also surprisingly remains the same for the RS racemic mixture surface. Therefore, the structures of the R-(+)-limonene and the S-(-)-limonene at the liquid interfaces are nevertheless not mirror images to each other, even though the corresponding groups have the same tilt angle from the interfacial normal, i.e., the R-(+)-limonene and the S-(-)-limonene at the surface are diastereomeric instead of enantiomeric. These results provide detailed information in understanding the structure and chirality of molecular interfaces and demonstrate the sensitivity and potential of SFG-VS as a unique spectroscopic tool for chirality characterization and chiral recognition at the molecular interface.

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

    Science.gov (United States)

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

    2015-03-01

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

  8. Excited-state intramolecular hydrogen transfer (ESIHT) of 1,8-Dihydroxy-9,10-anthraquinone (DHAQ) characterized by ultrafast electronic and vibrational spectroscopy and computational modeling

    KAUST Repository

    Mohammed, Omar F.

    2014-05-01

    We combine ultrafast electronic and vibrational spectroscopy and computational modeling to investigate the photoinduced excited-state intramolecular hydrogen-transfer dynamics in 1,8-dihydroxy-9,10-anthraquinone (DHAQ) in tetrachloroethene, acetonitrile, dimethyl sulfoxide, and methanol. We analyze the electronic excited states of DHAQ with various possible hydrogen-bonding schemes and provide a general description of the electronic excited-state dynamics based on a systematic analysis of femtosecond UV/vis and UV/IR pump-probe spectroscopic data. Upon photoabsorption at 400 nm, the S 2 electronic excited state is initially populated, followed by a rapid equilibration within 150 fs through population transfer to the S 1 state where DHAQ exhibits ESIHT dynamics. In this equilibration process, the excited-state population is distributed between the 9,10-quinone (S2) and 1,10-quinone (S1) states while undergoing vibrational energy redistribution, vibrational cooling, and solvation dynamics on the 0.1-50 ps time scale. Transient UV/vis pump-probe data in methanol also suggest additional relaxation dynamics on the subnanosecond time scale, which we tentatively ascribe to hydrogen bond dynamics of DHAQ with the protic solvent, affecting the equilibrium population dynamics within the S2 and S1 electronic excited states. Ultimately, the two excited singlet states decay with a solvent-dependent time constant ranging from 139 to 210 ps. The concomitant electronic ground-state recovery is, however, only partial because a large fraction of the population relaxes to the first triplet state. From the similarity of the time scales involved, we conjecture that the solvent plays a crucial role in breaking the intramolecular hydrogen bond of DHAQ during the S2/S1 relaxation to either the ground or triplet state. © 2014 American Chemical Society.

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

    Science.gov (United States)

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

    2015-03-05

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

  10. Vibrational spectroscopy of the phosphate mineral lazulite - (Mg, Fe)Al2(PO4)2·(OH)2 found in the Minas Gerais, Brazil

    Science.gov (United States)

    Frost, Ray L.; Xi, Yunfei; Beganovic, Martina; Belotti, Fernanda Maria; Scholz, Ricardo

    2013-04-01

    This research was done on lazulite samples from the Gentil mine, a lithium bearing pegmatite located in the municipality of Mendes Pimentel, Minas Gerais, Brazil. Chemical analysis was carried out by electron microprobe analysis and indicated a magnesium rich phase with partial substitution of iron. Traces of Ca and Mn, (which partially replaced Mg) were found. The calculated chemical formula of the studied sample is: (Mg0.88, Fe0.11)Al1.87(PO4)2.08(OH)2.02. The Raman spectrum of lazulite is dominated by an intense sharp band at 1060 cm-1 assigned to PO stretching vibrations of of tetrahedral [PO4] clusters presents into the HPO42- units. Two Raman bands at 1102 and 1137 cm-1 are attributed to both the HOP and PO antisymmetric stretching vibrations. The two infrared bands at 997 and 1007 cm-1 are attributed to the ν1PO43- symmetric stretching modes. The intense bands at 1035, 1054, 1081, 1118 and 1154 cm-1 are assigned to the ν3PO43- antisymmetric stretching modes from both the HOP and tetrahedral [PO4] clusters. A set of Raman bands at 605, 613, 633 and 648 cm-1 are assigned to the ν4 out of plane bending modes of the PO4, HPO4 and H2PO4 units. Raman bands observed at 414, 425, 460, and 479 cm-1 are attributed to the ν2 tetrahedral PO4 clusters, HPO4 and H2PO4 bending modes. The intense Raman band at 3402 and the infrared band at 3403 cm-1 are assigned to the stretching vibration of the OH units. A combination of Raman and infrared spectroscopy enabled aspects of the molecular structure of the mineral lazulite to be understood.

  11. Sum Frequency Generation Vibrational Spectroscopy and Kinetic Study of 2-Methylfuran and 2,5-Dimethylfuran Hydrogenation over 7 nm Platinum Cubic Nanoparticles

    KAUST Repository

    Aliaga, Cesar

    2011-04-28

    Sum frequency generation vibrational spectroscopy and kinetic measurements obtained from gas chromatography were used to study the adsorption and hydrogenation of 2-methylfuran (MF) and 2,5-dimethylfuran (DMF) over cubic Pt nanoparticles of 7 nm average size, synthesized by colloidal methods and cleaned by ultraviolet light and ozone treatment. Reactions carried out at atmospheric pressure in the temperature range of 20-120 °C produced dihydro and tetrahydro species, as well as ring-opening products (alcohols) and ring-cracking products, showing high selectivity toward ring opening throughout the entire temperature range. The aromatic rings (MF and DMF) adsorbed parallel to the nanoparticle surface. Results yield insight into various surface reaction intermediates and the reason for the significantly lower selectivity for ring cracking in DMF hydrogenation compared to MF hydrogenation. © 2011 American Chemical Society.

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

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hong-Fei

    2016-12-01

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

  13. Interpenetrating polymer network membranes for fuel cells: infrared vibrational spectroscopy; Membranes baseadas dm redes polimericas interpenetrantes para celulas a combustivel: estudo por espectroscopia vibracional no infravermelho

    Energy Technology Data Exchange (ETDEWEB)

    Loureiro, Felipe A.M.; Rocco, Ana Maria [Grupo de Materiais Condutores e Energia, Escola de Quimica, Universidade Federal do Rio de Janeiro, RJ (Brazil)], e-mail: amrocco@eq.ufrj.br; Pereira, Robson Pacheco [Instituto de Ciencias Exatas, Universidade Federal Fluminense (UFF), Volta Redonda, RJ (Brazil)

    2011-07-01

    In the present work, proton conductive membranes based on IPN matrices doped with H{sub 3}PO{sub 4} were developed. The characterization by infrared vibrational spectroscopy evidenced the polymerization of DGEBA and the immobilization of PEI chains, originating a structure containing basic sites suitable for proton coordination and conduction. The FTIR characterization evidenced the polymerization of DGEBA in the presence of PEI thus forming Semi-IPN membranes which, after doped with H{sub 3}PO{sub 4}, exhibited conductivity values of 10{sup -4} W{sup -1}cm{sup -1} at room temperature and 10{sup -3} {omega}{sup -1}cm{sup -1} at 80 degree C, as well as a dependency of conductivity with temperature following the Arrhenius model. The activation energy values (14,33 and 12,96 kJ.mol{sup -1}) indicated a proton conduction mechanism predominantly vehicular in the matrices studied under 100% relative humidity. (author)

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

    Science.gov (United States)

    Wang, Hong-Fei

    2016-12-01

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

  15. Adsorption and Vibrational Study of Folic Acid on Gold Nanopillar Structures Using Surface-enhanced Raman Scattering Spectroscopy

    DEFF Research Database (Denmark)

    Castillo, John J.; Rindzevicius, Tomas; Rozo, Ciro E.;

    2015-01-01

    on the nanopillars within the high electromagnetic field areas. The adsorption behaviour of folic acid and the band assignment of the main vibrations together with the optimized geometry of folic acid and folic acid in the presence of a cluster of 10 gold atoms were assessed using the density functional theory (B3...... that the interaction of folic acid with the Au NP occurred primarily through the nitrogen atoms, from their pteridine ring. Finally, the obtained adsorption isotherm for folic acid was deduced from the analysis of the SERS spectra and it followed a negative cooperative binding model....

  16. Determining Enzyme Kinetics for Systems Biology with Nuclear Magnetic Resonance Spectroscopy

    Directory of Open Access Journals (Sweden)

    Johann J. Eicher

    2012-11-01

    Full Text Available Enzyme kinetics for systems biology should ideally yield information about the enzyme’s activity under in vivo conditions, including such reaction features as substrate cooperativity, reversibility and allostery, and be applicable to enzymatic reactions with multiple substrates. A large body of enzyme-kinetic data in the literature is based on the uni-substrate Michaelis–Menten equation, which makes unnatural assumptions about enzymatic reactions (e.g., irreversibility, and its application in systems biology models is therefore limited. To overcome this limitation, we have utilised NMR time-course data in a combined theoretical and experimental approach to parameterize the generic reversible Hill equation, which is capable of describing enzymatic reactions in terms of all the properties mentioned above and has fewer parameters than detailed mechanistic kinetic equations; these parameters are moreover defined operationally. Traditionally, enzyme kinetic data have been obtained from initial-rate studies, often using assays coupled to NAD(PH-producing or NAD(PH-consuming reactions. However, these assays are very labour-intensive, especially for detailed characterisation of multi-substrate reactions. We here present a cost-effective and relatively rapid method for obtaining enzyme-kinetic parameters from metabolite time-course data generated using NMR spectroscopy. The method requires fewer runs than traditional initial-rate studies and yields more information per experiment, as whole time-courses are analyzed and used for parameter fitting. Additionally, this approach allows real-time simultaneous quantification of all metabolites present in the assay system (including products and allosteric modifiers, which demonstrates the superiority of NMR over traditional spectrophotometric coupled enzyme assays. The methodology presented is applied to the elucidation of kinetic parameters for two coupled glycolytic enzymes from Escherichia coli

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

    Science.gov (United States)

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

    2017-02-01

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

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

    Science.gov (United States)

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

    2016-12-01

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

  19. Low energy electron diffraction (LEED) and sum frequency generation (SFG) vibrational spectroscopy studies of solid-vacuum, solid-air and solid-liquid interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Hoffer, Saskia

    2002-08-19

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

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

    Science.gov (United States)

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

    2016-01-21

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

  1. Low energy electron diffraction (LEED) and sum frequency generation (SFG) vibrational spectroscopy studies of solid-vacuum, solid-air and solid-liquid interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Hoffer, Saskia [Univ. of California, Berkeley, CA (United States)

    2002-01-01

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

  2. Vibrational spectroscopies: a natural ''mesoscope'' for the study of spontaneous ordering in alloys

    Energy Technology Data Exchange (ETDEWEB)

    Chafi, Allal; Souhabi, Jihane; Pages, Olivier; Postnikov, Andrei; Gleize, Jerome [LPMD, Universite Paul Verlaine - Metz, 1 Bd Arago, 57078 Metz (France); Sallet, V. [GEMAC-CNRS, 1 Pl. Briand, 92195 Meudon (France); Li, L.H.; Harmand, J.C. [LPN-CNRS, Route de Nozay, 91460 Marcoussis (France)

    2009-05-15

    The novel paradigm of a 1-bond{yields}2-mode percolation-type behavior for the lattice dynamics at the zone-centre of random semiconductor alloys, that mirrors a lattice relaxation of the similar 1-bond{yields}2-length type, opens an attractive area for a (re-)discussion of spontaneous long-range clustering/anticlustering in terms of purely intrinsic effects. As examples, we show in this work how such antagonist effects as CuPt type spontaneous ordering of InGaP{sub 2} and N-induced In-anticlustering far from N-impurities in (N,In)-dilute InGaAsN can be discussed/evidenced from the transverse optical vibration spectra. The whole discussion is supported by full contour modelling of the TO Raman lineshapes via our percolation model. (copyright 2009 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  3. Quantitative terahertz time-domain spectroscopy and analysis in chemistry and biology

    DEFF Research Database (Denmark)

    Jepsen, Peter Uhd

    2005-01-01

    I will describe how Terahertz Time-Domain Spectroscopy (THz-TDS) can be used for quantitative, broadband spectroscopy in the far-infrared spectral region. Thz-TDS is sensitive to long-range, non-covalent interactions in the condensed phase, for instance intermolecular hydrogen bonding in molecular...

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

    Science.gov (United States)

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

    2014-11-11

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

  5. Electronic and vibrational spectroscopy of the cytochrome c:cytochrome c oxidase complexes from bovine and Paracoccus denitrificans.

    OpenAIRE

    Lynch, S. R.; Copeland, R. A.

    1992-01-01

    The 1:1 complex between horse heart cytochrome c and bovine cytochrome c oxidase, and between yeast cytochrome c and Paracoccus denitrificans cytochrome c oxidase have been studied by a combination of second derivative absorption, circular dichroism (CD), and resonance Raman spectroscopy. The second derivative absorption and CD spectra reveal changes in the electronic transitions of cytochrome a upon complex formation. These results could reflect changes in ground state heme structure or chan...

  6. Combined electron microscopy and vibrational spectroscopy study of corroded Magnox sludge from a legacy spent nuclear fuel storage pond

    Science.gov (United States)

    Gregson, Colin R.; Goddard, David T.; Sarsfield, Mark J.; Taylor, Robin J.

    2011-05-01

    Samples of filtered particulates and sludges, formed from corroding magnesium alloy clad uranium metal ("Magnox") fuel elements, collected from one of the legacy nuclear fuel storage ponds located at Sellafield (UK) were investigated by Environmental Scanning Electron Microscopy with Energy Dispersive X-Ray analysis (ESEM/EDX), micro-Raman spectroscopy and Fourier transform infra-red spectroscopy (FT-IR). ESEM imaging confirmed the dominant morphology to be clusters of interlocking platelets typical of brucite (Mg(OH) 2). EDX analysis was suggestive of some conversion to the related phase, hydrotalcite (Mg 6Al 2(CO 3)(OH) 16·4H 2O), due to elevated levels of Al associated with Mg. Other apparent morphologies were less commonly observed including flaky sheets, consistent with earlier stages of Magnox alloy corrosion. In a few specific cases, rods were also observed suggestive of some conversion to Mg-hydroxycarbonate phases. Discrete phases rich in U were also identified. Fluorescence in the Raman spectroscopy also indicated surface coatings of organic macromolecules and iron sulphide on hematite containing particles, attributed to microbial activity within the open air pond. Some specific differences in the solid phases between pond areas with differing conditions were apparent.

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

    Science.gov (United States)

    Kokaislová, A; Matějka, P

    2012-05-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Dao-Ling; Wang, Lai-Sheng, E-mail: Lai-Sheng-Wang@brown.edu [Department of Chemistry, Brown University, Providence, Rhode Island 02912 (United States); Liu, Hong-Tao [Department of Chemistry, Brown University, Providence, Rhode Island 02912 (United States); Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Ning, Chuan-Gang [Department of Physics, State Key Laboratory of Low-Dimensional Quantum Physics, Tsinghua University, Beijing 100084 (China)

    2015-03-28

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1981-12-16

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

  10. New light on protein folding: Unraveling folding and unfolding mechanisms using time-resolved and two-dimensional vibrational spectroscopy

    NARCIS (Netherlands)

    H. Meuzelaar

    2015-01-01

    How a protein folds from its one-dimensional sequence of amino acids into its three-dimensional, functional structure on biologically relevant time scales (typically on the micro- to millisecond time scale) is one of the most challenging questions currently investigated in several scientific discipl

  11. Variable-Temperature Tip-Enhanced Raman Spectroscopy of Single-Molecule Fluctuations and Dynamics.

    Science.gov (United States)

    Park, Kyoung-Duck; Muller, Eric A; Kravtsov, Vasily; Sass, Paul M; Dreyer, Jens; Atkin, Joanna M; Raschke, Markus B

    2016-01-13

    Structure, dynamics, and coupling involving single-molecules determine function in catalytic, electronic or biological systems. While vibrational spectroscopy provides insight into molecular structure, rapid fluctuations blur the molecular trajectory even in single-molecule spectroscopy, analogous to spatial averaging in measuring large ensembles. To gain insight into intramolecular coupling, substrate coupling, and dynamic processes, we use tip-enhanced Raman spectroscopy (TERS) at variable and cryogenic temperatures, to slow and control the motion of a single molecule. We resolve intrinsic line widths of individual normal modes, allowing detailed and quantitative investigation of the vibrational modes. From temperature dependent line narrowing and splitting, we quantify ultrafast vibrational dephasing, intramolecular coupling, and conformational heterogeneity. Through statistical correlation analysis of fluctuations of individual modes, we observe rotational motion and spectral fluctuations of the molecule. This work demonstrates single-molecule vibrational spectroscopy beyond chemical identification, opening the possibility for a complete picture of molecular motion ranging from femtoseconds to minutes.

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

    Energy Technology Data Exchange (ETDEWEB)

    Gracias, David Hugo [Univ. of California, Berkeley, CA (United States)

    1999-05-01

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

  13. Vibrational spectroscopy characterization of low level laser therapy on mammary culture cells: a micro-FTIR study

    Science.gov (United States)

    Magrini, Taciana D.; Villa dos Santos, Nathalia; Pecora Milazzotto, Marcella; Cerchiaro, Giselle; da Silva Martinho, Herculano

    2011-03-01

    Low level laser therapy (LLLT) is an emerging therapeutic approach for several clinical conditions. The clinical effects induced by LLLT presumably go from the photobiostimulation/photobioinibition at cellular level to the molecular level. The detailed mechanism underlying this effect is still obscure. This work is dedicated to quantify some relevant aspects of LLLT related to molecular and cellular variations. This goal was attached by exposing malignant breast cells (MCF7) to spatially filtered light of a He-Ne laser (633 nm) with 28.8 mJ/cm2 of fluency. The cell viability was evaluated by microscopic observation using Trypan Blue viability test. The vibrational spectra of each experimental group (micro- FTIR technique) were used to identify the relevant biochemical alterations occurred due the process. The red light had influence over RNA, phosphate and serine/threonine/tyrosine bands. Light effects on cell number or viability were not detected. However, the irradiation had direct influence on metabolic activity of cells.

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

    Science.gov (United States)

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

    2016-08-01

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

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

    Science.gov (United States)

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

    2007-06-15

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

  16. Vibrational spectroscopy of aluminate spinels at 1 atm and of MgAl2O4 to over 200 kbar

    Science.gov (United States)

    Chopelas, A.; Hofmeister, A. M.

    1991-12-01

    Single-crystal Raman and infrared reflectivity data including high pressure results to over 200 kbar on a natural, probably fully ordered MgAl2O4 spinel reveal that many of the reported frequencies from spectra of synthetic spinels are affected by disorder at the cation sites. The spectra are interpreted in terms of factor group analysis and show that the high energy modes are due to the octahedral internal modes, in contrast to the behavior of silicate spinels, but in agreement with previous data based on isotopic and chemical cation substitutions and with new Raman data on gahnite (˜ ZnAl2O4) and new IR reflectivity data on both gahnite and hercynite (˜Fe0.58Mg0.42Al2O4). Therefore, aluminate spinels are inappropriate as elastic or thermodynamic analogs for silicate spinels. Fluorescence sideband spectra yield complementary information on the vibrational modes and provide valuable information on the acoustic modes at high pressure. The transverse acoustic modes are nearly pressure independent, which is similar to the behavior of the shear modes previously measured by ultrasonic techniques. The pressure derivative of all acoustic modes become negative above 110 kbar, indicating a lattice instability, in agreement with previous predictions. This lattice instability lies at approximately the same pressure as the disproportionation of spinel to MgO and Al2O3 reported in high temperature, high pressure work.

  17. Surface-enhanced Raman spectroscopy at single-molecule scale and its implications in biology

    OpenAIRE

    Wang, Yuling; Irudayaraj, Joseph

    2013-01-01

    Single-molecule (SM) spectroscopy has been an exciting area of research offering significant promise and hope in the field of sensor development to detect targets at ultra-low levels down to SM resolution. To the experts and developers in the field of surface-enhanced Raman spectroscopy (SERS), this has often been a challenge and a significant opportunity for exploration. Needless to say, the opportunities and excitement of this multidisciplinary area impacts span the fields of physics, chemi...

  18. Infrared differential-absorption Mueller matrix spectroscopy and neural network-based data fusion for biological aerosol standoff detection.

    Science.gov (United States)

    Carrieri, Arthur H; Copper, Jack; Owens, David J; Roese, Erik S; Bottiger, Jerold R; Everly, Robert D; Hung, Kevin C

    2010-01-20

    An active spectrophotopolarimeter sensor and support system were developed for a military/civilian defense feasibility study concerning the identification and standoff detection of biological aerosols. Plumes of warfare agent surrogates gamma-irradiated Bacillus subtilis and chicken egg white albumen (analytes), Arizona road dust (terrestrial interferent), water mist (atmospheric interferent), and talcum powders (experiment controls) were dispersed inside windowless chambers and interrogated by multiple CO(2) laser beams spanning 9.1-12.0 microm wavelengths (lambda). Molecular vibration and vibration-rotation activities by the subject analyte are fundamentally strong within this "fingerprint" middle infrared spectral region. Distinct polarization-modulations of incident irradiance and backscatter radiance of tuned beams generate the Mueller matrix (M) of subject aerosol. Strings of all 15 normalized elements {M(ij)(lambda)/M(11)(lambda)}, which completely describe physical and geometric attributes of the aerosol particles, are input fields for training hybrid Kohonen self-organizing map feed-forward artificial neural networks (ANNs). The properly trained and validated ANN model performs pattern recognition and type-classification tasks via internal mappings. A typical ANN that mathematically clusters analyte, interferent, and control aerosols with nil overlap of species is illustrated, including sensitivity analysis of performance.

  19. Interactions of nitrogen and hydrogen with various 1D and 3D carbon materials probed via in-situ vibrational spectroscopy

    Science.gov (United States)

    Ray, Paramita

    Nanostructured carbon materials are perhaps the most widely studied adsorbents, and cryogenic nitrogen adsorption is likely the most common method to assess textural properties of adsorbents. Yet, in-situ vibrational spectroscopic studies of nitrogen's interactions with three nanostructured carbon materials have provided new insight into carbon-nitrogen interactions. In this dissertation I present the work of 2 projects: (i) Study of the interaction of N2 with different carbon geometries at a molecular level and (ii) exploration of novel C-H interactions on carbon materials via mechano-chemistry. Both of these projects utilize in-situ Raman spectroscopy for exploring gas-surface interactions. Chapters 2 and 3 explore the interaction of molecular Nitrogen on carbon surfaces. With complementary theoretical studies and systematic experimental studies at various temperatures and pressures for different surfaces, I demonstrate how the spectroscopic peak features of N2 gives an indication of gas-surface binding energy, pore structure, and surface chemistry. Using 1D and 3D carbon architectures, spectroscopic perturbation of N2 is probed as a function of adsorption potential and pore dimension, and the spectroscopic response is mapped to the cryogenic volumetric adsorption isotherms. Whereas the latter required multiple days and ˜100 mg of sample, the spectroscopic technique provided similar structural information in the matter of a few hours for a few micrograms of the sample. It is anticipated that the development of the site-specific spectroscopic technique will advance the understanding of adsorbent geometry versus chemical functionality in a way not possible with deconstruction of bulk gas adsorption measurements of pore dimension, surface area, and diffusivity. The second project probed mechanochemical means to polymerize aromatics and hydro-aromatics in the presence of hydrogen in an attempt to form localized carbon cages that trap hydrogen. Interesting aspects of

  20. Raman Spectroscopy and Related Techniques in Biomedicine

    Directory of Open Access Journals (Sweden)

    Alistair Elfick

    2010-03-01

    Full Text Available In this review we describe label-free optical spectroscopy techniques which are able to non-invasively measure the (biochemistry in biological systems. Raman spectroscopy uses visible or near-infrared light to measure a spectrum of vibrational bonds in seconds. Coherent anti-Stokes Raman (CARS microscopy and stimulated Raman loss (SRL microscopy are orders of magnitude more efficient than Raman spectroscopy, and are able to acquire high quality chemically-specific images in seconds. We discuss the benefits and limitations of all techniques, with particular emphasis on applications in biomedicine—both in vivo (using fiber endoscopes and in vitro (in optical microscopes.

  1. Liquid/liquid interface layering of 1-butanol and [bmim]PF6 ionic liquid: a nonlinear vibrational spectroscopy and molecular dynamics simulation study.

    Science.gov (United States)

    Iwahashi, Takashi; Ishiyama, Tatsuya; Sakai, Yasunari; Morita, Akihiro; Kim, Doseok; Ouchi, Yukio

    2015-10-14

    IR-visible sum-frequency generation (IV-SFG) vibrational spectroscopy and a molecular dynamics (MD) simulation were used to study the local layering order at the interface of 1-butanol-d9 and 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim]PF6), a room-temperature ionic liquid (RTIL). The presence of a local non-polar layer at the interface of the two polar liquids was successfully demonstrated. In the SFG spectra of 1-butanol-d9, we observed significant reduction and enhancement in the strength of the CD3 symmetric stretching (r(+)) mode and the antisymmetric stretching (r(-)) mode peaks, respectively. The results can be well explained by the presence of an oppositely oriented quasi-bilayer structure of butanol molecules, where the bottom layer is strongly bound by hydrogen-bonding with the PF6(-) anion. MD simulations reveal that the hydrogen-bonding of butanol with the PF6(-) anion causes the preferential orientation of the butanols; the restriction on the rotational distribution of the terminal methyl group along their C3 axis enhances the r(-) mode. As for the [bmim](+) cations, the SFG spectra taken within the CH stretch region indicate that the butyl chain of [bmim](+) points away from the bulk RTIL phase to the butanol phase at the interface. Combining the SFG spectroscopy and MD simulation results, we propose an interfacial model structure of layering, in which the butyl chains of the butanol molecules form a non-polar interfacial layer with the butyl chains of the [bmim](+) cations at the interface.

  2. Prediction for steatosis in type-2 diabetes: clinico-biological markers versus {sup 1}H-MR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Guiu, Boris; Krause, Denis; Cercueil, Jean-Pierre [University of Burgundy, INSERM U866, BP 87900, Dijon (France); CHU (University Hospital), Department of Radiology, 2 boulevard Marechal de Lattre de Tassigny, BP 77908, Dijon (France); Crevisy-Girod, Elodie [CHU (University Hospital), Department of Endocrinology, Diabetology, and Metabolic Diseases, BP 77908, Dijon (France); Binquet, Christine [University of Burgundy, INSERM U866, BP 87900, Dijon (France); CHU (University Hospital), Department of Biostatistics and Medical Informatics, BP 77908, Dijon (France); Duvillard, Laurence [University of Burgundy, INSERM U866, BP 87900, Dijon (France); Masson, David [University of Burgundy, INSERM U866, BP 87900, Dijon (France); CHU (University Hospital), Department of Biochemistry, BP 77908, Dijon (France); Lepage, Come; Hamza, Samia; Minello, Anne; Hillon, Patrick [University of Burgundy, INSERM U866, BP 87900, Dijon (France); CHU (University Hospital), Department of Hepatology, BP 77908, Dijon (France); Verges, Bruno; Petit, Jean-Michel [University of Burgundy, INSERM U866, BP 87900, Dijon (France); CHU (University Hospital), Department of Endocrinology, Diabetology, and Metabolic Diseases, BP 77908, Dijon (France)

    2012-04-15

    The SteatoTest, fatty liver index (FLI) and hepatic steatosis index (HSI) are clinico-biological scores of steatosis validated in general or selected populations. Serum adiponectin (s-adiponectin) and retinol binding protein 4 (s-RBP4) are adipokines that could predict liver steatosis. We investigated whether the Steatotest, FLI, HSI, s-adiponectin and s-RBP4 could be valid predictors of liver steatosis in type-2 diabetic (T2D) patients. We enrolled 220 consecutive T2D patients. Reference standard was 3.0 T {sup 1}H-MR spectroscopy (corrected for T1 and T2 decays). Intraclass correlation coefficients (ICCs), Kappa statistic measures of agreement, receiver operating characteristic (ROC) curves were assessed. Median liver fat content was 91 mg triglyceride/g liver tissue (range: 0-392). ICCs among the Steatotest, FLI, HSI, s-adiponectin, s-RBP4 and spectroscopy were low: 0.384, 0.281, 0.087, -0.297 and 0.048. Agreement between scores and spectroscopy was poor (Kappa range: 0.042-0.281). The areas under the ROC curves were low: 0.674, 0.647, 0.637, 0.616 and 0.540. S-adiponectin and s-RBP4 levels were strongly related to the presence of diabetic nephropathy (P = 0.0037 and P = 0.004; Mann-Whitney). The SteatoTest, FLI, HSI, s-adiponectin, s-RBP4 are not valid predictors of steatosis in T2D patients. Clino-biological markers cannot replace {sup 1}H-MR spectroscopy for the assessment of liver fat in this population. (orig.)

  3. Vibrational sum-frequency generation spectroscopy of ionic liquid 1-butyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate at the air-water interface

    Science.gov (United States)

    Saha, Ankur; SenGupta, Sumana; Kumar, Awadhesh; Choudhury, Sipra; Naik, Prakash D.

    2016-08-01

    The structure and orientation of room temperature ionic liquid (RTIL) 1-butyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate [PF3(C2F5)3], commonly known as [bmim][fap], have been investigated at the air-[bmim][fap] and air-water interfaces, employing vibrational sum-frequency generation (VSFG) spectroscopy. The VSFG spectra in the CH stretch region suggest presence of the [bmim] cation at the interfaces. Studies reveal that the butyl chain protrudes out into air, and the imidazolium ring lies almost planar to the interface. The CH stretch intensities get enhanced at the air-water interface, mainly because of polar orientation of imidazolium cation induced by interfacial water molecules. The OH stretch intensities are also enhanced at the air-water interface due to polar orientation of interfacial water molecules induced by [bmim][fap]. The Brewster angle microscopy suggests self aggregation of [bmim][fap] in the presence of water, and the aggregation becomes extensive showing dense surface domains with time. However, the surface pressure is almost unaffected due to aggregation.

  4. IR and SFG vibrational spectroscopy of the water bend in the bulk liquid and at the liquid-vapor interface, respectively

    Energy Technology Data Exchange (ETDEWEB)

    Ni, Yicun; Skinner, J. L. [Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706 (United States)

    2015-07-07

    Vibrational spectroscopy of the water bending mode has been investigated experimentally to study the structure of water in condensed phases. In the present work, we calculate the theoretical infrared (IR) and sum-frequency generation (SFG) spectra of the HOH bend in liquid water and at the water liquid/vapor interface using a mixed quantum/classical approach. Classical molecular dynamics simulation is performed by using a recently developed water model that explicitly includes three-body interactions and yields a better description of the water surface. Ab-initio-based transition frequency, dipole, polarizability, and intermolecular coupling maps are developed for the spectral calculations. The calculated IR and SFG spectra show good agreement with the experimental measurements. In the theoretical imaginary part of the SFG susceptibility for the water liquid/vapor interface, we find two features: a negative band centered at 1615 cm{sup −1} and a positive band centered at 1670 cm{sup −1}. We analyze this spectrum in terms of the contributions from molecules in different hydrogen-bond classes to the SFG spectral density and also compare to SFG results for the OH stretch. SFG of the water bending mode provides a complementary picture of the heterogeneous hydrogen-bond configurations at the water surface.

  5. Chemical synthesis, crystal structure, vibrational spectroscopy, non-linear optical properties and DFT calculation of bis (2,6-diaminopyridinium) sulfate monohydrate

    Science.gov (United States)

    Ben Hassen, Chaouki; Dammak, Thameur; Chniba-Boudjada, Nassira; Mhiri, Tahar; Boujelbene, Mohamed

    2017-01-01

    Single crystals of a new organic inorganic hybrid compound "bis (2,6-diaminopyridinium) sulfate monohydrate [C5H8N3]2SO4·H2O ([2,6-HDAP]2SO4·H2O)" was synthesized by slow evaporation method at room temperature and characterized by X-ray single crystal diffraction, infrared spectroscopy and DFT calculation. The new hybrid compound crystallizes in the orthorhombic system with the non-centro symmetric space group Pna21 and the following parameters a = 14.759(2) Å, b = 7.076 (2) Å and c = 28.159 (2) Å. The atomic arrangement can be described as inorganic chains following the b axis connected with the organic groups by means of Nsbnd H⋯O hydrogen bonds to form 3D network. Antiparallelly π-π stacked 2,6-HDAP cations form molecular columns in the spaces between the chains. The optimized molecular structure, vibrational spectra and the optical properties were calculated by the density functional theory (DFT) method using the B3LYP function with the LanL2DV basis set. The wavenumber calculated are in good agreement with the observed frequency values. The calculated hyperpolarizability βtot is about 4.5 times more than that of the reference crystal KDP. Hence, the large β value shows that the title compound is an attractive object for future studies of nonlinear optical properties.

  6. Further understanding of the adsorption mechanism of N719 sensitizer on anatase TiO2 films for DSSC applications using vibrational spectroscopy and confocal Raman imaging.

    Science.gov (United States)

    Lee, Kee Eun; Gomez, Mario A; Elouatik, Samir; Demopoulos, George P

    2010-06-15

    Vibrational spectroscopic studies of N719 dye-adsorbed TiO(2) films have been carried out by using SERRS, ATR-FTIR, and confocal Raman imaging. The high wavenumber region (3000-4000 cm(-1)) of dye adsorbed TiO(2) is analyzed via Raman and IR spectroscopy to investigate the role of surface hydroxyl groups in the anchoring mode. As a complementary technique, confocal Raman imaging is employed to study the distribution features of key dye groups (COO-, bipyridine, and C=O) on the anatase surface. Sensitized TiO(2) films made from two different nanocrystalline anatase powders are investigated: a commercial one (Dyesol) and our synthetic variety produced through aqueous synthesis. It is proposed the binding of the N719 dye to TiO(2) to occur through two neighboring carboxylic acid/carboxylate groups via a combination of bidentate-bridging and H-bonding involving a donating group from the N719 (and/or Ti-OH) units and acceptor from the Ti-OH (and/or N719) groups. The Raman imaging distribution of COO(-)(sym) on TiO(2) was used to show the covalent bonding, while the distribution of C=O mode was applied to observe the electrostatically bonded groups.

  7. Hydrogenation of the alpha,beta-Unsaturated Aldehydes Acrolein, Crotonaldehyde, and Prenal over Pt Single Crystals: A Kinetic and Sum-Frequency Generation Vibrational Spectroscopy Study

    Energy Technology Data Exchange (ETDEWEB)

    Kliewer, C.J.; Somorjai, G.A.

    2008-11-26

    Sum-frequency generation vibrational spectroscopy (SFG-VS) and kinetic measurements using gas chromatography have been used to study the surface reaction intermediates during the hydrogenation of three {alpha},{beta}-unsaturated aldehydes, acrolein, crotonaldehyde, and prenal, over Pt(111) at Torr pressures (1 Torr aldehyde, 100 Torr hydrogen) in the temperature range of 295K to 415K. SFG-VS data showed that acrolein has mixed adsorption species of {eta}{sub 2}-di-{sigma}(CC)-trans, {eta}{sub 2}-di-{sigma}(CC)-cis as well as highly coordinated {eta}{sub 3} or {eta}{sub 4} species. Crotonaldehyde adsorbed to Pt(111) as {eta}{sub 2} surface intermediates. SFG-VS during prenal hydrogenation also suggested the presence of the {eta}{sub 2} adsorption species, and became more highly coordinated as the temperature was raised to 415K, in agreement with its enhanced C=O hydrogenation. The effect of catalyst surface structure was clarified by carrying out the hydrogenation of crotonaldehyde over both Pt(111) and Pt(100) single crystals while acquiring the SFG-VS spectra in situ. Both the kinetics and SFG-VS showed little structure sensitivity. Pt(100) generated more decarbonylation 'cracking' product while Pt(111) had a higher selectivity for the formation of the desired unsaturated alcohol, crotylalcohol.

  8. IR and SFG vibrational spectroscopy of the water bend in the bulk liquid and at the liquid-vapor interface, respectively.

    Science.gov (United States)

    Ni, Yicun; Skinner, J L

    2015-07-07

    Vibrational spectroscopy of the water bending mode has been investigated experimentally to study the structure of water in condensed phases. In the present work, we calculate the theoretical infrared (IR) and sum-frequency generation (SFG) spectra of the HOH bend in liquid water and at the water liquid/vapor interface using a mixed quantum/classical approach. Classical molecular dynamics simulation is performed by using a recently developed water model that explicitly includes three-body interactions and yields a better description of the water surface. Ab-initio-based transition frequency, dipole, polarizability, and intermolecular coupling maps are developed for the spectral calculations. The calculated IR and SFG spectra show good agreement with the experimental measurements. In the theoretical imaginary part of the SFG susceptibility for the water liquid/vapor interface, we find two features: a negative band centered at 1615 cm(-1) and a positive band centered at 1670 cm(-1). We analyze this spectrum in terms of the contributions from molecules in different hydrogen-bond classes to the SFG spectral density and also compare to SFG results for the OH stretch. SFG of the water bending mode provides a complementary picture of the heterogeneous hydrogen-bond configurations at the water surface.

  9. Structure of butanol and hexanol at aqueous, ammonium bisulfate, and sulfuric acid solution surfaces investigated by vibrational sum frequency generation spectroscopy.

    Science.gov (United States)

    Van Loon, Lisa L; Minor, Rena N; Allen, Heather C

    2007-08-09

    The organization of 1-butanol and 1-hexanol at the air-liquid interface of aqueous, aqueous ammonium bisulfate, and sulfuric acid solutions was investigated using vibrational broad bandwidth sum frequency generation spectroscopy. There is spectroscopic evidence supporting the formation of centrosymmetric structures at the surface of pure butanol and pure hexanol. At aqueous, ammonium bisulfate, and at most sulfuric acid solution surfaces, butanol molecules organize in all-trans conformations. This suggests that butanol self-aggregates. The spectrum for the 0.052 M butanol in 59.5 wt % sulfuric acid solution is different from the other butanol solution spectra, that is, the surface butanol molecules are observed to possess a significant number of gauche defects. Relative to surface butanol, surface hexanol chains are more disordered at the surface of their respective solutions. Statistically, an increase in the number of gauche defects is expected for hexanol relative to butanol, a six carbon chain vs a four carbon chain. Yet, self-aggregation of hexanol at its aqueous solution surfaces is not ruled out because the methylene spectral contribution is relatively small. The surface spectra for butanol and hexanol also show evidence for salting out from the ammonium bisulfate solutions.

  10. AKARI near-infrared spectroscopy of the extended green object G318.05+0.09: Detection of CO fundamental ro-vibrational emission

    CERN Document Server

    Onaka, Takashi; Sakon, Itsuki; Ardaseva, Aleksandra

    2016-01-01

    We present the results of near-infrared (2.5--5.4um) long-slit spectroscopy of the extended green object (EGO) G318.05+0.09 with AKARI. Two distinct sources are found in the slit. The brighter source has strong red continuum emission with H2O ice, CO2 ice, and CO gas and ice absorption features at 3.0, 4.25um, 4.67um, respectively, while the other greenish object shows peculiar emission that has double peaks at around 4.5 and 4.7um. The former source is located close to the ultra compact HII region IRAS 14498-5856 and is identified as an embedded massive young stellar object. The spectrum of the latter source can be interpreted by blue-shifted (-3000 ~ -6000km/s) optically-thin emission of the fundamental ro-vibrational transitions (v=1-0) of CO molecules with temperatures of 12000--3700K without noticeable H2 and HI emission. We discuss the nature of this source in terms of outflow associated with the young stellar object and supernova ejecta associated with a supernova remnant.

  11. Synthesis, crystal structure, vibrational and 31P-NMR spectroscopy of the thiophosphate NaMg[PO3S]·9H2O

    Science.gov (United States)

    Höppe, Henning A.; Scharinger, Stefan W.; Heck, Joachim G.; Gross, Peter; Netzsch, Philip; Kazmierczak, Karolina

    2016-12-01

    NaMg[PO3S]·9H2O was obtained as single-phase crystalline powder starting from NaOH, PSCl3 and MgCl2·6H2O. At room temperature NaMg[PO3S]·9H2O crystallises in space group Cmc21 (no. 36) (a=638.58(4) pm, b=1632.31(10) pm, c=1217.16(7) pm, Z = 4; Rint = 0.032, Rσ = 0.034, R1 = 0.036, wR2 = 0.071). The data collection at 100 K reveals an ordering of the PO3S tetrahedra by undergoing a symmetry reduction to P21 (no. 4) and an according formation of twins (C1121, unconv. setting of P21, a=631.41(3) pm, b=1630.00(7) pm, c=1219.24(5) pm, γ=90.00(2)°, Z = 4; Rint = 0.115, Rσ = 0.064, R1 = 0.045, wR2 = 0.070). NaMg[PO3S]·9H2O comprises isolated PO3S tetrahedra, distorted MgO6 octahedra and trigonal NaO6 prisms. 31P NMR spectroscopy showed a chemical shift of 33.7 ppm. The vibrational spectra of NaMg[PO3S]·9H2O were recorded and the relevant bands were assigned.

  12. Hydrogenation of the alpha,beta-unsaturated aldehydes acrolein, crotonaldehyde, and prenal over Pt single crystals: a kinetic and sum-frequency generation vibrational spectroscopy study.

    Science.gov (United States)

    Kliewer, Christopher J; Bieri, Marco; Somorjai, Gabor A

    2009-07-29

    Sum-frequency generation vibrational spectroscopy (SFG-VS) and kinetic measurements using gas chromatography have been used to study the surface reaction intermediates during the hydrogenation of three alpha,beta-unsaturated aldehydes, acrolein, crotonaldehyde, and prenal, over Pt(111) at Torr pressures (1 Torr of aldehyde, 100 Torr of hydrogen) in the temperature range of 295-415 K. SFG-VS data showed that acrolein has mixed adsorption species of eta(2)-di-sigma(CC)-trans, eta(2)-di-sigma(CC)-cis as well as highly coordinated eta(3) or eta(4) species. Crotonaldehyde adsorbed to Pt(111) as eta(2) surface intermediates. SFG-VS during prenal hydrogenation also suggested the presence of the eta(2) adsorption species and became more highly coordinated as the temperature was raised to 415 K, in agreement with its enhanced C=O hydrogenation. The effect of catalyst surface structure was clarified by carrying out the hydrogenation of crotonaldehyde over both Pt(111) and Pt(100) single crystals while acquiring the SFG-VS spectra in situ. Both the kinetics and SFG-VS showed little structure sensitivity. Pt(100) generated more decarbonylation "cracking" product while Pt(111) had a higher selectivity for the formation of the desired unsaturated alcohol, crotyl alcohol.

  13. Characterization of the molecular structure and mechanical properties of polymer surfaces and protein/polymer interfaces by sum frequency generation vibrational spectroscopy and atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Koffas, Telly Stelianos [Univ. of California, Berkeley, CA (United States)

    2004-01-01

    Sum frequency generation (SFG) vibrational spectroscopy, atomic force microscopy (AFM), and other complementary surface-sensitive techniques have been used to study the surface molecular structure and surface mechanical behavior of biologically-relevant polymer systems. SFG and AFM have emerged as powerful analytical tools to deduce structure/property relationships, in situ, for polymers at air, liquid and solid interfaces. The experiments described in this dissertation have been performed to understand how polymer surface properties are linked to polymer bulk composition, substrate hydrophobicity, changes in the ambient environment (e.g., humidity and temperature), or the adsorption of macromolecules. The correlation of spectroscopic and mechanical data by SFG and AFM can become a powerful methodology to study and engineer materials with tailored surface properties. The overarching theme of this research is the interrogation of systems of increasing structural complexity, which allows us to extend conclusions made on simpler model systems. We begin by systematically describing the surface molecular composition and mechanical properties of polymers, copolymers, and blends having simple linear architectures. Subsequent chapters focus on networked hydrogel materials used as soft contact lenses and the adsorption of protein and surfactant at the polymer/liquid interface. The power of SFG is immediately demonstrated in experiments which identify the chemical parameters that influence the molecular composition and ordering of a polymer chain's side groups at the polymer/air and polymer/liquid interfaces. In general, side groups with increasingly greater hydrophobic character will be more surface active in air. Larger side groups impose steric restrictions, thus they will tend to be more randomly ordered than smaller hydrophobic groups. If exposed to a hydrophilic environment, such as water, the polymer chain will attempt to orient more of its hydrophilic groups to

  14. Characterization of the molecular structure and mechanical properties of polymer surfaces and protein/polymer interfaces by sum frequency generation vibrational spectroscopy and atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Koffas, Telly Stelianos

    2004-05-15

    Sum frequency generation (SFG) vibrational spectroscopy, atomic force microscopy (AFM), and other complementary surface-sensitive techniques have been used to study the surface molecular structure and surface mechanical behavior of biologically-relevant polymer systems. SFG and AFM have emerged as powerful analytical tools to deduce structure/property relationships, in situ, for polymers at air, liquid and solid interfaces. The experiments described in this dissertation have been performed to understand how polymer surface properties are linked to polymer bulk composition, substrate hydrophobicity, changes in the ambient environment (e.g., humidity and temperature), or the adsorption of macromolecules. The correlation of spectroscopic and mechanical data by SFG and AFM can become a powerful methodology to study and engineer materials with tailored surface properties. The overarching theme of this research is the interrogation of systems of increasing structural complexity, which allows us to extend conclusions made on simpler model systems. We begin by systematically describing the surface molecular composition and mechanical properties of polymers, copolymers, and blends having simple linear architectures. Subsequent chapters focus on networked hydrogel materials used as soft contact lenses and the adsorption of protein and surfactant at the polymer/liquid interface. The power of SFG is immediately demonstrated in experiments which identify the chemical parameters that influence the molecular composition and ordering of a polymer chain's side groups at the polymer/air and polymer/liquid interfaces. In general, side groups with increasingly greater hydrophobic character will be more surface active in air. Larger side groups impose steric restrictions, thus they will tend to be more randomly ordered than smaller hydrophobic groups. If exposed to a hydrophilic environment, such as water, the polymer chain will attempt to orient more of its hydrophilic groups to

  15. Aqueous Cu(II)-organic complexation studied in situ using soft X-ray and vibrational spectroscopies.

    Science.gov (United States)

    Phillips, Courtney L; Regier, Tom Z; Peak, Derek

    2013-12-17

    In situ aqueous solutions containing copper-ligand mixtures were measured at the Cu L-edge using X-ray absorption near edge structure (XANES) and with attenuated total reflectance infrared (ATR-FTIR) spectroscopies. Copper complexation with environmentally relevant ligands such as EDTA, citrate, and malate provided a bridge between spectroscopic studies and general environmental behavior and will allow for future study of complex environmental samples. XANES results show that the lowest unoccupied molecular orbital (LUMO) energy is governed by the ligand field strength and is related to Lewis acid/base properties of the ligand functional groups. Complementary ATR-FTIR studies confirmed the importance of water molecules in the structure of these Cu-ligand complexes and provided in-depth structural analysis to support the XANES data. Copper-malate is shown to have a 5/6-O-ring structure, and Cu-ethylenediaminetetraacetate has pentadentate coordination. Cu L-edge XANES also revealed direct Cu-N coordination in these aqueous solutions with amide functional groups.

  16. Characterization of extracellular vesicles by IR spectroscopy: Fast and simple classification based on amide and CH stretching vibrations.

    Science.gov (United States)

    Mihály, Judith; Deák, Róbert; Szigyártó, Imola Csilla; Bóta, Attila; Beke-Somfai, Tamás; Varga, Zoltán

    2017-03-01

    Extracellular vesicles isolated by differential centrifugation from Jurkat T-cell line were investigated by attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR). Amide and CH stretching band intensity ratios calculated from IR bands, characteristic of protein and lipid components, proved to be distinctive for the different extracellular vesicle subpopulations. This proposed 'spectroscopic protein-to-lipid ratio', combined with the outlined spectrum-analysis protocol is valid also for low sample concentrations (0.15-0.05mg/ml total protein content) and can carry information about the presence of other non-vesicular formations such as aggregated proteins, lipoproteins and immune complexes. Detailed analysis of IR data reveals compositional changes of extracellular vesicles subpopulations: second derivative spectra suggest changes in protein composition from parent cell towards exosomes favoring proteins with β-turns and unordered motifs at the expense of intermolecular β-sheet structures. The IR-based protein-to-lipid assessment protocol was tested also for red blood cell derived microvesicles for which similar values were obtained. The potential applicability of this technique for fast and efficient characterization of vesicular components is high as the investigated samples require no further preparations and all the different molecular species can be determined in the same sample. The results indicate that ATR-FTIR measurements provide a simple and reproducible method for the screening of extracellular vesicle preparations. It is hoped that this sophisticated technique will have further impact in extracellular vesicle research.

  17. Vibrational spectroscopy and analytical electron microscopy studies of Fe-V-O and In-V-O thin films

    CERN Document Server

    Vuk, A S; Drazic, G; Colomban, P

    2002-01-01

    Orthovanadate (M sup 3 sup + VO sub 4; M= Fe, In) and vanadate (Fe sub 2 V sub 4 O sub 1 sub 3) thin films were prepared using sol-gel synthesis and dip coating deposition. Using analytical electron microscopy (AEM), the chemical composition and the degree of crystallization of the phases present in the thin Fe-V-O films were investigated. TEM samples were prepared in both orientations: parallel (plan view) and perpendicular (cross section) to the substrate. In the first stages of crystallization, when the particle sizes were in the nanometer range, the classical identification of phases using electron diffraction was not possible. Instead of measuring d values, experimentally selected area electron diffraction (SAED) patterns were compared to calculated (simulated) patterns in order to determine the phase composition. The problems of evaluating the ratio of amorphous and crystalline phases in thin films are reported. Results of TEM and XRD as well as IR and Raman spectroscopy showed that the films made at lo...

  18. Femtosecond nonlinear spectroscopy at surfaces: Second-harmonic probing of hole burning at the Si(111)7x7 surface and fourier-transform sum-frequency vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    McGuire, John Andrew [Univ. of California, Berkeley, CA (United States)

    2004-11-24

    The high temporal resolution and broad bandwidth of a femtosecond laser system are exploited in a pair of nonlinear optical studies of surfaces. The dephasing dynamics of resonances associated with the adatom dangling bonds of the Si(111)7 x 7 surface are explored by transient second-harmonic hole burning, a process that can be described as a fourth-order nonlinear optical process. Spectral holes produced by a 100 fs pump pulse at about 800 nm are probed by the second harmonic signal of a 100 fs pulse tunable around 800 nm. The measured spectral holes yield homogeneous dephasing times of a few tens of femtoseconds. Fits with a Lorentzian spectral hole centered at zero probe detuning show a linear dependence of the hole width on pump fluence, which suggests that charge carrier-carrier scattering dominates the dephasing dynamics at the measured excitation densities. Extrapolation of the deduced homogeneous dephasing times to zero excitation density yields an intrinsic dephasing time of {approx} 70 fs. The presence of a secondary spectral hole indicates that scattering of the surface electrons with surface optical phonons at 570 cm-1 occurs within the first 200 fs after excitation. The broad bandwidth of femtosecond IR pulses is used to perform IR-visible sum frequency vibrational spectroscopy. By implementing a Fourier-transform technique, we demonstrate the ability to obtain sub-laser-bandwidth spectral resolution. FT-SFG yields a greater signal when implemented with a stretched visible pulse than with a femtosecond visible pulse. However, when compared with multichannel spectroscopy using a femtosecond IR pulse but a narrowband visible pulse, Fourier-transform SFG is found to have an inferior signal-to-noise ratio. A mathematical analysis of the signal-to-noise ratio illustrates the constraints on the Fourier-transform approach.

  19. Sulfur K-edge absorption spectroscopy on selected biological systems; Schwefel-K-Kanten-Absorptionsspektroskopie an ausgewaehlten biologischen Systemen

    Energy Technology Data Exchange (ETDEWEB)

    Lichtenberg, Henning

    2008-07-15

    Sulfur is an essential element in organisms. In this thesis investigations of sulfur compounds in selected biological systems by XANES (X-ray Absorption Near Edge Structure) spectroscopy are reported. XANES spectroscopy at the sulfur K-edge provides an excellent tool to gain information about the local environments of sulfur atoms in intact biological samples - no extraction processes are required. Spatially resolved measurements using a Kirkpatrick-Baez mirror focusing system were carried out to investigate the infection of wheat leaves by rust fungi. The results give information about changes in the sulfur metabolism of the host induced by the parasite and about the extension of the infection into visibly uninfected plant tissue. Furthermore, XANES spectra of microbial mats from sulfidic caves were measured. These mats are dominated by microbial groups involved in cycling sulfur. Additionally, the influence of sulfate deprivation and H{sub 2}S exposure on sulfur compounds in onion was investigated. To gain an insight into the thermal degradation of organic material the influence of roasting of sulfur compounds in coffee beans was studied. (orig.)

  20. Femtosecond laser spectroscopy

    CERN Document Server

    Hannaford, Peter

    2005-01-01

    As concepts and methodologies have evolved over the past two decades, the realm of ultrafast science has become vast and exciting and has impacted many areas of chemistry, biology and physics, and other fields such as materials science, electrical engineering, and optical communication. The field has recently exploded with the announcement of a series of remarkable new developments and advances. This volume surveys this recent growth in eleven chapters written by leading international researchers in the field. It includes sections on femtosecond optical frequency combs, soft x-ray femtosecond laser sources, and attosecond laser sources. In addition, the contributors address real-time spectroscopy of molecular vibrations with sub-5-fs pulses and multidimensional femtosecond coherent spectroscopies for studying molecular and electron dynamics. Novel methods for measuring and characterizing ultrashort laser pulses and ultrashort pulses of light are also described. The topics covered are revolutionizing the field...

  1. Parallel β-sheet vibrational couplings revealed by 2D IR spectroscopy of an isotopically labeled macrocycle: quantitative benchmark for the interpretation of amyloid and protein infrared spectra.

    Science.gov (United States)

    Woys, Ann Marie; Almeida, Aaron M; Wang, Lu; Chiu, Chi-Cheng; McGovern, Michael; de Pablo, Juan J; Skinner, James L; Gellman, Samuel H; Zanni, Martin T

    2012-11-21

    Infrared spectroscopy is playing an important role in the elucidation of amyloid fiber formation, but the coupling models that link spectra to structure are not well tested for parallel β-sheets. Using a synthetic macrocycle that enforces a two stranded parallel β-sheet conformation, we measured the lifetimes and frequency for six combinations of doubly (13)C═(18)O labeled amide I modes using 2D IR spectroscopy. The average vibrational lifetime of the isotope labeled residues was 550 fs. The frequencies of the labels ranged from 1585 to 1595 cm(-1), with the largest frequency shift occurring for in-register amino acids. The 2D IR spectra of the coupled isotope labels were calculated from molecular dynamics simulations of a series of macrocycle structures generated from replica exchange dynamics to fully sample the conformational distribution. The models used to simulate the spectra include through-space coupling, through-bond coupling, and local frequency shifts caused by environment electrostatics and hydrogen bonding. The calculated spectra predict the line widths and frequencies nearly quantitatively. Historically, the characteristic features of β-sheet infrared spectra have been attributed to through-space couplings such as transition dipole coupling. We find that frequency shifts of the local carbonyl groups due to nearest neighbor couplings and environmental factors are more important, while the through-space couplings dictate the spectral intensities. As a result, the characteristic absorption spectra empirically used for decades to assign parallel β-sheet secondary structure arises because of a redistribution of oscillator strength, but the through-space couplings do not themselves dramatically alter the frequency distribution of eigenstates much more than already exists in random coil structures. Moreover, solvent exposed residues have amide I bands with >20 cm(-1) line width. Narrower line widths indicate that the amide I backbone is solvent

  2. Retrieving the optical parameters of biological tissues using diffuse reflectance spectroscopy and Fourier series expansions. I. theory and application.

    Science.gov (United States)

    Muñoz Morales, Aarón A; Vázquez Y Montiel, Sergio

    2012-10-01

    The determination of optical parameters of biological tissues is essential for the application of optical techniques in the diagnosis and treatment of diseases. Diffuse Reflection Spectroscopy is a widely used technique to analyze the optical characteristics of biological tissues. In this paper we show that by using diffuse reflectance spectra and a new mathematical model we can retrieve the optical parameters by applying an adjustment of the data with nonlinear least squares. In our model we represent the spectra using a Fourier series expansion finding mathematical relations between the polynomial coefficients and the optical parameters. In this first paper we use spectra generated by the Monte Carlo Multilayered Technique to simulate the propagation of photons in turbid media. Using these spectra we determine the behavior of Fourier series coefficients when varying the optical parameters of the medium under study. With this procedure we find mathematical relations between Fourier series coefficients and optical parameters. Finally, the results show that our method can retrieve the optical parameters of biological tissues with accuracy that is adequate for medical applications.

  3. Synthesis and vibrational spectroscopy of 57Fe-labeled models of [NiFe] hydrogenase: first direct observation of a nickel–iron interaction† †Electronic supplementary information (ESI) available: Experimental procedures, spectral data, computational chemistry details, animated vibrational modes as GIFs. See DOI: 10.1039/c4cc04572f Click here for additional data file. Click here for additional data file.

    Science.gov (United States)

    Pelmenschikov, Vladimir; Wang, Hongxin; Meier, Florian; Gee, Leland B.; Yoda, Yoshitaka; Kaupp, Martin; Rauchfuss, Thomas B.

    2014-01-01

    A new route to iron carbonyls has enabled synthesis of 57Fe-labeled [NiFe] hydrogenase mimic (OC)3 57Fe(pdt)Ni(dppe). Its study by nuclear resonance vibrational spectroscopy revealed Ni–57Fe vibrations, as confirmed by calculations. The modes are absent for [(OC)3 57Fe(pdt)Ni(dppe)]+, which lacks Ni–57Fe bonding, underscoring the utility of the analyses in identifying metal–metal interactions. PMID:25237680

  4. Infrared vibrational nanocrystallography and nanoimaging

    Science.gov (United States)

    Muller, Eric A.; Pollard, Benjamin; Bechtel, Hans A.; van Blerkom, Peter; Raschke, Markus B.

    2016-01-01

    Molecular solids and polymers can form low-symmetry crystal structures that exhibit anisotropic electron and ion mobility in engineered devices or biological systems. The distribution of molecular orientation and disorder then controls the macroscopic material response, yet it is difficult to image with conventional techniques on the nanoscale. We demonstrated a new form of optical nanocrystallography that combines scattering-type scanning near-field optical microscopy with both optical antenna and tip-selective infrared vibrational spectroscopy. From the symmetry-selective probing of molecular bond orientation with nanometer spatial resolution, we determined crystalline phases and orientation in aggregates and films of the organic electronic material perylenetetracarboxylic dianhydride. Mapping disorder within and between individual nanoscale domains, the correlative hybrid imaging of nanoscale heterogeneity provides insight into defect formation and propagation during growth in functional molecular solids. PMID:27730212

  5. Infrared vibrational nanocrystallography and nanoimaging.

    Science.gov (United States)

    Muller, Eric A; Pollard, Benjamin; Bechtel, Hans A; van Blerkom, Peter; Raschke, Markus B

    2016-10-01

    Molecular solids and polymers can form low-symmetry crystal structures that exhibit anisotropic electron and ion mobility in engineered devices or biological systems. The distribution of molecular orientation and disorder then controls the macroscopic material response, yet it is difficult to image with conventional techniques on the nanoscale. We demonstrated a new form of optical nanocrystallography that combines scattering-type scanning near-field optical microscopy with both optical antenna and tip-selective infrared vibrational spectroscopy. From the symmetry-selective probing of molecular bond orientation with nanometer spatial resolution, we determined crystalline phases and orientation in aggregates and films of the organic electronic material perylenetetracarboxylic dianhydride. Mapping disorder within and between individual nanoscale domains, the correlative hybrid imaging of nanoscale heterogeneity provides insight into defect formation and propagation during growth in functional molecular solids.

  6. Advanced techniques for actinide spectroscopy (ATAS 2012). Abstract book

    Energy Technology Data Exchange (ETDEWEB)

    Foerstendorf, Harald; Mueller, Katharina; Steudtner, Robin (eds.)

    2012-07-01

    The abstract book of the International workshop on advanced techniques for actinide spectroscopy (ATAS 2012) include contributions concerning the following issues: environmental applications, NMR spectroscopy, vibrational spectroscopy, X-ray spectroscopy and theory, technical application: separation processes, emission spectroscopy.

  7. Application of gas phase cryogenic vibrational spectroscopy to characterize the CO2, CO, N2 and N2O interactions with the open coordination site on a Ni(I) macrocycle using dual cryogenic ion traps

    Science.gov (United States)

    Craig, Stephanie M.; Menges, Fabian S.; Johnson, Mark A.

    2017-02-01

    Recent advances in gas phase ion chemistry, coupled with cryogenic ion vibrational predissociation spectroscopy, provide a powerful way to characterize the structures of small molecules bound to open coordination sites of organometallic compounds. Here we extend our previous measurements on the relatively weakly interacting CO2 molecule with a Ni(I) tetraaza-macrocyclic compound to enable the characterization of more strongly interacting substrates. We first confirm the calculated η2-C,O binding motif of CO2 using isotopic labeling by direct, one photon vibrational predissociation of the Ni(I)-CO2 complex. We then apply this approach to study complexation of N2 at the active site. The generality of the method is then expanded to include application to more strongly bound systems that cannot be photodissociated with one IR photon. This involves implementation of a recently developed scheme (Marsh et al., 2015) involving two temperature-controlled ion traps. The first is optimized to complex the substrate molecule to the active site and the second is cooled to around 10 K to enable condensation of weakly bound "tag" molecules onto the target complex so as to enable its characterization by linear vibrational predissociation spectroscopy. We demonstrate this capability by applying it to the coordination of CO to the active Ni(I) site, as well as to elucidate the nature of the products that are formed upon reaction with N2O.

  8. Slow-spinning low-sideband HR-MAS NMR spectroscopy: delicate analysis of biological samples

    Science.gov (United States)

    Renault, Marie; Shintu, Laetitia; Piotto, Martial; Caldarelli, Stefano

    2013-11-01

    High-Resolution Magic-Angle Spinning (HR-MAS) NMR spectroscopy has become an extremely versatile analytical tool to study heterogeneous systems endowed with liquid-like dynamics. Spinning frequencies of several kHz are however required to obtain NMR spectra, devoid of spinning sidebands, with a resolution approaching that of purely isotropic liquid samples. An important limitation of the method is the large centrifugal forces that can damage the structure of the sample. In this communication, we show that optimizing the sample preparation, particularly avoiding air bubbles, and the geometry of the sample chamber of the HR-MAS rotor leads to high-quality low-sideband NMR spectra even at very moderate spinning frequencies, thus allowing the use of well-established solution-state NMR procedures for the characterization of small and highly dynamic molecules in the most fragile samples, such as live cells and intact tissues.

  9. Non-invasive chemically specific measurement of subsurface temperature in biological tissues using surface-enhanced spatially offset Raman spectroscopy.

    Science.gov (United States)

    Gardner, Benjamin; Stone, Nicholas; Matousek, Pavel

    2016-06-23

    Here we demonstrate for the first time the viability of characterising non-invasively the subsurface temperature of SERS nanoparticles embedded within biological tissues using spatially offset Raman spectroscopy (SORS). The proposed analytical method (T-SESORS) is applicable in general to diffusely scattering (turbid) media and features high sensitivity and high chemical selectivity. The method relies on monitoring the Stokes and anti-Stokes bands of SERS nanoparticles in depth using SORS. The approach has been conceptually demonstrated using a SORS variant, transmission Raman spectroscopy (TRS), by measuring subsurface temperatures within a slab of porcine tissue (5 mm thick). Root-mean-square errors (RMSEs) of 0.20 °C were achieved when measuring temperatures over ranges between 25 and 44 °C. This unique capability complements the array of existing, predominantly surface-based, temperature monitoring techniques. It expands on a previously demonstrated SORS temperature monitoring capability by adding extra sensitivity stemming from SERS to low concentration analytes. The technique paves the way for a wide range of applications including subsurface, chemical-specific, non-invasive temperature analysis within turbid translucent media including: the human body, subsurface monitoring of chemical (e.g. catalytic) processes in manufacture quality and process control and research. Additionally, the method opens prospects for control of thermal treatment of cancer in vivo with direct non-invasive feedback on the temperature of mediating plasmonic nanoparticles.

  10. Determination of resonance Raman cross-sections for use in biological SERS sensing with femtosecond stimulated Raman spectroscopy.

    Science.gov (United States)

    Silva, W Ruchira; Keller, Emily L; Frontiera, Renee R

    2014-08-05

    Surface-enhanced Raman spectroscopy (SERS) is a promising technique for in vivo bioanalyte detection, but accurate characterization of SERS biosensors can be challenging due to difficulties in differentiating resonance and surface enhancement contributions to the Raman signal. Here, we quantitate the resonance Raman cross-sections for a commonly used near-infrared SERS dye, 3,3'-diethylthiatricarbocyanine (DTTC). It is typically challenging to measure resonance Raman cross-sections for fluorescent dye molecules due to the overwhelming isoenergetic fluorescence signal. To overcome this issue, we used etalon-based femtosecond stimulated Raman spectroscopy, which is intrinsically designed to acquire a stimulated Raman signal without strong fluorescence or interference from signals resulting from other four-wave mixing pathways. Using this technique, we found that the cross-sections for most of the resonantly enhanced modes in DTTC exceed 10(-25) cm(2)/molecule. These cross-sections lead to high signal magnitude SERS signals from even weakly enhancing SERS substrates, as much of what appears to be a SERS signal is actually coming from the intrinsically strong resonance Raman signal. Our work will lead to a more accurate determination of SERS enhancement factors and SERS substrate characterization in the biologically relevant near-infrared region, ultimately leading to a more widespread use of SERS for biosensing and bioimaging applications.

  11. Terahertz underdamped vibrational motion governs protein-ligand binding in solution.

    Science.gov (United States)

    Turton, David A; Senn, Hans Martin; Harwood, Thomas; Lapthorn, Adrian J; Ellis, Elizabeth M; Wynne, Klaas

    2014-06-03

    Low-frequency collective vibrational modes in proteins have been proposed as being responsible for efficiently directing biochemical reactions and biological energy transport. However, evidence of the existence of delocalized vibrational modes is scarce and proof of their involvement in biological function absent. Here we apply extremely sensitive femtosecond optical Kerr-effect spectroscopy to study the depolarized Raman spectra of lysozyme and its complex with the inhibitor triacetylchitotriose in solution. Underdamped delocalized vibrational modes in the terahertz frequency domain are identified and shown to blue-shift and strengthen upon inhibitor binding. This demonstrates that the ligand-binding coordinate in proteins is underdamped and not simply solvent-controlled as previously assumed. The presence of such underdamped delocalized modes in proteins may have significant implications for the understanding of the efficiency of ligand binding and protein-molecule interactions, and has wider implications for biochemical reactivity and biological function.

  12. Surface-enhanced and tip-enhanced Raman spectroscopy of biological molecules on nanostructured metallic surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Hennemann, Laura E.; Mihaljevic, Josip; Braun, Kai; Meixner, Alfred J.; Zhang, Dai [Institute of Physical and Theoretical Chemistry, University of Tuebingen, Tuebingen (Germany); Kolloch, Andreas [Department of Physics, University of Konstanz, Universitaetsstrasse 10, 78457 Konstanz (Germany)

    2011-07-01

    We use a custom built apertureless scanning near-field optical microscope (SNOM) to investigate several kinds of biological molecules. The setup is an extended parabolic mirror based confocal microscope working with higher order laser modes in order to tune the polarization of the light in its focus. We detected the presence of a (sub)monolayer of biological molecules ranging from DNA bases to double stranded DNA by collecting their unique Raman fingerprint spectrum. In order to detect such small amounts of molecules, we performed surface-enhanced Raman scattering (SERS) or tip-enhanced Raman scattering (TERS). For SERS, either the irregular rough edges of evaporated noble metal grids or regular arrays of gold nano triangles served as enhancing substrates. We compared the plasmonic properties of gold triangles of different aspect ratios and on different substrates to optimize the electromagnetic enhancement for the 632.8 nm laser excitation. The obtained optical patterns were compared to those computed in simulations. In the case of TERS, an electrochemically etched sharp gold tip (approx. 20 nm tip apex diameter) was approached to the surface, thus acting simultaneously as a scanning probe microscopy tip for topographic measurements and as a near-field antenna collecting optical information. We collected TERS spectra of single calf thymus DNA molecules immobilized on smooth Au(111) surfaces. Strongly enhanced spectra were obtained both in the SERS and in the TERS measurements.

  13. High-Pressure Vibrational Spectroscopy.

    Science.gov (United States)

    Pogson, Mark

    1987-09-01

    Available from UMI in association with The British Library. Requires signed TDF. The study of solids at high pressure and variable temperature enables development of accurate interatomic potential functions over wide ranges of interatomic distances. A review of the main models used in the determination of these potentials is given in Chapter one. A discussion of phonon frequency as a variable physical parameter reflecting the interatomic potential is given. A high pressure Raman study of inorganic salts of the types MSCN, (M = K,Rb,Cs & NH_4^+ ) and MNO_2, (M = K,Na) has been completed. The studies have revealed two new phases in KNO_2 and one new phase in NaNO _2 at high pressure. The accurate phonon shift data have enabled the determination of the pure and biphasic stability regions of the phases of KNO _2. A discussion of the B1, B2 relationship of univalent nitrites is also given. In the series of thiocyanates studied new phases have been found in all four materials. In both the potassium and rubidium salts two new phases have been detected, and in the ceasium salt one new phase has been detected, all at high pressure, from accurate phonon shift data. These transitions are discussed in terms of second-order mechanisms with space groups suggested for all phases, based on Landau's theory of second-order phase transitions. In the ammonium salt one new phase has been detected. This new phase transition has been interpreted as a second-order transition. The series of molecular crystals CH_3 HgX, (X = Cl,Br & I) has been studied at high pressure and at variable temperature. In Chapter five, their phase behaviour at high pressure is detailed along with the pressure dependencies of their phonon frequencies. In the chloride and the bromide two new phases have been detected. In the bromide one has been detected at high temperature and one at high pressure, and latter being interpreted as the stopping of the methyl rotation. In the chloride one phase has been found at both low temperature as well as high pressure, and the other only at high pressure, the latter again associated with the stopping of methyl rotation. The iodide displays two high pressure transitions. A Raman -active soft-mode has been observed in all three analogues, at both high pressure and variable temperature. For the chloride and bromide analogues there is a discussion of the nature of the soft-mode along with the mechanism associated with the I/II transition. The results of the X-ray crystal structure determination of CH_3HgBr at ambient temperature and pressure are given.

  14. Early Warning of Biological Threats via Surface-Enhanced Raman Spectroscopy: A Case Study of Bacillus Spores

    Directory of Open Access Journals (Sweden)

    Antonia Lai

    2016-12-01

    Full Text Available A study on the application of surface-enhanced Raman spectroscopy (SERS in detecting biological threats is here reported. Simulants of deadly Bacillus anthracis endospores were used. This study proposes an automated device where SERS is used as a fast, pre-alarm technique of a two-stage sensor equipped with a real-time polymerase chain reaction (PCR. In order to check the potentialities of SERS in terms of sensitivity and specificity for on-site, real-time, automatic detection and identification of biological agents, two strains of genetically and harmless closely B. anthracis-related spores, Bacillus thuringiensis and Bacillus atrophaeus, were used as simulants. In order to assure the selectivity of the SERS substrate against B. thuringiensis spores, the substrate was functionalized by specific peptides. The obtained SERS measurements are classified as positive or negative hits by applying a special data evaluation based on the Euclidian distance between each spectrum and a reference spectrum of blank measurement. Principal component analysis (PCA was applied for discriminating between different strains representing dangerous and harmless spores. The results show that the SERS sensor is capable of detecting a few tenths of spores in a few minutes, and is particularly sensitive and fast for this purpose. Post-process analysis of the spectra allowed for discrimination between the contaminated and uncontaminated SERS sensors and even between different strains of spores, although not as clearly. For this purpose, the use of a non-functionalized SERS substrate is suggested.

  15. Vibrations of the S{sub 1} state of fluorobenzene-h{sub 5} and fluorobenzene-d{sub 5} via resonance-enhanced multiphoton ionization (REMPI) spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Joe P.; Andrejeva, Anna; Tuttle, William D.; Wright, Timothy G., E-mail: Tim.Wright@nottingham.ac.uk [School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD (United Kingdom); Pugliesi, Igor; Schriever, Christian [Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 München (Germany)

    2014-12-28

    We report resonance-enhanced multiphoton ionization spectra of the isotopologues fluorobenzene-h{sub 5} and fluorobenzene-d{sub 5}. By making use of quantum chemical calculations, the changes in the wavenumber of the vibrational modes upon deuteration are examined. Additionally, the mixing of vibrational modes both between isotopologues and also between the two electronic states is discussed. The isotopic shifts lead to dramatic changes in the appearance of the spectrum as vibrations shift in and out of Fermi resonance. Assignments of the majority of the fluorobenzene-d{sub 5} observed bands are provided, aided by previous results on fluorobenzene-h{sub 5}.

  16. Resonant Mie scattering in infrared spectroscopy of biological materials--understanding the 'dispersion artefact'.

    Science.gov (United States)

    Bassan, Paul; Byrne, Hugh J; Bonnier, Franck; Lee, Joe; Dumas, Paul; Gardner, Peter

    2009-08-01

    Infrared spectroscopic cytology is potentially a powerful clinical tool. However, in order for it to be successful, practitioners must be able to extract reliably a pure absorption spectrum from a measured spectrum that often contains many confounding factors. The most intractable problem to date is the, so called, dispersion artefact which most prominently manifests itself as a sharp decrease in absorbance on the high wavenumber side of the amide I band in the measured spectrum, exhibiting a derivative-like line shape. In this paper we use synchrotron radiation FTIR micro-spectroscopy to record spectra of mono-dispersed poly(methyl methacrylate) (PMMA) spheres of systematically varying size and demonstrate that the spectral distortions in the data can be understood in terms of resonant Mie scattering. A full understanding of this effect will enable us to develop strategies for deconvolving the scattering contribution and recovering the pure absorption spectrum, thus removing one of the last technological barriers to the development of clinical spectroscopic cytology.

  17. High-extinction VIPA-based Brillouin spectroscopy of turbid biological media

    CERN Document Server

    Fiore, Antonio; Shao, Peng; Yun, Seok Hyun; Scarcelli, Giuliano

    2016-01-01

    Brillouin microscopy has recently emerged as powerful technique to characterize the mechanical properties of biological tissue, cell and biomaterials. However, the potential of Brillouin microscopy is currently limited to transparent samples, because Brillouin spectrometers do not have sufficient spectral extinction to reject the predominant non-Brillouin scattered light of turbid media. To overcome this issue, we developed a spectrometer composed of a two VIPA stages and a multi-pass Fabry-Perot interferometer. The Fabry-Perot etalon acts as an ultra-narrow band-pass filter for Brillouin light with high spectral extinction and low loss. We report background-free Brillouin spectra from Intralipid solutions and up to 100 microns deep within chicken muscle tissue.

  18. HNS+ and HSN+ cations: Electronic states, spin-rovibronic spectroscopy with planetary and biological implications

    Science.gov (United States)

    Trabelsi, Tarek; Ben Yaghlane, Saida; Al Mogren, Muneerah Mogren; Francisco, Joseph S.; Hochlaf, Majdi

    2016-08-01

    Ab initio methods in conjunction with a large basis set are used to compute the potential energy surfaces of the 12 lowest electronic states of the HNS+ and HSN+ isomeric forms. These potentials are used in discussions of the metastability of these cations and plausible mechanisms for the H+/H + SN+/SN, S/S+ + NH+/NH, N/N+ + SH+/SH ion-molecule reactions. Interestingly, the low rovibrational levels of HSN+(12A″) and HNS+(12A″) electronically excited ions are predicted to be long-lived. Both ions are suggested to be a suitable candidate for light-sensitive NOṡ donor in vivo and as a possible marker for the detection of intermediates in nitrites + H2S reactions at the cellular level. The full spin rovibronic levels of HNS+ are presented, which may assist in the experimental identification of HNS+ and HSN+ ions and in elucidating their roles in astrophysical and biological media.

  19. Animal Communications Through Seismic Vibrations

    Energy Technology Data Exchange (ETDEWEB)

    Hill, Peggy (University of Tulsa)

    2001-05-02

    Substrate vibration has been important to animals as a channel of communication for millions of years, but our literature on vibration in this context of biologically relevant information is only decades old. The jaw mechanism of the earliest land vertebrates allowed them to perceive substrate vibrations as their heads lay on the ground long before airborne sounds could be heard. Although the exact mechanism of vibration production and the precise nature of the wave produced are not always understood, recent development of affordable instrumentation to detect and measure vibrations has allowed researchers to answer increasingly sophisticated questions about how animals send and receive vibration signals. We now know that vibration provides information used in predator defense, prey detection, recruitment to food, mate choice, intrasexual competition, and maternal/brood social interactions in a variety of insect orders, spiders, crabs, scorpions, chameleons, frogs, golden moles, mole rats, kangaroos rats, wallabies, elephants and bison.

  20. Applications of High Resolution Laser Induced Breakdown Spectroscopy for Environmental and Biological Samples

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Madhavi Z [ORNL; Labbe, Nicole [ORNL; Wagner, Rebekah J. [Pennsylvania State University, University Park, PA

    2013-01-01

    This chapter details the application of LIBS in a number of environmental areas of research such as carbon sequestration and climate change. LIBS has also been shown to be useful in other high resolution environmental applications for example, elemental mapping and detection of metals in plant materials. LIBS has also been used in phytoremediation applications. Other biological research involves a detailed understanding of wood chemistry response to precipitation variations and also to forest fires. A cross-section of Mountain pine (pinceae Pinus pungen Lamb.) was scanned using a translational stage to determine the differences in the chemical features both before and after a fire event. Consequently, by monitoring the elemental composition pattern of a tree and by looking for abrupt changes, one can reconstruct the disturbance history of a tree and a forest. Lastly we have shown that multivariate analysis of the LIBS data is necessary to standardize the analysis and correlate to other standard laboratory techniques. LIBS along with multivariate statistical analysis makes it a very powerful technology that can be transferred from laboratory to field applications with ease.

  1. PREFACE: Vibrations at surfaces Vibrations at surfaces

    Science.gov (United States)

    Rahman, Talat S.

    2011-12-01

    This special issue is dedicated to the phenomenon of vibrations at surfaces—a topic that was indispensible a couple of decades ago, since it was one of the few phenomena capable of revealing the nature of binding at solid surfaces. For clean surfaces, the frequencies of modes with characteristic displacement patterns revealed how surface geometry, as well as the nature of binding between atoms in the surface layers, could be different from that in the bulk solid. Dispersion of the surface phonons provided further measures of interatomic interactions. For chemisorbed molecules on surfaces, frequencies and dispersion of the vibrational modes were also critical for determining adsorption sites. In other words, vibrations at surfaces served as a reliable means of extracting information about surface structure, chemisorption and overlayer formation. Experimental techniques, such as electron energy loss spectroscopy and helium-atom-surface scattering, coupled with infra-red spectroscopy, were continually refined and their resolutions enhanced to capture subtleties in the dynamics of atoms and molecules at surfaces. Theoretical methods, whether based on empirical and semi-empirical interatomic potential or on ab initio electronic structure calculations, helped decipher experimental observations and provide deeper insights into the nature of the bond between atoms and molecules in regions of reduced symmetry, as encountered on solid surfaces. Vibrations at surfaces were thus an integral part of the set of phenomena that characterized surface science. Dedicated workshops and conferences were held to explore the variety of interesting and puzzling features revealed in experimental and theoretical investigations of surface vibrational modes and their dispersion. One such conference, Vibrations at Surfaces, first organized by Harald Ibach in Juelich in 1980, continues to this day. The 13th International Conference on Vibrations at Surfaces was held at the University of

  2. Quantitative generalized ratiometric fluorescence spectroscopy for turbid media based on probe encapsulated by biologically localized embedding

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Xiu-Fang; Chen, Zeng-Ping, E-mail: zpchen2002@hotmail.com; Cui, Yin-Yin; Hu, Yuan-Liang; Yu, Ru-Qin

    2016-05-19

    PEBBLE (probe encapsulated by biologically localized embedding) nanosensor encapsulating an intensity-based fluorescence indicator and an inert reference fluorescence dye inside the pores of stable matrix can be used as a generalized wavelength-ratiometric probe. However, the lack of an efficient quantitative model render the choices of inert reference dyes and intensity-based fluorescence indicators used in PEBBLEs based generalized wavelength-ratiometric probes rather limited. In this contribution, an extended quantitative fluorescence model was derived specifically for generalized wavelength-ratiometric probes based on PEBBLE technique (QFM{sub GRP}) with a view to simplify the design of PEBBLEs and hence further extend their application potentials. The effectiveness of QFM{sub GRP} has been tested on the quantitative determination of free Ca{sup 2+} in both simulated and real turbid media using a Ca{sup 2+} sensitive PEBBLE nanosensor encapsulating Rhod-2 and eosin B inside the micropores of stable polyacrylamide matrix. Experimental results demonstrated that QFM{sub GRP} could realize precise and accurate quantification of free Ca{sup 2+} in turbid samples, even though there is serious overlapping between the fluorescence excitation peaks of eosin B and Ca{sup 2+} bound Rhod-2. The average relative predictive error value of QFM{sub GRP} for the test simulated turbid samples was 5.9%, about 2–4 times lower than the corresponding values of partial least squares calibration model and the empirical ratiometric model based on the ratio of fluorescence intensities at the excitation peaks of Ca{sup 2+} bound Rhod-2 and eosin B. The recovery rates of QFM{sub GRP} for the real and spiked turbid samples varied from 93.1% to 101%, comparable to the corresponding results of atomic absorption spectrometry. - Highlights: • An advanced model was derived for generalized wavelength-ratiometric PEBBLEs. • The model can simplify the design of generalized wavelength

  3. Luminescence spectroscopy of singlet oxygen enables monitoring of oxygen consumption in biological systems consisting of fatty acids.

    Science.gov (United States)

    Gollmer, Anita; Regensburger, Johannes; Maisch, Tim; Bäumler, Wolfgang

    2013-07-21

    The interaction of singlet oxygen ((1)O2) generated in a photosensitized process with well-known reference photosensitizers Perinaphthenone (PN) and TMPyP is investigated in a model system consisting of fatty acids and the respective exogenous photosensitizer (PS) in solution by direct detection of the luminescence photons of (1)O2 at 1270 nm. Such a model system is a first approach to mimic the complex environment of (1)O2 in a biological cell which consists mainly of water, proteins, sugars and lipids. Firstly, the important issue of oxygen consumption is evaluated which has to be considered during luminescence detection of (1)O2. It is known that the luminescence signal of (1)O2 is dependent on the oxygen concentration of the environment. Cellular components such as lipids represent oxygen consumers due to peroxidation of their unsaturated double bonds. Secondly, the experimental conditions for this model system regarding oxygen consumption are optimized to estimate the rates and rate constants of the coupled system. Thirdly, the triplet decay of the PS can provide more precise information about the actual oxygen concentration close to the PS and can be used, therefore, as a more precise method to determine the oxygen concentration in more complex systems such as a biological cell. The aim is to get a better understanding of photosensitized reactions of (1)O2 with cellular components to further improve methodologies, in particular at a cellular level using luminescence spectroscopy. In conclusion, luminescence detection might be a helpful tool to monitor precisely and promptly changes in oxygen concentration in a complex environment.

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

    Science.gov (United States)

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

    2014-07-14

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

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

    Indian Academy of Sciences (India)

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

    2012-01-01

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

  6. Molecular structure and vibrational analysis of Trifluoperazine by FT-IR, FT-Raman and UV-Vis spectroscopies combined with DFT calculations.

    Science.gov (United States)

    Rajesh, P; Gunasekaran, S; Gnanasambandan, T; Seshadri, S

    2015-02-25

    The complete vibrational assignment and analysis of the fundamental vibrational modes of Trifluoperazine (TFZ) was carried out using the experimental FT-IR, FT-Raman and UV-Vis data and quantum chemical studies. The observed vibrational data were compared with the wavenumbers derived theoretically for the optimized geometry of the compound from the DFT-B3LYP gradient calculations employing 6-31G (d,p) basis set. Thermodynamic properties like entropy, heat capacity and enthalpy have been calculated for the molecule. The HOMO-LUMO energy gap has been calculated. The intramolecular contacts have been interpreted using natural bond orbital (NBO) and natural localized molecular orbital (NLMO) analysis. Important non-linear properties such as first hyperpolarizability of TFZ have been computed using B3LYP quantum chemical calculation.

  7. Application of picosecond laser-induced breakdown spectroscopy to quantitative analysis of boron in meatballs and other biological samples.

    Science.gov (United States)

    Hedwig, Rinda; Lahna, Kurnia; Lie, Zener Sukra; Pardede, Marincan; Kurniawan, Koo Hendrik; Tjia, May On; Kagawa, Kiichiro

    2016-11-10

    This report presents the results of laser-induced breakdown spectroscopy (LIBS) study on biological and food samples of high water content using a picosecond (ps) laser at low output energy of 10 mJ and low-pressure helium ambient gas at 2 kPa. Evidence of excellent emission spectra of various analyte elements with very low background is demonstrated for a variety of samples without the need of sample pretreatment. Specifically, limits of detection in the range of sub-ppm are obtained for hazardous Pb and B impurities in carrots and meatballs. This study also shows the inferior performance of LIBS using a nanosecond laser and atmospheric ambient air for a soft sample of high water content and thereby explains its less successful applications in previous attempts. The present result has instead demonstrated the feasibility and favorable results of employing LIBS with a ps laser and low-pressure helium ambient gas as a less costly and more practical alternative to inductively coupled plasma for regular high sensitive inspection of harmful food preservatives and environmental pollutants.

  8. Evaluation of a multi-electrode bioimpedance spectroscopy tensor probe to detect the anisotropic conductivity spectra of biological tissues

    Science.gov (United States)

    Karki, Bishal; Wi, Hun; McEwan, Alistair; Kwon, Hyeuknam; In Oh, Tong; Woo, Eung Je; Seo, Jin Keun

    2014-07-01

    This paper presents bioimpedance spectroscopy measurements of anisotropic tissues using a 16 electrode probe and reconstruction method of estimating the anisotropic impedance spectrum in a local region just underneath the center of the probe. This may enable in-vivo surface bioimpedance measurements with similar performance to the ex-vivo gold standard that requires excising and placing the entire tissue sample in a unit measurement cell with uniform electric field. The multiple surface electrodes enable us to create a focused current pattern so that the resulting measured voltage is more sensitive to a local region and less sensitive to other areas. This is exploited in a reconstruction method to provide improved bioimpedance and anisotropy measurements. In this paper, we describe the current pattern for localized electrical energy concentration, performance with the spring loaded pin electrodes, data calibration and experimental results on anisotropic agar phantoms and different tissue types. The anisotropic conductivity spectra are able to differentiate insulating films of different thickness and detect their orientation. Bioimpedance spectra of biological tissues are in agreement with published data and reference instruments. The anisotropy expressed as the ratio of eigenvalues and the orientation of eigenfunctions were reconstructed at 45° intervals. This information is used to predict the underlying anisotropy of the region under the probe. Tissue measurements clearly demonstrate the expected higher anisotropy of muscle tissue compared to liver tissue and spectral changes.

  9. Vibrational spectroscopy (FT-IR and FT-Raman) investigation, and hybrid computational (HF and DFT) analysis on the structure of 2,3-naphthalenediol.

    Science.gov (United States)

    Shoba, D; Periandy, S; Karabacak, M; Ramalingam, S

    2011-12-01

    The FT-IR and FT-Raman vibrational spectra of 2,3-naphthalenediol (C(10)H(8)O(2)) have been recorded using Bruker IFS 66V spectrometer in the range of 4000-100 cm(-1) in solid phase. A detailed vibrational spectral analysis has been carried out and the assignments of the observed fundamental bands have been proposed on the basis of peak positions and relative intensities. The optimized molecular geometry and vibrational frequencies in the ground state are calculated by using the ab initio Hartree-Fock (HF) and DFT (LSDA and B3LYP) methods with 6-31+G(d,p) and 6-311+G(d,p) basis sets. There are three conformers, C1, C2 and C3 for this molecule. The computational results diagnose the most stable conformer of title molecule as the C1 form. The isotropic computational analysis showed good agreement with the experimental observations. Comparison of the fundamental vibrational frequencies with calculated results by HF and DFT methods. Comparison of the simulated spectra provides important information about the capability of computational method to describe the vibrational modes. A study on the electronic properties, such as absorption wavelengths, excitation energy, dipole moment and Frontier molecular orbital energies, are performed by time dependent DFT approach. The electronic structure and the assignment of the absorption bands in the electronic spectra of steady compounds are discussed. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. On the basis of the thermodynamic properties of the title compound at different temperatures have been calculated. The statistical thermodynamic properties (standard heat capacities, standard entropies, and standard enthalpy changes) and their correlations with temperature have been obtained from the theoretical vibrations.

  10. Homogeneous and inhomogeneous broadenings and the Voigt line shapes in the phase-resolved and intensity sum-frequency generation vibrational spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-01-21

    In this report we show that the ability to measure the sub-1 cm-1 resolution phase-resolved and intensity high-resolution broadband sum frequency generation vibrational spectra (HR-BB-SFG-VS) of the –CN stretch vibration of the Langmuir-Blodgett (LB) monolayer of the 4-n-octyl-4’-cyanobiphenyl (8CB) on the z-cut α-quartz surface allows for the first time the direct comparison and understanding of the homogeneous and inhomogeneous broadenings in the imaginary and intensity SFG vibrational spectral lineshapes in detail. The difference of the full width at half maxima (FWHM) of the imaginary and intensity SFG-VS spectra of the same vibrational mode is the signature of the Voigt lineshape and it measures the relative contribution to the overall lineshape from the homogeneous and inhomogeneous broadenings in SFG vibrational spectra. From the phase-resolved and intensity spectra, we found that the FWHM of the 2238.00 ±0.02 cm-1 peak in the phase-resolved imaginary and intensity spectra is 19.2 ± 0.2 cm-1 and 21.6 ± 0.4 cm-1, respectively, for the –CN group of the 8CB LB monolayer on the z-cut α-quartz crystal surface. The FWHM width difference of 2.4 cm-1 agrees quantitatively with a Voigt lineshape with a homogeneous broadening half width of Γ = 5.29 ± 0.08 cm-1 and a inhomogeneous standard derivation width Δω = 5.42 ± 0.07 cm-1. These results shed new lights on the understanding and interpretation of the lineshapes of both the phase-resolved and the intensity SFG vibrational spectra, as well as other incoherent and coherent spectroscopic techniques in general.

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

    Science.gov (United States)

    Ramalingam, S; Periandy, S

    2011-03-01

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

  12. Biologic

    CERN Document Server

    Kauffman, L H

    2002-01-01

    In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers but also extainers ><, entities open to interaction and distinguishing the space that they are not. The boundary algebra of containers and extainers is to biologic what boolean algebra is to classical logic. We show how this formalism encompasses significant parts of the logic of DNA replication, the Dirac formalism for quantum mechanics, formalisms for protein folding and the basic structure of the Temperley Lieb algebra at the foundations of topological invariants of knots and links.

  13. Raman and infrared spectroscopy, DFT calculations, and vibrational assignment of the anticancer agent picoplatin: performance of long-range corrected/hybrid functionals for a platinum(II) complex.

    Science.gov (United States)

    Malik, Magdalena; Wysokiński, Rafał; Zierkiewicz, Wiktor; Helios, Katarzyna; Michalska, Danuta

    2014-08-28

    Picoplatin, cis-[PtCl2(NH3)(2-picoline)], is a new promising anticancer agent undergoing clinical trials, which reveals high efficacy against many tumors and greatly reduced toxicity, in comparison to cisplatin. In this work, we present for the first time the Fourier-transform Raman and infrared spectra of picoplatin, in the region of 3500-50 cm(-1). The comprehensive theoretical studies on the molecular structure, the nature of Pt-ligand bonding, vibrational frequencies, and intensities were performed by employing different DFT methods, including hybrid (PBE0, mPW1PW, and B3LYP) and long-range-corrected hybrid density functionals (LC-ωPBE, CAM-B3LYP). Various effective core potentials (ECP) and basis sets have been used. In the prediction of the molecular structure of picoplatin, the best results have been obtained by LC-ωPBE, followed by PBE0, mPW1PW, and CAM-B3LYP density functionals, while the least accurate is B3LYP. The use of the LanL2TZ(f) ECP/basis set for Pt, in conjunction with all tested DFT methods, improves the calculated geometry of the title complex. The PBE0, mPW1PW, and CAM-B3LYP methods have shown the best performance in the calculations of the frequencies of Pt-ligand vibrations. A clear-cut assignment of all the bands in the IR and Raman spectra have been made on the basis of the calculated potential energy distribution (PED). The nature of the "vibrational signatures" of picoplatin have been determined. These results are indispensable for further investigation on drug-target interactions using vibrational spectroscopy.

  14. Vibrational Microspectroscopy for Cancer Screening

    Directory of Open Access Journals (Sweden)

    Fiona M. Lyng

    2015-02-01

    Full Text Available Vibrational spectroscopy analyses vibrations within a molecule and can be used to characterise a molecular structure. Raman spectroscopy is one of the vibrational spectroscopic techniques, in which incident radiation is used to induce vibrations in the molecules of a sample, and the scattered radiation may be used to characterise the sample in a rapid and non-destructive manner. Infrared (IR spectroscopy is a complementary vibrational spectroscopic technique based on the absorption of IR radiation by the sample. Molecules absorb specific frequencies of the incident light which are characteristic of their structure. IR and Raman spectroscopy are sensitive to subtle biochemical changes occurring at the molecular level allowing spectral variations corresponding to disease onset to be detected. Over the past 15 years, there have been numerous reports demonstrating the potential of IR and Raman spectroscopy together with multivariate statistical analysis techniques for the detection of a variety of cancers including, breast, lung, brain, colon, oral, oesophageal, prostate and cervical cancer. This paper discusses the recent advances and the future perspectives in relation to cancer screening applications, focussing on cervical and oral cancer.

  15. Vibrational spectroscopy of the double complex salt Pd(NH3)4(ReO4)2, a bimetallic catalyst precursor

    Science.gov (United States)

    Thompson, Simon T.; Lamb, H. Henry; Delley, Bernard; Franzen, Stefan

    2017-02-01

    Tetraamminepalladium(II) perrhenate, a double complex salt, has significant utility in PdRe catalyst preparation; however, the vibrational spectra of this readily prepared compound have not been described in the literature. Herein, we present the infrared (IR) and Raman spectra of tetraamminepalladium(II) perrhenate and several related compounds. The experimental spectra are complemented by an analysis of normal vibrational modes that compares the experimentally obtained spectra with spectra calculated using DFT (DMol3). The spectra are dominated by features due to the ammine groups and the Resbnd O stretch in Td ReO4-; lattice vibrations due to the D4h Pd(NH3)42+ are also observed in the Raman spectrum. Generally, we observe good agreement between ab initio calculations and experimental spectra. The calculated IR spectrum closely matches experimental results for peak positions and their relative intensities. The methods for calculating resonance Raman intensities are implemented using the time correlator formalism using two methods to obtain the excited state displacements and electron-vibration coupling constants, which are the needed inputs in addition to the normal mode wave numbers. Calculated excited state energy surfaces of Raman-active modes correctly predict relative intensities of the peaks and Franck-Condon activity; however, the position of Raman bands are predicted at lower frequencies than observed. Factor group splitting of Raman peaks observed in spectra of pure compounds is not predicted by DFT.

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

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    1979-01-01

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

  17. Use of vibrational spectroscopy to study protein and DNA structure, hydration, and binding of biomolecules: A combined theoretical and experimental approach

    DEFF Research Database (Denmark)

    Jalkanen, Karl J.; Jürgensen, Vibeke Würtz; Claussen, Anetta

    2006-01-01

    +disp, RHF, MP2, and DFT methodologies for the modeling studies with the goal of interpreting the experimentally measured vibrational spectra for these molecules to the greatest extent possible and to use this combined approach to understand the structure, function, and electronic properties...

  18. Fluorescence spectroscopy

    DEFF Research Database (Denmark)

    Bagatolli, Luis

    2016-01-01

    Fluorescence spectroscopy is a powerful experimental tool used by scientists from many disciplines. During the last decades there have been important developments on distinct fluorescence methods, particularly those related to the study of biological phenomena. This chapter discusses the foundati......Fluorescence spectroscopy is a powerful experimental tool used by scientists from many disciplines. During the last decades there have been important developments on distinct fluorescence methods, particularly those related to the study of biological phenomena. This chapter discusses...

  19. Basic molecular spectroscopy

    CERN Document Server

    Gorry, PA

    1985-01-01

    BASIC Molecular Spectroscopy discusses the utilization of the Beginner's All-purpose Symbolic Instruction Code (BASIC) programming language in molecular spectroscopy. The book is comprised of five chapters that provide an introduction to molecular spectroscopy through programs written in BASIC. The coverage of the text includes rotational spectra, vibrational spectra, and Raman and electronic spectra. The book will be of great use to students who are currently taking a course in molecular spectroscopy.

  20. On the effect of experimental noise on the classification of biological samples using Raman micro-spectroscopy

    Science.gov (United States)

    Barton, Sinead J.; Kerr, Laura T.; Domijan, Katarina; Hennelly, Bryan M.

    2016-04-01

    Raman micro-spectroscopy is an optoelectronic technique that can be used to evaluate the chemical composition of biological samples and has been shown to be a powerful diagnostic tool for the investigation of various cancer related diseases including bladder, breast, and cervical cancer. Raman scattering is an inherently weak process with approximately 1 in 107 photons undergoing scattering and for this reason, noise from the recording system can have a significant impact on the quality of the signal, and its suitability for diagnostic classification. The main sources of noise in the recorded signal are shot noise, CCD dark current, and CCD readout noise. Shot noise results from the low signal photon count while dark current results from thermally generated electrons in the semiconductor pixels. Both of these noise sources are time dependent; readout noise is time independent but is inherent in each individual recording and results in the fundamental limit of measurement, arising from the internal electronics of the camera. In this paper, each of the aforementioned noise sources are analysed in isolation, and used to experimentally validate a mathematical model. This model is then used to simulate spectra that might be acquired under various experimental conditions including the use of different cameras, different source wavelength, and power etc. Simulated noisy datasets of T24 and RT112 cell line spectra are generated based on true cell Raman spectrum irradiance values (recorded using very long exposure times) and the addition of simulated noise. These datasets are then input to multivariate classification using Principal Components Analysis and Linear Discriminant Analysis. This method enables an investigation into the effect of noise on the sensitivity and specificity of Raman based classification under various experimental conditions and using different equipment.

  1. Resonance-enhanced multiphoton ionization (REMPI) spectroscopy of bromobenzene and its perdeuterated isotopologue: Assignment of the vibrations of the S{sub 0}, S{sub 1}, and D{sub 0}{sup +} states of bromobenzene and the S{sub 0} and D{sub 0}{sup +} states of iodobenzene

    Energy Technology Data Exchange (ETDEWEB)

    Andrejeva, Anna; Tuttle, William D.; Harris, Joe P.; Wright, Timothy G., E-mail: Tim.Wright@nottingham.ac.uk [School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD (United Kingdom)

    2015-12-28

    We report vibrationally resolved spectra of the S{sub 1}←S{sub 0} transition of bromobenzene using resonance-enhanced multiphoton ionization spectroscopy. We study bromobenzene-h{sub 5} as well as its perdeuterated isotopologue, bromobenzene-d{sub 5}. The form of the vibrational modes between the isotopologues and also between the S{sub 0} and S{sub 1} electronic states is discussed for each species, allowing assignment of the bands to be achieved and the activity between states and isotopologues to be established. Vibrational bands are assigned utilizing quantum chemical calculations, previous experimental results, and isotopic shifts. Previous work and assignments of the S{sub 1} spectra are discussed. Additionally, the vibrations in the ground state cation, D{sub 0}{sup +}, are considered, since these have also been used by previous workers in assigning the excited neutral state spectra. We also examine the vibrations of iodobenzene in the S{sub 0} and D{sub 0}{sup +} states and comment on the previous assignments of these. In summary, we have been able to assign the corresponding vibrations across the whole monohalobenzene series of molecules, in the S{sub 0}, S{sub 1}, and D{sub 0}{sup +} states, gaining insight into vibrational activity and vibrational couplings.

  2. Dynamics of an [Fe4S4(SPh)4]2- cluster explored via IR, Raman, and nuclear resonance vibrational spectroscopy (NRVS)-analysis using 36S substitution, DFT calculations, and empirical force fields.

    Science.gov (United States)

    Xiao, Yuming; Koutmos, Markos; Case, David A; Coucouvanis, Dimitri; Wang, Hongxin; Cramer, Stephen P

    2006-05-14

    We have used four vibrational spectroscopies--FT-IR, FT-Raman, resonance Raman, and 57Fe nuclear resonance vibrational spectroscopy (NRVS)--to study the normal modes of the Fe-S cluster in [(n-Bu)4N]2[Fe4S4(SPh)4]. This [Fe4S4(SR)4]2- complex serves as a model for the clusters in 4Fe ferredoxins and high-potential iron proteins (HiPIPs). The IR spectra exhibited differences above and below the 243 K phase transition. Significant shifts with 36S substitution into the bridging S positions were also observed. The NRVS results were in good agreement with the low temperature data from the conventional spectroscopies. The NRVS spectra were interpreted by normal mode analysis using optimized Urey-Bradley force fields (UBFF) as well as from DFT theory. For the UBFF calculations, the parameters were refined by comparing calculated and observed NRVS frequencies and intensities. The frequency shifts after 36S substitution were used as an additional constraint. A D 2d symmetry Fe4S4S'4 model could explain most of the observed frequencies, but a better match to the observed intensities was obtained when the ligand aromatic rings were included for a D 2d Fe4S4(SPh)4 model. The best results were obtained using the low temperature structure without symmetry constraints. In addition to stretching and bending vibrations, low frequency modes between approximately 50 and 100 cm(-1) were observed. These modes, which have not been seen before, are interpreted as twisting motions with opposing sides of the cube rotating in opposite directions. In contrast with a recent paper on a related Fe4S4 cluster, we find no need to assign a large fraction of the low frequency NRVS intensity to 'rotational lattice modes'. We also reassign the 430 cm(-1) band as primarily an elongation of the thiophenolate ring, with approximately 10% terminal Fe-S stretch character. This study illustrates the benefits of combining NRVS with conventional Raman and IR analysis for characterization of Fe-S centers. DFT

  3. Characterization of 1,5-dimethoxynaphthalene by vibrational spectroscopy (FT-IR and FT-Raman) and density functional theory calculations.

    Science.gov (United States)

    Kandasamy, M; Velraj, G; Kalaichelvan, S; Mariappan, G

    2015-01-05

    In this work, we reported a combined experimental and theoretical study on molecular structure, vibrational spectra and natural bond orbital (NBO) analysis of 1,5-dimethoxynaphthalene. The optimized molecular structure, atomic charges, vibrational frequencies and natural bond orbital analysis of 1,5-dimethoxynaphthalene have been studied by performing DFT/B3LYP/6-31G(d,p) level of theory. The FTIR, FT-Raman spectra were recorded in the region of 4000-400 cm(-1) and 3500-50 cm(-1) respectively. The scaled wavenumbers are compared with the experimental values. The difference between the observed and scaled wavenumber values of the most fundamentals is very small. The formation of hydrogen bond was investigated in terms of the charge density by the NBO analysis. Natural Population Analysis (NPA) was used for charge determination in the title molecule. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis were investigated using theoretical calculations.

  4. Molecular dynamics simulation and vibrational spectroscopy of molecules (Ⅰ)——A method of internal coordinate correlation for band assignment

    Institute of Scientific and Technical Information of China (English)

    杨小震

    1995-01-01

    A method of simulation of vibrational spectra by using the "internal coordinatecorrelation" based on molecular dynamics algorithms and auto-correlation function has been developed.The in-ternal coordinates,such as bond stretching,bond angle bending,out-of-plane bending and torsion,are treatedas the dynamic variables to obtain a density spectrum or the "internal coordinate correlation" spectrum Theadvantages of this method are as follows:i)it is easier to assign vibration modes for the density spectra;ii)itsimply connects the Fourier transformed "internal coordinate correlation" function to the eigenvectors innormal coordinate analysis;iii)it is a basis for simulating IR and Raman active spectra of a large molecularsystem.

  5. Complex vibrational analysis of an antiferroelectric liquid crystal based on solid-state oriented quantum chemical calculations and experimental molecular spectroscopy.

    Science.gov (United States)

    Drużbicki, Kacper; Mikuli, Edward; Kocot, Antoni; Ossowska-Chruściel, Mirosława Danuta; Chruściel, Janusz; Zalewski, Sławomir

    2012-08-02

    The experimental and theoretical vibrational spectroscopic study of one of a novel antiferroelectric liquid crystals (AFLC), known under the MHPSBO10 acronym, have been undertaken. The interpretation of both FT-IR and FT-Raman spectra was focused mainly on the solid-state data. To analyze the experimental results along with the molecular properties, density functional theory (DFT) computations were performed using several modern theoretical approaches. The presented calculations were performed within the isolated molecule model, probing the performance of modern exchange-correlations functionals, as well as going beyond, i.e., within hybrid (ONIOM) and periodic boundary conditions (PBC) methodologies. A detailed band assignment was supported by the normal-mode analysis with SQM ab initio force field scaling. The results are supplemented by the noncovalent interactions analysis (NCI). The relatively noticeable spectral differences observed upon Crystal to AFLC phase transition have also been reported. For the most prominent vibrational modes, the geometries of the transition dipole moments along with the main components of vibrational polarizability were analyzed in terms of the molecular frame. One of the goals of the paper was to optimize the procedure of solid-state calculations to obtain the results comparable with the all electron calculations, performed routinely for isolated molecules, and to test their performance. The presented study delivers a complex insight into the vibrational spectrum with a noticeable improvement of the theoretical results obtained for significantly attracting mesogens using modern molecular modeling approaches. The presented modeling conditions are very promising for further description of similar large molecular crystals.

  6. Waves & vibrations

    OpenAIRE

    Nicolas, Maxime

    2016-01-01

    Engineering school; This course is designed for students of Polytech Marseille, engineering school. It covers first the physics of vibration of the harmonic oscillator with damping and forcing, coupled oscillators. After a presentation of the wave equation, the vibration of strings, beams and membranes are studied.

  7. Pyrrole Hydrogenation over Rh(111) and Pt(111) Single-Crystal Surfaces and Hydrogenation Promotion Mediated by 1-Methylpyrrole: A Kinetic and Sum-Frequency Generation Vibrational Spectroscopy Study

    Energy Technology Data Exchange (ETDEWEB)

    Kliewer, Christopher J.; Bieri, Marco; Somorjai, Gabor A.

    2008-03-04

    Sum-frequency generation (SFG) surface vibrational spectroscopy and kinetic measurements using gas chromatography have been used to study the adsorption and hydrogenation of pyrrole over both Pt(111) and Rh(111) single-crystal surfaces at Torr pressures (3 Torr pyrrole, 30 Torr H{sub 2}) to form pyrrolidine and the minor product butylamine. Over Pt(111) at 298 K it was found that pyrrole adsorbs in an upright geometry cleaving the N-H bond to bind through the nitrogen evidenced by SFG data. Over Rh(111) at 298 K pyrrole adsorbs in a tilted geometry relative to the surface through the p-aromatic system. A pyrroline surface reaction intermediate, which was not detected in the gas phase, was seen by SFG during the hydrogenation over both surfaces. Significant enhancement of the reaction rate was achieved over both metal surfaces by adsorbing 1-methylpyrrole before reaction. SFG vibrational spectroscopic results indicate that reaction promotion is achieved by weakening the bonding between the N-containing products and the metal surface because of lateral interactions on the surface between 1-methylpyrrole and the reaction species, reducing the desorption energy of the products. It was found that the ring-opening product butylamine was a reaction poison over both surfaces, but this effect can be minimized by treating the catalyst surfaces with 1-methylpyrrole before reaction. The reaction rate was not enhanced with elevated temperatures, and SFG suggests desorption of pyrrole at elevated temperatures.

  8. Sum Frequency Generation Vibrational Spectroscopy of 1,3-Butadiene Hydrogenation on 4 nm Pt@SiO 2 , Pd@SiO 2 , and Rh@SiO 2 Core–Shell Catalysts

    KAUST Repository

    Krier, James M.

    2015-01-14

    © 2014 American Chemical Society. 1,3-Butadiene (1,3-BD) hydrogenation was performed on 4 nm Pt, Pd, and Rh nanoparticles (NPs) encapsulated in SiO2 shells at 20, 60, and 100 °C. The core-shells were grown around polyvinylpyrrolidone (PVP) coated NPs (Stöber encapsulation) prepared by colloidal synthesis. Sum frequency generation (SFG) vibrational spectroscopy was performed to correlate surface intermediates observed in situ with reaction selectivity. It is shown that calcination is effective in removing PVP, and the SFG signal can be generated from the metal surface. Using SFG, it is possible to compare the surface vibrational spectrum of Pt@SiO2 (1,3-BD is hydrogenated through multiple paths and produces butane, 1-butene, and cis/trans-2-butene) to Pd@SiO2 (1,3-BD favors one path and produces 1-butene and cis/trans-2-butene). In contrast to Pt@SiO2 and Pd@SiO2, SFG and kinetic experiments of Rh@SiO2 show a permanent accumulation of organic material.

  9. Deducing the molecular properties of zwitterionic, protonated, deprotonated, and double-deprotonated forms of L-cysteine from vibrational spectroscopy (IR, Raman, VCD) and quantum chemical calculations.

    Science.gov (United States)

    Quesada-Moreno, María Mar; Avilés-Moreno, Juan Ramón; Márquez-García, A A; López-González, Juan Jesús

    2014-06-01

    The behavior of L-cysteine (C3H7NO2S, (2R)-2-amino-3-sulfanylpropanoic acid) in water at different pH values was analyzed both experimentally and theoretically. The behavior was studied at pH values of 5.21 (at this pH, L-cysteine is a zwitterionic species), 1.00 (protonated species), 8.84 (monodeprotonated species), and 13.00 (dideprotonated species). We carried out a vibrational study using nonchiroptical (IR-Raman) and chiroptical (VCD) techniques complemented by quantum chemical calculations. We adopted a dual strategy, as follows. (i) The hybrid density functionals B3LYP and M062X and the ab initio MP2 method were employed, with the same 6-311++G (d,p) basis set, in order to characterize the relative energies and structures of an extensive set of conformers of L-cysteine. The presence of water was included by utilizing the IEF-PCM implicit solvation model. (ii) The vibrational analysis was made using a chirality-sensitive using a chirality-sensitive technique (VCD) and chirality-insensitive techniques (IR, including MIR and FIR, and Raman), especially in aqueous solution. The results obtained theoretically and experimentally were compared in order to deduce the most stable structures at each pH. Moreover, for the first time, the monodeprotonated anion of L-cysteine was detected in aqueous solution by means of IR, Raman and vibrational circular dichroism (VCD). Finally, analysis of the low-frequency region using the IR and Raman techniques was shown to be a very important way to understanding the conformational preference of the zwitterionic species.

  10. Direct observation of the cyclic dimer in liquid acetic acid by probing the C=O vibration with ultrafast coherent Raman spectroscopy.

    Science.gov (United States)

    Lütgens, Matthias; Friedriszik, Frank; Lochbrunner, Stefan

    2014-09-01

    We present a comparison of spontaneous Raman and ultrafast coherent anti-Stokes Raman scattering (CARS) spectra of the C=O vibration of liquid acetic acid. The former technique cannot clearly reveal the number of contributions in the spectrum. However, the additional time and spectrally resolved CARS experiment supports strictly the existence of four modes, which proves the coexistence of more than one H-bonded configuration in liquid acetic acid. A comparably slowly dephasing mode which is obscured by a broad band in the linear Raman spectrum is assigned to the cyclic dimer and can be observed freed from all other contributions by ultrafast CARS.

  11. Characterizing the Biological and Geochemical Architecture of Hydrothermally Derived Sedimentary Deposits: Coupling Micro Raman Spectroscopy with Noble Gas Spectrometry

    Science.gov (United States)

    Bower, D. M.; Conrad, P. G.; Steele, A.; Fries, M. D.

    2016-05-01

    The chemical species in cherts and glass fragments were analyzed using micro Raman spectroscopy in conjunction with measurements of heavy noble gas isotopes to characterize hydrothermally derived sedimentary environments.

  12. Threshold photoelectron spectroscopy of unstable N-containing compounds: Resolution of ΔK subbands in HNCO{sup +} and vibrational resolution in NCO{sup +}

    Energy Technology Data Exchange (ETDEWEB)

    Holzmeier, Fabian; Lang, Melanie; Fischer, Ingo, E-mail: ingo.fischer@uni-wuerzburg.de [Institute of Physical and Theoretical Chemistry, University of Würzburg, Am Hubland, D-97074 Würzburg (Germany); Tang, Xiaofeng [Synchrotron SOLEIL, l’Orme des Merisiers, Saint Aubin BP 48, F-91192 Gif sur Yvette Cedex (France); Cunha de Miranda, Barbara; Romanzin, Claire; Alcaraz, Christian [Laboratoire de Chimie-Physique, UMR 8000 CNRS and Université Paris-Sud 11, F-91405 Orsay Cedex (France); Hemberger, Patrick [Molecular Dynamics Group, Paul Scherrer Institute (PSI), CH-5232 Villigen (Switzerland)

    2015-05-14

    The threshold photoelectron spectra (TPES) of two unstable nitrogen-containing species, HNCO and NCO, were recorded utilizing vacuum ultraviolet synchrotron radiation. Both are intermediates in combustion processes and play a role in the removal of nitrogen oxides from exhaust gases. The rovibronic structure of the first band in the TPES of HNCO{sup +} was analyzed within the framework of an orbital ionization model, and the resolved structure of the origin band was assigned to ΔK subbands. An ionization energy of 11.602 ± 0.005 eV was determined and the vibrational structure of the cationic ground state was analyzed by a Franck-Condon fit. Low lying electronically excited states of HNCO{sup +} were also observed. In a second series of experiments, the NCO radical was generated by flash pyrolysis from chlorine isocyanate. The ionization energy to the X{sup +} {sup 3}Σ{sup −} ground state was determined to be 11.76 ± 0.02 eV, while for the a{sup +1}Δ state, a value of 12.93 ± 0.02 eV was obtained. Vibrational structure was observed for both states, and bands were assigned by Franck-Condon simulations.

  13. Infrared spectroscopy of OD vibrators in minerals at natural dilution: hydroxyl groups in talc and kaolinite, and structural water in beryl and emerald.

    Science.gov (United States)

    de Donato, Philippe; Cheilletz, Alain; Barres, Odile; Yvon, Jacques

    2004-05-01

    An infrared (IR) study of natural deuteration is conducted on minerals containing hydroxyl groups (talc and kaolinite) and channel-water-bearing minerals (beryl and emerald). In talc, the OD valence vibration is located at 2710 cm(-1), corresponding to OD groups surrounded by 3 Mg atoms. In kaolinite, the OD valence vibrations are located at 2671 cm(-1) (inner OD group), 2712, 2706, and 2700 cm(-1) (three inner-surface OD groups). In beryl and emerald, natural deuteration of channel water is observed for the first time by infrared microspectroscopy. In beryl from Minas Gerais (Brazil), the OD profiles are characterized by four bands at 2735, 2686, 2672, and 2641 cm(-1). In emeralds from Colombia and Brazil, the OD profiles are characterized by five or four bands, respectively, at 2816, 2737, 2685, 2673, and 2641 cm(-1) (Colombia) and 2730, 2684, 2672, and 2640 cm(-1) (Brazil). The band at 2816 cm(-1) can be assigned to -OD or OD(-), and bands at 2686-2684, 2673-2672, and 2641-2640 cm(-1) can be assigned to type-I and type-II HOD molecules. The band at 2737-2730 cm(-1) is partially disturbed by combination bands of the mineral. Such OD profiles are different from those obtained by artificial deuteration at higher OD dilution.

  14. Good Vibrations

    OpenAIRE

    Panesar, Lucy

    2007-01-01

    Good Vibrations was a market research exercise conducted by Felicity (my alter-ego) and assistants to help develop marketing and packaging for an electro-therapeutic device (vibrator) used to treat hysteria and other female stress related disorders. It was a live art work commissioned by The Live Art Development Agency for East End Collaborations on 6th May 2007 and the South London Gallery for Bonkersfest on 2nd June 2007.

  15. Vibration sensors

    Science.gov (United States)

    Gupta, Amita; Singh, Ranvir; Ahmad, Amir; Kumar, Mahesh

    2003-10-01

    Today, vibration sensors with low and medium sensitivities are in great demand. Their applications include robotics, navigation, machine vibration monitoring, isolation of precision equipment & activation of safety systems e.g. airbags in automobiles. Vibration sensors have been developed at SSPL, using silicon micromachining to sense vibrations in a system in the 30 - 200 Hz frequency band. The sensing element in the silicon vibration sensor is a seismic mass suspended by thin silicon hinges mounted on a metallized glass plate forming a parallel plate capacitor. The movement of the seismic mass along the vertical axis is monitored to sense vibrations. This is obtained by measuring the change in capacitance. The movable plate of the parallel plate capacitor is formed by a block connected to a surrounding frame by four cantilever beams located on sides or corners of the seismic mass. This element is fabricated by silicon micromachining. Several sensors in the chip sizes 1.6 cm x 1.6 cm, 1 cm x 1 cm and 0.7 cm x 0.7 cm have been fabricated. Work done on these sensors, techniques used in processing and silicon to glass bonding are presented in the paper. Performance evaluation of these sensors is also discussed.

  16. Preface - From molecules to molecular materials, biological molecular systems and nanostructures: A collection of contributions presented at the XIIIth International Conference on Molecular Spectroscopy

    Science.gov (United States)

    Ratajczak, Henryk; Drozd, Marek; Fausto, Rui

    2016-12-01

    This volume contains a series of selected contributions presented at the XIIIth International Conference on Molecular Spectroscopy (ICMS): "From Molecules to Molecular Materials, Biological Molecular Systems and Nanostructures" held in Wrocław, Poland, 9-12 September 2015, under the auspices of the Mayor of Wrocław and the European Academy of Sciences, Arts and Humanities. Wrocław was chosen not accidentally as venue for the conference. With more than a thousand years of history, Wrocław is the location of one of the oldest universities in Central Europe. Being a place where education and science play major roles in the daily life of its inhabitants, Wrocław is also a privileged center for spectroscopy in Poland.

  17. Theoretical investigation on the non-linear optical properties, vibrational spectroscopy and frontier molecular orbital of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide molecule.

    Science.gov (United States)

    Xiao-Hong, Li; Hong-Ling, Cui; Rui-Zhou, Zhang; Xian-Zhou, Zhang

    2015-02-25

    The vibrational frequencies of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide (HB-CA) in the ground state have been calculated using density functional method (B3LYP) with B3LYP/6-311++G(d,p) basis set. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exists C-H⋯O hydrogen bond in the title compound, which is confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as nonlinear optical material. The analysis of frontier molecular orbitals shows that HB-CA has high excitation energies, good stability and high chemical hardness. The analysis of MEP map shows the negative and the positive potential sites.

  18. Theoretical investigation on the non-linear optical properties, vibrational spectroscopy and frontier molecular orbital of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide molecule

    Science.gov (United States)

    Xiao-Hong, Li; Hong-Ling, Cui; Rui-Zhou, Zhang; Xian-Zhou, Zhang

    2015-02-01

    The vibrational frequencies of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide (HB-CA) in the ground state have been calculated using density functional method (B3LYP) with B3LYP/6-311++G(d,p) basis set. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exists Csbnd H⋯O hydrogen bond in the title compound, which is confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as nonlinear optical material. The analysis of frontier molecular orbitals shows that HB-CA has high excitation energies, good stability and high chemical hardness. The analysis of MEP map shows the negative and the positive potential sites.

  19. Contrasting organic aerosol particles from boreal and tropical forests during HUMPPA-COPEC-2010 and AMAZE-08 using coherent vibrational spectroscopy

    Directory of Open Access Journals (Sweden)

    C. J. Ebben

    2011-06-01

    Full Text Available We present the vibrational sum frequency generation spectra of organic particles collected in a boreal forest in Finland and a tropical forest in Brazil. These spectra are compared to those of secondary organic material produced in the Harvard Environmental Chamber. By comparing coherent vibrational spectra of a variety of terpene and olefin reference compounds, along with the secondary organic material synthesized in the environmental chamber, we show that submicron aerosol particles sampled in Southern Finland during HUMPPA-COPEC-2010 are composed to a large degree of material similar in chemical composition to synthetic α-pinene-derived material. For material collected in Brazil as part of AMAZE-08, the organic component is found to be chemically complex in the coarse mode but highly uniform in the fine mode. When combined with histogram analyses of the isoprene and monoterpene abundance recorded during the HUMPPA-COPEC-2010 and AMAZE-08 campaigns, the findings presented here indicate that if air is rich in monoterpenes, submicron-sized secondary aerosol particles that form under normal OH and O3 concentration levels can be described in terms of their hydrocarbon content as being similar to α-pinene-derived model secondary organic aerosol particles. If the isoprene concentration dominates the chemical composition of organic compounds in forest air, then the hydrocarbon component of secondary organic material in the submicron size range is not simply well-represented by that of isoprene-derived model secondary organic aerosol particles but is more complex. Throughout the climate-relevant size range of the fine mode, however, we find that the chemical composition of the secondary organic particle material from such air is invariant with size, suggesting that the particle growth does not change the chemical composition of the hydrocarbon component of the particles in a significant way.

  20. Contrasting organic aerosol particles from boreal and tropical forests during HUMPPA-COPEC-2010 and AMAZE-08 using coherent vibrational spectroscopy

    Directory of Open Access Journals (Sweden)

    C. J. Ebben

    2011-10-01

    Full Text Available We present the vibrational sum frequency generation spectra of organic particles collected in a boreal forest in Finland and a tropical forest in Brazil. These spectra are compared to those of secondary organic material produced in the Harvard Environmental Chamber. By comparing coherent vibrational spectra of a variety of terpene and olefin reference compounds, along with the secondary organic material synthesized in the environmental chamber, we show that submicron aerosol particles sampled in Southern Finland during HUMPPA-COPEC-2010 are composed to a large degree of material similar in chemical composition to synthetic α-pinene-derived material. For material collected in Brazil as part of AMAZE-08, the organic component is found to be chemically complex in the coarse mode but highly uniform in the fine mode. When combined with histogram analyses of the isoprene and monoterpene abundance recorded during the HUMPPA-COPEC-2010 and AMAZE-08 campaigns, the findings presented here indicate that if air is rich in monoterpenes, submicron-sized secondary aerosol particles that form under normal OH and O3 concentration levels can be described in terms of their hydrocarbon content as being similar to α-pinene-derived model secondary organic aerosol particles. If the isoprene concentration dominates the chemical composition of organic compounds in forest air, then the hydrocarbon component of secondary organic material in the submicron size range is not simply well-represented by that of isoprene-derived model secondary organic aerosol particles but is more complex. Throughout the climate-relevant size range of the fine mode, however, we find that the chemical composition of the secondary organic particle material from such air is invariant with size, suggesting that the particle growth does not change the chemical composition of the hydrocarbon component of the particles in a significant way.

  1. Insight into the Local Solvent Environment of Biologically Relevant Iron-nitroysl Systems through Two-Dimensional Infrared Spectroscopy

    Science.gov (United States)

    Brookes, Jennifer Faith

    Iron-nitrosyl systems, particularly in the form of heme proteins, with their iron metal active sites play an important role in biological systems. Heme proteins act as storage, transporters, and receptors for nitric oxide (NO), a signaling molecule that is important in immune, nervous, and cardiovascular systems of mammals. By better understanding the local environment of the active site of NO binding heme proteins we can gain insight into disease in which the NO pathways have been implicated. This is an important step to being able to develop pharmaceuticals targeting NO pathways in humans. Sodium nitroprusside ((SNP, Na2[Fe(CN)5is NO]·2H 2O) investigated as a model system for the active site of nitric oxide binding heme proteins. Using two-dimensional infrared spectroscopy (2D IR) to obtain dephasing dynamics of the nitrosyl stretch (nuNO) in a series of solvents we are able to better understand the local environment of the more complicated metalloproteins. Rigorous line shape analysis is performed by using nonlinear response theory to simulate 2D IR spectra which are then fit to experimental data in an iterative process to extract frequency-frequency correlation functions (FFCFs). The time scales obtained are then correlated to empirical solvent polarity parameters. The analysis of the 2D IR lineshapes reveal that the spectral diffusion timescale of the nuNO in SNP varies from 0.8 -- 4 ps and is negatively correlated with the empirical solvent polarity scales. We continue to investigate NO binding of metalloproteins through 2D IR experiments on nitrophorin 4 (NP4). NP4 is a pH-sensitive NO transporter protein present in the salivary gland of the blood sucking insect Rhodius prolixus which undergoes a pH sensitive structural change between a closed and open conformation allowing for the storage and delivery of NO. The two structures are observed spectroscopically as two distinct pH-dependent nu NO frequencies at ~1904 and ~1917 cm-1. We obtain FFCFs by globally

  2. Combining gravimetric and vibrational spectroscopy measurements to quantify first- and second-shell hydration layers in polyimides with different molecular architectures.

    Science.gov (United States)

    Musto, Pellegrino; Mensitieri, Giuseppe; Lavorgna, Marino; Scarinzi, Gennaro; Scherillo, Giuseppe

    2012-02-02

    In-situ Fourier transform infrared (FTIR) measurements have been carried out at different relative pressures of water vapor to study the H(2)O diffusion in three polyimides differing in their molecular structure and fluorine substitution. Spectral data have been analyzed by difference spectroscopy, least-squares curve fitting, and two-dimensional (2D) correlation spectroscopy, which provided molecular level information on the diffusion mechanism. In particular, two distinct water species were identified corresponding, respectively, to the first and second-shell hydration layers. The spectroscopic analysis demonstrated that the relative population of these species is a function of the total water content in the system. A method has been devised to quantify the water concentration in the two hydration layers, based on a combination of spectroscopic and gravimetric data. The results have been compared with those from an earlier spectroscopic approach reported in the literature and based on the analysis of the carbonyl region.

  3. A Review on the Role of Vibrational Spectroscopy as An Analytical Method to Measure Starch Biochemical and Biophysical Properties in Cereals and Starchy Foods

    Directory of Open Access Journals (Sweden)

    D. Cozzolino

    2014-12-01

    Full Text Available Starch is the major component of cereal grains and starchy foods, and changes in its biophysical and biochemical properties (e.g., amylose, amylopectin, pasting, gelatinization, viscosity will have a direct effect on its end use properties (e.g., bread, malt, polymers. The use of rapid and non-destructive methods to study and monitor starch properties, such as gelatinization, retrogradation, water absorption in cereals and starchy foods, is of great interest in order to improve and assess their quality. In recent years, near infrared reflectance (NIR and mid infrared (MIR spectroscopy have been explored to predict several quality parameters, such as those generated by instrumental methods commonly used in routine analysis like the rapid visco analyser (RVA or viscometers. In this review, applications of both NIR and MIR spectroscopy to measure and monitor starch biochemical (amylose, amylopectin, starch and biophysical properties (e.g., pasting properties will be presented and discussed.

  4. Systematic metabolite annotation and identification in complex biological extracts : combining robust mass spectrometry fragmentation and nuclear magnetic resonance spectroscopy

    NARCIS (Netherlands)

    Hooft, van der J.J.J.

    2012-01-01

    Detailed knowledge of the chemical content of organisms, organs, tissues, and cells is needed to fully characterize complex biological systems. The high chemical variety of compounds present in biological systems is illustrated by the presence of a large variety of compounds, ranging from apolar lip

  5. Mid-infrared upconversion spectroscopy

    DEFF Research Database (Denmark)

    Tidemand-Lichtenberg, Peter; Dam, Jeppe Seidelin; Andersen, H. V.

    2016-01-01

    Mid-infrared (MIR) spectroscopy is emerging as an attractive alternative to near-infrared or visible spectroscopy. MIR spectroscopy offers a unique possibility to probe the fundamental absorption bands of a large number of gases as well as the vibrational spectra of complex molecules. In this paper...

  6. Analysis of red and yellow ochre samples from Clearwell Caves and Çatalhöyük by vibrational spectroscopy and other techniques

    Science.gov (United States)

    Mortimore, Joanne L.; Marshall, Lisa-Jane R.; Almond, Matthew J.; Hollins, Peter; Matthews, Wendy

    2004-04-01

    Ochre samples excavated from the neolithic site at Çatalhöyük, Turkey have been compared with "native" ochres from Clearwell Caves, UK using infrared spectroscopy backed up by Raman spectroscopy, scanning electron microscopy (with energy-dispersive X-rays (EDX) analysis), powder X-ray diffraction, diffuse reflection UV-Vis and atomic absorption spectroscopies. For the Clearwell Caves ochres, which range in colour from yellow-orange to red-brown, it is shown that the colour is related to the nature of the chromophore present and not to any differences in particle size. The darker red ochres contain predominantly haematite while the yellow ochre contains only goethite. The ochres from Çatalhöyük contain only about one-twentieth of the levels of iron found in the Clearwell Caves ochres. The iron oxide pigment (haematite in all cases studied here) has been mixed with a soft lime plaster which also contains calcite and silicate (clay) minerals.

  7. Analysis of red and yellow ochre samples from Clearwell Caves and Catalhöyük by vibrational spectroscopy and other techniques.

    Science.gov (United States)

    Mortimore, Joanne L; Marshall, Lisa-Jane R; Almond, Matthew J; Hollins, Peter; Matthews, Wendy

    2004-04-01

    Ochre samples excavated from the neolithic site at Catalhöyük, Turkey have been compared with "native" ochres from Clearwell Caves, UK using infrared spectroscopy backed up by Raman spectroscopy, scanning electron microscopy (with energy-dispersive X-rays (EDX) analysis), powder X-ray diffraction, diffuse reflection UV-Vis and atomic absorption spectroscopies. For the Clearwell Caves ochres, which range in colour from yellow-orange to red-brown, it is shown that the colour is related to the nature of the chromophore present and not to any differences in particle size. The darker red ochres contain predominantly haematite while the yellow ochre contains only goethite. The ochres from Catalhöyük contain only about one-twentieth of the levels of iron found in the Clearwell Caves ochres. The iron oxide pigment (haematite in all cases studied here) has been mixed with a soft lime plaster which also contains calcite and silicate (clay) minerals.

  8. Urban vibrations

    DEFF Research Database (Denmark)

    Morrison, Ann; Knudsen, L.; Andersen, Hans Jørgen

    2012-01-01

    In   this   paper   we   describe   a   field   study   conducted   with   a   wearable   vibration   belt   where   we   test   to   determine   the   vibration   intensity   sensitivity   ranges   on   a   large   diverse   group   of   participants   with   evenly   distributed  ages  and......   lab   studies   in   that   we   found   a   decreased   detection   rate   in   busy   environments.   Here   we   test   with   a   much   larger   sample   and   age   range,   and   contribute   with   the   first   vibration  sensitivity  testing  outside  the  lab  in  an  urban   public...

  9. Molecular Structures, Vibrational Spectroscopy, and Normal-Mode Analysis of M(2)(C&tbd1;CR)(4)(PMe(3))(4) Dimetallatetraynes. Observation of Strongly Mixed Metal-Metal and Metal-Ligand Vibrational Modes.

    Science.gov (United States)

    John, Kevin D.; Miskowski, Vincent M.; Vance, Michael A.; Dallinger, Richard F.; Wang, Louis C.; Geib, Steven J.; Hopkins, Michael D.

    1998-12-28

    The nature of the skeletal vibrational modes of complexes of the type M(2)(C&tbd1;CR)(4)(PMe(3))(4) (M = Mo, W; R = H, Me, Bu(t)(), SiMe(3)) has been deduced. Metrical data from X-ray crystallographic studies of Mo(2)(C&tbd1;CR)(4)(PMe(3))(4) (R = Me, Bu(t)(), SiMe(3)) and W(2)(C&tbd1;CMe)(4)(PMe(3))(4) reveal that the core bond distances and angles are within normal ranges and do not differ in a statistically significant way as a function of the alkynyl substituent, indicating that their associated force constants should be similarly invariant among these compounds. The crystal structures of Mo(2)(C&tbd1;CSiMe(3))(4)(PMe(3))(4) and Mo(2)(C&tbd1;CBu(t)())(4)(PMe(3))(4) are complicated by 3-fold disorder of the Mo(2) unit within apparently ordered ligand arrays. Resonance-Raman spectra ((1)(delta-->delta) excitation, THF solution) of Mo(2)(C&tbd1;CSiMe(3))(4)(PMe(3))(4) and its isotopomers (PMe(3)-d(9), C&tbd1;CSiMe(3)-d(9), (13)C&tbd1;(13)CSiMe(3)) exhibit resonance-enhanced bands due to a(1)-symmetry fundamentals (nu(a) = 362, nu(b) = 397, nu(c) = 254 cm(-)(1) for the natural-abundance complex) and their overtones and combinations. The frequencies and relative intensities of the fundamentals are highly sensitive to isotopic substitution of the C&tbd1;CSiMe(3) ligands, but are insensitive to deuteration of the PMe(3) ligands. Nonresonance-Raman spectra (FT-Raman, 1064 nm excitation, crystalline samples) for the Mo(2)(C&tbd1;CSiMe(3))(4)(PMe(3))(4) compounds and for Mo(2)(C&tbd1;CR)(4)(PMe(3))(4) (R = H, D, Me, Bu(t)(), SiMe(3)) and W(2)(C&tbd1;CMe)(4)(PMe(3))(4) exhibit nu(a), nu(b), and nu(c) and numerous bands due to alkynyl- and phosphine-localized modes, the latter of which are assigned by comparisons to FT-Raman spectra of Mo(2)X(4)L(4) (X = Cl, Br, I; L = PMe(3), PMe(3)-d(9))(4) and Mo(2)Cl(4)(AsMe(3))(4). Valence force-field normal-coordinate calculations on the model compound Mo(2)(C&tbd1;CH)(4)P(4), using core force constants transferred from a calculation

  10. Syntheses, Vibrational Spectroscopy, and Crystal Structure Determination from X-Ray Powder Diffraction Data of Alkaline Earth Dicyanamides M[N(CN)

    Energy Technology Data Exchange (ETDEWEB)

    Juergens, Barbara; Irran, Elisabeth; Schnick, Wolfgang

    2001-03-01

    The alkaline earth dicyanamides Mg[N(CN){sub 2}]{sub 2}, Ca[N(CN){sub 2}]{sub 2}, Sr[N(CN){sub 2}]{sub 2}, and Ba[N(CN){sub 2}]{sub 2} were synthesized by ion exchange using Na[N(CN){sub 2}] and the respective nitrates or bromides as starting materials. The crystal structures were determined from X-ray powder diffractometry: Mg[N(CN){sub 2}]{sub 2}, Pnnm, Z=2, a=617.14(3), b=716.97(3), and c=740.35(5) pm; Ca[N(CN){sub 2}]{sub 2} and Sr[N(CN){sub 2}]{sub 2}, C2/c, Z=4; Ca[N(CN){sub 2}]{sub 2}, a=1244.55(3), b=607.97(1), and c=789.81(1) pm, {beta}=98.864(2){degree}; Sr[N(CN){sub 2}]{sub 2}, a=1279.63(2), b=624.756(8), and c=817.56(1) pm, {beta}=99.787(1){degree}; Ba[N(CN){sub 2}]{sub 2}, Pnma, Z=4, a=1368.68(7), b=429.07(7), and c=1226.26(2) pm. The dicyanamides consist of the respective alkaline earth cations and bent planar [N(CN){sub 2}]{sup -} ions. The structural features were correlated with vibrational spectroscopic data. The thermal behavior was studied by thermoanalytical experiments.

  11. Resonance Raman spectroscopy of chemically modified and isotopically labelled purple membranes: I. A critical examination of the carbon-nitrogen vibrational modes

    Energy Technology Data Exchange (ETDEWEB)

    Ehrenberg, B. (Cornell Univ., Ithaca, NY); Lemley, A.T.; Lewis, A.; Zastrow, M.V.; Crespi, H.L.

    1980-01-01

    Resonance Raman spectra of bacteriorhodopsin are compared to the spectra of this protein modified in the following ways: (1) selective deuteration at the C-15 carbon atom of retinal, (2) full deuteration of the retinal, (3) the addition of a conjugated double bond in the ..beta..-ionone ring (3-dehydroretinal), (4) full deuteration of the protein and lipid components, (5) /sup 15/N enrichment of the entire membrane and (6) deuteration of the entire membrane. A detailed comparison of the /sup 15/N-enriched membrane and naturally occurring purple membrane from 800 cm/sup -1/ to 1700 cm/sup -1/ reveals that /sup 15/N enrichment affects the frequency of only two vibrational modes. These occur at 1642 cm/sup -1/ and 1620 cm/sup -1/ in naturally occurring purple membrane and at 1628 cm/sup -1/ and 1615 cm/sup -1/ in the /sup 15/N-enriched samples. Therefore, this pair of bands reflects the states of protonation of the Schiff base.

  12. Insight into the packing pattern of β2 fibrils: a model study of glutamic acid rich oligomers with 13C isotopic edited vibrational spectroscopy.

    Science.gov (United States)

    Chi, Heng; Welch, William R W; Kubelka, Jan; Keiderling, Timothy A

    2013-11-11

    Polyglutamic acid at low pH forms aggregates and self-assembles into a spiral, fibril-like superstructure formed as a β2-type sheet conformation that has a more compact intersheet packing than commonly found. This is stabilized by three-centered bifurcated hydrogen bonding of the amide carbonyl involving the protonated glutamic acid side chain. We report vibrational spectroscopic results and analyses for oligopeptides rich in glutamic acid enhanced with (13)C isotope labeling in a study modeling low pH poly-Glu self-assembly. Our results indicate bifurcated H-bonding and β2 aggregation can be attained in these model decamers, confirming they have the same conformations as poly-Glu. We also prepared conventional β1-sheet aggregates by rapid precipitation from the residual peptides in the higher pH supernatant. By comparing the isotope-enhanced IR and VCD spectra with theoretical predictions, we deduced that the oligo-Glu β2 structure is based on stacked, twisted, antiparallel β-sheets. The best fit to theoretical predictions was obtained for the strands being out of register, sequentially stepped by one residue, in a ladder-like fashion. The alternate β1 conformer for this oligopeptide was similarly shown to be antiparallel but was less ordered and apparently had a different registry in its aggregate structure.

  13. Raman spectroscopy measurements of the vibrational properties of uv-polymerized C60 thin film and C60 powder compressed in a diamond anvil cell

    Science.gov (United States)

    Li, Y.; Singh, D.; Sharma, S. C.

    2002-03-01

    We present results from a series of experiments designed to further study the effects of pressure on the vibrational properties of C60 compressed under high pressures (10 GPa) in a diamond anvil cell. The Raman scattering measurements were made by using a high resolution optical spectrometer that consists of a 1.25 m, f/11 monochromator, 2400 g/mm, ion-etched blazed holographic diffraction grating, 2048x512 pixel back illuminated liquid nitrogen cooled CCD camera, Super-Notch-Plus filter, argon-ion laser operating at 514.5 nm, and SpectraMax for Windows software. The Raman scattering measurements on C60 thin films show a large ( 10 cm-1) and characteristic red shift in the pentagonal pinch mode Ag(2) of pristine C60 upon irradiation by 21.2 eV photons. Upon heating this film under 10(-3) Torr vacuum at 413 and 473 K, the Raman spectra shift towards the pentagonal pinch mode of pristine C60. These results are in agreement with previously published data (1,2) and they show that the film is polymerized because of uv irradiation. We have also measured spectra for C60 powder compressed under high pressures in a diamond anvil cell. We present results for several frequencies of the Raman active modes of C60. 1. A. M. Rao et al, Science 259, 955 (1993); 2. S. C. Sharma et al, Mat. Res. Symp. Proc. 695, L3.10 (2002)

  14. Isolating Site-Specific Spectral Signatures of Individual Water Molecules in H-Bonded Networks with Isotopomer-Selective Ir-Ir Double Resonance Vibrational Predissociation Spectroscopy

    Science.gov (United States)

    Wolke, Conrad T.; Johnson, Mark

    2016-06-01

    We will discuss an experimental method that directly yields the embedded correlations between the two OH stretches and the intramolecular bending modes associated with a single H2O water molecule embedded in an otherwise all-D isotopologue. This is accomplished using isotopomer-selective IR-IR hole-burning on the Cs+(D2O)5(H2O) clusters formed by gas-phase exchange of a single, intact H2O molecule for D2O in the Cs+(D2O)6 ion. The OH stretching pattern of the Cs+(H2O)6 isotopologue is accurately recovered by superposition of the isotopomer spectra, thus establishing that the H2O incorporation is random and that the OH stretching manifold is largely due to contributions from decoupled water molecules. This behavior enables a powerful new way to extract structural information from vibrational spectra of size-selected clusters by explicitly identifying the local environments responsible for specific infrared features. Extension of this method to address the degree to which OH stretches are decoupled in the protonated water clusters will also be discussed.

  15. Vibrational properties of SrCu{sub 2}O{sub 2} studied via Density Functional Theory calculations and compared to Raman and infrared spectroscopy measurements

    Energy Technology Data Exchange (ETDEWEB)

    Even, J., E-mail: jacky.even@insa.rennes.fr [Université Européenne de Bretagne, INSA, FOTON, UMR CNRS 6082, 20 Avenue des Buttes de Coësmes, F-35708 Rennes (France); Pedesseau, L.; Durand, O. [Université Européenne de Bretagne, INSA, FOTON, UMR CNRS 6082, 20 Avenue des Buttes de Coësmes, F-35708 Rennes (France); Modreanu, M. [Tyndall National Institute, Lee Maltings, Prospect Row, Cork (Ireland); Huyberechts, G. [FLAMAC, Technologiepark 903, 9052 Zwijnaarde (Belgium); Servet, B. [Thales Research and Technology France, Campus Polytechnique, 1, avenue Augustin Fresnel, 91767 Palaiseau cedex France (France); Chaix-Pluchery, O. [Laboratoire des Matériaux et du Génie Physique, Grenoble INP—Minatec, 3, parvis Louis Néel, BP 257, 38016 Grenoble Cedex 1 (France)

    2013-08-31

    The SrCu{sub 2}O{sub 2} material is a p-type transparent conductive oxide. A theoretical study of the SrCu{sub 2}O{sub 2} crystal is performed with a state of the art implementation of the Density Functional Theory. The simulated crystal structure is compared with available X-ray diffraction data and previous theoretical modeling. Density Functional Perturbation Theory is used to study the vibrational properties of the SrCu{sub 2}O{sub 2} crystal. A symmetry analysis of the optical phonon eigenvectors at the Brillouin zone center is proposed. The Raman spectra simulated using the derivatives of the dielectric susceptibility, show a good agreement with Raman scattering experimental results. - Highlights: ► The symmetry properties of the optical phonons of the SrCu{sub 2}O{sub 2} crystal are analyzed. ► Born charges and the dynamical matrix are calculated at the Brillouin zone center. ► Density Functional Perturbation Theory (DFPT) is used to compute Raman spectrum. ► DFPT Raman spectrum is compared with experimental results.

  16. Vibrational spectroscopy and density functional theory study of 3-[4,5-dimethyl-2-thiazolyl]-2,5-diphenyl-2H-tetrazolium bromide.

    Science.gov (United States)

    Li, Ran; Mao, Zhu; Chen, Lei; Lv, Haiming; Cheng, Jianbo; Zhao, Bing

    2015-01-25

    In this work, the structural parameters of the title molecule (MTT) have been obtained at the B3LYP/6-311++G(**) level of theory. The two phenyl rings and the two heterocyclic rings are found in four different planes. The tetrazolium ring was connected with other three rings and their distances are also different in decrease order of 1.461 Å (from tetrazolium ring to carbon connected phenyl)>1.445 Å (from tetrazolium ring to nitrogen connected phenyl)>1.425 Å (from tetrazolium ring to thiazolyl ring). Fourier transform infrared (FTIR) and Raman spectra of the compound were 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. The calculated vibrational frequencies were in good agreement with the experimental values. In addition, the UV-Vis spectra were obtained experimentally and theoretically. Considering the effect of the PCM modelling error, the calculated absorbance peaks obtained at the B3LYP/6-311++G(**) level were also in good agreement with the experimental values. The HOMO-LUMO gap was predicted to be 1.83 eV at the B3LYP/6-311++G(**) level.

  17. Specificity and mechanism of action of alpha-helical membrane-active peptides interacting with model and biological membranes by single-molecule force spectroscopy.

    Science.gov (United States)

    Sun, Shiyu; Zhao, Guangxu; Huang, Yibing; Cai, Mingjun; Shan, Yuping; Wang, Hongda; Chen, Yuxin

    2016-07-01

    In this study, to systematically investigate the targeting specificity of membrane-active peptides on different types of cell membranes, we evaluated the effects of peptides on different large unilamellar vesicles mimicking prokaryotic, normal eukaryotic, and cancer cell membranes by single-molecule force spectroscopy and spectrum technology. We revealed that cationic membrane-active peptides can exclusively target negatively charged prokaryotic and cancer cell model membranes rather than normal eukaryotic cell model membranes. Using Acholeplasma laidlawii, 3T3-L1, and HeLa cells to represent prokaryotic cells, normal eukaryotic cells, and cancer cells in atomic force microscopy experiments, respectively, we further studied that the single-molecule targeting interaction between peptides and biological membranes. Antimicrobial and anticancer activities of peptides exhibited strong correlations with the interaction probability determined by single-molecule force spectroscopy, which illustrates strong correlations of peptide biological activities and peptide hydrophobicity and charge. Peptide specificity significantly depends on the lipid compositions of different cell membranes, which validates the de novo design of peptide therapeutics against bacteria and cancers.

  18. Experimental and Theoretical Investigations on the Terahertz Vibrational Spectroscopy of Alanine Crystal%丙氨酸晶体太赫兹振动光谱的实验和理论研究

    Institute of Scientific and Technical Information of China (English)

    王果; 王卫宁

    2012-01-01

    利用太赫兹时域光谱和低频拉曼光谱仪研究了丙氨酸晶体在0.2-2.6 THz范围内的太赫兹吸收和拉曼散射光谱.研究表明:在该低频范围有四个振动模式,其中两个只具有拉曼活性,其余两个同时具有红外和拉曼活性.基于B3LYP杂化密度泛函的自洽场晶体轨道法对丙氨酸周期性结构进行了理论研究和光谱计算.通过比较实验和理论结果,指认了实验光谱特征峰所属的不可约表示.通过理论计算得到的图形,得出在此低频范围的振动模式主要包含分子间氢键的扭转和摇摆运动.%The terahertz absorption and Raman scattering spectra of an alanine crystal in the range of 0.2-2.6 THz were obtained using terahertz time-domain spectroscopy and low-frequency Raman spectroscopy. The results indicated that there were four vibrational modes in this low-frequency region. Two modes were Raman active whereas the other two were both infrared and Raman active. A theoretical investigation on the periodic structure of alanine was performed using a self-consistent field crystal orbital method based on the B3LYP hybrid density functional. By comparing the experimental and theoretical results, irreducible representations were assigned to the corresponding peaks in the spectra. It was indicated that the vibrational modes in this low-frequency region were mainly torsion or rocking modes involving inter-molecular hydrogen bonds which have been described using schematic representations.

  19. Dispersed fluorescence spectroscopy of the SiCN A ˜ 2 Δ - X ˜ 2 Π system: Observation of some vibrational levels with chaotic characteristics

    Science.gov (United States)

    Fukushima, Masaru; Ishiwata, Takashi

    2016-12-01

    The laser induced fluorescence (LIF) spectrum of the A ˜ 2Δ - X ˜ 2Π transition was obtained for SiCN generated by laser ablation under supersonic free jet expansion. The vibrational structures of the dispersed fluorescence (DF) spectra from single vibronic levels (SVL's) were analyzed with consideration of the Renner-Teller (R-T) interaction. Analysis of the pure bending (ν2) structure by a perturbation approach including R-T, anharmonicity, spin-orbit (SO), and Herzberg-Teller (H-T) interactions indicated considerably different spin splitting for the μ and κ levels of the X ˜ 2Π state of SiCN, in contrast to identical spin splitting for general species derived from the perturbation approach, where μ and κ specify the lower and upper levels, respectively, separated by R-T. Further analysis of the vibrational structure including R-T, anharmonicity, SO, H-T, Fermi, and Sears interactions was carried out via a direct diagonalization procedure, where Sears resonance is a second-order interaction combined from SO and H-T interactions with Δ K = ± 1, ΔΣ = ∓1, and Δ P = 0, and where P is a quantum number, P = K + Σ. The later numerical analysis reproduced the observed structure, not only the pure ν2 structure but also the combination structure of the ν2 and the Si-CN stretching (ν3) modes. As an example, the analysis demonstrates Sears resonance between vibronic levels, (0110) κ Σ(+) and ( 0 2 0 0 ) μ Π /1 2 , with Δ K = ± 1 and Δ P = 0. On the basis of coefficients of their eigen vectors derived from the numerical analysis, it is interpreted as an almost one-to-one mixing between the two levels. The mixing coefficients of the two vibronic levels agree with those obtained from computational studies. The numerical analysis also indicates that some of the vibronic levels show chaotic characteristics in view of the two-dimensional harmonic oscillator (2D-HO) basis which is used as the basis function in the present numerical analysis; i.e., the

  20. Vibrating minds

    CERN Multimedia

    2009-01-01

    Ed Witten is one of the leading scientists in the field of string theory, the theory that describes elementary particles as vibrating strings. This week he leaves CERN after having spent a few months here on sabbatical. His wish is that the LHC will unveil supersymmetry.

  1. NEW ACCURATE MEASUREMENT OF {sup 36}ArH{sup +} AND {sup 38}ArH{sup +} RO-VIBRATIONAL TRANSITIONS BY HIGH RESOLUTION IR ABSORPTION SPECTROSCOPY

    Energy Technology Data Exchange (ETDEWEB)

    Cueto, M.; Herrero, V. J.; Tanarro, I.; Doménech, J. L. [Molecular Physics Department, Instituto de Estructura de la Materia (IEM-CSIC), Serrano 123, E-28006 Madrid (Spain); Cernicharo, J. [Department of Astrophysics, CAB. INTA-CSIC. Crta Torrejón-Ajalvir Km 4, E-28850 Torrejón de Ardoz, Madrid (Spain); Barlow, M. J.; Swinyard, B. M., E-mail: jl.domenech@csic.es [Department of Physics and Astronomy, University College London. Gower Street, London WC1E 6BT (United Kingdom)

    2014-03-01

    The protonated argon ion, {sup 36}ArH{sup +}, was recently identified in the Crab Nebula from Herschel spectra. Given the atmospheric opacity at the frequency of its J = 1-0 and J = 2-1 rotational transitions (617.5 and 1234.6 GHz, respectively), and the current lack of appropriate space observatories after the recent end of the Herschel mission, future studies on this molecule will rely on mid-infrared observations. We report on accurate wavenumber measurements of {sup 36}ArH{sup +} and {sup 38}ArH{sup +} rotation-vibration transitions in the v = 1-0 band in the range 4.1-3.7 μm (2450-2715 cm{sup –1}). The wavenumbers of the R(0) transitions of the v = 1-0 band are 2612.50135 ± 0.00033 and 2610.70177 ± 0.00042 cm{sup –1} (±3σ) for {sup 36}ArH{sup +} and {sup 38}ArH{sup +}, respectively. The calculated opacity for a gas thermalized at a temperature of 100 K and with a linewidth of 1 km s{sup –1} of the R(0) line is 1.6 × 10{sup –15} × N({sup 36}ArH{sup +}). For column densities of {sup 36}ArH{sup +} larger than 1 × 10{sup 13} cm{sup –2}, significant absorption by the R(0) line can be expected against bright mid-IR sources.

  2. Development of Efficient and Robust Heteronuclear Cross-Polarization Techniques for Biological Solid-State Nuclear Magnetic Resonance Spectroscopy

    DEFF Research Database (Denmark)

    Jain, Sheetal Kumar

    2014-01-01

    of biological macromolecules. A new method for polarization transfer called Rotor Echo Short Pulse IRradiATION mediated Cross-Polarization (RESPIRATIONCP) is introduced with a theoretical explanation of its polarization transfer efficiency. An analysis of robustness towards experimental imperfections......) and Silver Hepta Fluoro Butyrate (SHFB) are presented at high magnetic fields. It is demonstrated that important information about dynamics may be extracted from 19F→13C RESPIRATIONCP buildup curves, which are central to the dynamics studies of important biological and synthetic polymers....

  3. Vibrational spectroscopic studies of newly developed synthetic biopolymers.

    Science.gov (United States)

    Bista, Rajan K; Bruch, Reinhard F; Covington, Aaron M

    2010-05-01

    Vibrational spectroscopic techniques such as near-infrared (NIR), Fourier transform infrared (FTIR), and Raman spectroscopy are valuable diagnostic tools that can be used to elucidate comprehensive structural information of numerous biological samples. In this review article, we have highlighted the advantages of nanotechnology and biophotonics in conjunction with vibrational spectroscopic techniques in order to understand the various aspects of new kind of synthetic biopolymers termed as polyethylene glycol (PEG)ylated lipids. In contrast to conventional phospholipids, these novel lipids spontaneously form liposomes or nanovesicles upon hydration, without the supply of external activation energy. The amphiphiles considered in this study differ in their hydrophobic acyl chain length and contain different units of PEG hydrophilic headgroups. We have further explored the thermotropic phase behaviors and associated changes in the conformational order/disorder of such lipids by using variable-temperature FTIR and Raman spectroscopy. Phase transition temperature profiles and correlation between various spectral indicators have been identified by either monitoring the shifts in the vibrational peak positions or plotting vibrational peak intensity ratios in the C--H stretching region as a function of temperature. To supplement our observations of phase transformations, a thermodynamic approach known as differential scanning calorimetry (DSC) has been applied and revealed a good agreement with the infrared and Raman spectroscopic data. Finally, the investigation of thermal properties of lipids is extremely crucial for numerous purposes, thus the results obtained in this work may find application in a wide variety of studies including the development of PEGylated lipid based drug and substances delivery vehicles.

  4. Unusual Synthetic Pathway for an {Fe(NO)2}(9) Dinitrosyl Iron Complex (DNIC) and Insight into DNIC Electronic Structure via Nuclear Resonance Vibrational Spectroscopy.

    Science.gov (United States)

    Speelman, Amy L; Zhang, Bo; Silakov, Alexey; Skodje, Kelsey M; Alp, E Ercan; Zhao, Jiyong; Hu, Michael Y; Kim, Eunsuk; Krebs, Carsten; Lehnert, Nicolai

    2016-06-01

    Dinitrosyl iron complexes (DNICs) are among the most abundant NO-derived cellular species. Monomeric DNICs can exist in the {Fe(NO)2}(9) or {Fe(NO)2}(10) oxidation state (in the Enemark-Feltham notation). However, experimental studies of analogous DNICs in both oxidation states are rare, which prevents a thorough understanding of the differences in the electronic structures of these species. Here, the {Fe(NO)2}(9) DNIC [Fe(dmp)(NO)2](OTf) (1; dmp = 2,9-dimethyl-1,10-phenanthroline) is synthesized from a ferrous precursor via an unusual pathway, involving disproportionation of an {FeNO}(7) complex to yield the {Fe(NO)2}(9) DNIC and a ferric species, which is subsequently reduced by NO gas to generate a ferrous complex that re-enters the reaction cycle. In contrast to most {Fe(NO)2}(9) DNICs with neutral N-donor ligands, 1 exhibits high solution stability and can be characterized structurally and spectroscopically. Reduction of 1 yields the corresponding {Fe(NO)2}(10) DNIC [Fe(dmp)(NO)2] (2). The Mössbauer isomer shift of 2 is 0.08 mm/s smaller than that of 1, which indicates that the iron center is slightly more oxidized in the reduced complex. The nuclear resonance vibrational spectra (NRVS) of 1 and 2 are distinct and provide direct experimental insight into differences in bonding in these complexes. In particular, the symmetric out-of-plane Fe-N-O bending mode is shifted to higher energy by 188 cm(-1) in 2 in comparison to 1. Using quantum chemistry centered normal coordinate analysis (QCC-NCA), this is shown to arise from an increase in Fe-NO bond order and a stiffening of the Fe(NO)2 unit upon reduction of 1 to 2. DFT calculations demonstrate that the changes in bonding arise from an iron-centered reduction which leads to a distinct increase in Fe-NO π-back-bonding in {Fe(NO)2}(10) DNICs in comparison to the corresponding {Fe(NO)2}(9) complexes, in agreement with all experimental findings. Finally, the implications of the electronic structure of DNICs for

  5. Biomedical applications of X-ray absorption and vibrational spectroscopic microscopies in obtaining structural information from complex systems

    Science.gov (United States)

    Aitken, Jade B.; Carter, Elizabeth A.; Eastgate, Harold; Hackett, Mark J.; Harris, Hugh H.; Levina, Aviva; Lee, Yao-Chang; Chen, Ching-Iue; Lai, Barry; Vogt, Stefan; Lay, Peter A.

    2010-02-01

    Protein crystallography and NMR spectroscopy took decades to emerge as routine techniques in structural biology. X-ray absorption spectroscopy now has reached a similar stage of maturity for obtaining complementary local structural information around metals in metalloproteins. However, the relatively recent emergence of X-ray and vibrational spectroscopic microprobes that build on these techniques has enabled the structural information obtained from the "mature" techniques on isolated biomolecules to be translated into in situ structural information from inhomogeneous complex systems, such as whole cells and tissues.

  6. Molecular structure, Normal Coordinate Analysis, harmonic vibrational frequencies, Natural Bond Orbital, TD-DFT calculations and biological activity analysis of antioxidant drug 7-hydroxycoumarin

    Science.gov (United States)

    Sebastian, S.; Sylvestre, S.; Jayarajan, D.; Amalanathan, M.; Oudayakumar, K.; Gnanapoongothai, T.; Jayavarthanan, T.

    2013-01-01

    In this work, we report harmonic vibrational frequencies, molecular structure, NBO and HOMO, LUMO analysis of Umbelliferone also known as 7-hydroxycoumarin (7HC). The optimized geometric bond lengths and bond angles obtained by computation (monomer and dimmer) shows good agreement with experimental XRD data. Harmonic frequencies of 7HC were determined and analyzed by DFT utilizing 6-311+G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of Normal Coordinate Analysis (NCA) following the Scaled Quantum Mechanical Force Field Methodology (SQMFF). The change in electron density (ED) in the σ* and π* antibonding orbitals and stabilization energies E(2) have been calculated by Natural Bond Orbital (NBO) analysis to give clear evidence of stabilization originating in the hyperconjugation of hydrogen-bonded interaction. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) complements with the experimental findings. The simulated spectra satisfactorily coincides with the experimental spectra. Microbial activity of studied compounds was tested against Staphylococcus aureus, Streptococcus pyogenes, Bacillus subtilis, Escherichia coli, Psuedomonas aeruginosa, Klebsiella pneumoniae, Proteus mirabilis, Shigella flexneri, Salmonella typhi and Enterococcus faecalis.

  7. Influence of magnetic fields on the hydration process of amino acids: vibrational spectroscopy study of L-phenylalanine and L-glutamine.

    Science.gov (United States)

    De Ninno, Antonella; Congiu Castellano, Agostina

    2014-02-01

    Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy has been used to investigate the effect of weak electromagnetic fields on the structure of L-glutamine (L-Gln) and L-phenylalnine (L-Phe) in aqueous solution. It has been found that the exposure to a DC field or a 50 Hz AC field, for a short time induces modifications in the spectra of exposed samples in agreement with our preceding observations on glutamic acid. Furthermore, the acid-base equilibrium has been investigated by using the ratio of the intensity of the deprotonated on protonated species. In the case of L-Phe, the exposure induces a measurable shift of acid dissociation constant pKa1 out of the experimental errors, while in case of L-Gln, the effect is under the limit detectable with this method. The phenomenon of the shift of the acid-base equilibrium has been connected elsewhere to modification of the water-water hydrogen bonds in the water around both the backbone and the residue (R). Here we suggest that the magnetic field modifies the water structure around the molecules and changes the hydrophobic interactions allowing the molecules of amino acids to aggregate. The differences observed in the behavior of L-Phe and L-Gln may be related to the differences in the polarity of their residues.

  8. Nature of phase transitions in ammonium oxofluorovanadates, a vibrational spectroscopy study of (NH4)3VO2F4 and (NH4)3VOF5

    Science.gov (United States)

    Gerasimova, Yu. V.; Oreshonkov, A. S.; Laptash, N. M.; Vtyurin, A. N.; Krylov, A. S.; Shestakov, N. P.; Ershov, A. A.; Kocharova, A. G.

    2017-04-01

    Two ammonium oxofluorovanadates, (NH4)3VO2F4 and (NH4)3VOF5, have been investigated by temperature-dependent infrared and Raman spectroscopy methods to determine the nature of phase transitions (PT) in these compounds. Dynamics of quasioctahedral groups was simulated within the framework of semi-empirical approach, which justified the cis-conformation of VO2F43 - (C2v) and the C4v geometry of VOF53 -. The observed infrared and Raman spectra of both compounds at room temperature (RT) revealed the presence at least of two crystallographically independent octahedral groups. The first order PT at elevated temperatures is connected with a complete dynamic disordering of these groups with only single octahedral state. At lower temperatures, the octahedra are ordered and several octahedral states appear. This PT is the most pronounced in the case of (NH4)3VOF5, when at least seven independent VOF53 - octahedra are present in the structure below 50 K, in accordance with the Raman spectra. Ammonium groups do not take part in PTs at higher and room temperatures but their reorientational motion freezes at lower temperatures.

  9. Combining vibrational biomolecular spectroscopy with chemometric techniques for the study of response and sensitivity of molecular structures/functional groups mainly related to lipid biopolymer to various processing applications.

    Science.gov (United States)

    Yu, Gloria Qingyu; Yu, Peiqiang

    2015-09-01

    The objectives of this project were to (1) combine vibrational spectroscopy with chemometric multivariate techniques to determine the effect of processing applications on molecular structural changes of lipid biopolymer that mainly related to functional groups in green- and yellow-type Crop Development Centre (CDC) pea varieties [CDC strike (green-type) vs. CDC meadow (yellow-type)] that occurred during various processing applications; (2) relatively quantify the effect of processing applications on the antisymmetric CH3 ("CH3as") and CH2 ("CH2as") (ca. 2960 and 2923 cm(-1), respectively), symmetric CH3 ("CH3s") and CH2 ("CH2s") (ca. 2873 and 2954 cm(-1), respectively) functional groups and carbonyl C=O ester (ca. 1745 cm(-1)) spectral intensities as well as their ratios of antisymmetric CH3 to antisymmetric CH2 (ratio of CH3as to CH2as), ratios of symmetric CH3 to symmetric CH2 (ratio of CH3s to CH2s), and ratios of carbonyl C=O ester peak area to total CH peak area (ratio of C=O ester to CH); and (3) illustrate non-invasive techniques to detect the sensitivity of individual molecular functional group to the various processing applications in the recently developed different types of pea varieties. The hypothesis of this research was that processing applications modified the molecular structure profiles in the processed products as opposed to original unprocessed pea seeds. The results showed that the different processing methods had different impacts on lipid molecular functional groups. Different lipid functional groups had different sensitivity to various heat processing applications. These changes were detected by advanced molecular spectroscopy with chemometric techniques which may be highly related to lipid utilization and availability. The multivariate molecular spectral analyses, cluster analysis, and principal component analysis of original spectra (without spectral parameterization) are unable to fully distinguish the structural differences in the

  10. The AstroBiology Explorer (ABE) MIDEX Mission: Using Infrared Spectroscopy to Identify Organic Molecules in Space

    Science.gov (United States)

    Sandford, S. A.

    2002-01-01

    The AstroBiology Explorer (ABE) mission is one of four selected for Phase A Concept Study in NASA's current call for MIDEX class missions. ABE is a cooled space telescope equipped with spectrographs covering the 2.5-20 micron spectral range. The ABE mission is devoted to the detection and identification of organic and related molecular species in space. ABE is currently under study at NASA's Ames Research Center in collaboration with Ball Aerospace.

  11. Study of energetic-particle-irradiation induced biological effect on Rhizopus oryzae through synchrotron-FTIR micro-spectroscopy

    Science.gov (United States)

    Liu, Jinghua; Qi, Zeming; Huang, Qing; Wei, Xiaoli; Ke, Zhigang; Fang, Yusheng; Tian, Yangchao; Yu, Zengliang

    2013-01-01

    Energetic particles exist ubiquitously and cause varied biological effects such as DNA strand breaks, lipid peroxidation, protein modification, cell apoptosis or death. An emerging biotechnology based on ion-beam technique has been developed to serve as an effective tool for mutation breeding of crops and microbes. In order to improve the effectiveness of ion-beam biotechnology for mutation breeding, it is indispensible to gain a better understanding of the mechanism of the interactions between the energetic ions and biological systems which is still elusive. A new trend is to conduct more comprehensive research which is based on micro-scaled observation of the changes of the cellular structures and compositions under the interactions. For this purpose, advanced synchrotron FTIR (s-FTIR) microscopy was employed to monitor the cellular changes of single fungal hyphae under irradiation of α-particles from 241Am. Intracellular contents of ROS, MDA, GSSG/GSH and activities of CAT and SOD were measured via biochemical assay. Ion-irradiation on Rhizopus oryzae causes localized vacuolation, autolysis of cell wall and membrane, lipid peroxidation, DNA damage and conformational changes of proteins, which have been clearly revealed by the s-FTIR microspectroscopy. The different changes of cell viability, SOD and CAT activities can be explained by the ROS-involved chemical reactions. Evidently, the elevated level of ROS in hyphal cells upon irradiation plays the key role in the caused biological effect. This study demonstrates that s-FTIR microspectroscopy is an effective tool to study the damage of fungal hyphae caused by ionizing radiation and it facilitates the exploit of the mechanism for the interactions between the energetic ions and biological systems.

  12. Vibrational spectroscopy to support the link between rheology and continuous twin-screw melt granulation on molecular level: A case study.

    Science.gov (United States)

    Monteyne, Tinne; Heeze, Liza; Oldörp, Klaus; Vervaet, Chris; Remon, Jean-Paul; De Beer, Thomas

    2016-06-01

    Twin screw hot melt granulation (TSHMG) is an innovative and continuous drug formulation process allowing granulation of moisture sensitive drugs. However, due to the lack of experience and in-depth process understanding, this technique is not yet widely used. During the TSHMG process, the microstructure of the granules is generated and modified and strongly depends on the flow behavior of the material. Hence, rheology might be a suitable tool to simulate and examine this process. However, chemical interactions of the material are influencing the physical properties leading to the microstructure. In this research project it is spectroscopically investigated whether the heat applied in a rheometer induces the same molecular effects as these occurring during TSHMG of the model formulation caffeine anhydrous/Soluplus®. Hence, it is evaluated whether rheology can be used as a simulation tool to improve the understanding of the material behavior at molecular level during continuous melt granulation. Therefore, in-line Raman spectroscopy is executed during TSHMG and in situ Fourier Transform Infra-red (FTIR) during oscillatory rheological experiments. The results from the in-line Raman monitoring revealed polymorph transition of caffeine anhydrous during twin screw melt granulation with Soluplus® which is stimulated depending on the binder concentration and/or granulation temperature. A correlation was seen between the FTIR spectra obtained during the rheological temperature ramp and the in-line collected Raman spectra during the melt granulation runs. The polymorphic conversion of caffeine anhydrous could be detected in the same temperature range with both techniques, proving the comparability of plate-plate rheometry and hot melt granulation (HMG) for this case with the used parameter settings. Process simulation using rheology combined with in situ FTIR seems a promising approach to increase process understanding and to facilitate binder and parameter selection for

  13. Vibrational Signatures of Isomeric Lithiated N-acetyl-D-hexosamines by Gas-Phase Infrared Multiple-Photon Dissociation (IRMPD) Spectroscopy

    Science.gov (United States)

    Tan, Yanglan; Zhao, Ning; Liu, Jinfeng; Li, Pengfei; Stedwell, Corey N.; Yu, Long; Polfer, Nicolas C.

    2017-03-01

    Three lithiated N-acetyl-D-hexosamine (HexNAc) isomers, N-acetyl-D-glucosamine (GlcNAc), N-acetyl-D-galactosamine (GalNAc), and N-acetyl-D-mannosamine (ManNAc) are investigated as model monosaccharide derivatives by gas-phase infrared multiple-photon dissociation (IRMPD) spectroscopy. The hydrogen stretching region, which is attributed to OH and NH stretching modes, reveals some distinguishing spectral features of the lithium-adducted complexes that are useful in terms of differentiating these isomers. In order to understand the effect of lithium coordination on saccharide structure, and therefore anomericity, chair configuration, and hydrogen bonding networks, the conformational preferences of lithiated GlcNAc, GalNAc, and ManNAc are studied by comparing the experimental measurements with density functional theory (DFT) calculations. The experimental results of lithiated GlcNAc and GalNAc show a good match to the theoretical spectra of low-energy structures adopting a 4 C 1 chair conformation, consistent with this motif being the dominant conformation in condensed-phase monosaccharides. The epimerization effect upon going to lithiated ManNAc is significant, as in this case the 1 C 4 chair conformers give a more compelling match with the experimental results, consistent with their lower calculated energies. A contrasting computational study of these monosaccharides in their neutral form suggests that the lithium cation coordination with Lewis base oxygens can play a key role in favoring particular structural motifs (e.g., a 4 C 1 versus 1 C 4 ) and disrupting hydrogen bond networks, thus exhibiting specific IR spectral features between these closely related lithium-chelated complexes.

  14. Vibrational Signatures of Isomeric Lithiated N-acetyl-D-hexosamines by Gas-Phase Infrared Multiple-Photon Dissociation (IRMPD) Spectroscopy

    Science.gov (United States)

    Tan, Yanglan; Zhao, Ning; Liu, Jinfeng; Li, Pengfei; Stedwell, Corey N.; Yu, Long; Polfer, Nicolas C.

    2017-01-01

    Three lithiated N-acetyl-D-hexosamine (HexNAc) isomers, N-acetyl-D-glucosamine (GlcNAc), N-acetyl-D-galactosamine (GalNAc), and N-acetyl-D-mannosamine (ManNAc) are investigated as model monosaccharide derivatives by gas-phase infrared multiple-photon dissociation (IRMPD) spectroscopy. The hydrogen stretching region, which is attributed to OH and NH stretching modes, reveals some distinguishing spectral features of the lithium-adducted complexes that are useful in terms of differentiating these isomers. In order to understand the effect of lithium coordination on saccharide structure, and therefore anomericity, chair configuration, and hydrogen bonding networks, the conformational preferences of lithiated GlcNAc, GalNAc, and ManNAc are studied by comparing the experimental measurements with density functional theory (DFT) calculations. The experimental results of lithiated GlcNAc and GalNAc show a good match to the theoretical spectra of low-energy structures adopting a 4 C 1 chair conformation, consistent with this motif being the dominant conformation in condensed-phase monosaccharides. The epimerization effect upon going to lithiated ManNAc is significant, as in this case the 1 C 4 chair conformers give a more compelling match with the experimental results, consistent with their lower calculated energies. A contrasting computational study of these monosaccharides in their neutral form suggests that the lithium cation coordination with Lewis base oxygens can play a key role in favoring particular structural motifs (e.g., a 4 C 1 versus 1 C 4 ) and disrupting hydrogen bond networks, thus exhibiting specific IR spectral features between these closely related lithium-chelated complexes.

  15. Energy-dispersive x-ray fluorescence spectroscopy and inductively coupled plasma emission spectrometry evaluated for multielement analysis in complex biological matrices.

    Science.gov (United States)

    Irons, R D; Schenk, E A; Giauque, R D

    1976-12-01

    Energy-dispersive x-ray spectroscopy and inductively coupled plasma emission spectrometry were evaluated as methods for routine multielement analysis of biological material. Standard samples included Standard Reference Materials (National Bureau of Standards), compounded mixtures, and supplements that provided a wide range of elemental concentrations for analysis. Elements included in this study were Zn, Pb, Ni, Mn, Fe, Mg, Cu, Ca, As, Se, Br, Rb, and Sr. Standards were analyzed as unknowns by participating laboratories. The two methods were evaluated for sensitivity, precision, and accuracy, and the results compared to those obtained for atomic absorption spectrometric analysis of identical standard unknowns. Both methods compared favorably and both were determined to be highly reliable for such an application. Advantages and disadvantages of each method are compared and discussed.

  16. Mapping the metal uptake in plants from Jasper Ridge Biological Preserve using synchrotron micro-focused X-ray fluorescence spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Lo, Allison [Univ. of California, Davis, CA (United States)

    2015-08-20

    Serpentine soil originates in the Earth’s mantle and contains high concentrations of potentially toxic transition metals. Although serpentine soil limits plant growth, endemic and adapted plants at Jasper Ridge Biological Preserve, located behind SLAC National Accelerator Laboratory, can tolerate these conditions. Serpentine soil and seeds belonging to native California and invasive plants were collected at Jasper Ridge. The seeds were grown hydroponically and on serpentine and potting soil to examine the uptake and distribution of ions in the roots and shoots using synchrotron micro-focused X-ray fluorescence spectroscopy. The results were used to determine differences between serpentine-tolerant plants. Rye grown on potting soil was enriched in Ni, Fe, Mn, and Cr compared to purple needlegrass grown on serpentine soil. Serpentine vegetation equally suppressed the uptake of Mn, Ni, and Fe in the roots and shoots. The uptake of Ca and Mg affected the uptake of other elements such as K, S, and P.

  17. Structure of the dimeric N-glycosylated form of fungal β-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies

    Directory of Open Access Journals (Sweden)

    Sklenář Jan

    2007-05-01

    Full Text Available Abstract Background Fungal β-N-acetylhexosaminidases catalyze the hydrolysis of chitobiose into its constituent monosaccharides. These enzymes are physiologically important during the life cycle of the fungus for the formation of septa, germ tubes and fruit-bodies. Crystal structures are known for two monomeric bacterial enzymes and the dimeric human lysosomal β-N-acetylhexosaminidase. The fungal β-N-acetylhexosaminidases are robust enzymes commonly used in chemoenzymatic syntheses of oligosaccharides. The enzyme from Aspergillus oryzae was purified and its sequence was determined. Results The complete primary structure of the fungal β-N-acetylhexosaminidase from Aspergillus oryzae CCF1066 was used to construct molecular models of the catalytic subunit of the enzyme, the enzyme dimer, and the N-glycosylated dimer. Experimental data were obtained from infrared and Raman spectroscopy, and biochemical studies of the native and deglycosylated enzyme, and are in good agreement with the models. Enzyme deglycosylated under native conditions displays identical kinetic parameters but is significantly less stable in acidic conditions, consistent with model predictions. The molecular model of the deglycosylated enzyme was solvated and a molecular dynamics simulation was run over 20 ns. The molecular model is able to bind the natural substrate – chitobiose with a stable value of binding energy during the molecular dynamics simulation. Conclusion Whereas the intracellular bacterial β-N-acetylhexosaminidases are monomeric, the extracellular secreted enzymes of fungi and humans occur as dimers. Dimerization of the fungal β-N-acetylhexosaminidase appears to be a reversible process that is strictly pH dependent. Oligosaccharide moieties may also participate in the dimerization process that might represent a unique feature of the exclusively extracellular enzymes. Deglycosylation had only limited effect on enzyme activity, but it significantly affected

  18. Monothiodibenzoylmethane: Structural and vibrational assignments

    DEFF Research Database (Denmark)

    Hansen, Bjarke Knud Vilster; Gorski, Alexander; Posokhov, Yevgen

    2007-01-01

    The vibrational structure of the title compound (1,3-diphenyl-3-thioxopropane-1-one, TDBM) was studied by a variety of experimental and theoretical methods. The stable ground state configuration of TDBM was investigated by IR absorption measurements in different media, by LD polarization spectros......The vibrational structure of the title compound (1,3-diphenyl-3-thioxopropane-1-one, TDBM) was studied by a variety of experimental and theoretical methods. The stable ground state configuration of TDBM was investigated by IR absorption measurements in different media, by LD polarization...... spectroscopy of samples partially aligned in a stretched polymer matrix, and by Raman spectroscopy. The investigation of the metastable photoproduct of TDBM was based on the previously published spectrum of the product trapped in argon matrix (Posokhov et al., Chem. Phys. Lett. 350 (2001) 502). The observed...

  19. Final report on LDRD project: Semiconductor surface-emitting microcavity laser spectroscopy for analysis of biological cells and microstructures

    Energy Technology Data Exchange (ETDEWEB)

    Gourley, P.L.; McDonald, A.E. [Sandia National Labs., Albuquerque, NM (United States). Nanostructure and Semiconductor Physics Dept.; Gourley, M.F. [Washington Hospital Center, DC (United States); Bellum, J. [Coherent Technologies, Boulder, CO (United States)

    1997-08-01

    This article discusses a new intracavity laser technique that uses living or fixed cells as an integral part of the laser. The cells are placed on a GaAs based semiconductor wafer comprising one half of a vertical cavity surface-emitting laser. After placement, the cells are covered with a dielectric mirror to close the laser cavity. When photo-pumped with an external laser, this hybrid laser emits coherent light images and spectra that depend sensitively on the cell size, shape, and dielectric properties. The light spectra can be used to identify different cell types and distinguish normal and abnormal cells. The laser can be used to study single cells in real time as a cell-biology lab-on-a-chip, or to study large populations of cells by scanning the pump laser at high speed. The laser is well-suited to be integrated with other micro-optical or micro-fluidic components to lead to micro-optical-mechanical systems for analysis of fluids, particulates, and biological cells.

  20. Transient absorption spectroscopy in biology using the Super-ACO storage ring FEL and the synchrotron radiation combination

    CERN Document Server

    Renault, E; De Ninno, G; Garzella, D; Hirsch, M; Nahon, L; Nutarelli, D

    2001-01-01

    The Super-ACO storage ring FEL, covering the UV range down to 300 nm with a high average power (300 mW at 350 nm) together with a high stability and long lifetime, is a unique tool for the performance of users applications. We present here the first pump-probe two color experiments on biological species using a storage ring FEL coupled to the synchrotron radiation. The intense UV pulse of the Super-ACO FEL is used to prepare a high initial concentration of chromophores in their first singlet electronic excited state. The nearby bending magnet synchrotron radiation provides, on the other hand a pulsed, white light continuum (UV-IR), naturally synchronized with the FEL pulses and used to probe the photochemical subsequent events and the associated transient species. We have demonstrated the feasibility with a dye molecule (POPOP) observing a two-color effect, signature of excited state absorption and a temporal signature with Acridine. Applications on various chromophores of biological interest are carried out,...

  1. Microorganisms detection on substrates using QCL spectroscopy

    Science.gov (United States)

    Padilla-Jiménez, Amira C.; Ortiz-Rivera, William; Castro-Suarez, John R.; Ríos-Velázquez, Carlos; Vázquez-Ayala, Iris; Hernández-Rivera, Samuel P.

    2013-05-01

    Recent investigations have focused on the improvement of rapid and accurate methods to develop spectroscopic markers of compounds constituting microorganisms that are considered biological threats. Quantum cascade lasers (QCL) systems have revolutionized many areas of research and development in defense and security applications, including his area of research. Infrared spectroscopy detection based on QCL was employed to acquire mid infrared (MIR) spectral signatures of Bacillus thuringiensis (Bt), Escherichia coli (Ec) and Staphylococcus epidermidis (Se), which were used as biological agent simulants of biothreats. The experiments were carried out in reflection mode on various substrates such as cardboard, glass, travel baggage, wood and stainless steel. Chemometrics statistical routines such as principal component analysis (PCA) regression and partial least squares-discriminant analysis (PLS-DA) were applied to the recorded MIR spectra. The results show that the infrared vibrational techniques investigated are useful for classification/detection of the target microorganisms on the types of substrates studied.

  2. The AstroBiology Explorer (ABE) MIDEX Mission Concept: Using Infrared Spectroscopy to Identify Organic Molecules in Space

    Science.gov (United States)

    Sandford, Scott A.; Ennico, Kimberly; Allamandola, Louis; Bregman, Jesse; Greene, Thomas; Hudgins, Douglas

    2002-01-01

    One of the principal means by which organic compounds are detected and identified in space is by infrared spectroscopy. Past IR telescopic and laboratory studies have shown that much of the carbon in the interstellar medium (ISM) is in complex organic species but the distribution, abundance and evolutionary relationships of these materials are not well understood. The Astrobiology Explorer (ABE) is a MIDEX mission concept designed to conduct IR spectroscopic observations to detect and identify these materials and address outstanding problems in astrobiology, astrochemistry, and astrophysics. ABE's core science program includes observations of planetary nebulae and stellar outflows, protostellar objects, Solar System objects, and galaxies, and lines of sight through dense molecular clouds and the diffuse ISM. ABE is a cryogenically-cooled 60 cm diameter space telescope equipped with 3 cross-dispersed R-2000 spectrometers that share a single common slit. Each spectrometer measures one spectral octave and together cover the entire 2.5-20 micron region simultaneously. The spectrometers use state-of-the-art InSb and Si:As 1024x1024 pixel detectors. ABE would operate in a heliocentric, Earth drift-away orbit and have a core science mission lasting approximately 1.5 years. ABE is currently under study at NASA's Ames Research Center in collaboration with Ball Aerospace and Technologies Corp.

  3. The photodissociation and reaction dynamics of vibrationally excited molecules

    Energy Technology Data Exchange (ETDEWEB)

    Crim, F.F. [Univ. of Wisconsin, Madison (United States)

    1993-12-01

    This research determines the nature of highly vibrationally excited molecules, their unimolecular reactions, and their photodissociation dynamics. The goal is to characterize vibrationally excited molecules and to exploit that understanding to discover and control their chemical pathways. Most recently the author has used a combination of vibrational overtone excitation and laser induced fluorescence both to characterize vibrationally excited molecules and to study their photodissociation dynamics. The author has also begun laser induced grating spectroscopy experiments designed to obtain the electronic absorption spectra of highly vibrationally excited molecules.

  4. Innovative nanostructures for highly sensitive vibrational biosensing (Conference Presentation)

    Science.gov (United States)

    Popp, Juergen; Mayerhöfer, Thomas; Cialla-May, Dana; Weber, Karina; Huebner, Uwe

    2016-03-01

    Employing vibrational spectroscopy (IR-absorption and Raman spectroscopy) allows for the labelfree detection of molecular specific fingerprints of inorganic, organic and biological substances. The sensitivity of vibrational spectroscopy can be improved by several orders of magnitude via the application of plasmonic active surfaces. Within this contribution we will discuss two such approaches, namely surface enhanced Raman spectroscopy (SERS) as well as surface enhanced IR absorption (SEIRA). It will be shown that SERS using metal colloids as SERS active substrate in combination with a microfluidic lab-on-a-chip (LOC) device enables high throughput and reproducible measurements with highest sensitivity and specificity. The application of such a LOC-SERS approach for therapeutic drug monitoring (e.g. quantitative detection of antibiotics in a urine matrix) will be presented. Furthermore, we will introduce innovative bottom-up strategies to prepare SERS-active nanostructures coated with a lipophilic sensor layer as one-time use SERS substrates for specific food analysis (e.g. quantitative detection of toxic food colorants). The second part of this contribution presents a slit array metamaterial perfect absorber for IR sensing applications consisting of a dielectric layer sandwiched between two metallic layers of which the upper layer is perforated with a periodic array of slits. Light-matter interaction is greatly amplified in the slits, where also the analyte is concentrated, as the surface of the substrate is covered by a thin silica layer. Thus, already small concentrations of analytes down to a monolayer can be detected by refractive index sensing and identified by their spectral fingerprints with a standard mid-infrared lab spectrometer.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-09-15

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

  6. Study of the lithiated phenylacetonitrile monoanions and dianions formed according to the lithiated base used (LHMDS, LDA, or n-BuLi). 2. Alkylation and deuteriation mechanism study by vibrational and NMR spectroscopy and quantum chemistry calculations.

    Science.gov (United States)

    Strzalko, Tekla; Wartski, Lya; Corset, Jacques; Castellà-Ventura, Martine; Froment, Françoise

    2012-08-01

    Mechanisms of alkylation by PhCH(2)Cl or CH(3)I in THF and of deuteriation by DCl (4 N in D(2)O) in THF or THF-toluene of lithiated phenylacetonitrile monoanions and dianions obtained with LHMDS, LDA, or n-BuLi are studied by vibrational and NMR spectroscopy and quantum chemistry calculations. Dialkylation of the three dilithio dianions generated with n-BuLi (2.0-2.7 equiv, THF-hexane) depends on their structure: N-lithio (PhCCNLi)(-)Li(+) and (C,N)-dilithio PhCLiCNLi dianions afford PhCR(2)CN (R = PhCH(2), CH(3)) from the intermediate N-lithio monoalkylated monoanion PhCRCNLi 10; C-lithio dianion (PhCLiCN)(-)Li(+) leads to a carbenoid species, the C-lithio monoalkylated nitrile PhCLiRCN 11, which either eliminates carbene Ph-C-R and different LiCN species or isomerizes to PhCRCNLi in the presence of LiX (X = Cl, I). Dialkylation or dideuteriation of monoanions (monomers, dimers, and heterodimers [PhCHCNLi·LiR'], R' = (SiMe(3))(2)N, (i-Pr)(2)N) obtained with LHMDS or LDA (2.4 equiv, THF) proceeds via a sequential mechanism involving monometalation-monoalkylation (or monodeuteriation) reactions. Some carbene and (LiCNLi)(+) are also observed, and explained by another mechanism implying the C-lithio monoalkylated monoanion PhCLiRCN 9 in the presence of LiX. These results show the ambiphilic behavior of PhCLiRCN as a carbenoid (11) or a carbanion (9) and the importance of LiX formed in situ in the first alkylation step.

  7. Photoacoustic detection and optical spectroscopy of high-intensity focused ultrasound-induced thermal lesions in biologic tissue

    Energy Technology Data Exchange (ETDEWEB)

    Alhamami, Mosa; Kolios, Michael C.; Tavakkoli, Jahan, E-mail: jtavakkoli@ryerson.ca [Department of Physics, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3 (Canada)

    2014-05-15

    Purpose: The aims of this study are: (a) to investigate the capability of photoacoustic (PA) method in detecting high-intensity focused ultrasound (HIFU) treatments in muscle tissuesin vitro; and (b) to determine the optical properties of HIFU-treated and native tissues in order to assist in the interpretation of the observed contrast in PA detection of HIFU treatments. Methods: A single-element, spherically concaved HIFU transducer with a centre frequency of 1 MHz was utilized to create thermal lesions in chicken breast tissuesin vitro. To investigate the detectability of HIFU treatments photoacoustically, PA detection was performed at 720 and 845 nm on seven HIFU-treated tissue samples. Within each tissue sample, PA signals were acquired from 22 locations equally divided between two regions of interest within two volumes in tissue – a HIFU-treated volume and an untreated volume. Optical spectroscopy was then carried out on 10 HIFU-treated chicken breast specimens in the wavelength range of 500–900 nm, in 1-nm increments, using a spectrophotometer with an integrating sphere attachment. The authors’ optical spectroscopy raw data (total transmittance and diffuse reflectance) were used to obtain the optical absorption and reduced scattering coefficients of HIFU-induced thermal lesions and native tissues by employing the inverse adding-doubling method. The aforementioned interaction coefficients were subsequently used to calculate the effective attenuation coefficient and light penetration depth of HIFU-treated and native tissues in the wavelength range of 500–900 nm. Results: HIFU-treated tissues produced greater PA signals than native tissues at 720 and 845 nm. At 720 nm, the averaged ratio of the peak-to-peak PA signal amplitude of HIFU-treated tissue to that of native tissue was 3.68 ± 0.25 (mean ± standard error of the mean). At 845 nm, the averaged ratio of the peak-to-peak PA signal amplitude of HIFU-treated tissue to that of native tissue was 3.75

  8. Comprehensive Chiroptical Spectroscopy, Applications in Stereochemical Analysis of Synthetic Compounds, Natural Products, and Biomolecules

    CERN Document Server

    Berova, Nina; Nakanishi, Koji; Woody, Robert W

    2012-01-01

    This book provides an introduction to the important methods of chiroptical spectroscopy in general, and circular dichroism (CD) in particular, which are increasingly important in all areas of chemistry, biochemistry, and structural biology. The book can be used as a text for undergraduate and graduate students and as a reference for researchers in academia and industry. Experimental methods and instrumentation are described with topics ranging from the most widely used methods (electronic and vibrational CD) to frontier areas such as nonlinear spectroscopy and photoelectron CD,

  9. Real-time observation of vibrational quantum beat in condensed phase by 20 fs time-resolved spectroscopy%凝聚相分子振动量子拍的20fs时间分辨光谱实时观测

    Institute of Scientific and Technical Information of China (English)

    王云鹏; 王专; 翁羽翔

    2012-01-01

    Impulsive coherent vibrational spectroscopy is a kind of time-resolved spectroscopy methodology with a pulse duration of the femtosecond laser shorter than the molecular vibrational period. Usually, it is based on pump-probe technique and is utilized to real-time observation of the molecular vibrational dynamics coupled to the electronic ground or excited state. We have built an impulsive coherent vibrational spectroscopy setup based on a sub-20 fs, 550 to 700 nm tunable non-collinear optical parametric amplifier and performed pump-probe experiment with an Oxazine 720 methanol solution as the sample. Two vibrational quantum beats with frequency of 592 and 678 cm-1 were observed and the corresponding vibrational periods are 56.3 and 49.2 fs respectively.%冲击相干振动光谱是以脉冲宽度比分子振动周期短的飞秒激光作为激发光源的一种光谱学实验方法,通常是以泵浦-探测实验装置为基础,可以实时观测与电子基态或激发态相耦合的分子振动动力学过程.中国科学院物理研究所以小于20 fs,550~700 nm光谱范围内可调谐的非共线光参量放大器为光源,建立了一套冲击相干振动光谱学实验装置,并以染料分子Oxazine 720的甲醇溶液为样品进行了实验测试.实验中样品被泵浦光脉冲激发后在电子基态形成振动波包,并观测到振动波包在电子势能曲面上运动所形成的振动量子拍信号.经分析有两个分子振动模式被激发,其振动频率分别为592与678cm-1,所对应的振动周期分别为56.3与49.2 fs.

  10. Comprehensive chiroptical spectroscopy, instrumentation, methodologies, and theoretical simulations

    CERN Document Server

    Berova, Nina; Nakanishi, Koji

    2011-01-01

    This book provides an introduction to the important methods of chiroptical spectroscopy in general, and circular dichroism (CD) in particular, which are increasingly important in all areas of chemistry, biochemistry, and structural biology. The book can be used as a text for undergraduate and graduate students and as a reference for researchers in academia and industry, with or without the companion volume in this set. Experimental methods and instrumentation are described with topics ranging from the most widely used methods (electronic and vibrational CD) to frontier areas such as nonlinear

  11. Theory of vibration protection

    CERN Document Server

    Karnovsky, Igor A

    2016-01-01

    This text is an advancement of the theory of vibration protection of mechanical systems with lumped and distributed parameters. The book offers various concepts and methods of solving vibration protection problems, discusses the advantages and disadvantages of different methods, and the fields of their effective applications. Fundamental approaches of vibration protection, which are considered in this book, are the passive, parametric and optimal active vibration protection. The passive vibration protection is based on vibration isolation, vibration damping and dynamic absorbers. Parametric vibration protection theory is based on the Shchipanov-Luzin invariance principle. Optimal active vibration protection theory is based on the Pontryagin principle and the Krein moment method. The book also contains special topics such as suppression of vibrations at the source of their occurrence and the harmful influence of vibrations on humans. Numerous examples, which illustrate the theoretical ideas of each chapter, ar...

  12. Vibrational Spectroscopy of Microhydrated Conjugate Base Anions

    NARCIS (Netherlands)

    Asmis, K. R.; Neumark, D. M.

    2012-01-01

    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 aeros

  13. Vibrational Overtone Spectroscopy of Pyrrole and Pyrrolidine

    Science.gov (United States)

    1991-05-23

    general pattern is a strong peak accompanied by two or three weaker peaks to lower energy. For instance, the 13,305 cm-I band in pyrrole has three weaker...Orza, J.M. Anales de Quimica 1984, 80, 59. 29. Navarro, R.; Orza, J.M. Anales de Quimica 1982, 79, 557. 30. Xie, Y; Fan, K.; Boggs,J., Molec. Phys

  14. Low temperature vibrational spectroscopy. I. Hexachlorotellurates

    DEFF Research Database (Denmark)

    Berg, Rolf W.; Poulsen, Finn Willy; Bjerrum, Niels

    1977-01-01

    frequency lattice modes were observed and interpreted in terms of a phase transition near 165 K, similar to transitions in other K2[MX6] salts. The cubic tetramethylammonium hexachlorotellurate salt undergoes a phase transition of supposed first order at a temperature near 110 K, corresponding...... to transitions known in analogous uranium and tin compounds. Possible reasons for the transitions are discussed. In the low temperature phases the nu4 and nu6 bendings of [TeCl6]2− have been identified with bands near ~130 and ~110 cm−1. No evidence seemed to favor any stereochemical distortion due to the lone...

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

    Science.gov (United States)

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

    2003-12-01

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

  16. Feasibility study for the rapid screening of target molecules using translational diffusion coefficients: diffusion-ordered NMR spectroscopy of biological toxins.

    Science.gov (United States)

    Henderson, Terry J

    2010-02-01

    A panel of 15 biological toxins ranging between approximately 60-28,000 g/mol was used to evaluate the feasibility of screening aqueous samples for toxin analytes based on their translational diffusion coefficients, D(t). Toxin D(t) values were measured by pulsed-field gradient (1)H NMR spectroscopy using a bipolar pulse pair, longitudinal eddy current delay pulse sequence incorporating water suppression to achieve the maximum dynamic range for toxin signals. To collect data for an effective screening protocol, reference D(t) values were determined from five independent measurements at both 25 and 37 degrees C for all toxins in the panel. In the protocol, D(t) values are measured at both temperatures for a suspected toxin target in a sample, and for assignment as a potential toxin analyte, the measurements are required to fall within +/-0.25 x 10(-6) cm(2)/s of both reference D(t) values for at least one toxin in the panel. Only solution viscosity was found to influence sample D(t) measurements appreciably; however, the measurements are easily corrected for viscosity effects by calculating the D(t) value of the suspected toxin at infinite dilution. In conclusion, the protocol provides a rapid and effective means for screening aqueous samples for all toxins in the panel, narrowing toxin identification to < or = 2 possibilities in virtually all cases.

  17. Electrical impedance spectroscopy (EIS)-based evaluation of biological tissue phantoms to study multifrequency electrical impedance tomography (Mf-EIT) systems

    KAUST Repository

    Bera, Tushar Kanti

    2016-03-18

    Abstract: Electrical impedance tomography (EIT) phantoms are essential for the calibration, comparison and evaluation of the EIT systems. In EIT, the practical phantoms are typically developed based on inhomogeneities surrounded by a homogeneous background to simulate a suitable conductivity contrast. In multifrequency EIT (Mf-EIT) evaluation, the phantoms must be developed with the materials which have recognizable or distinguishable impedance variations over a wide range of frequencies. In this direction the impedance responses of the saline solution (background) and a number vegetable and fruit tissues (inhomogeneities) are studied with electrical impedance spectroscopy (EIS) and the frequency responses of bioelectrical impedance and conductivity are analyzed. A number of practical phantoms with different tissue inhomogeneities and different inhomogeneity configurations are developed and the multifrequency impedance imaging is studied with the Mf-EIT system to evaluate the phantoms. The conductivity of the vegetable inhomogeneities reconstructed from the EIT imaging is compared with the conductivity values obtained from the EIS studies. Experimental results obtained from multifrequency EIT reconstruction demonstrate that the electrical impedance of all the biological tissues inhomogenity decreases with frequency. The potato tissue phantom produces better impedance image in high frequency ranges compared to the cucumber phantom, because the cucumber impedance at high frequency becomes lesser than that of the potato at the same frequency range. Graphical Abstract: [Figure not available: see fulltext.] © 2016 The Visualization Society of Japan

  18. In-situ Studies of the Reactions of Bifunctional and Heterocyclic Molecules over Noble Metal Single Crystal and Nanoparticle Catalysts Studied with Kinetics and Sum-Frequency Generation Vibrational Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-06-30

    Sum frequency generation surface vibrational spectroscopy (SFG-VS) in combination with gas chromatography (GC) was used in-situ to monitor surface bound reaction intermediates and reaction selectivities for the hydrogenation reactions of pyrrole, furan, pyridine, acrolein, crotonaldehyde, and prenal over Pt(111), Pt(100), Rh(111), and platinum nanoparticles under Torr reactant pressures and temperatures of 300K to 450K. The focus of this work is the correlation between the SFG-VS observed surface bound reaction intermediates and adsorption modes with the reaction selectivity, and how this is affected by catalyst structure and temperature. Pyrrole hydrogenation was investigated over Pt(111) and Rh(111) single crystals at Torr pressures. It was found that pyrrole adsorbs to Pt(111) perpendicularly by cleaving the N-H bond and binding through the nitrogen. However, over Rh(111) pyrrole adsorbs in a tilted geometry binding through the {pi}-aromatic orbitals. A surface-bound pyrroline reaction intermediate was detected over both surfaces with SFG-VS. It was found that the ring-cracking product butylamine is a reaction poison over both surfaces studied. Furan hydrogenation was studied over Pt(111), Pt(100), 10 nm cubic platinum nanoparticles and 1 nm platinum nanoparticles. The product distribution was observed to be highly structure sensitive and the acquired SFG-VS spectra reflected this sensitivity. Pt(100) exhibited more ring-cracking to form butanol than Pt(111), while the nanoparticles yielded higher selectivities for the partially saturated ring dihydrofuran. Pyridine hydrogenation was investigated over Pt(111) and Pt(100). The α-pyridyl surface adsorption mode was observed with SFG-VS over both surfaces. 1,4-dihydropyridine was seen as a surface intermediate over Pt(100) but not Pt(111). Upon heating the surfaces to 350K, the adsorbed pyridine changes to a flat-lying adsorption mode. No evidence was found for the pyridinium cation. The hydrogenation of the

  19. Quantum Effects in Biology

    Science.gov (United States)

    Mohseni, Masoud; Omar, Yasser; Engel, Gregory S.; Plenio, Martin B.

    2014-08-01

    List of contributors; Preface; Part I. Introduction: 1. Quantum biology: introduction Graham R. Fleming and Gregory D. Scholes; 2. Open quantum system approaches to biological systems Alireza Shabani, Masoud Mohseni, Seogjoo Jang, Akihito Ishizaki, Martin Plenio, Patrick Rebentrost, Alàn Aspuru-Guzik, Jianshu Cao, Seth Lloyd and Robert Silbey; 3. Generalized Förster resonance energy transfer Seogjoo Jang, Hoda Hossein-Nejad and Gregory D. Scholes; 4. Multidimensional electronic spectroscopy Tomáš Mančal; Part II. Quantum Effects in Bacterial Photosynthetic Energy Transfer: 5. Structure, function, and quantum dynamics of pigment protein complexes Ioan Kosztin and Klaus Schulten; 6. Direct observation of quantum coherence Gregory S. Engel; 7. Environment-assisted quantum transport Masoud Mohseni, Alàn Aspuru-Guzik, Patrick Rebentrost, Alireza Shabani, Seth Lloyd, Susana F. Huelga and Martin B. Plenio; Part III. Quantum Effects in Higher Organisms and Applications: 8. Excitation energy transfer in higher plants Elisabet Romero, Vladimir I. Novoderezhkin and Rienk van Grondelle; 9. Electron transfer in proteins Spiros S. Skourtis; 10. A chemical compass for bird navigation Ilia A. Solov'yov, Thorsten Ritz, Klaus Schulten and Peter J. Hore; 11. Quantum biology of retinal Klaus Schulten and Shigehiko Hayashi; 12. Quantum vibrational effects on sense of smell A. M. Stoneham, L. Turin, J. C. Brookes and A. P. Horsfield; 13. A perspective on possible manifestations of entanglement in biological systems Hans J. Briegel and Sandu Popescu; 14. Design and applications of bio-inspired quantum materials Mohan Sarovar, Dörthe M. Eisele and K. Birgitta Whaley; 15. Coherent excitons in carbon nanotubes Leonas Valkunas and Darius Abramavicius; Glossary; References; Index.

  20. Vibrational Spectra of a Mechanosensitive Channel

    NARCIS (Netherlands)

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

    2013-01-01

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

  1. Vibrational relaxation of pure liquid water

    NARCIS (Netherlands)

    Lindner, J; Vohringer, P; Pshenichnikov, MS; Cringus, D; Wiersma, DA; Mostovoy, M; Vöhringer, Peter; Pshenichnikov, Maxim S.

    2006-01-01

    Multicolor infrared ultrafast spectroscopy is applied to investigate the vibrational relaxation dynamics in liquid water at room temperature. In a sequence of experiments, both the stretching and the bending mode are photoexcited and probed. A unified model, capable of the reproduction of as much as

  2. Application of Raman spectroscopy technology to studying Sudan I

    Science.gov (United States)

    Li, Gang; Zhang, Guoping; Chen, Chen

    2006-06-01

    Being an industrial dye, the Sudan I may have a toxic effect after oral intake on the body, and has recently been shown to cause cancer in rats, mice and rabbits. Because China and some other countries have detected the Sudan I in samples of the hot chilli powder and the chilli products, it is necessary to study the characteristics of this dye. As one kind of molecule scattering spectroscopy, Raman spectroscopy is characterized by the frequency excursion caused by interactions of molecules and photons. The frequency excursion reflects the margin between certain two vibrational or rotational energy states, and shows the information of the molecule. Because Raman spectroscopy can provides quick, easy, reproducible, and non-destructive analysis, both qualitative and quantitative, with no sample preparation required, Raman spectroscopy has been a particularly promising technique for analyzing the characteristics and structures of molecules, especially organic ones. Now, it has a broad application in biological, chemical, environmental and industrial applications. This paper firstly introduces Sudan I dye and the Raman spectroscopy technology, and then describes its application to the Sudan I. Secondly, the fingerprint spectra of the Sudan I are respectively assigned and analyzed in detail. Finally, the conclusion that the Raman spectroscopy technology is a powerful tool to determine the Sudan I is drawn.

  3. A lab-on-a-chip for hypoxic patch clamp measurements combined with optical tweezers and spectroscopy- first investigations of single biological cells.

    Science.gov (United States)

    Alrifaiy, Ahmed; Borg, Johan; Lindahl, Olof A; Ramser, Kerstin

    2015-04-18

    The response and the reaction of the brain system to hypoxia is a vital research subject that requires special instrumentation. With this research subject in focus, a new multifunctional lab-on-a-chip (LOC) system with control over the oxygen content for studies on biological cells was developed. The chip was designed to incorporate the patch clamp technique, optical tweezers and absorption spectroscopy. The performance of the LOC was tested by a series of experiments. The oxygen content within the channels of the LOC was monitored by an oxygen sensor and verified by simultaneously studying the oxygenation state of chicken red blood cells (RBCs) with absorption spectra. The chicken RBCs were manipulated optically and steered in three dimensions towards a patch-clamp micropipette in a closed microfluidic channel. The oxygen level within the channels could be changed from a normoxic value of 18% O 2 to an anoxic value of 0.0-0.5% O 2. A time series of 3 experiments were performed, showing that the spectral transfer from the oxygenated to the deoxygenated state occurred after about 227 ± 1 s and a fully developed deoxygenated spectrum was observed after 298 ± 1 s, a mean value of 3 experiments. The tightness of the chamber to oxygen diffusion was verified by stopping the flow into the channel system while continuously recording absorption spectra showing an unchanged deoxygenated state during 5400 ± 2 s. A transfer of the oxygenated absorption spectra was achieved after 426 ± 1 s when exposing the cell to normoxic buffer. This showed the long time viability of the investigated cells. Successful patching and sealing were established on a trapped RBC and the whole-cell access (Ra) and membrane (Rm) resistances were measured to be 5.033 ± 0.412 M Ω and 889.7 ± 1.74 M Ω respectively.

  4. Role of Raman spectroscopy and surface enhanced Raman spectroscopy in colorectal cancer

    Institute of Scientific and Technical Information of China (English)

    Cerys A Jenkins; Paul D Lewis; Peter R Dunstan; Dean A Harris

    2016-01-01

    Colorectal cancer(CRC) is the fourth most commoncancer in the United Kingdom and is the second largest cause of cancer related death in the United Kingdom after lung cancer.Currently in the United Kingdom there is not a diagnostic test that has sufficient differentiation between patients with cancer and those without cancer so the current referral system relies on symptomatic presentation in a primary care setting.Raman spectroscopy and surface enhanced Raman spectroscopy(SERS) are forms of vibrational spectroscopy that offer a nondestructive method to gain molecular information about biological samples.The techniques offer a wide range of applications from in vivo or in vitro diagnostics using endoscopic probes,to the use of micro-spectrometers for analysis of biofluids.The techniques have the potential to detect molecular changes prior to any morphological changes occurring in the tissue and therefore could offer many possibilities to aid the detection of CRC.The purpose of this review is to look at the current state of diagnostic technology in the United Kingdom.The development of Raman spectroscopy and SERS in clinical applications relation for CRC will then be discussed.Finally,future areas of research of Raman/SERS as a clinical tool for the diagnosis of CRC are also discussed.

  5. Vibrational Spectroscopy Investigation Using Ab Initio and Density Functional Theory Analysis on the Structure of tert-Butyl 3a-Chloroperhydro-2,6a-epoxyoxireno[e]isoindole-5-carboxylate

    Directory of Open Access Journals (Sweden)

    Hakan Arslan

    2013-01-01

    Full Text Available The molecular structure, vibrational frequencies, and infrared intensities of the tert-butyl 3a-chloroperhydro-2,6a-epoxyoxireno[e]isoindole-5-carboxylate were calculated by the HF and DFT (BLYP and B3LYP methods using 6-31G(d and 6-31G(d,p basis sets. The FT infrared spectrum of the solid sample was measured under standard condition. We obtained two stable conformers for the title compound; however Conformer 1 is approximately 0.2 kcal/mol more stable than the Conformer 2. The comparison of the theoretical and experimental geometry of the title compound shows that the X-ray parameters fairly well reproduce the geometry of Conformer 2. Comparison of the observed fundamental vibrational frequencies of the title molecule and calculated results by HF and DFT methods indicates that B3LYP is superior for molecular vibrational problems. The harmonic vibrations computed by the B3LYP/6-31G(d,p method are in a good agreement with the observed IR spectral data. Theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions (PEDs using VEDA 4 program.

  6. Tip-enhanced Raman spectroscopy: From concepts to practical applications

    Science.gov (United States)

    Jiang, Nan; Kurouski, Dmitry; Pozzi, Eric A.; Chiang, Naihao; Hersam, Mark C.; Van Duyne, Richard P.

    2016-08-01

    Tip-enhanced Raman spectroscopy (TERS) is a powerful technique that integrates the vibrational fingerprinting of Raman spectroscopy and the sub-nanometer resolution of scanning probe microscopy (SPM). As a result, TERS is capable of obtaining chemical maps of analyzed specimens with exceptional lateral resolution. This is extremely valuable for the study of interactions between molecules and substrates, in addition to structural characterization of biological objects, such as viruses and amyloid fibrils, 2D polymeric materials, and monitoring electrochemical and photo-catalytic processes. In this mini-review, we discuss the most significant advances of TERS, including: super high resolution chemical imaging, monitoring of catalytic processes, incorporation of pulsed-excitation techniques, single-site electrochemistry, biosensing, and art conservation. We begin with a short overview of TERS, comparing it with other surface analytical techniques, followed by an overview of recent developments and future applications in TERS.

  7. Portable vibration exciter

    Science.gov (United States)

    Beecher, L. C.; Williams, F. T.

    1970-01-01

    Gas-driven vibration exciter produces a sinusoidal excitation function controllable in frequency and in amplitude. It allows direct vibration testing of components under normal loads, removing the possibility of component damage due to high static pressure.

  8. Vibrational spectroscopy (FT-IR and Laser-Raman) investigation, and computational (M06-2X and B3LYP) analysis on the structure of 4-(3-fluorophenyl)-1-(propan-2-ylidene)-thiosemicarbazone.

    Science.gov (United States)

    Sert, Yusuf; Miroslaw, Barbara; Çırak, Çağrı; Doğan, Hatice; Szulczyk, Daniel; Struga, Marta

    2014-07-15

    In this study, the experimental and theoretical vibrational spectral analysis of 4-(3-fluorophenyl)-1-(propan-2-ylidene)-thiosemicarbazone have been carried out. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) have been recorded for the solid state samples. The theoretical vibrational frequencies and the optimized geometric parameters (bond lengths and angles) have been calculated for gas phase using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set. The diversity in molecular geometry of fluorophenyl substituted thiosemicarbazones has been discussed based on the X-ray crystal structure reports and theoretical calculation results from the literature. The assignments of the vibrational frequencies have been done on the basis of potential energy distribution (PED) analysis by using VEDA4 software. A good correlation was found between the computed and experimental geometric and vibrational data. In addition, the highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbital energy levels and other related molecular energy values of the compound have been determined using the same level of theoretical calculations.

  9. FT-IR光谱在电离辐射作用于微生物研究中的应用%Application of FT-IR Spectroscopy in Study of Biological Effects on Microorganisms Induced by Ionizing Radiation

    Institute of Scientific and Technical Information of China (English)

    刘京华; 黄青

    2012-01-01

    傅里叶变换红外光谱(Fourier transform infrared spectroscopy,FT-IR)是一种很有用的生物分析检测技术,通过FT-IR光谱技术可以得到有关蛋白质、脂类、核酸和多糖等微生物和细胞各类组成成分的信息.基于同步辐射光源的显微FT-IR光谱具有更高的空间分辨率和更快的测量速度,因而在生物学研究中具有进行快速、实时、动态和无损检测等优势.本文介绍了FT-IR光谱技术在微生物及电离辐射作用于微生物引起的生物学效应研究中的应用,并对该领域未来研究的发展趋势进行了展望.%Fourier transform infrared (FT-IR) spectroscopy is a useful and powerful technique that can provide rich information on proteins,lipids,nucleic acids and carbohydrates in biological systems. Especially,the high-resolution synchrotron Fourier-transform infrared (SR-FTIR) microspectroscopy and imaging technique can be employed as an excellent tool for convenient,fast,non-invasive,and real-time monitoring of varied complicated processes occuring in a biological system. In this review,the authors discuss the recent progress on the application of FT-IR spectroscopy in the study of biological effects on microorganisms induced by ionizing radiation,and also give an outlook for the future FT-IR spectroscopy research in this field.

  10. A new Density Functional Theory (DFT) based method for supporting the assignment of vibrational signatures of mannan and cellulose—Analysis of palm kernel cake hydrolysis by ATR-FT-IR spectroscopy as a case study

    DEFF Research Database (Denmark)

    Barsberg, Søren Talbro; Sanadi, Anand Ramesh; Jørgensen, Henning

    2011-01-01

    Attenuated Total Reflectance (ATR) FT-IR spectroscopy gives in situ information on molecular concentration, organization and interactions in plant cell walls. We demonstrate its potential for further developments by a case study which combines ATR-FT-IR spectroscopy with a recently published DFT...

  11. Vibrational spectroscopic characterization of fluoroquinolones

    Science.gov (United States)

    Neugebauer, U.; Szeghalmi, A.; Schmitt, M.; Kiefer, W.; Popp, J.; Holzgrabe, U.

    2005-05-01

    Quinolones are important gyrase inhibitors. Even though they are used as active agents in many antibiotics, the detailed mechanism of action on a molecular level is so far not known. It is of greatest interest to shed light on this drug-target interaction to provide useful information in the fight against growing resistances and obtain new insights for the development of new powerful drugs. To reach this goal, on a first step it is essential to understand the structural characteristics of the drugs and the effects that are caused by the environment in detail. In this work we report on Raman spectroscopical investigations of a variety of gyrase inhibitors (nalidixic acid, oxolinic acid, cinoxacin, flumequine, norfloxacin, ciprofloxacin, lomefloxacin, ofloxacin, enoxacin, sarafloxacin and moxifloxacin) by means of micro-Raman spectroscopy excited with various excitation wavelengths, both in the off-resonance region (532, 633, 830 and 1064 nm) and in the resonance region (resonance Raman spectroscopy at 244, 257 and 275 nm). Furthermore DFT calculations were performed to assign the vibrational modes, as well as for an identification of intramolecular hydrogen bonding motifs. The effect of small changes in the drug environment was studied by adding successively small amounts of water until physiological low concentrations of the drugs in aqueous solution were obtained. At these low concentrations resonance Raman spectroscopy proved to be a useful and sensitive technique. Supplementary information was obtained from IR and UV/vis spectroscopy.

  12. Vibrational Relaxation of the Aqueous Proton in Acetonitrile: Ultrafast Cluster Cooling and Vibrational Predissociation.

    Science.gov (United States)

    Ottosson, N; Liu, L; Bakker, H J

    2016-07-28

    We study the ultrafast O-H stretch vibrational relaxation dynamics of protonated water clusters embedded in a matrix of deuterated acetonitrile, using polarization-resolved mid-IR femtosecond spectroscopy. The clusters are produced by mixing triflic (trifluoromethanesulfonic) acid and H2O in molar ratios of 1:1, 1:2, and 1:3, thus varying the degree of hydration of the proton. At all hydration levels the excited O-H stretch vibration of the hydrated proton shows an ultrafast vibrational relaxation with a time constant T1 cooling of the clusters reveals a long-living, underlying transient absorption change with high anisotropy. We argue that this feature stems from the vibrational predissociation of a small fraction of the proton hydration structures, directly following the ultrafast infrared excitation.

  13. Vibration of hydraulic machinery

    CERN Document Server

    Wu, Yulin; Liu, Shuhong; Dou, Hua-Shu; Qian, Zhongdong

    2013-01-01

    Vibration of Hydraulic Machinery deals with the vibration problem which has significant influence on the safety and reliable operation of hydraulic machinery. It provides new achievements and the latest developments in these areas, even in the basic areas of this subject. The present book covers the fundamentals of mechanical vibration and rotordynamics as well as their main numerical models and analysis methods for the vibration prediction. The mechanical and hydraulic excitations to the vibration are analyzed, and the pressure fluctuations induced by the unsteady turbulent flow is predicted in order to obtain the unsteady loads. This book also discusses the loads, constraint conditions and the elastic and damping characters of the mechanical system, the structure dynamic analysis, the rotor dynamic analysis and the system instability of hydraulic machines, including the illustration of monitoring system for the instability and the vibration in hydraulic units. All the problems are necessary for vibration pr...

  14. Cβ-H stretching vibration as a new probe for conformation of n-propanol in gaseous and liquid states.

    Science.gov (United States)

    Yu, Yuanqin; Wang, Yuxi; Hu, Naiyin; Lin, Ke; Zhou, Xiaoguo; Liu, Shilin

    2016-04-21

    The development of potential probes to identify molecular conformation is essential in organic and biological chemistry. In this work, we investigated a site-specific C-H stretching vibration as a conformational probe for a model compound, 1,1,3,3,3-deuterated n-propanol (CD3CH2CD2OH), using stimulated photoacoustic Raman spectroscopy in the gas phase and conventional spontaneous Raman spectroscopy in the liquid state. Along with quantum chemistry calculations, the experiment shows that the CH2 symmetric stretching mode at the β-carbon position is very sensitive to the conformational structure of n-propanol and can serve as a new probe for all five of its conformers. Compared with the O-H stretching vibration, a well-established conformational sensor for n-propanol, the Cβ-H stretching vibration presented here shows better conformational resolution in the liquid state. Furthermore, using this probe, we investigated the conformational preference of n-propanol in pure liquid and in dilute water solution. It is revealed that in pure liquid, n-propanol molecules prefer the trans-OH conformation, and in dilute water solution, this preference is enhanced, indicating that the water molecules play a role of further stabilizing the trans-OH n-propanol conformers. This leads to conformational evolution that n-propanol molecules with gauche-OH structure are transferred to the trans-OH structure upon diluting with water. These results not only provide important information on structures of n-propanol in different environments, but also demonstrate the potential of the C-H stretching vibration as a new tool for conformational analysis. This is especially important when considering that hydrocarbon chains are structural units in organic and biological molecules.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-02-14

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

  16. Thermal Vibrational Convection

    Science.gov (United States)

    Gershuni, G. Z.; Lyubimov, D. V.

    1998-08-01

    Recent increasing awareness of the ways in which vibrational effects can affect low-gravity experiments have renewed interest in the study of thermal vibrational convection across a wide range of fields. For example, in applications where vibrational effects are used to provide active control of heat and mass transfer, such as in heat exchangers, stirrers, mineral separators and crystal growth, a sound understanding of the fundamental theory is required. In Thermal Vibrational Convection, the authors present the theory of vibrational effects caused by a static gravity field, and of fluid flows which appear under vibration in fluid-filled cavities. The first part of the book discusses fluid-filled cavities where the fluid motion only appears in the presence of temperature non-uniformities, while the second considers those situations where the vibrational effects are caused by a non-uniform field. Throughout, the authors concentrate on consideration of high frequency vibrations, where averaging methods can be successfully applied in the study of the phenomena. Written by two of the pioneers in this field, Thermal Vibrational Convection will be of great interest to scientists and engineers working in the many areas that are concerned with vibration, and its effect on heat and mass transfer. These include hydrodynamics, hydro-mechanics, low gravity physics and mechanics, and geophysics. The rigorous approach adopted in presenting the theory of this fascinating and highly topical area will facilitate a greater understanding of the phenomena involved, and will lead to the development of more and better-designed experiments.

  17. Normal coordinate analysis and vibrational spectroscopy (FT-IR and FT-Raman) studies of 5-methyl-N-[4-(trifluoromethyl) phenyl]-isoxazole-4-carboxamide using density functional method.

    Science.gov (United States)

    Shahidha, R; Muthu, S; Elamurugu Porchelvi, E; Govindarajan, M

    2014-11-11

    Vibrational spectral analysis of 5-methyl-N-[4-(trifluoromethyl) phenyl]-isoxazole-4-carboxamide is (5MN4TPI4C) molecule was carried out using FT-IR and FT-Raman spectroscopic techniques. The equilibrium geometry, harmonic vibrational wavenumbers, various bonding features have been computed using density functional B3LYP method with 6-311G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFFM). Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The non-linear optical (NLO) behavior of 5MN4TPI4C has been studied by determination of the electric dipole moment (μ) and hyperpolarizability (β) by using B3LYP/6-311G(d,p) method. The molecular orbital compositions and their contributions to the chemical bonding are studied by Total density of energy states (TDOS), sum of α and β electron (αβDOS) density of states. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound at different temperatures are calculated.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-02-14

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

  19. Application of Raman Spectroscopy and Infrared Spectroscopy in the Identification of Breast Cancer.

    Science.gov (United States)

    Depciuch, Joanna; Kaznowska, Ewa; Zawlik, Izabela; Wojnarowska, Renata; Cholewa, Marian; Heraud, Philip; Cebulski, Józef

    2016-02-01

    Raman spectroscopy and infrared (IR) spectroscopy are both techniques that allow for the investigation of vibrating chemical particles. These techniques provide information not only about chemical particles through the identification of functional groups and spectral analysis of so-called "fingerprints", these methods allow for the qualitative and quantitative analyses of chemical substances in the sample. Both of these spectral techniques are frequently being used in biology and medicine in diagnosing illnesses and monitoring methods of therapy. The type of breast cancer found in woman is often a malignant tumor, causing 1.38 million new cases of breast cancer and 458 000 deaths in the world in 2013. The most important risk factors for breast cancer development are: sex, age, family history, specific benign breast conditions in the breast, ionizing radiation, and lifestyle. The main purpose of breast cancer screening tests is to establish early diagnostics and to apply proper treatment. Diagnoses of breast cancer are based on: (1) physical techniques (e.g., ultrasonography, mammography, elastography, magnetic resonance, positron emission tomography [PET]); (2) histopathological techniques; (3) biological techniques; and (4) optical techniques (e.g., photo acoustic imaging, fluorescence tomography). However, none of these techniques provides unique or especially revealing answers. The aim of our study is comparative spectroscopic measurements on patients with the following: normal non-cancerous breast tissue; breast cancer tissues before chemotherapy; breast cancer tissues after chemotherapy; and normal breast tissues received around the cancerous breast region. Spectra collected from breast cancer patients shows changes in amounts of carotenoids and fats. We also observed changes in carbohydrate and protein levels (e.g., lack of amino acids, changes in the concentration of amino acids, structural changes) in comparison with normal breast tissues. This fact

  20. Synthesis, Spectroscopy, Thermal Analysis, Magnetic Properties and Biological Activity Studies of Cu(II and Co(II Complexes with Schiff Base Dye Ligands

    Directory of Open Access Journals (Sweden)

    Saeid Amani

    2012-05-01

    Full Text Available Three azo group-containing Schiff base ligands, namely 1-{3-[(3-hydroxy-propyliminomethyl]-4-hydroxyphenylazo}-4-nitrobenzene (2a, 1-{3-[(3-hydroxypropyl-iminomethyl]-4-hydroxyphenylazo}-2-chloro-4-nitrobenzene (2b and 1-{3-[(3-hydroxy-propyliminomethyl]-4-hydroxyphenylazo}-4-chloro-3-nitrobenzene (2c were prepared. The ligands were characterized by elemental analysis, FTIR spectroscopy, UV-Vis spectroscopy, 13C- and 1H-NMR spectroscopy and thermogravimetric analysis. Next the corresponding copper(II and cobalt(II metal complexes were synthesized and characterized by the physicochemical and spectroscopic methods of elemental analysis, FTIR spectroscopy, UV-Vis spectroscopy, magnetic moment measurements, and thermogravimetric analysis (TGA and (DSC. The room temperature effective magnetic moments of complexes are 1.45, 1.56, 1.62, 2.16, 2.26 and 2.80 B.M. for complexes 3a, 3b, 3c, 4a 4b, and 4c, respectively, indicating that the complexes are paramagnetic with considerable electronic communication between the two metal centers.

  1. Synthesis, spectroscopy, thermal analysis, magnetic properties and biological activity studies of Cu(II) and Co(II) complexes with Schiff base dye ligands.

    Science.gov (United States)

    Ahmadi, Raziyeh Arab; Amani, Saeid

    2012-05-29

    Three azo group-containing Schiff base ligands, namely 1-{3-[(3-hydroxypropylimino) methyl]-4-hydroxyphenylazo}-4-nitrobenzene (2a), 1-{3-[(3-hydroxypropylimino) methyl]-4-hydroxyphenylazo}-2-chloro-4-nitrobenzene (2b) and 1-{3-[(3-hydroxypropylimino) methyl]-4-hydroxyphenylazo}-4-chloro-3-nitrobenzene (2c) were prepared. The ligands were characterized by elemental analysis, FTIR spectroscopy, UV-Vis spectroscopy, ¹³C- and ¹H-NMR spectroscopy and thermogravimetric analysis. Next the corresponding copper(II) and cobalt(II) metal complexes were synthesized and characterized by the physicochemical and spectroscopic methods of elemental analysis, FTIR spectroscopy, UV-Vis spectroscopy, magnetic moment measurements, and thermogravimetric analysis (TGA) and (DSC). The room temperature effective magnetic moments of complexes are 1.45, 1.56, 1.62, 2.16, 2.26 and 2.80 B.M. for complexes 3a, 3b, 3c, 4a 4b, and 4c, respectively, indicating that the complexes are paramagnetic with considerable electronic communication between the two metal centers.

  2. Global nonresonant vibrational-photoelectron coupling in molecular photoionization

    Science.gov (United States)

    Poliakoff, Erwin; Das, Aloke; Hardy, David; Bozek, John; Aguilar, Alex; Lucchese, Robert

    2009-05-01

    Using photoelectron spectroscopy and Schwinger variational scattering theory, we have investigated the coupling between vibrational motion and the exiting photoelectron over extended ranges of photoelectron kinetic energy. Photoelectron spectroscopy is performed with vibrational resolution over uncommonly large ranges of energy (ca. 200 eV). We find clear and significant changes in vibrational branching ratios as a function of photon energy, in direct contradiction to predictions of the Franck-Condon principle. While it is well known that resonances lead to coupling between electronic and vibrational degrees of freedom, nonresonant mechanisms that result in such coupling are not expected or well-documented. Photoelectron spectra are presented for several electronic states of N2^+, CO^+, and NO^+, and we find that valence isoelectronic channels behave very differently, which is also surprising. Theoretical results indicate that Cooper minima are the underlying cause of these effects, and we are currently working to understand the reasons for the sensitivity of the Cooper minima on bond length.

  3. Vibrating fuel grapple. [LMFBR

    Science.gov (United States)

    Chertock, A.J.; Fox, J.N.; Weissinger, R.B.

    A reactor refueling method is described which utilizes a vibrating fuel grapple for removing spent fuel assemblies from a reactor core. It incorporates a pneumatic vibrator in the grapple head which allows additional withdrawal capability without exceeding the allowable axial force limit. The only moving part in the vibrator is a steel ball, pneumatically driven by a gas, such as argon, around a track, with centrifugal force created by the ball being transmitted through the grapple to the assembly handling socket.

  4. Vibrational optical activity principles and applications

    CERN Document Server

    Nafie, Laurence A

    2011-01-01

    This unique book stands as the only comprehensive introduction to vibrational optical activity (VOA) and is the first single book that serves as a complete reference for this relatively new, but increasingly important area of molecular spectroscopy. Key features:A single-source reference on this topic that introduces, describes the background and foundation of this area of spectroscopy.Serves as a guide on how to use it to carry out applications with relevant problem solving.Depth and breadth of the subject is presented in a logical, complete and progressive fashion. A

  5. Vibrational properties of uracil

    Institute of Scientific and Technical Information of China (English)

    WANG Zhiping; ZHANG Fengshou; ZENG Xianghua; ZHOU Hongyu; GU Bin; CHENG Wei

    2006-01-01

    A semiempirical molecular dynamics model is developed to study the vibrational frequencies of uracil at very low kinetic temperature by using the Fourier transform of velocity autocorrelation function of trajectories of molecular dynamics simulations. The finite difference harmonic method is used to assign the vibrational frequency of each mode. The calculated frequencies are found to be in good agreement with experimental measurements. Moreover, we make up for the lost vibrational modes in experiments self-consistently. A total of 30 vibrational modes and their corresponding frequencies are reported.

  6. Hydrogen Bonds and Vibrations of Water on (110) Rutile

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Nitin [ORNL; Neogi, Sanghamitra [Pennsylvania State University; Kent, Paul R [ORNL; Bandura, Andrei V. [St. Petersburg State University, St. Petersburg, Russia; Wesolowski, David J [ORNL; Cole, David R [ORNL; Sofo, Jorge O. [Pennsylvania State University

    2009-01-01

    We study the relation between hydrogen bonding and the vibrational frequency spectra of water on the (110) surface of rutile (α-TiO2) with three structural layers of adsorbed water. Using ab-initio molecular dynamics simulations at 280, 300 and 320K, we find strong, crystallographically-controlled adsorption sites, in general agreement with synchrotron X-ray and classical MD simulations. We demonstrate that these sites are produced by strong hydrogen bonds formed between the surface oxygen atoms and sorbed water molecules. The strength of these bonds is manifested by substantial broadening of the stretching mode vibrational band. The overall vibrational spectrum obtained from our simulations is in good agreement with inelastic neutron scattering experiments. We correlate the vibrational spectrum with different bonds at the surface in order to transform these vibrational measurements into a spectroscopy of surface interactions.

  7. Raman spectroscopy as a tool for investigating lipid protein interactions

    DEFF Research Database (Denmark)

    Petersen, Frederic Nicolas Rønne; Helix Nielsen, Claus

    2009-01-01

    Raman spectroscopy is a very well-established technique for noninvasive probing of chemical compounds. The fad that Raman scattering is an inherently weak effect has prompted many new developments in sample signal enhancement and techniques (such as surface-enhancement Raman spectroscopy [SERS]) ...... to study using noninvasive vibrational spectroscopy....

  8. Ultrafast vibrational energy relaxation of the water bridge.

    Science.gov (United States)

    Piatkowski, Lukasz; Wexler, Adam D; Fuchs, Elmar C; Schoenmaker, Hinco; Bakker, Huib J

    2012-05-14

    We report the energy relaxation of the OH stretch vibration of HDO molecules contained in an HDO:D(2)O water bridge using femtosecond mid-infrared pump-probe spectroscopy. We found that the vibrational lifetime is shorter (~630 ± 50 fs) than for HDO molecules in bulk HDO:D(2)O (~740 ± 40 fs). In contrast, the thermalization dynamics following the vibrational relaxation are much slower (~1.5 ± 0.4 ps) than in bulk HDO:D(2)O (~250 ± 90 fs). These differences in energy relaxation dynamics strongly indicate that the water bridge and bulk water differ on a molecular scale.

  9. Vibration-rotation-tunneling dynamics in small water clusters

    Energy Technology Data Exchange (ETDEWEB)

    Pugliano, N.

    1992-11-01

    The goal of this work is to characterize the intermolecular vibrations of small water clusters. Using tunable far infrared laser absorption spectroscopy, large amplitude vibration-rotation-tunneling (VRT) dynamics in vibrationally excited states of the water dimer and the water trimer are investigated. This study begins with the measurement of 12 VRT subbands, consisting of approximately 230 transitions, which are assigned to an 82.6 cm{sup {minus}1} intermolecular vibration of the water dimer-d{sub 4}. Each of the VRT subbands originate from K{sub a}{double_prime}=0 and terminate in either K{sub a}{prime}=0 or 1. These data provide a complete characterization of the tunneling dynamics in the vibrationally excited state as well as definitive symmetry labels for all VRT energy levels. Furthermore, an accurate value for the A{prime} rotational constant is found to agree well with its corresponding ground state value. All other excited state rotational constants are fitted, and discussed in terms of the corresponding ground state constants. In this vibration, the quantum tunneling motions are determined to exhibit large dependencies with both the K{sub a}{prime} quantum number and the vibrational coordinate, as is evidenced by the measured tunneling splittings. The generalized internal-axis-method treatment which has been developed to model the tunneling dynamics, is considered for the qualitative description of each tunneling pathway, however, the variation of tunneling splittings with vibrational excitation indicate that the high barrier approximation does not appear to be applicable for this vibrational coordinate. The data are consistent with a motion possessing a{prime} symmetry, and the vibration is assigned as the {nu}{sub 12} acceptor bending coordinate. This assignment is in agreement with the vibrational symmetry, the resultsof high level ab initio calculations, and preliminary data assigned to the analogous vibration in the D{sub 2}O-DOH isotopomer.

  10. Vibration-rotation-tunneling dynamics in small water clusters

    Energy Technology Data Exchange (ETDEWEB)

    Pugliano, N.

    1992-11-01

    The goal of this work is to characterize the intermolecular vibrations of small water clusters. Using tunable far infrared laser absorption spectroscopy, large amplitude vibration-rotation-tunneling (VRT) dynamics in vibrationally excited states of the water dimer and the water trimer are investigated. This study begins with the measurement of 12 VRT subbands, consisting of approximately 230 transitions, which are assigned to an 82.6 cm[sup [minus]1] intermolecular vibration of the water dimer-d[sub 4]. Each of the VRT subbands originate from K[sub a][double prime]=0 and terminate in either K[sub a][prime]=0 or 1. These data provide a complete characterization of the tunneling dynamics in the vibrationally excited state as well as definitive symmetry labels for all VRT energy levels. Furthermore, an accurate value for the A[prime] rotational constant is found to agree well with its corresponding ground state value. All other excited state rotational constants are fitted, and discussed in terms of the corresponding ground state constants. In this vibration, the quantum tunneling motions are determined to exhibit large dependencies with both the K[sub a][prime] quantum number and the vibrational coordinate, as is evidenced by the measured tunneling splittings. The generalized internal-axis-method treatment which has been developed to model the tunneling dynamics, is considered for the qualitative description of each tunneling pathway, however, the variation of tunneling splittings with vibrational excitation indicate that the high barrier approximation does not appear to be applicable for this vibrational coordinate. The data are consistent with a motion possessing a[prime] symmetry, and the vibration is assigned as the [nu][sub 12] acceptor bending coordinate. This assignment is in agreement with the vibrational symmetry, the resultsof high level ab initio calculations, and preliminary data assigned to the analogous vibration in the D[sub 2]O-DOH isotopomer.

  11. Vibrationally Resolved Electron Transfer Rates in Solution

    Science.gov (United States)

    Spears, Kenneth G.

    2002-03-01

    We have re-examined our earlier report of electron transfer in the [Co(Cp)_2|V(CO)_6] radical-pair using ultrafast infrared transient absorption spectroscopy in room temperature solutions. The radical-pair is created from the [Co(Cp)_2^+|V(CO)_6^-] ion-pair by ultrafast visible charge-transfer excitation. Transient absorption experiments with ps time constants. A small ET component with a 75 ps time constant is due to some separation and reformation of the radical-pairs. Transient absorption experiments monitoring the recovery of the ion-pair state shows that both fast components are due to ET rather than some other vibrational relaxation (VR) process in the radical state. We analyze the visible charge-transfer band and assign the two fast ET decay times to two ion-pair contact geometries with absorption origins different by about 1250 ± 350 cm-1. For excitation at 800 and 700 nm the 700 fs ET lifetime depends on the vibrational quantum state of the nontotally symmetric CO stretch in the V(CO)6 radical, where the lifetime decreases by 10% for the first vibrational quantum and 45% for the second quantum. There is no quantum effect for the second ion-pair geometry with a 5 ps ET lifetime. Standard ET rate models cannot explain the rate dependence upon vibrational quantum state for a nontotally symmetric vibration, and it may arise from a breakdown of the Condon approximation. We also report rates for IVR of CO stretching modes and for VR of low frequency vibrations. At excitation wavelengths of 620 and 555 nm there is sufficient internal vibrational energy in low-frequency vibrations to cause geometric inter-conversion between energetically similar Jahn-Teller geometries in the V(CO)6 radical. This process creates a 200 fs rise time for the V(CO)6 radical species to assume a stable geometry, which requires VR of low frequency vibrations to the solvent. These results demonstrate that earlier ET measurements from our group on the same molecule had insufficient time

  12. Normal coordinate analysis and vibrational spectroscopy (FT-IR and FT-Raman) studies of (2S)-2-amino-3-(3,4-dihydroxyphenyl)-2-methylpropanoic acid using ab initio HF and DFT method.

    Science.gov (United States)

    Prabakaran, A; Muthu, S

    2012-12-01

    The FT-IR and FT-Raman spectra of (2S)-2-amino-3-(3,4-dihydroxyphenyl)-2-methylpropanoic acid (2ADMA) were recorded in the region 4000-400 cm(-1) and 4000-100 cm(-1), respectively. The geometrical structure, harmonic vibrational frequency, infrared intensity, Raman activities and bonding features of this compound was carried out by ab initio HF and DFT methods with 6-31G (d,p) basis set. The complete vibrational frequency assignments were made by normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMF). The electric dipole moment (μ) and the first-order hyperpolarizability (β(0)) values have been the computed quantum mechanically. The calculated HOMO and LUMO energies show that, the charge transfer occurs within the molecule. The charge delocalizations of these molecules have been analyzed using NBO analysis. The solvent effects have been calculated using TD-DFT in combination with the polarized continuum model (PCM), and the results are in good agreement with experimental measurements. The other molecular properties like Mulliken population analysis, electrostatic potential (ESP) and thermodynamic properties of the title compound at the different temperatures have been calculated. Finally, the calculation results were applied to simulate infrared and Raman spectra of the title compound which shows good agreement with observed spectra.

  13. Mechanical vibration and shock analysis, sinusoidal vibration

    CERN Document Server

    Lalanne, Christian

    2014-01-01

    Everything engineers need to know about mechanical vibration and shock...in one authoritative reference work! This fully updated and revised 3rd edition addresses the entire field of mechanical vibration and shock as one of the most important types of load and stress applied to structures, machines and components in the real world. Examples include everything from the regular and predictable loads applied to turbines, motors or helicopters by the spinning of their constituent parts to the ability of buildings to withstand damage from wind loads or explosions, and the need for cars to m

  14. [Vibration on agricultural tractors].

    Science.gov (United States)

    Peretti, Alessandro; Delvecchio, Simone; Bonomini, Francesco; di Bisceglie, Anita Pasqua; Colosio, Claudio

    2013-01-01

    In the article, details related to the diffusion of agricultural tractors in Italy are given and considerations about the effects of vibration on operators, the sources of vibration and suggestions to reduce them are presented. The acceleration values observed in Italy amongst 244 tractors and levels of worker exposure are shown by means of histograms. The relevant data variability is discussed.

  15. Picking up good vibrations

    NARCIS (Netherlands)

    Eijk, A.

    2010-01-01

    The methods that need to be employed to develop the better vibration guidelines to assess the integrity of a reciprocating compressor system are discussed. An R&D project of the European Forum of Reciprocating Compressors (EFRC) has been initiated to develop guidelines for vibrations in reciprocatin

  16. Vibrational Schroedinger Cats

    Science.gov (United States)

    Kis, Z.; Janszky, J.; Vinogradov, An. V.; Kobayashi, T.

    1996-01-01

    The optical Schroedinger cat states are simple realizations of quantum states having nonclassical features. It is shown that vibrational analogues of such states can be realized in an experiment of double pulse excitation of vibrionic transitions. To track the evolution of the vibrational wave packet we derive a non-unitary time evolution operator so that calculations are made in a quasi Heisenberg picture.

  17. Vibration Theory, Vol. 3

    DEFF Research Database (Denmark)

    Nielsen, Søren R. K.

    The present textbook has been written based on previous lecture notes for a course on stochastic vibration theory that is being given on the 9th semester at Aalborg University for M. Sc. students in structural engineering. The present 4th edition of this textbook on linear stochastic vibration...

  18. Vibration Theory, Vol. 3

    DEFF Research Database (Denmark)

    Nielsen, Søren R. K.

    The present textbook has been written based on previous lecture notes for a course on stochastic vibration theory that is being given on the 9th semester at Aalborg University for M. Sc. students in structural engineering. The present 2nd edition of this textbook on linear stochastic vibration th...

  19. Raman Spectroscopy for Clinical Oncology

    Directory of Open Access Journals (Sweden)

    Michael B. Fenn

    2011-01-01

    Full Text Available Cancer is one of the leading causes of death throughout the world. Advancements in early and improved diagnosis could help prevent a significant number of these deaths. Raman spectroscopy is a vibrational spectroscopic technique which has received considerable attention recently with regards to applications in clinical oncology. Raman spectroscopy has the potential not only to improve diagnosis of cancer but also to advance the treatment of cancer. A number of studies have investigated Raman spectroscopy for its potential to improve diagnosis and treatment of a wide variety of cancers. In this paper the most recent advances in dispersive Raman spectroscopy, which have demonstrated promising leads to real world application for clinical oncology are reviewed. The application of Raman spectroscopy to breast, brain, skin, cervical, gastrointestinal, oral, and lung cancers is reviewed as well as a special focus on the data analysis techniques, which have been employed in the studies.

  20. 基于原子力显微镜的单分子力谱在生物研究中的应用%Application of Atomic Force Microscopy Based Single Molecule Force Spectroscopy in Biological Research

    Institute of Scientific and Technical Information of China (English)

    黎虹颖; 古宁宇; 唐纪琳

    2012-01-01

    Atomic force microscopy(AFM) is widely used in biological research,AFM based single molecule force spectroscopy can be applied to study the intramolecular and intermolecular interactions of biomolecules at the single-molecule and single-cell levels.In this paper,we present the latest progress of AFM based single molecule force spectroscopy in biomolecular interaction,protein unfolding,cell surface biomolecules,cell mechanical properties and single molecule force spectroscopy imaging.%原子力显微镜被广泛应用于生物研究领域,基于原子力显微镜的单分子力谱可以在单分子、单细胞水平上研究生物分子内和分子间的相互作用.本文介绍了原子力显微镜单分子力谱在生物分子间相互作用、蛋白质去折叠、细胞表面生物分子、细胞力学性质和基于单分子力谱成像等研究中的最新进展.

  1. Vibration control in accelerators

    Energy Technology Data Exchange (ETDEWEB)

    Montag, C.

    2011-01-01

    In the vast majority of accelerator applications, ground vibration amplitudes are well below tolerable magnet jitter amplitudes. In these cases, it is necessary and sufficient to design a rigid magnet support structure that does not amplify ground vibration. Since accelerator beam lines are typically installed at an elevation of 1-2m above ground level, special care has to be taken in order to avoid designing a support structure that acts like an inverted pendulum with a low resonance frequency, resulting in untolerable lateral vibration amplitudes of the accelerator components when excited by either ambient ground motion or vibration sources within the accelerator itself, such as cooling water pumps or helium flow in superconducting magnets. In cases where ground motion amplitudes already exceed the required jiter tolerances, for instance in future linear colliders, passive vibration damping or active stabilization may be considered.

  2. Cars Spectroscopy of Propellant Flames

    Science.gov (United States)

    1983-11-01

    Harris, K. Aron, and J. Fendell "N2 and 00 Vibrational CARS and H2 Rotational CARS Spectroscopy of CHI/N20 Flames," Proceedings of the Nineteenth...JANNAF Combustion Meeting, CIIA Publication No. 366, 1982, p 123. 21. K. Aron, L. E. Harris, and J. Fendell , "N and CO Vibrational CARS and H2 Rotational...9 6 5 . p 3 8 4 . . . . . 23. J. Fendell , L. E, Harris, and K. Aron, "Theoretical Calculation of 11 CARS S-Branches for Propellant Flames

  3. Perspective: Electrospray photoelectron spectroscopy: From multiply-charged anions to ultracold anions

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lai-Sheng, E-mail: Lai-Sheng-Wang@brown.edu [Department of Chemistry, Brown University, Providence, Rhode Island 02912 (United States)

    2015-07-28

    Electrospray ionization (ESI) has become an essential tool in chemical physics and physical chemistry for the production of novel molecular ions from solution samples for a variety of spectroscopic experiments. ESI was used to produce free multiply-charged anions (MCAs) for photoelectron spectroscopy (PES) in the late 1990 s, allowing many interesting properties of this class of exotic species to be investigated. Free MCAs are characterized by strong intramolecular Coulomb repulsions, which create a repulsive Coulomb barrier (RCB) for electron emission. The RCB endows many fascinating properties to MCAs, giving rise to meta-stable anions with negative electron binding energies. Recent development in the PES of MCAs includes photoelectron imaging to examine the influence of the RCB on the electron emission dynamics, pump-probe experiments to examine electron tunneling through the RCB, and isomer-specific experiments by coupling PES with ion mobility for biological MCAs. The development of a cryogenically cooled Paul trap has led to much better resolved PE spectra for MCAs by creating vibrationally cold anions from the room temperature ESI source. Recent advances in coupling the cryogenic Paul trap with PE imaging have allowed high-resolution PE spectra to be obtained for singly charged anions produced by ESI. In particular, the observation of dipole-bound excited states has made it possible to conduct vibrational autodetachment spectroscopy and resonant PES, which yield much richer vibrational spectroscopic information for dipolar free radicals than traditional PES.

  4. Studies of the electronic structure and biological activity of chosen 1,4-benzodiazepines by {sup 35}Cl NQR spectroscopy and DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Bronisz, K. [Department of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan (Poland); Ostafin, M. [Department of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan (Poland)], E-mail: ostifnqr@amu.edu.pl; Poleshchuk, O. Kh. [Department of Chemistry, Tomsk Pedagogical University, Komsomolskii 75, 634041 Tomsk (Russian Federation); Mielcarek, J. [Faculty of Pharmacy, University of Medical Sciences, Grunwaldzka 6, 60-780 Poznan (Poland); Nogaj, B. [Department of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan (Poland)

    2006-11-08

    Selected derivatives of 1,4-benzodiazepine: lorazepam, lormetazepam, oxazepam and temazepam, used as active substances in anxiolytic drugs, have been studied by {sup 35}Cl NQR method in order to find the correlation between electronic structure and biological activity. The {sup 35}Cl NQR resonance frequencies ({nu} {sub Q}) measured at 77 K have been correlated with the following parameters characterising their biological activity: biological half-life period (t {sub 0.5}), affinity to benzodiazepine receptor (IC{sub 50}) and mean dose equivalent. The results of experimental study of some benzodiazepine derivatives by nuclear quadrupole resonance of {sup 35}Cl nuclei are compared with theoretical results based on DFT calculations which were carried out by means of Gaussian'98 W software.

  5. Studies of the electronic structure and biological activity of chosen 1,4-benzodiazepines by 35Cl NQR spectroscopy and DFT calculations

    Science.gov (United States)

    Bronisz, K.; Ostafin, M.; Poleshchuk, O. Kh.; Mielcarek, J.; Nogaj, B.

    2006-11-01

    Selected derivatives of 1,4-benzodiazepine: lorazepam, lormetazepam, oxazepam and temazepam, used as active substances in anxiolytic drugs, have been studied by 35Cl NQR method in order to find the correlation between electronic structure and biological activity. The 35Cl NQR resonance frequencies ( νQ) measured at 77 K have been correlated with the following parameters characterising their biological activity: biological half-life period ( t0.5), affinity to benzodiazepine receptor (IC 50) and mean dose equivalent. The results of experimental study of some benzodiazepine derivatives by nuclear quadrupole resonance of 35Cl nuclei are compared with theoretical results based on DFT calculations which were carried out by means of Gaussian'98 W software.

  6. Low temperature vibrational spectroscopy. II. Evidence for order–disorder phase transitions due to weak C–H···Cl hydrogen bonding in tetramethylammonium hexachloroplatinate (IV), -tellurate (IV), and -stannate (IV) and the related perdeuterated compounds

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    1978-01-01

    torsions and other noncubic features play a role, especially in spectra at low temperatures. Possible site symmetries of the [PtCl6]2− ion, which cannot have strictly Oh symmetry in either phase, have been deduced. The spectra of a mixed Pt : Te compound showed that the hexachlorometallate anions vibrate...... approximately independent of each other. The results have been compared with von der Ohe's recent extensive low temperature Raman study on protonated compounds with M=U, Sn, and Zr, and his conclusions are discussed. It is shown that crystals of this kind can be characterized by methyl–chlorine interaction...... and it is suggested that the phase transitions are caused by an ordering of rotationally disordered methyl groups via the formation of weak C–H···Cl hydrogen bonds at low temperatures. The transition temperatures and hence the interactions are shown to depend on both the kind of hydrogen isotope and metal present...

  7. The vibrational spectrum of the atoms in the grain boundaries of nanocrystalline Pd

    Energy Technology Data Exchange (ETDEWEB)

    Stuhr, U. [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Wipf, H.; Hahn, H. [Technische Hochschule Darmstadt (Germany); Natter, H.; Hemperlmann, R. [Universitaet des Saarlandes, Saarbruecken (Germany); Andersen, K. [Institut Max von Laue - Paul Langevin (ILL), 38 - Grenoble (France)

    1997-09-01

    The vibrational excitations of the atoms in nanocrystalline Pd was investigated by neutron-time-of-flight spectroscopy. Hydrogen was used as a probe for the vibrations in the grain boundaries. The separation between the H and Pd vibrations was done by spin analysis. The results show that in the grain boundary the density of states of low energy excitations ({<=}5 meV) is drastically increased. (author) 3 figs., 3 refs.

  8. [The characteristics of the development of gallbladder and biliary tract pathology under the influence of vibration].

    Science.gov (United States)

    Preobrazhenskiĭ, V N; Merkulov, V M; Vasil'ev, A Iu; Ermakova, T I; Borisov, B P

    1995-01-01

    The examination of 86 helicopter pilots has shown that their exposure to vibration leads to biliary and gallbladder damage which aggravates with longer service. As indicated by spectroscopy and gas-liquid chromatography, vibration affects colloid-osmotic properties of bile: molecules grow in size, bile acids retention becomes longer.

  9. Two-dimensional spectroscopy of molecular excitons in a model dimer system

    Science.gov (United States)

    Halpin, Alexei

    The physics of molecular excitons has been the subject of many recent studies using electronic two-dimensional photon-echo spectroscopy (2DPE), particularly in the context of light harvesting in photosynthesis. Since the spectra for multichromophoric aggregates are congested, particularly so at room temperature, we present a study of a model dimer comprised of identical chromophores with a well defined electronic coupling strength, to provide clear signatures for coherences between vibronic excitons in 2D spectra. We begin by describing the design of a broadband passively phase-stabilized interferometer for collection of 2D spectra, which also allows for the investigation of state preparation in 2D spectroscopy by using shaped excitation pulses. In experiments on the model dimer we observe strong oscillating off-diagonal features in the 2D spectra which are present only before the onset of dephasing, which occurs in less than 100 fs due to strong system-bath coupling. This is in contrast with the parent dye, where low amplitude oscillations associated with Raman active vibrations persist for several ps following excitation. The results of this comparative study indicate that the signals observed earlier in photosynthetic proteins likely reflect vibrational motion in isolated pigments, and not delocalized quantum coherence. While long-lived vibrational coherences are of questionable biological relevance at face value, we conclude with a discussion on initial findings using coherently controlled 2D spectroscopy, where we observe long-lived signatures associated to vibronic coherences at room temperature. These results point to new directions of study using multidimensional spectroscopy to unravel the role of coherence in excitation energy transfer in molecular aggregates in an experimentally direct fashion.

  10. Ultrafast infrared near-field molecular nano-spectroscopy

    Directory of Open Access Journals (Sweden)

    Rang Matthias

    2013-03-01

    Full Text Available We demonstrate molecular radiative infrared vibrational free-induction decay on the nano-scale and its control via near-field coupling between the transient molecular polarization and optical antenna properties of the metallic scanning near-field probe tip. This allows for pushing the sensitivity of infrared vibrational spectroscopy into the single molecule regime.

  11. Electronic Spectroscopy & Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Mark Maroncelli, Nancy Ryan Gray

    2010-06-08

    The Gordon Research Conference (GRC) on Electronic Spectroscopy and Dynamics was held at Colby College, Waterville, NH from 07/19/2009 thru 07/24/2009. The Conference was well-attended with participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. The GRC on Electronic Spectroscopy & Dynamics showcases some of the most recent experimental and theoretical developments in electronic spectroscopy that probes the structure and dynamics of isolated molecules, molecules embedded in clusters and condensed phases, and bulk materials. Electronic spectroscopy is an important tool in many fields of research, and this GRC brings together experts having diverse backgrounds in physics, chemistry, biophysics, and materials science, making the meeting an excellent opportunity for the interdisciplinary exchange of ideas and techniques. Topics covered in this GRC include high-resolution spectroscopy, biological molecules in the gas phase, electronic structure theory for excited states, multi-chromophore and single-molecule spectroscopies, and excited state dynamics in chemical and biological systems.

  12. Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers.

    Science.gov (United States)

    Kern, Jan; Yachandra, Vittal K; Yano, Junko

    2015-10-01

    Although the structure of enzymes and the chemistry at the catalytic sites have been studied intensively, an understanding of the atomic-scale chemistry requires a new approach beyond steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure of metallo-enzymes at ambient conditions, while overcoming the severe X-ray-induced changes to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by the intense and ultra-short femtosecond (fs) X-ray pulses from an X-ray free electron laser (XFEL) by acquiring a signal before the sample is destroyed. This review describes the recent and pioneering uses of XFELs to study the protein structure and dynamics of metallo-enzymes using crystallography and scattering, as well as the chemical structure and dynamics of the catalytic complexes (charge, spin, and covalency) using spectroscopy during the reaction to understand the electron-transfer processes and elucidate the mechanism.

  13. The structure and function of quinones in biological solar energy transduction: a cyclic voltammetry, EPR, and hyperfine sub-level correlation (HYSCORE) spectroscopy study of model naphthoquinones.

    Science.gov (United States)

    Coates, Christopher S; Ziegler, Jessica; Manz, Katherine; Good, Jacob; Kang, Bernard; Milikisiyants, Sergey; Chatterjee, Ruchira; Hao, Sijie; Golbeck, John H; Lakshmi, K V

    2013-06-20

    Quinones function as electron transport cofactors in photosynthesis and cellular respiration. The versatility and functional diversity of quinones is primarily due to the diverse midpoint potentials that are tuned by the substituent effects and interactions with surrounding amino acid residues in the binding site in the protein. In the present study, a library of substituted 1,4-naphthoquinones are analyzed by cyclic voltammetry in both protic and aprotic solvents to determine effects of substituent groups and hydrogen bonds on the midpoint potential. We use continuous-wave electron paramagnetic resonance (EPR) spectroscopy to determine the influence of substituent groups on the electronic properties of the 1,4-naphthoquinone models in an aprotic solvent. The results establish a correlation between the presence of substituent group(s) and the modification of electronic properties and a corresponding shift in the midpoint potential of the naphthoquinone models. Further, we use pulsed EPR spectroscopy to determine the effect of substituent groups on the strength and planarity of the hydrogen bonds of naphthoquinone models in a protic solvent. This study provides support for the tuning of the electronic properties of quinone cofactors by the influence of substituent groups and hydrogen bonding interactions.

  14. Vibration enhanced quantum transport

    CERN Document Server

    Semião, F L; Milburn, G J

    2009-01-01

    In this paper, we study the role of a collective vibrational motion in the phenomenon of electronic energy transfer (EET) between chromophores with different electronic transition frequencies. Previous experimental work on EET in conjugated polymer samples has suggested that the common structural framework of the macromolecule introduce correlations in the energy gap fluctuations which cause coherent EET. We present a simple model describing the coupling between the chromophores and a common vibrational mode, and find that vibration can indeed lead to an enhancement in the transport of excitations across the quantum network. Furthermore, in our model phase information is partially retained in the transfer process from a donor to an acceptor, as experimentally demonstrated in the conjugated polymer system. Consequently, this mechanism of vibration enhanced quantum transport might find applications in quantum information transfer of qubit states or entanglement.

  15. NIF Ambient Vibration Measurements

    Energy Technology Data Exchange (ETDEWEB)

    Noble, C.R.; Hoehler, M.S., S.C. Sommer

    1999-11-29

    LLNL has an ongoing research and development project that includes developing data acquisition systems with remote wireless communication for monitoring the vibrations of large civil engineering structures. In order to establish the capability of performing remote sensing over an extended period of time, the researchers needed to apply this technology to a real structure. The construction of the National Ignition Facility provided an opportunity to test the data acquisition system on a large structure to monitor whether the facility is remaining within the strict ambient vibration guidelines. This document will briefly discuss the NIF ambient vibration requirements and summarize the vibration measurements performed during the Spring and Summer of 1999. In addition, a brief description of the sensors and the data acquisition systems will be provided in Appendix B.

  16. Vibrating wire alignment technique

    CERN Document Server

    Xiao-Long, Wang; lei, Wu; Chun-Hua, Li

    2013-01-01

    Vibrating wire alignment technique is a kind of method which through measuring the spatial distribution of magnetic field to do the alignment and it can achieve very high alignment accuracy. Vibrating wire alignment technique can be applied for magnet fiducialization and accelerator straight section components alignment, it is a necessary supplement for conventional alignment method. This article will systematically expound the international research achievements of vibrating wire alignment technique, including vibrating wire model analysis, system frequency calculation, wire sag calculation and the relation between wire amplitude and magnetic induction intensity. On the basis of model analysis this article will introduce the alignment method which based on magnetic field measurement and the alignment method which based on amplitude and phase measurement. Finally, some basic questions will be discussed and the solutions will be given.

  17. Multifrequency EPR Spectroscopy: A Toolkit for the Characterization of Mono- and Di-nuclear Metal Ion Centers in Complex Biological Systems

    Science.gov (United States)

    Hanson, Graeme R.

    Metalloenzymes are ubiquitous in nature containing complex metal ion cofactors intimately involved in the enzymes' biological function. The application of multifrequency continuous wave and orientation selective pulsed EPR in conjunction with computer simulation and density functional theory calculations has proven to be a powerful toolkit for the geometric and electronic structural characterization of these metal ion cofactors in the resting enzyme, enzyme-substrate and -product complexes, which in turn provides a detailed understanding of the enzymes' catalytic mechanism. In this chapter, a brief description of the multifrequency EPR toolkit used to structurally (geometric and electronic) characterize metal ion binding sites in complex biological systems and its application in the structural characterization of (i) molybdenum containing enzymes and model complexes, (ii) mono- and di-nuclear copper(II) cyclic peptide complexes (marine and synthetic analogues) and (iii) dinuclear metal ion centers in purple acid phosphatases will be presented.

  18. Vibrational Spectra and Quantum Calculations of Ethylbenzene

    Institute of Scientific and Technical Information of China (English)

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

    2012-01-01

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

  19. Characterization of the primary hydration shell of the hydroxide ion with H2 tagging vibrational spectroscopy of the OH- ṡ (H2O)n=2,3 and OD- ṡ (D2O)n=2,3 clusters

    Science.gov (United States)

    Gorlova, Olga; DePalma, Joseph W.; Wolke, Conrad T.; Brathwaite, Antonio; Odbadrakh, Tuguldur T.; Jordan, Kenneth D.; McCoy, Anne B.; Johnson, Mark A.

    2016-10-01

    We report the isotope-dependent vibrational predissociation spectra of the H2-tagged OH- ṡ (H2O)n=2,3 clusters, from which we determine the strongly coordination-dependent energies of the fundamentals due to the OH groups bound to the ion and the intramolecular bending modes of the water molecules. The HOH bending fundamental is completely missing in the delocalized OH- ṡ (H2O) binary complex but is recovered upon adding the second water molecule, thereby establishing that the dihydrate behaves as a hydroxide ion solvated by two essentially intact water molecules. The energies of the observed OH stretches are in good agreement with the values predicted by Takahashi and co-workers [Phys. Chem. Chem. Phys. 17, 25505 (2015); 15, 114 (2013)] with a theoretical model that treats the strong anharmonicities at play in this system with explicit coupling between the bound OH groups and the O-O stretching modes on an extended potential energy surface. We highlight a surprising similarity between the spectral signatures of OH- ṡ (H2O)3 and the excess proton analogue, H3O+ ṡ (H2O)3, both of which correspond to completed hydration shells around the proton defect. We discuss the origin of the extreme solvatochromicity displayed by both OH- and H+ in the context of the anomalously large "proton polarizabilities" of the H5O2+ and H3O2- binary complexes.

  20. Syntheses, Vibrational Spectroscopy, and Crystal Structure Determination from X-Ray Powder Diffraction Data of Alkaline Earth Dicyanamides M[N(CN) 2] 2 with M=Mg, Ca, Sr, and Ba

    Science.gov (United States)

    Jürgens, Barbara; Irran, Elisabeth; Schnick, Wolfgang

    2001-03-01

    The alkaline earth dicyanamides Mg[N(CN)2]2, Ca[N(CN)2]2, Sr[N(CN)2]2, and Ba[N(CN)2]2 were synthesized by ion exchange using Na[N(CN)2] and the respective nitrates or bromides as starting materials. The crystal structures were determined from X-ray powder diffractometry: Mg[N(CN)2]2, Pnnm, Z=2, a=617.14(3), b=716.97(3), and c=740.35(5) pm; Ca[N(CN)2]2 and Sr[N(CN)2]2, C2/c, Z=4; Ca[N(CN)2]2, a=1244.55(3), b=607.97(1), and c=789.81(1) pm, β=98.864(2)°; Sr[N(CN)2]2, a=1279.63(2), b=624.756(8), and c=817.56(1) pm, β=99.787(1)°; Ba[N(CN)2]2, Pnma, Z=4, a=1368.68(7), b=429.07(7), and c=1226.26(2) pm. The dicyanamides consist of the respective alkaline earth cations and bent planar [N(CN)2]- ions. The structural features were correlated with vibrational spectroscopic data. The thermal behavior was studied by thermoanalytical experiments.