New approach for determination of the influence of long-range order and selected ring oscillations on IR spectra in zeolites.

PubMed

Mikuła, Andrzej; Król, Magdalena; Mozgawa, Włodzimierz; Koleżyński, Andrzej

2018-04-15

Vibrational spectroscopy can be considered as one of the most important methods used for structural characterization of various porous aluminosilicate materials, including zeolites. On the other hand, vibrational spectra of zeolites are still difficult to interpret, particularly in the pseudolattice region, where bands related to ring oscillations can be observed. Using combination of theoretical and computational approach, a detailed analysis of these regions of spectra is possible; such analysis should be, however, carried out employing models with different level of complexity and simultaneously the same theory level. In this work, an attempt was made to identify ring oscillations in vibrational spectra of selected zeolite structures. A series of ab initio calculations focused on S4R, S6R, and as a novelty, 5-1 isolated clusters, as well as periodic siliceous frameworks built from those building units (ferrierite (FER), mordenite (MOR) and heulandite (HEU) type) have been carried out. Due to the hierarchical structure of zeolite frameworks it can be expected that the total envelope of the zeolite spectra should be with good accuracy a sum of the spectra of structural elements that build each zeolite framework. Based on the results of HF calculations, normal vibrations have been visualized and detailed analysis of pseudolattice range of resulting theoretical spectra have been carried out. Obtained results have been applied for interpretation of experimental spectra of selected zeolites. Copyright © 2018 Elsevier B.V. All rights reserved.

Understanding Reflectance Anisotropy: Surface-structure signatures and bulk-related features

NASA Astrophysics Data System (ADS)

Gero Schmidt, W.

2000-03-01

Reflectance anisotropy spectroscopy (RAS) is becoming an increasingly important tool for in situ control of semiconductor processing with real-time feedback. The understanding and interpretation of the measured spectra, however, has been hampered by relatively slow theoretical progress. Using a massively parallel real-space multigrid technique [1] and ab initio pseudopotentials we calculated the optical spectra of a variety of III-V(001) growth structures and stepped Si(111):H surfaces. Our results agree well with experiment, notably with respect to the stoichiometric changes induced by different surface preparations. We identify two distinct sources for the optical anisotropy: (i) highly structure-dependent features are caused by transitions involving electronic surface states, and (ii) derivative-like oscillations or peaks at the bulk critical point energies arise from transitions between surface-modified bulk wave functions. The latter are nearly independent from the actual surface structure. The agreement between the calculated and measured spectra is further improved by applying quasi-particle corrections obtained from numerically efficient, simplified GW calculations [2]. The combination of converged first-principles calculations with an approximate treatment of many-particle effects allows the reliable identification of ``surface-structure fingerprints'' in the optical spectra, paving the way for the exploitation of their rich technological potential. [1ex] [1] EL Briggs, DJ Sullivan, J Bernholc, Phys. Rev. B 54, 14362 (1996). [2] F Bechstedt, R Del Sole, G Cappellini, L Reining, Solid State Commun. 84, 765 (1992).

First-principles calculations of phonons and Raman and infrared spectra in Cd-IV-N2 compounds

NASA Astrophysics Data System (ADS)

Lyu, Sai; Lambrecht, Walter R. L.

2018-05-01

A first-principles study of the phonons at the zone center in Cd-IV-N2 compounds is presented with IV = Si, Ge, Sn. The calculations are performed for the most likely Pbn21 crystal structure, after showing that it is indeed lower in total energy compared to the closely related Pmc21 structure. The normal mode frequencies are calculated using density functional perturbation theory and symmetry labeled. The longitudinal optical-transverse optical splittings are determined using the Born effective charges which are also reported. These are used to simulate polarized Raman spectra for different scattering configurations as well as the infrared absorption and reflection spectra. The mode frequencies are found to decrease from Si to Ge to Sn as group-IV cation. The spectra show a wide variety of number of prominent peaks and relative intensities in spite of the great similarities of these three materials. Phonon densities of states and their analysis in atom by atom contributions are also reported.

Baseline estimation in flame's spectra by using neural networks and robust statistics

NASA Astrophysics Data System (ADS)

Garces, Hugo; Arias, Luis; Rojas, Alejandro

2014-09-01

This work presents a baseline estimation method in flame spectra based on artificial intelligence structure as a neural network, combining robust statistics with multivariate analysis to automatically discriminate measured wavelengths belonging to continuous feature for model adaptation, surpassing restriction of measuring target baseline for training. The main contributions of this paper are: to analyze a flame spectra database computing Jolliffe statistics from Principal Components Analysis detecting wavelengths not correlated with most of the measured data corresponding to baseline; to systematically determine the optimal number of neurons in hidden layers based on Akaike's Final Prediction Error; to estimate baseline in full wavelength range sampling measured spectra; and to train an artificial intelligence structure as a Neural Network which allows to generalize the relation between measured and baseline spectra. The main application of our research is to compute total radiation with baseline information, allowing to diagnose combustion process state for optimization in early stages.

PDB2CD: a web-based application for the generation of circular dichroism spectra from protein atomic coordinates.

PubMed

Mavridis, Lazaros; Janes, Robert W

2017-01-01

Circular dichroism (CD) spectroscopy is extensively utilized for determining the percentages of secondary structure content present in proteins. However, although a large contributor, secondary structure is not the only factor that influences the shape and magnitude of the CD spectrum produced. Other structural features can make contributions so an entire protein structural conformation can give rise to a CD spectrum. There is a need for an application capable of generating protein CD spectra from atomic coordinates. However, no empirically derived method to do this currently exists. PDB2CD has been created as an empirical-based approach to the generation of protein CD spectra from atomic coordinates. The method utilizes a combination of structural features within the conformation of a protein; not only its percentage secondary structure content, but also the juxtaposition of these structural components relative to one another, and the overall structure similarity of the query protein to proteins in our dataset, the SP175 dataset, the 'gold standard' set obtained from the Protein Circular Dichroism Data Bank (PCDDB). A significant number of the CD spectra associated with the 71 proteins in this dataset have been produced with excellent accuracy using a leave-one-out cross-validation process. The method also creates spectra in good agreement with those of a test set of 14 proteins from the PCDDB. The PDB2CD package provides a web-based, user friendly approach to enable researchers to produce CD spectra from protein atomic coordinates. http://pdb2cd.cryst.bbk.ac.uk CONTACT: r.w.janes@qmul.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Correlating the vibrational spectra of structurally related molecules: A spectroscopic measure of similarity.

PubMed

Tao, Yunwen; Zou, Wenli; Cremer, Dieter; Kraka, Elfi

2018-03-05

Using catastrophe theory and the concept of a mutation path, an algorithm is developed that leads to the direct correlation of the normal vibrational modes of two structurally related molecules. The mutation path is defined by weighted incremental changes in mass and geometry of the molecules in question, which are successively applied to mutate a molecule into a structurally related molecule and thus continuously converting their normal vibrational spectra from one into the other. Correlation diagrams are generated that accurately relate the normal vibrational modes to each other by utilizing mode-mode overlap criteria and resolving allowed and avoided crossings of vibrational eigenstates. The limitations of normal mode correlation, however, foster the correlation of local vibrational modes, which offer a novel vibrational measure of similarity. It will be shown how this will open new avenues for chemical studies. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Pressure effect on the Raman and photoluminescence spectra of Eu3+-doped Na2Ti6O13 nanorods

NASA Astrophysics Data System (ADS)

Zeng, Q. G.; Yang, G. T.; Chen, F.; Luo, J. Y.; Zhang, Z. M.; Leung, C. W.; Ding, Z. J.; Sheng, Y. Q.

2013-12-01

Eu3+-doped Na2Ti6O13 (Na2Ti6O13:Eu) nanorods with diameters of 30 nm and lengths 400 nm were synthesized by hydrothermal and heat treatment methods. Raman spectra at ambient conditions indicated a pure monoclinic phase (space group C2/m) of the nanorods. The relations between structural and optical properties of Na2Ti6O13:Eu nanorods under high pressures were obtained by photoluminescence and Raman spectra. Two structural transition points at 1.39 and 15.48 GPa were observed when the samples were pressurized. The first transition point was attributed to the crystalline structural distortion. The later transition point was the result of pressure-induced amorphization, and the high-density amorphous (HDA) phase formed after 15.48 GPa was structurally related to the monoclinic baddeleyite structured TiO2 (P21/c). However, the site symmetry of the local environment around the Eu3+ ions in Na2Ti6O13 increased with the rising pressure. These above results indicate the occurrence of short-range order for the local asymmetry around the Eu3+ ions and long-range disorder for the crystalline structure of Na2Ti6O13:Eu nanorods by applying pressure. After releasing the pressure from 22.74 GPa, the HDA phase is transformed to low-density amorphous form, which is attributed to be structurally related to the α-PbO2-type TiO2.

[Effects of dynamic high-pressure microfluidization on the structure of waxy rice starch].

PubMed

Tu, Zong-Cai; Zhu, Xiu-Mei; Chen, Gang; Wang, Hui; Zhang, Bo; Huang, Xiao-Qin; Li, Zhi

2010-03-01

The effects of dynamic ultra high-pressure microfluidization on the structure of waxy rice starch solutions (6%) were analyzed using SEM, UV-Vis spectra, polarized light microscopy, and X-ray diffraction spectra. The results showed that: SEM graphs demonstrated that the crystal structure of waxy rice starch under different pressure treatment was destroyed with different degrees and impacted into flake up to 160 MPa; from the ultraviolet-visible spectrum we know the reduction in the blue iodine value and the decrease in the amylopectin content, which illustrated that the structure of waxy rice starch was fractured; polarized microscopic images showed that the polarization crosses of starch molecules became misty with the pressure increasing, and most of starch molecules lost polarization cross when the pressure reached 160 MPa; X-ray diffraction spectra indicated that relative crystallinity began to decline at 120 MPa with pressure treatment, and the decreased amplitude was slightly lower.

Raman effect in icosahedral boron-rich solids

PubMed Central

Werheit, Helmut; Filipov, Volodymyr; Kuhlmann, Udo; Schwarz, Ulrich; Armbrüster, Marc; Leithe-Jasper, Andreas; Tanaka, Takaho; Higashi, Iwami; Lundström, Torsten; Gurin, Vladimir N; Korsukova, Maria M

2010-01-01

We present Raman spectra of numerous icosahedral boron-rich solids having the structure of α-rhombohedral, β-rhombohedral, α-tetragonal, β-tetragonal, YB66, orthorhombic or amorphous boron. The spectra were newly measured and, in some cases, compared with reported data and discussed. We emphasize the importance of a high signal-to-noise ratio in the Raman spectra for detecting weak effects evoked by the modification of compounds, accommodation of interstitial atoms and other structural defects. Vibrations of the icosahedra, occurring in all the spectra, are interpreted using the description of modes in α-rhombohedral boron by Beckel et al. The Raman spectrum of boron carbide is largely clarified. Relative intra- and inter-icosahedral bonding forces are estimated for the different structural groups and for vanadium-doped β-rhombohedral boron. The validity of Badger's rule is demonstrated for the force constants of inter-icosahedral B–B bonds, whereas the agreement is less satisfactory for the intra-icosahedral B–B bonds. PMID:27877328

Symmetry and electronic structure of noble-metal nanoparticles and the role of relativity.

PubMed

Häkkinen, Hannu; Moseler, Michael; Kostko, Oleg; Morgner, Nina; Hoffmann, Margarita Astruc; von Issendorff, Bernd

2004-08-27

We present high resolution UV-photoelectron spectra of cold mass selected Cun-, Agn-, and Aun- with n=53-58. The observed electron density of states is not the expected simple electron shell structure, but is strongly influenced by electron-lattice interactions. Only Cu55- and Ag55- exhibit highly degenerate states. This is a direct consequence of their icosahedral symmetry, as is confirmed by density functional theory calculations. Neighboring sizes exhibit perturbed electronic structures, as they are formed by removal or addition of atoms to the icosahedron and therefore have lower symmetries. Gold clusters in the same size range show completely different spectra with almost no degeneracy, which indicates that they have structures of much lower symmetry. This behavior is related to strong relativistic bonding effects in gold, as demonstrated by ab initio calculations for Au55-.

Theoretical Prediction of Si 2–Si 33 Absorption Spectra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Li -Zhen; Lu, Wen -Cai; Qin, Wei

Here, the optical absorption spectra of Si 2–Si 33 clusters were systematically studied by a time-dependent density functional theory approach. The calculations revealed that the absorption spectrum becomes significantly broad with increasing cluster size, stretching from ultraviolet to the infrared region. The absorption spectra are closely related to the structural motifs. With increasing cluster size, the absorption intensity of cage structures gradually increases, but the absorption curves of the prolate and the Y-shaped structures are very sensitive to cluster size. If the transition energy reaches ~12 eV, it is noted that all the clusters have remarkable absorption in deep ultravioletmore » region of 100–200 nm, and the maximum absorption intensity is ~100 times that in the visible region. Further, the optical responses to doping in the Si clusters were studied.« less

Theoretical Prediction of Si 2–Si 33 Absorption Spectra

DOE PAGES

Zhao, Li -Zhen; Lu, Wen -Cai; Qin, Wei; ...

2017-07-07

Here, the optical absorption spectra of Si 2–Si 33 clusters were systematically studied by a time-dependent density functional theory approach. The calculations revealed that the absorption spectrum becomes significantly broad with increasing cluster size, stretching from ultraviolet to the infrared region. The absorption spectra are closely related to the structural motifs. With increasing cluster size, the absorption intensity of cage structures gradually increases, but the absorption curves of the prolate and the Y-shaped structures are very sensitive to cluster size. If the transition energy reaches ~12 eV, it is noted that all the clusters have remarkable absorption in deep ultravioletmore » region of 100–200 nm, and the maximum absorption intensity is ~100 times that in the visible region. Further, the optical responses to doping in the Si clusters were studied.« less

Electronic structure and x-ray spectroscopy of Cu2MnAl1-xGax

NASA Astrophysics Data System (ADS)

Rai, D. P.; Ekuma, C. E.; Boochani, A.; Solaymani, S.; Thapa, R. K.

2018-04-01

We explore the electronic and related properties of Cu2MnAl1-xGax with a first-principles, relativistic multiscattering Green function approach. We discuss our results in relation to existing experimental data and show that the electron-core hole interaction is essential for the description of the optical spectra especially in describing the X-ray absorption and magnetic circular dichroism spectra at the L2,3 edges of Cu and Mn.

Spontaneous polarization and dielectric relaxation dynamics of ferroelectric liquid crystals derived from 2(S)-[2(S)-ethylhexyolxy] propionic acid and its (S, R)-diastereomer

NASA Astrophysics Data System (ADS)

Huang, Lei-Ching; Fu, Chao-Ming

2015-09-01

The spontaneous polarization and molecular dynamics of four ferroelectric liquid crystals (FLCs) with two different kinds of core rings and two types of diastereomeric structures were investigated in this study. The FLCs with a biphenyl ring core structure showed higher spontaneous polarization than the FLCs with a naphthalene ring core structure. The complex dielectric spectra exhibited the Goldstone mode in the ferroelectric (SmC*) phase for all FLCs. The complex dielectric spectra of the four FLCs can be optimally fitted by the Debye model and the Cole-Cole model. Moreover, the Goldstone mode was enhanced under low DC bias fields for the FLCs with the (S, R)- diastereomeric structure, whereas the mode was suppressed for the FLCs with the (S, S)- diastereomeric structure. A microscopic molecular dynamic model is proposed to describe the underlying mechanism of the particular enhancement of the Goldstone mode. The experimental results of dielectric spectra and spontaneous polarization are explained in the discussion of the mesomorphic properties related to the FLC molecular structure.

Raman spectroscopy of glasses in the As-Te system

NASA Astrophysics Data System (ADS)

Tverjanovich, A.; Rodionov, K.; Bychkov, E.

2012-06-01

For the first time, the Raman spectra of AsxTe1-x glasses, 0.2≤x≤0.6, have been measured over the entire glass-forming range. The spectra exhibit three broad spectral features attributed to vibrations of structural units having Te-Te, As-Te and As-As bonds. The observed chemical disorder in the glasses is discussed on the basis of partial bond fractions derived from the integrated intensity of the Raman modes. The underlying structural model suggests a dissociation of AsTe- or As2Te3-related units in the glass melt. The spectra of glasses quenched from different temperatures, as well as those of the annealed vitreous alloys, are consistent with predictions of the model.

Ion dynamics in AgI doped silver selenium-tellurite mixed former glasses

NASA Astrophysics Data System (ADS)

Palui, A.; Ghosh, A.

2017-03-01

The ionic conductivity and the conductivity spectra of the glass compositions xAgI-(1-x)[yAg2O-(1-y)(0.5SeO2-0.5TeO2)] have been studied at different temperatures The activation energy for the dc conduction has been analyzed using the Anderson-Stuart model, and a correlation between the dc conductivity and the doorway radius has been obtained. We have analyzed the conductivity spectra using the random free-energy barrier model, taking into account the contribution of electrode polarization. It is observed that the Barton-Nakajima-Namikawa relation between the conductivity and the relaxation time is valid for these glasses. The time-temperature superposition principle has been verified using the scaling of the conductivity spectra in the framework of the random barrier model. The charge carrier density, obtained from the Nernst-Einstein relation, is found to be almost independent of temperature, but dependent weakly on composition. We have also studied the influence of the modification of the network structure of these glasses on ion migration and correlated the conductivity with the relative strength of the structural units.

Path integral Monte Carlo study on the structure and absorption spectra of alkali atoms (Li, Na, K) attached to superfluid helium clusters

NASA Astrophysics Data System (ADS)

Nakayama, Akira; Yamashita, Koichi

2001-01-01

Path integral Monte Carlo calculations have been performed to investigate the microscopic structure and thermodynamic properties of the AkṡHeN (Ak=Li, Na, K,N⩽300) clusters at T=0.5 K. Absorption spectra which correspond to the 2P←2S transitions of alkali atoms are also calculated within a pairwise additive model, which employs diatomic Ak-He potential energy curves. The size dependences of the cluster structure and absorption spectra that show the influence of the helium cluster environment are examined in detail. It is found that alkali atoms are trapped in a dimple on the helium cluster's surface and that, from the asymptotic behavior, the AkṡHe300 cluster, at least semiquantitatively, mimics the local structure of experimentally produced large helium clusters in the vicinity of alkali atoms. We have successfully reproduced the overall shapes of the spectra and explained their features from a static and structural point of view. The positions, relative intensities, and line widths of the absorption maxima are calculated to be in moderate agreement with experiments [F. Stienkemeier, J. Higgins, C. Callegari, S. I. Kanorsky, W. E. Ernst, and G. Scoles, Z. Phys. D 38, 253 (1996)].

External reflection FTIR of peptide monolayer films in situ at the air/water interface: experimental design, spectra-structure correlations, and effects of hydrogen-deuterium exchange.

PubMed Central

Flach, C R; Brauner, J W; Taylor, J W; Baldwin, R C; Mendelsohn, R

1994-01-01

A Fourier transform infrared spectrometer has been interfaced with a surface balance and a new external reflection infrared sampling accessory, which permits the acquisition of spectra from protein monolayers in situ at the air/water interface. The accessory, a sample shuttle that permits the collection of spectra in alternating fashion from sample and background troughs, reduces interference from water vapor rotation-vibration bands in the amide I and amide II regions of protein spectra (1520-1690 cm-1) by nearly an order of magnitude. Residual interference from water vapor absorbance ranges from 50 to 200 microabsorbance units. The performance of the device is demonstrated through spectra of synthetic peptides designed to adopt alpha-helical, antiparallel beta-sheet, mixed beta-sheet/beta-turn, and unordered conformations at the air/water interface. The extent of exchange on the surface can be monitored from the relative intensities of the amide II and amide I modes. Hydrogen-deuterium exchange may lower the amide I frequency by as much as 11-12 cm-1 for helical secondary structures. This shifts the vibrational mode into a region normally associated with unordered structures and leads to uncertainties in the application of algorithms commonly used for determination of secondary structure from amide I contours of proteins in D2O solution. PMID:7919013

Liquid-crystal projection image depixelization by spatial phase scrambling

NASA Astrophysics Data System (ADS)

Yang, Xiangyang; Jutamulia, Suganda; Li, Nan

1996-08-01

A technique that removes the pixel structure by scrambling the relative phases among multiple spatial spectra is described. Because of the pixel structure of the liquid-crystal-display (LCD) panel, multiple spectra are generated at the Fourier-spectrum plane (usually at the back focal plane of the imaging lens). A transparent phase mask is placed at the Fourier-spectrum plane such that each spectral order is modulated by one of the subareas of the phase mask, and the phase delay resulting from each pair of subareas is longer than the coherent length of the light source, which is approximately 1 m for the wideband white light sources used in most of LCD s. Such a phase-scrambling technique eliminates the coherence between different spectral orders; therefore, the reconstructed images from the multiple spectra will superimpose incoherently, and the pixel structure will not be observed in the projection image.

Effect of aluminum on the local structure of silicon in zeolites as studied by Si K edge X-ray absorption near-edge fine structure: spectra simulation with a non-muffin tin atomic background.

PubMed

Bugaev, Lusegen A; Bokhoven, Jeroen A van; Khrapko, Valerii V

2009-04-09

Experimental Si K edge X-ray absorption near-edge fine structure (XANES) of zeolite faujasite, mordenite, and beta are interpreted by means of the FEFF8 code, replacing the theoretical atomic background mu(0) by a background that was extracted from an experimental spectrum. To some extent, this diminished the effect of the inaccuracy introduced by the MT potential and accounted for the intrinsic loss of photoelectrons. The agreement of the theoretical and experimental spectra at energies above the white lines enabled us to identify structural distortion around silicon, which occurs with increasing aluminum content. The Si K edge XANES spectra are very sensitive to slight distortions in the silicon coordination. Placing an aluminum atom on a nearest neighboring T site causes a distortion in the silicon tetrahedron, shortening one of the silicon-oxygen bonds relative to the other three.

Water in Betelgeuse and Antares

NASA Technical Reports Server (NTRS)

Jennings, D. E.; Sada, P. V.

1998-01-01

Absorption lines of hot water have been identified in the infrared spectra of Betelgeuse (alpha Orionis) and Antares (alpha Scorpii) near 12.3 micrometers (811 to 819 wavenumbers). The water lines originate in the atmospheres of the stars, not in their circumstellar material. The spectra are similar in structure to umbral sunspot spectra. Pure rotation water lines of this type will occur throughout the spectra of cool stars at wavelengths greater than 10 micrometers. From the water spectra, the upper limit for the temperature in the line formation region in both stars is 2800 kelvin. The water column density in both stars is (3 +/- 2) x 10(18) molecules per square centimeter, yielding an abundance relative to atomic hydrogen of n(H2O)/n(H) approximately 10(-)7.

Modeling the Conformation-Specific Infrared Spectra of N-Alkylbenzenes

NASA Astrophysics Data System (ADS)

Tabor, Daniel P.; Sibert, Edwin; Hewett, Daniel M.; Korn, Joseph A.; Zwier, Timothy S.

2016-06-01

Conformation-specific UV-IR double resonance spectra are presented for n-alkylbenzenes. With the aid of a local mode Hamiltonian that includes the effects of stretch-bend Fermi coupling, the spectra of ethyl, n-propyl, and n-butylbenzene are assigned to individual conformers. These molecules allow for further development of the work on a first principles method for calculating alkyl stretch spectra. Due to the consistency of the anharmonic couplings from conformer to conformer, construction of the model Hamiltonian for a given conformer only requires a harmonic frequency calculation at the conformer's minimum geometry as an input. The model Hamiltonian can be parameterized with either density functional theory or MP2 electronic structure calculations. The relative strengths and weaknesses of these methods are evaluated, including their predictions of the relative energetics of the conformers. Finally, the IR spectra for conformers that have the alkyl chain bend back and interact with the π cloud of the benzene ring are modeled.

Structure and reactivity of thiazolium azo dyes: UV-visible, resonance Raman, NMR, and computational studies of the reaction mechanism in alkaline solution.

PubMed

Abbott, Laurence C; Batchelor, Stephen N; Moore, John N

2013-03-07

UV-visible absorption, resonance Raman, and (1)H NMR spectroscopy, allied with density functional theory (DFT) calculations, have been used to study the structure, bonding, and alkaline hydrolysis mechanism of the cationic thiazloium azo dye, 2-[2-[4-(diethylamino)phenyl]diazenyl]-3-methyl-thiazolium (1a), along with a series of six related dyes with different 4-dialkylamino groups and/or other phenyl ring substituents (2a-c, 3a-c) and the related isothiazolium azo dye, 5-[2-[4-(dimethylamino)phenyl]diazenyl]-2-methyl-isothiazolium (4). These diazahemicyanine dyes are calculated to have a similar low-energy structure that is cis, trans at the (iso)thiazolium-azo group, and for which the calculated Raman spectra provide a good match with the experimental data; the calculations on these structures are used to assign and discuss the transitions giving rise to the experimental spectra, and to consider the bonding and its variation between the dyes. UV-visible, Raman, and NMR spectra recorded from minutes to several weeks after raising the pH of an aqueous solution of 1a to ca. 11.5 show that the dominant initial step in the reaction is loss of diethylamine to produce a quinonimine (ca. hours), with subsequent reactions occurring on longer time scales (ca. days to weeks); kinetic analyses give a rate constant of 2.6 × 10(-2) dm(3) mol(-1) s(-1) for reaction of 1a with OH(-). UV-visible spectra recorded on raising the pH of the other dyes in solution show similar changes that are attributed to the same general reaction mechanism, but with different rate constants for which the dependence on structure is discussed.

Infrared spectra of some sulfides and their analogs of binary composition in the long-wave region

NASA Technical Reports Server (NTRS)

Povarennykh, A. S.; Sidorenko, G. A.; Solntseva, L. S.; Solntsev, B. P.

1981-01-01

The far infrared spectra (500-60/cm) of some simple sulfides and their analogs were studied. In all, 22 minerals with different structure types were investigated, out of which 14 are sulfides (galena, alabandite, pyrrhotite, sphalerite, wurtzite, cinnabar, realgar, orpiment, getchelite antimonite, molybdenite, pyrite, marcasite and heazlewoodite) 6 arsenides (niccolite, domeykite, arsenopyrite, lollingite, rammelsbergite and skutterudite), one telluride (tetradymite) and native arsenic. The main bands of infrared absorption spectra of the minerals are compared with the relative strength of the interatomic bonds and their interpretation is given.

Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system.

PubMed

Ikeya, Teppei; Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune; Güntert, Peter

2009-08-01

Stereo-array isotope labeling (SAIL) has been combined with the fully automated NMR structure determination algorithm FLYA to determine the three-dimensional structure of the protein ubiquitin from different sets of input NMR spectra. SAIL provides a complete stereo- and regio-specific pattern of stable isotopes that results in sharper resonance lines and reduced signal overlap, without information loss. Here we show that as a result of the superior quality of the SAIL NMR spectra, reliable, fully automated analyses of the NMR spectra and structure calculations are possible using fewer input spectra than with conventional uniformly 13C/15N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional "through-bond" spectrum (and 2D HSQC spectra) in addition to the 13C-edited and 15N-edited NOESY spectra for conformational restraints, yielded structures with an accuracy of 0.83-1.15 A for the backbone RMSD to the conventionally determined solution structure of SAIL ubiquitin. NMR structures can thus be determined almost exclusively from the NOESY spectra that yield the conformational restraints, without the need to record many spectra only for determining intermediate, auxiliary data of the chemical shift assignments. The FLYA calculations for this report resulted in 252 ubiquitin structure bundles, obtained with different input data but identical structure calculation and refinement methods. These structures cover the entire range from highly accurate structures to seriously, but not trivially, wrong structures, and thus constitute a valuable database for the substantiation of structure validation methods.

Boron difluoride dibenzoylmethane derivatives: Electronic structure and luminescence

NASA Astrophysics Data System (ADS)

Tikhonov, Sergey A.; Vovna, Vitaliy I.; Osmushko, Ivan S.; Fedorenko, Elena V.; Mirochnik, Anatoliy G.

2018-01-01

Electronic structure and optical properties of boron difluoride dibenzoylmethanate and four of its derivatives have been studied by X-ray photoelectron spectroscopy, absorption and luminescence spectroscopy and quantum chemistry (DFT, TDDFT). The relative quantum luminescence yields have been revealed to correlate with charge transfers of HOMO-LUMO transitions, energy barriers of aromatic substituents rotation and the lifetime of excited states in the investigated complexes. The bathochromic shift of intensive bands in the optical spectra has been observed to occur when the functional groups are introduced into p-positions of phenyl cycles due to destabilizing HOMO levels. Calculated energy intervals between electronic levels correlate well with XPS spectra structure of valence and core electrons.

Importance of many-body dispersion and temperature effects on gas-phase gold cluster (meta)stability

NASA Astrophysics Data System (ADS)

Goldsmith, Bryan R.; Gruene, Philipp; Lyon, Jonathan T.; Rayner, David M.; Fielicke, André; Scheffler, Matthias; Ghiringhelli, Luca M.

Gold clusters in the gas phase exhibit many structural isomers that are shown to intercovert frequently, even at room temperature. We performed ab initio replica-exchange molecular dynamics (REMD) calculations on gold clusters (of sizes 5-14 atoms) to identify metastable states and their relative populations at finite temperature, as well as to examine the importance of temperature and van der Waals (vdW) on their isomer energetic ordering. Free energies of the gold cluster isomers are optimally estimated using the Multistate Bennett Acceptance Ratio. The distribution of bond coordination numbers and radius of gyration are used to address the challenge of discriminating isomers along their dynamical trajectories. Dispersion effects are important for stabilizing three-dimensional structures relative to planar structures and brings isomer energetic predictions to closer quantitative agreement compared with RPA@PBE calculations. We find that higher temperatures typically stabilize metastable three-dimensional structures relative to planar/quasiplanar structures. Computed IR spectra of low free energy Au9, Au10, and Au12 isomers are in agreement with experimental spectra obtained by far-IR multiple photon dissociation in a molecular beam at 100 K.

Neutron spectra measurement and calculations using data libraries CIELO, JEFF-3.2 and ENDF/B-VII.1 in iron benchmark assemblies

NASA Astrophysics Data System (ADS)

Jansky, Bohumil; Rejchrt, Jiri; Novak, Evzen; Losa, Evzen; Blokhin, Anatoly I.; Mitenkova, Elena

2017-09-01

The leakage neutron spectra measurements have been done on benchmark spherical assemblies - iron spheres with diameter of 20, 30, 50 and 100 cm. The Cf-252 neutron source was placed into the centre of iron sphere. The proton recoil method was used for neutron spectra measurement using spherical hydrogen proportional counters with diameter of 4 cm and with pressure of 400 and 1000 kPa. The neutron energy range of spectrometer is from 0.1 to 1.3 MeV. This energy interval represents about 85 % of all leakage neutrons from Fe sphere of diameter 50 cm and about of 74% for Fe sphere of diameter 100 cm. The adequate MCNP neutron spectra calculations based on data libraries CIELO, JEFF-3.2 and ENDF/B-VII.1 were done. Two calculations were done with CIELO library. The first one used data for all Fe-isotopes from CIELO and the second one (CIELO-56) used only Fe-56 data from CIELO and data for other Fe isotopes were from ENDF/B-VII.1. The energy structure used for calculations and measurements was 40 gpd (groups per decade) and 200 gpd. Structure 200 gpd represents lethargy step about of 1%. This relatively fine energy structure enables to analyze the Fe resonance neutron energy structure. The evaluated cross section data of Fe were validated on comparisons between the calculated and experimental spectra.

Analysis of protein circular dichroism spectra for secondary structure using a simple matrix multiplication.

PubMed

Compton, L A; Johnson, W C

1986-05-15

Inverse circular dichroism (CD) spectra are presented for each of the five major secondary structures of proteins: alpha-helix, antiparallel and parallel beta-sheet, beta-turn, and other (random) structures. The fraction of the each secondary structure in a protein is predicted by forming the dot product of the corresponding inverse CD spectrum, expressed as a vector, with the CD spectrum of the protein digitized in the same way. We show how this method is based on the construction of the generalized inverse from the singular value decomposition of a set of CD spectra corresponding to proteins whose secondary structures are known from X-ray crystallography. These inverse spectra compute secondary structure directly from protein CD spectra without resorting to least-squares fitting and standard matrix inversion techniques. In addition, spectra corresponding to the individual secondary structures, analogous to the CD spectra of synthetic polypeptides, are generated from the five most significant CD eigenvectors.

Functional brain connectivity is predictable from anatomic network's Laplacian eigen-structure.

PubMed

Abdelnour, Farras; Dayan, Michael; Devinsky, Orrin; Thesen, Thomas; Raj, Ashish

2018-05-15

How structural connectivity (SC) gives rise to functional connectivity (FC) is not fully understood. Here we mathematically derive a simple relationship between SC measured from diffusion tensor imaging, and FC from resting state fMRI. We establish that SC and FC are related via (structural) Laplacian spectra, whereby FC and SC share eigenvectors and their eigenvalues are exponentially related. This gives, for the first time, a simple and analytical relationship between the graph spectra of structural and functional networks. Laplacian eigenvectors are shown to be good predictors of functional eigenvectors and networks based on independent component analysis of functional time series. A small number of Laplacian eigenmodes are shown to be sufficient to reconstruct FC matrices, serving as basis functions. This approach is fast, and requires no time-consuming simulations. It was tested on two empirical SC/FC datasets, and was found to significantly outperform generative model simulations of coupled neural masses. Copyright © 2018. Published by Elsevier Inc.

Theory of Parabolic Arcs in Interstellar Scintillation Spectra

NASA Astrophysics Data System (ADS)

Cordes, James M.; Rickett, Barney J.; Stinebring, Daniel R.; Coles, William A.

2006-01-01

Interstellar scintillation (ISS), observed as time variation in the intensity of a compact radio source, is caused by small-scale structure in the electron density of the interstellar plasma. Dynamic spectra of ISS show modulation in radio frequency and time. Here we relate the (two-dimensional) power spectrum of the dynamic spectrum-the secondary spectrum-to the scattered image of the source. Recent work has identified remarkable parabolic arcs in secondary spectra. Each point in a secondary spectrum corresponds to interference between points in the scattered image with a certain Doppler shift and a certain delay. The parabolic arc corresponds to the quadratic relation between differential Doppler shift and delay through their common dependence on scattering angle. We show that arcs will occur in all media that scatter significant power at angles larger than the rms angle. Thus, effects such as source diameter, steep spectra, and dissipation scales, which truncate high angle scattering, also truncate arcs. Arcs are equally visible in simulations of nondispersive scattering. They are enhanced by anisotropic scattering when the spatial structure is elongated perpendicular to the velocity. In weak scattering the secondary spectrum is directly mapped from the scattered image, and this mapping can be inverted. We discuss additional observed phenomena including multiple arcs and reverse arclets oriented oppositely to the main arc. These phenomena persist for many refractive scattering times, suggesting that they are due to large-scale density structures, rather than low-frequency components of Kolmogorov turbulence.

BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra.

PubMed

Micsonai, András; Wien, Frank; Bulyáki, Éva; Kun, Judit; Moussong, Éva; Lee, Young-Ho; Goto, Yuji; Réfrégiers, Matthieu; Kardos, József

2018-06-11

Circular dichroism (CD) spectroscopy is a widely used method to study the protein secondary structure. However, for decades, the general opinion was that the correct estimation of β-sheet content is challenging because of the large spectral and structural diversity of β-sheets. Recently, we showed that the orientation and twisting of β-sheets account for the observed spectral diversity, and developed a new method to estimate accurately the secondary structure (PNAS, 112, E3095). BeStSel web server provides the Beta Structure Selection method to analyze the CD spectra recorded by conventional or synchrotron radiation CD equipment. Both normalized and measured data can be uploaded to the server either as a single spectrum or series of spectra. The originality of BeStSel is that it carries out a detailed secondary structure analysis providing information on eight secondary structure components including parallel-β structure and antiparallel β-sheets with three different groups of twist. Based on these, it predicts the protein fold down to the topology/homology level of the CATH protein fold classification. The server also provides a module to analyze the structures deposited in the PDB for BeStSel secondary structure contents in relation to Dictionary of Secondary Structure of Proteins data. The BeStSel server is freely accessible at http://bestsel.elte.hu.

Classification model based on Raman spectra of selected morphological and biochemical tissue constituents for identification of atherosclerosis in human coronary arteries.

PubMed

Peres, Marines Bertolo; Silveira, Landulfo; Zângaro, Renato Amaro; Pacheco, Marcos Tadeu Tavares; Pasqualucci, Carlos Augusto

2011-09-01

This study presents the results of Raman spectroscopy applied to the classification of arterial tissue based on a simplified model using basal morphological and biochemical information extracted from the Raman spectra of arteries. The Raman spectrograph uses an 830-nm diode laser, imaging spectrograph, and a CCD camera. A total of 111 Raman spectra from arterial fragments were used to develop the model, and those spectra were compared to the spectra of collagen, fat cells, smooth muscle cells, calcification, and cholesterol in a linear fit model. Non-atherosclerotic (NA), fatty and fibrous-fatty atherosclerotic plaques (A) and calcified (C) arteries exhibited different spectral signatures related to different morphological structures presented in each tissue type. Discriminant analysis based on Mahalanobis distance was employed to classify the tissue type with respect to the relative intensity of each compound. This model was subsequently tested prospectively in a set of 55 spectra. The simplified diagnostic model showed that cholesterol, collagen, and adipocytes were the tissue constituents that gave the best classification capability and that those changes were correlated to histopathology. The simplified model, using spectra obtained from a few tissue morphological and biochemical constituents, showed feasibility by using a small amount of variables, easily extracted from gross samples.

Excitonic and band-band transitions of Cu2ZnSiS4 determined from reflectivity spectra

NASA Astrophysics Data System (ADS)

Guc, M.; Levcenko, S.; Dermenji, L.; Gurieva, G.; Schorr, S.; Syrbu, N. N.; Arushanov, E.

2014-07-01

Exciton spectra of Cu2ZnSiS4 single crystals are investigated by reflection spectroscopy at 10 and 300 K for light polarized perpendicular (E⊥c) and parallel (E∥c) to the optical axis. The parameters of the excitons and dielectric constant are determined. The free carriers effective masses have been estimated. The room temperature reflectivity spectra at photon energies higher than the fundamental band gap in the polarization Е⊥с and E∥с were measured and related to the electronic band structure of Cu2ZnSiS4.

Molecular dynamics study of structure and vibrational spectra at zwitterionoic lipid/aqueous KCl, NaCl, and CaCl2 solution interfaces

NASA Astrophysics Data System (ADS)

Ishiyama, Tatsuya; Shirai, Shinnosuke; Okumura, Tomoaki; Morita, Akihiro

2018-06-01

Molecular dynamics (MD) simulations of KCl, NaCl, and CaCl2 solution/dipalmytoylphosphatidylcholine lipid interfaces were performed to analyze heterodyne-detected vibrational sum frequency generation (HD-VSFG) spectra in relation to the interfacial water structure. The present MD simulation well reproduces the experimental spectra and elucidates a specific cation effect on the interfacial structure. The K+, Na+, and Ca2+ cation species penetrate in the lipid layer more than the anions in this order, due to the electrostatic interaction with negative polar groups of lipid, and the electric double layer between the cations and anions cancels the intrinsic orientation of water at the water/lipid interface. These mechanisms explain the HD-VSFG spectrum of the water/lipid interface and its spectral perturbation by adding the ions. The lipid monolayer reverses the order of surface preference of the cations at the solution/lipid interface from that at the solution/air interface.

Comparative analysis of the heme iron electronic structure and stereochemistry in tetrameric rabbit hemoglobin and monomeric soybean leghemoglobin a using Mössbauer spectroscopy with a high velocity resolution

NASA Astrophysics Data System (ADS)

Alenkina, I. V.; Kumar, A.; Berkovsky, A. L.; Oshtrakh, M. I.

2018-02-01

A comparative study of tetrameric rabbit hemoglobin and monomeric soybean leghemoglobin a in the oxy- and deoxy-forms was carried out using 57Fe Mössbauer spectroscopy with a high velocity resolution in order to analyze the heme iron electronic structure and stereochemistry in relation to the Mössbauer hyperfine parameters. The Mössbauer spectra of tetrameric rabbit hemoglobin in both forms were fitted using two quadrupole doublets related to the 57Fe in ɑ- and β-subunits. In contrast, the Mössbauer spectra of monomeric soybean leghemoglobin a were fitted using: (i) two quadrupole doublets for the oxy-form related to two conformational states of the distal His E7 imidazole ring and different hydrogen bonding of oxygen molecule in the oxy-form and (ii) using three quadrupole doublets for deoxy-form related to three conformational states of the proximal His F8 imidazole ring. Small variations of Mössbauer hyperfine parameters related to small differences in the heme iron electronic structure and stereochemistry in tetrameric rabbit hemoglobin and monomeric soybean leghemoglobin a are discussed.

Optical study of gamma irradiated sodium metaphosphate glasses containing divalent metal oxide MO (ZnO or CdO)

NASA Astrophysics Data System (ADS)

Nabhan, E.; Abd-Allah, W. M.; Ezz-El-Din, F. M.

Sodium metaphosphate glasses containing divalent metal oxide, ZnO or CdO with composition 50 P2O5 - (50 - x) Na2O - x MO (ZnO, or CdO) where x = 0, 10, 20 (mol%) were prepared by conventional melt method. UV/visible spectroscopy and FTIR spectroscopy are measured before and after exposing to successive gamma irradiation doses (5-80 kGy). The optical absorption spectra results of the samples before irradiation reveal a strong UV absorption band at (∼230 nm) which is related to unavoided iron impurities. The effects of gamma irradiation on the optical spectral properties of the various glasses have been compared. From the optical absorption spectral data, the optical band gap is evaluated. The main structural groups and the influence of both divalent metal oxide and gamma irradiation effect on the structural vibrational groups are realized through IR spectroscopy. The FTIR spectra of γ-irradiated samples are characterized by the stability of the number and position for the main characteristic band of phosphate groups. To better understood the structural changes during γ-irradiation, a deconvolution of FTIR spectra in the range 650-1450 cm-1 is made. The FTIR deconvolution results found evidence that, the changes occurring after gamma irradiation have been related to irradiation induced structural defects and compositional changes.

A Comparison of the Raman Spectra and Crystal Chemistry of Norbergite and Clinohumite at High Pressure

NASA Astrophysics Data System (ADS)

Pease, A. M.; Gramsch, S. A.

2017-12-01

Humite group minerals n(Mg.Fe)2SiO4 - (Mg,Fe)(OH)2 have been suggested as possible candidates for water storage and transport in the mantle, and clinohumite in particular has been proposed as the source of ilmenite lamellae in Alpine ultrahigh pressure metamorphic terranes via its decomposition at high pressure and temperature. In this study, a comparison is made between the Raman spectra of norbergite (n = 1) and clinohumite (n = 4) up to 15 GPa to correlate the structural and vibrational properties of these two members of the group. All observed vibrational modes in the Raman spectra of both minerals increase in frequency with pressure, although the change in frequencies with pressure is much steeper in norbergite than for clinohumite. In norbergite, antisymmetric stretching modes of the SiO4 tetrahedra merge, but no such merging of modes occurs in clinohumite. In addition, the intensity of the antisymmetric stretching mode for clinohumite decreases dramatically in pressure compared to the intensity of the symmetric stretching mode. In the spectra of norbergite, these two modes retain their relative intensities with increasing pressure. The most striking difference between the spectra of norbergite and clinohumite is in the deformation modes of the brucite layer, which within the clinohumite structure retain their intensities with increasing pressure, while these modes are not observed in the spectra of norbergite. The nature of the Raman spectra and their evolution with pressure are correlated with the structural properties of the two minerals in terms of the interactions between olivine and brucite layers and the crystal chemistry of the humite group minerals.

Crystal structures and infrared spectra of two Fe-bearing hydrous magnesium silicates synthesized at high temperature and pressure

NASA Technical Reports Server (NTRS)

Yang, H.; Prewitt, C. T.; Liu, Z.

2002-01-01

The synthesis and characterization of Fe-bearing phase E and phase E' demonstrate that the phase E-type structures can be rather compliant and complex, and that as we further explore the temperature-pressure-composition space, other types of structures that are similar to or related to the structure of phase E may be discovered.

H I anisotropies associated with radio-polarimetric filaments . Steep power spectra associated with cold gas

NASA Astrophysics Data System (ADS)

Kalberla, P. M. W.; Kerp, J.; Haud, U.; Haverkorn, M.

2017-10-01

Context. LOFAR detected toward 3C 196 linear polarization structures which were found subsequently to be closely correlated with cold filamentary H I structures. The derived direction-dependent H I power spectra revealed marked anisotropies for narrow ranges in velocity, sharing the orientation of the magnetic field as expected for magneto-hydrodynamical (MHD) turbulence. Aims: Using the Galactic portion of the Effelsberg-Bonn H I Survey (EBHIS) we continue our study of such anisotropies in the H I distribution in direction of two WSRT fields, Horologium and Auriga; both are well known for their prominent radio-polarimetric depolarization canals. At 349 MHz the observed pattern in total intensity is insignificant but polarized intensity and polarization angle show prominent ubiquitous structures with so far unknown origin. Methods: Apodizing the H I survey data by applying a rotational symmetric 50% Tukey window, we derive average and position angle dependent power spectra. We fit power laws and characterize anisotropies in the power distribution. We used a Gaussian analysis to determine relative abundances for the cold and warm neutral medium. Results: For the analyzed radio-polarimetric targets significant anisotropies are detected in the H I power spectra; their position angles are aligned to the prominent depolarization canals, initially detected by WSRT. H I anisotropies are associated with steep power spectra. Steep power spectra, associated with cold gas, are detected also in other fields. Conclusions: Radio-polarimetric depolarization canals are associated with filamentary H I structures that belong to the cold neutral medium (CNM). Anisotropies in the CNM are in this case linked to a steepening of the power-spectrum spectral index, indicating that phase transitions in a turbulent medium occur on all scales. Filamentary H I structures, driven by thermal instabilities, and radio-polarimetric filaments are associated with each other. The magneto-ionic medium that causes the radio-polarimetric filaments is probably wrapped around the H I.

Electronic structures and population dynamics of excited states of xanthione and its derivatives

NASA Astrophysics Data System (ADS)

Fedunov, Roman G.; Rogozina, Marina V.; Khokhlova, Svetlana S.; Ivanov, Anatoly I.; Tikhomirov, Sergei A.; Bondarev, Stanislav L.; Raichenok, Tamara F.; Buganov, Oleg V.; Olkhovik, Vyacheslav K.; Vasilevskii, Dmitrii A.

2017-09-01

A new compound, 1,3-dimethoxy xanthione (DXT), has been synthesized and its absorption (stationary and transient) and luminescence spectra have been measured in n-hexane and compared with xanthione (XT) spectra. The pronounced broadening of xanthione vibronic absorption band related to the electronic transition to the second singlet excited state has been observed. Distinctions between the spectra of xanthione and its methoxy derivatives are discussed. Quantum chemical calculations of these compounds in the ground and excited electronic states have been accomplished to clarify the nature of electronic spectra changes due to modification of xanthione by methoxy groups. Appearance of a new absorption band of DXT caused by symmetry changes has been discussed. Calculations of the second excited state structure of xanthione and its methoxy derivatives confirm noticeable charge transfer (about 0.1 of the charge of an electron) from the methoxy group to thiocarbonyl group. Fitting of the transient spectra of XT and DXT has been fulfilled and the time constants of internal conversion S2 →S1 and intersystem crossing S1 →T1 have been determined. A considerable difference between the time constants of internal conversion S2 →S1 in XT and DXT is uncovered.

Reduction of chemical formulas from the isotopic peak distributions of high-resolution mass spectra.

PubMed

Roussis, Stilianos G; Proulx, Richard

2003-03-15

A method has been developed for the reduction of the chemical formulas of compounds in complex mixtures from the isotopic peak distributions of high-resolution mass spectra. The method is based on the principle that the observed isotopic peak distribution of a mixture of compounds is a linear combination of the isotopic peak distributions of the individual compounds in the mixture. All possible chemical formulas that meet specific criteria (e.g., type and number of atoms in structure, limits of unsaturation, etc.) are enumerated, and theoretical isotopic peak distributions are generated for each formula. The relative amount of each formula is obtained from the accurately measured isotopic peak distribution and the calculated isotopic peak distributions of all candidate formulas. The formulas of compounds in simple spectra, where peak components are fully resolved, are rapidly determined by direct comparison of the calculated and experimental isotopic peak distributions. The singular value decomposition linear algebra method is used to determine the contributions of compounds in complex spectra containing unresolved peak components. The principles of the approach and typical application examples are presented. The method is most useful for the characterization of complex spectra containing partially resolved peaks and structures with multiisotopic elements.

Investigation of traveling ionospheric disturbances using the differential Doppler data from the Apollo-Soyuz mission

NASA Technical Reports Server (NTRS)

Gross, S. H.

1981-01-01

The ASTP Doppler data were recalibrated, analyzed and related to geophysical phenomena and found consistent. Spectra were computed for data intervals covering each hemisphere. As many as 14 such intervals were analyzed. Wave structure is seen in much of the data. The spectra for all those intervals are very similar in a number of respects. They all decrease with frequency, or with decreasing wavelength. Power law fits are reasonable and spectral indices are found to range from about -2.0 to about -3.5. Both large scale (thousands of kilometers) and medium scale (hundreds of kilometers) waves are evident. These spectra are very similar to spectra of in situ measurements of neutrals and ionization measured by Atmosphere Explorer C.

Elemental and Molecular Relative Abundances in the Ejecta of Eta Carinae

NASA Technical Reports Server (NTRS)

Kober, G. V.; Gull, T. R.; Nielsen, K.; Bruhweiler, F.; Verner, K.; Stahl, O.; Weis, K.; Bomans, D.

2006-01-01

We are measuring relative elemental abundances for the ejecta in the line of sight from Eta Carinae using high dispersion spectroscopy with the HST/STIS and the VLT/UVES. While multiple velocity components have been identified, we focus on the -513 and -146 km/s components originating from the Homunculus and the Little Homunculus. Complicating factors are the complex nebular structures in the immediate vicinity of the bright, massive star: the very bright emission structures, Weigelt blobs B, C and D, the broad, clumpy structures of the extended wind apparently not photoionized by Eta Car B, and general scattered starlight from the extended wind and the dusty core of the circumstellar material. We have used the 3050 to 3160A region of overlap between STIS and UVES to intercompare equivalent widths of absorption lines to estimate the 'contributing factor', namely the amount of light originating from the star compared to nebular structures. While the extracted STIS spectra are from 0.1" wide aperture, the UVES spectra are limited by the 1" seeing conditions. Curiously we find that the scattering contribution in the UVES spectra changes with time, apparently with orbital phase of the 5.54-year period. This indicates that the dust may be modified by changes in the central source with phase. The noticeable drop in scattered light appears to occur about 1.7 years (phase 0.35) after the spectroscopic minimum. Relative abundances of iron peak elements and some molecules will be estimated. Observations in this study were accomplished with HST through STSci and with VLT through ESO and funded under STIS GTO resources.

S2p core level spectroscopy of short chain oligothiophenes

NASA Astrophysics Data System (ADS)

Baseggio, O.; Toffoli, D.; Stener, M.; Fronzoni, G.; de Simone, M.; Grazioli, C.; Coreno, M.; Guarnaccio, A.; Santagata, A.; D'Auria, M.

2017-12-01

The Near-Edge X-ray-Absorption Fine-Structure (NEXAFS) and X-ray Photoemission Spectroscopy (XPS) of short-chain oligothiophenes (thiophene, 2,2'-bithiophene, and 2,2':5',2″-terthiophene) in the gas phase have been measured in the sulfur L2,3-edge region. The assignment of the spectral features is based on the relativistic two-component zeroth-order regular approximation time dependent density functional theory approach. The calculations allow us to estimate both the contribution of the spin-orbit splitting and of the molecular-field splitting to the sulfur binding energies and give results in good agreement with the experimental measurements. The deconvolution of the calculated S2p NEXAFS spectra into the two manifolds of excited states converging to the LIII and LII edges facilitates the attribution of the spectral structures. The main S2p NEXAFS features are preserved along the series both as concerns the energy positions and the nature of the transitions. This behaviour suggests that the electronic and geometrical environment of the sulfur atom in the three oligomers is relatively unaffected by the increasing chain length. This trend is also observed in the XPS spectra. The relatively simple structure of S2p NEXAFS spectra along the series reflects the localized nature of the virtual states involved in the core excitation process.

Irmpd Action Spectroscopy and Computational Approaches to Elucidate Gas-Phase Structures and Energetics of 2'-DEOXYCYTIDINE and Cytidine Sodium Complexes

NASA Astrophysics Data System (ADS)

Zhu, Yanlong; Hamlow, Lucas; He, Chenchen; Gao, Juehan; Oomens, Jos; Rodgers, M. T.

2016-06-01

The local structures of DNA and RNA are influenced by protonation, deprotonation and noncovalent interactions with cations. In order to determine the effects of Na+ cationization on the gas-phase structures of 2'-deoxycytidine, [dCyd+Na]+, and cytidine, [Cyd+Na]+, infrared multiple photon dissociation (IRMPD) action spectra of these sodium cationized nucleosides are measured over the range extending from 500 to 1850 wn using the FELIX free electron laser. Complementary electronic structure calculations are performed to determine the stable low-energy conformations of these complexes. Geometry optimizations, frequency analyses, and IR spectra of these species are determined at the B3LYP/6-311+G(d,p) level of theory. Single-point energies are calculated at the B3LYP/6-311+G(2d,2p) level of theory to determine the relative stabilities of these conformations. Comparison of the measure IRMPD action spectra and computed linear IR spectra enable the conformations accessed in the experiments to be elucidated. For both cytosine nucleosides, tridentate binding of the Na+ cation to the O2, O4' and O5' atoms of the nucleobase and sugar is observed. Present results for the sodium cationized nucleosides are compared to results for the analogous protonated forms of these nucleosides to elucidate the effects of multiple chelating interactions with the sodium cation vs. hydrogen bonding interactions in the protonated systems on the structures and stabilities of these nucleosides.

Helium induced fine structure in the electronic spectra of anthracene derivatives doped into superfluid helium nanodroplets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pentlehner, D.; Slenczka, A., E-mail: alkwin.slenczka@chemie.uni-regensburg.de

2015-01-07

Electronic spectra of organic molecules doped into superfluid helium nanodroplets show characteristic features induced by the helium environment. Besides a solvent induced shift of the electronic transition frequency, in many cases, a spectral fine structure can be resolved for electronic and vibronic transitions which goes beyond the expected feature of a zero phonon line accompanied by a phonon wing as known from matrix isolation spectroscopy. The spectral shape of the zero phonon line and the helium induced phonon wing depends strongly on the dopant species. Phonon wings, for example, are reported ranging from single or multiple sharp transitions to broadmore » (Δν > 100 cm{sup −1}) diffuse signals. Despite the large number of example spectra in the literature, a quantitative understanding of the helium induced fine structure of the zero phonon line and the phonon wing is missing. Our approach is a systematic investigation of related molecular compounds, which may help to shed light on this key feature of microsolvation in superfluid helium droplets. This paper is part of a comparative study of the helium induced fine structure observed in electronic spectra of anthracene derivatives with particular emphasis on a spectrally sharp multiplet splitting at the electronic origin. In addition to previously discussed species, 9-cyanoanthracene and 9-chloroanthracene will be presented in this study for the first time.« less

The study on molecular structure and microbiological activity of alkali metal 3-hydroxyphenylycetates

NASA Astrophysics Data System (ADS)

Samsonowicz, M.; Regulska, E.; Kowczyk-Sadowy, M.; Butarewicz, A.; Lewandowski, W.

2017-10-01

The biological activity of chemical compounds depends on their molecular structure. In this paper molecular structure of 3-hydroxyphenylacetates in comparison to 3-hydroxyphenylacetic acid was studied. FT-IR, FT-Raman and NMR spectroscopy and density functional theory (DFT) calculations was used. The B3LYP/6-311++G(d,p) hybrid functional method was used to calculate optimized geometrical structures of studied compounds. The Mulliken, APT, MK, ChelpG and NBO atomic charges as well as dipole moment and energy values were calculated. Theoretical chemical shifts in NMR spectra and the wavenumbers and intensities of the bands in vibrational spectra were analyzed. Calculated parameters were compared to experimental characteristic of studied compounds. Microbiological analysis of studied compounds was performed relative to: Bacillus subtilis, Pseudomonas aeruginosa, Escherichia coli and Klebsiella oxytoca. The relationship between spectroscopic and structure parameters of studied compounds in regard to their activity was analyzed.

Near-edge X-ray absorption spectra for metallic Cu and Mn

NASA Astrophysics Data System (ADS)

Greaves, G. N.; Durham, P. J.; Diakun, G.; Quinn, P.

1981-11-01

The measurement of X-ray absorption fine structure of metals- both in the extended region (EXAFS) as well as in the near edge region (XANES)-has been widely discussed (see refs 1-6 for Cu and refs 7-9 for Mn). The recent availability of intense X-ray fluxes from storage rings has usually been exploited for EXAFS leaving the XANES often with poorer resolution than earlier work performed on conventional sources (for example, compare the near edge structure for copper in ref. 1 with refs 3 or 6). In addition, whilst the theory and analysis of EXAFS is relatively well-established2,10, a theory for the strong scattering regime near to the absorption edge has only recently been developed11. We report here the first high resolution XANES spectra for Cu and Mn which were performed at the SRS storage ring at Daresbury. Although both metals have close-packed structures consisting of atoms of similar size their local atomic structure is different in detail. Significant differences are found in their respective XANES reflecting the senstivity of this region of the X-ray absorption fine structure to the local atomic structure. Spectra for the two metals have been analysed using the new multiple scattering formalism. This is a real space calculation and unlike a conventional band structure approach it does not require structural periodicity but works from the local arrangement of atoms.

Linear Optical and SERS Study on Metallic Membranes with Subwavelength Complementary Patterns

NASA Astrophysics Data System (ADS)

Hao, Qingzhen; Zeng, Yong; Jensen, Lasse; Werner, Douglas; Crespi, Vincent; Huang, Tony Jun; Interdepartmental Collaboration

2011-03-01

An efficient technique is developed to fabricate optically thin metallic films with subwavelength patterns and their complements simultaneously. By comparing the spectra of the complementary films, we show that Babinet's principle nearly holds in the optical domain. A discrete-dipole approximation can qualitatively describe their spectral dependence on the geometry of the constituent particles and the illuminating polarization. Using pyridine as probe molecules, we studied surface-enhanced Raman spectroscopy (SERS) from the complementary structure. Although the complementary structure posses closely related linear spectra, they have quite different near-field behaviors. For hole arrays, their averaged local field gains as well as the SERS enhancements are strongly correlated to their transmission spectra. We therefore can use cos 4 θ to approximately describe the dependence of the Raman intensity on the excitation polarization angle θ , while the complementary particle arrays present maximal local field gains at wavelengths generally much bigger than their localized surface plasmonic resonant wavelengths.

The effect of structurally related impurities on crystallinity reduction of sulfamethazine by grinding.

PubMed

Hamada, Yoshito; Ono, Makoto; Ohara, Motomu; Yonemochi, Etsuo

2016-12-30

In this study, the effect of structurally related impurities on crystallinity reduction of sulfamethazine by grinding was evaluated. The crystallinity of sulfamethazine was not decreased when it was ground alone. However, when structurally related impurities with sulfonamide derivatives were blended, the crystallinity of sulfamethazine was decreased by grinding. Other materials without a sulfonamide moiety showed no such effect. The Raman spectra of sulfamethazine demonstrated that there was a difference between its crystalline and amorphous states within its sulfonamide structure. It was suggested that the sulfonamide structure of the impurities was important in causing the inhibition of recrystallization of sulfamethazine during grinding. Copyright © 2016 Elsevier B.V. All rights reserved.

Structural comparison of nickel electrodes and precursor phases

NASA Technical Reports Server (NTRS)

Cornilsen, Bahne C.; Shan, Xiaoyin; Loyselle, Patricia

1989-01-01

A summary of previous Raman spectroscopic results and a discussion of important structural differences in the various phases of active mass and active mass precurors are presented. Raman spectra provide unique signatures for these phases, and allow one to distinguish each phase, even when the compound is amorphous to X-rays (i.e., does not scatter X-rays because of a lack of order and/or small particle size). The structural changes incurred during formation, charge and discharge, cobalt addition, and aging will be discussed and related to electrode properties. Important structural differences include NiO2 layer stacking, nonstoichiometry (especially cation-deficit nonstoichiometry), disorder, dopant content, and water content. The results indicate that optimal nickel active mass is non-close packed and nonstoichiometric. The formation process transforms precursor phases into this structure. Therefore, the precursor disorder, or lack thereof, influences this final active mass structure and the rate of formation. Aging processes induce structural change which is believed to be detrimental. The role of cobalt addition can be appreciated in terms of structures favored or stabilized by the dopant. In recent work, the in situ Raman technique to characterize the critical structural parameters was developed. An in situ method relates structure, electrochemistry, and preparation. In situ Raman spectra of cells during charge and discharge, either during cyclic voltammetry or under constant current conditions were collected. With the structure-preparation knowledge and the in situ Raman tool, it will be possible to define the structure-property-preparation relations in more detail. This instrumentation has application to a variety of electrode systems.

Progesterone and testosterone studies by neutron-scattering methods and quantum chemistry calculations

NASA Astrophysics Data System (ADS)

Holderna-Natkaniec, K.; Szyczewski, A.; Natkaniec, I.; Khavryutchenko, V. D.; Pawlukojc, A.

Inelastic incoherent neutron scattering (IINS) and neutron diffraction spectra of progesterone and testosterone were measured simultaneously on the NERA spectrometer at the IBR-2 pulsed reactor in Dubna. Both studied samples do not indicate any phase transition in the temperature range from 20 to 290K. The IINS spectra have been transformed to the phonon density of states (PDS) in the one-phonon scattering approximation. The PDS spectra display well-resolved peaks of low-frequency internal vibration modes up to 600cm-1. The assignment of these modes was proposed taking into account the results of calculations of the structure and dynamics of isolated molecules of the investigated substances. The quantum chemistry calculations were performed by the semi-empirical PM3 method and at the restricted Hartree-Fock level with the 6-31* basis set. The lower internal modes assigned to torsional vibration of the androstane skeleton mix with the lattice vibrations. The intense bands in the PDS spectra in the frequency range from 150 to 300cm-1 are related to librations of structurally inequivalent methyl groups.

Quantum-chemical calculations and electron diffraction study of the equilibrium molecular structure of vitamin K3

NASA Astrophysics Data System (ADS)

Khaikin, L. S.; Tikhonov, D. S.; Grikina, O. E.; Rykov, A. N.; Stepanov, N. F.

2014-05-01

The equilibrium molecular structure of 2-methyl-1,4-naphthoquinone (vitamin K3) having C s symmetry is experimentally characterized for the first time by means of gas-phase electron diffraction using quantum-chemical calculations and data on the vibrational spectra of related compounds.

Application of terahertz spectroscopy and theoretical calculation in dimethylurea isomers investigation

NASA Astrophysics Data System (ADS)

Zhao, Yonghong; Li, Zhi; Liu, Jianjun; Chen, Tao; Zhang, Huo; Qin, Binyi; Wu, Yifang

2018-03-01

The characteristic absorption spectra of two structural isomers of dimethylurea(DMU) in 0.6-1.8 THz region have been measured using terahertz time-domain spectroscopy (THZ-TDS) at room temperature. Significant differences have been found between their terahertz spectra and implied that the THZ-TDS is an effective means of identifying structural isomers. To simulate their spectra, calculations on single molecule and cluster of 1,1-DMU and 1,3-DMU were performed, and we found that the cluster calculations using DFT-D3 method are better to predict the experimental spectra. Using the normal mode as displacements in redundant internal coordinates and the GaussView program, most observed THz vibrational modes are assigned to bending and rocking modes related to the intermolecular hydrogen bonding interactions, and twisting mode of ethyl groups. The different spectral features of two isomers mainly arise from different intermolecular hydrogen bonds resulting from different atom arrangements in molecules and different molecule arrangements in crystals. Using the reduced-density-gradient (RDG) analysis, the positions and types of intermolecular hydrogen bonding interactions in 1,1-DMU and 1,3-DMU crystals are visualized. Therefore, we can confirm that THz-TDS can be used as an effective means for the recognition of structural isomers and detection of intermolecular hydrogen bonding interactions in these crystals.

Structural properties and FTIR-Raman spectra of the anti-hypertensive clonidine hydrochloride agent and their dimeric species

NASA Astrophysics Data System (ADS)

Romano, Elida; Davies, Lilian; Brandán, Silvia Antonia

2017-04-01

The structural and vibrational properties of the α-adrenergic agonist clonidine hydrochloride agent and their anionic and dimeric species were studied combining the experimental FT-IR and Raman spectra in solid phase with ab-initio calculations based on the density functional theory (DFT). All the calculations were performed by using the hybrid B3LYP with the 6-31G* and 6-311++G** basis sets. The structural properties for those species were studied employing the Natural Bond Orbital (NBO), Atoms in Molecules theory (AIM) and frontier orbitals calculations. The complete assignments of the FTIR and Raman spectra were performed combining the DFT calculations with the Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology. Very good concordances between the theoretical and experimental spectra were found. In addition, the force constants for those three species were computed and compared with the values reported for similar antihypertensive agents. The ionic nature of the H→Cl bond and the high value of the LP(1)N4 → LP*(1)H18 charge transfer could explain the high reactivity of clonidine hydrochloride in relation to other antihypertensive agent and the strong shifthing of the band assigned to the Nsbnd H stretching mode linked to the Hsbnd Cl bond toward lower wavenumbers.

Compositional Dependence of Optical and Structural Properties of Nanogranular Mixed ZrO2/ZnO/SnO2 Thin Film

NASA Astrophysics Data System (ADS)

Salari, S.; Ghodsi, F. E.

2018-06-01

A study on the optical properties and photoluminescence (PL) spectra of ternary oxide nanogranular thin films comprising Zr, Zn, and Sn revealed that the change in component ratio could direct the roadmap to improve characteristics of the films. Grazing angle X-ray diffraction analysis showed that incorporation of Sn atoms into the tetragonal structure of Zn/Zr thin film resulted in an amorphous structure. The band gap of film was tunable by precisely controlling the concentration of components. The widening of band gap could correlate to the quantum confinement effect. PL spectra of the composite thin films under excitation at 365 nm showed a sharp red emission with relatively Gaussian line shape, which was intensified in the optimum percentage ratio of 50/30/20. This nearly red emission is attributed to the radiative emission of electrons captured at low-energy traps located near the valence band. An optimum red emission is strongly desirable for use in white LEDs. The comparative study on FTIR spectra of unary, binary, and ternary thin films confirmed successful composition of three different metal oxides in ternary thin films. Detailed investigation on FTIR spectra of ternary compounds revealed that the quenching in PL emission at higher percentage of Sn was originally due to the hydroxyl group.

Electronic structures and abnormal phonon behaviors of cobalt-modified Na0.5Bi0.5TiO3-6%BaTiO3 single crystals

NASA Astrophysics Data System (ADS)

Huang, T.; Zhang, P.; Xu, L. P.; Chen, C.; Zhang, J. Z.; Hu, Z. G.; Luo, H. S.; Chu, J. H.

2016-10-01

Optical properties, electronic structures, and structural variations of x wt% cobalt (Co) doped Na0.5Bi0.5TiO3-6%BaTiO3 (x=0%, 0.5%, 0.8%) single crystals have been studied by temperature-dependent optical ellipsometry and Raman spectra from 250 to 650 K. Based on the temperature evolution of electronic transitions (Ecp1 and Ecp2) and the phonon modes involving Ti-O vibrations, two critical temperature points exhibit an increasing trend with Co dopants, which are related to structural variations for ferroelectric to anti-ferroelectric, and anti-ferroelectric to paraelectric transition, respectively. Additionally, distinguishing abnormal phonon behaviors can be observed from Raman spectra for the crystal of x=0.5% and 0.8%, which show reverse frequency shift of the modes involving Ti-O vibration. It can be ascribed to different relative concentration of Co2+ and Co3+ in the crystals, which has been confirmed by X-ray Photoelectron Spectroscopy data.

Structure Prediction of Self-Assembled Dye Aggregates from Cryogenic Transmission Electron Microscopy, Molecular Mechanics, and Theory of Optical Spectra.

PubMed

Friedl, Christian; Renger, Thomas; Berlepsch, Hans V; Ludwig, Kai; Schmidt Am Busch, Marcel; Megow, Jörg

2016-09-01

Cryogenic transmission electron microscopy (cryo-TEM) studies suggest that TTBC molecules self-assemble in aqueous solution to form single-walled tubes with a diameter of about 35 Å. In order to reveal the arrangement and mutual orientations of the individual molecules in the tube, we combine information from crystal structure data of this dye with a calculation of linear absorbance and linear dichroism spectra and molecular dynamics simulations. We start with wrapping crystal planes in different directions to obtain tubes of suitable diameter. This set of tube models is evaluated by comparing the resulting optical spectra with experimental data. The tubes that can explain the spectra are investigated further by molecular dynamics simulations, including explicit solvent molecules. From the trajectories of the most stable tube models, the short-range ordering of the dye molecules is extracted and the optimization of the structure is iteratively completed. The final structural model is a tube of rings with 6-fold rotational symmetry, where neighboring rings are rotated by 30° and the transition dipole moments of the chromophores form an angle of 74° with respect to the symmetry axis of the tube. This model is in agreement with cryo-TEM images and can explain the optical spectra, consisting of a sharp red-shifted J-band that is polarized parallel to to the symmetry axis of the tube and a broad blue-shifted H-band polarized perpendicular to this axis. The general structure of the homogeneous spectrum of this hybrid HJ-aggregate is described by an analytical model that explains the difference in redistribution of oscillator strength inside the vibrational manifolds of the J- and H-bands and the relative intensities and excitation energies of those bands. In addition to the particular system investigated here, the present methodology can be expected to aid the structure prediction for a wide range of self-assembled dye aggregates.

[The change in optical spectra from solid and liquid solution of copper phthalocyanines derivatives].

PubMed

Zheng, Xiao-pan; He, Zhi-qun; Zhang, Chun-xiu; Xu, Zheng; Wang, Yong-sheng

2006-06-01

In the present work, the change in electronic absorption spectra from three copper phthalocyanines (CuPc, tb-CuPc, oo-CuPc) in different environments was investigated. The mechanism of red shift Q-band absorption from the three species in an organic solvent before and after protonation was discussed. This was used to compare with those dispersed in solid films. The relation between the molecular interactions and the spectra change was studied. In a combination of POM, DSC and XRD techniques, the structure and morphology of the thin films were characterised. It was found that the molecules in the doped matrices of PC were associated or aggregated. This association and hence the corresponding change in absorption spectra cannot be altered by the modification of dopant concentration.

Indentation creep behaviors of amorphous Cu-based composite alloys

NASA Astrophysics Data System (ADS)

Song, Defeng; Ma, Xiangdong; Qian, Linfang

2018-04-01

This work reports the indentation creep behaviors of two Si2Zr3/amorphous Cu-based composite alloys utilizing nanoindentation technique. By analysis with Kelvin model, the retardation spectra of alloys at different positions, detached and attached regions to the intermetallics, were deduced. For the indentation of detached regions to Si2Zr3 intermetallics in both alloys, very similarity in creep displacement can be observed and retardation spectra show a distinct disparity in the second retardation peak. For the indentation of detached regions, the second retardation spectra also display distinct disparity. At both positions, the retardation spectra suggest that Si elements may lead to the relatively dense structure in the amorphous matrix and to form excessive Si2Zr3 intermetallics which may deteriorate the plastic deformation of current Cu-based composite alloys.

Photoluminescence of Porous Silicon-Zinc Oxide Hybrid structures

NASA Astrophysics Data System (ADS)

Olenych, I. B.; Monastyrskii, L. S.; Luchechko, A. P.

2017-03-01

Arrays of ZnO nanostructures, which are optically transparent in the visible range, were grown on the surface of porous silicon by electrochemical deposition. Photoluminescence excitation and emission spectra of the obtained hybrid structures were investigated in 220-450 and 400-800 nm regions, respectively. It is established that multicolor emission is formed by combining the luminescence bands of porous silicon and zinc oxide. The possibility of controlling the photoluminescence spectra by changing the excitation energy is demonstrated. It is revealed that thermal annealing has an effect on the luminescent properties of porous silicon/zinc oxide hybrid structures. Thermal processing at 500°C leads to a sharp decrease of long-wavelength luminescence associated with porous silicon and to an increase of short-wavelength luminescence intensity related to zinc oxide.

π-Stacking, C-H/π, and halogen bonding interactions in bromobenzene and mixed bromobenzene-benzene clusters.

PubMed

Reid, Scott A; Nyambo, Silver; Muzangwa, Lloyd; Uhler, Brandon

2013-12-19

Noncovalent interactions play an important role in many chemical and biochemical processes. Building upon our recent study of the homoclusters of chlorobenzene, where π-π stacking and CH/π interactions were identified as the most important binding motifs, in this work we present a study of bromobenzene (PhBr) and mixed bromobenzene-benzene clusters. Electronic spectra in the region of the PhBr monomer S0-S1 (ππ*) transition were obtained using resonant two-photon ionization (R2PI) methods combined with time-of-flight mass analysis. As previously found for related systems, the PhBr cluster spectra show a broad feature whose center is red-shifted from the monomer absorption, and electronic structure calculations indicate the presence of multiple isomers and Franck-Condon activity in low-frequency intermolecular modes. Calculations at the M06-2X/aug-cc-pVDZ level find in total eight minimum energy structures for the PhBr dimer: four π-stacked structures differing in the relative orientation of the Br atoms (denoted D1-D4), one T-shaped structure (D5), and three halogen bonded structures (D6-D8). The calculated binding energies of these complexes, corrected for basis set superposition error (BSSE) and zero-point energy (ZPE), are in the range of -6 to -24 kJ/mol. Time-dependent density functional theory (TDDFT) calculations predict that these isomers absorb over a range that is roughly consistent with the breadth of the experimental spectrum. To examine the influence of dipole-dipole interaction, R2PI spectra were also obtained for the mixed PhBr···benzene dimer, where the spectral congestion is reduced and clear vibrational structure is observed. This structure is well-simulated by Franck-Condon calculations that incorporate the lowest frequency intermolecular modes. Calculations find four minimum energy structures for the mixed dimer and predict that the binding energy of the global minimum is reduced by ~30% relative to the global minimum PhBr dimer structure.

Development of in-structure design spectra for dome mounted equipment on underground waste storage tanks at the Hanford Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Julyk, L.J.

1995-09-01

In-structure response spectra for dome mounted equipment on underground waste storage tanks at the Hanford Site are developed on the basis of recent soil-structure-interaction analyses. Recommended design spectra are provided for various locations on the tank dome.

Characterization of Tissue Structure at Varying Length Scales Using Temporal Diffusion Spectroscopy

PubMed Central

Gore, John C.; Xu, Junzhong; Colvin, Daniel C.; Yankeelov, Thomas E.; Parsons, Edward C.; Does, Mark D.

2011-01-01

The concepts, theoretical behavior and experimental applications of temporal diffusion spectroscopy are reviewed and illustrated. Temporal diffusion spectra are obtained by using oscillating gradient waveforms in diffusion-weighted measurements, and represent the manner in which various spectral components of molecular velocity correlations vary in different geometrical structures that restrict or hinder free movements. Measurements made at different gradient frequencies reveal information on the scale of restrictions or hindrances to free diffusion, and the shape of a spectrum reveals the relative contributions of spatial restrictions at different distance scales. Such spectra differ from other so-called diffusion spectra which depict spatial frequencies and are defined at a fixed diffusion time. Experimentally, oscillating gradients at moderate frequency are more feasible for exploring restrictions at very short distances, which in tissues correspond to structures smaller than cells. We describe the underlying concepts of temporal diffusion spectra and provide analytical expressions for the behavior of the diffusion coefficient as a function of gradient frequency in simple geometries with different dimensions. Diffusion in more complex model media that mimic tissues has been simulated using numerical methods. Experimental measurements of diffusion spectra have been obtained in suspensions of particles and cells, as well as in vivo in intact animals. An observation of particular interest is the increased contrast and heterogeneity observed in tumors using oscillating gradients at moderate frequency compared to conventional pulse gradient methods, and the potential for detecting changes in tumors early in their response to treatment. Computer simulations suggest that diffusion spectral measurements may be sensitive to intracellular structures such as nuclear size, and that changes in tissue diffusion properties may be measured before there are changes in cell density. PMID:20677208

Structural, electronic and vibrational properties of LaF3 according to density functional theory and Raman spectroscopy

NASA Astrophysics Data System (ADS)

Oreshonkov, A. S.; Roginskii, E. M.; Krylov, A. S.; Ershov, A. A.; Voronov, V. N.

2018-06-01

Crystal structure of LaF3 single crystal is refined in tysonite-type trigonal unit cell P c1 using density functional theory calculations and Raman spectroscopy. It is shown that trigonal structure with P c1 space group is more energy-efficient than hexagonal structure with space group P63 cm. Simulated Raman spectra obtained using LDA approximation is in much better agreement with experimental data than that obtained with PBE and PBEsol functionals of GGA. The calculated frequency value of silent mode B 2 in case of hexagonal structure P63 cm was found to be imaginary (unstable mode), thus the energy surface obtains negative curvature with respect to the corresponding normal coordinates of the mode which leads to instability of the hexagonal structure in harmonic approximation. The A 1g line at 214 cm‑1 in Raman spectra of LaF3 related to the translation of F2 ions along c axis can be connected with F2 ionic conductivity.

A theoretical description of the polarization dependence of the sum frequency generation spectroscopy of the water/vapor interface

NASA Astrophysics Data System (ADS)

Perry, Angela; Neipert, Christine; Kasprzyk, Christina Ridley; Green, Tony; Space, Brian; Moore, Preston B.

2005-10-01

An improved time correlation function (TCF) description of sum frequency generation (SFG) spectroscopy was developed and applied to theoretically describing the spectroscopy of the ambient water/vapor interface. A more general TCF expression than was published previously is presented—it is valid over the entire vibrational spectrum for both the real and imaginary parts of the signal. Computationally, earlier time correlation function approaches were limited to short correlation times that made signal processing challenging. Here, this limitation is overcome, and well-averaged spectra are presented for the three independent polarization conditions that are possible for electronically nonresonant SFG. The theoretical spectra compare quite favorably in shape and relative magnitude to extant experimental results in the O H stretching region of water for all polarization geometries. The methodological improvements also allow the calculation of intermolecular SFG spectra. While the intermolecular spectrum of bulk water shows relatively little structure, the interfacial spectra (for polarizations that are sensitive to dipole derivatives normal to the interface—SSP and PPP) show a well-defined intermolecular mode at 875cm-1 that is comparable in intensity to the rest of the intermolecular structure, and has an intensity that is approximately one-sixth of the magnitude of the intense free OH stretching peak. Using instantaneous normal mode methods, the resonance is shown to be due to a wagging mode localized on a single water molecule, almost parallel to the interface, with two hydrogens displaced normal to the interface, and the oxygen anchored in the interface. We have also uncovered the origin of another intermolecular mode at 95cm-1 for the SSP and PPP spectra, and at 220cm-1 for the SPS spectra. These resonances are due to hindered translations perpendicular to the interface for the SSP and PPP spectra, and translations parallel to the interface for the SPS spectra. Further, by examining the real and imaginary parts of the SFG signal, several resonances are shown to be due to a single spectroscopic species while the "donor" OH region is shown to consist of three distinct species—consistent with an earlier experimental analysis.

Electronic structure of the La 1 + xBa 2 - xCu 3O 7 + δ system studied by photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Lindberg, P. A. P.; Shen, Z.-X.; Hwang, J.; Shih, C. K.; Lindau, I.; Spicer, W. E.; Mitzi, D. B.; Kapitulnik, A.

1989-01-01

Photoemission experiments utilizing synchrotron radiation have been carried out on the high temperature superconductor La 1.075Ba 1.925Cu 3O 7.0. The valence band spectra show similar spectral features as those of YBa 2Cu 3O 6.9, even though large differences in relative peak intensities are observed. Oxygen-related states are identified by scanning the photon energy through the O2 s → O2 p absorption edge. The stability of the sample surface, and changes in the valence band spectra after annealing in ultrahigh vacuum are also briefly discussed.

Rotational Spectra of Hydrogen Bonded Networks of Amino Alcohols

NASA Astrophysics Data System (ADS)

Zhang, Di; Zwier, Timothy S.

2014-06-01

The rotational spectra of several different amino alcohols including D/L-allo-threoninol, 2-amino-1,3-propanediol and 1,3-diamino-2-propanol over the 6.5-18.5 GHz range have been investigated under jet-cooled conditions using chirped-pulsed Fourier transform microwave spectroscopy. Despite the small size of these molecules, a great variety of conformations have been observed in the molecular expansion. While the NH2 group is typically thought of as a H-bond acceptor, it often acts both as acceptor and donor in forming H-bonded networks. With three adjacent H-bonding substituents (a combination of OH and NH2 groups), many different hydrogen bonding patterns are possible, including H-bonded chains and H-bonded cycles. Since many of these structures differ primarily by the relative orientation of the H-atoms, the analysis of these rotational spectra are challenging. Only through an exhaustive conformational search and the comparison with the experimental rotational constants, nuclear quadrupolar splittings, and line strengths are we able to understand the complex nature of these interactions. The ways in which the presence and number of NH2 groups affects the relative energies, and distorts the structures will be explored.

Medium-range structural properties of vitreous germania obtained through first-principles analysis of vibrational spectra.

PubMed

Giacomazzi, Luigi; Umari, P; Pasquarello, Alfredo

2005-08-12

We analyze the principal vibrational spectra of vitreous GeO(2) and derive therefrom structural properties referring to length scales beyond the basic tetrahedral unit. We generate a model structure that yields a neutron structure factor in accord with experiment. The inelastic-neutron, the infrared, and the Raman spectra, calculated within a density-functional approach, also agree with respective experimental spectra. The accord for the Raman spectrum supports a Ge-O-Ge angle distribution centered at 135 degrees. The Raman feature X(2) is found to result from vibrations in three-membered rings, and therefore constitutes a distinctive characteristic of the medium-range structure.

First-Principles Predictions of Near-Edge X-ray Absorption Fine Structure Spectra of Semiconducting Polymers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Su, Gregory M.; Patel, Shrayesh N.; Pemmaraju, C. D.

The electronic structure and molecular orientation of semiconducting polymers in thin films determine their ability to transport charge. Methods based on near-edge X-ray absorption fine structure (NEXAFS) spectroscopy can be used to probe both the electronic structure and microstructure of semiconducting polymers in both crystalline and amorphous films. However, it can be challenging to interpret NEXAFS spectra on the basis of experimental data alone, and accurate, predictive calculations are needed to complement experiments. Here, we show that first-principles density functional theory (DFT) can be used to model NEXAFS spectra of semiconducting polymers and to identify the nature of transitions inmore » complicated NEXAFS spectra. Core-level X-ray absorption spectra of a set of semiconducting polymers were calculated using the excited electron and core-hole (XCH) approach based on constrained-occupancy DFT. A comparison of calculations on model oligomers and periodic structures with experimental data revealed the requirements for accurate prediction of NEXAFS spectra of both conjugated homopolymers and donor–acceptor polymers. The NEXAFS spectra predicted by the XCH approach were applied to study molecular orientation in donor–acceptor polymers using experimental spectra and revealed the complexity of using carbon edge spectra in systems with large monomeric units. The XCH approach has sufficient accuracy in predicting experimental NEXAFS spectra of polymers that it should be considered for design and analysis of measurements using soft X-ray techniques, such as resonant soft X-ray scattering and scanning transmission X-ray microscopy.« less

Structure Optimization of 21,23-Core-Modified Porphyrins Absorbing Long-Wavelength Light as Potential Photosensitizers Against Breast Cancer Cells

DTIC Science & Technology

2006-04-01

recording singlet oxygen emission spectra. A diode -pumped solid-state laser (Millenia X, Spectra-Physics) at 532 nm was the excitation source. The sample...biological properties in vitro Youngjae You,a,* Scott L. Gibsonb and Michael R. Dettya aInstitute for Lasers , Photonics, and Biophotonics, Department...relative to the exciting laser beam. An additional long-pass filter (850LP) was used to attenuate the excitation laser and the fluorescence from the

Composition and structure of fresh ammonia clouds on Jupiter based on quantitative analysis of Galileo/NIMS and New Horizons/LEISA spectra

NASA Astrophysics Data System (ADS)

Sromovsky, L. A.; Fry, P. M.

2018-06-01

Ammonia gas has long been assumed to be the main source of condensables for the upper cloud layer on Jupiter, but distinctive spectral features associated with ammonia have been seen only rarely. Since both ammonia and NH4SH absorb in the 3 μm region, and widespread absorption in the 3 μm region was present (Sromovsky and Fry, 2010), identification of the 2 μm absorption feature of NH3 provided an opportunity to clearly establish its presence in Jovian clouds. Baines et al. (2002) succeeded in finding in Near Infrared Mapping Spectrometer (NIMS) observations one feature that had both 2 μm and 3 μm absorption, and many which were known to have absorption at 2.73 μm. They named these Spectrally Identifiable Ammonia Clouds (SIACs). They also argued that these were fresh ammonia clouds that would eventually succumb to some process that would obscure their absorption features. Detection of many more of the 2 μm features was later achieved by New Horizon's Linear Etalon Imaging Spectral Array (LEISA) instrument, which provided both the spatial and spectral resolution needed to identify these features. Here we report on the first quantitative modeling that uses NIMS spectra over a broad (1-5.2 μm) spectral range and LEISA spectra over a much narrower (1.25-2.5 μm) spectral range to constrain the cloud structure and composition of these rare cloud features and compare them to background clouds. We find that the absorption signature at 2 μm, which is well characterized in LEISA spectra, is relatively subtle and easily matched by model clouds containing spherical particles of ammonia ice with radii of 2-4 μm. The NIMS spectra, which cover both reflected sunlight as well as thermal emission regions are more difficult to model with cloud materials plausibly present in Jupiter's atmosphere. The best signal/noise spectra obtained from NIMS provide a relatively sparse sampling of the spectrum, which does not establish the detailed shape of the 3 μm absorption region. NIMS SIAC spectra with much denser spectral sampling are limited by much higher noise levels that degrade the features that are key to identifying cloud composition. The structure which best matches the wide range NIMS SIAC spectra contains two overlapping NH3 clouds with a bi-modal size distribution over an optically thick NH4SH cloud. The bi-modal distribution may be a result of modeling non-spherical, possibly fractal aggregate, particles with spheres.

Vibrational, X-ray absorption, and Mössbauer spectra of sulfate minerals from the weathered massive sulfide deposit at Iron Mountain, California

USGS Publications Warehouse

Majzlan, Juraj; Alpers, Charles N.; Bender Koch, Christian; McCleskey, R. Blaine; Myneni, Satish B.C.; Neil, John M.

2011-01-01

The Iron Mountain Mine Superfund site in California is a prime example of an acid mine drainage (AMD) system with well developed assemblages of sulfate minerals typical for such settings. Here we present and discuss the vibrational (infrared), X-ray absorption, and M??ssbauer spectra of a number of these phases, augmented by spectra of a few synthetic sulfates related to the AMD phases. The minerals and related phases studied in this work are (in order of increasing Fe2O3/FeO): szomolnokite, rozenite, siderotil, halotrichite, r??merite, voltaite, copiapite, monoclinic Fe2(SO4)3, Fe2(SO4)3??5H2O, kornelite, coquimbite, Fe(SO4)(OH), jarosite and rhomboclase. Fourier transform infrared spectra in the region 750-4000cm-1 are presented for all studied phases. Position of the FTIR bands is discussed in terms of the vibrations of sulfate ions, hydroxyl groups, and water molecules. Sulfur K-edge X-ray absorption near-edge structure (XANES) spectra were collected for selected samples. The feature of greatest interest is a series of weak pre-edge peaks whose position is determined by the number of bridging oxygen atoms between Fe3+ octahedra and sulfate tetrahedra. M??ssbauer spectra of selected samples were obtained at room temperature and 80K for ferric minerals jarosite and rhomboclase and mixed ferric-ferrous minerals r??merite, voltaite, and copiapite. Values of Fe2+/[Fe2++Fe3+] determined by M??ssbauer spectroscopy agree well with those determined by wet chemical analysis. The data presented here can be used as standards in spectroscopic work where spectra of well-characterized compounds are required to identify complex mixtures of minerals and related phases. ?? 2011 Elsevier B.V.

Influence of the nature of the ligand on the structure and spectra of boron-containing iron(II) dioximates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pol'shin, E.V.; Trachevskii, V.V.; Tyukhtenko, S.I.

1987-11-01

The Moessbauer (/sup 57/Fe) and NMR (/sup 1/H, /sup 13/C, /sup 11/B) spectra of the macrobicyclic dioximates FeD/sub 3/(BF)/sub 2/, where H/sub 2/D stands for glyoxime, methylglyoxime, 1,2-cyclohexanedione dioxime (Nioxime), furildioxime, and benzil dioxime, have been investigated. The values of the isomer shifts for these compounds range from 0.31 to 0.37 mm/sec relative to sodium nitroprusside, and the Raman scattering ranges from 0.6 to 0.9 for the aliphatic oximes and is equal to approx. 0.2 for the aromatic oximes. The changes in the Raman scattering have been related to the angle of distortion of the trigonal prism. The greatest changesmore » in the /sup 13/C and /sup 1/H NMR spectra are observed for the atoms of the substituents.« less

Two-dimensional fourier transform spectrometer

DOEpatents

DeFlores, Lauren; Tokmakoff, Andrei

2016-10-25

The present invention relates to a system and methods for acquiring two-dimensional Fourier transform (2D FT) spectra. Overlap of a collinear pulse pair and probe induce a molecular response which is collected by spectral dispersion of the signal modulated probe beam. Simultaneous collection of the molecular response, pulse timing and characteristics permit real time phasing and rapid acquisition of spectra. Full spectra are acquired as a function of pulse pair timings and numerically transformed to achieve the full frequency-frequency spectrum. This method demonstrates the ability to acquire information on molecular dynamics, couplings and structure in a simple apparatus. Multi-dimensional methods can be used for diagnostic and analytical measurements in the biological, biomedical, and chemical fields.

Two-dimensional fourier transform spectrometer

DOEpatents

DeFlores, Lauren; Tokmakoff, Andrei

2013-09-03

The present invention relates to a system and methods for acquiring two-dimensional Fourier transform (2D FT) spectra. Overlap of a collinear pulse pair and probe induce a molecular response which is collected by spectral dispersion of the signal modulated probe beam. Simultaneous collection of the molecular response, pulse timing and characteristics permit real time phasing and rapid acquisition of spectra. Full spectra are acquired as a function of pulse pair timings and numerically transformed to achieve the full frequency-frequency spectrum. This method demonstrates the ability to acquire information on molecular dynamics, couplings and structure in a simple apparatus. Multi-dimensional methods can be used for diagnostic and analytical measurements in the biological, biomedical, and chemical fields.

Two-dimensional sum-frequency generation (2D SFG) reveals structure and dynamics of a surface-bound peptide

PubMed Central

Laaser, Jennifer E.; Skoff, David R.; Ho, Jia-Jung; Joo, Yongho; Serrano, Arnaldo L.; Steinkruger, Jay D.; Gopalan, Padma; Gellman, Samuel H.; Zanni, Martin T.

2014-01-01

Surface-bound polypeptides and proteins are increasingly used to functionalize inorganic interfaces such as electrodes, but their structural characterization is exceedingly difficult with standard technologies. In this paper, we report the first two-dimensional sum-frequency generation (2D SFG) spectra of a peptide monolayer, which is collected by adding a mid-IR pulse shaper to a standard femtosecond SFG spectrometer. On a gold surface, standard FTIR spectroscopy is inconclusive about the peptide structure because of solvation-induced frequency shifts, but the 2D lineshapes, anharmonic shifts, and lifetimes obtained from 2D SFG reveal that the peptide is largely α-helical and upright. Random coil residues are also observed, which do not themselves appear in SFG spectra due to their isotropic structural distribution, but which still absorb infrared light and so can be detected by cross-peaks in 2D SFG spectra. We discuss these results in the context of peptide design. Because of the similar way in which the spectra are collected, these 2D SFG spectra can be directly compared to 2D IR spectra, thereby enabling structural interpretations of surface-bound peptides and biomolecules based on the well-studied structure/2D IR spectra relationships established from soluble proteins. PMID:24372101

The simulation of UV spectroscopy and electronic analysis of temozolomide and dacarbazine chemical decomposition to their metabolites.

PubMed

Khalilian, M Hossein; Mirzaei, Saber; Taherpour, Avat Arman

2016-11-01

The electronic features of anti-tumor agent, temozolomide, and its degradation products (MTIC and metabolite AIC) have been traced by means of UV absorption spectroscopy in vacuo and aqueous media. For comparison, electronic spectra of related structures and drugs (e.g., dacarbazine) were also investigated. These investigations were carried out using time-dependent density functional theory (TD-DFT) method while the conductor like screening model (COSMO) were applied for the inclusion of solvent effects in electronic spectra. From functional benchmarking, two methods; B3LYP and O3LYP were selected among several other methods with 6-311+G(2d,p) basis set aiming to get the best results in accord with the experimental values. An assessment of the obtained spectra has shown that O3LYP functional gives a mean absolute error (MAE) from experimental absorption peaks of 4.3 nm compared to the 7.2 nm MAE value at B3LYP level in aqueous media. Furthermore, since the structural and tautomeric conformers affect the electronic spectra, conformational preferences have been analyzed in temozolomide, dacarbazine, and their related structures. Temozolomide structure possesses two rotamers that differ in the orientation of carboxamide moiety with a small energy difference (energy difference of 1.39 kcal mol -1 in vacuo and 0.35 kcal mol -1 in aqueous media at B3LYP/6-311++G(2df,3pd). The more stable and meta-stable TMZ rotamer have shown their absorption maxima at 329-334 nm, respectively, at O3LYP level in aqueous media. Applying statistical calculation according to Boltzmann population formula at 25 °C and computed weighed mean estimates the λ max of temozolomide at 331 nm, which is in notable agreement with the experimental value (330 nm). Moreover, molecular orbital composition analysis has been conducted in order to interpret these findings. Graphical Abstract Temozolomide and dacarbazine.

Low-temperature and low atmospheric pressure infrared reflectance spectroscopy of Mars soil analog materials

NASA Technical Reports Server (NTRS)

Bishop, Janice L.; Pieters, Carle M.

1995-01-01

Infrared reflectance spectra of carefully selected Mars soil analog materials have been measured under low atmospheric pressures and temperatures. Chemically altered montmorillonites containing ferrihydrite and hydrated ferric sulfate complexes are examined, as well as synthetic ferrihydrite and a palagonitic soil from Haleakala, Maui. Reflectance spectra of these analog materials exhibit subtle visible to near-infrared features, which are indicative of nanophase ferric oxides or oxyhydroxides and are similar to features observed in the spectra of the bright regions of Mars. Infrared reflectance spectra of these analogs include hydration features due to structural OH, bound H2O, and adsorbed H2O. The spectral character of these hydration features is highly dependent on the sample environment and on the nature of the H2O/OH in the analogs. The behavior of the hydration features near 1.9 micron, 2.2 micron, 2.7 micron, 3 micron, and 6 microns are reported here in spectra measured under a Marslike atmospheric environment. In spectra of these analogs measured under dry Earth atmospheric conditions the 1.9-micron band depth is 8-17%; this band is much stronger under moist conditions. Under Marslike atmospheric conditions the 1.9-micron feature is broad and barely discernible (1-3% band depth) in spectra of the ferrihydrite and palagonitic soil samples. In comparable spectra of the ferric sulfate-bearing montmorillonite the 1.9-micron feature is also broad, but stronger (6% band depth). In the low atmospheric pressure and temperature spectra of the ferrihydrite-bearing montmorillonite this feature is sharper than the other analogs and relatively stronger (6% band depth). Although the intensity of the 3-micron band is weaker in spectra of each of the analogs when measured under Marslike conditions, the 3-micron band remains a dominant feature and is especially broad in spectra of the ferrihydrite and palagonitic soil. The structural OH features observed in these materials at 2.2-2.3 micron and 2.75 microns remain largely unaffected by the environmental conditions. A shift in the Christiansen feature towards shorter wavelengths has also been observed with decreasing atmospheric pressure and temperature in the midinfrared spectra of these samples.

Size resolved infrared spectroscopy of Na(CH3OH)n (n = 4-7) clusters in the OH stretching region: unravelling the interaction of methanol clusters with a sodium atom and the emergence of the solvated electron.

PubMed

Forck, Richard M; Pradzynski, Christoph C; Wolff, Sabine; Ončák, Milan; Slavíček, Petr; Zeuch, Thomas

2012-03-07

Size resolved IR action spectra of neutral sodium doped methanol clusters have been measured using IR excitation modulated photoionisation mass spectroscopy. The Na(CH(3)OH)(n) clusters were generated in a supersonic He seeded expansion of methanol by subsequent Na doping in a pick-up cell. A combined analysis of IR action spectra, IP evolutions and harmonic predictions of IR spectra (using density functional theory) of the most stable structures revealed that for n = 4, 5 structures with an exterior Na atom showing high ionisation potentials (IPs) of ~4 eV dominate, while for n = 6, 7 clusters with lower IPs (~3.2 eV) featuring fully solvated Na atoms and solvated electrons emerge and dominate the IR action spectra. For n = 4 simulations of photoionisation spectra using an ab initio MD approach confirm the dominance of exterior structures and explain the previously reported appearance IP of 3.48 eV by small fractions of clusters with partly solvated Na atoms. Only for this cluster size a shift in the isomer composition with cluster temperature has been observed, which may be related to kinetic stabilisation of less Na solvated clusters at low temperatures. Features of slow fragmentation dynamics of cationic Na(+)(CH(3)OH)(6) clusters have been observed for the photoionisation near the adiabatic limit. This finding points to the relevance of previously proposed non-vertical photoionisation dynamics of this system.

Development of a NIR-based blend uniformity method for a drug product containing multiple structurally similar actives by using the quality by design principles.

PubMed

Lin, Yiqing; Li, Weiyong; Xu, Jin; Boulas, Pierre

2015-07-05

The aim of this study is to develop an at-line near infrared (NIR) method for the rapid and simultaneous determination of four structurally similar active pharmaceutical ingredients (APIs) in powder blends intended for the manufacturing of tablets. Two of the four APIs in the formula are present in relatively small amounts, one at 0.95% and the other at 0.57%. Such small amounts in addition to the similarity in structures add significant complexity to the blend uniformity analysis. The NIR method is developed using spectra from six laboratory-created calibration samples augmented by a small set of spectra from a large-scale blending sample. Applying the quality by design (QbD) principles, the calibration design included concentration variations of the four APIs and a main excipient, microcrystalline cellulose. A bench-top FT-NIR instrument was used to acquire the spectra. The obtained NIR spectra were analyzed by applying principal component analysis (PCA) before calibration model development. Score patterns from the PCA were analyzed to reveal relationship between latent variables and concentration variations of the APIs. In calibration model development, both PLS-1 and PLS-2 models were created and evaluated for their effectiveness in predicting API concentrations in the blending samples. The final NIR method shows satisfactory specificity and accuracy. Copyright © 2015 Elsevier B.V. All rights reserved.

Propagation Diagnostic Simulations Using High-Resolution Equatorial Plasma Bubble Simulations

NASA Astrophysics Data System (ADS)

Rino, C. L.; Carrano, C. S.; Yokoyama, T.

2017-12-01

In a recent paper, under review, equatorial-plasma-bubble (EPB) simulations were used to conduct a comparative analysis of the EPB spectra characteristics with high-resolution in-situ measurements from the C/NOFS satellite. EPB realizations sampled in planes perpendicular to magnetic field lines provided well-defined EPB structure at altitudes penetrating both high and low-density regions. The average C/NOFS structure in highly disturbed regions showed nearly identical two-component inverse-power-law spectral characteristics as the measured EPB structure. This paper describes the results of PWE simulations using the same two-dimensional cross-field EPB realizations. New Irregularity Parameter Estimation (IPE) diagnostics, which are based on two-dimensional equivalent-phase-screen theory [A theory of scintillation for two-component power law irregularity spectra: Overview and numerical results, by Charles Carrano and Charles Rino, DOI: 10.1002/2015RS005903], have been successfully applied to extract two-component inverse-power-law parameters from measured intensity spectra. The EPB simulations [Low and Midlatitude Ionospheric Plasma DensityIrregularities and Their Effects on Geomagnetic Field, by Tatsuhiro Yokoyama and Claudia Stolle, DOI 10.1007/s11214-016-0295-7] have sufficient resolution to populate the structure scales (tens of km to hundreds of meters) that cause strong scintillation at GPS frequencies. The simulations provide an ideal geometry whereby the ramifications of varying structure along the propagation path can be investigated. It is well known path-integrated one-dimensional spectra increase the one-dimensional index by one. The relation requires decorrelation along the propagation path. Correlated structure would be interpreted as stochastic total-electron-content (TEC). The simulations are performed with unmodified structure. Because the EPB structure is confined to the central region of the sample planes, edge effects are minimized. Consequently, the propagated signal phase can be comparted to path-integrated phase for evaluating TEC extraction. Only the frequency dependence of phase scintillation distinguishes phase scintillation. The simulations allow scale-dependent exploration of remote-sensing diagnostics.

Fragmentation pathways and structural characterization of organophosphorus compounds related to the Chemical Weapons Convention by electron ionization and electrospray ionization tandem mass spectrometry.

PubMed

Hosseini, Seyed Esmaeil; Saeidian, Hamid; Amozadeh, Ali; Naseri, Mohammad Taghi; Babri, Mehran

2016-12-30

For unambiguous identification of Chemical Weapons Convention (CWC)-related chemicals in environmental samples, the availability of mass spectra, interpretation skills and rapid microsynthesis of suspected chemicals are essential requirements. For the first time, the electron ionization single quadrupole and electrospray ionization tandem mass spectra of a series of O-alkyl N-[bis(dimethylamino)methylidene]-P-methylphosphonamidates (Scheme 1, cpd 4) were studied for CWC verification purposes. O-Alkyl N-[bis(dimethylamino)methylidene]-P-methylphosphonamidates were prepared through a microsynthetic method and were analyzed using electron ionization and electrospray ionization mass spectrometry with gas and liquid chromatography, respectively, as MS-inlet systems. General EI and ESI fragmentation pathways were proposed and discussed, and collision-induced dissociation studies of the protonated derivatives of these compounds were performed to confirm proposed fragment ion structures by analyzing mass spectra of deuterated analogs. Mass spectrometric studies revealed some interesting fragmentation pathways during the ionization process, such as McLafferty rearrangement, hydrogen rearrangement and a previously unknown intramolecular electrophilic aromatic substitution reaction. The EI and ESI fragmentation routes of the synthesized compounds 4 were investigated with the aim of detecting and identifying CWC-related chemicals during on-site inspection and/or off-site analysis and toxic chemical destruction monitoring. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

First light with Trident: multi-platform synthetic quasar spectra

NASA Astrophysics Data System (ADS)

Silvia, Devin W.; Hummels, Cameron B.; Smith, Britton

2017-01-01

Observational efforts to better understand the nature of the intergalactic and circumgalactic media have relied heavily on the information encoded in the absorption line systems of quasar spectra. Numerical simulations of large-scale structure and galaxy evolution are well-suited to explore the properties of those same media owing to the relative ease with which one can access physical quantities from complex, three-dimensional data. However, a difficulty arises when one tries to make direct “apple-to-apples” comparisons between observed spectra and simulated data. In an effort to provide a common language capable of linking theory and observation, we announce the release of Trident. Trident is a publicly available software tool that enables the creation of realistic synthetic absorption spectra from virtually all widely-used hydrodynamics simulation codes. Through user-controlled levels of spectral realism, direct comparisons between simulated and observed data become not only possible, but greatly simplified. We present the methods for extracting artificial quasar sightlines and generating spectra as well as early-stage applications of those spectra to intergalactic and circumgalactic absorption line studies.

Spatial variations in annual cycles of body-size spectra of planktonic ciliates and their environmental drivers in marine ecosystems.

PubMed

Xu, Henglong; Jiang, Yong; Xu, Guangjian

2016-11-15

Body-size spectra has proved to be a useful taxon-free resolution to summarize a community structure for bioassessment. The spatial variations in annual cycles of body-size spectra of planktonic ciliates and their environmental drivers were studied based on an annual dataset. Samples were biweekly collected at five stations in a bay of the Yellow Sea, northern China during a 1-year cycle. Based on a multivariate approach, the second-stage analysis, it was shown that the annual cycles of the body-size spectra were significantly different among five sampling stations. Correlation analysis demonstrated that the spatial variations in the body-size spectra were significantly related to changes of environmental conditions, especially dissolved nitrogen, alone or in combination with salinity and dissolve oxygen. Based on results, it is suggested that the nutrients may be the environmental drivers to shape the spatial variations in annual cycles of planktonic ciliates in terms of body-size spectra in marine ecosystems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Complex polarization propagator approach in the restricted open-shell, self-consistent field approximation: the near K-edge X-ray absorption fine structure spectra of allyl and copper phthalocyanine.

PubMed

Linares, Mathieu; Stafström, Sven; Rinkevicius, Zilvinas; Ågren, Hans; Norman, Patrick

2011-05-12

A presentation of the complex polarization propagator in the restricted open-shell self-consistent field approximation is given. It rests on a formulation of a resonant-convergent, first-order polarization propagator approach that makes it possible to directly calculate the X-ray absorption cross section at a particular frequency without explicitly addressing the excited states. The quality of the predicted X-ray spectra relates only to the type of density functional applied without any separate treatment of dynamical relaxation effects. The method is applied to the calculation of the near K-edge X-ray absorption fine structure spectra of allyl and copper phthalocyanine. Comparison is made between the spectra of the radicals and those of the corresponding cations and anions to assess the effect of the increase of electron charge in the frontier orbital. The method offers the possibility for unique assignment of symmetry-independent atoms. The overall excellent spectral agreement motivates the application of the method as a routine precise tool for analyzing X-ray absorption of large systems of technological interest.

Structural properties, vibrational spectra and surface-enhanced Raman scattering of 2,4,6-trichloro- and tribromoanilines: A comparative study

NASA Astrophysics Data System (ADS)

Haruna, Kabiru; Saleh, Tawfik A.; Al Thagfi, Jameel; Al-Saadi, Abdulaziz A.

2016-10-01

A comparative electronic and spectroscopic analysis of 2,4,6-trichloroaniline (TCA) and 2,4,6-tribromoaniline (TBA) was carried out by theoretical and experimental techniques. The NH2 inversion barrier in TCA and TBA molecules was predicted to be three times less than that in aniline and 2,4,6-trifluoroaniline. The size of the halogen substituents in the ortho positions is shown by density functional theory to play an important role in determining the electronic and structural properties of the amino group in the investigated haloaniline derivatives. A thorough interpretation of the infrared and Raman spectra has been performed on the basis of the observed and calculated infrared and Raman spectra as well as calculated potential energy distribution values. In addition, the SERS spectra for both trihaloanilines were successfully collected up to a concentration of 10-6 M using aged hydroxylamine-reduced silver colloid as an active substrate for TCA and TBA. SERS intensities of several peaks were found to linearly change with concentration allowing quantitative analyses of TCA and TBA. A relatively stronger interaction in the case of TBA-silver colloids is predicted compared to the TCA analogue.

Structure, spectra and antioxidant action of ascorbic acid studied by density functional theory, Raman spectroscopic and nuclear magnetic resonance techniques.

PubMed

Singh, Gurpreet; Mohanty, B P; Saini, G S S

2016-02-15

Structure, vibrational and nuclear magnetic resonance spectra, and antioxidant action of ascorbic acid towards hydroxyl radicals have been studied computationally and in vitro by ultraviolet-visible, nuclear magnetic resonance and vibrational spectroscopic techniques. Time dependant density functional theory calculations have been employed to specify various electronic transitions in ultraviolet-visible spectra. Observed chemical shifts and vibrational bands in nuclear magnetic resonance and vibrational spectra, respectively have been assigned with the help of calculations. Changes in the structure of ascorbic acid in aqueous phase have been examined computationally and experimentally by recording Raman spectra in aqueous medium. Theoretical calculations of the interaction between ascorbic acid molecule and hydroxyl radical predicted the formation of dehydroascorbic acid as first product, which has been confirmed by comparing its simulated spectra with the corresponding spectra of ascorbic acid in presence of hydrogen peroxide. Copyright © 2015 Elsevier B.V. All rights reserved.

[A method for obtaining redshifts of quasars based on wavelet multi-scaling feature matching].

PubMed

Liu, Zhong-Tian; Li, Xiang-Ru; Wu, Fu-Chao; Zhao, Yong-Heng

2006-09-01

The LAMOST project, the world's largest sky survey project being implemented in China, is expected to obtain 10(5) quasar spectra. The main objective of the present article is to explore methods that can be used to estimate the redshifts of quasar spectra from LAMOST. Firstly, the features of the broad emission lines are extracted from the quasar spectra to overcome the disadvantage of low signal-to-noise ratio. Then the redshifts of quasar spectra can be estimated by using the multi-scaling feature matching. The experiment with the 15, 715 quasars from the SDSS DR2 shows that the correct rate of redshift estimated by the method is 95.13% within an error range of 0. 02. This method was designed to obtain the redshifts of quasar spectra with relative flux and a low signal-to-noise ratio, which is applicable to the LAMOST data and helps to study quasars and the large-scale structure of the universe etc.

Transient Spectra in TDDFT: Corrections and Correlations

NASA Astrophysics Data System (ADS)

Parkhill, John; Nguyen, Triet

We introduce an atomistic, all-electron, black-box electronic structure code to simulate transient absorption (TA) spectra and apply it to simulate pyrazole and a GFP chromophore derivative. The method is an application of OSCF2, our dissipative extension of time-dependent density functional theory. We compare our simulated spectra directly with recent ultra-fast spectroscopic experiments, showing that they are usefully predicted. We also relate bleaches in the TA signal to Fermi-blocking which would be missed in a simplified model. An important ingredient in the method is the stationary-TDDFT correction scheme recently put forwards by Fischer, Govind, and Cramer which allows us to overcome a limitation of adiabatic TDDFT. We demonstrate that OSCF2 is able to predict both the energies of bleaches and induced absorptions, as well as the decay of the transient spectrum, with only the molecular structure as input. With remaining time we will discuss corrections which resolve the non-resonant behavior of driven TDDFT, and correlated corrections to mean-field dynamics.

Rapid approach to analyze biochemical variation in rat organs by ATR FTIR spectroscopy

NASA Astrophysics Data System (ADS)

Staniszewska, Emilia; Malek, Kamilla; Baranska, Malgorzata

2014-01-01

ATR FTIR spectra were collected from rat tissue homogenates (myocardium, brain, liver, lung, intestine, and kidney) to analyze their biochemical content. Based on the second derivative of an average spectral profile it was possible to assign bands e.g. to triglycerides and cholesterol esters, proteins, phosphate macromolecules (DNA, RNA, phospholipids, phosphorylated proteins) and others (glycogen, lactate). Peaks in the region of 1600-1700 cm-1 related to amide I mode revealed the secondary structure of proteins. The collected spectra do not characterize morphological structure of the investigated tissues but show their different composition. The comparison of spectral information gathered from FTIR spectra of the homogenates and those obtained previously from FTIR imaging of the tissue sections implicates that the presented here approach can be successfully employed in the investigations of biochemical variation in animal tissues. Moreover, it can be used in the pharmacological and pharmacokinetic studies to correlate the overall biochemical status of the tissue with the pathological changes it has undergone.

Hybrid accretion disks in active galactic nuclei. I - Structure and spectra

NASA Technical Reports Server (NTRS)

Wandel, Amri; Liang, Edison P.

1991-01-01

A unified treatment is presented of the two distinct states of vertically thin AGN accretion disks: a cool (about 10 to the 6th K) optically thick solution, and a hot (about 10 to the 9th K) optically thin solution. A generalized formalism and a new radiative cooling equation valid in both regimes are introduced. A new luminosity limit is found at which the hot and cool alpha solutions merge into a single solution of intermediate optical depth. Analytic solutions for the disk structure are given, and output spectra are computed numerically. This is used to demonstrate the prospect of fitting AGN broadband spectra containing both the UV bump as well as the hard X-ray and gamma-ray tail, using a single accretion disk model. Such models are found to make definite predictions about the observed spectrum, such as the relation between the hard X-ray spectral index, the UV-to-X-ray luminosity ratio, and a feature of about 1 MeV.

Recent Development in Spectroscopic and Chemical Characterization of Cellulose

DTIC Science & Technology

2005-01-01

specific to the reducing end groups of the polysaccharides , confirmed the parallel alignment of molecular chains within the microfibrils in native...they include primary, secondary, and tertiary structures. And indeed, crystallographic studies of the monosaccharides and of related structures...Two approaches were adopted for this purpose. The first was based on examining the Raman spectra of polysaccharide polymers and oligomers that

Study of defects and vacancies in structural properties of Mn, co-doped oxides: ZnO

NASA Astrophysics Data System (ADS)

Kumar, Harish; Kaushik, A.; Alvi, P. A.; Dalela, B.; Dalela, S.

2018-05-01

The paper deals with the Structural properties on Mn, Co doped oxides ZnO samples using XRD, Positron Annihilation Lifetime (PAL) Spectra and Raman Spectra. The Mn, Co doped ZnO samples crystallize in a wurtzite structure without any impurity phases in XRD Spectra. The defect state of these samples has been investigated by using positron annihilation lifetime (PAL) spectroscopy technique in which all the relevant lifetime parameters are measured for all the spectra. The results are explained in the direction of doping concentration in these samples in terms of defects structure on Zn lattice site VZn and oxygen defects Vo.

Iridescence from photonic crystals and its suppression in butterfly scales

PubMed Central

Poladian, Leon; Wickham, Shelley; Lee, Kwan; Large, Maryanne C.J.

2008-01-01

Regular three-dimensional periodic structures have been observed in the scales of over half a dozen butterfly species. We compare several of these structures: we calculate their photonic bandgap properties; measure the angular variation of the reflection spectra; and relate the observed iridescence (or its suppression) to the structures. We compare the mechanisms for iridescence suppression in different species and conclude with some speculations about form, function, development and evolution. PMID:18980932

Multivariate Analysis of Two-Dimensional 1H, 13C Methyl NMR Spectra of Monoclonal Antibody Therapeutics To Facilitate Assessment of Higher Order Structure.

PubMed

Arbogast, Luke W; Delaglio, Frank; Schiel, John E; Marino, John P

2017-11-07

Two-dimensional (2D) 1 H- 13 C methyl NMR provides a powerful tool to probe the higher order structure (HOS) of monoclonal antibodies (mAbs), since spectra can readily be acquired on intact mAbs at natural isotopic abundance, and small changes in chemical environment and structure give rise to observable changes in corresponding spectra, which can be interpreted at atomic resolution. This makes it possible to apply 2D NMR spectral fingerprinting approaches directly to drug products in order to systematically characterize structure and excipient effects. Systematic collections of NMR spectra are often analyzed in terms of the changes in specifically identified peak positions, as well as changes in peak height and line widths. A complementary approach is to apply principal component analysis (PCA) directly to the matrix of spectral data, correlating spectra according to similarities and differences in their overall shapes, rather than according to parameters of individually identified peaks. This is particularly well-suited for spectra of mAbs, where some of the individual peaks might not be well resolved. Here we demonstrate the performance of the PCA method for discriminating structural variation among systematic sets of 2D NMR fingerprint spectra using the NISTmAb and illustrate how spectral variability identified by PCA may be correlated to structure.

Low-temperature and low atmospheric pressure infrared reflectance spectroscopy of Mars soil analog materials

NASA Technical Reports Server (NTRS)

Bishop, Janice L.; Pieters, Carle M.

1995-01-01

Infrared reflectance spectra of carefully selected Mars soil analog materials have been measured under low atmospheric pressures and temperatures. Chemically altered montmorillonites containing ferrihydrite and hydrated ferric sulfate complexes are examined, as well as synthetic ferrihydrate and a palagonitic soil from Haleakala, Maui. Reflectance spectra of these analog materials exhibit subtle visible to near-infrared features, which are indicative of nanophase ferric oxides or oxyhydroxides and are similar to features observed in the spectra of the bright regions of Mars. Infrared reflectance spectra of these analogs include hydration features due to structural OH, bound H2O and adsorbed H2O. The spectal character of these hydration features is highly dependent on the sample environment and on the nature of the H2O/OH in the analogs. The behavior of the hydration features near 1.9 micrometers, 2.2 micrometers, 2.7 micrometers, 3 micrometers, and 6 micrometers are reported here in spetra measured under Marslike atmospheric environment. In spectra of these analogs measured under dry Earth atmospheric conditions the 1.9-micrometer band depth is 8-17%; this band is much stonger under moist conditions. Under Marslike atmospheric conditions the 1.9-micrometer feature is broad and barely discernible (1-3% band depth) in spectra of the ferrihydrite and palagonitic soil samples. In comparable spectra of the ferric sulfate-bearing montmorillonite the 1.9-micrometer feature is also broad, but stronger (6% band depth). In the low atmospheric pressure and temperature spectra of the ferrihydrite-bearing montmorillonite this feature is sharper than the other analogs and relatively stronger (6% band depth). Although the intensity of the 3- micrometer band is weaker in spectra of each of the analogs when measured under Marslike conditions, the 3-micromter band remains a dominant feature and is especially broad in spectra of the ferrihydrite and palagonitic soil. The structural OH features observed in these materials at 2.2-2.3 micrometers and 2.27 micrometers remain largely unaffected by the environmental conditions. A shift in the Christiansen feature towards shorter wavelengths has also been observed with decreasing atmospheric pressure and temperature in the midinfrared spectra of these samples.

Revisiting the origin of satellites in core-level photoemission of transparent conducting oxides: The case of n -doped SnO2

NASA Astrophysics Data System (ADS)

Borgatti, Francesco; Berger, J. A.; Céolin, Denis; Zhou, Jianqiang Sky; Kas, Joshua J.; Guzzo, Matteo; McConville, C. F.; Offi, Francesco; Panaccione, Giancarlo; Regoutz, Anna; Payne, David J.; Rueff, Jean-Pascal; Bierwagen, Oliver; White, Mark E.; Speck, James S.; Gatti, Matteo; Egdell, Russell G.

2018-04-01

The longstanding problem of interpretation of satellite structures in core-level photoemission spectra of metallic systems with a low density of conduction electrons is addressed using the specific example of Sb-doped SnO2. Comparison of ab initio many-body calculations with experimental hard x-ray photoemission spectra of the Sn 4 d states shows that strong satellites are produced by coupling of the Sn core hole to the plasma oscillations of the free electrons introduced by doping. Within the same theoretical framework, spectral changes of the valence band spectra are also related to dynamical screening effects. These results demonstrate that, for the interpretation of electron correlation features in the core-level photoelectron spectra of such narrow-band materials, going beyond the homogeneous electron gas electron-plasmon coupling model is essential.

Analytic calculations of hyper-Raman spectra from density functional theory hyperpolarizability gradients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ringholm, Magnus; Ruud, Kenneth; Bast, Radovan

We present the first analytic calculations of the geometrical gradients of the first hyperpolarizability tensors at the density-functional theory (DFT) level. We use the analytically calculated hyperpolarizability gradients to explore the importance of electron correlation effects, as described by DFT, on hyper-Raman spectra. In particular, we calculate the hyper-Raman spectra of the all-trans and 11-cis isomers of retinal at the Hartree-Fock (HF) and density-functional levels of theory, also allowing us to explore the sensitivity of the hyper-Raman spectra on the geometrical characteristics of these structurally related molecules. We show that the HF results, using B3LYP-calculated vibrational frequencies and force fields,more » reproduce the experimental data for all-trans-retinal well, and that electron correlation effects are of minor importance for the hyper-Raman intensities.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vidmer, Alexandre, E-mail: alexandre@vidmer.com; Sclauzero, Gabriele; Pasquarello, Alfredo

The infrared absorption spectra of jennite, tobermorite 14 Å, anomalous tobermorite 11 Å, and normal tobermorite 11 Å are simulated within a density-functional-theory scheme. The atomic coordinates and the cell parameters are optimized resulting in structures which agree with previous studies. The vibrational frequencies and modes are obtained for each mineral. The vibrational density of states is analyzed through extensive projections on silicon tetrahedra, oxygen atoms, OH groups, and water molecules. The coupling with the electric field is achieved through the use of density functional perturbation theory, which yields Born effective charges and dielectric constants. The simulated absorption spectra reproducemore » well the experimental spectra, thereby allowing for a detailed interpretation of the spectral features in terms of the underlying vibrational modes. In the far-infrared part of the absorption spectra, the interplay between Ca and Si related vibrations leads to differences which are sensitive to the calcium/silicon ratio of the mineral.« less

Excitonic spectra and energy band structure of ZnAl2Se4 crystals

NASA Astrophysics Data System (ADS)

Syrbu, N. N.; Zalamai, V. V.; Tiron, A. V.; Tiginyanu, I. M.

2015-11-01

Absorption, reflection and wavelength modulated reflection spectra were investigated in ZnAl2Se4 crystals. The energy positions of ground and excited states for three excitonic series (А, В and С) were determined. The main parameters of excitons and more precise values of energy intervals V1(Γ7)-C1(Γ6), V2(Γ6)-C1(Γ6), and V3(Γ7)-C1(Γ6) were estimated. Values of splitting due to crystal field and spin-orbital interaction were calculated. Effective masses of electrons (mC1∗) and holes (mV1∗, mV2∗, mV3∗) were estimated. Reflection spectra contours in excitonic region were calculated using dispersion equations. Optical functions for E > Eg from measured reflection spectra were assigned on the base of Kramers-Kronig relations.

Electronic structure of some adenosine receptor antagonists. III. Quantitative investigation of the electronic absorption spectra of alkyl xanthines

NASA Astrophysics Data System (ADS)

Moustafa, H.; Shalaby, Samia H.; El-sawy, K. M.; Hilal, Rifaat

2002-07-01

Quantitative and comparative investigation of the electronic absorption spectra of theophylline, caffeine and their derivatives is reported. The spectra of theophylline, caffeine and theobromine were compared to establish the predominant tautomeric species in solution. This comparison, analysis of solvent effects and assignments of the observed transitions via MO computations indicate the exits of only one tautomeric species in solution that is the N7 form. A low-lying triplet state was identified which corresponds to a HOMO-LUMO transition. This relatively long-lived T 1 state is always less polar than the ground state and may very well underlie the photochemical reactivity of alkyl xanthines. Substituents of different electron donating or withdrawing strengths and solvent effects are investigated and analyzed. The present analysis is facilitated via computer deconvolution of the observed spectra and MO computation.

FBRDLR: Fast blind reconstruction approach with dictionary learning regularization for infrared microscopy spectra

NASA Astrophysics Data System (ADS)

Liu, Tingting; Liu, Hai; Chen, Zengzhao; Chen, Yingying; Wang, Shengming; Liu, Zhi; Zhang, Hao

2018-05-01

Infrared (IR) spectra are the fingerprints of the molecules, and the spectral band location closely relates to the structure of a molecule. Thus, specimen identification can be performed based on IR spectroscopy. However, spectrally overlapping components prevent the specific identification of hyperfine molecular information of different substances. In this paper, we propose a fast blind reconstruction approach for IR spectra, which is based on sparse and redundant representations over a dictionary. The proposed method recovers the spectrum with the discrete wavelet transform dictionary on its content. The experimental results demonstrate that the proposed method is superior because of the better performance when compared with other state-of-the-art methods. The method the authors used remove the instrument aging issue to a large extent, thus leading the reconstruction IR spectra a more convenient tool for extracting features of an unknown material and interpreting it.

Structural, optical and dielectric properties of transition metal (MFe2O4; M = Co, Ni and Zn) nanoferrites

NASA Astrophysics Data System (ADS)

Chand, Prakash; Vaish, Swapnil; Kumar, Praveen

2017-11-01

In the present work, transition metal spinel ferrite (MFe2O4; M = Co, Ni, Zn) nanostructures synthesized by chemical co-precipitation method. XRD analysis confirms the formation of cubic spinel-type structure with space group Fd3m and the average crystallite size calculated by Scherrer's formula found to be in 9-14 nm range. Scanning electron microscopy was used to study surface morphology of the samples. Moreover, Raman and PL spectra also confirm the formation of the cubic structure. The Raman spectra measured on cobalt, nickel and zinc ferrite revealed a larger number of phonon bands than expected for the cubic spinel structure. The calculated optical energy band gaps, obtained by Tauc's relation from UV-Vis absorption spectra are found to be as 2.44, 3.54 and 3.25 eV for CoFe2O4, NiFe2O4&ZnFe2O, respectively. The analysis of the complex impedance spectra of all ferrites samples shows the presence of one semicircular arc at all selected temperatures, signifying a key role of the grain boundary contribution. The dielectric constants (ε ‧) were measured in the frequency range from 10 Hz to 5 MHz at different temperatures and is found to be decreased suddenly with an increase in frequency and maintain a steady state or constant at higher frequencies for all the three samples. The AC conductivity is found to be increased with frequency and temperature of all the three samples which is explained on the basis of Koop's phenomenological theory.

A conformational study of protonated noradrenaline by UV-UV and IR dip double resonance laser spectroscopy combined with an electrospray and a cold ion trap method.

PubMed

Wako, Hiromichi; Ishiuchi, Shun-Ichi; Kato, Daichi; Féraud, Géraldine; Dedonder-Lardeux, Claude; Jouvet, Christophe; Fujii, Masaaki

2017-05-03

The conformer-selected ultraviolet (UV) and infrared (IR) spectra of protonated noradrenaline were measured using an electrospray/cryogenic ion trap technique combined with photo-dissociation spectroscopy. By comparing the UV photo dissociation (UVPD) spectra with the UV-UV hole burning (HB) spectra, it was found that five conformers coexist under ultra-cold conditions. Based on the spectral features of the IR dip spectra of each conformer, two different conformations on the amine side chain were identified. Three conformers (group I) were assigned to folded and others (group II) to extended structures by comparing the observed IR spectra with the calculated ones. Observation of the significantly less-stable extended conformers strongly suggests that the extended structures are dominant in solution and are detected in the gas phase by kinetic trapping. The conformers in each group are assignable to rotamers of OH orientations in the catechol ring. By comparing the UV-UV HB spectra and the calculated Franck-Condon spectra obtained by harmonic vibrational analysis of the S 1 state, with the aid of relative stabilization energies of each conformer in the S 0 state, the absolute orientations of catechol OHs of the observed five conformers were successfully determined. It was found that the 0-0 transition of one folded conformer is red-shifted by about 1000 cm -1 from the others. The significant red-shift was explained by a large contribution of the πσ* state to S 1 in the conformer in which an oxygen atom of the meta-OH group is close to the ammonium group.

Microscopic FTIR studies of lung cancer cells in pleural fluid.

PubMed

Wang, H P; Wang, H C; Huang, Y J

1997-10-01

Structural changes associated with lung cancer and tuberculous cells in pleural fluid were studied by microscopic FTIR spectroscopy. Infrared spectra demonstrate significant spectral differences between normal, lung cancer and tuberculous cells. The ratio of the peak intensities of the 1030 and 1080 cm-1 bands (originated mainly in glycogen and phosphodiester groups of nucleic acids) differs greatly between normal and lung cancer samples. Such findings prompt the consideration that recording infrared spectra from lung cancer and tuberculous cells may be of diagnostic value. Since measurements of IR spectra of lung cancer cells in the pleural fluid can be a very rapid inexpensive process, our finding warrant exploration of this possibility in the investigation of the mechanism whereby the environmental pollution related cancers develop.

Effect of Cr doping on structural and magnetic properties of ZnS nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Virpal,; Singh, Jasvir; Sharma, Sandeep

2016-05-23

The structural, optical and magnetic properties of pure and Cr doped ZnS nanoparticles were studied at room temperature. X-ray diffraction analysis confirmed the absence of any mixed phase and the cubic structure of ZnS in pure and Cr doped ZnS nanoparticles. Fourier transfer infrared spectra confirmed the Zn-S stretching bond at 664 cm{sup −1} of ZnS in all prepared nanoparticles. The UV-Visible absorption spectra showed blue shift which became even more pronounced in Cr doped ZnS nanoparticles. However, at relatively higher Cr concentrations a slower red shift was shown by the doped nanoparticles. This phenomenon is attributed to sp-d exchange interactionmore » that becomes prevalent at higher doping concentrations. Further, magnetic hysteresis measurements showed that Cr doped ZnS nanoparticles exhibited ferromagnetic behavior at room temperature.« less

High quality x-ray absorption spectroscopy measurements with long energy range at high pressure using diamond anvil cell.

PubMed

Hong, Xinguo; Newville, Matthew; Prakapenka, Vitali B; Rivers, Mark L; Sutton, Stephen R

2009-07-01

We describe an approach for acquiring high quality x-ray absorption fine structure (XAFS) spectroscopy spectra with wide energy range at high pressure using diamond anvil cell (DAC). Overcoming the serious interference of diamond Bragg peaks is essential for combining XAFS and DAC techniques in high pressure research, yet an effective method to obtain accurate XAFS spectrum free from DAC induced glitches has been lacking. It was found that these glitches, whose energy positions are very sensitive to the relative orientation between DAC and incident x-ray beam, can be effectively eliminated using an iterative algorithm based on repeated measurements over a small angular range of DAC orientation, e.g., within +/-3 degrees relative to the x-ray beam direction. Demonstration XAFS spectra are reported for rutile-type GeO2 recorded by traditional ambient pressure and high pressure DAC methods, showing similar quality at 440 eV above the absorption edge. Accurate XAFS spectra of GeO2 glass were obtained at high pressure up to 53 GPa, providing important insight into the structural polymorphism of GeO2 glass at high pressure. This method is expected be applicable for in situ XAFS measurements using a diamond anvil cell up to ultrahigh pressures.

High quality x-ray absorption spectroscopy measurements with long energy range at high pressure using diamond anvil cell

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong, X.; Newville, M.; Prakapenka, V.B.

We describe an approach for acquiring high quality x-ray absorption fine structure (XAFS) spectroscopy spectra with wide energy range at high pressure using diamond anvil cell (DAC). Overcoming the serious interference of diamond Bragg peaks is essential for combining XAFS and DAC techniques in high pressure research, yet an effective method to obtain accurate XAFS spectrum free from DAC induced glitches has been lacking. It was found that these glitches, whose energy positions are very sensitive to the relative orientation between DAC and incident x-ray beam, can be effectively eliminated using an iterative algorithm based on repeated measurements over amore » small angular range of DAC orientation, e.g., within {+-}3{sup o} relative to the x-ray beam direction. Demonstration XAFS spectra are reported for rutile-type GeO{sub 2} recorded by traditional ambient pressure and high pressure DAC methods, showing similar quality at 440 eV above the absorption edge. Accurate XAFS spectra of GeO{sub 2} glass were obtained at high pressure up to 53 GPa, providing important insight into the structural polymorphism of GeO{sub 2} glass at high pressure. This method is expected be applicable for in situ XAFS measurements using a diamond anvil cell up to ultrahigh pressures.« less

Fraction of boroxol rings in vitreous boron oxide from a first-principles analysis of Raman and NMR spectra.

PubMed

Umari, P; Pasquarello, Alfredo

2005-09-23

We determine the fraction f of B atoms belonging to boroxol rings in vitreous boron oxide through a first-principles analysis. After generating a model structure of vitreous B2O3 by first-principles molecular dynamics, we address a large set of properties, including the neutron structure factor, the neutron density of vibrational states, the infrared spectra, the Raman spectra, and the 11B NMR spectra, and find overall good agreement with corresponding experimental data. From the analysis of Raman and 11B NMR spectra, we yield consistently for both probes a fraction f of approximately 0.75. This result indicates that the structure of vitreous boron oxide is largely dominated by boroxol rings.

X-ray spectra and electron structure of A15 compounds of transition metals

NASA Astrophysics Data System (ADS)

Kurmaev, E. Z.; Iarmoshenko, Iu. M.

1988-01-01

Results of an X-ray emission spectroscopy study of the electron structure of A15 compounds are reported. In particular, attention is given to the X-ray spectra of A15 compounds of the A3B type with transition and nontransition elements, effect of alloying on the formation of the electron structure of ternary phases, and effect of atomic ordering in the X-ray spectra of A15 compounds with changes in heat treament and concentration. The X-ray spectra of A15 compounds irradiated by fast neutrons are also examined.

A 125Te and 23Na NMR investigation of the structure and crystallisation of sodium tellurite glasses.

PubMed

Holland, D; Bailey, J; Ward, G; Turner, B; Tierney, P; Dupree, R

2005-01-01

125Te static nuclear magnetic resonance (NMR) and 23Na and 125Te magic angle spinning (MAS) NMR have been used, in conjunction with X-ray diffraction, to examine the structure and crystallisation behaviour of glasses of composition xNa2O.(1-x)TeO2 (0.075 x 0.4). The MAS NMR 23Na spectra from the glasses are broad and featureless but shift by approximately +5 ppm with increased x, i.e. as the system becomes more ionic. The static 125Te NMR spectra show an increase in axial symmetry with increasing x, indicating a shift from predominantly [TeO4] to [TeO3] structural units. The 23Na and 125Te spectra from the crystallised samples have been fitted to obtain information on the sites in the metastable crystal phases, which are the first to form on heating and which are therefore more closely related to the glass structure than thermodynamically stable crystal phases. New sodium tellurite phases are reported, including a sodium stabilised, face centred cubic phase related to delta-TeO2; a metastable form of Na2Te4O9 containing 3 sodium and 4 tellurium sites; and a metastable form of Na2Te2O5 containing 2 sodium sites. There is evidence of oxidation of TeIV to TeVI occurring in glasses with high values of x and, at x=0.40 and 0.50 (outside the glass forming range), some sodium metatellurate (Na2TeO4) is formed at the same time as sodium metatellurite (Na2TeO3). The 125Te shift is very sensitive to environment within the sodium tellurite system, covering more than 320 ppm, with anisotropies varying from 640 to 1540 ppm. The lack of features in the 125Te spectra of the glass phases, combined with the large shift range and high but variable anisotropy, means than it is not possible to obtain a unique fit to any presumed species present. Furthermore, the chemical shift anisotropy parameters for three of the four Te sites in the Na2Te4O9 phase are found to lie outside the range used for previous simulations of glass spectra.

Silica deposits on Mars with features resembling hot spring biosignatures at El Tatio in Chile

PubMed Central

Ruff, Steven W.; Farmer, Jack D.

2016-01-01

The Mars rover Spirit encountered outcrops and regolith composed of opaline silica (amorphous SiO2·nH2O) in an ancient volcanic hydrothermal setting in Gusev crater. An origin via either fumarole-related acid-sulfate leaching or precipitation from hot spring fluids was suggested previously. However, the potential significance of the characteristic nodular and mm-scale digitate opaline silica structures was not recognized. Here we report remarkably similar features within active hot spring/geyser discharge channels at El Tatio in northern Chile, where halite-encrusted silica yields infrared spectra that are the best match yet to spectra from Spirit. Furthermore, we show that the nodular and digitate silica structures at El Tatio that most closely resemble those on Mars include complex sedimentary structures produced by a combination of biotic and abiotic processes. Although fully abiotic processes are not ruled out for the Martian silica structures, they satisfy an a priori definition of potential biosignatures. PMID:27853166

Understanding the Electronic Structure of 4d Metal Complexes: From Molecular Spinors to L-Edge Spectra of a di-Ru Catalyst

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alperovich, Igor; Smolentsev, Grigory; Moonshiram, Dooshaye

2015-09-17

L{sub 2,3}-edge X-ray absorption spectroscopy (XAS) has demonstrated unique capabilities for the analysis of the electronic structure of di-Ru complexes such as the blue dimer cis,cis-[Ru{sub 2}{sup III}O(H{sub 2}O){sub 2}(bpy){sub 4}]{sup 4+} water oxidation catalyst. Spectra of the blue dimer and the monomeric [Ru(NH{sub 3}){sub 6}]{sup 3+} model complex show considerably different splitting of the Ru L{sub 2,3} absorption edge, which reflects changes in the relative energies of the Ru 4d orbitals caused by hybridization with a bridging ligand and spin-orbit coupling effects. To aid the interpretation of spectroscopic data, we developed a new approach, which computes L{sub 2,3}-edges XASmore » spectra as dipole transitions between molecular spinors of 4d transition metal complexes. This allows for careful inclusion of the spin-orbit coupling effects and the hybridization of the Ru 4d and ligand orbitals. The obtained theoretical Ru L{sub 2,3}-edge spectra are in close agreement with experiment. Critically, existing single-electron methods (FEFF, FDMNES) broadly used to simulate XAS could not reproduce the experimental Ru L-edge spectra for the [Ru(NH{sub 3}){sub 6}]{sup 3+} model complex nor for the blue dimer, while charge transfer multiplet (CTM) calculations were not applicable due to the complexity and low symmetry of the blue dimer water oxidation catalyst. We demonstrated that L-edge spectroscopy is informative for analysis of bridging metal complexes. The developed computational approach enhances L-edge spectroscopy as a tool for analysis of the electronic structures of complexes, materials, catalysts, and reactive intermediates with 4d transition metals.« less

Investigation of Local Structures in Cation-ordered Microwave Dielectric A Solid-state NMR and First Principle Calculation Study

NASA Astrophysics Data System (ADS)

Kalfarisi, Rony G.

Solid-state Nuclear Magnetic Resonance (ssNMR) spectroscopy has proven to be a powerful method to probe the local structure and dynamics of a system. In powdered solids, the nuclear spins experience various anisotropic interactions which depend on the molecular orientation. These anisotropic interactions make ssNMR very useful as they give a specific appearance to the resonance lines of the spectra. The position and shape of these resonance lines can be related to local structure and dynamics of the system under study. My research interest has focused around studying local structures and dynamics of quadrupolar nuclei in materials using ssNMR spectroscopy. 7Li and 93Nb ssNMR magic angle spinning (MAS) spectra, acquired at 17.6 and 7.06 T, have been used to evaluate the structural and dynamical properties of cation-ordered microwave dielectric materials. Microwave dielectric materials are essential in the application of wireless telecommunication, biomedical engineering, and other scientific and industrial implementations that use radio and microwave signals. The study of the local environment with respect to average structure, such as X-ray diffraction study, is essential for the better understanding of the correlations between structures and properties of these materials. The investigation for short and medium range can be performed with the use of ssNMR techniques. Even though XRD results show cationic ordering at the B-site (third coordination sphere), NMR spectra show a presence of disorder materials. This was indicated by the observation of a distribution in NMR parameters derived from experimental . {93}Nb NMR spectraand supported by theoretical calculations.

Secondary Electron Emission Spectroscopy of Diamond Surfaces

NASA Technical Reports Server (NTRS)

Krainsky, Isay L.; Asnin, Vladimir M.; Petukhov, Andre G.

1999-01-01

This report presents the results of the secondary electron emission spectroscopy study of hydrogenated diamond surfaces for single crystals and chemical vapor-deposited polycrystalline films. One-electron calculations of Auger spectra of diamond surfaces having various hydrogen coverages are presented, the major features of the experimental spectra are explained, and a theoretical model for Auger spectra of hydrogenated diamond surfaces is proposed. An energy shift and a change in the line shape of the carbon core-valence-valence (KVV) Auger spectra were observed for diamond surfaces after exposure to an electron beam or by annealing at temperatures higher than 950 C. This change is related to the redistribution of the valence-band local density of states caused by hydrogen desorption from the surface. A strong negative electron affinity (NEA) effect, which appeared as a large, narrow peak in the low-energy portion of the spectrum of the secondary electron energy distribution, was also observed on the diamond surfaces. A fine structure in this peak, which was found for the first time, reflected the energy structure of the bottom of the conduction band. Further, the breakup of the bulk excitons at the surface during secondary electron emission was attributed to one of the features of this structure. The study demonstrated that the NEA type depends on the extent of hydrogen coverage of the diamond surface, changing from the true type for the completely hydrogenated surface to the effective type for the partially hydrogenated surface.

Assessment of nonenzymatic glycation in protein by FTIR spectroscopy

NASA Astrophysics Data System (ADS)

Otero de Joshi, Virginia; Joshi, Narahari V.; Gil, Herminia; Velasquez, William; Contreras, Silvia; Marquez, Glevis

1999-04-01

Detection of nonenzymatic glycated proteins is a very significant feature in diabetes, aging and related diseases, therefore we have carried out an FTIR spectroscopic study for glycated and native proteins such as (gamma) -globulin, human serum albumin. For this purpose, commercially available proteins were glycated by a usual procedure and their FTIR spectra were recorded together with that of the native ones. In order to follow the changes in time, (gamma) -globulin was glycated during 1, 2, 3, 5 and 8 weeks and their spectra were recorded. Direct verification was obtained by examining a model unit where the -NH2 group was attached to glucose. The spectrum shows a strong peak at 3500 cm-1 confirming the observed variation in time dependent spectra. The general features of the spectra are very similar and there was no additional structure or change in the peaks. This is understandable as not all the lysine residues are glycated, only a small fraction. Glucose is attached to the (epsilon) -amino group of lysine to form Amadori products, and therefore, the vibrational modes corresponding to the (epsilon) -NH2 unit of lysine are expected to be altered. This region exactly lies in the Amide I region of protein structure. Careful investigation of this part, indeed, shows a complex structure originated from alternations of -NH2 group. Thus, the present investigation indicates that an optical approach could be a rapid and effective method to identify the nonenzymatic glycation process.

Reaction of. beta. -propiolactone with derivatives of adenine and with DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, R.; Mieyal, J.J.; Goldthwait, D.A.

1982-01-01

The reaction of deoxyadenosine with ..beta..-propiolactone produces two derivatives. One is 1-(2-carboxyethyl)-2-deoxyadenosine (CEdA). The proposed structure for the other is 3-(..beta..-D-2-deoxyribosyl)-7,8-dihydropyrimido-(2,l-i)purine-9-one (dDPP). Spectral characteristics of both compounds are presented. These include u.v. spectra of each in acidic, neutral and alkaline solutions, i.r. spectra, fluorescence spectra, and n.m.r. spectra. The dDPP can be converted to CEdA by mild acid hydrolysis, and the CEdA can be converted to dDPP by reaction with a carbodiimide derivative. When poly A was reacted with ..beta..-propiolactone, the yield of dDPP in the polymer was 7-9%. When double-stranded DNA was alkylated by (/sup 3/H)..beta..-propiolactone at relatively highmore » concentrations and then acid hydrolyzed to separate 1-(2-carboxyethyl)adenine (CEA) and 7-(2-carboxyethyl)guanine (CEG), and CEA to CEG ratio of up to 0.62 was obtained. With relatively low concentrations of (/sup 3/H)..beta..-propiolactone, the yield of CEA was low with double-stranded DNA but was 5-6 fold greater with single-stranded DNA.« less

Effects of structure distortion on optical phonon properties of crystalline beta-BaTeMo{sub 2}O{sub 9}—A novel nonlinear optical material: Infrared and Raman spectra as well as first-principles calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, S. T.; Huang, Y.; Qiu, W. Y.

2013-12-21

The infrared dielectric property of monoclinic BaTeMo{sub 2}O{sub 9} single crystals is studied by polarized IR reflectance spectra from 20 to 1800 cm{sup −1}. Based on the modified Lorentz model, the frequencies, strengths, and dampings of TO modes as well as the orientations of the dipole momenta are determined, agreeing well with Raman spectra and results from First-principles calculation. The observed modes are visually assigned to the specific atoms' motions in the primitive cell based on the theory calculations. A large shift of the internal modes of the anion groups relative to free anion co-ordination polyhedra is observed, which can bemore » used to indicate the distortions of co-ordination polyhedra related to the nonlinear optical properties. Further, the experimental results of the strengths of the oscillators support the elimination and splitting of degenerate modes in free regular polyhedrons. These results offer a way to evaluate the nonlinear optical properties by use of traditional IR reflectivity spectra.« less

X-ray spectra and atmospheric structures of bursting neutron stars

NASA Technical Reports Server (NTRS)

Ebisuzaki, Toshikazu

1987-01-01

Atmospheric structures and emitted X-ray spectra of bursting neutron stars are investigated. Theoretical curves are fitted to observational ones on the color temperature vs. luminosity diagram and two relations among mass, radius, and distance of the bursters are obtained. The fit of the theoretical curve to observations is statistically acceptable. Two possible sets of mass, radius, and distance to the X-ray bursts source MXB 1636-536 are derived, taking into account absorption lines at 4.1 keV, theoretical mass-radius relations of neutron star models, and the distance to the Galactic center. If the absorption line is due to Cr XX III, then M = 1.7-2.0 solar masses, R = 11-12 km, and d = 6.3-6.7 kpc, and if it is due to Fe XXV, then M = 1.8-2.1 solar masses, R = 8-10 km, and d = 5.8-6,4 kpc. The distance to the Galactic center is almost the same as that to MXB 1636-536.

Oxidation of 2,6-di-tert-butyl-4-methylphenol. The structure of C14H22O3

USGS Publications Warehouse

Yohe, G.R.; Dunbar, J.E.; Lansford, M.W.; Pedrotti, R.L.; Scheidt, F.M.; Lee, F.G.H.; Smith, E.C.

1959-01-01

The acidic compound C14H22O3, previously reported without assignment of structure as an oxidation product of 2,6-di-tert-butyl-4-methylphenol, is now believed to be DL-trans-5,6-di-tert-butyl-2-hydroxy-1,4-diketo-2-cyclohexene (I). Chemical properties are described and infrared spectra are presented in support of this structure. This structure is of interest in relation to the problem of the existence of o-di-tert-alkylbenzene derivatives. The relatively easy racemization of optically active I suggests that its completely enolized form, 5,6-di-tert-butyl-1,2,4-trihydroxybenzene, is capable of transitory existence.

Raman spectroscopy of the multianion mineral gartrellite-PbCu(Fe3+,Cu)(AsO4)2(OH,H2O)2

NASA Astrophysics Data System (ADS)

Frost, Ray L.; Xi, Yunfei; Palmer, Sara J.

2012-04-01

The multianion mineral gartrellite PbCu(Fe3+,Cu)(AsO4)2(OH,H2O)2 has been studied by a combination of Raman and infrared spectroscopy. The vibrational spectra of two gartrellite samples from Durango and Ashburton Downs were compared. Gartrellite is one of the tsumcorite mineral group based upon arsenate and sulphate anions. Crystal symmetry is either triclinic in the case of an ordered occupation of two cationic sites, triclinic due to ordering of the H bonds in the case of species with 2 water molecules per formula unit, or monoclinic in the other cases. Characteristic Raman spectra of the minerals enable the assignment of the bands to specific vibrational modes. These spectra are related to the structure of gartrellite. The position of the hydroxyl and water stretching vibrations are related to the strength of the hydrogen bond formed between the OH unit and the AsO4 anion.

The influence of the long-range order on the vibrational spectra of structures based on sodalite cage.

PubMed

Mikuła, A; Król, M; Koleżyński, A

2015-06-05

Zeolites are a group of tecto-aluminosilicates with numerous practical applications, e.g. gas separators, molecular sieves and sorbents. The unique properties result from porous structure of channels and cages which are built from smaller units - the so-called Secondary Building Units (SBU), and sometimes also larger groups (Breck, 1974; Ciciszwili et al., 1974; Mozgawa, 2008; Čejka and van Bekkum, 2005). The aim of this study was the examination of the influence of long-range order on vibrational spectra of sodalite and zeolite A. Ab initio calculations (geometry optimizations and vibrational spectra calculations) of sodalite cage and selected SBU were carried out by means of Gaussian09 (Frisch et al., 2009) (in the case of isolated clusters) and Crystal09 (Dovesi et al., 2005, 2009) (for periodic structures). The obtained results were compared with the experimental spectra of sodalite and zeolite A crystal structures, synthesized under hydrothermal conditions. These results allowed analyzing of the long-range ordering influence on the vibrational spectra, as well as the identification of the characteristic vibrations in β cage based frameworks. It has been found, that based on small structural fragment (SBU) models a characteristic vibrations can be identify. However, full spectra analysis and especially the interpretation of far-infrared region of the spectra require using periodic models under the influence of translational crystal lattice. Copyright © 2015 Elsevier B.V. All rights reserved.

Human- and computer-accessible 2D correlation data for a more reliable structure determination of organic compounds. Future roles of researchers, software developers, spectrometer managers, journal editors, reviewers, publisher and database managers toward artificial-intelligence analysis of NMR spectra.

PubMed

Jeannerat, Damien

2017-01-01

The introduction of a universal data format to report the correlation data of 2D NMR spectra such as COSY, HSQC and HMBC spectra will have a large impact on the reliability of structure determination of small organic molecules. These lists of assigned cross peaks will bridge signals found in NMR 1D and 2D spectra and the assigned chemical structure. The record could be very compact, human and computer readable so that it can be included in the supplementary material of publications and easily transferred into databases of scientific literature and chemical compounds. The records will allow authors, reviewers and future users to test the consistency and, in favorable situations, the uniqueness of the assignment of the correlation data to the associated chemical structures. Ideally, the data format of the correlation data should include direct links to the NMR spectra to make it possible to validate their reliability and allow direct comparison of spectra. In order to take the full benefits of their potential, the correlation data and the NMR spectra should therefore follow any manuscript in the review process and be stored in open-access database after publication. Keeping all NMR spectra, correlation data and assigned structures together at all time will allow the future development of validation tools increasing the reliability of past and future NMR data. This will facilitate the development of artificial intelligence analysis of NMR spectra by providing a source of data than can be used efficiently because they have been validated or can be validated by future users. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Infrared spectroscopic characterization of monocytic microvesicles (microparticles) released upon lipopolysaccharide stimulation.

PubMed

Lee, Joonsup; Wen, Beryl; Carter, Elizabeth A; Combes, Valery; Grau, Georges E R; Lay, Peter A

2017-07-01

Microvesicles (MVs) are involved in cell-cell interactions, including disease pathogenesis. Nondestructive Fourier-transform infrared (FTIR) spectra from MVs were assessed as a technique to provide new biochemical insights into a LPS-induced monocyte model of septic shock. FTIR spectroscopy provided a quick method to investigate relative differences in biomolecular content of different MV populations that was complementary to traditional semiquantitative omics approaches, with which it is difficult to provide information on relative changes between classes (proteins, lipids, nucleic acids, carbohydrates) or protein conformations. Time-dependent changes were detected in biomolecular contents of MVs and in the monocytes from which they were released. Differences in phosphatidylcholine and phosphatidylserine contents were observed in MVs released under stimulation, and higher relative concentrations of RNA and α-helical structured proteins were present in stimulated MVs compared with MVs from resting cells. FTIR spectra of stimulated monocytes displayed changes that were consistent with those observed in the corresponding MVs they released. LPS-stimulated monocytes had reduced concentrations of nucleic acids, α-helical structured proteins, and phosphatidylcholine compared with resting monocytes but had an increase in total lipids. FTIR spectra of MV biomolecular content will be important in shedding new light on the mechanisms of MVs and the different roles they play in physiology and disease pathogenesis.-Lee, J., Wen, B., Carter, E. A., Combes, V., Grau, G. E. R., Lay, P. A. Infrared spectroscopic characterization of monocytic microvesicles (microparticles) released upon lipopolysaccharide stimulation. © FASEB.

The structural and electrical evolution of graphene by oxygen plasma-induced disorder.

PubMed

Kim, Dong Chul; Jeon, Dae-Young; Chung, Hyun-Jong; Woo, YunSung; Shin, Jai Kwang; Seo, Sunae

2009-09-16

Evolution of a single graphene layer with disorder generated by remote oxygen plasma irradiation is investigated using atomic force microscopy, Raman spectroscopy and electrical measurement. Gradual changes of surface morphology from planar graphene to isolated granular structure associated with a decrease of transconductance are accounted for by two-dimensional percolative conduction by disorder and the oxygen plasma-induced doping effect. The corresponding evolution of Raman spectra of graphene shows several peculiarities such as a sudden appearance of a saturated D peak followed by a linear decrease in its intensity, a relatively inert characteristic of a D' peak and a monotonic increase of a G peak position as the exposure time to oxygen plasma increases. These are discussed in terms of a disorder-induced change of Raman spectra in the graphite system.

The use of UV, FT-IR and Raman spectra for the identification of the newest penem analogs: solutions based on mathematic procedure and the density functional theory.

PubMed

Cielecka-Piontek, J; Lewandowska, K; Barszcz, B; Paczkowska, M

2013-02-15

The application of ultraviolet, FT-IR and Raman spectra was proposed for identification studies of the newest penem analogs (doripenem, biapenem and faropenem). An identification of the newest penem analogs based on their separation from related substances was achieved after the application of first derivative of direct spectra in ultraviolet which permitted elimination of overlapping effects. A combination of experimental and theoretical studies was performed for analyzing the structure and vibrational spectra (FT-IR and Raman spectra) of doripenem, biapenem and faropenem. The calculations were conducted using the density functional theory with the B3LYP hybrid functional and 6-31G(d,p) basis set. The confirmation of the applicability of the DFT methodology for interpretation of vibrational IR and Raman spectra of the newest penem analogs contributed to determination of changes of vibrations in the area of the most labile bonds. By employing the theoretical approach it was possible to eliminate necessity of using reference standards which - considering the instability of penem analogs - require that correction coefficients are factored in. Copyright © 2012 Elsevier B.V. All rights reserved.

A Comparative Cathodoluminescence Emission Study of Feldspathic Glasses in SNC Meteorites and Quenched Melts of These Glasses

NASA Astrophysics Data System (ADS)

Kubny, A.; Jagoutz, E.

2001-12-01

In this study the cathodoluminescence (electron-excited luminescence) emission spectra were measured in the range 200 to 900 nm of individual feldspathic glass grains in the SNC meteorites Shergotty 101, Shergotty 232, ALHA 84001, EETA 79001-47, EETA 79001-276, and Dar al Gani 476 and those of quenched melts of the feldspathic glass grains. The quenching experiments of the original feldspathic glasses were conducted at 1500° C and atmospheric pressure. The aim of this CL emission study was the characterization of feldspathic glasses of SNC meteorites by comparison of the diagnostic spectral features of the feldspathic glasses of SNC meteorites with those of their quenched melts. In the CL emission spectra of the studied feldspathic glasses generally broad bands in the blue (ca. 460 nm), green (ca. 560 nm), and red (ca. 700 nm) can appear. These emission bands are assigned to structural defects (Al-O--Al centers), and the structural incorporation of Mn2+ and Fe3+ , respectively. The blue emission band at about 460 nm attributed to Al-O--Al centers is observed in the spectra of the original feldspathic glasses whereas it is not present (or only in low relative intensity) in the spectra of the quenched melts. The green emission band at 550 to 575 nm assigned to electronic transitions of Mn2+ in M sites is observed in the spectra of the original feldspathic glasses. It is shifted to longer wavelengths of 590 to 605 nm in the spectra of the quenched melts. The occurrence of the red emission band at about 700 nm attributed to electronic transition of Fe3+ in the spectra of the quenched melts of the feldspathic glasses indicates the presence of structural units which allow the occupancy of Fe3+ on tetrahedral sites. The results obtained by CL emission spectroscopy confirm results of Raman spectroscopic studies that the stuctures of feldspathic glasses of the studied SNC meteorites are modified by melting and quenching at atmospheric pressure. Additionally, comparison with published work on CL emission of shocked oligoclases shows that the feldspathic glasses of the studied SNC meteorites are not diaplectic but melt glasses.

Structural stability, vibrational, and bonding properties of potassium 1, 1'-dinitroamino-5, 5'-bistetrazolate: An emerging green primary explosive.

PubMed

Yedukondalu, N; Vaitheeswaran, G

2015-08-14

Potassium 1,1'-dinitroamino-5,5'-bistetrazolate (K2DNABT) is a nitrogen rich (50.3% by weight, K2C2N12O4) green primary explosive with high performance characteristics, namely, velocity of detonation (D = 8.33 km/s), detonation pressure (P = 31.7 GPa), and fast initiating power to replace existing toxic primaries. In the present work, we report density functional theory (DFT) calculations on structural, equation of state, vibrational spectra, electronic structure, and absorption spectra of K2DNABT. We have discussed the influence of weak dispersive interactions on structural and vibrational properties through the DFT-D2 method. We find anisotropic compressibility behavior (b

Structural stability, vibrational, and bonding properties of potassium 1, 1'-dinitroamino-5, 5'-bistetrazolate: An emerging green primary explosive

NASA Astrophysics Data System (ADS)

Yedukondalu, N.; Vaitheeswaran, G.

2015-08-01

Potassium 1,1'-dinitroamino-5,5'-bistetrazolate (K2DNABT) is a nitrogen rich (50.3% by weight, K2C2N12O4) green primary explosive with high performance characteristics, namely, velocity of detonation (D = 8.33 km/s), detonation pressure (P = 31.7 GPa), and fast initiating power to replace existing toxic primaries. In the present work, we report density functional theory (DFT) calculations on structural, equation of state, vibrational spectra, electronic structure, and absorption spectra of K2DNABT. We have discussed the influence of weak dispersive interactions on structural and vibrational properties through the DFT-D2 method. We find anisotropic compressibility behavior (b

Association Mechanisms of Unsaturated C2 Hydrocarbons with Their Cations: Acetylene and Ethylene

NASA Technical Reports Server (NTRS)

Bera, Partha P.; Head-Gordon, Martin; Lee, Timothy J.

2013-01-01

The ion-molecule association mechanism of acetylene and ethylene with their cations is investigated by ab initio quantum chemical methods to understand the structures, association energies, and the vibrational and electronic spectra of the products. Stable puckered cyclic isomers are found as the result of first forming less stable linear and bridge isomers. The puckered cyclic complexes are calculated to be strongly bound, by 87, 35 and 56 kcal/mol for acetylene-acetylene cation, ethylene-ethylene cation and acetylene-ethylene cation, respectively. These stable complexes may be intermediates that participate in further association reactions. There are no association barriers, and no significant inter-conversion barriers, so the initial linear and bridge encounter complexes are unlikely to be observable. However, the energy gap between the bridged and cyclic puckered isomers greatly differs from complex to complex: it is 44 kcal/mol in C4H4 +, but only 6 kcal/mol in C4H8 +. The accurate CCSD(T) calculations summarized above are also compared against less computationally expensive MP2 and density functional theory (DFT) calculations for structures, relative energies, and vibrational spectra. Calculated vibrational spectra are compared against available experiments for cyclobutadiene cation. Electronic spectra are also calculated using time-dependent DFT.

The structure of BPS spectra

NASA Astrophysics Data System (ADS)

Longhi, Pietro

In this thesis we develop and apply novel techniques for analyzing BPS spectra of supersymmetric quantum field theories of class S. By a combination of wall-crossing, spectral networks and quiver methods we explore the BPS spectra of higher rank four-dimensional N = 2 super Yang-Mills, uncovering surprising new phenomena. Focusing on the SU(3) case, we prove the existence of wild BPS spectra in field theory, featuring BPS states of higher spin whose degeneracies grow exponentially with the energy. The occurrence of wild BPS states is surprising because it appears to be in tension with physical expectations on the behavior of the entropy as a function of the energy scale. The solution to this puzzle comes from realizing that the size of wild BPS states grows rapidly with their mass, and carefully analyzing the volume-dependence of the entropy of BPS states. We also find some interesting structures underlying wild BPS spectra, such as a Regge-like relation between the maximal spin of a BPS multiplet and the square of its mass, and the existence of a universal asymptotic distribution of spin-j irreps within a multiplet of given charge. We also extend the spectral networks construction by introducing a refinement in the topological classification of 2d-4d BPS states, and identifying their spin with a topological invariant known as the "writhe of soliton paths". A careful analysis of the 2d-4d wall-crossing behavior of this refined data reveals that it is described by motivic Kontsevich-Soibelman transformations, controlled by the Protected Spin Character, a protected deformation of the BPS index encoding the spin of BPS states. Our construction opens the way for the systematic study of refined BPS spectra in class S theories. We apply it to several examples, including ones featuring wild BPS spectra, where we find an interesting relation between spectral networks and certain functional equations. For class S theories of A 1 type, we derive an alternative technique for computing generating functions of 2d-4d BPS spectra, based on the topological data of an ideal triangulation of the Riemann surface defining the theory. We provide a set of building blocks and corresponding rules, from which the 2d-4d spectra of a vast class of theories can be algorithmically recovered. Finally, we present previously unpublished exact results on the BPS spectrum of the SU(2) N = 2* theory, and briefly comment on its wall crossing.

Vibrational, X-ray absorption, and Mössbauer spectra of sulfate minerals from the weathered massive sulfide deposit at Iron Mountain, California

USGS Publications Warehouse

Majzlan, Juraj; Alpers, Charles N.; Bender Koch, Christian; McCleskey, R. Blaine; Myneni, Satish B.C.; Neil, John M.

2014-01-01

The Iron Mountain Mine Superfund site in California is a prime example of an acid mine drainage (AMD) system with well developed assemblages of sulfate minerals typical for such settings. Here we present and discuss the vibrational (infrared), X-ray absorption, and Mössbauer spectra of a number of these phases, augmented by spectra of a few synthetic sulfates related to the AMD phases. The minerals and related phases studied in this work are (in order of increasing Fe2O3/FeO): szomolnokite, rozenite, siderotil, halotrichite, römerite, voltaite, copiapite, monoclinic Fe2(SO4)3, Fe2(SO4)3·5H2O, kornelite, coquimbite, Fe(SO4)(OH), jarosite and rhomboclase. Fourier transform infrared spectra in the region 750–4000 cm−1 are presented for all studied phases. Position of the FTIR bands is discussed in terms of the vibrations of sulfate ions, hydroxyl groups, and water molecules. Sulfur K-edge X-ray absorption near-edge structure (XANES) spectra were collected for selected samples. The feature of greatest interest is a series of weak pre-edge peaks whose position is determined by the number of bridging oxygen atoms between Fe3+ octahedra and sulfate tetrahedra. Mössbauer spectra of selected samples were obtained at room temperature and 80 K for ferric minerals jarosite and rhomboclase and mixed ferric–ferrous minerals römerite, voltaite, and copiapite. Values of Fe2+/[Fe2+ + Fe3+] determined by Mössbauer spectroscopy agree well with those determined by wet chemical analysis. The data presented here can be used as standards in spectroscopic work where spectra of well-characterized compounds are required to identify complex mixtures of minerals and related phases.

In situ observations of a high-pressure phase of H2O ice

USGS Publications Warehouse

Chou, I.-Ming; Blank, J.G.; Goncharov, A.F.; Mao, Ho-kwang; Hemley, R.J.

1998-01-01

A previously unknown solid phase of H2O has been identified by its peculiar growth patterns, distinct pressure-temperature melting relations, and vibrational Raman spectra. Morphologies of ice crystals and their pressure-temperature melting relations were directly observed in a hydrothermal diamond-anvil cell for H2O bulk densities between 1203 and 1257 kilograms per cubic meter at temperatures between -10??and 50??C. Under these conditions, four different ice forms were observed to melt: two stable phases, ice V and ice VI, and two metastable phases, ice IV and the new ice phase. The Raman spectra and crystal morphology are consistent with a disordered anisotropic structure with some similarities to ice VI.

A Butterfly in the Making: Revealing the Near-Infrared Structure of Hubble 12

NASA Technical Reports Server (NTRS)

Hora, Joseph L.; Latter, William B.

1996-01-01

We present deep narrowband near-IR images and moderate resolution spectra of the young planetary nebula Hubble 12. These data are the first to show clearly the complex structure for this important planetary nebula. Images were obtained at lambda = 2.12, 2.16, and 2.26 micron. The lambda = 2.12 Am image reveals the bipolar nature of the nebula, as well as complex structure near the central star in the equatorial region. The images show an elliptical region of emission, which may indicate a ring or a cylindrical source structure. This structure is possibly related to the mechanism that is producing the bipolar flow. The spectra show the nature of several distinct components. The central object is dominated by recombination lines of H I and He I. The core is not a significant source of molecular hydrogen emission. The east position in the equatorial region is rich in lines of ultraviolet-excited fluorescent H2. A spectrum of part of the central region shows strong [Fe II] emission, which might indicate the presence of shocks.

Observations using Phosphorus-31 nuclear magnetic resonance (31P-NMR) of structural changes in freeze-thawed hen egg yolk.

PubMed

Wakamatsu, Hiroki; Handa, Akihiro; Chiba, Kazuhiro

2018-04-01

Hen egg yolk (EY) has a complicated structure consisting of lipids and proteins, and its structure is deeply related with its functional properties. 31 P-NMR is an efficient technique to non-destructively detect the dynamic behaviour of phospholipids, the main component of bio-membranes. We determined conditions for measuring the 31 P NMR spectra of EY and identified the components. 31 P-NMR was used to detect phosvitin, inorganic phosphate, and lipoprotein as well as structural changes such as granule collapse and freeze-thaw denaturation as signal changes. Freeze-thaw denaturation generated a new denaturation peak. We separated aggregates of LDL from freeze-thawed plasma using centrifugation. TEM and 31 P-NMR observations revealed that the denaturation peak corresponded to LDL aggregates. The 31 P-NMR spectra suggested the formation of multiple forms of LDL aggregates in which the head groups of phospholipid molecules adopt a face-to-face orientation, similar to that observed following the flocculation of lipoproteins or in the lamellar-like structures of phospholipids. Copyright © 2017 Elsevier Ltd. All rights reserved.

Zeolites on Mars: Prospects for Remote Sensing

NASA Technical Reports Server (NTRS)

Gaffney, E. S.; Singer, R. B.; Kunkle, T. D.

1985-01-01

The Martian surface composition measured by Viking can be represented by several combinations of minerals incorporating major fractions of zeolites known to occur in altered mafic rocks and polar soils on Earth. The abundant occurrence of zeolites on Mars is consistent with what is known about both the physical and chemical environment of that planet. The laboratory reflectance spectra (0.65 to 2.55 microns) of a number of relatively pure zeolite minerals and some naturally occurring zeolite-clay soils were measured. All of the spectra measured are dominated by strong absorption near 1.4 and 1.9 microns and a steep reflectance drop longward of about 2.2 microns, all of which are due to abundant H2O. Weaker water overtone bands are also apparent, and in most cases there is spectral evidence for minor Fe(3+). In these features the zeolite spectra are similar to spectra of smectite clays which have abundant interlayer water. The most diagnostic difference between clay and zeolite spectra is the total absence in the zeolites of the weak structural OH absorption.

FT-IR, FT-Raman spectra and DFT calculations of melaminium perchlorate monohydrate

NASA Astrophysics Data System (ADS)

Kanagathara, N.; Marchewka, M. K.; Drozd, M.; Renganathan, N. G.; Gunasekaran, S.; Anbalagan, G.

2013-08-01

Melaminium perchlorate monohydrate (MPM), an organic material has been synthesized by slow solvent evaporation method at room temperature. Powder X-ray diffraction analysis confirms that MPM crystal belongs to triclinic system with space group P-1. FTIR and FT Raman spectra are recorded at room temperature. Functional group assignment has been made for the melaminium cations and perchlorate anions. Vibrational spectra have also been discussed on the basis of quantum chemical density functional theory (DFT) calculations using Firefly (PC GAMESS) version 7.1 G. Vibrational frequencies are calculated and scaled values are compared with experimental values. The assignment of the bands has been made on the basis of the calculated PED. The Mulliken charges, HOMO-LUMO orbital energies are analyzed directly from Firefly program log files and graphically illustrated. HOMO-LUMO energy gap and other related molecular properties are also calculated. The theoretically constructed FT-IR and FT-Raman spectra of MPM coincide with the experimental one. The chemical structure of the compound has been established by 1H and 13C NMR spectra. No detectable signal was observed during powder test for second harmonic generation.

Pectin functionalised by fatty acids: Diffuse reflectance infrared Fourier transform (DRIFT) spectroscopic characterisation

NASA Astrophysics Data System (ADS)

Kamnev, Alexander A.; Calce, Enrica; Tarantilis, Petros A.; Tugarova, Anna V.; De Luca, Stefania

2015-01-01

Chemically modified pectin derivatives obtained by partial esterification of its hydroxyl moieties with fatty acids (FA; oleic, linoleic and palmitic acids), as well as the initial apple peel pectin were comparatively characterised using diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy. Characteristic changes observed in DRIFT spectra in going from pectin to its FA esters are related to the corresponding chemical modifications. Comparing the DRIFT spectra with some reported data on FTIR spectra of the same materials measured in KBr or NaCl matrices has revealed noticeable shifts of several polar functional groups both in pectin and in its FA-esterified products induced by the halide salts. The results obtained have implications for careful structural analyses of biopolymers with hydrophilic functional groups by means of different FTIR spectroscopic methodologies.

Structures of cage, prism, and book isomers of water hexamer from broadband rotational spectroscopy.

PubMed

Pérez, Cristóbal; Muckle, Matt T; Zaleski, Daniel P; Seifert, Nathan A; Temelso, Berhane; Shields, George C; Kisiel, Zbigniew; Pate, Brooks H

2012-05-18

Theory predicts the water hexamer to be the smallest water cluster with a three-dimensional hydrogen-bonding network as its minimum energy structure. There are several possible low-energy isomers, and calculations with different methods and basis sets assign them different relative stabilities. Previous experimental work has provided evidence for the cage, book, and cyclic isomers, but no experiment has identified multiple coexisting structures. Here, we report that broadband rotational spectroscopy in a pulsed supersonic expansion unambiguously identifies all three isomers; we determined their oxygen framework structures by means of oxygen-18-substituted water (H(2)(18)O). Relative isomer populations at different expansion conditions establish that the cage isomer is the minimum energy structure. Rotational spectra consistent with predicted heptamer and nonamer structures have also been identified.

Identification of structural relaxation in the dielectric response of water

DOE PAGES

Hansen, Jesper S.; Kisliuk, Alexander; Sokolov, Alexei P.; ...

2016-06-09

One century ago pioneering dielectric results obtained for water and n-alcohols triggered the advent of molecular rotation diffusion theory considered by Debye to describe the primary dielectric absorption in these liquids. Here, comparing dielectric, viscoelastic, and light scattering results, we unambiguously demonstrate that the structural relaxation appears only as a high-frequency shoulder in the dielectric spectra of water. In contrast, the main dielectric peak is related to a supramolecular structure, analogous to the Debye-like peak observed in monoalcohols.

Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of mannitol

NASA Astrophysics Data System (ADS)

Moorthi, P. P.; Gunasekaran, S.; Swaminathan, S.; Ramkumaar, G. R.

2015-02-01

A collective experimental and theoretical study was conducted on the molecular structure and vibrational spectra of mannitol. The FT-IR and FT-Raman spectra of mannitol were recorded in the solid phase. The molecular geometry, vibrational frequencies, thermodynamic functions and atomic charges of mannitol in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking cc-pVDZ basis set. The complete vibrational assignments were performed on the basis of Total Energy Distribution (TED) of the vibrational modes. The UV absorption spectra of the title compound dissolved in water. Natural bond orbital analysis has been carried out to explain the charge transfer or delocalization of charge due to the intra-molecular interactions. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO methods. The first order hyperpolarizability (β0) of this novel molecular system and related properties (β, α0 and Δα) of mannitol are calculated using B3LYP/cc-pVDZ and HF/cc-pVDZ methods on the finite-field approach. By using TD-DFT calculation, electronic absorption spectra of the title compound have been predicted and a good agreement with experimental one is established. In addition, the molecular electrostatic potential (MEP) have been investigated using theoretical calculations, the calculated HOMO and LUMO energies shows that the charge transfer within the molecule.

Microsynthesis and electron ionization mass spectral studies of O(S)-alkyl N,N-dimethyl alkylphosphono(thiolo)thionoamidates for Chemical Weapons Convention verification.

PubMed

Saeidian, Hamdollah; Babri, Mehran; Abdoli, Morteza; Sarabadani, Mansour; Ashrafi, Davood; Naseri, Mohammad Taghi

2012-12-15

The availability of mass spectra and interpretation skills are essential for unambiguous identification of the Chemical Weapons Convention (CWC)-related chemicals. The O(S)-alkyl N,N-dimethyl alkylphosphono(thiolo)thionoamidates are included in the list of scheduled CWC-related compounds, but there are very few spectra from these compounds in the literature. This paper examines these spectra and their mass spectral fragmentation routes. The title chemicals were prepared through microsynthetic protocols and were analyzed using electron ionization mass spectrometry with gas chromatography as a MS-inlet system. Structures of fragments were confirmed using analysis of fragment ions of deuterated analogs, tandem mass spectrometry and density functional theory (DFT) calculations. Mass spectrometric studies revealed some interesting fragmentation pathways during the ionization process, such as alkene and amine elimination and McLafferty-type rearrangements. The most important fragmentation route of the chemicals is the thiono-thiolo rearrangement. DFT calculations are used to support MS results and to reveal relative preference formation of fragment ions. The retention indices (RIs) of all the studied compounds are also reported. Mass spectra of the synthesized compounds were investigated with the aim to enrich the Organization for the Prohibition of Chemical Weapons (OPCW) Central Analytical Database (OCAD) which may be used for detection and identification of CWC-related chemicals during on-site inspection and/or off-site analysis such as OPCW proficiency tests. Copyright © 2012 John Wiley & Sons, Ltd.

Aromatic Cluster Sensor of Protein Folding: Near-UV Electronic Circular Dichroism Bands Assigned to Fold Compactness.

PubMed

Farkas, Viktor; Jákli, Imre; Tóth, Gábor K; Perczel, András

2016-09-19

Both far- and near-UV electronic circular dichroism (ECD) spectra have bands sensitive to thermal unfolding of Trp and Tyr residues containing proteins. Beside spectral changes at 222 nm reporting secondary structural variations (far-UV range), L b bands (near-UV range) are applicable as 3D-fold sensors of protein's core structure. In this study we show that both L b (Tyr) and L b (Trp) ECD bands could be used as sensors of fold compactness. ECD is a relative method and thus requires NMR referencing and cross-validation, also provided here. The ensemble of 204 ECD spectra of Trp-cage miniproteins is analysed as a training set for "calibrating" Trp↔Tyr folded systems of known NMR structure. While in the far-UV ECD spectra changes are linear as a function of the temperature, near-UV ECD data indicate a non-linear and thus, cooperative unfolding mechanism of these proteins. Ensemble of ECD spectra deconvoluted gives both conformational weights and insight to a protein folding↔unfolding mechanism. We found that the L b 293 band is reporting on the 3D-structure compactness. In addition, the pure near-UV ECD spectrum of the unfolded state is described here for the first time. Thus, ECD folding information now validated can be applied with confidence in a large thermal window (5≤T≤85 °C) compared to NMR for studying the unfolding of Trp↔Tyr residue pairs. In conclusion, folding propensities of important proteins (RNA polymerase II, ubiquitin protein ligase, tryptase-inhibitor etc.) can now be analysed with higher confidence. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The acidic pH-induced structural changes in Pin1 as revealed by spectral methodologies

NASA Astrophysics Data System (ADS)

Wang, Jing-Zhang; Xi, Lei; Zhu, Guo-Fei; Han, Yong-Guang; Luo, Yue; Wang, Mei; Du, Lin-Fang

2012-12-01

Pin1 is closely associated with the pathogenesis of cancers and Alzheimer's disease (AD). Previously, we have shown the characteristics of the thermal denaturation of Pin1. Herein, the acid-induced denaturation of Pin1 was determined by means of fluorescence emission, synchronous fluorescence, far-UV CD, ANS fluorescence and RLS spectroscopies. The fluorescence emission spectra and the synchronous fluorescence spectra suggested the partially reversible unfolding (approximately from pH 7.0 to 4.0) and refolding (approximately from pH 4.0 to 1.0) of the structures around the chromophores in Pin1, apparently with an intermediate state at about pH 4.0-4.5. The far-UV CD spectra indicated that acidic pH (below pH 4.0) induced the structural transition from α-helix and random coils to β-sheet in Pin1. The ANS fluorescence and the RLS spectra further suggested the exposure of the hydrophobic side-chains of Pin1 and the aggregation of it especially below pH 2.3, and the aggregation possibly resulted in the formation of extra intermolecular β-sheet. The present work primarily shows that acidic pH can induce kinds of irreversible structural changes in Pin1, such as the exposure of the hydrophobic side-chains, the transition from α-helix to β-sheet and the aggregation of Pin1, and also explains why Pin1 loses most of its activity below pH 5.0. The results emphasize the important role of decreased pH in the pathogenesis of some Pin1-related diseases, and support the therapeutic approach for them by targeting acidosis and modifying the intracellular pH gradients.

Advanced aircraft service life monitoring method via flight-by-flight load spectra

NASA Astrophysics Data System (ADS)

Lee, Hongchul

This research is an effort to understand current method and to propose an advanced method for Damage Tolerance Analysis (DTA) for the purpose of monitoring the aircraft service life. As one of tasks in the DTA, the current indirect Individual Aircraft Tracking (IAT) method for the F-16C/D Block 32 does not properly represent changes in flight usage severity affecting structural fatigue life. Therefore, an advanced aircraft service life monitoring method based on flight-by-flight load spectra is proposed and recommended for IAT program to track consumed fatigue life as an alternative to the current method which is based on the crack severity index (CSI) value. Damage Tolerance is one of aircraft design philosophies to ensure that aging aircrafts satisfy structural reliability in terms of fatigue failures throughout their service periods. IAT program, one of the most important tasks of DTA, is able to track potential structural crack growth at critical areas in the major airframe structural components of individual aircraft. The F-16C/D aircraft is equipped with a flight data recorder to monitor flight usage and provide the data to support structural load analysis. However, limited memory of flight data recorder allows user to monitor individual aircraft fatigue usage in terms of only the vertical inertia (NzW) data for calculating Crack Severity Index (CSI) value which defines the relative maneuver severity. Current IAT method for the F-16C/D Block 32 based on CSI value calculated from NzW is shown to be not accurate enough to monitor individual aircraft fatigue usage due to several problems. The proposed advanced aircraft service life monitoring method based on flight-by-flight load spectra is recommended as an improved method for the F-16C/D Block 32 aircraft. Flight-by-flight load spectra was generated from downloaded Crash Survival Flight Data Recorder (CSFDR) data by calculating loads for each time hack in selected flight data utilizing loads equations. From the comparison of interpolated fatigue life using CSI value and fatigue test results, it is obvious that proposed advanced IAT method via flight-by-flight load spectra is more reliable and accurate than current IAT method. Therefore, the advanced aircraft service life monitoring method based on flight-by-flight load spectra not only monitors the individual aircraft consumed fatigue life for inspection but also ensures the structural reliability of aging aircrafts throughout their service periods.

The 2012 Ferrara seismic sequence: Regional crustal structure, earthquake sources, and seismic hazard

NASA Astrophysics Data System (ADS)

Malagnini, Luca; Herrmann, Robert B.; Munafò, Irene; Buttinelli, Mauro; Anselmi, Mario; Akinci, Aybige; Boschi, E.

2012-10-01

Inadequate seismic design codes can be dangerous, particularly when they underestimate the true hazard. In this study we use data from a sequence of moderate-sized earthquakes in northeast Italy to validate and test a regional wave propagation model which, in turn, is used to understand some weaknesses of the current design spectra. Our velocity model, while regionalized and somewhat ad hoc, is consistent with geophysical observations and the local geology. In the 0.02-0.1 Hz band, this model is validated by using it to calculate moment tensor solutions of 20 earthquakes (5.6 ≥ MW ≥ 3.2) in the 2012 Ferrara, Italy, seismic sequence. The seismic spectra observed for the relatively small main shock significantly exceeded the design spectra to be used in the area for critical structures. Observations and synthetics reveal that the ground motions are dominated by long-duration surface waves, which, apparently, the design codes do not adequately anticipate. In light of our results, the present seismic hazard assessment in the entire Pianura Padana, including the city of Milan, needs to be re-evaluated.

Photoluminescence and reflectivity of polymethylmethacrylate implanted by low-energy carbon ions at high fluences

NASA Astrophysics Data System (ADS)

Wang, Jun; Zhu, Fei; Zhang, Bei; Liu, Huixian; Jia, Guangyi; Liu, Changlong

2012-11-01

Polymethylmethacrylate (PMMA) specimens were implanted with 30 keV carbon ions in a fluence range of 1 × 1016 to 2 × 1017 cm-2, and photoluminescence (PL) and reflectivity of the implanted samples were examined. A luminescent band with one peak was found in PL spectra excited by 480 nm line, but its intensity did not vary in parallel with ion fluence. The strongest PL occurred at the fluence of 5 × 1016 cm-2. Results from visible-light-excited micro-Raman spectra indicated that the formation of hydrogenated amorphous carbon structures in subsurface layer and their evolutions with ion fluence could be responsible for the observed PL responses. Measurements of the small-angle reflectance spectra from both the implanted and rear surfaces of samples in the ultraviolet-visible (UV-vis) range demonstrated a kind of both fluence-dependent and wavelength-related reflectivity variations, which were attributed to the structural changes induced by ion implantation. A noticeable reflectivity modification, which may be practically used, could be found at the fluence of 1 × 1016 cm-2.

Giant molecular cloud scaling relations: the role of the cloud definition

NASA Astrophysics Data System (ADS)

Khoperskov, S. A.; Vasiliev, E. O.; Ladeyschikov, D. A.; Sobolev, A. M.; Khoperskov, A. V.

2016-01-01

We investigate the physical properties of molecular clouds in disc galaxies with different morphologies: a galaxy without prominent structure, a spiral barred galaxy and a galaxy with flocculent structure. Our N-body/hydrodynamical simulations take into account non-equilibrium H2 and CO chemical kinetics, self-gravity, star formation and feedback processes. For the simulated galaxies, the scaling relations of giant molecular clouds, or so-called Larson's relations, are studied for two types of cloud definition (or extraction method): the first is based on total column density position-position (PP) data sets and the second is indicated by the CO (1-0) line emission used in position-position-velocity (PPV) data. We find that the cloud populations obtained using both cloud extraction methods generally have similar physical parameters, except that for the CO data the mass spectrum of clouds has a tail with low-mass objects M ˜ 103-104 M⊙. Owing toa varying column density threshold, the power-law indices in the scaling relations are significantly changed. In contrast, the relations are invariant to the CO brightness temperature threshold. Finally, we find that the mass spectra of clouds for PPV data are almost insensitive to the galactic morphology, whereas the spectra for PP data demonstrate significant variation.

Theoretical research and experimental validation of quasi-static load spectra on bogie frame structures of high-speed trains

NASA Astrophysics Data System (ADS)

Zhu, Ning; Sun, Shou-Guang; Li, Qiang; Zou, Hua

2014-12-01

One of the major problems in structural fatigue life analysis is establishing structural load spectra under actual operating conditions. This study conducts theoretical research and experimental validation of quasi-static load spectra on bogie frame structures of high-speed trains. The quasistatic load series that corresponds to quasi-static deformation modes are identified according to the structural form and bearing conditions of high-speed train bogie frames. Moreover, a force-measuring frame is designed and manufactured based on the quasi-static load series. The load decoupling model of the quasi-static load series is then established via calibration tests. Quasi-static load-time histories, together with online tests and decoupling analysis, are obtained for the intermediate range of the Beijing—Shanghai dedicated passenger line. The damage consistency calibration of the quasi-static discrete load spectra is performed according to a damage consistency criterion and a genetic algorithm. The calibrated damage that corresponds with the quasi-static discrete load spectra satisfies the safety requirements of bogie frames.

The vibrational spectra and structure of 4-methyl oxaloacetate (carbomethoxypyruvic acid)

NASA Astrophysics Data System (ADS)

Schiering, David W.; Katon, J. E.

1986-04-01

The vibrational spectra of solid 4-methyl oxalocetate have been recorded. Infrared spectra were collected at ambient and liquid nitrogen temperatures; Raman spectra were collected at ambient temperature only. A tentative vibrational assignment of the solid is proposed based on a dimer structure composed of two enolic monomer units hydrogen bonded through the carboxylic acid group. 4-Methyl oxaloacetate was found to undergo keto—enol tautomerization in solution, and the solvent dependency of this equilibrium was demonstrated.

Change in Glutenin Macropolymer Secondary Structure in Wheat Sourdough Fermentation by FTIR.

PubMed

Wang, Jinshui; Yue, Yuanyuan; Liu, Tiantian; Zhang, Bin; Wang, Zhenlei; Zhang, Changfu

2017-06-01

Wheat sourdough was prepared by fermentation with Lactobacillus plantarum M616 and yeast in the present study. The change in secondary structure of glutenin macropolymer (GMP) in wheat sourdough fermentation for 4 and 12 h was determined using Fourier transform infrared spectroscopy, and then the resultant spectra were Fourier self-deconvoluted of the amide I band in the region from 1600 to 1700 cm -1 . Significant different spectra especially in the amide I band for GMP from sourdough fermented with L. plantarum M616 (SL) and with L. plantarum M616 and yeast (SLY) were found in respect of control dough (CK), dough with acids (SA), and sourdough fermented with yeast (SY) at 4 and 12 h of fermentation. The loss of α-helix structure in SL, SLY, and SA samples was noticed during fermentation. Compared with CK and SY, SL, SLY, and SA samples showed significant decrease (p < 0.05) in the relative areas of α-helix at the same stage of fermentation. In addition, β-turns in SL sourdough decrease, and the relative areas of random coil increase significantly (p < 0.05). These changes in the secondary structure mean that the flexibility of glutenin macropolymer in sourdough increases and it makes GMP degradation easier during fermentation. The modified secondary structure of GMP makes more sensitive to proteolysis by means of cereal enzymes.

Structure, vibrational spectra and DFT characterization of the intra- and inter-molecular interactions in 2-hydroxy-5-methylpyridine-3-carboxylic acid--normal modes of the eight-membered HB ring.

PubMed

Godlewska, P; Jańczak, J; Kucharska, E; Hanuza, J; Lorenc, J; Michalski, J; Dymińska, L; Węgliński, Z

2014-01-01

Fourier transform IR and Raman spectra, XRD studies and DFT quantum chemical calculations have been used to characterize the structural and vibrational properties of 2-hydroxy-5-methylpyridine-3-carboxylic acid. In the unit-cell of this compound two molecules related by the inversion center interact via OH⋯N hydrogen bonds. The double hydrogen bridge system is spaced parallel to the (102) crystallographic plane forming eight-membered arrangement characteristic for pyridine derivatives. The six-membered ring is the second characteristic unit formed via the intramolecular OH⋯O hydrogen bond. The geometry optimization of the monomer and dimer have been performed applying the Gaussian03 program package. All calculations were performed in the B3LYP/6-31G(d,p) basis set using the XRD data as input parameters. The relation between the molecular and crystal structures has been discussed in terms of the hydrogen bonds formed in the unit cell. The vibrations of the dimer have been discussed in terms of the resonance inside the system built of five rings coupled via hydrogen bonds. Copyright © 2013 Elsevier B.V. All rights reserved.

Surface-enhanced Raman spectroscopy study on the structure changes of 4-Mercaptophenylboronic Acid under different pH conditions

NASA Astrophysics Data System (ADS)

Su, Hongyang; Wang, Yue; Yu, Zhi; Liu, Yawen; Zhang, Xiaolei; Wang, Xiaolei; Sui, Huimin; Sun, Chengbin; Zhao, Bing

2017-10-01

4-Mercaptophenylboronic Acid (4-MPBA) plays pivotal role in various fields. The orientation and existing form of the 4-MPBA strongly depend on the pH value of the media. The general aim of this work is to obtain information about the structure changes of 4-MPBA absorbed on Ag nanoparticles in different pH environment. Surface-enhanced Raman spectroscopy (SERS) technique is a simple and rapid method to study adsorption phenomena at molecule level. The investigation is done by means of SERS. In order to interpret the experimental information, a series of SERS spectra is carried out. The relative intensities of the totally symmetric (a1 mode) and non-totally symmetric (b2 mode) bands in the SERS spectra of 4-MPBA change depend on the environmental pH values, which is a manifestation of charge transfer (CT) processes. The degree of charge transfer increases with the pH value of the media changing from acidity to alkalinity. The structure changes of MPBA had been carried out in different pH environment. We envision that this approach will be of great significance in related fields of 4-MPBA-involved detection.

On the origin of the low-temperature band in depolarization current spectra of poled multicomponent silicate glasses

NASA Astrophysics Data System (ADS)

Brunkov, P. N.; Kaasik, V. P.; Lipovskii, A. A.; Tagantsev, D. K.

2018-04-01

Thermally stimulated depolarization current spectra of poled silicate multicomponent glasses in the vicinity of room temperature (220-320 K) have been recorded and two bands, typical for such glasses, have been observed. It was shown that the high-temperature band (at about 290 K) is related to the relaxation of poled glass structure in the bulk, while the low-temperature band (at about 230-270 K) should be attributed to the surface phenomenon—absorption/desorption of positive species of ambient atmosphere, supposedly, water cluster ions H+(H2O)n.

Manipulation of spontaneous emission in a tapered photonic crystal fibre

NASA Astrophysics Data System (ADS)

Myers, S. J.; Fussell, D. P.; Dawes, J. M.; Mägi, E.; McPhedran, R. C.; Eggleton, B. J.; de Sterke, C. Martijn

2006-12-01

We characterize the spontaneous emission of dye that is introduced into the central core of a tapered photonic crystal fiber. Since the photonic crystal period in the fibre cladding varies along the taper, the transmission and spontaneous emission spectra over a wide range of relative frequencies can be observed. The spontaneous emission spectra of the fibre transverse to the fiber axis show suppression due to partial band-gaps of the structure, and also enhancement of spontaneous emission near the band edges. We associate these with van Hove features, as well as finite cluster size effects.

NMR-based automated protein structure determination.

PubMed

Würz, Julia M; Kazemi, Sina; Schmidt, Elena; Bagaria, Anurag; Güntert, Peter

2017-08-15

NMR spectra analysis for protein structure determination can now in many cases be performed by automated computational methods. This overview of the computational methods for NMR protein structure analysis presents recent automated methods for signal identification in multidimensional NMR spectra, sequence-specific resonance assignment, collection of conformational restraints, and structure calculation, as implemented in the CYANA software package. These algorithms are sufficiently reliable and integrated into one software package to enable the fully automated structure determination of proteins starting from NMR spectra without manual interventions or corrections at intermediate steps, with an accuracy of 1-2 Å backbone RMSD in comparison with manually solved reference structures. Copyright © 2017 Elsevier Inc. All rights reserved.

The effect of annulation of benzene rings on the photophysics and electronic structure of tetraazachlorin molecules

NASA Astrophysics Data System (ADS)

Pershukevich, P. P.; Volkovich, D. I.; Gladkov, L. L.; Dudkin, S. V.; Kuzmitsky, V. A.; Makarova, E. A.; Solovyev, K. N.

2017-10-01

The photophysics and electronic structure of tribenzotetraazachlorins (H2, Zn, and Mg), which are novel analogues of phtalocyanines, have been studied experimentally and theoretically. At 293 K, the electronic absorption, fluorescence, and fluorescence excitation spectra are recorded and the fluorescence quantum yield and lifetime, as well as the quantum yield of singlet oxygen generation, are measured; at 77 K, the fluorescence, fluorescence excitation, and fluorescence polarization spectra are recorded and the fluorescence lifetime values are measured. The dependences of the absorption spectra and photophysical parameters on the structure variation are analyzed in detail. Quantum-chemical calculations of the electronic structure and absorption spectra of tribenzotetraazachlorins (H2, Mg) are performed using the INDO/Sm method (modified INDO/S method) based on molecular-geometry optimization by the DFT PBE/TZVP method. The results of quantum-chemical calculations of the electronic absorption spectra are in very good agreement with the experimental data for the transitions to two lower electronic states.

N3 and O2 protonated tautomeric conformations of 2'-deoxycytidine and cytidine coexist in the gas phase.

PubMed

Wu, R R; Yang, Bo; Frieler, C E; Berden, G; Oomens, J; Rodgers, M T

2015-05-07

Infrared multiple photon dissociation action spectra of the protonated forms of the cytidyl nucleosides, 2'-deoxycytidine, [dCyd+H](+), and cytidine, [Cyd+H](+), are acquired over the IR fingerprint and hydrogen-stretching regions. Electronic structure calculations are performed at the B3LYP/6-311+G(d,p) level to determine the stable low-energy tautomeric conformations of these species generated upon electrospray ionization (ESI) and to generate the linear IR absorption spectra of these protonated nucleosides. Comparison between the experimental and theoretical spectra allows the tautomeric conformations of [dCyd+H](+) and [Cyd+H](+) populated by ESI to be determined. B3LYP predicts N3 as the preferred protonation site for both [dCyd+H](+) and [Cyd+H](+), whereas MP2 suggests that protonation at O2 is more favorable. The 2'-hydroxyl substituent does not significantly alter the structures of the B3LYP N3 and MP2 O2 protonated ground tautomeric conformations of [dCyd+H](+) vs [Cyd+H](+). [dCyd+H](+) and [Cyd+H](+) exhibit very similar spectral signatures in both regions. Nonetheless, the 2'-hydroxyl does affect the relative intensities of the IRMPD bands of [dCyd+H](+) vs [Cyd+H](+). The spectral features observed in the hydrogen-stretching region complement those of the fingerprint region and allow the N3 and O2 protonated tautomeric conformations to be readily distinguished. Comparison between the measured and computed spectra indicates that both N3 and O2 protonated tautomeric conformations coexist in the experiments, and the populations are dominated by the most stable N3 and O2 protonated tautomeric conformations. Least-squares fitting of the IRMPD spectra to the IR spectra for these most stable conformers suggests relative populations of ∼55% N3 vs 45% O2 protonated conformers of [dCyd+H](+), whereas ∼47% N3 vs 53% O2 protonated conformers of [Cyd+H](+). This change in the preferred site of protonation indicates that the 2'-hydroxyl substituent plays an important role in controlling the reactivity of the cytidyl nucleosides.

Electroluminescence and cathodoluminescence from polyethylene and polypropylene films: Spectra reconstruction from elementary components and underlying mechanisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qiao, B.; Teyssedre, G.; Laurent, C.

The mechanisms of electroluminescence from large band gap polymers used as insulation in electric components are still under debate. It becomes important to unravel the underlying physics of the emission because of increasing thermo-electric stress and a possible relationship between electroluminescence and field withstand. We report herein on the cathodoluminescence spectra of polyethylene and polypropylene films as a way to uncover the nature of its contributions to electroluminescence emission. It is shown that spectra from the two materials are structured around four elementary components, each of them being associated with a specific process contributing to the overall emission with differentmore » weights depending on excitation conditions and on materials. The cathodoluminescence and electroluminescence spectra of each material are reconstructed from the four spectral components and their relative contribution are discussed. It is shown that electroluminescence from polyethylene and polypropylene has the same origin pointing towards generic mechanisms in both.« less

Spectra of variations and cosmic ray anisotropy during GLE of June 11, 1991

NASA Astrophysics Data System (ADS)

Kravtsova, Marina; Sdobnov, Valeriy

2015-03-01

We have studied variation spectra and cosmic-ray (CR) anisotropy, using the ground-based and satellite observations of the CR intensity on the worldwide network of stations during the ground level enhancement (GLE) of June 11, 1991. The spectrographic global survey has been used. Variation spectra of primary CRs at different moments of the event are presented. Note that the CR variation spectra during this period are not described by a power or an exponential function of particle rigidity. The maximum rigidity, up to which the protons were accelerated on June 11, 1991, was ~2.8 GV (06:00 UT; i.e., two hours after GLE started). We show relative variations in the CR intensity in the geocentric solar ecliptic coordinate system during certain periods of the event under study. On June 11, 1991, the bidirectional anisotropy dominated in the distribution of particles with rigidity of 4 GV and 10 GV, which implies that the Earth passed the loop-like IMF structure.

Molecular structure, natural bond analysis, vibrational and electronic spectra, surface enhanced Raman scattering and Mulliken atomic charges of the normal modes of [Mn(DDTC)2] complex.

PubMed

Téllez S, Claudio A; Costa, Anilton C; Mondragón, M A; Ferreira, Glaucio B; Versiane, O; Rangel, J L; Lima, G Müller; Martin, A A

2016-12-05

Theoretical and experimental bands have been assigned for the Fourier Transform Infrared and Raman spectra of the bis(diethyldithiocarbamate)Mn(II) complex, [Mn(DDTC)2]. The calculations have been based on the DFT/B3LYP method, second derivative spectra and band deconvolution analysis. The UV-vis experimental spectra were measured in acetonitrile solution, and the calculated electronic spectrum was obtained using the TD/B3LYP method with 6-311G(d, p) basis set for all atoms. Charge transfer bands and those d-d spin forbidden were assigned in the UV-vis spectrum. The natural bond orbital analysis was carried out using the DFT/B3LYP method and the Mn(II) hybridization leading to the planar geometry of the framework was discussed. Surface enhanced Raman scattering (SERS) was also performed. Mulliken charges of the normal modes were obtained and related to the SERS enhanced bands. Copyright © 2016 Elsevier B.V. All rights reserved.

Multivariate Analysis of Electron Detachment Dissociation and Infrared Multiphoton Dissociation Mass Spectra of Heparan Sulfate Tetrasaccharides Differing Only in Hexuronic acid Stereochemistry

NASA Astrophysics Data System (ADS)

Oh, Han Bin; Leach, Franklin E.; Arungundram, Sailaja; Al-Mafraji, Kanar; Venot, Andre; Boons, Geert-Jan; Amster, I. Jonathan

2011-03-01

The structural characterization of glycosaminoglycan (GAG) carbohydrates by mass spectrometry has been a long-standing analytical challenge due to the inherent heterogeneity of these biomolecules, specifically polydispersity, variability in sulfation, and hexuronic acid stereochemistry. Recent advances in tandem mass spectrometry methods employing threshold and electron-based ion activation have resulted in the ability to determine the location of the labile sulfate modification as well as assign the stereochemistry of hexuronic acid residues. To facilitate the analysis of complex electron detachment dissociation (EDD) spectra, principal component analysis (PCA) is employed to differentiate the hexuronic acid stereochemistry of four synthetic GAG epimers whose EDD spectra are nearly identical upon visual inspection. For comparison, PCA is also applied to infrared multiphoton dissociation spectra (IRMPD) of the examined epimers. To assess the applicability of multivariate methods in GAG mixture analysis, PCA is utilized to identify the relative content of two epimers in a binary mixture.

Detecting molecular features of spectra mainly associated with structural and non-structural carbohydrates in co-products from bioEthanol production using DRIFT with uni- and multivariate molecular spectral analyses.

PubMed

Yu, Peiqiang; Damiran, Daalkhaijav; Azarfar, Arash; Niu, Zhiyuan

2011-01-01

The objective of this study was to use DRIFT spectroscopy with uni- and multivariate molecular spectral analyses as a novel approach to detect molecular features of spectra mainly associated with carbohydrate in the co-products (wheat DDGS, corn DDGS, blend DDGS) from bioethanol processing in comparison with original feedstock (wheat (Triticum), corn (Zea mays)). The carbohydrates related molecular spectral bands included: A_Cell (structural carbohydrates, peaks area region and baseline: ca. 1485-1188 cm(-1)), A_1240 (structural carbohydrates, peak area centered at ca. 1240 cm(-1) with region and baseline: ca. 1292-1198 cm(-1)), A_CHO (total carbohydrates, peaks region and baseline: ca. 1187-950 cm(-1)), A_928 (non-structural carbohydrates, peak area centered at ca. 928 cm(-1) with region and baseline: ca. 952-910 cm(-1)), A_860 (non-structural carbohydrates, peak area centered at ca. 860 cm(-1) with region and baseline: ca. 880-827 cm(-1)), H_1415 (structural carbohydrate, peak height centered at ca. 1415 cm(-1) with baseline: ca. 1485-1188 cm(-1)), H_1370 (structural carbohydrate, peak height at ca. 1370 cm(-1) with a baseline: ca. 1485-1188 cm(-1)). The study shows that the grains had lower spectral intensity (KM Unit) of the cellulosic compounds of A_1240 (8.5 vs. 36.6, P < 0.05), higher (P < 0.05) intensities of the non-structural carbohydrate of A_928 (17.3 vs. 2.0) and A_860 (20.7 vs. 7.6) than their co-products from bioethanol processing. There were no differences (P > 0.05) in the peak area intensities of A_Cell (structural CHO) at 1292-1198 cm(-1) and A_CHO (total CHO) at 1187-950 cm(-1) with average molecular infrared intensity KM unit of 226.8 and 508.1, respectively. There were no differences (P > 0.05) in the peak height intensities of H_1415 and H_1370 (structural CHOs) with average intensities 1.35 and 1.15, respectively. The multivariate molecular spectral analyses were able to discriminate and classify between the corn and corn DDGS molecular spectra, but not wheat and wheat DDGS. This study indicated that the bioethanol processing changes carbohydrate molecular structural profiles, compared with the original grains. However, the sensitivities of different types of carbohydrates and different grains (corn and wheat) to the processing differ. In general, the bioethanol processing increases the molecular spectral intensities for the structural carbohydrates and decreases the intensities for the non-structural carbohydrates. Further study is needed to quantify carbohydrate related molecular spectral features of the bioethanol co-products in relation to nutrient supply and availability of carbohydrates.

Solution NMR Structures of Oxidized and Reduced Ehrlichia chaffeensis thioredoxin: NMR-Invisible Structure Owing to Backbone Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buchko, Garry W.; Hewitt, Stephen N.; Van Voorhis, Wesley C.

Thioredoxins (Trxs) are small ubiquitous proteins that participate in a diverse variety of redox reactions via the reversible oxidation of two cysteine thiol groups in a structurally conserved active site, CGPC. Here, we describe the NMR solution structures of a Trx from Ehrlichia chaffeensis (Ec-Trx, ECH_0218), the etiological agent responsible for human monocytic ehrlichiosis, in both the oxidized and reduced states. The overall topology of the calculated structures is similar in both redox states and similar to other Trx structures, a five-strand, mixed -sheet (1:3:2:4:5) surrounded by four -helices. Unlike other Trxs studied by NMR in both redox states, themore » 1H-15N HSQC spectra of reduced Ec-Trx was missing eight amide cross peaks relative to the spectra of oxidized Ec-Trx. These missing amides correspond to residues C32-E39 in the active site containing helix (2) and S72-I75 in a loop near the active site and suggest a substantial change in the backbone dynamics associated with the formation of an intramolecular C32-C35 disulfide bond.« less

Estimating Eulerian spectra from pairs of drifters

NASA Astrophysics Data System (ADS)

LaCasce, Joe

2017-04-01

GPS-tracked surface drifters offer the possibility of sampling energetic variations at the ocean surface on scales of only 10s of meters, much less than that resolved by satellite. Here we investigate whether velocity differences between pairs of drifters can be used to estimate kinetic energy spectra. Theoretical relations between the spectrum and the second-order longitudinal structure function for 2D non-divergent flow are derived. The structure function is a natural statistic for particle pairs and is easily calculated. However it integrates contributions across wavenumber, and this tends to obscure the spectral dependencies when turbulent inertial ranges are of finite extent. Nevertheless, the transform from spectrum to structure function is robust, as illustrated with Eulerian data collected from aircraft. The inverse transform, from structure function to spectrum, is much less robust, yielding poor results in particular at large wavenumbers. This occurs because the transform involves a filter function which magnifies contributions from large pair separations, which tend to be noisy. Fitting the structure function to a polynomial improves the spectral estimate, but not sufficiently to distinguish correct inertial range dependencies. Thus with Lagrangian data, it is appears preferable to focus on structure functions, despite their shortcomings.

Structural characterization of rondorfite, calcium silica chlorine mineral containing magnesium in tetrahedral position [MgO4]6-, with the aid of the vibrational spectroscopies and fluorescence.

PubMed

Dulski, M; Bulou, A; Marzec, K M; Galuskin, E V; Wrzalik, R

2013-01-15

Raman and infrared spectra of rondorfite Ca8Mg(SiO4)4Cl2, a calcium chlorosilica mineral containing magnesium in tetrahedral position, has been studied in terms of spectra-structure relations. Raman spectra have been measured at different excited laser lines: 780 nm, 532 nm, 488 nm and 457 nm. This mineral is characterized by a single sharp intense Raman band at 863 cm(-1) assigned to the ν1 [SiO4]4- (Ag) symmetric stretching mode in the magnesiosilicate pentamer. Due to symmetry restriction the other Raman bands have a small intensity. Two Raman bands observed at 564 cm(-1) and 526 cm(-1) are associated simultaneously with ν4 [MgO4]6- and ν4 [SiO4]4- symmetric and antisymmetric modes where magnesium occurs in the tetrahedral configuration. The weak bands at 422 cm(-1) and 386 cm(-1) are associated with the ν2 bending mode of CaO6 in octahedral configuration, respectively. Moreover the infrared spectrum shows very weak bands associated with the hydroxyl group and/or water molecule. Additionally, the strong fluorescence phenomenon was observed and related to the presence of chlorine atoms, magnesium Mg2+ ions in atypical configuration or point defects. Copyright © 2012 Elsevier B.V. All rights reserved.

Structural model of the amyloid fibril formed by beta(2)-microglobulin #21-31 fragment based on vibrational spectroscopy.

PubMed

Hiramatsu, Hirotsugu; Goto, Yuji; Naiki, Hironobu; Kitagawa, Teizo

2005-06-08

A structural model of amyloid fibril formed by the #21-31 fragment of beta2-microglobulin is proposed from microscope IR measurements on specifically 13C-labeled peptide fibrils and Raman spectra of the dispersed fibril solution. The 13C-shifted amide frequency indicated the secondary structure of the labeled residues. The IR spectra have demonstrated that the region between F22 and V27 forms the core part with the extended beta-sheet structure. Raman spectra indicated the formation of a dimer with a disulfide bridge between C25 residues.

Spectral analysis of the structure of ultradispersed diamonds

NASA Astrophysics Data System (ADS)

Uglov, V. V.; Shimanski, V. I.; Rusalsky, D. P.; Samtsov, M. P.

2008-07-01

The structure of ultradispersed diamonds (UDD) is studied by spectral methods. The presence of diamond crystal phase in the UDD is found based on x-ray analysis and Raman spectra. The Raman spectra also show sp2-and sp3-hybridized carbon. Analysis of IR absorption spectra suggests that the composition of functional groups present in the particles changes during the treatment.

Validation of the French Autism Spectrum Quotient scale and its relationships with schizotypy and Eysenckian personality traits.

PubMed

Sierro, Guillaume; Rossier, Jérôme; Mohr, Christine

2016-07-01

Autism and schizophrenia spectra were long considered distinct entities. Yet, recent studies emphasized overlapping clinical and personality features suggesting common mechanisms and liabilities. Independent notions, however, highlight that the two spectra oppose each other socially (positive schizotypal hyper-mentalism versus autistic hypo-mentalism). To clarify these relationships, we used data from 921 French-speaking Swiss undergraduates to firstly validate the French Autism Spectrum Questionnaire (AQ) identifying an optimal factor structure. Secondly, we assessed relationships between this AQ structure and schizotypic personality traits. Results from correlational and principal component analyses replicated both overlapping and opposing relationships. We conjecture that autistic traits opposing positive schizotypy represent autistic mentalizing deficits. We discuss implications of our findings relative to theories of autism and schizophrenia spectrum relationships. Copyright © 2016 Elsevier Inc. All rights reserved.

Al3+ environments in nanostructured ZnAl2O4 and their effects on the luminescence properties.

PubMed

da Silva, Alison A; Gonçalves, Agnaldo S; Davolos, Marian R; Santagneli, Silvia H

2008-11-01

Single-phase zinc aluminate (ZnAl2O4) with the spinel structure was successfully obtained by the Pechini method at different calcining temperatures for 4 hours. The nanoparticles are highly crystalline with no impurities related to ZnO or Al2O3 residues. The microstructural environment of aluminium ions changes with heat treatment temperature, as observed by Fourier transform infrared spectroscopy. The spinel structure might present two different AlO6 sites as evidenced by 27Al solid-state magic-angle-spinning nuclear magnetic resonance spectra. Some AlO4 sites were also detected for samples calcined at a temperature lower than 900 degrees C. The photoluminescence spectra show that the emission can be tuned depending on the calcining temperature. This effect was discussed on the basis of symmetry and oxygen vacancies.

Soft X-Ray Absorption Spectroscopy of High-Abrasion-Furnace Carbon Black

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muramatsu, Yasuji; Harada, Ryusuke; Gullikson, Eric M.

2007-02-02

The soft x-ray absorption spectra of high-abrasion-furnace carbon black were measured to obtain local-structure/chemical-states information of the primary particles and/or crystallites. The soft x-ray absorption spectral features of carbon black represent broader {pi}* and {sigma}* peak structures compared to highly oriented pyrolytic graphite (HOPG). The subtracted spectra between the carbon black and HOPG, (carbon black) - (HOPG), show double-peak structures on both sides of the {pi}* peak. The lower-energy peak, denoted as the 'pre-peak', in the subtracted spectra and the {pi}*/{sigma}* peak intensity ratio in the absorption spectra clearly depend on the specific surface area by nitrogen adsorption (NSA). Therefore,more » it is concluded that the pre-peak intensity and the {pi}*/{sigma}* ratio reflect the local graphitic structure of carbon black.« less

[Preparation and spectral analysis of a new type of blue light-emitting material delta-Alq3].

PubMed

Wang, Hua; Hao, Yu-ying; Gao, Zhi-xiang; Zhou, He-feng; Xu, Bing-she

2006-10-01

In the present article, delta-Alq3, a new type of blue light-emitting material, was synthesized and investigated by IR spectra, XRD spectra, UV-Vis absorption spectra, photoluminescence (PL) spectra, and electroluminescence (EL) spectra. The relationship between molecular spatial structure and spectral characteristics was studied by the spectral analysis of delta-Alq3 and alpha-Alq3. Results show that a new phase of Alq3 (delta-Alq3) can be obtained by vacuum heating alpha-Alq3, and the molecular spatial structure of alpha-Alq3 changes during the vacuum heating. The molecular spatial structure of delta-Alq3 lacks symmetry compared to alpha-Alq3. This transformation can reduce the electron cloud density on phenoxide of Alq3 and weaken the intermolecular conjugated interaction between adjacent Alq3 molecules. Hence, the pi--pi* electron transition absorption peak of delta-Alq3 shifts toward short wavelength in UV-Vis absorption spectra, and the maximum emission peak of delta-Alq3 (lamda max = 480 nm) blue-shifts by 35 nm compared with that of alpha-Alq3 (lamda max = 515 nm) in PL spectra. The maximum emission peaks of delta-Alq3 and alpha-Alq3 are all at 520 nm in EL spectra.

Resonant Raman spectra of diindenoperylene thin films

NASA Astrophysics Data System (ADS)

Scholz, R.; Gisslén, L.; Schuster, B.-E.; Casu, M. B.; Chassé, T.; Heinemeyer, U.; Schreiber, F.

2011-01-01

Resonant and preresonant Raman spectra obtained on diindenoperylene (DIP) thin films are interpreted with calculations of the deformation of a relaxed excited molecule with density functional theory (DFT). The comparison of excited state geometries based on time-dependent DFT or on a constrained DFT scheme with observed absorption spectra of dissolved DIP reveals that the deformation pattern deduced from constrained DFT is more reliable. Most observed Raman peaks can be assigned to calculated A_g-symmetric breathing modes of DIP or their combinations. As the position of one of the laser lines used falls into a highly structured absorption band, we have carefully analyzed the Raman excitation profile arising from the frequency dependence of the dielectric tensor. This procedure gives Raman cross sections in good agreement with the observed relative intensities, both in the fully resonant and in the preresonant case.

Resonant Raman spectra of diindenoperylene thin films.

PubMed

Scholz, R; Gisslén, L; Schuster, B-E; Casu, M B; Chassé, T; Heinemeyer, U; Schreiber, F

2011-01-07

Resonant and preresonant Raman spectra obtained on diindenoperylene (DIP) thin films are interpreted with calculations of the deformation of a relaxed excited molecule with density functional theory (DFT). The comparison of excited state geometries based on time-dependent DFT or on a constrained DFT scheme with observed absorption spectra of dissolved DIP reveals that the deformation pattern deduced from constrained DFT is more reliable. Most observed Raman peaks can be assigned to calculated A(g)-symmetric breathing modes of DIP or their combinations. As the position of one of the laser lines used falls into a highly structured absorption band, we have carefully analyzed the Raman excitation profile arising from the frequency dependence of the dielectric tensor. This procedure gives Raman cross sections in good agreement with the observed relative intensities, both in the fully resonant and in the preresonant case.

Kohonen and counterpropagation neural networks applied for mapping and interpretation of IR spectra.

PubMed

Novic, Marjana

2008-01-01

The principles of learning strategy of Kohonen and counterpropagation neural networks are introduced. The advantages of unsupervised learning are discussed. The self-organizing maps produced in both methods are suitable for a wide range of applications. Here, we present an example of Kohonen and counterpropagation neural networks used for mapping, interpretation, and simulation of infrared (IR) spectra. The artificial neural network models were trained for prediction of structural fragments of an unknown compound from its infrared spectrum. The training set contained over 3,200 IR spectra of diverse compounds of known chemical structure. The structure-spectra relationship was encompassed by the counterpropagation neural network, which assigned structural fragments to individual compounds within certain probability limits, assessed from the predictions of test compounds. The counterpropagation neural network model for prediction of fragments of chemical structure is reversible, which means that, for a given structural domain, limited to the training data set in the study, it can be used to simulate the IR spectrum of a chemical defined with a set of structural fragments.

Identifying Broadband Rotational Spectra with Neural Networks

NASA Astrophysics Data System (ADS)

Zaleski, Daniel P.; Prozument, Kirill

2017-06-01

A typical broadband rotational spectrum may contain several thousand observable transitions, spanning many species. Identifying the individual spectra, particularly when the dynamic range reaches 1,000:1 or even 10,000:1, can be challenging. One approach is to apply automated fitting routines. In this approach, combinations of 3 transitions can be created to form a "triple", which allows fitting of the A, B, and C rotational constants in a Watson-type Hamiltonian. On a standard desktop computer, with a target molecule of interest, a typical AUTOFIT routine takes 2-12 hours depending on the spectral density. A new approach is to utilize machine learning to train a computer to recognize the patterns (frequency spacing and relative intensities) inherit in rotational spectra and to identify the individual spectra in a raw broadband rotational spectrum. Here, recurrent neural networks have been trained to identify different types of rotational spectra and classify them accordingly. Furthermore, early results in applying convolutional neural networks for spectral object recognition in broadband rotational spectra appear promising. Perez et al. "Broadband Fourier transform rotational spectroscopy for structure determination: The water heptamer." Chem. Phys. Lett., 2013, 571, 1-15. Seifert et al. "AUTOFIT, an Automated Fitting Tool for Broadband Rotational Spectra, and Applications to 1-Hexanal." J. Mol. Spectrosc., 2015, 312, 13-21. Bishop. "Neural networks for pattern recognition." Oxford university press, 1995.

Eta Carinae: Viewed from Multiple Vantage Points

NASA Technical Reports Server (NTRS)

Gull, Theodore

2007-01-01

The central source of Eta Carinae and its ejecta is a massive binary system buried within a massive interacting wind structure which envelops the two stars. However the hot, less massive companion blows a small cavity in the very massive primary wind, plus ionizes a portion of the massive wind just beyond the wind-wind boundary. We gain insight on this complex structure by examining the spatially-resolved Space Telescope Imaging Spectrograph (STIS) spectra of the central source (0.1") with the wind structure which extends out to nearly an arcsecond (2300AU) and the wind-blown boundaries, plus the ejecta of the Little Homunculus. Moreover, the spatially resolved Very Large Telescope/UltraViolet Echelle Spectrograph (VLT/UVES) stellar spectrum (one arcsecond) and spatially sampled spectra across the foreground lobe of the Homunculus provide us vantage points from different angles relative to line of sight. Examples of wind line profiles of Fe II, and the.highly excited [Fe III], [Ne III], [Ar III] and [S III)], plus other lines will be presented.

Structural and optical study of tellurite-barium glasses

NASA Astrophysics Data System (ADS)

Grelowska, I.; Reben, M.; Burtan, B.; Sitarz, M.; Cisowski, J.; Yousef, El Sayed; Knapik, A.; Dudek, M.

2016-12-01

The goal of this work was to determine the effect of barium oxide on the structural, thermal and optical properties of the TeO2-BaO-Na2O (TBN) and TeO2-BaO-WO3 (TBW) glass systems. Raman spectra allow relating the glass structure and vibration properties (i.e. vibrational frequencies and Raman intensities) with the glass composition. Raman spectra show the presence of TeO4 and TeO3+1/TeO3 units that conform with the glass matrix. Differential thermal analysis DTA, XRD measurements have been considered in term of BaO addition. The spectral dependence of ellipsometric angles of the tellurite-barium glass has been studied. The optical measurements were conducted on Woollam M2000 spectroscopic ellipsometer in spectral range of 190-1700 nm. The reflectance and transmittance measurements have been done on spectrophotometer Perkin Elmer, Lambda 900 in the range of 200-2500 nm (UV-VIS-NIR). From the transmittance spectrum, the energy gap was determined.

Ab initio and density functional force field studies on the IR spectra and structure of diazonium dicyanomethylide (diazodicyanomethane)

NASA Astrophysics Data System (ADS)

Georgieva, Miglena K.

2004-03-01

The structure of diazonium dicyanomethylide (diazodicyanomethane) +N 2-C(CN) 2-↔N 2C(CN) 2 has been studied on the basis of ab initio HF, MP2 and DFT BLYP force field calculations, as well as of literature IR spectra and X-ray diffraction structural data. The results have been compared with those obtained for a series of chemical relatives of the title compound, i.e. molecules, push-pull molecules, anions and zwitterions, containing α-dicyano or diazo fragments, and especially substituted ammonium dicyanomethylides and diazomethane +N 2-CH 2-↔N 2CH 2. It has been found on the basis of spectral, bond length, bond order and electric charge analyses that the diazonium (or carbanionic, left) canonical form is much more important for the title zwitterion, than the corresponding one for diazomethane. So, the title compound can be named (and considered as) both diazonium dicyanomethylide and dicyanodiazomethane.

Finite temperature effects on the X-ray absorption spectra of energy related materials

NASA Astrophysics Data System (ADS)

Pascal, Tod; Prendergast, David

2014-03-01

We elucidate the role of room-temperature-induced instantaneous structural distortions in the Li K-edge X-ray absorption spectra (XAS) of crystalline LiF, Li2SO4, Li2O, Li3N and Li2CO3 using high resolution X-ray Raman spectroscopy (XRS) measurements and first-principles density functional theory calculations within the eXcited electron and Core Hole (XCH) approach. Based on thermodynamic sampling via ab-initio molecular dynamics (MD) simulations, we find calculated XAS in much better agreement with experiment than those computed using the rigid crystal structure alone. We show that local instantaneous distortion of the atomic lattice perturbs the symmetry of the Li 1 s core-excited-state electronic structure, broadening spectral line-shapes and, in some cases, producing additional spectral features. This work was conducted within the Batteries for Advanced Transportation Technologies (BATT) Program, supported by the U.S. Department of Energy Vehicle Technologies Program under Contract No. DE-AC02-05CH11231.

Reflectance spectra characteristics from an SPR grating fabricated by nano-imprint lithography technique for biochemical nanosensor applications

NASA Astrophysics Data System (ADS)

Setiya Pradana, Jalu; Hidayat, Rahmat

2018-04-01

In this paper, we report our research work on developing a Surface Plasmon Resonance (SPR) element with sub-micron (hundreds of nanometers) periodicity grating structure. This grating structure was fabricated by using a simple nano-imprint lithography technique from an organically siloxane polymers, which was then covered by nanometer thin gold layer. The formed grating structure was a very well defined square-shaped periodic structure. The measured reflectance spectra indicate the SPR wave excitation on this grating structure. For comparison, the simulations of reflectance spectra have been also carried out by using Rigorous Coupled-Wave Analysis (RCWA) method. The experimental results are in very good agreement with the simulation results.

[Infrared spectroscopic analysis of Guilin watermelon frost products].

PubMed

Huang, Dong-lan; Chen, Xiao-kang; Xu, Yong-qun; Sun, Su-qin; Zhou, Qun; Lu, Wen-guan

2012-08-01

The objective of the present study is to analyze different products of Guilin watermelon frost by Fourier transform infrared spectroscopy (FTIR), second derivative infrared spectroscopy and two-dimensional correlation spectroscopy (2D-IR) under thermal perturbation. The structural information of the samples indicates that samples from the same factory but of different brands had some dissimilarities in the IR spectra, and the type and content of accessories of them were different compared with conventional IR spectra of samples, peaks at 638 and 616 cm(-1) all arise from anhydrous sodium sulfate in watermelon frost spray and watermelon frost capsule; the characteristic absorption peaks of the sucrose, dextrin or other accessories can be seen clearly in the spectra of watermelon frost throat-clearing buccal tablets, watermelon frost throat tablets and watermelon frost lozenge. And the IR spectra of watermelon frost lozenge is very similar to the IR spectra of sucrose, so it can be easily proved that the content of sucrose in watermelon frost lozenge is high. In the 2D-IR correlation spectra, the samples presented the differences in the position, number and relative intensity of autopeaks and correlation peak clusters. Consequently, the macroscopical fingerprint characters of FTIR, second derivative infrared spectra and 2D-IR spectra can not only provide the information about main chemical constituents in medical materials, but also analyze and identify the type and content of accessories in Guilin watermelon frost. In conclusion, the multi-steps IR macro-fingerprint method is rapid, effective, visual and accurate for pharmaceutical research.

Investigation of biochemical property changes in activation-induced CD 8 + T cell apoptosis using Raman spectroscopy

NASA Astrophysics Data System (ADS)

Lee, Young Ju; Ahn, Hyung Joon; Lee, Gi-Ja; Jung, Gyeong Bok; Lee, Gihyun; Kim, Dohyun; Shin, Jae-Ho; Jin, Kyung-Hyun; Park, Hun-Kuk

2015-07-01

The study was to investigate the changes in biochemical properties of activated mature CD8+ T cells related to apoptosis at a molecular level. We confirmed the activation and apoptosis of CD8+ T cells by fluorescence-activated cell sorting and atomic force microscopy and then performed Raman spectral measurements on activated mature CD8+ T cells and cellular deoxyribose nucleic acid (DNA). In the activated mature CD8+ T cells, there were increases in protein spectra at 1002 and 1234 cm-1. In particular, to assess the apoptosis-related DNA spectral signatures, we investigated the spectra of the cellular DNA isolated from resting and activated mature CD8+ T cells. Raman spectra at 765 to 786 cm-1 and 1053 to 1087 cm-1 were decreased in activated mature DNA. In addition, we analyzed Raman spectrum using the multivariate statistical method including principal component analysis. Raman spectra of activated mature DNA are especially well-discriminated from those of resting DNA. Our findings regarding the biochemical and structural changes associated with apoptosis in activated mature T cells and cellular DNA according to Raman spectroscopy provide important insights into allospecific immune responses generated after organ transplantation, and may be useful for therapeutic manipulation of the immune response.

Weathering and precipitation after meteorite impact of Ni, Cr, Fe, Ca and Mn in K-T boundary clays from Stevns Klint

NASA Astrophysics Data System (ADS)

Miyano, Yumiko; Yoshiasa, Akira; Tobase, Tsubasa; Isobe, Hiroshi; Hongu, Hidetomo; Okube, Maki; Nakatsuka, Akihiko; Sugiyama, Kazumasa

2016-05-01

Ni, Cr, Fe, Ca and Mn K-edge XANES and EXAFS spectra were measured on K-T boundary clays from Stevns Klint in Denmark. According to XANES spectra and EXAFS analyses, the local structures of Ni, Cr and Fe in K-T boundary clays is similar to Ni(OH)2, Cr2O3 and FeOOH, respectively. It is assumed that the Ni, Cr and Fe elements in impact related glasses is changing into stable hydrate and oxide by the weathering and diagenesis at the surface of the Earth. Ca in K-T boundary clays maintains the diopside-like structure. Local structure of Ca in K-T clays seems to keep information on the condition at meteorite impact. Mn has a local structure like MnCO3 with divalent state. It is assumed that the origin on low abundant of Mn in the Fe-group element in K-T clays was the consumption by life activity and the diffusion to other parts.

Attached flow structure and streamwise energy spectra in a turbulent boundary layer

NASA Astrophysics Data System (ADS)

Srinath, S.; Vassilicos, J. C.; Cuvier, C.; Laval, J.-P.; Stanislas, M.; Foucaut, J.-M.

2018-05-01

On the basis of (i) particle image velocimetry data of a turbulent boundary layer with large field of view and good spatial resolution and (ii) a mathematical relation between the energy spectrum and specifically modeled flow structures, we show that the scalings of the streamwise energy spectrum E11(kx) in a wave-number range directly affected by the wall are determined by wall-attached eddies but are not given by the Townsend-Perry attached eddy model's prediction of these spectra, at least at the Reynolds numbers Reτ considered here which are between 103 and 104. Instead, we find E11(kx) ˜kx-1 -p where p varies smoothly with distance to the wall from negative values in the buffer layer to positive values in the inertial layer. The exponent p characterizes the turbulence levels inside wall-attached streaky structures conditional on the length of these structures. A particular consequence is that the skin friction velocity is not sufficient to scale E11(kx) for wave numbers directly affected by the wall.

Fine Structure in the Secondary Electron Emission Peak for Diamond Crystal with (100) Negative Electron Affinity Surface

NASA Technical Reports Server (NTRS)

Asnin, V. M.; Krainsky, I. L.

1998-01-01

A fine structure was discovered in the low-energy peak of the secondary electron emission spectra of the diamond surface with negative electron affinity. We studied this structure for the (100) surface of the natural type-IIb diamond crystal. We have found that the low-energy peak consists of a total of four maxima. The relative energy positions of three of them could be related to the electron energy minima near the bottom of the conduction band. The fourth peak, having the lowest energy, was attributed to the breakup of the bulk exciton at the surface during the process of secondary electron emission.

Phosphorescence/microwave double-resonance spectra of tryptophan perturbed by methylmercury(II).

PubMed Central

Davis, J M; Maki, A H

1982-01-01

Amplitude-modulated phosphorescence/microwave double-resonance (AM-PMDR) spectra are reported for complexes of methylmercury(II) cation, designated CH3Hg(II), with tryptophan and glyceraldehyde-3-phosphate dehydrogenase (GPDHase; from rabbit muscle). Wavelength shifts are observed in the AM-PMDR spectra of CH3Hg(II)-tryptophan, which are obtained by microwave pumping in distinct zero-field D + E magnetic resonance transitions, demonstrating that AM-PMDR can be used to display selectively the phosphorescence spectra of structurally distinct complexes with different zero-field splittings. The AM-PMDR spectra accurately represent the phosphorescence of CH3Hg(II)-tryptophan. Binding of CH3Hg(II) to a cysteine site of GDPHase perturbs the luminescence of one of the two optically resolved tryptophan. The AM-PMDR spectrum of the perturbed tryptophan is obtained by microwave pumping of the D + E magnetic resonance signal, which can be observed optically only in the presence of a heavy atom perturbation. The resulting spectrum is broadened and shifted to the blue relative to the corresponding tryptophan phosphorescence spectrum of the uncomplexed enzyme. Comparison of the AM-PMDR spectra of CH3Hg(II)-tryptophan and CH3Hg(II)-GPDHase suggests that there are differences in the mechanisms of heavy atom perturbation in these complexes. PMID:6956860

Spectral Analysis of Vector Magnetic Field Profiles

NASA Technical Reports Server (NTRS)

Parker, Robert L.; OBrien, Michael S.

1997-01-01

We investigate the power spectra and cross spectra derived from the three components of the vector magnetic field measured on a straight horizontal path above a statistically stationary source. All of these spectra, which can be estimated from the recorded time series, are related to a single two-dimensional power spectral density via integrals that run in the across-track direction in the wavenumber domain. Thus the measured spectra must obey a number of strong constraints: for example, the sum of the two power spectral densities of the two horizontal field components equals the power spectral density of the vertical component at every wavenumber and the phase spectrum between the vertical and along-track components is always pi/2. These constraints provide powerful checks on the quality of the measured data; if they are violated, measurement or environmental noise should be suspected. The noise due to errors of orientation has a clear characteristic; both the power and phase spectra of the components differ from those of crustal signals, which makes orientation noise easy to detect and to quantify. The spectra of the crustal signals can be inverted to obtain information about the cross-track structure of the field. We illustrate these ideas using a high-altitude Project Magnet profile flown in the southeastern Pacific Ocean.

Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters using Density Functional Theory

DTIC Science & Technology

2017-05-05

dependent density functional theory (TD-DFT). The size of the clusters considered is relatively large compared to those considered in previous studies...are characterized by many different geometries, which potentially can be optimized with respect to specific materials design criteria, i.e., molecular...SixOy molecular clusters using density functional theory (DFT). The size of the clusters considered, however, is relatively large compared to those

Quantum chemistry calculation of resveratrol and related stilbenes

NASA Astrophysics Data System (ADS)

Del Nero, J.; de Melo, C. P.

2003-01-01

We report a semiempirical investigation of the first excited states and of the spectroscopic properties of resveratrol, a phytoalexin with well-known antioxidative properties, and of structurally related stilbenes. The analysis of the calculated bond length and charge rearrangements resulting from the photoexcitation and of the corresponding theoretical spectra gives us some insight of how chemical modifications of these molecules could affect the possible physiological properties of resveratrol.

Carbohydrate and lipid spectroscopic molecular structures of different alfalfa hay and their relationship with nutrient availability in ruminants

PubMed Central

Yari, Mojtaba; Valizadeh, Reza; Nnaserian, Abbas Ali; Jonker, Arjan; Yu, Peiqiang

2017-01-01

Objective This study was conducted to determine molecular structures related to carbohydrates and lipid in alfalfa hay cut at early bud, late bud and early flower and in the afternoon and next morning using Fourier transform infrared spectroscopy (FT/IR) and to determine their relationship with alfalfa hay nutrient profile and availability in ruminants. Methods Chemical composition analysis, carbohydrate fractionation, in situ ruminal degradability, and DVE/OEB model were used to measure nutrient profile and availability of alfalfa hay. Univariate analysis, hierarchical cluster analysis (CLA) and principal components analysis (PCA) were conducted to identify FT/IR spectra differences. Results The FT/IR non-structural carbohydrate (NSCHO) to total carbohydrates and NSCHO to structural carbohydrate ratios decreased (p<0.05), while lignin to NSCHO and lipid CH3 symmetric to CH2 symmetric ratios increased with advancing maturity (p<0.05). The FT/IR spectra related to structural carbohydrates, lignin and lipids were distinguished for alfalfa hay at three maturities by PCA and CLA, while FT/IR molecular structures related to carbohydrates and lipids were similar between alfalfa hay cut in the morning and afternoon when analyzed by PCA and CLA analysis. Positive correlations were found for FT/IR NSCHO to total carbohydrate and NSCHO to structural carbohydrate ratios with non-fiber carbohydrate (by wet chemistry), ruminal fast and intermediately degradable carbohydrate fractions and total ruminal degradability of carbohydrates and predicted intestinal nutrient availability in dairy cows (r≥0.60; p<0.05) whereas FT/IR lignin to NSCHO and CH3 to CH2 symmetric stretching ratio had negative correlation with predicted ruminal and intestinal nutrient availability of alfalfa hay in dairy cows (r≥−0.60; p<0.05). Conclusion FT/IR carbohydrate and lipid molecular structures in alfalfa hay changed with advancing maturity from early bud to early flower, but not during the day, and these molecular structures correlated with predicted nutrient supply of alfalfa hay in ruminants. PMID:28335093

Amide or Amine: Determining the Origin of the 3300 cm−1 NH Mode in Protein SFG Spectra Using 15N Isotope Labels

PubMed Central

Weidner, Tobias; Breen, Nicholas F.; Drobny, Gary P.; Castner, David G.

2009-01-01

Sum frequency generation (SFG) vibrational spectroscopy has been employed in biomaterials research and protein adsorption studies with growing success in recent years. A number of studies focusing on understanding SFG spectra of proteins and peptides at different interfaces have laid the foundation for future, more complex studies. In many cases a strong NH mode near 3300 cm−1 is observed in the SFG spectra, but the relationship of this mode to the peptide structure is uncertain since it has been assigned to either a backbone amide mode or a side chain related amine resonance. A thorough understanding of the SFG spectra of these first model systems is an important first step for future experiments. To clarify the origin of the NH SFG mode we studied 15N isotopically labeled 14-amino acid amphiphilic model peptides composed of lysine (K) and leucine (L) in an α-helical secondary structure (LKα14) that were adsorbed onto charged surfaces in situ at the solid-liquid interface. 15N substitution at the terminal amine group of the lysine side chains resulted in a red-shift of the NH mode of 9 cm−1 on SiO2 and 13 cm−1 on CaF2. This clearly shows the 3300 cm−1 NH feature is associated with side chain NH stretches and not with backbone amide modes. PMID:19873996

Amide or amine: determining the origin of the 3300 cm(-1) NH mode in protein SFG spectra using 15N isotope labels.

PubMed

Weidner, Tobias; Breen, Nicholas F; Drobny, Gary P; Castner, David G

2009-11-26

Sum frequency generation (SFG) vibrational spectroscopy has been employed in biomaterials research and protein adsorption studies with growing success in recent years. A number of studies focusing on understanding SFG spectra of proteins and peptides at different interfaces have laid the foundation for future, more complex studies. In many cases, a strong NH mode near 3300 cm(-1) is observed in the SFG spectra, but the relationship of this mode to the peptide structure is uncertain, since it has been assigned to either a backbone amide mode or a side chain related amine resonance. A thorough understanding of the SFG spectra of these first model systems is an important first step for future experiments. To clarify the origin of the NH SFG mode, we studied (15)N isotopically labeled 14-amino acid amphiphilic model peptides composed of lysine (K) and leucine (L) in an alpha-helical secondary structure (LKalpha14) that were adsorbed onto charged surfaces in situ at the solid-liquid interface. (15)N substitution at the terminal amine group of the lysine side chains resulted in a red-shift of the NH mode of 9 cm(-1) on SiO(2) and 13 cm(-1) on CaF(2). This clearly shows the 3300 cm(-1) NH feature is associated with side chain NH stretches and not with backbone amide modes.

A UV resonance Raman (UVRR) spectroscopic study on the extractable compounds in Scots pine (Pinus sylvestris) wood. Part II. Hydrophilic compounds.

PubMed

Nuopponen, M; Willför, S; Jääskeläinen, A-S; Vuorinen, T

2004-11-01

Hydrophilic extracts of Scots pine (Pinus sylvestris) heartwood and sapwood and a solid Scots pine knotwood sample were studied by UV resonance Raman spectroscopy (UVRRS). In addition, UVRR spectra of two hydrophilic model compounds (pinosylvin and chrysin) were analysed. UV Raman spectra were collected using 244 and 257 nm excitation wavelengths. The chemical composition of the acetone:water (95:5 v/v) extracts were also determined by gas chromatography. The aromatic and oleophilic structures of pinosylvin and chrysin showed three intense resonance enhanced bands in the spectral region of 1649-1548 cm(-1). Pinosylvin showed also a relatively intense band in the aromatic substitution region at 996 cm(-1). The spectra of the heartwood acetone:water extract showed many bands typical of pinosylvin. In addition, the extract included bands distinctive for resin and fatty acids. The sapwood acetone:water extract showed bands due to oleophilic structures at 1655-1650 cm(-1). The extract probably also contained oligomeric lignans because the UVRR spectra were in parts similar to that of guaiacyl lignin. The characteristic band of pinosylvin (996 cm(-1)) was detected in the UVRR spectrum of the resin rich knotwood. In addition, several other bands typical for wood resin were observed, which indicated that the wood resin in the knotwood was resonance enhanced even more than lignin.

A UV resonance Raman (UVRR) spectroscopic study on the extractable compounds in Scots pine ( Pinus sylvestris) wood . Part II. Hydrophilic compounds

NASA Astrophysics Data System (ADS)

Nuopponen, M.; Willför, S.; Jääskeläinen, A.-S.; Vuorinen, T.

2004-11-01

Hydrophilic extracts of Scots pine ( Pinus sylvestris) heartwood and sapwood and a solid Scots pine knotwood sample were studied by UV resonance Raman spectroscopy (UVRRS). In addition, UVRR spectra of two hydrophilic model compounds (pinosylvin and chrysin) were analysed. UV Raman spectra were collected using 244 and 257 nm excitation wavelengths. The chemical composition of the acetone:water (95:5 v/v) extracts were also determined by gas chromatography. The aromatic and oleophilic structures of pinosylvin and chrysin showed three intense resonance enhanced bands in the spectral region of 1649-1548 cm -1. Pinosylvin showed also a relatively intense band in the aromatic substitution region at 996 cm -1. The spectra of the heartwood acetone:water extract showed many bands typical of pinosylvin. In addition, the extract included bands distinctive for resin and fatty acids. The sapwood acetone:water extract showed bands due to oleophilic structures at 1655-1650 cm -1. The extract probably also contained oligomeric lignans because the UVRR spectra were in parts similar to that of guaiacyl lignin. The characteristic band of pinosylvin (996 cm -1) was detected in the UVRR spectrum of the resin rich knotwood. In addition, several other bands typical for wood resin were observed, which indicated that the wood resin in the knotwood was resonance enhanced even more than lignin.

Balancing act: Evidence for a strong subdominant d -wave pairing channel in Ba 0.6 K 0.4 Fe 2 As 2

DOE PAGES

Böhm, T.; Kemper, A. F.; Moritz, B.; ...

2014-12-18

We present detailed measurements of the temperature-dependent Raman spectra of optimally doped Ba 0.6K 0.4Fe 2As 2 and analyze the low-temperature spectra based on local-density-approximation band-structure calculations and the subsequent estimation of effective Raman vertices. Experimentally, a narrow, emergent mode appears in the B 1g (d x2-y2) Raman spectra only below T c, well into the superconducting state and at an energy below twice the energy gap on the electron Fermi-surface sheets. The Raman spectra can be reproduced quantitatively with estimates for the magnitude and momentum-space structure of an A 1g (s-wave) pairing gap on different Fermi-surface sheets, as wellmore » as the identification of the emergent sharp feature as a Bardasis-Schrieffer exciton. Formed as a Cooper-pair bound state in a subdominant d x2-y2 channel, the binding energy of the exciton relative to the gap edge shows that the coupling strength in the subdominant channel is as strong as 60% of that in the dominant s-wave channel. This result suggests that d x2-y2 may be the dominant pairing symmetry in Fe-based superconductors that lack central hole bands.« less

Photoreflectance and photoluminescence spectroscopy of the lattice-matched InGaAs/InAlAs single quantum well

NASA Astrophysics Data System (ADS)

Wang, Y. C.; Tyan, S. L.; Juang, Y. D.

2002-07-01

A lattice-matched In0.53Ga0.47As/In0.52Al0.48As single quantum well (SQW) structure grown by gas source molecular beam epitaxy has been investigated by photoreflectance (PR) and photoluminescence (PL). The PR measurements allowed the observation of interband transitions from the heavy- and light-hole valence subbands to the conduction subbands. The transition energies measured from the PR spectra agree with those calculated theoretically. Two features corresponding to the ground state transition coming from the SQW and the band gap transition generated from the buffer layer are observed in the PL spectra and are in good agreement with the PR data. The effect of the temperature on the transition energies is essentially same as that in the gap transition of the bulk structure. The values of the Varshni coefficients of InGaAs/InAlAs were obtained from the relation between the exciton transition energy and the temperature. The built-in electric field could be determined and located from a series of PR spectra by sequential etching processes. The phase spectra obtained from the PR spectra by the Kramers-Kronig transformation were analyzed in terms of the two-ray model, and calculated the etching depth in each etching, and thus leading to the etching rate. The etching rate obtained from phase shift analysis agrees with that measured by atomic force microscopy. The etching results suggest that a built-in electric field exists at the buffer/substrate interface and it also enables us to determine the etching rate.

Synergic application of spectroscopic and theoretical methods to the chlorogenic acid structure elucidation

NASA Astrophysics Data System (ADS)

Marković, Svetlana; Tošović, Jelena; Dimitrić Marković, Jasmina M.

2016-07-01

Although chlorogenic acid (5-O-caffeoylquinic acid, 5CQA) is a dietary polyphenol known for its pharmacological and nutritional properties, its structural features have not been completely elucidated. This is the first study whose aim is to contribute to clarification of the 5CQA structure by comparing the experimental and simulated IR, Raman, 1H NMR, 13C NMR, and UV spectra. For this purpose, a comprehensive conformational analysis of 5CQA was performed to reveal its most stable conformations in the gas-state and solution (DMSO and methanol). The lowest-energy conformers were used to predict the spectra at two levels of theory: B3LYP-D3/and M06-2X/6-311+G(d,p) in combination with the CPCM solvation model. Both methods provide very good agreement between all experimental and simulated spectra, thus indicating correct arrangement of the atoms in the 5CQA molecule. The quinic moiety is characterized with directed hydrogen bonds, where the carboxylic hydrogen is not oriented towards the carbonyl oxygen of the carboxylic group, but towards the oxygen of the proximate hydroxyl group. In the gas-state the lowest-energy conformers are characterized with the O4sbnd H4 ⋯ O9‧ hydrogen bond, whereas in the solvated state the structures with the O4sbnd H4 ⋯ O10‧ hydrogen bond prevail. Knowing the fine structural details, i.e. the proper conformation of 5CQA, provides a solid base for all further investigations related to this compound.

Probing the Structural, Electronic, and Magnetic Properties of Ag n V (n = 1-12) Clusters.

PubMed

Xiong, Ran; Die, Dong; Xiao, Lu; Xu, Yong-Gen; Shen, Xu-Ying

2017-12-16

The structural, electronic, and magnetic properties of Ag n V (n = 1-12) clusters have been studied using density functional theory and CALYPSO structure searching method. Geometry optimizations manifest that a vanadium atom in low-energy Ag n V clusters favors the most highly coordinated location. The substitution of one V atom for an Ag atom in Ag n + 1 (n ≥ 5) cluster modifies the lowest energy structure of the host cluster. The infrared spectra, Raman spectra, and photoelectron spectra of Ag n V (n = 1-12) clusters are simulated and can be used to determine the most stable structure in the future. The relative stability, dissociation channel, and chemical activity of the ground states are analyzed through atomic averaged binding energy, dissociation energy, and energy gap. It is found that V atom can improve the stability of the host cluster, Ag 2 excepted. The most possible dissociation channels are Ag n V = Ag + Ag n - 1 V for n = 1 and 4-12 and Ag n V = Ag 2  + Ag n - 2 V for n = 2 and 3. The energy gap of Ag n V cluster with odd n is much smaller than that of Ag n + 1 cluster. Analyses of magnetic property indicate that the total magnetic moment of Ag n V cluster mostly comes from V atom and varies from 1 to 5 μ B . The charge transfer between V and Ag atoms should be responsible for the change of magnetic moment.

XANES study on Fe, U and Th in hydrous melts at high temperature and pressure

NASA Astrophysics Data System (ADS)

Wilke, M.; Schmidt, C.; Farges, F.; Borchert, M.; Simionovici, A.; Hahn, M.

2005-12-01

Insight to the structural units of melts is an important key to model properties of magmas. The effect of water and pressure on the local structure around minor to trace elements in silicate melts was investigated at in-situ conditions. The study was performed using XANES spectroscopy and a diamond anvil-cell. This was done to characterize spurious effects observed on glasses that are potentially invoked by quenching [1] and to understand better the processes occurring during the quench. We present results of in-situ XANES measurements on iron, uranium and thorium in hydrous silicate melt up to 1 GPa and 700° C. In-situ XANES spectra were recorded at the ESRF (Grenoble, France), beamline ID 22, using a hydrothermal diamond anvil cell with a design optimized for such measurements [2], i.e. recesses on the front and the back-side of one of the diamond anvils that provide the possibility to collect spectra at relatively low energies (down to 7 keV) and relatively low concentrations (0.1-1 wt%). In-situ Fe K-edge XANES spectra of Fe(II) in hydrous haplogranitic melt at 700° C and 500 MPa suggests that the local structure around Fe in hydrous glass observed previously is probably due to ordering during the quench. Additionally, the XANES is very similar to in-situ spectra taken on Fe(II) in anhydrous haplogranitic melt at 1150° C and ambient pressure. This indicates that the combined effect of water and pressure (0-500 MPa range) does not influence drastically the local structure of Fe in this type of melt composition. In-situ LIII-edge XANES of U in hydrous haplogranitic melt (1 wt% U) at 700° C and 620 MPa show that, upon reduction, U precipitated as uraninite. This suggests a low amount of NBO's (to which tetravalent actinides preferentially bond [3]) in this water-saturated melt. In contrast, U-bearing (1000 ppm) hydrous sodium-tri-silicate melt shows the presence of U(IV) dissolved in the melt as 6-7 coordinated species, as in dry glasses [3]. Similar structural information is obtained for Th(IV). Spectra taken above and below the complete miscibility of the silicate and aqueous phase (ca. 460° C) also reveal no difference in speciation. The aqueous fluid measured at ambient conditions after the run did not show any significant amount of dissolved tetravalent actinides [1] Wilke et al. (2002) Chem. Geol., 189, 55-67. [2] Schmidt C., Rickers K. (2003) Am. Mineral., 88, 288-292. [3] Farges F. (1991) Geochim. Cosmochim. Acta, 55, 3303-3319.

Atomic site preferences and structural evolution in vanadium-doped ZrSiO4 from multinuclear solid-state NMR

NASA Astrophysics Data System (ADS)

Dajda, N.; Dixon, J. M.; Smith, M. E.; Carthey, N.; Bishop, P. T.

2003-01-01

Solid state NMR spectra of 29Si are reported from pure and vanadium-doped zircon (V-ZrSiO4) samples. The vanadium concentration is varied up to ˜1-mol % V4+ by using both conventional-firing and sol-gel routes, and 51V NMR data are also recorded. 17O NMR of 17O isotopically enriched samples shows that the initial gel is completely amorphous with the whole range of possible M-O-M' linkages detected, and that this structure evolves into a fully ordered ZrSiO4 structure with calcination. Static 91Zr NMR data is reported from a pure zircon sample. The NMR data are used to quantify the amount of vanadium entering the zircon structure, and to elucidate its site preference within the lattice. Two contact shifted peaks with very different T1 relaxation from the main zircon peak but attributable to the zircon lattice are observed in the 29Si NMR spectra for all samples. These spectra are consistent with vanadium substitution on both the tetrahedral and dodecahedral sites, with a slight preference for the silicon site. The data show that the relative occupation of these two sites is almost independent of the preparation method and vanadium concentration. At a higher vanadium concentration a third additional peak is observed which may indicate another substitution site. Variable temperature NMR and susceptibility measurements indicate the hyperfine nature of the interactions influencing silicon from V4+ ions in the different sites.

Rheo-optical two-dimensional (2D) near-infrared (NIR) correlation spectroscopy for probing strain-induced molecular chain deformation of annealed and quenched Nylon 6 films

NASA Astrophysics Data System (ADS)

Shinzawa, Hideyuki; Mizukado, Junji

2018-04-01

A rheo-optical characterization technique based on the combination of a near-infrared (NIR) spectrometer and a tensile testing machine is presented here. In the rheo-optical NIR spectroscopy, tensile deformations are applied to polymers to induce displacement of ordered or disordered molecular chains. The molecular-level variation of the sample occurring on short time scales is readily captured as a form of strain-dependent NIR spectra by taking an advantage of an acousto-optic tunable filter (AOTF) equipped with the NIR spectrometer. In addition, the utilization of NIR with much less intense absorption makes it possible to measure transmittance spectra of relatively thick samples which are often required for conventional tensile testing. An illustrative example of the rheo-optical technique is given with annealed and quenched Nylon 6 samples to show how this technique can be utilized to derive more penetrating insight even from the seemingly simple polymers. The analysis of the sets of strain-dependent NIR spectra suggests the presence of polymer structures undergoing different variations during the tensile elongation. For instance, the tensile deformation of the semi-crystalline Nylon 6 involves a separate step of elongation of the rubbery amorphous chains and subsequent disintegration of the rigid crystalline structure. Excess amount of crystalline phase in Nylon 6, however, results in the retardation of the elastic deformation mainly achieved by the amorphous structure, which eventually leads to the simultaneous orientation of both amorphous and crystalline structures.

Identification and classification of cathinone unknowns by statistical analysis processing of direct analysis in real time-high resolution mass spectrometry-derived "neutral loss" spectra.

PubMed

Fowble, Kristen L; Shepard, Jason R E; Musah, Rabi A

2018-03-01

An approach to the rapid determination of the structures of novel synthetic cathinone designer drugs, also known as bath salts, is reported. While cathinones fragment so extensively by electron impact mass spectrometry that their mass spectra often cannot be used to identify the structure, collision-induced dissociation (CID) direct analysis in real time-high resolution mass spectrometry (DART-HRMS) experiments furnished spectra that provided diagnostic fragmentation patterns for the analyzed cathinones. From this data, neutral loss spectra, which reflect the presence of specific chemical moieties, could be acquired. These spectra showed striking similarities between cathinones sharing structural features such as pyrrolidine rings and methylenedioxy moieties. Principle component analysis (PCA) of the neutral loss spectra of nine synthetic cathinones of various types including ethcathinones, those containing a methylenedioxy moiety appended to the benzene ring, and pyrrolidine-containing structures, illustrated that cathinones falling within the same class clustered together and could be distinguished from those of other classes. Furthermore, hierarchical clustering analysis of the neutral loss data of a model set derived from 44 synthetic cathinones, furnished a dendrogram in which structurally similar cathinones clustered together. The ability of this model system to facilitate structure determination was tested using 4-fluoroethcathinone, 3,4-methylenedioxy-α-pyrrolidinohexanophenone (MDPHP), and ethylone, which fall into the ethcathinone, pyrrolidine-containing, and methylenedioxy-containing subclasses respectively. The results showed that their neutral loss spectra correctly fell within the ethcathinone, pyrrolidine-containing and methylenedioxy-containing cathinone clades of the dendrogram, and that the neutral loss information could be used to infer the structures of these compounds. The analysis and data processing steps are rapid and samples can be analyzed in their native form without any sample processing steps. The robustness of the dendrogram dataset can be readily increased by continued addition of newly discovered structures. The approach can be broadly applied to structure determination of unknowns, and would be particularly useful for analyses where sample amounts are limited. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of Imidazole Deprotonation on Vibrational Spectra of High-Spin Iron(II) Porphyrinates

PubMed Central

Hu, Chuanjiang; Peng, Qian; Silvernail, Nathan J.; Barabanschikov, Alexander; Zhao, Jiyong; Alp, E. Ercan; Sturhahn, Wolfgang; Sage, J. Timothy; Scheidt, W. Robert

2013-01-01

The effects of the deprotonation of coordinated imidazole on the dynamics of five-coordinate high-spin iron(II) porphyrinates have been investigated using nuclear resonance vibrational spectroscopy. Two complexes have been studied in detail with both powder and oriented single-crystal measurements. Changes in the vibrational spectra are clearly related to structural differences in the molecular structures that occur when imidazole is deprotonated. Most modes involving the simultaneous motion of iron and imidazolate are unresolved but the one mode that is resolved is found at higher frequency in the imidazolates. These out-of-plane results are in accord with earlier resonance Raman studies of heme proteins. We also show the imidazole vs. imidazolate differences in the in-plane vibrations that are not accessible to resonance Raman studies. The in-plane vibrations are at lower frequency in the imidazolate derivatives; the doming mode shifts are inconclusive. The stiffness, an experimentally determined force constant that averages the vibrational details to quantify the nearest-neighbor interactions, confirms that deprotonation inverts the relative strengths of axial and equatorial coordination. PMID:23470205

Optical, electrical and ferromagnetic studies of ZnO:Fe diluted magnetic semiconductor nanoparticles for spintronic applications

NASA Astrophysics Data System (ADS)

Elilarassi, R.; Chandrasekaran, G.

2017-11-01

In the present investigation, diluted magnetic semiconductor (Zn1-xFexO) nanoparticles with different doping concentrations (x = 0, 0.02, 0.04, 0.06, and 0.08) were successfully synthesized by sol-gel auto-combustion method. The crystal structure, morphology, optical, electrical and magnetic properties of the prepared samples were characterized by X-ray diffraction (XRD), scanning electron microscope (SEM), energy dispersive analysis using x-rays (EDAX), ultraviolet-visible spectrophotometer, fluorescence spectroscope (FS), vibrating sample magnetometer (VSM) and broad band dielectric spectrometer (BDS). XRD results reveal that all the samples possess hexagonal wurtzite crystal structure with good crystalline quality. The absence of impurity phases divulge that Fe ions are well incorporated into the ZnO crystal lattice. The substitutional incorporation of Fe3+ at Zn sites is reflected in optical absorption spectra of the samples. Flouorescence spectra of the samples show a strong near-band edge related UV emission as well as defect related visible emissions. The semiconducting behavior of the samples has been confirmed through electrical conductivity measurements. Magnetic measurements indicated that all the samples possess ferromagnetism at room temperature.

Experimental and theoretical study of the structural environment of magnesium in minerals and silicate glasses using X-ray absorption near-edge structure

NASA Astrophysics Data System (ADS)

Trcera, Nicolas; Cabaret, Delphine; Rossano, Stéphanie; Farges, François; Flank, Anne-Marie; Lagarde, Pierre

2009-05-01

X-ray absorption spectroscopy at the Mg K-edge is used to obtain information on magnesium environment in minerals, silicate and alumino-silicate glasses. First-principles XANES calculations are performed for minerals using a plane-wave density functional formalism with core-hole effects treated in a supercell approach. The good agreement obtained between experimental and theoretical spectra provides useful information to interpret the spectral features. With the help of calculation, the position of the first peak of XANES spectra is related to both coordination and polyhedron distortion changes. In alumino-silicate glasses, magnesium is found to be mainly 5-fold coordinated to oxygen whatever the aluminum saturation index value. In silicate glasses, magnesium coordination increases from 4 in Cs-, Rb- and K-bearing glasses to 5 in Na- and Li-bearing glasses but remains equal as the polymerization degree of the glass varies. The variation of the C feature (position and intensity) is strongly related to the alkali type providing information on the medium range order.

Effects of a high-pressure treatment on the wheat alpha-amylase inhibitor and its relationship to elimination of allergenicity

NASA Astrophysics Data System (ADS)

Yamamoto, S.; Takanohashi, K.; Hara, T.; Odani, S.; Suzuki, A.; Nishiumi, T.

2010-03-01

In this study, the effects of high-pressure treatment on structure and allergeincity of alpha amylase inhibitor (a-AI) were investigated. The pressure-induced structural changes of α-AI were estimated by fluorescence spectra and by fourth derivative UV-spectroscopy for probed tyrosine residues and by circular dichroism (CD) spectroscopy. The changes in the tertiary structure detected by fluorescence spectra and by fourth derivative UV-spectroscopy under high pressure were indicated at over 300 MPa. Measurements of CD spectroscopy suggested that the effects of a high-pressure treatment on changes in the secondary structure of α-AI were little. From our results, pressure-induced changes of the α-AI structure were not apparent. On the other hands, the IgE-specific binding activities of pressurized α-AI to sera from allergic patients against wheat, which is estimated by observations of dot-blotting, were decreased by high-pressure treatment. It is known that the pressure-induced elimination of allergenicity is related to the tertiary structural changes of allergen molecules. This study are suspected that the epitopes of α-AI do not contain tyrosine residues, and thus the decrease of IgE-specific binding activities is probably caused by the tertiary structural changes of these parts of α-AI.

A Novel Acoustic Sensor Approach to Classify Seeds Based on Sound Absorption Spectra

PubMed Central

Gasso-Tortajada, Vicent; Ward, Alastair J.; Mansur, Hasib; Brøchner, Torben; Sørensen, Claus G.; Green, Ole

2010-01-01

A non-destructive and novel in situ acoustic sensor approach based on the sound absorption spectra was developed for identifying and classifying different seed types. The absorption coefficient spectra were determined by using the impedance tube measurement method. Subsequently, a multivariate statistical analysis, i.e., principal component analysis (PCA), was performed as a way to generate a classification of the seeds based on the soft independent modelling of class analogy (SIMCA) method. The results show that the sound absorption coefficient spectra of different seed types present characteristic patterns which are highly dependent on seed size and shape. In general, seed particle size and sphericity were inversely related with the absorption coefficient. PCA presented reliable grouping capabilities within the diverse seed types, since the 95% of the total spectral variance was described by the first two principal components. Furthermore, the SIMCA classification model based on the absorption spectra achieved optimal results as 100% of the evaluation samples were correctly classified. This study contains the initial structuring of an innovative method that will present new possibilities in agriculture and industry for classifying and determining physical properties of seeds and other materials. PMID:22163455

Fragmentation of negative ions from N-linked carbohydrates, part 4. Fragmentation of complex glycans lacking substitution on the 6-antenna.

PubMed

Harvey, David J; Jaeken, Jaak; Butler, Mike; Armitage, Alison J; Rudd, Pauline M; Dwek, Raymond A

2010-05-01

Negative ion CID spectra of N-linked glycans released from glycoproteins contain many ions that are diagnostic for specific structural features such as the detailed arrangement of antennae and the location of fucose residues. Identification of such ions requires reference glycans that are often difficult to acquire in a pure state. The recent acquisition of a sample of N-glycans from a patient lacking the enzyme N-acetylglucosaminyltransferase-2 provided an opportunity to investigate fragmentation of glycans lacking a 6-antenna. These glycans contained one or two galactose-N-acetylglucosamine-chains attached to the 3-linked mannose residue of the trimannosyl-chitobiose core with and without fucose substitution. The spectra from the patient sample clearly defined the antenna distribution and showed striking differences from the spectra of isomeric compounds obtained from normal subjects. Furthermore, they provided additional information on previously identified antenna-specific fragment ions and indicated the presence of additional ions that were diagnostic of fucose substitution. Glycans obtained from such enzyme-deficient patients can, thus, be a valuable way of obtaining spectra of specific isomers in a relatively pure state for interpretation of mass spectra. 2010 John Wiley & Sons, Ltd.

Optical Studies of CaS:Eu, Sm Infrared Stimulable Phosphors

NASA Astrophysics Data System (ADS)

Tamura, Yasuaki; Shibukawa, Atsushi

1993-07-01

The photoluminescence (PL) and infrared stimulated luminescence (ISL) spectra of CaS:Eu,Sm infrared stimulable phosphors (ISPs) are studied. In addition, the concentration dependence of ISL intensity is examined. Sm3+- and Eu2+-related structures are found in both the PL excitation and emission spectra. Two types of Sm3+ are found, one of which exhibits strong emission at around 650 nm and the other, weak emission compared to the other emissions at around 565 nm and 605 nm. These are assigned to an asymmetric and a symmetric site, respectively. ISL excitation spectra coincide with the Eu2+ 4f7 to 4f65d1 and 4f66s1 transitions and range from 220 to 650 nm. ISL emission spectra coincide with the Eu2+ 4f65d1 to 4f7 transition and range from 550 to 750 nm. ISL stimulation spectra range from 0.8 μm to 1.7 μm and are thought to indicate the Sm2+ ion transition from 4f6 to 4f55d1. The maximum ISL intensity is obtained from a sample with Eu and Sm concentrations of 500 and 130 ppm, respectively.

FT-IR, FT-Raman spectra and DFT calculations of melaminium perchlorate monohydrate.

PubMed

Kanagathara, N; Marchewka, M K; Drozd, M; Renganathan, N G; Gunasekaran, S; Anbalagan, G

2013-08-01

Melaminium perchlorate monohydrate (MPM), an organic material has been synthesized by slow solvent evaporation method at room temperature. Powder X-ray diffraction analysis confirms that MPM crystal belongs to triclinic system with space group P-1. FTIR and FT Raman spectra are recorded at room temperature. Functional group assignment has been made for the melaminium cations and perchlorate anions. Vibrational spectra have also been discussed on the basis of quantum chemical density functional theory (DFT) calculations using Firefly (PC GAMESS) version 7.1 G. Vibrational frequencies are calculated and scaled values are compared with experimental values. The assignment of the bands has been made on the basis of the calculated PED. The Mulliken charges, HOMO-LUMO orbital energies are analyzed directly from Firefly program log files and graphically illustrated. HOMO-LUMO energy gap and other related molecular properties are also calculated. The theoretically constructed FT-IR and FT-Raman spectra of MPM coincide with the experimental one. The chemical structure of the compound has been established by (1)H and (13)C NMR spectra. No detectable signal was observed during powder test for second harmonic generation. Copyright © 2013 Elsevier B.V. All rights reserved.

Real-Time Continuous Response Spectra Exceedance Calculation Displayed in a Web-Browser Enables Rapid and Robust Damage Evaluation by First Responders

NASA Astrophysics Data System (ADS)

Franke, M.; Skolnik, D. A.; Harvey, D.; Lindquist, K.

2014-12-01

A novel and robust approach is presented that provides near real-time earthquake alarms for critical structures at distributed locations and large facilities using real-time estimation of response spectra obtained from near free-field motions. Influential studies dating back to the 1980s identified spectral response acceleration as a key ground motion characteristic that correlates well with observed damage in structures. Thus, monitoring and reporting on exceedance of spectra-based thresholds are useful tools for assessing the potential for damage to facilities or multi-structure campuses based on input ground motions only. With as little as one strong-motion station per site, this scalable approach can provide rapid alarms on the damage status of remote towns, critical infrastructure (e.g., hospitals, schools) and points of interests (e.g., bridges) for a very large number of locations enabling better rapid decision making during critical and difficult immediate post-earthquake response actions. Details on the novel approach are presented along with an example implementation for a large energy company. Real-time calculation of PSA exceedance and alarm dissemination are enabled with Bighorn, an extension module based on the Antelope software package that combines real-time spectral monitoring and alarm capabilities with a robust built-in web display server. Antelope is an environmental data collection software package from Boulder Real Time Technologies (BRTT) typically used for very large seismic networks and real-time seismic data analyses. The primary processing engine produces continuous time-dependent response spectra for incoming acceleration streams. It utilizes expanded floating-point data representations within object ring-buffer packets and waveform files in a relational database. This leads to a very fast method for computing response spectra for a large number of channels. A Python script evaluates these response spectra for exceedance of one or more specified spectral limits, reporting any such exceedances via alarm packets that are put in the object ring-buffer for use by any alarm processes that need them. The web-display subsystem allows alert dissemination, interactive exploration, and alarm cancellation via the WWW.

Real Time Spectroscopic Ellipsometry Analysis of First Stage CuIn1−xGaxSe2 Growth: Indium-Gallium Selenide Co-Evaporation

PubMed Central

Pradhan, Puja; Aryal, Puruswottam; Attygalle, Dinesh; Ibdah, Abdel-Rahman; Koirala, Prakash; Li, Jian; Bhandari, Khagendra P.; Liyanage, Geethika K.; Ellingson, Randy J.; Heben, Michael J.; Marsillac, Sylvain; Collins, Robert W.; Podraza, Nikolas J.

2018-01-01

Real time spectroscopic ellipsometry (RTSE) has been applied for in-situ monitoring of the first stage of copper indium-gallium diselenide (CIGS) thin film deposition by the three-stage co-evaporation process used for fabrication of high efficiency thin film photovoltaic (PV) devices. The first stage entails the growth of indium-gallium selenide (In1−xGax)2Se3 (IGS) on a substrate of Mo-coated soda lime glass maintained at a temperature of 400 °C. This is a critical stage of CIGS deposition because a large fraction of the final film thickness is deposited, and as a result precise compositional control is desired in order to achieve the optimum performance of the resulting CIGS solar cell. RTSE is sensitive to monolayer level film growth processes and can provide accurate measurements of bulk and surface roughness layer thicknesses. These in turn enable accurate measurements of the bulk layer optical response in the form of the complex dielectric function ε = ε1 − iε2, spectra. Here, RTSE has been used to obtain the (ε1, ε2) spectra at the measurement temperature of 400 °C for IGS thin films of different Ga contents (x) deduced from different ranges of accumulated bulk layer thickness during the deposition process. Applying an analytical expression in common for each of the (ε1, ε2) spectra of these IGS films, oscillator parameters have been obtained in the best fits and these parameters in turn have been fitted with polynomials in x. From the resulting database of polynomial coefficients, the (ε1, ε2) spectra can be generated for any composition of IGS from the single parameter, x. The results have served as an RTSE fingerprint for IGS composition and have provided further structural information beyond simply thicknesses, for example information related to film density and grain size. The deduced IGS structural evolution and the (ε1, ε2) spectra have been interpreted as well in relation to observations from scanning electron microscopy, X-ray diffractometry and energy-dispersive X-ray spectroscopy profiling analyses. Overall the structural, optical and compositional analysis possible by RTSE has assisted in understanding the growth and properties of three stage CIGS absorbers for solar cells and shows future promise for enhancing cell performance through monitoring and control. PMID:29337931

Real Time Spectroscopic Ellipsometry Analysis of First Stage CuIn1-xGaxSe₂ Growth: Indium-Gallium Selenide Co-Evaporation.

PubMed

Pradhan, Puja; Aryal, Puruswottam; Attygalle, Dinesh; Ibdah, Abdel-Rahman; Koirala, Prakash; Li, Jian; Bhandari, Khagendra P; Liyanage, Geethika K; Ellingson, Randy J; Heben, Michael J; Marsillac, Sylvain; Collins, Robert W; Podraza, Nikolas J

2018-01-16

Real time spectroscopic ellipsometry (RTSE) has been applied for in-situ monitoring of the first stage of copper indium-gallium diselenide (CIGS) thin film deposition by the three-stage co-evaporation process used for fabrication of high efficiency thin film photovoltaic (PV) devices. The first stage entails the growth of indium-gallium selenide (In 1- x Ga x )₂Se₃ (IGS) on a substrate of Mo-coated soda lime glass maintained at a temperature of 400 °C. This is a critical stage of CIGS deposition because a large fraction of the final film thickness is deposited, and as a result precise compositional control is desired in order to achieve the optimum performance of the resulting CIGS solar cell. RTSE is sensitive to monolayer level film growth processes and can provide accurate measurements of bulk and surface roughness layer thicknesses. These in turn enable accurate measurements of the bulk layer optical response in the form of the complex dielectric function ε = ε₁ - iε₂, spectra. Here, RTSE has been used to obtain the (ε₁, ε₂) spectra at the measurement temperature of 400 °C for IGS thin films of different Ga contents ( x ) deduced from different ranges of accumulated bulk layer thickness during the deposition process. Applying an analytical expression in common for each of the (ε₁, ε₂) spectra of these IGS films, oscillator parameters have been obtained in the best fits and these parameters in turn have been fitted with polynomials in x . From the resulting database of polynomial coefficients, the (ε₁, ε₂) spectra can be generated for any composition of IGS from the single parameter, x . The results have served as an RTSE fingerprint for IGS composition and have provided further structural information beyond simply thicknesses, for example information related to film density and grain size. The deduced IGS structural evolution and the (ε₁, ε₂) spectra have been interpreted as well in relation to observations from scanning electron microscopy, X-ray diffractometry and energy-dispersive X-ray spectroscopy profiling analyses. Overall the structural, optical and compositional analysis possible by RTSE has assisted in understanding the growth and properties of three stage CIGS absorbers for solar cells and shows future promise for enhancing cell performance through monitoring and control.

Catalysis of GTP Hydrolysis by Small GTPases at Atomic Detail by Integration of X-ray Crystallography, Experimental, and Theoretical IR Spectroscopy*

PubMed Central

Rudack, Till; Jenrich, Sarah; Brucker, Sven; Vetter, Ingrid R.; Gerwert, Klaus; Kötting, Carsten

2015-01-01

Small GTPases regulate key processes in cells. Malfunction of their GTPase reaction by mutations is involved in severe diseases. Here, we compare the GTPase reaction of the slower hydrolyzing GTPase Ran with Ras. By combination of time-resolved FTIR difference spectroscopy and QM/MM simulations we elucidate that the Mg2+ coordination by the phosphate groups, which varies largely among the x-ray structures, is the same for Ran and Ras. A new x-ray structure of a Ran·RanBD1 complex with improved resolution confirmed this finding and revealed a general problem with the refinement of Mg2+ in GTPases. The Mg2+ coordination is not responsible for the much slower GTPase reaction of Ran. Instead, the location of the Tyr-39 side chain of Ran between the γ-phosphate and Gln-69 prevents the optimal positioning of the attacking water molecule by the Gln-69 relative to the γ-phosphate. This is confirmed in the RanY39A·RanBD1 crystal structure. The QM/MM simulations provide IR spectra of the catalytic center, which agree very nicely with the experimental ones. The combination of both methods can correlate spectra with structure at atomic detail. For example the FTIR difference spectra of RasA18T and RanT25A mutants show that spectral differences are mainly due to the hydrogen bond of Thr-25 to the α-phosphate in Ran. By integration of x-ray structure analysis, experimental, and theoretical IR spectroscopy the catalytic center of the x-ray structural models are further refined to sub-Å resolution, allowing an improved understanding of catalysis. PMID:26272610

Catalysis of GTP hydrolysis by small GTPases at atomic detail by integration of X-ray crystallography, experimental, and theoretical IR spectroscopy.

PubMed

Rudack, Till; Jenrich, Sarah; Brucker, Sven; Vetter, Ingrid R; Gerwert, Klaus; Kötting, Carsten

2015-10-02

Small GTPases regulate key processes in cells. Malfunction of their GTPase reaction by mutations is involved in severe diseases. Here, we compare the GTPase reaction of the slower hydrolyzing GTPase Ran with Ras. By combination of time-resolved FTIR difference spectroscopy and QM/MM simulations we elucidate that the Mg(2+) coordination by the phosphate groups, which varies largely among the x-ray structures, is the same for Ran and Ras. A new x-ray structure of a Ran·RanBD1 complex with improved resolution confirmed this finding and revealed a general problem with the refinement of Mg(2+) in GTPases. The Mg(2+) coordination is not responsible for the much slower GTPase reaction of Ran. Instead, the location of the Tyr-39 side chain of Ran between the γ-phosphate and Gln-69 prevents the optimal positioning of the attacking water molecule by the Gln-69 relative to the γ-phosphate. This is confirmed in the RanY39A·RanBD1 crystal structure. The QM/MM simulations provide IR spectra of the catalytic center, which agree very nicely with the experimental ones. The combination of both methods can correlate spectra with structure at atomic detail. For example the FTIR difference spectra of RasA18T and RanT25A mutants show that spectral differences are mainly due to the hydrogen bond of Thr-25 to the α-phosphate in Ran. By integration of x-ray structure analysis, experimental, and theoretical IR spectroscopy the catalytic center of the x-ray structural models are further refined to sub-Å resolution, allowing an improved understanding of catalysis. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Essential Parameters for Structural Analysis and Dereplication by 1H NMR Spectroscopy

PubMed Central

2015-01-01

The present study demonstrates the importance of adequate precision when reporting the δ and J parameters of frequency domain 1H NMR (HNMR) data. Using a variety of structural classes (terpenoids, phenolics, alkaloids) from different taxa (plants, cyanobacteria), this study develops rationales that explain the importance of enhanced precision in NMR spectroscopic analysis and rationalizes the need for reporting Δδ and ΔJ values at the 0.1–1 ppb and 10 mHz level, respectively. Spectral simulations paired with iteration are shown to be essential tools for complete spectral interpretation, adequate precision, and unambiguous HNMR-driven dereplication and metabolomic analysis. The broader applicability of the recommendation relates to the physicochemical properties of hydrogen (1H) and its ubiquity in organic molecules, making HNMR spectra an integral component of structure elucidation and verification. Regardless of origin or molecular weight, the HNMR spectrum of a compound can be very complex and encode a wealth of structural information that is often obscured by limited spectral dispersion and the occurrence of higher order effects. This altogether limits spectral interpretation, confines decoding of the underlying spin parameters, and explains the major challenge associated with the translation of HNMR spectra into tabulated information. On the other hand, the reproducibility of the spectral data set of any (new) chemical entity is essential for its structure elucidation and subsequent dereplication. Handling and documenting HNMR data with adequate precision is critical for establishing unequivocal links between chemical structure, analytical data, metabolomes, and biological activity. Using the full potential of HNMR spectra will facilitate the general reproducibility for future studies of bioactive chemicals, especially of compounds obtained from the diversity of terrestrial and marine organisms. PMID:24895010

Sodiated Sugar Structures: Cryogenic Ion Vibrational Spectroscopy of Na^+(GLUCOSE) Adducts

NASA Astrophysics Data System (ADS)

Voss, Jonathan; Kregel, Steven J.; Fischer, Kaitlyn C.; Garand, Etienne

2017-06-01

The recent discovery that ionic liquids help facilitate the dissolution of cellulose has renewed interest in understanding how ionic species interact with carbohydrates. Here we present infrared spectra in the 2800 - 3800 \\wn range of gas-phase mass-selected Na^+(Glucose) adducts. These adducts are further probed with IR-dip spectroscopy to yield conformer specific spectra of at least seven unique species. The relative abundances of conformers show that gas-phase interconversion barriers are sufficiently high to preserve the solution-phase populations. Additionally, our results demonstrate that mM concentrations of NaCl do not strongly perturb the anomeric ratio of glucose in solution.

High Si-H local mode overtones in SiHD/sub 3/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernheim, R.A.; Lampe, F.W.; O'Keefe, J.F.

1984-01-01

Spectra for SiHD/sub 3/ obtained using a nonresonant photoacoustic cell mounted within the cavity of a CR490 tunable CW laser are reported herein. The symmetric top spectra exhibit partial rotational resolution. A relation for determining the Si-H bond distance is reported, and the Si-D bond distance is taken to be the same as the Si-H distance in the ground vibrational state. The bond angle is assumed to remain tetrahedral in both situations. The noted spectral vibrational band widths arise only from rotational structure with contributions from fast vibrational relaxation not being evident. 10 references, 2 figures, 1 table.

Investigation of low-loss spectra and near-edge fine structure of polymers by PEELS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heckmann, W.

Transmission electron microscopy has changed from a purely imaging method to an analytical method. This has been facilitated particularly by equipping electron microscopes with energy filters and with parallel electron energy loss spectrometers (PEELS). Because of their relatively high energy resolution (1 to 2 eV) they provide information not only on the elements present but also on the type of bonds between the molecular groups. Polymers are radiation sensitive and the molecular bonds change as the spectrum is being recorded. This can be observed with PEEL spectrometers that are able to record spectra with high sensitivity and in rapid succession.

Unveiling the Sweet Conformations of Ketohexoses

NASA Astrophysics Data System (ADS)

Bermudez, C.; Pena, I.; Cabezas, C.; Daly, A. M.; Mata, S.; Alonso, J. L.

2013-06-01

The conformational behavior of ketohexoses D-Fructose, L-Sorbose, D-Tagatose and D-Psicose has been revealed from their rotational spectra. A broadband microwave spectrometer (CP-FTMW) has been used to rapidly acquire the rotational spectra in the 6 to 12 GHz frequency range. All observed species are stabilized by complicated intramolecular hydrogen-bonding networks. Structural motifs related to the sweetness of ketohexoses are revealed. G. G. Brown, B. C. Dian, K. O. Douglass, S. M. Geyer, S. T. Shipman, B. H. Pate, Rev. Sci. Instrum. 2008, 79, 053103. S. Mata, I. Peña, C. Cabezas, J. C. López, J. L. Alonso, J. Mol. Spectrosc. 2012, 280, 91.

Density functional calculations of the Mössbauer parameters in hexagonal ferrite SrFe12O19

NASA Astrophysics Data System (ADS)

Ikeno, Hidekazu

2018-03-01

Mössbauer parameters in a magnetoplumbite-type hexagonal ferrite, SrFe12O19, are computed using the all-electron band structure calculation based on the density functional theory. The theoretical isomer shift and quadrupole splitting are consistent with experimentally obtained values. The absolute values of hyperfine splitting parameters are found to be underestimated, but the relative scale can be reproduced. The present results validate the site-dependence of Mössbauer parameters obtained by analyzing experimental spectra of hexagonal ferrites. The results also show the usefulness of theoretical calculations for increasing the reliability of interpretation of the Mössbauer spectra.

Raman spectra and phase transitions in Rb{sub 2}KInF{sub 6} elpasolite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krylov, A. S.; Krylova, S. N., E-mail: slanky@iph.krasn.ru; Vtyurin, A. N.

2011-01-15

The Raman spectra of Rb{sub 2}KInF{sub 6} elpasolite crystal have been studied in a wide temperature range, including two phase transitions: from the cubic phase to the tetragonal phase and then to the monoclinic phase. Several anomalies of internal modes of InF{sub 6} octahedra and low-frequency lattice vibrations, which are related to the structural changes at the transition points, have been found and quantitatively analyzed. The results of a quantitative analysis of the temperature dependences of the parameters of spectral lines are in good agreement with the thermodynamic data on the phase transitions.

Utilization of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for structural studies related to biology and disease

NASA Astrophysics Data System (ADS)

Costello, Catherine E.; Helin, Jari; Ngoka, Lambert C. M.

1996-04-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), because of its high sensitivity and relatively straightforward requirements for sample preparation, is contributing to the solution of structural problems in biology and to the development of therapeutic approaches through increased understanding of pharmacology and enhanced capabilities for quality control of pharmaceuticals. We are using a reflectron TOF- MS for the determination of molecular weights of individual compounds and the components of mixtures that are naturally occurring or are generated through enzymic digests, and employing the post-source decay mode to elucidate structural details. To maximize the sensitivity and information content of the spectra, varied matrices, derivative, and stepwise degradation procedures are being explored. Present studies include investigations of oligosaccharides, neutral glycolipids, gangliosides, glycoproteins, neuropeptides and proteins. Rules for fragmentation are being developed with model compounds and used for the structural elucidation of unknowns. When adequate sample amounts are available, the results are compared with low- and high-energy collision-induced decomposition spectra obtained with tandem MS in order to provide a data base for the correlation of spectral features and guidance in selection of approaches for scarce biological samples. Current projects include biophysical studies of glycoplipids, glycoproteins and oligosaccharides and investigations of the substance P receptor, transthyretin genetic variants and cisplatin-DNA interactions.

INFERRING THE CORONAL DENSITY IRREGULARITY FROM EUV SPECTRA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hahn, M.; Savin, D. W., E-mail: mhahn@astro.columbia.edu

2016-09-20

Understanding the density structure of the solar corona is important for modeling both coronal heating and the solar wind. Direct measurements are difficult because of line-of-sight integration and possible unresolved structures. We present a new method for quantifying such structures using density-sensitive extreme ultraviolet line intensities to derive a density irregularity parameter, a relative measure of the amount of structure along the line of sight. We also present a simple model to relate the inferred irregularities to physical quantities, such as the filling factor and density contrast. For quiet-Sun regions and interplume regions of coronal holes, we find a densitymore » contrast of at least a factor of 3–10 and corresponding filling factors of about 10%–20%. Our results are in rough agreement with other estimates of the density structures in these regions. The irregularity diagnostic provides a useful relative measure of unresolved structure in various regions of the corona.« less

Soft x-ray absorption spectra of ilmenite family.

PubMed

Agui, A; Mizumaki, M; Saitoh, Y; Matsushita, T; Nakatani, T; Fukaya, A; Torikai, E

2001-03-01

We have carried out soft x-ray absorption spectroscopy to study the electronic structure of ilmenite family, such as MnTiO3, FeTiO3, and CoTiO3 at the soft x-ray beamline, BL23SU, at the SPring-8. The Ti and M L2,3 absorption spectra of MTiO3 (M=Mn, Fe, and Co) show spectra of Ti4+ and M2+ electron configurations, respectively. Except the Fe L2,3 spectrum, those spectra were understood within the O(h) symmetry around the transition metal ions. The Fe L3-edge spectrum clearly shows a doublet peak at the L3 edge, which is attributed to Fe2+ state, moreover the very high-resolution the L-edge spectra of transition metals show fine structures. The spectra of those ilmenites are compared.

Raman and infrared spectra and theoretical calculations of dipicolinic acid, dinicotinic acid, and their dianions

NASA Astrophysics Data System (ADS)

McCann, Kathleen; Laane, Jaan

2008-11-01

The Raman and infrared spectra of dipicolinic acid (DPA) and dinicotinic acid (DNic) and their salts (CaDPA, Na 2DPA, and CaDNic) have been recorded and the spectra have been assigned. Ab initio and DFT calculations were carried out to predict the structures and vibrational spectra and were compared to the experimental results. Because of extensive intermolecular hydrogen bonding in the crystals of these molecules, the calculated structures and spectra for the individual molecules agree only moderately well with the experimental values. Theoretical calculations were also carried out for DPA dimers and DPA·2H 2O to better understand the intermolecular interactions. The spectra do show that DPA and its calcium salt, which are present in anthrax spores, can be distinguished from the very similar DNic and CaDNic.

Simulations of iron K pre-edge X-ray absorption spectra using the restricted active space method.

PubMed

Guo, Meiyuan; Sørensen, Lasse Kragh; Delcey, Mickaël G; Pinjari, Rahul V; Lundberg, Marcus

2016-01-28

The intensities and relative energies of metal K pre-edge features are sensitive to both geometric and electronic structures. With the possibility to collect high-resolution spectral data it is important to find theoretical methods that include all important spectral effects: ligand-field splitting, multiplet structures, 3d-4p orbital hybridization, and charge-transfer excitations. Here the restricted active space (RAS) method is used for the first time to calculate metal K pre-edge spectra of open-shell systems, and its performance is tested against on six iron complexes: [FeCl6](n-), [FeCl4](n-), and [Fe(CN)6](n-) in ferrous and ferric oxidation states. The method gives good descriptions of the spectral shapes for all six systems. The mean absolute deviation for the relative energies of different peaks is only 0.1 eV. For the two systems that lack centrosymmetry [FeCl4](2-/1-), the ratios between dipole and quadrupole intensity contributions are reproduced with an error of 10%, which leads to good descriptions of the integrated pre-edge intensities. To gain further chemical insight, the origins of the pre-edge features have been analyzed with a chemically intuitive molecular orbital picture that serves as a bridge between the spectra and the electronic structures. The pre-edges contain information about both ligand-field strengths and orbital covalencies, which can be understood by analyzing the RAS wavefunction. The RAS method can thus be used to predict and rationalize the effects of changes in both the oxidation state and ligand environment in a number of hard X-ray studies of small and medium-sized molecular systems.

Investigation of formalin influence over hard and soft biological tissues fluorescent spectra in vitro

NASA Astrophysics Data System (ADS)

Borisova, E.; Uzunov, Tz.; Vladimirov, B.; Avramov, L.

2007-05-01

In order to investigate the formalin influence over fluorescence properties of hard and soft biological tissues during conservation, emission spectra have been registered. Nitrogen laser at 337 nm and light-emitting diode with maximum at 405 nm have been used as excitation sources. For investigation of formalin influence over hard tissues, an experiment was made on teeth samples. Sound teeth were demineralized with a phosphoric acid for 10 seconds to obtain enamel structure near to the tooth lesion, and were fixed in formalin. Before and after teeth treatment spectra from the areas of interest were detected. There were not observed changes in the shape of the teeth spectra, related to the introduction of formalin fluorescence. Samples from mucosa of esophagus and stomach, where initially an ALA/Protoporphyrin IX diagnosis was applied, were used as soft tissue specimens. After fluorescent diagnosis in vivo biopsy samples were obtained from normal and cancerous areas and were conserved in formalin. Initially, spectrum observed has one autofluorescence maximum from the mucous tissue at 500-600 nm and secondary maxima from the protoporphyrin fluorescence at 635 nm and 720 nm, as well as pronounced minima at 540 and 575 nm related to hemoglobin absorption. After formalin conservation hemoglobin absorption was strongly reduced that increases mucous emission signal in green-yellow spectral region. Simultaneously the maxima at 635 nm and 720 nm were reduced. As conclusion we could say that formalin has negligible influence over fluorescence spectra of conserved hard tissues and has more pronounced influence over fluorescence spectra obtained in the case of soft tissue conservation, which has to be taking into account in measurements in vitro.

Relation between Kitaev magnetism and structure in α -RuCl3

NASA Astrophysics Data System (ADS)

Glamazda, A.; Lemmens, P.; Do, S.-H.; Kwon, Y. S.; Choi, K.-Y.

2017-05-01

Raman scattering has been employed to investigate lattice and magnetic excitations of the honeycomb Kitaev material α -RuCl3 and its Heisenberg counterpart CrCl3. Our phonon Raman spectra give evidence for a first-order structural transition from a monoclinic to a rhombohedral structure for both compounds. Significantly, only α -RuCl3 features a large thermal hysteresis, consistent with the formation of a wide phase of coexistence. In the related temperature interval of 70 -170 K, we observe a hysteretic behavior of magnetic excitations as well. The stronger magnetic response in the rhombohedral compared to the monoclinic phase evidences a coupling between the crystallographic structure and low-energy magnetic response. Our results demonstrate that the Kitaev magnetism concomitant with fractionalized excitations is susceptible to small variations of bonding geometry.

Structure, stability, thermodynamic properties, and infrared spectra of the protonated water octamer H(+)(H2O)8.

PubMed

Karthikeyan, S; Park, Mina; Shin, Ilgyou; Kim, Kwang S

2008-10-16

We investigated various two-dimensional (2D) and three-dimensional (3D) structures of H (+)(H 2O) 8, using density functional theory (DFT), Moller-Plesset second-order perturbation theory (MP2), and coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)). The 3D structure is more stable than the 2D structure at all levels of theory on the Born-Oppenheimer surface. With the zero-point energy (ZPE) correction, the predicted structure varies depending on the level of theory. The DFT employing Becke's three parameters with Lee-Yang-Parr functionals (B3LYP) favors the 2D structure. At the complete basis set (CBS) limit, the MP2 calculation favors the 3D structure by 0.29 kcal/mol, and the CCSD(T) calculation favors the 3D structure by 0.27 kcal/mol. It is thus expected that both 2D and 3D structures are nearly isoenergetic near 0 K. At 100 K, all the calculations show that the 2D structure is much more stable in free binding energy than the 3D structure. The DFT and MP2 vibrational spectra of the 2D structure are consistent with the experimental spectra. First-principles Car-Parrinello molecular dynamics (CPMD) simulations show that the 2D Zundel-type vibrational spectra are in good agreement with the experiment.

Support vector machine based classification of fast Fourier transform spectroscopy of proteins

NASA Astrophysics Data System (ADS)

Lazarevic, Aleksandar; Pokrajac, Dragoljub; Marcano, Aristides; Melikechi, Noureddine

2009-02-01

Fast Fourier transform spectroscopy has proved to be a powerful method for study of the secondary structure of proteins since peak positions and their relative amplitude are affected by the number of hydrogen bridges that sustain this secondary structure. However, to our best knowledge, the method has not been used yet for identification of proteins within a complex matrix like a blood sample. The principal reason is the apparent similarity of protein infrared spectra with actual differences usually masked by the solvent contribution and other interactions. In this paper, we propose a novel machine learning based method that uses protein spectra for classification and identification of such proteins within a given sample. The proposed method uses principal component analysis (PCA) to identify most important linear combinations of original spectral components and then employs support vector machine (SVM) classification model applied on such identified combinations to categorize proteins into one of given groups. Our experiments have been performed on the set of four different proteins, namely: Bovine Serum Albumin, Leptin, Insulin-like Growth Factor 2 and Osteopontin. Our proposed method of applying principal component analysis along with support vector machines exhibits excellent classification accuracy when identifying proteins using their infrared spectra.

Nature of the high-binding-energy dip in the low-temperature photoemission spectra of Bi2Sr2CaCu2O8+δ

NASA Astrophysics Data System (ADS)

Dessau, D. S.; Shen, Z.-X.; Wells, B. O.; King, D. M.; Spicer, W. E.; Arko, A. J.; Lombardo, L. W.; Mitzi, D. B.; Kapitulnik, A.

1992-03-01

At the transition to superconductivity, an anomalous high-binding-energy (~=-90 meV) dip appears in the low-temperature photoemission spectra taken along the Γ-M¯ high-symmetry direction of Bi2Sr2CaCu2O8+δ. This paper details experiments which further characterize the energy and k-space dependence of this dip structure. The dip occurs over a wide portion of the Γ-M¯ zone diagonal (110), yet shows minimal energy dispersion. In the spectra taken along the Γ-X zone edge (100), the dip is very weak or not present. We show that these results imply that the dip is not an artifact dependent on the experiment or special features of the band structure and therefore is an intrinsic feature of the superconducting state of Bi2Sr2CaCu2O8+δ. The behavior of the normal-state bands along Γ-M¯ in relation to the local-density-approximation prediction of a Bi-O-based electron ``pocket'' is also discussed, with our data explained most naturally if the Bi-O band remains above the Fermi level for all k.

Spectrophotometric Study of the Region of the Sky Around the Galaxies Markarian 261 and 262

NASA Astrophysics Data System (ADS)

Khachikian, E. Ye.; Sargsyan, L. A.

2005-10-01

Results are presented from a detailed spectrophotometric study of a unique system of physically coupled galaxies whose spectra contain identical emission lines. This system consists of four galaxies, three of which have a double or multiple structure in their central portions and are, by definition, galaxies with two or multiple nuclei. Two of these objects are the galaxies with an ultraviolet excess (UVE), Mark 261 and Mark 262, while one is a galaxy made up of two identical starlike nuclei that are referred to as the “twin objects.” In the DSS2 charts, the latter show up as two adjacent stars without any surroundings. However, there are two condensations between these starlike nuclei. The fourth object has a triplet structure. It is shown here that all these objects have the same emission (line) spectra and red shifts. All the physical characteristics that can be determined from the spectra are determined: red shifts, relative intensities of emission lines, their equivalent widths, distances to the galaxies, etc. It is concluded that the members of this system have a common origin, more or less consistent with Ambartsumyan's idea of the fragmentation of an isolated, high density body.

Optical and Electron Spin Resonance Studies of Destruction of Porous Structures Formed by Nitrogen-Rare Gas Nanoclusters in Bulk Superfluid Helium

NASA Astrophysics Data System (ADS)

McColgan, Patrick T.; Meraki, Adil; Boltnev, Roman E.; Lee, David M.; Khmelenko, Vladimir V.

2017-04-01

We studied optical and electron spin resonance spectra during destruction of porous structures formed by nitrogen-rare gas (RG) nanoclusters in bulk superfluid helium containing high concentrations of stabilized nitrogen atoms. Samples were created by injecting products of a radio frequency discharge of nitrogen-rare gas-helium gas mixtures into bulk superfluid helium. These samples have a high energy density allowing the study of energy release in chemical processes inside of nanocluster aggregates. The rare gases used in the studies were neon, argon, and krypton. We also studied the effects of changing the relative concentrations between nitrogen and rare gas on thermoluminescence spectra during destruction of the samples. At the beginning of the destructions, α -group of nitrogen atoms, Vegard-Kaplan bands of N_2 molecules, and β -group of O atoms were observed. The final destruction of the samples were characterized by a series bright flashes. Spectra obtained during these flashes contain M- and β -bands of NO molecules, the intensities of which depend on the concentration of molecular nitrogen in the gas mixture as well as the type of rare gas present in the gas mixture.

Infrared spectra and other properties predictions of 5-amino-3-methyl-4-isoxazolecarbohydrazide with electric field simulation using CPC model

NASA Astrophysics Data System (ADS)

Regiec, Andrzej; Wojciechowski, Piotr; Pietraszko, Adam; Mączyński, Marcin

2018-06-01

Here, the Conductor-like Polarizable Continuum Model (CPCM) was used as a less demanding substitute of Periodic Boundary Conditions (PBC) method to attempt to reliably simulate infrared spectra and some structural parameters of solid compound - 5-amino-3-methyl-4-isoxazolecarbohydrazide (HIX). The measured relative electric permittivity of HIX was used as a simplified equivalent of electric intensity generating by other molecules of 5-amino-3-methyl-4-isoxazolecarbohydrazide in crystal structure. The application of CPCM has resulted in better conformity of calculated molecular parameters with experimentally found. Theoretical geometry was compared with data obtained with X-ray crystallography. Comparison of harmonic approximation with anharmonic one, based on the six selected characteristic vibrations, shows that non-scaled harmonic wavenumbers, calculated with CPCM, well correspond to experimental spectra. Additionally, the results point out that anharmonic approximation appeared to be strong sensitive for input geometry and calculation parameters used, so the results are sometimes unreliable, especially for low wavenumbers. Also, the new feasible ways of the synthesis of the titled compound is presented, one of which is particularly easy and highly efficient.

Photo-degradation of CT-DNA with a series of carbothioamide ruthenium (II) complexes - Synthesis and structural analysis

NASA Astrophysics Data System (ADS)

Muthuraj, V.; Umadevi, M.

2018-04-01

The present research article is related with the method of preparation, structure and spectroscopic properties of a series of carbothioamide ruthenium (II) complexes with N and S donor ligands namely, 2-((6-chloro-4-oxo-4H-chromen-3-yl)methylene) hydrazine carbothioamide (ClChrTs)/2-((6-methoxy-4-oxo-4H-chromen-3-yl)methylene)hydrazine carbothioamide (MeOChrTS). The synthesized complexes were characterized by several techniques using analytical methods as well as by spectral techniques such as FT-IR, 1HNMR, 13CNMR, ESI mass and thermogravimetry/differential thermal analysis (TG-DTA). The IR spectra shows that the ligand acts as a neutral bidentate with N and S donor atoms. The biological activity of the prepared compounds and metal complexes were tested against cell line of calf-thymus DNA via an intercalation mechanism (MCF-7). In addition, the interaction of Ru(II) complexes and its free ligands with CT-DNA were also investigated by titration with UV-Vis spectra, fluorescence spectra, and Circular dichroism studies. Results suggest that both of the two Ru(II) complexes can bind with calf-thymus DNA via an intercalation mechanism.

Effect of relativity on the ionization spectra of the xenon fluorides XeFn (n=2, 4, 6).

PubMed

Pernpointner, Markus; Cederbaum, Lorenz S

2005-06-01

Noble gas compounds exhibit special chemical bonding situations and have been investigated by various spectroscopic and theoretical techniques. In this work we calculate the ionization spectra of the xenon fluorides (XeF2,XeF4, and XeF6) in the valence and subvalence (down to Xe 4d) areas by application of the recently developed Dirac-Hartree-Fock one-particle propagator technique. In this technique, the relativistic (four-component) and electron correlation effects are computed simultaneously. The xenon compounds show considerable spin-orbit splitting strongly influencing the photoelectron spectrum not reproducible in prior calculations. Comparison to one-component methods is made and the occurring satellite structures are interpreted. The satellite structures can be attributed either to the breakdown of the one-particle picture or to a reflection of intra-atomic and interatomic Auger decay processes within the molecule.

Mg II-Absorbing Galaxies in the UltraVISTA Survey

NASA Astrophysics Data System (ADS)

Stroupe, Darren; Lundgren, Britt

2018-01-01

Light that is emitted from distant quasars can become partially absorbed by intervening gaseous structures, including galaxies, in its path toward Earth, revealing information about the chemical content, degree of ionization, organization and evolution of these structures through time. In this project, quasar spectra are used to probe the halos of foreground galaxies at a mean redshift of z=1.1 in the COSMOS Field. Mg II absorption lines in Sloan Digital Sky Survey quasar spectra are paired with galaxies in the UltraVISTA catalog at an impact parameter less than 200 kpc. A sample of 77 strong Mg II absorbers with a rest-frame equivalent width ≥ 0.3 Å and redshift from 0.34 < z < 2.21 are investigated to find equivalent width ratios of Mg II, C IV and Fe II absorption lines, and their relation to the impact parameter and the star formation rates, stellar masses, environments and redshifts of their host galaxies.

Molecular and structural characteristics in toxic algae cultures of Ostreopsis ovata and Ostreopsis spp. evidenced by FTIR and FTNIR spectroscopy

NASA Astrophysics Data System (ADS)

Mecozzi, Mauro; Pietroletti, Marco; Tornambè, Andrea

2011-05-01

In this article we investigated the compositional and structural characteristics of the principal biomolecules such as carbohydrates, proteins, lipids, nucleic acids and chlorophyll pigments present in biofilm cultures of Ostreopsis spp. and in batch cultures of Ostreopsis ovata. Our approach based on the use of infrared (FTIR) and near infrared (FTNIR) spectroscopy showed the marked differences existing between biofilm cultures and batch cultures. FTIR spectroscopy showed the higher contents of polysaccharides and chlorophyll pigments in O. ovata from batch cultures with respect to Ostreopsis spp. Second derivative FTIR spectroscopy showed different features concerning the secondary structure of proteins because in O. ovata samples the beta sheet and beta turn structures were observed whereas in Ostreopsis spp. samples the alpha helix structure was the most evident. FTNIR spectroscopy showed other structural differences observed existing between O. ovata and Ostreopsis spp. mainly related to hydrogen bond interactions determining more packed structures in the nucleus of O. ovata. In addition, the interpretation of FTIR and FTNIR spectral information was also supported by the application of two statistical methods, the independent component analysis (ICA) and the spectral cross correlation analysis (SCCA). ICA was used as spectral deconvolution technique to separate the effects of the interference bicarbonate ion from algal FTIR spectra so to verify the high similar qualitative composition of the three biofilm samples of Ostreopsis spp. At last, SCCA applied to FTIR and FTNIR spectra was useful to evidence some structural differences involving -CH and CH 2 groups of aliphatic chains in O. ovata and Ostreopsis spp. samples. Though preliminary, these results agree with some previous studies suggesting that the presence of different ecophysiological characteristics in O. ovata and Ostreopsis spp. depending on the parameters related to the condition growth.

Raman spectroscopic study of plasma-treated salmon DNA

NASA Astrophysics Data System (ADS)

Joon Lee, Geon; Kwon, Young-Wan; Hee Kim, Yong; Ha Choi, Eun

2013-01-01

In this research, we studied the effect of plasma treatment on the optical/structural properties of the deoxyribonucleic acid (DNA) extracted from salmon sperm. DNA-cetyltrimethylammonium (CTMA) films were obtained by complexation of DNA with CTMA. Circular dichroism (CD) and Raman spectra indicated that DNA retained its double helical structure in the solid film. The Raman spectra exhibited several vibration modes corresponding to the nuclear bases and the deoxyribose-phosphate backbones of the DNA, as well as the alkylchains of CTMA. Dielectric-barrier-discharge (DBD) plasma treatment induced structural modification and damage to the DNA, as observed by changes in the ultraviolet-visible absorption, CD, and Raman spectra. The optical emission spectra of the DBD plasma confirmed that DNA modification was induced by plasma ions such as reactive oxygen species and reactive nitrogen species.

Effect of gamma radiation on the optical and structural properties of ZnO nanowires with various diameters

NASA Astrophysics Data System (ADS)

Reyhani, A.; Gholizadeh, A.; vahedi, V.; Khanlary, M. R.

2018-01-01

The effects of gamma-irradiation are studied on the morphology and structural properties of ZnO nanowire with various diameters. The ZnO nanowires are grown using Zn thin films at various initial thicknesses including 125, 250 and 500 nm in air ambient. The results illustrate dramatic effects of Gamma-irradiation on the deformation of ZnO nanowires. Thus, radiation induce ripple ZnO surfaces instead ZnO nanowires. Gamma-irradiation has also been effective on the optical and crystalline properties of the nanowires. X-ray diffraction attests that size of the ZnO nano-structures has changed and (l00) crystalline direction related to Zn metal has been created after irradiation. UV-Visible spectra display two areas for transmittance of irradiated ZnO nanowires, one in the Visible-light and the other in IR sub-region. In the Visible-light area, the layer gets thicker from 125 to 500 nm; the difference between the layer transmittance spectra is reduced before and after gamma irradiation. In the IR-light region, with increasing of ZnO initial thickness, the difference between the layer transmittance spectra is increased before and after gamma irradiation. The photoluminescence spectroscopy displays that intensity of green-yellow band improves in compared to near-band-edge emission due to formation of Zn metal and oxygen vacancies after gamma irradiation.

Stepwise microhydration of aromatic amide cations: water solvation networks revealed by the infrared spectra of acetanilide+-(H2O)n clusters (n ≤ 3).

PubMed

Klyne, Johanna; Schmies, Matthias; Miyazaki, Mitsuhiko; Fujii, Masaaki; Dopfer, Otto

2018-01-31

The structure and activity of peptides and proteins strongly rely on their charge state and the interaction with their hydration environment. Here, infrared photodissociation (IRPD) spectra of size-selected microhydrated clusters of cationic acetanilide (AA + , N-phenylacetamide), AA + -(H 2 O) n with n ≤ 3, are analysed by dispersion-corrected density functional theory calculations at the ωB97X-D/aug-cc-pVTZ level to determine the stepwise microhydration process of this aromatic peptide model. The IRPD spectra are recorded in the informative X-H stretch (ν OH , ν NH , ν CH , amide A, 2800-3800 cm -1 ) and fingerprint (amide I-II, 1000-1900 cm -1 ) ranges to probe the preferred hydration motifs and the cluster growth. In the most stable AA + -(H 2 O) n structures, the H 2 O ligands solvate the acidic NH proton of the amide by forming a hydrogen-bonded solvent network, which strongly benefits from cooperative effects arising from the excess positive charge. Comparison with neutral AA-H 2 O reveals the strong impact of ionization on the acidity of the NH proton and the topology of the interaction potential. Comparison with related hydrated formanilide clusters demonstrates the influence of methylation of the amide group (H → CH 3 ) on the shape of the intermolecular potential and the structure of the hydration shell.

Entangled scalar and tensor fluctuations during inflation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Collins, Hael; Vardanyan, Tereza

2016-11-29

We show how the choice of an inflationary state that entangles scalar and tensor fluctuations affects the angular two-point correlation functions of the T, E, and B modes of the cosmic microwave background. The propagators for a state starting with some general quadratic entanglement are solved exactly, leading to predictions for the primordial scalar-scalar, tensor-tensor, and scalar-tensor power spectra. These power spectra are expressed in terms of general functions that describe the entangling structure of the initial state relative to the standard Bunch-Davies vacuum. We illustrate how such a state would modify the angular correlations in the CMB with amore » simple example where the initial state is a small perturbation away from the Bunch-Davies state. Because the state breaks some of the rotational symmetries, the angular power spectra no longer need be strictly diagonal.« less

Collection, analysis, and archival of LDEF activation data

NASA Technical Reports Server (NTRS)

Laird, C. E.; Harmon, B. A.; Fishman, G. J.; Parnell, T. A.

1993-01-01

The study of the induced radioactivity of samples intentionally placed aboard the Long Duration Exposure Facility (LDEF) and samples obtained from the LDEF structure is reviewed. The eight laboratories involved in the gamma-ray counting are listed and the scientists and the associated counting facilities are described. Presently, most of the gamma-ray counting has been completed and the spectra are being analyzed and corrected for efficiency and self absorption. The acquired spectra are being collected at Eastern Kentucky University for future reference. The results of these analyses are being compiled and reviewed for possible inconsistencies as well as for comparison with model calculations. These model calculations are being revised to include the changes in trapped-proton flux caused by the onset of the period of maximum solar activity and the rapidly decreasing spacecraft orbit. Tentative plans are given for the storage of the approximately 1000 gamma-ray spectra acquired in this study and the related experimental data.

N-propyl nitrate vibrational spectrum analysis using DFT B3LYP quantum-chemical method

NASA Astrophysics Data System (ADS)

Shaikhullina, R. M.; Hrapkovsky, G. M.; Shaikhullina, M. M.

2018-05-01

Calculation of a molecular structure, conformation and related vibrational spectra of the n- propyl nitrate C3H7NO3 was carried out by means of density functional theory (DFT) by employing the Gaussian 03 package. The molecular geometries were fully optimized by using the Becker's three-parameter hybrid exchange functional combined with the Lee–Yang–Parr correlation functional (B3LYP) and using the 6-31G(d) basis set. By scanning the dihedral angles around C-O and C-C bonds, five energetically most favorable conformers of n-propyl nitrate - TG, TT, GT, GG and G´G forms were found. Vibrational spectra of the most energetically favorable conformers were calculated. The comparative analysis of calculated and experimental spectra is carried out, the spectral features of the conformational state of n-propyl nitrate and the spectral effects of formation of intramolecular hydrogen bonds are established.

Ground level enhancements of cosmic rays in solar cycle 24

NASA Astrophysics Data System (ADS)

Kravtsova, M. V.; Sdobnov, V. E.

2017-07-01

Using data from ground-based observations of cosmic rays (CRs) on the worldwide network of stations and spacecraft, we have investigated the proton spectra and the CR anisotropy during the ground level enhancements of CRs on May 17, 2012 (GLE71) and January 6, 2014 (GLE72) occurred in solar cycle 24 by the spectrographic global survey method. We provide the CR rigidity spectra and the relative changes in the intensity of CRs with a rigidity of 2 GV in the solar-ecliptic geocentric coordinate system in specific periods of these events. We show that the proton acceleration during GLE71 and GLE72 occurred up to rigidities R 2.3-2.5 GV, while the differential rigidity spectra of solar CRs are described neither by a power nor by an exponential function of particle rigidity. At the times of the events considered the Earth was in a loop-like structure of the interplanetary magnetic field.

Bulk Nuclear Hyperpolarization of Inorganic Solids by Relay from the Surface.

PubMed

Björgvinsdóttir, Snædís; Walder, Brennan J; Pinon, Arthur C; Emsley, Lyndon

2018-06-14

NMR is a method of choice to determine structural and electronic features in inorganic materials, and has been widely used in the past, but its application is severely limited by its low relative sensitivity. We show how the bulk of proton-free inorganic solids can be hyperpolarized with a general strategy using impregnation dynamic nuclear polarization through homonuclear spin diffusion between low-γ nuclei. This is achieved either through direct hyperpolarization or with a pulse cooling cross-polarization method, transferring hyperpolarization from protons to heteronuclei at particle surfaces. We demonstrate a factor of 50 gain in overall sensitivity for the 119 Sn spectrum of powdered SnO 2 , corresponding to an acceleration of a factor >2500 in acquisition times. The method is also shown for 31 P spectra of GaP, 113 Cd spectra of CdTe, and 29 Si spectra of α-quartz.

Photonic band gap spectra in Octonacci metamaterial quasicrystals

NASA Astrophysics Data System (ADS)

Brandão, E. R.; Vasconcelos, M. S.; Albuquerque, E. L.; Fulco, U. L.

2017-02-01

In this work we study theoretically the photonic band gap spectra for a one-dimensional quasicrystal made up of SiO2 (layer A) and a metamaterial (layer B) organized following the Octonacci sequence, where its nth-stage Sn is given by the inflation rule Sn =Sn - 1Sn - 2Sn - 1 for n ≥ 3 , with initial conditions S1 = A and S2 = B . The metamaterial is characterized by a frequency dependent electric permittivity ε(ω) and magnetic permeability μ(ω) . The polariton dispersion relation is obtained analytically by employing a theoretical calculation based on a transfer-matrix approach. A quantitative analysis of the spectra is then discussed, stressing the distribution of the allowed photonic band widths for high generations of the Octonacci structure, which depict a self-similar scaling property behavior, with a power law depending on the common in-plane wavevector kx .

Computer simulation of backscattering spectra from paint

NASA Astrophysics Data System (ADS)

Mayer, M.; Silva, T. F.

2017-09-01

To study the role of lateral non-homogeneity on backscattering analysis of paintings, a simplified model of paint consisting of randomly distributed spherical pigment particles embedded in oil/binder has been developed. Backscattering spectra for lead white pigment particles in linseed oil have been calculated for 3 MeV H+ at a scattering angle of 165° for pigment volume concentrations ranging from 30 vol.% to 70 vol.% using the program STRUCTNRA. For identical pigment volume concentrations the heights and shapes of the backscattering spectra depend on the diameter of the pigment particles: This is a structural ambiguity for identical mean atomic concentrations but different lateral arrangement of materials. Only for very small pigment particles the resulting spectra are close to spectra calculated supposing atomic mixing and assuming identical concentrations of all elements. Generally, a good fit can be achieved when evaluating spectra from structured materials assuming atomic mixing of all elements and laterally homogeneous depth distributions. However, the derived depth profiles are inaccurate by a factor of up to 3. The depth range affected by this structural ambiguity ranges from the surface to a depth of roughly 0.5-1 pigment particle diameters. Accurate quantitative evaluation of backscattering spectra from paintings therefore requires taking the correct microstructure of the paint layer into account.

Vibrational spectra and fragmentation pathways of size-selected, D2-tagged ammonium/methylammonium bisulfate clusters.

PubMed

Johnson, Christopher J; Johnson, Mark A

2013-12-19

Particles consisting of ammonia and sulfuric acid are widely regarded as seeds for atmospheric aerosol nucleation, and incorporation of alkylamines has been suggested to substantially accelerate their growth. Despite significant efforts, little direct experimental evidence exists for the structures and chemical processes underlying multicomponent particle nucleation. Here we are concerned with the positively charged clusters of ammonia and sulfuric acid with compositions H(+)(NH3)m(H2SO4)n (2 ≤ m ≤ 5, 1 ≤ n ≤ 4), for which equilibrium geometry structures have been reported in recent computational searches. The computed harmonic vibrational spectra of such minimum energy structures can be directly compared with the experimental spectra of each cluster composition isolated in the laboratory using cryogenic ion chemistry methods. We present one-photon (i.e., linear) infrared action spectra of the isolated gas phase ions cryogenically cooled to 10 K, allowing us to resolve the characteristic vibrational signatures of these clusters. Because the available calculated spectra for different structural candidates have been obtained using different levels of theory, we reoptimized the previously reported structures with several common electronic structure methods and find excellent agreement can be achieved for the (m = 3, n = 2) cluster using CAM-B3LYP with only minor structural differences from the previously identified geometries. At the larger sizes, the experimental spectra strongly resemble that observed for 180 nm ammonium bisulfate particles. The characteristic ammonium- and bisulfate-localized bands are clearly evident at all sizes studied, indicating that the cluster structures are indeed ionic in nature. With the likely (3,2) structure in hand, we then explore the spectral and structural changes caused when methylamine is substituted for ammonia. This process is found to occur with minimal perturbation of the unsubstituted cluster. The thermal decomposition pathways were also evaluated using multiple-photon induced dissociation and are, in all cases, dominated (>100:1) by evaporation of a neutral ammonia molecule rather than methylamine. Spectra obtained for the product cluster ions resulting from this evaporation are consistent with the formation of a single hydrogen bond between two neighboring bisulfate ions, partially regenerating a sulfuric acid molecule. These results provide critical experimental benchmarks for ongoing theoretical efforts to understand the early stages of aerosol growth.

Rotational temperatures of Venus upper atmosphere as measured by SOIR on board Venus Express

NASA Astrophysics Data System (ADS)

Mahieux, A.; Vandaele, A. C.; Robert, S.; Wilquet, V.; Drummond, R.; López Valverde, M. A.; López Puertas, M.; Funke, B.; Bertaux, J. L.

2015-08-01

SOIR is a powerful infrared spectrometer flying on board the Venus Express spacecraft since mid-2006. It sounds the Venus atmosphere above the cloud layer using the solar occultation technique. In the recorded spectra, absorption structures from many species are observed, among them carbon dioxide, the main constituent of the Venus atmosphere. Previously, temperature vertical profiles were derived from the carbon dioxide density retrieved from the SOIR spectra by assuming hydrostatic equilibrium. These profiles show a permanent cold layer at 125 km with temperatures of ~100 K, surrounded by two warmer layers at 90 and 140 km, reaching temperatures of ~200 K and 250-300 K, respectively. In this work, temperature profiles are derived from the SOIR spectra using another technique based on the ro-vibrational structure of carbon dioxide observed in the spectra. The error budget is extensively investigated. Temperature profiles obtained by both techniques are comparable within their respective uncertainties and they confirm the vertical structure previously determined from SOIR spectra.

A theoretical and experimental study on the molecular and electronic structures of artemisinin and related drug molecules

NASA Astrophysics Data System (ADS)

Galasso, V.; Kovač, B.; Modelli, A.

2007-06-01

The equilibrium structures of artemisinin and a selection of its derivatives (potent antimalarial drugs) have been studied with the density functional theory ansatz B3LYP. Of the five rings of the artemisinin framework, it is only the pyranose ring B that exhibits a marked conformational flexibility, especially on addition of a pendant side chain at C-10. For the derivatives, the β isomer with the axial substituent group is found to be energetically more stable than the α isomer with the equatorial group. The assignment of the vibrational fundamentals has been supported by calculations on related model molecules and a normal coordinate analysis. This allows for a reliable characterization of the normal modes, mainly involving the peroxide linkage, in the claimed fingerprint region of 1,2,4-trioxanes. The electronic structures have also been studied by measuring and calculating significant features of the NMR, photoelectron and electron transmission spectra. In particular, a representative set of NMR chemical shifts and nuclear spin-spin coupling constants, obtained with DFT formalisms, compares favourably with experiment and fits expectation in terms of stereoelectronic effects of the vicinal oxygen lone pairs. Based on ab initio outer valence Green's function calculations, a consistent interpretation of the uppermost bands in the photoelectron spectra of artemisinin and derivatives has been advanced. The top ionization energies reflect a complex interaction of the various oxygen lone pair orbitals. Electron transmission spectroscopy is applied for the first time to compounds containing the peroxide bond and elucidates the empty level electronic structure of artemisinin and derivatives in the 0-6 eV energy range, with the support of MO calculations and comparison with the spectra of reference molecules. Electron attachment to the lowest-lying empty σ∗ MO, mainly localized on the O-O bridge, occurs at an energy (1.7 eV) exceptionally low for compounds not containing third-row or heavier elements.

Structure determination of butylone as a new psychoactive substance using chiroptical and vibrational spectroscopies.

PubMed

Spálovská, Dita; Králík, František; Kohout, Michal; Jurásek, Bronislav; Habartová, Lucie; Kuchař, Martin; Setnička, Vladimír

2018-05-01

Recently, there has been a worldwide substantial increase in the consumption of new psychoactive substances (NPS), compounds that mimic the structure of illicit drugs, such as amphetamines or ecstasy. The producers try to avoid the law by a slight modification of illicit structures, thereby developing dozens of temporarily legal NPS every year. The current trends in the detection and monitoring of such substances demand a fast and reliable analysis. Molecular spectroscopy represents a highly effective tool for the identification of NPS and chiroptical methods can provide further information on their 3D structure, which is the key for the determination of their biological activity. We present the first systematic study of NPS, specifically butylone, combining chiroptical and vibrational spectroscopies with ab initio calculations. According to density functional theory calculations, 6 stable lowest energy conformers of butylone were found and their molecular structure was described. For each conformer, the relative abundance based on the Boltzmann distribution was estimated, their population weighted spectra predicted and compared to the experimental results. Very good agreement between the experimental and the simulated spectra was achieved, which allowed not only the assignment of the absolute configuration, but also a precise description of the molecular structure. © 2018 Wiley Periodicals, Inc.

Photonic-magnonic crystals: Multifunctional periodic structures for magnonic and photonic applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kłos, J. W., E-mail: klos@amu.edu.pl; Krawczyk, M.; Dadoenkova, Yu. S.

2014-05-07

We investigate the properties of a photonic-magnonic crystal, a complex multifunctional one-dimensional structure with magnonic and photonic band gaps in the GHz and PHz frequency ranges for spin waves and light, respectively. The system consists of periodically distributed dielectric magnetic slabs of yttrium iron garnet and nonmagnetic spacers with an internal structure of alternating TiO{sub 2} and SiO{sub 2} layers which form finite-size dielectric photonic crystals. We show that the spin-wave coupling between the magnetic layers, and thus the formation of the magnonic band structure, necessitates a nonzero in-plane component of the spin-wave wave vector. A more complex structure perceivedmore » by light is evidenced by the photonic miniband structure and the transmission spectra in which we have observed transmission peaks related to the repetition of the magnetic slabs in the frequency ranges corresponding to the photonic band gaps of the TiO{sub 2}/SiO{sub 2} stack. Moreover, we show that these modes split to very high sharp (a few THz wide) subpeaks in the transmittance spectra. The proposed novel multifunctional artificial crystals can have interesting applications and be used for creating common resonant cavities for spin waves and light to enhance the mutual influence between them.« less

Detecting Molecular Features of Spectra Mainly Associated with Structural and Non-Structural Carbohydrates in Co-Products from BioEthanol Production Using DRIFT with Uni- and Multivariate Molecular Spectral Analyses

PubMed Central

Yu, Peiqiang; Damiran, Daalkhaijav; Azarfar, Arash; Niu, Zhiyuan

2011-01-01

The objective of this study was to use DRIFT spectroscopy with uni- and multivariate molecular spectral analyses as a novel approach to detect molecular features of spectra mainly associated with carbohydrate in the co-products (wheat DDGS, corn DDGS, blend DDGS) from bioethanol processing in comparison with original feedstock (wheat (Triticum), corn (Zea mays)). The carbohydrates related molecular spectral bands included: A_Cell (structural carbohydrates, peaks area region and baseline: ca. 1485–1188 cm−1), A_1240 (structural carbohydrates, peak area centered at ca. 1240 cm−1 with region and baseline: ca. 1292–1198 cm−1), A_CHO (total carbohydrates, peaks region and baseline: ca. 1187–950 cm−1), A_928 (non-structural carbohydrates, peak area centered at ca. 928 cm−1 with region and baseline: ca. 952–910 cm−1), A_860 (non-structural carbohydrates, peak area centered at ca. 860 cm−1 with region and baseline: ca. 880–827 cm−1), H_1415 (structural carbohydrate, peak height centered at ca. 1415 cm−1 with baseline: ca. 1485–1188 cm−1), H_1370 (structural carbohydrate, peak height at ca. 1370 cm−1 with a baseline: ca. 1485–1188 cm−1). The study shows that the grains had lower spectral intensity (KM Unit) of the cellulosic compounds of A_1240 (8.5 vs. 36.6, P < 0.05), higher (P < 0.05) intensities of the non-structural carbohydrate of A_928 (17.3 vs. 2.0) and A_860 (20.7 vs. 7.6) than their co-products from bioethanol processing. There were no differences (P > 0.05) in the peak area intensities of A_Cell (structural CHO) at 1292–1198 cm−1 and A_CHO (total CHO) at 1187–950 cm−1 with average molecular infrared intensity KM unit of 226.8 and 508.1, respectively. There were no differences (P > 0.05) in the peak height intensities of H_1415 and H_1370 (structural CHOs) with average intensities 1.35 and 1.15, respectively. The multivariate molecular spectral analyses were able to discriminate and classify between the corn and corn DDGS molecular spectra, but not wheat and wheat DDGS. This study indicated that the bioethanol processing changes carbohydrate molecular structural profiles, compared with the original grains. However, the sensitivities of different types of carbohydrates and different grains (corn and wheat) to the processing differ. In general, the bioethanol processing increases the molecular spectral intensities for the structural carbohydrates and decreases the intensities for the non-structural carbohydrates. Further study is needed to quantify carbohydrate related molecular spectral features of the bioethanol co-products in relation to nutrient supply and availability of carbohydrates. PMID:21673931

Rich magneto-absorption spectra of AAB-stacked trilayer graphene.

PubMed

Do, Thi-Nga; Shih, Po-Hsin; Chang, Cheng-Peng; Lin, Chiun-Yan; Lin, Ming-Fa

2016-06-29

A generalized tight-binding model is developed to investigate the feature-rich magneto-optical properties of AAB-stacked trilayer graphene. Three intragroup and six intergroup inter-Landau-level (inter-LL) optical excitations largely enrich magneto-absorption peaks. In general, the former are much higher than the latter, depending on the phases and amplitudes of LL wavefunctions. The absorption spectra exhibit single- or twin-peak structures which are determined by quantum modes, LL energy spectra and Fermion distribution. The splitting LLs, with different localization centers (2/6 and 4/6 positions in a unit cell), can generate very distinct absorption spectra. There exist extra single peaks because of LL anti-crossings. AAB, AAA, ABA, and ABC stackings considerably differ from one another in terms of the inter-LL category, frequency, intensity, and structure of absorption peaks. The main characteristics of LL wavefunctions and energy spectra and the Fermi-Dirac function are responsible for the configuration-enriched magneto-optical spectra.

Comparative NEXAFS study of the selected icefish hard tissues and hydroxyapatite

NASA Astrophysics Data System (ADS)

Petrova, O. V.; Nekipelov, S. V.; Sivkov, D. V.; Mingaleva, A. E.; Nikolaev, A.; Frank-Kamenetskaya, O. V.; Bazhenov, V. V.; Vyalikh, D. V.; Molodtsov, S. L.; Sivkov, V. N.; Ehrlich, H.

2017-11-01

The structure of native Champsocephalus gunnari icefish otoliths, scales, teeth, bones and pristine hydroxyapatite (HA) were examined using Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy. NEXAFS Cls-absorption spectra of the selected icefish hard tissues indicate that otoliths contain anion [CO3]2-. NEXAFS P2p-spectra clearly indicate the absence of phosphorus atoms only within otoliths and scales samples. However, the icefish teeth and bones P2p-spectra demonstrate identical spectral feature typical for the HA. NEXAFS Ca2p-spectra of the icefish hard tissues studied also shows features, which are in good correspondence with HA spectra. Interestingly, there is a red shift ≈ 0.1 eV of the 2p1/2,3/2 → 3d transition energies in NEXAFS Ca2p-spectra of teethes and bones of the C. gunnari in comparison to HA.

Trident: A Universal Tool for Generating Synthetic Absorption Spectra from Astrophysical Simulations

NASA Astrophysics Data System (ADS)

Hummels, Cameron B.; Smith, Britton D.; Silvia, Devin W.

2017-09-01

Hydrodynamical simulations are increasingly able to accurately model physical systems on stellar, galactic, and cosmological scales; however, the utility of these simulations is often limited by our ability to directly compare them with the data sets produced by observers: spectra, photometry, etc. To address this problem, we have created trident, a Python-based open-source tool for post-processing hydrodynamical simulations to produce synthetic absorption spectra and related data. trident can (I) create absorption-line spectra for any trajectory through a simulated data set mimicking both background quasar and down-the-barrel configurations; (II) reproduce the spectral characteristics of common instruments like the Cosmic Origins Spectrograph; (III) operate across the ultraviolet, optical, and infrared using customizable absorption-line lists; (IV) trace simulated physical structures directly to spectral features; (v) approximate the presence of ion species absent from the simulation outputs; (VI) generate column density maps for any ion; and (vii) provide support for all major astrophysical hydrodynamical codes. trident was originally developed to aid in the interpretation of observations of the circumgalactic medium and intergalactic medium, but it remains a general tool applicable in other contexts.

Thermal infrared spectroscopy and modeling of experimentally shocked basalts

USGS Publications Warehouse

Johnson, J. R.; Staid, M.I.; Kraft, M.D.

2007-01-01

New measurements of thermal infrared emission spectra (250-1400 cm-1; ???7-40 ??m) of experimentally shocked basalt and basaltic andesite (17-56 GPa) exhibit changes in spectral features with increasing pressure consistent with changes in the structure of plagioclase feldspars. Major spectral absorptions in unshocked rocks between 350-700 cm-1 (due to Si-O-Si octahedral bending vibrations) and between 1000-1250 cm-1 (due to Si-O antisymmetric stretch motions of the silica tetrahedra) transform at pressures >20-25 GPa to two broad spectral features centered near 950-1050 and 400-450 cm-1. Linear deconvolution models using spectral libraries composed of common mineral and glass spectra replicate the spectra of shocked basalt relatively well up to shock pressures of 20-25 GPa, above which model errors increase substantially, coincident with the onset of diaplectic glass formation in plagioclase. Inclusion of shocked feldspar spectra in the libraries improves fits for more highly shocked basalt. However, deconvolution models of the basaltic andesite select shocked feldspar end-members even for unshocked samples, likely caused by the higher primary glass content in the basaltic andesite sample.

Experimental and time-dependent density functional theory characterization of the UV-visible spectra of monomeric and μ-oxo dimeric ferriprotoporphyrin IX.

PubMed

Kuter, David; Venter, Gerhard A; Naidoo, Kevin J; Egan, Timothy J

2012-10-01

Speciation of ferriprotoporphyrin IX, Fe(III)PPIX, in aqueous solution is complex. Despite the use of its characteristic spectroscopic features for identification, the theoretical basis of the unique UV-visible absorbance spectrum of μ-[Fe(III)PPIX](2)O has not been explored. To investigate this and to establish a structural and spectroscopic model for Fe(III)PPIX species, density functional theory (DFT) calculations were undertaken for H(2)O-Fe(III)PPIX and μ-[Fe(III)PPIX](2)O. The models agreed with related Fe(III)porphyrin crystal structures and reproduced vibrational spectra well. The UV-visible absorbance spectra of H(2)O-Fe(III)PPIX and μ-[Fe(III)PPIX](2)O were calculated using time-dependent DFT and reproduced major features of the experimental spectra of both. Transitions contributing to calculated excitations have been identified. The features of the electronic spectrum calculated for μ-[Fe(III)PPIX](2)O were attributed to delocalization of electron density between the two porphyrin rings of the dimer, the weaker ligand field of the axial ligand, and antiferromagnetic coupling of the Fe(III) centers. Room temperature magnetic circular dichroism (MCD) spectra have been recorded and are shown to be useful in distinguishing between these two Fe(III)PPIX species. Bands underlying major spectroscopic features were identified through simultaneous deconvolution of UV-visible and MCD spectra. Computed UV-visible spectra were compared to deconvoluted spectra. Interpretation of the prominent bands of H(2)O-Fe(III)PPIX largely conforms to previous literature. Owing to the weak paramagnetism of μ-[Fe(III)PPIX](2)O at room temperature and the larger number of underlying excitations, interpretation of its experimental UV-visible spectrum was necessarily tentative. Nonetheless, comparison with the calculated spectra of antiferromagnetically coupled and paramagnetic forms of the μ-oxo dimer of Fe(III)porphine suggested that the composition of the Soret band involves a mixture of π→π* and π→d(π) charge transfer transitions. The Q-band and charge transfer bands appear to amalgamate into a mixed low energy envelope consisting of excitations with heavily admixed π→π* and charge transfer transitions.

NMR Relaxometry to Characterize the Drug Structural Phase in a Porous Construct.

PubMed

Thrane, Linn W; Berglund, Emily A; Wilking, James N; Vodak, David; Seymour, Joseph D

2018-06-14

Nuclear magnetic resonance (NMR) frequency spectra and T 2 relaxation time measurements, using a high-power radio frequency probe, are shown to characterize the presence of an amorphous drug in a porous silica construct. The results indicate the ability of non-solid-state NMR methods to characterize crystalline and amorphous solid structural phases in drugs. Two-dimensional T 1 - T 2 magnetic relaxation time correlation experiments are shown to monitor the impact of relative humidity on the drug in a porous silica tablet.

Vibrational-Rotational Spectroscopy For Planetary Atmospheres, volume 1

NASA Technical Reports Server (NTRS)

Mumma, M. J. (Editor); Fox, K. (Editor); Hornstein, J. (Editor)

1982-01-01

Comprehensive information on the composition and dynamics of the varied planetary atmospheres is summarized. New observations resulted in new demands for supporting laboratory studies. Spectra observed from spacecraft used to interpret planetary atmospheric structure measurements, to aid in greenhouse and cloud physics calculations, and to plan future experiments are discussed. Current findings and new ideas of physicists, chemists, and planetry astronomers relating to the knowledge of the structure of things large and small, of planets and of molecules are summarized.

Mechanical impedance and acoustic mobility measurement techniques of specifying vibration environments

NASA Technical Reports Server (NTRS)

Kao, G. C.

1973-01-01

Method has been developed for predicting interaction between components and corresponding support structures subjected to acoustic excitations. Force environments determined in spectral form are called force spectra. Force-spectra equation is determined based on one-dimensional structural impedance model.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kopaczek, J.; Polak, M. P.; Scharoch, P.

Modulated reflectance (contactless electroreflectance (CER), photoreflectance (PR), and piezoreflectance (PzR)) has been applied to study direct optical transitions in bulk MoS{sub 2}, MoSe{sub 2}, WS{sub 2}, and WSe{sub 2}. In order to interpret optical transitions observed in CER, PR, and PzR spectra, the electronic band structure for the four crystals has been calculated from the first principles within the density functional theory for various points of Brillouin zone including K and H points. It is clearly shown that the electronic band structure at H point of Brillouin zone is very symmetric and similar to the electronic band structure at Kmore » point, and therefore, direct optical transitions at H point should be expected in modulated reflectance spectra besides the direct optical transitions at the K point of Brillouin zone. This prediction is confirmed by experimental studies of the electronic band structure of MoS{sub 2}, MoSe{sub 2}, WS{sub 2}, and WSe{sub 2} crystals by CER, PR, and PzR spectroscopy, i.e., techniques which are very sensitive to critical points of Brillouin zone. For the four crystals besides the A transition at K point, an A{sub H} transition at H point has been observed in CER, PR, and PzR spectra a few tens of meV above the A transition. The spectral difference between A and A{sub H} transition has been found to be in a very good agreement with theoretical predictions. The second transition at the H point of Brillouin zone (B{sub H} transition) overlaps spectrally with the B transition at K point because of small energy differences in the valence (conduction) band positions at H and K points. Therefore, an extra resonance which could be related to the B{sub H} transition is not resolved in modulated reflectance spectra at room temperature for the four crystals.« less

Direct optical transitions at K- and H-point of Brillouin zone in bulk MoS2, MoSe2, WS2, and WSe2

NASA Astrophysics Data System (ADS)

Kopaczek, J.; Polak, M. P.; Scharoch, P.; Wu, K.; Chen, B.; Tongay, S.; Kudrawiec, R.

2016-06-01

Modulated reflectance (contactless electroreflectance (CER), photoreflectance (PR), and piezoreflectance (PzR)) has been applied to study direct optical transitions in bulk MoS2, MoSe2, WS2, and WSe2. In order to interpret optical transitions observed in CER, PR, and PzR spectra, the electronic band structure for the four crystals has been calculated from the first principles within the density functional theory for various points of Brillouin zone including K and H points. It is clearly shown that the electronic band structure at H point of Brillouin zone is very symmetric and similar to the electronic band structure at K point, and therefore, direct optical transitions at H point should be expected in modulated reflectance spectra besides the direct optical transitions at the K point of Brillouin zone. This prediction is confirmed by experimental studies of the electronic band structure of MoS2, MoSe2, WS2, and WSe2 crystals by CER, PR, and PzR spectroscopy, i.e., techniques which are very sensitive to critical points of Brillouin zone. For the four crystals besides the A transition at K point, an AH transition at H point has been observed in CER, PR, and PzR spectra a few tens of meV above the A transition. The spectral difference between A and AH transition has been found to be in a very good agreement with theoretical predictions. The second transition at the H point of Brillouin zone (BH transition) overlaps spectrally with the B transition at K point because of small energy differences in the valence (conduction) band positions at H and K points. Therefore, an extra resonance which could be related to the BH transition is not resolved in modulated reflectance spectra at room temperature for the four crystals.

The structure of oleamide films at the aluminum/oil interface and aluminum/air interface studied by Sum Frequency Generation (SFG) vibrational spectroscopy and Reflection Absorption Infrared Spectroscopy (RAIRS).

PubMed

Casford, Michael T L; Davies, Paul B

2009-08-01

The structure of oleamide (cis-9-octadecenamide) films on aluminum has been investigated by sum frequency generation vibrational spectroscopy (SFG) and reflection absorption infrared spectroscopy (RAIRS). Three different film deposition strategies were investigated: (i) films formed by equilibrium adsorption from oleamide solutions in oil, (ii) Langmuir-Blodgett films cast at 1 and 25 mN m(-1), (iii) thick spin-cast films. Both L-B and spin-cast films were examined in air and under oil. The adsorbate formed in the 1 mN m(-1) film in air showed little orientational order. For this film, the spectroscopic results and the ellipsometric thickness point to a relatively conformationally disordered monolayer that is oriented principally in the plane of the interface. Direct adsorption to the metal interface from oil results in SFG spectra of oleamide that are comparable to those observed for the 1 mN m(-1) L-B film in air. In contrast, SFG and RAIRS results for the 25 mN m(-1) film in air and SFG spectra of the spin-cast film in air both show strong conformational ordering and orientational alignment normal to the interface. The 25 mN m(-1) film has an ellipsometric thickness almost twice that of the 1 mN m(-1) L-B film. Taken in combination with the spectroscopic results, this is indicative of a well packed monolayer in air in which the hydrocarbon chain is in an essentially defect-free extended conformation with the methyl terminus oriented away from the surface. A similar structure is also deduced for the surface of the spin-cast film in air. Upon immersion of the 25 mN m(-1) L-B film in oil the SFG spectra show that this film rapidly adopts a relatively disordered structure similar to that seen for the 1 mN m(-1) L-B film in air. Immersion of the spin-cast film in oil results in the gradual disordering of the amide film over a period of several days until the observed spectra become essentially identical to those observed for direct adsorption of oleamide from oil.

Infrared absorption of methanol-water clusters (CH3OH)n(H2O), n = 1-4, recorded with the VUV-ionization/IR-depletion technique

NASA Astrophysics Data System (ADS)

Lee, Yu-Fang; Kelterer, Anne-Marie; Matisz, Gergely; Kunsági-Máté, Sándor; Chung, Chao-Yu; Lee, Yuan-Pern

2017-04-01

We recorded infrared (IR) spectra in the CH- and OH-stretching regions of size-selected clusters of methanol (M) with one water molecule (W), represented as MnW, n = 1-4, in a pulsed supersonic jet using the photoionization/IR-depletion technique. Vacuum ultraviolet emission at 118 nm served as the source of ionization in a time-of-flight mass spectrometer to detect clusters MnW as protonated forms Mn-1WH+. The variations in intensities of Mn-1WH+ were monitored as the wavelength of the IR laser light was tuned across the range 2700-3800 cm-1. IR spectra of size-selected clusters were obtained on processing of the observed action spectra of the related cluster-ions according to a mechanism that takes into account the production and loss of each cluster due to IR photodissociation. Spectra of methanol-water clusters in the OH region show significant variations as the number of methanol molecules increases, whereas those in the CH region are similar for all clusters. Scaled harmonic vibrational wavenumbers and relative IR intensities predicted with the M06-2X/aug-cc-pVTZ method for the methanol-water clusters are consistent with our experimental results. For dimers, absorption bands of a structure WM with H2O as a hydrogen-bond donor were observed at 3570, 3682, and 3722 cm-1, whereas weak bands of MW with methanol as a hydrogen-bond donor were observed at 3611 and 3753 cm-1. For M2W, the free OH band of H2O was observed at 3721 cm-1, whereas a broad feature was deconvoluted to three bands near 3425, 3472, and 3536 cm-1, corresponding to the three hydrogen-bonded OH-stretching modes in a cyclic structure. For M3W, the free OH shifted to 3715 cm-1, and the hydrogen-bonded OH-stretching bands became much broader, with a weak feature near 3179 cm-1 corresponding to the symmetric OH-stretching mode of a cyclic structure. For M4W, the observed spectrum agrees unsatisfactorily with predictions for the most stable cyclic structure, indicating significant contributions from branched isomers, which is distinctly different from M5 of which the cyclic form dominates.

Infrared absorption of methanol-water clusters (CH3OH)n(H2O), n = 1-4, recorded with the VUV-ionization/IR-depletion technique.

PubMed

Lee, Yu-Fang; Kelterer, Anne-Marie; Matisz, Gergely; Kunsági-Máté, Sándor; Chung, Chao-Yu; Lee, Yuan-Pern

2017-04-14

We recorded infrared (IR) spectra in the CH- and OH-stretching regions of size-selected clusters of methanol (M) with one water molecule (W), represented as M n W, n = 1-4, in a pulsed supersonic jet using the photoionization/IR-depletion technique. Vacuum ultraviolet emission at 118 nm served as the source of ionization in a time-of-flight mass spectrometer to detect clusters M n W as protonated forms M n-1 WH + . The variations in intensities of M n-1 WH + were monitored as the wavelength of the IR laser light was tuned across the range 2700-3800 cm -1 . IR spectra of size-selected clusters were obtained on processing of the observed action spectra of the related cluster-ions according to a mechanism that takes into account the production and loss of each cluster due to IR photodissociation. Spectra of methanol-water clusters in the OH region show significant variations as the number of methanol molecules increases, whereas those in the CH region are similar for all clusters. Scaled harmonic vibrational wavenumbers and relative IR intensities predicted with the M06-2X/aug-cc-pVTZ method for the methanol-water clusters are consistent with our experimental results. For dimers, absorption bands of a structure WM with H 2 O as a hydrogen-bond donor were observed at 3570, 3682, and 3722 cm -1 , whereas weak bands of MW with methanol as a hydrogen-bond donor were observed at 3611 and 3753 cm -1 . For M 2 W, the free OH band of H 2 O was observed at 3721 cm -1 , whereas a broad feature was deconvoluted to three bands near 3425, 3472, and 3536 cm -1 , corresponding to the three hydrogen-bonded OH-stretching modes in a cyclic structure. For M 3 W, the free OH shifted to 3715 cm -1 , and the hydrogen-bonded OH-stretching bands became much broader, with a weak feature near 3179 cm -1 corresponding to the symmetric OH-stretching mode of a cyclic structure. For M 4 W, the observed spectrum agrees unsatisfactorily with predictions for the most stable cyclic structure, indicating significant contributions from branched isomers, which is distinctly different from M 5 of which the cyclic form dominates.

Impurity-induced photoconductivity of narrow-gap Cadmium–Mercury–Telluride structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kozlov, D. V., E-mail: dvkoz@impras.ru; Rumyantsev, V. V.; Morozov, S. V.

2015-12-15

The photoconductivity (PC) spectra of CdHgTe (MCT) solid solutions with a Cd fraction of 17 and 19% are measured. A simple model for calculating the states of doubly charged acceptors in MCT solid solutions, which makes it possible to describe satisfactorily the observed photoconductivity spectra, is proposed. The found lines in the photoconductivity spectra of narrow-gap MCT structures are associated with transitions between the states of both charged and neutral acceptor centers.

INTERFERENCE AS AN ORIGIN OF THE PEAKED NOISE IN ACCRETING X-RAY BINARIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Veledina, Alexandra, E-mail: alexandra.veledina@gmail.com

2016-12-01

We propose a physical model for the peaked noise in the X-ray power density spectra of accreting X-ray binaries. We interpret its appearance as an interference of two Comptonization continua: one coming from the upscattering of seed photons from the cold thin disk and the other fed by the synchrotron emission of the hot flow. Variations of both X-ray components are caused by fluctuations in mass accretion rate, but there is a delay between them corresponding to the propagation timescale from the disk Comptonization radius to the region of synchrotron Comptonization. If the disk and synchrotron Comptonization are correlated, themore » humps in the power spectra are harmonically related and the dips between them appear at frequencies related as odd numbers 1:3:5. If they are anti-correlated, the humps are related as 1:3:5, but the dips are harmonically related. Similar structures are expected to be observed in accreting neutron star binaries and supermassive black holes. The delay can be easily recovered from the frequency of peaked noise and further used to constrain the combination of the viscosity parameter and disk height-to-radius ratio α ( H / R ){sup 2} of the accretion flow. We model multi-peak power spectra of black hole X-ray binaries GX 339–4 and XTE J1748–288 to constrain these parameters.« less

Synthesis, NMR, FT-IR, X-ray structural characterization, DFT analysis and isomerism aspects of 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione.

PubMed

Barakat, Assem; Al-Najjar, Hany J; Al-Majid, Abdullah Mohammed; Soliman, Saied M; Mabkhot, Yahia Nasser; Shaik, Mohammed Rafi; Ghabbour, Hazem A; Fun, Hoong-Kun

2015-08-05

The synthesis and spectral characterization of the 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione;3 was reported. The solid state molecular structure of 3 was studied using X-ray crystallography. The relative stabilities of the seven possible isomers of 3 were calculated by DFT/B3LYP method using 6-311 G(d,p) basis set. The calculated total energies and thermodynamic parameters were used to predict the relative stabilities of these isomers. The effect of solvent polarity on the relative stability of these isomers was studied at the same level of theory using PCM. It was found that the keto form, (T0), is the most stable isomer both in the gaseous state and solution. In solution, the calculated total energies of all isomers are decreased indicating that all isomers are stabilized by the solvent effect. The vibrational spectra of the most stable isomer, 3(T0) are calculated using the same level of theory and the results are compared with the experimentally measured FTIR spectra. Good correlation was obtained between the experimental and calculated vibrational frequencies (R(2)=0.9992). The electronic spectra of 3(T0) in gas phase as well as in solutions were calculated using the TD-DFT method. All the predicted electronic transitions showed very little spectral shifts and increase in the intensity of absorption due to solvent effect. Also the (1)H- and (13)C-NMR chemical shifts of the stable isomer were calculated and the results were correlated with the experimental data. Good correlations between the experimental and calculated chemical shifts were obtained. Copyright © 2015 Elsevier B.V. All rights reserved.

The molecular, electronic structures and vibrational spectra of metal-free, N,N'-dideuterio and magnesium tetra-2,3-pyridino-porphyrazines: Density functional calculations.

PubMed

Liu, Zhongqiang; Zhang, Xianxi; Zhang, Yuexing; Li, Renjie; Jiang, Jianzhuang

2006-10-01

A theoretical investigation of the fully optimized geometries and electronic structures of the metal-free (TPdPzH(2)), N,N'-dideuterio (TPdPzD(2)), and magnesium (TPdPzMg) tetra-2,3-pyridino-porphyrazine has been conducted based on density functional theory. The optimized geometries at density functional theory level for these compounds are reported here for the first time. A comparison between the different molecules for the geometry, molecular orbital, and atomic charge is made. The substituent effect of the N atoms on the molecular structures of these compounds is discussed. The IR and Raman spectra for these three compounds have also been calculated at density functional B3LYP level using the 6-31G(d) basis set. Detailed assignments of the NH, NM, and pyridine ring vibrational bands in the IR and Raman spectra have been made based on assistance of animated pictures. The simulated IR spectra of TPdPzH(2) are compared with the experimental absorption spectra, and very good consistency has been found. The isotope effect on the IR and Raman spectra is also discussed.

Anisotropy of atomic bonds formed by p-type dopants in bulk GaN crystals

NASA Astrophysics Data System (ADS)

Lawniczak-Jablonska, K.; Suski, T.; Gorczyca, I.; Christensen, N. E.; Libera, J.; Kachniarz, J.; Lagarde, P.; Cortes, R.; Grzegory, I.

The anisotropy of atomic bonds formed by acceptor dopants with nitrogen in bulk wurtzite GaN crystals was studied by means of linearly polarized synchrotron radiation used in measurements of X-ray-absorption spectra for the K-edgeof Mg and Zn dopants. These spectra correspond to i) a single acceptor N bond along the c-axis and ii) three bonds realized with N atoms occupying the ab-plane perpendicular to the c-axis. The Zn dopant formed resonant spectra similar to that characteristic for Ga cations. In the case of the Mg dopant, similarity to Ga cations was observed for triple bonds in the ab-plane, only. Practically no resonant structure for spectra detected along the c-axis was observed. The absorption spectra were compared with ab initio calculations using the full-potential linear muffin-tin-orbital method. These calculations were also used for determination of the bond length for Mg-N and Zn-N in wurtzite GaN crystals and show that introducing dopants causes an increase of the lengths of the bonds formed by both dopants. Extended X-ray-absorption fine-structure measurements performed for bulk GaN:Zn confirmed the prediction of the theory in the case of the Zn-N bond. Finally, it is suggested that the anisotropy in the length of the Mg-N bonds, related to their larger strength in the case of bonds in the ab-plane, can explain preferential formation of a superlattice consisting of Mg-rich layers arranged in ab-planes of several bulk GaN:Mg crystals observed by transmission electron microscopy. Within the sensitivity of the method used, no parasitic metallic clusters or oxide compounds formed by the considered acceptors in GaN crystals were found.

Toward ab initio molecular dynamics modeling for sum-frequency generation spectra; an efficient algorithm based on surface-specific velocity-velocity correlation function.

PubMed

Ohto, Tatsuhiko; Usui, Kota; Hasegawa, Taisuke; Bonn, Mischa; Nagata, Yuki

2015-09-28

Interfacial water structures have been studied intensively by probing the O-H stretch mode of water molecules using sum-frequency generation (SFG) spectroscopy. This surface-specific technique is finding increasingly widespread use, and accordingly, computational approaches to calculate SFG spectra using molecular dynamics (MD) trajectories of interfacial water molecules have been developed and employed to correlate specific spectral signatures with distinct interfacial water structures. Such simulations typically require relatively long (several nanoseconds) MD trajectories to allow reliable calculation of the SFG response functions through the dipole moment-polarizability time correlation function. These long trajectories limit the use of computationally expensive MD techniques such as ab initio MD and centroid MD simulations. Here, we present an efficient algorithm determining the SFG response from the surface-specific velocity-velocity correlation function (ssVVCF). This ssVVCF formalism allows us to calculate SFG spectra using a MD trajectory of only ∼100 ps, resulting in the substantial reduction of the computational costs, by almost an order of magnitude. We demonstrate that the O-H stretch SFG spectra at the water-air interface calculated by using the ssVVCF formalism well reproduce those calculated by using the dipole moment-polarizability time correlation function. Furthermore, we applied this ssVVCF technique for computing the SFG spectra from the ab initio MD trajectories with various density functionals. We report that the SFG responses computed from both ab initio MD simulations and MD simulations with an ab initio based force field model do not show a positive feature in its imaginary component at 3100 cm(-1).

Ring distributions in alkali- and alkaline-earth aluminosilicate framework glasses- a raman spectroscopic study

USGS Publications Warehouse

Sharma, S.K.; Philpotts, J.A.; Matson, D.W.

1985-01-01

Raman spectra of crystalline polymorphs of a number of tectosilicate minerals having various sizes of smallest rings of TO4 tetrahedra (T = Si, Al) have been investigated to identify the bands that are sensitive indicators of the smallest rings in the network. The information obtained from the Raman spectra of tectosilicate minerals (e.g., SiO2 polymorphs, NaAlSi3O8 (Ab), NaAlSiO4 (Ne), KAlSi3O8 (Or), and KAlSi2O6 (Lc)) is used to interpret the Raman spectra of the isochemical glasses. It is shown that the frequency of the dominant ??s (TOT) band in the spectra of both crystals and glasses is related to the dominant size of TO4 rings in the structure. In agreement with previous X-ray RDF work, it is found that in the glasses of Ab and Jd (NaAlSi2O6) compositions, six-membered rings of TO4 tetrahedra predominate. The Raman spectrum of Or glass, however, indicates that clusters of intermixed four- and six-membered rings of TO4 tetrahedra, similar to those existing in crystalline leucite, are also present in the glass. Raman evidence indicates that four-membered rings of TO4 tetrahedra predominate in the glass of An composition. Similarly, the higher frequency of the ??s (TOT) band in the spectrum of Ne glass as compared with the frequency the ??s (TOT) band in the spectra of crystalline cargenieite and nephelite indicates either an admixture of the four- and six-membered rings or the puckering of six-membered rings in the glass structure. ?? 1985.

The Structure of Li7 and K7

NASA Technical Reports Server (NTRS)

Bauschlicher. Charles W., Jr.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The self-consistent-field (SCF) approach and density functional theory, using the B3LYP hybrid functional, yield three low-lying structures for Li7(-). The relative separations differ for the SCF and B3LYP approaches, however the B3LYP results are in good agreement with the coupled cluster results. For K7(-), only an octahedron with one face capped is found to be a minimum; this the second most stable structure for Li7(-). A comparison of the computed separations between the low-lying states of K7 and the photoelectron detachment spectra does not allow an unambiguous assignment of the structure of K7(-).

Electronic structure of rare-earth chromium antimonides RECrSb{sub 3} (RE=La-Nd, Sm, Gd-Dy, Yb) by X-ray photoelectron spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crerar, Shane J.; Mar, Arthur, E-mail: arthur.mar@ualberta.ca; Grosvenor, Andrew P.

The electronic structure of the ternary rare-earth chromium antimonides RECrSb{sub 3} (RE=La-Nd, Sm, Gd-Dy, Yb) has been examined by high-resolution X-ray photoelectron spectroscopy (XPS) for the first time. The RE 3d or 4d core-line spectra are substantially complicated by the presence of satellite peaks but their general resemblance to those of RE{sub 2}O{sub 3} tends to support the presence of trivalent RE atoms in RECrSb{sub 3}. However, the Yb 4d spectrum of YbCrSb{sub 3} also shows peaks that are characteristic of divalent ytterbium. The Cr 2p core-line spectra exhibit asymmetric lineshapes and little change in binding energy (BE) relative tomore » Cr metal, providing strong evidence for electronic delocalization. The Sb 3d core-line spectra reveal slightly negative BE shifts relative to elemental antimony, supporting the presence of anionic Sb species in RECrSb{sub 3}. The experimental valence band spectrum of LaCrSb{sub 3} matches well with the calculated density of states, and it can be fitted to component peaks belonging to individual atoms to yield an average formulation that agrees well with expectations ('La{sup 3+}Cr{sup 3+}(Sb{sup 2-}){sub 3}'). On progressing from LaCrSb{sub 3} to NdCrSb{sub 3}, the 4f-band in the valence band spectra grows in intensity and shifts to higher BE. The valence band spectrum for YbCrSb{sub 3} also supports the presence of divalent ytterbium. - Graphical Abstract: In their valence band spectra, the 4f-band intensifies and shifts to higher BE on progressing from LaCrSb{sub 3} to NdCrSb{sub 3}. Highlights: Black-Right-Pointing-Pointer High-resolution core-line and valence band XPS spectra were measured for RECrSb{sub 3}. Black-Right-Pointing-Pointer Divalent Yb is present in YbCrSb{sub 3}, in contrast to trivalent RE in other members. Black-Right-Pointing-Pointer Asymmetric Cr 2p spectral lineshape confirms delocalization of Cr valence electrons. Black-Right-Pointing-Pointer Small negative Sb 3d BE shifts support assignment of anionic Sb atoms. Black-Right-Pointing-Pointer Fitted valence band spectra show shifts in the 4f band as RE is changed.« less

Structural characterization of ZnCl2 modified tellurite based glasses

NASA Astrophysics Data System (ADS)

Dhankhar, Sunil; Kundu, R. S.; Punia, R.; Sunita, Parmar, R.; Sanjay, Kishore, N.

2016-05-01

Glass composition 70 TeO2-(30-x) BaO - x ZnCl2; x = 5, 10, 15, 20 and 25 have been prepared by rapid melt quenching technique under controlled atmospheric conditions. Amorphous nature of the samples was confirmed by x-ray diffractogram. The glass transition temperature (Tg) has been determined using differential scanning calorimetry (DSC) and its value is observed to decrease with increase in ZnCl2 content. The peaks in the Raman and FTIR spectra have been estimated by deconvolutation of the spectra and each of deconvoluted spectra exhibits several peaks. IR and Raman spectra of the present glass system indicate that TeO2 exists as TeO3 trigonal pyramidal (tp), TeO4 trigonal bipyramidal (tbp) and TeO6 polyhedra structural units. With increase in zinc halide content, transformation of some of TeO4 structural units into TeO3 structural units is observed Increase in TeO3 structural units shows that non-bridging oxygen contribution increases which confirms the decrease in glass transition temperature.

Simulated infrared spectra of triflic acid during proton dissociation.

PubMed

Laflamme, Patrick; Beaudoin, Alexandre; Chapaton, Thomas; Spino, Claude; Soldera, Armand

2012-05-05

Vibrational analysis of triflic acid (TfOH) at different water uptakes was conducted. This molecule mimics the sulfonate end of the Nafion side-chain. As the proton leaves the sulfonic acid group, structural changes within the Nafion side-chain take place. They are revealed by signal shifts in the infrared spectrum. Molecular modeling is used to follow structural modifications that occur during proton dissociation. To confirm the accuracy of the proposed structures, infrared spectra were computed via quantum chemical modeling based on density functional theory. The requirement to use additional diffuse functions in the basis set is discussed. Comparison between simulated infrared spectra of 1 and 2 acid molecules with different water contents and experimental data was performed. An accurate description of infrared spectra for systems containing 2 TfOH was obtained. Copyright © 2012 Wiley Periodicals, Inc.

Study of Nb2O(y) (y = 2-5) anion and neutral clusters using anion photoelectron spectroscopy and density functional theory calculations.

PubMed

Mann, Jennifer E; Waller, Sarah E; Rothgeb, David W; Jarrold, Caroline Chick

2011-09-14

A study combining anion photoelectron spectroscopy and density functional theory calculations on the transition metal suboxide series, Nb(2)O(y)(-) (y = 2-5), is described. Photoelectron spectra of the clusters are obtained, and Franck-Condon simulations using calculated anion and neutral structures and frequencies are used to evaluate the calculations and assign transitions observed in the spectra. The spectra, several of which exhibit partially resolved vibrational structure, show an increase in electron affinity with increasing cluster oxidation state. Hole-burning experiments suggest that the photoelectron spectra of both Nb(2)O(2)(-) and Nb(2)O(3)(-) have contributions from more than one structural isomer. Reasonable agreement between experiment and computational results is found among all oxides. © 2011 American Institute of Physics

Tautomerism and spectroscopic properties of the immunosuppressant azathioprine.

PubMed

Makhyoun, Mohamed A; Massoud, Raghdaa A; Soliman, Saied M

2013-10-01

The molecular structure and the relative stabilities of the four possible tautomers of the immunosuppressant azathioprine (AZA) are calculated by DFT/B3LYP method using different basis sets. The results of the energy analysis and thermodynamic treatment of the obtained data are used to predict the relative stabilities of the AZA tautomers. The effect of solvents such as DMSO and water on the stability of the AZA tautomers was studied using the polarized continuum method (PCM) at the same level of theory. The calculation predicted that, the total energies of all tautomers are decreased indicating that all tautomers are more or less stabilized by the solvent effect. The vibrational spectra of AZA are calculated using the same level of theory and the results are compared with the experimentally measured FTIR spectra. Good correlation is obtained between the experimental and calculated vibrational frequencies (R(2)=0.997). The electronic spectra of AZA in gas phase and in methanol as solvent are calculated using the TD-DFT method. The calculations predicted bathochromic shift in all the spectral bands in presence of solvent compared to the gas phase. Also the NMR spectra of all tautomers are calculated and the results are correlated with the experimental NMR chemical shifts where the most stable tautomer gives the best correlation coefficient (R(2)=0.996). Copyright © 2013 Elsevier B.V. All rights reserved.

Fine structure in RF spectra of lightning return stroke wave forms

NASA Technical Reports Server (NTRS)

Lanzerotti, L. J.; Thomson, D. J.; Maclennan, C. G.; Rinnert, K.; Krider, E. P.

1988-01-01

The power spectra of the wide-band (10 Hz to 100 kHz) magnetic-field signals for a number of lightning return strokes measured during a thunderstorm which occurred in Lindau in August, 1984 have been calculated. The RF magnetic field data are obtained with the engineering unit of the Galileo Jupiter Probe lightning experiment. Each return stroke data stream is passed through an adaptive filter designed to whiten its spectrum. The spectra of the magnetic field data definitely show fine structure, with two or three distinct peaks in the spectra of many of the waveforms. A peak at f of about 60-70 kHz is often seen in the power spectra of the waveform time segments preceding and following the rise-to-peak amplitude of the return stroke.

Influence of molecular electronic properties on the IR spectra of dimeric hydrogen bond systems: polarized spectra of 2-hydroxybenzothiazole and 2-mercaptobenzothiazole crystals

NASA Astrophysics Data System (ADS)

Flakus, Henryk T.; Miros, Artur; Jones, Peter G.

2002-01-01

We have studied the polarized IR spectra of the hydrogen-bonded molecular crystals of 2-hydroxybenzothiazole (HBT) and 2-mercaptobenzothiazole (MBT). The crystal structure of 2-hydroxybenzothiazole was determined by X-ray diffraction. The polarized spectra of the crystals were measured, in the frequency ranges of the νN-H and νN-D bands, at room temperature, and at 77 K. In both systems an extremely strong H/D isotopic effect in the spectra was observed, involving reduction of the well-developed νN-H band fine structure to a single prominent νN-D line only. The two νN-H bands were also shown to exhibit almost identical properties, band shapes, temperature and dichroic properties included. The spectra were quantitatively reconstituted, along with the strong isotopic effect, when calculated using the 'strong-coupling' theory, assuming the centrosymmetric dimers of HBT or MBT to be the structural units responsible for the crystalline spectral properties. The similarity of the spectra of the two crystalline systems was considered to be a result of longer-distance couplings between the proton vibrations in the dimers, via the aromatic ring electrons. When investigating the 'residual' νN-H band shapes for crystals isotopically diluted by deuterium, we observed some 'self-organization' effects in the spectra, indicating the energetically favored presence of two identical hydrogen isotopes in each hydrogen bond dimer.

[Study of alkaline lignin from Arundo donax linn based on FT Raman spectroscopy].

PubMed

You, Ting-ting; Ma, Jian-feng; Guo, Si-qin; Xu, Feng

2014-08-01

Arundo donax linn, as a perennial energy crop, has promising application prospect. In the present study, Fourier transform Raman (FT Raman) spectroscopy was applied to determine the structural information of materials, milled wood lignin (MWL), and alkaline lignins (AL, under different treated time) from A. donax stem nondestructively. The results indicated that, extractable compounds in A. donax had negative contribution to the Raman spectra without rising new Raman peaks. FT Raman spectrum of MWL indicated that MWL from A. donax was HGS type lignins. Compared with the spectra of MWL from wood materials, the peak at 1173 cm(-1) was much higher in intensity for the MWL from A. donax stem, which may be assigned to hydroxycinnamic acid by analyzing the standard. With respect to FT Raman spectra of ALs, the relatively highest intensity of 1173 cm(-1) was found in alkaline lignin (AL2), which was treated for 40 min by alkaline. Moreover, the peak of coniferaldehyde/sinapaldehyde (1630 cm(-1)) was lowest in intensity while the band attributed to coniferyl alcohol/sinapyl alcohol (1660 cm(-1)) was almost disappeared in AL2. It could be inferred that AL2 demonstrated a highest content of phenolic acid, which may improve its potential application, such as for antioxidant activity. Furthermore, the results obtained by FT Raman spectra were verified by two dimensional heteronuclear singlequantum coherence nuclear magnetic resonance analyses. Above all, FT Raman spectroscopy provided alternative safe, rapid, accurate, and nondestructive technology for lignin structure determination.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zarkevich, Nikolai A; Johnson, Duane D

Nitinol (NiTi), the most widely used shape-memory alloy, exhibits an austenite phase that has yet to be identified. The usually assumed austenitic structure is cubic B2, which has imaginary phonon modes, hence it is unstable. We suggest a stable austenitic structure that “on average” has B2 symmetry (observed by x-ray and neutron diffraction), but it exhibits finite atomic displacements from the ideal B2 sites. The proposed structure has a phonon spectrum that agrees with that from neutron scattering, has diffraction spectra in agreement with x-ray diffraction, and has an energy relative to the ground state that agrees with calorimetry data.

Semiclassical Origin of Superdeformed Shell Structure in the Spheroidal Cavity Model

NASA Astrophysics Data System (ADS)

Arita, K.; Sugita, A.; Matsuyanagi, K.

1998-12-01

Classical periodic orbits responsible for emergence of the superdeformed shell structures of single-particle motion in spheroidal cavities are identified and their relative contributions to the shell structures are evaluated. Both prolate and oblate superdeformations (axis ratio approximately 2:1) as well as prolate hyperdeformation (axis ratio approximately 3:1) are investigated. Fourier transforms of quantum spectra clearly show that three-dimensional periodic orbits born out of bifurcations of planar orbits in the equatorial plane become predominant at large prolate deformations, while butterfly-shaped planar orbits bifurcated from linear orbits along the minor axis are important at large oblate deformations.

Chemical composition and surfactant characteristics of marine foams investigated by means of UV-vis, FTIR and FTNIR spectroscopy.

PubMed

Mecozzi, Mauro; Pietroletti, Marco

2016-11-01

In this study, we collected the ultraviolet-visible (UV-vis), Fourier transform infrared (FTIR) and Fourier transform near-infrared (FTNIR) spectra of marine foams from different sites and foams produced by marine living organisms (i.e. algae and molluscs) to retrieve information about their molecular and structural composition. UV-vis spectra gave information concerning the lipid and pigment contents of foams. FTIR spectroscopy gave a more detailed qualitative information regarding carbohydrates, lipids and proteins in addition with information about the mineral contents of foams. FTNIR spectra confirmed the presence of carbohydrates, lipids and proteins in foams. Then, due to the higher content of structural information of FTIR spectroscopy with respect to FTNIR and UV-vis, we join the FTIR spectra of marine foams to those of humic substance from marine sediments and to the spectra of foams obtained by living organisms. We submitted this resulting FTIR spectral dataset to statistical multivariate methods to investigate specific aspects of foams such as structural similarity among foams and in addition, contributions from the organic matter of living organisms. Cluster analysis (CA) evidenced several cases (i.e. clusters) of marine foams having high structural similarity with foams from vegetal and animal samples and with humic substance extracted from sediments. These results suggested that all the living organisms of the marine environment can give contributions to the chemical composition of foams. Moreover, as CA also evidenced cases of structural differences within foam samples, we applied two-dimensional correlation analysis (2DCORR) to the FTIR spectra of marine foams to investigate the molecular characteristics which caused these structural differences. Asynchronous spectra of two-dimensional correlation analysis showed that the structural heterogeneity among foam samples depended reasonably on the presence and on the qualitative difference of electrostatic (hydrogen bonds) and nonpolar (van der Waals and π-π) interactions involving carbohydrate proteins and lipids present. The presence and relevance of these interactions agree with the supramolecular and surfactant characteristics of marine organic matter described in the scientific literature.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pease, J.H.

The three dimensional structures of several small peptides were determined using a combination of {sup 1}H nuclear magnetic resonance (NMR) and distance geometry calculations. These techniques were found to be particularly helpful for analyzing structural differences between related peptides since all of the peptides' {sup 1}H NMR spectra are very similar. The structures of peptides from two separate classes are presented. Peptides in the first class are related to apamin, an 18 amino acid peptide toxin from honey bee venom. The {sup 1}H NMR assignments and secondary structure determination of apamin were done previously. Quantitative NMR measurements and distance geometrymore » calculations were done to calculate apamin's three dimensional structure. Peptides in the second class are 48 amino acid toxins from the sea anemone Radianthus paumotensis. The {sup 1}H NMR assignments of toxin II were done previously. The {sup 1}H NMR assignments of toxin III and the distance geometry calculations for both peptides are presented.« less

Higher order moments, structure functions and spectral ratios in near- and far-wakes of a wind turbine array

NASA Astrophysics Data System (ADS)

Ali, Naseem; Aseyev, A.; McCraney, J.; Vuppuluri, V.; Abbass, O.; Al Jubaree, T.; Melius, M.; Cal, R. B.

2014-11-01

Hot-wire measurements obtained in a 3 × 3 wind turbine array boundary layer are utilized to analyze higher order statistics which include skewness, kurtosis as well as the ratios of structure functions and spectra. The ratios consist of wall-normal to streamwise components for both quantities. The aim is to understand the degree of anisotropy in the flow for the near- and far-wakes of the flow field where profiles at one diameter and five diameters are considered, respectively. The skewness at top tip for both wakes show a negative skewness while below the turbine canopy, this terms are positive. The kurtosis shows a Gaussian behavior in the near-wake immediately at hub-height. In addition, the effect due to the passage of the rotor in tandem with the shear layer at the top tip renders relatively high differences in the fourth order moment. The second order structure function and spectral ratios are found to exhibit anisotropic behavior at the top and bottom-tips for the large scales. Mixed structure functions and co-spectra are also considered in the context of isotropy.

Molecular Eigensolution Symmetry Analysis and Fine Structure

PubMed Central

Harter, William G.; Mitchell, Justin C.

2013-01-01

Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES). Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES) used in Born–Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v), then applied to families of Oh clusters in SF6 spectra and to extreme clusters. PMID:23344041

Metal isotope and density functional study of the tetracarboxylatodicopper(II) core vibrations

NASA Astrophysics Data System (ADS)

Drożdżewski, Piotr; Brożyna, Anna

2005-11-01

Vibrational spectra of tetrakis(acetato)diaquadicopper(II) complex have been deeply examined in order to provide a detailed description of dynamics of [Cu 2O 8C 4] core being a typical structural unit of most copper(II) carboxylates. Low frequency bands related to significant motions of metal atoms were detected by metal isotope substitution. Observed spectra and isotope shifts were reproduced in DFT calculations. For clear presentation of computed normal vibrations, a D 4h symmetry approximation was successfully applied. Basing on observed isotope shifts and calculation results, all skeletal vibrations have been analyzed including normal mode with the largest Cu ⋯Cu stretching amplitude assigned to Raman band at 178 cm -1.

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

PubMed

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

2015-07-28

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

Calculation of density of states of transition metals: From bulk sample to nanocluster

NASA Astrophysics Data System (ADS)

Krasavin, Andrey V.; Borisyuk, Petr V.; Vasiliev, Oleg S.; Zhumagulov, Yaroslav V.; Kashurnikov, Vladimir A.; Kurelchuk, Uliana N.; Lebedinskii, Yuriy Yu.

2018-03-01

A technique is presented of restoring the electronic density of states of the valence band from data of X-ray photoelectron spectroscopy (XPS). The originality of the technique consists in using a stochastic procedure to solve an integral equation relating the density of states and the experimental X-ray photoelectron spectra via the broadening function. To obtain the broadening function, only the XPS spectra of the core levels are needed. The results are presented for bulk sample of gold and tungsten and nanoclusters of tantalum; the possibility of using the results to determine the density of states of low-dimensional structures, including ensembles of metal nanoclusters, is demonstrated.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Albert, Julian; Falge, Mirjam; Hildenbrand, Heiko

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.

[IR study on a series of tungsten clusters].

PubMed

Yu, R; Chen, J; Lu, S

2000-10-01

In this paper, the IR study on a series of tungsten clusters which contain a [W2S4]2+ or [W2MM'S4]4+ (M,M'=Cu,Ag) core is reported. According to the results of X-ray structural analysis and the IR spectra of the clusters, some characteristic IR absorptions of the clusters were assigned. The study of IR spectra of these clusters shows that the variation of structure can reflect on the IR spectra significantly.

The vibrational spectra and structures of dimethyl oxaloacetate and dimethyl oxaloacetate- d2

NASA Astrophysics Data System (ADS)

Schiering, David W.; Katon, J. E.

The complete vibrational spectra of dimethyl oxaloacetate and dimethyl oxaloacetate- d2 have been recorded and analyzed. The i.r. spectra were recorded at liquid N 2 as well as ambient temperature. Tentative vibrational assignments are proposed based on an enol structure in the crystalline phase. In solution, dimethyl oxaloacetate exists as a tautomeric mixture of keto and enol forms. Evidence for the existence of different enol conformers in CCl 4 and CS 2 solutions is also presented.

Two-dimensional NMR spectroscopy links structural moieties of soil organic matter to the temperature sensitivity of its decomposition

NASA Astrophysics Data System (ADS)

Soucemarianadin, Laure; Erhagen, Björn; Öquist, Mats; Nilsson, Mats; Schleucher, Jürgen

2015-04-01

Soil organic matter (SOM) represents a huge carbon pool, specifically in boreal ecosystems. Warming-induced release of large amounts of CO2 from the soil carbon pool might become a significant exacerbating feedback to global warming, if decomposition rates of boreal soils were more sensitive to increased temperatures. Despite a large number of studies dedicated to the topic, it has proven difficult to elucidate how the organo-chemical composition of SOM influences its decomposition, or its quality as a substrate for microbial metabolism. A great part of this challenge results from our inability to achieve a detailed characterization of the complex composition of SOM on the level of molecular structural moieties. 13C nuclear magnetic resonance (NMR) spectroscopy is a common tool to characterize SOM. However, SOM is a very complex mixture and the chemical shift regions distinguished in the 13C NMR spectra often represent many different molecular fragments. For example, in the carbohydrates region, signals of all monosaccharides present in many different polymers overlap. This overlap thwarts attempts to identify molecular moieties, resulting in insufficient information to characterize SOM composition. We applied two-dimensional (2D) NMR to characterize SOM with highly increased resolution. We directly dissolved finely ground litters and forest floors'fibric and humic horizons'of both coniferous and deciduous boreal forests in dimethyl sulfoxide and analyzed the resulting solution with a 2D 1H-13C NMR experiment. In the 2D planes of these spectra, signals of CH groups can be resolved based on their 13C and 1H chemical shifts, hence the resolving power and information content of these NMR spectra is hugely increased. The 2D spectra indeed resolved overlaps observed in 1D 13C spectra, so that hundreds of distinct CH groups could be observed and many molecular fragments could be identified. For instance, in the aromatics region, signals from individual lignin units could be recognized. It was hence possible to follow the fate of specific structural moieties in soils. We observed differences between litter and soil samples, and were able to relate them to the decomposition of identifiable moieties. Using multivariate data analysis, we aimed at linking the detailed chemical fingerprints of SOM to turnover rates in a soil incubation experiment. With the multivariate models, we were able to relate signal patterns in the 2D spectra and intensities of identifiable molecular moieties to variability in the temperature response of organic matter decomposition, as assessed by Q10. In conclusion, the characterization of SOM composition at the molecular level by solution-state 2D NMR spectroscopy is highly promising; it offers unprecedented possibilities to link SOM molecular composition to ecosystem processes, and their responses to environmental changes.

Thermal analysis and vibrational spectroscopic characterization of the boro silicate mineral datolite - CaBSiO4(OH)

NASA Astrophysics Data System (ADS)

Frost, Ray L.; Xi, Yunfei; Scholz, Ricardo; Lima, Rosa Malena Fernandes; Horta, Laura Frota Campos; Lopez, Andres

2013-11-01

The objective of this work is to determine the thermal stability and vibrational spectra of datolite CaBSiO4(OH) and relate these properties to the structure of the mineral. The thermal analysis of datolite shows a mass loss of 5.83% over a 700-775 °C temperature range. This mass loss corresponds to 1 water (H2O) molecules pfu. A quantitative chemical analysis using electron probe was undertaken. The Raman spectrum of datolite is characterized by bands at 917 and 1077 cm-1 assigned to the symmetric stretching modes of BO and SiO tetrahedra. A very intense Raman band is observed at 3498 cm-1 assigned to the stretching vibration of the OH units in the structure of datolite. BOH out-of-plane vibrations are characterized by the infrared band at 782 cm-1. The vibrational spectra are based upon the structure of datolite based on sheets of four- and eight-membered rings of alternating SiO4 and BO3(OH) tetrahedra with the sheets bonded together by calcium atoms.

Intramolecular structural model for photoinduced plasticity in chalcogenide glasses

NASA Astrophysics Data System (ADS)

Yannopoulos, S. N.

2003-08-01

Selected spectral features of Raman spectra of glassy As2S3 subjected to elongation stress and sub-band-gap light illumination are analyzed and compared with polarization-dependent information obtained from the bulk glass at room temperature and near the glass transition temperature. The data are suggestive of specific structural changes which involve the transformation of atomic arrangements from realgarlike As4S4 molecules, originally present in virgin (untreated) fibers, into planar orpimentlike clusters. Implications of these atomic rearrangements to the incipient photoinduced fluidity—the onset of plastic deformation—in As2S3 glass are discussed. Kinetics of photoinduced plastic changes is compared to that of Raman spectra changes, revealing a qualitative similar behavior. An approximate estimation of the relative contribution of intermolecular rearrangements and the intramolecular structural mechanism proposed in this paper has revealed that the latter is responsible for almost 30% of the photoinduced elongation of the fiber’s length at room temperature. The proposed mechanism can as well serve as rationale for understanding the photoinduced volume expansion observed in chalcogenide glasses.

Simulation of Two Dimensional Ultraviolet (2DUV) Spectroscopy of Amyloid Fibrils

PubMed Central

Jiang, Jun; Abramavicius, Darius; Falvo, Cyril; Bulheller, Benjamin M.; Hirst, Jonathan D.; Mukamel, Shaul

2010-01-01

Revealing the structure and aggregation mechanism of amyloid fibrils is essential for the treatment of over 20 diseases related to protein misfolding. Coherent two dimensional (2D) infrared spectroscopy is a novel tool that provides a wealth of new insight into the structure and dynamics of biomolecular systems. Recently developed ultrafast laser sources are extending multidimensional spectroscopy into the ultraviolet (UV) region, and this opens up new opportunities for probing fibrils. In a simulation study, we show that 2DUV spectra of the backbone of a 32-residue β-amyloid (Aβ9–40) fibril associated with Alzheimer’s disease, and two intermediate prefibrillar structures carry characteristic signatures of fibril size and geometry that could be used to monitor its formation kinetics. The dependence of these signals on the fibril size and geometry is explored. We demonstrate that the dominant features of the β-amyloid fibril spectra are determined by intramolecular interactions within a single Aβ9–40, while intermolecular interactions at the “external interface” have clear signatures in the fine details of these signals. PMID:20795695

Structures and spectroscopic properties of nonperipherally and peripherally substituted metal-free phthalocyanines: a substitution effect study based on density functional theory calculations.

PubMed

Zhong, Aimin; Zhang, Yuexing; Bian, Yongzhong

2010-11-01

The molecular structures, molecular orbitals, atomic charges, electronic absorption spectra, and infrared (IR) and Raman spectra of a series of substituted metal-free phthalocyanine compounds with four (1, 3, 5, 7) or eight (2, 4, 6, 8) methoxyl (1, 2, 5, 6) or methylthio groups (3, 4, 7, 8) on the nonperipheral (1-4) or peripheral positions (5-8) of the phthalocyanine ring are studied by density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations. The calculated structural parameters and simulated electronic absorption and IR spectra are compared with the X-ray crystallography structures and the experimentally observed electronic absorption and IR spectra of the similar molecules, and good agreement between the calculated and experimental results is found. The substitution of the methoxyl or methylthio groups at the nonperipheral positions of the phthalocyanine ring has obvious effects on the molecular structure and spectroscopic properties of the metal-free phthalocyanine. Nonperipheral substitution has a more significant influence than peripheral substitution. The substitution effect increases with an increase in the number of substituents. The methylthio group shows more significant influence than the methoxyl group, despite the stronger electron-donating property of the methoxyl group than the methylthio group. The octa-methylthio-substituted metal-free phthalocyanine compounds have nonplanar structures whose low-lying occupied molecular orbitals and electronic absorption spectra are significantly changed by the substituents. The present systematical study will be helpful for understanding the relationship between structures and properties in phthalocyanine compounds and designing phthalocyanines with typical properties. Copyright © 2010 Elsevier Inc. All rights reserved.

Excitonic nature of optical transitions in electroabsorption spectra of perovskite solar cells

NASA Astrophysics Data System (ADS)

Ruf, Fabian; Magin, Alice; Schultes, Moritz; Ahlswede, Erik; Kalt, Heinz; Hetterich, Michael

2018-02-01

We investigate the electronic structure of solution-processed perovskite solar cells using temperature-dependent electroabsorption (EA) spectroscopy. Simultaneous measurements of absorption and electromodulated spectra of semitransparent methylammonium lead iodide solar cells facilitate a direct comparison of the specific features. The EA spectra can be transformed to peak-like line shapes utilizing an approach based on the Kramers-Kronig relations. The resulting peak positions correspond well to the discrete excitonic—rather than the continuum—contribution of the absorption spectra derived from generalized Elliott fits. This indicates the excitonic nature of the observed EA resonance and is found to be consistent over the whole temperature range investigated (from T = 10 K up to room temperature). To further confirm these findings, a line shape analysis of the measured EA spectra was performed. The best agreement was achieved using a first-derivative-like functional form which is expected for excitonic systems and supports the conclusion of an excitonic optical transition. Exciton binding energies EB are estimated for the orthorhombic and tetragonal phases as 26 meV and 19 meV, respectively. Nevertheless, power-conversion efficiencies η up to 13% (11.5% stabilized) demonstrate good charge-carrier separation in the devices due to sufficient thermal dissociation and Sommerfeld-enhanced absorption.

Optical studies of CaS:Eu,Sm infrared stimulable phosphors

NASA Astrophysics Data System (ADS)

Tamura, Yasuaki; Shibukawa, Atsushi

1993-07-01

The photoluminescence (PL) and infrared stimulated luminescence (ISL) spectra of CaS:Eu,Sm infrared stimulable phosphors (ISPs) are studied. In addition, the concentration dependence of ISL intensity is examined. Sm(3+) and Eu(2+) related structures are found in both the PL excitation and emission spectra. Two types of Sm(3+) are found, one of which exhibits strong emission at around 650 nm and the other weak emission compared to the other emissions at around 565 nm and 605 nm. These are assigned to an asymmetric and a symmetric site, respectively. ISL excitation spectra coincide with the Eu(2+) 4f(sup 7) to 4f(sup 6)5d(sup 1) and 4f(sup 6)6s(sup 1) transitions and range from 220 to 650 nm. ISL emission spectra coincide with the Eu(2+) 4f(sup 6)5d(sup 1) to 4f(sup 7) transition and range from 550 to 750 nm. ISL stimulation spectra range from 0.8 micron to 1.7 micron and are thought to indicate the Sm(2+) ion transition from 4f(sup 6) to 4f(sup 5)5d(sup 1). The maximum ISL intensity is obtained from a sample with Eu and Sm concentrations of 500 and 130 ppm, respectively.

The structural and Raman spectral studies on Ni0.5Cu0.5Fe2O4 ferrite

NASA Astrophysics Data System (ADS)

Somani, M.; Saleem, M.

2018-05-01

Spinel ferrite Ni0.5Cu0.5Fe2O4 has been successfully prepared via solid state reaction. The crystal structure studies using XRD technique revealed cubic structure of the sample. The XRD spectra was further refined via Retvield Refinement and all the parameters regarding structure were obtained which confirmed cubic structure. The assigned space group was found to be Fd-3m. Particle size was calculated to be 56 nm. The Raman Spectra revealed five active Raman modes which confirmed spinel structure.

Coupling CP-MD simulations and X-ray absorption spectroscopy: exploring the structure of oxaliplatin in aqueous solution.

PubMed

Beret, Elizabeth C; Provost, Karine; Müller, Diane; Marcos, Enrique Sánchez

2009-09-10

A combined experimental-theoretical approach applying X-ray absorption spectroscopy and ab initio molecular dynamics (CP-MD) simulations is used to get insight into the structural determination of oxaliplatin, a third-generation anticancer drug of the cisplatin family, in aqueous solution. Experimental Pt L(III)-edge EXAFS and XANES spectra of oxaliplatin in water are compared with theoretical XAS spectra. The latter are obtained as statistically averaged spectra computed for a set of selected snapshots extracted from the MD trajectory of ethyldiamineoxalatoplatinum(II) (EDO-Pt) in liquid water. This compound is a simplified structure of oxaliplatin, where the outer part of the cyclohexane ring contained in the cyclohexanediamine ligand of oxaliplatin has been removed. We show that EDO-Pt is an appropriate model to simulate the spectroscopical properties of oxaliplatin given that the cyclohexane ring does not generate particular features in neither the EXAFS nor the XANES spectra. The computation of average EXAFS spectra using structures from the MD simulation in which atoms are selected according to different cutoff radii around the Pt center allows the assignment of spectral features to particular structural motifs, both in k and R-spaces. The outer oxygen atoms of the oxalate ligand (R(Pt-O(II)) = 3.97 +/- 0.03 A) are responsible for a well-defined hump at around 6.5 A(-1) in the k(2)-weighted EXAFS spectrum. The conventional EXAFS analysis data procedure is reexamined by its application to the simulated average EXAFS spectra. The structural parameters resulting from the fit may then be compared with those obtained from the simulation, providing an estimation of the methodological error associated with the global fitting procedure. A thorough discussion on the synergy between the experimental and theoretical XAS approaches is presented, and evidence for the detection of a slight hydration structure around the Pt complex is shown, leading to the suggestion of a new challenge to experimental XAS measurements.

WSEAT Shock Testing Margin Assessment Using Energy Spectra Final Report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sisemore, Carl; Babuska, Vit; Booher, Jason

Several programs at Sandia National Laboratories have adopted energy spectra as a metric to relate the severity of mechanical insults to structural capacity. The purpose being to gain insight into the system's capability, reliability, and to quantify the ultimate margin between the normal operating envelope and the likely system failure point -- a system margin assessment. The fundamental concern with the use of energy metrics was that the applicability domain and implementation details were not completely defined for many problems of interest. The goal of this WSEAT project was to examine that domain of applicability and work out the necessarymore » implementation details. The goal of this project was to provide experimental validation for the energy spectra based methods in the context of margin assessment as they relate to shock environments. The extensive test results concluded that failure predictions using energy methods did not agree with failure predictions using S-N data. As a result, a modification to the energy methods was developed following the form of Basquin's equation to incorporate the power law exponent for fatigue damage. This update to the energy-based framework brings the energy based metrics into agreement with experimental data and historical S-N data.« less

Impact of Ocean Surface Waves on Air-Sea Momentum Flux

NASA Astrophysics Data System (ADS)

Tamura, H.; Drennan, W. M.; Collins, C. O., III; Graber, H. C.

2016-02-01

In this study, we investigated the structure of turbulent air flow over ocean waves. Observations of wind and waves were retrieved by air-sea interaction spar (ASIS) buoys during the shoaling waves experiment (SHOWEX) in Duck, NC in 1999. It is shown that the turbulent velocity spectra and co-spectra for pure wind sea conditions follow the universal forms estimated by Miyake et al [1970]. In the presence of strong swells, the wave boundary layer was extended and the universal spectral scaling of u'w' broke down [Drennan et al, 1999]. On the other hand, the use of the peak wave frequency (fp) to reproduce the "universal spectra" succeeded at explaining the spectral structure of turbulent flow field. The u'w' co-spectra become negative near the fp, which suggests the upward momentum transport (i.e., negative wind stress) induced by ocean waves. Finally, we propose three turbulent flow structures for different wind-wave regimes.

13C NMR spectroscopy of the insoluble carbon of carbonaceous chondrites

NASA Technical Reports Server (NTRS)

Cronin, J. R.; Pizzarello, S.; Frye, J. S.

1987-01-01

13C NMR spectra have been obtained of the insoluble carbon residues resulting from HF-digestion of three carbonaceous chondrites, Orgueil (C1), Murchison (CM2), and Allende (CV3). Spectra obtained using the cross polarization magic-angle spinning technique show two major features attributable respectively to carbon in aliphatic/olefinic structures. The spectrum obtained from the Allende sample was weak, presumably as a consequence of its low hydrogen content. Single pulse excitation spectra, which do not depend on 1H-13C polarization transfer for signal enhancement were also obtained. These spectra, which may be more representative of the total carbon in the meteorite samples, indicate a greater content of carbon in aromatic/olefinic structures. These results suggest that extensive polycyclic aromatic sheets are important structural features of the insoluble carbon of all three meteorites. The Orgueil and Murchison materials contain additional hydrogenated aromatic/olefinic and aliphatic groups.

Angle-resolved PED and AED calculations for different structures of the diamond C(111) surface

NASA Astrophysics Data System (ADS)

Niebergall, L.; Rennert, P.; Chassé, A.; Kucherenko, Yu

1998-05-01

Angle-resolved (AR) photoelectron diffraction (PED) spectra for electrons excited from the C 1s core state and angle-resolved KVV Auger electron diffraction (AED) spectra are calculated for the Pandey and the Tsai stucture models of diamond C(111) which extend previous investigations of the ideal structure. It is shown how to decide on the structure model by comparing PE spectra for different directions and by comparing PED and AED spectra. Calculations have been performed by evaluating the scattering path operator for a finite cluster in a curved-wave approximation. The different matrix elements for the photoelectron excitation and for the Auger process, respectively, are included. It is shown that the PED intensities are very sensitive to the surface reconstruction for polar angles in the range of 80°. In the AED intensities, polar scans in the plane perpendicular to the chain direction can be considered.

ON PREDICTING INFRAGRAVITY ENERGY IN THE SURF ZONE.

USGS Publications Warehouse

Sallenger,, Asbury H.; Holman, Robert A.; Edge, Billy L.

1985-01-01

Flow data were obtained in the surf zone across a barred profile during a storm. RMS cross-shore velocities due to waves in the intragravity band (wave periods greater than 20 s) had maxima in excess of 0. 5 m/s over the bar crest. For comparison to measured spectra, synthetic spectra of cross-shore flow were computed using measured nearshore profiles. The structure, in the infragravity band, of these synthetic spectra corresponded reasonably well with the structure of the measured spectra. Total variances of measured cross-shore flow within the infragravity band were nondimensionalized by dividing by total infragravity variances of synthetic spectra. These nondimensional variances were independent of distance offshore and increased with the square of the breaker height. Thus, cross-shore flow due to infragravity waves can be estimated with knowledge of the nearshore profile and incident wave conditions. Refs.

Effect of ferroelastic domain pattern changes on the EPR spectra in TDM

NASA Astrophysics Data System (ADS)

Zapart, W.; Zapart, M. B.

2011-09-01

This article presents polarized light microscopy studies of the ferroelastic domain structure and the analysis of electron paramagnetic resonance spectra of Cr3+ admixture ions in trigonal double molybdates. The correlation has been found between abnormal EPR lineshape and domain structure in ferroelastic phases of these crystals.

Structure of selected basic zinc/copper (II) phosphate minerals based upon near-infrared spectroscopy--implications for hydrogen bonding.

PubMed

Frost, Ray L; Reddy, B Jagannadha; Palmer, Sara J; Keeffe, Eloise C

2011-03-01

The NIR spectra of reichenbachite, scholzite and parascholzite have been studied at 298 K. The spectra of the minerals are different, in line with composition and crystal structural variations. Cation substitution effects are significant in their electronic spectra and three distinctly different electronic transition bands are observed in the near-infrared spectra at high wavenumbers in the 12,000-7600 cm(-1) spectral region. Reichenbachite electronic spectrum is characterised by Cu(II) transition bands at 9755 and 7520 cm(-1). A broad spectral feature observed for ferrous ion in the 12,000-9000 cm(-1) region both in scholzite and parascholzite. Some what similarities in the vibrational spectra of the three phosphate minerals are observed particularly in the OH stretching region. The observation of strong band at 5090 cm(-1) indicates strong hydrogen bonding in the structure of the dimorphs, scholzite and parascholzite. The three phosphates exhibit overlapping bands in the 4800-4000 cm(-1) region resulting from the combinations of vibrational modes of (PO(4))(3-) units. Copyright © 2010 Elsevier B.V. All rights reserved.

Configuration interaction in charge exchange spectra of tin and xenon

NASA Astrophysics Data System (ADS)

D'Arcy, R.; Morris, O.; Ohashi, H.; Suda, S.; Tanuma, H.; Fujioka, S.; Nishimura, H.; Nishihara, K.; Suzuki, C.; Kato, T.; Koike, F.; O'Sullivan, G.

2011-06-01

Charge-state-specific extreme ultraviolet spectra from both tin ions and xenon ions have been recorded at Tokyo Metropolitan University. The electron cyclotron resonance source spectra were produced from charge exchange collisions between the ions and rare gas target atoms. To identify unknown spectral lines of tin and xenon, atomic structure calculations were performed for Sn14+-Sn17+ and Xe16+-Xe20+ using the Hartree-Fock configuration interaction code of Cowan (1981 The Theory of Atomic Structure and Spectra (Berkeley, CA: University of California Press)). The energies of the capture states involved in the single-electron process that occurs in these slow collisions were estimated using the classical over-barrier model.

Vibrational spectra of cyclopentadienyl chlorides of titanium, zirconium and hafnium. internal rotation and thermodynamic functions

NASA Astrophysics Data System (ADS)

Balducci, G.; Bencivenni, L.; De Rosa, G.; Gigli, R.; Martine, B.; Cesaro, S. Nunziante

1980-05-01

The infrared and Raman spectra of some cyclopentadienyl compounds of the transition metals, namely Ti(C 5H 5)Cl 3 and M(C 5H 5) 2Cl 2 (M = Ti, Zr and Hf), are reported and discussed. The infrared spectra of the gaseous species isolated in argon matrices at 10 K provide structural information about the single molecules. Particular attention has been paid to the low-frequency region in order to achieve more reliable assignments for the internal-rotation modes. The structural data and the fundamental frequencies derived from the spectra are employed in a calculation of the thermodynamic functions for these compounds in the ideal gas state.

Evaluation of stereo-array isotope labeling (SAIL) patterns for automated structural analysis of proteins with CYANA.

PubMed

Ikeya, Teppei; Terauchi, Tsutomu; Güntert, Peter; Kainosho, Masatsune

2006-07-01

Recently we have developed the stereo-array isotope labeling (SAIL) technique to overcome the conventional molecular size limitation in NMR protein structure determination by employing complete stereo- and regiospecific patterns of stable isotopes. SAIL sharpens signals and simplifies spectra without the loss of requisite structural information, thus making large classes of proteins newly accessible to detailed solution structure determination. The automated structure calculation program CYANA can efficiently analyze SAIL-NOESY spectra and calculate structures without manual analysis. Nevertheless, the original SAIL method might not be capable of determining the structures of proteins larger than 50 kDa or membrane proteins, for which the spectra are characterized by many broadened and overlapped peaks. Here we have carried out simulations of new SAIL patterns optimized for minimal relaxation and overlap, to evaluate the combined use of SAIL and CYANA for solving the structures of larger proteins and membrane proteins. The modified approach reduces the number of peaks to nearly half of that observed with uniform labeling, while still yielding well-defined structures and is expected to enable NMR structure determinations of these challenging systems.

Optical, electrical and ferromagnetic studies of ZnO:Fe diluted magnetic semiconductor nanoparticles for spintronic applications.

PubMed

Elilarassi, R; Chandrasekaran, G

2017-11-05

In the present investigation, diluted magnetic semiconductor (Zn 1-x Fe x O) nanoparticles with different doping concentrations (x=0, 0.02, 0.04, 0.06, and 0.08) were successfully synthesized by sol-gel auto-combustion method. The crystal structure, morphology, optical, electrical and magnetic properties of the prepared samples were characterized by X-ray diffraction (XRD), scanning electron microscope (SEM), energy dispersive analysis using x-rays (EDAX), ultraviolet-visible spectrophotometer, fluorescence spectroscope (FS), vibrating sample magnetometer (VSM) and broad band dielectric spectrometer (BDS). XRD results reveal that all the samples possess hexagonal wurtzite crystal structure with good crystalline quality. The absence of impurity phases divulge that Fe ions are well incorporated into the ZnO crystal lattice. The substitutional incorporation of Fe 3+ at Zn sites is reflected in optical absorption spectra of the samples. Flouorescence spectra of the samples show a strong near-band edge related UV emission as well as defect related visible emissions. The semiconducting behavior of the samples has been confirmed through electrical conductivity measurements. Magnetic measurements indicated that all the samples possess ferromagnetism at room temperature. Copyright © 2017 Elsevier B.V. All rights reserved.

Understanding reliability and some limitations of the images and spectra reconstructed from a multi-monochromatic x-ray imager

DOE PAGES

Nagayama, T.; Mancini, R. C.; Mayes, D.; ...

2015-11-18

Temperature and density asymmetry diagnosis is critical to advance inertial confinement fusion (ICF) science. A multi-monochromatic x-ray imager (MMI) is an attractive diagnostic for this purpose. The MMI records the spectral signature from an ICF implosion core with time resolution, 2-D space resolution, and spectral resolution. While narrow-band images and 2-D space-resolved spectra from the MMI data constrain temperature and density spatial structure of the core, the accuracy of the images and spectra depends not only on the quality of the MMI data but also on the reliability of the post-processing tools. In this paper, we synthetically quantify the accuracymore » of images and spectra reconstructed from MMI data. Errors in the reconstructed images are less than a few percent when the space-resolution effect is applied to the modeled images. The errors in the reconstructed 2-D space-resolved spectra are also less than a few percent except those for the peripheral regions. Spectra reconstructed for the peripheral regions have slightly but systematically lower intensities by ~6% due to the instrumental spatial-resolution effects. However, this does not alter the relative line ratios and widths and thus does not affect the temperature and density diagnostics. We also investigate the impact of the pinhole size variation on the extracted images and spectra. A 10% pinhole size variation could introduce spatial bias to the images and spectra of ~10%. A correction algorithm is developed, and it successfully reduces the errors to a few percent. Finally, it is desirable to perform similar synthetic investigations to fully understand the reliability and limitations of each MMI application.« less

Simulations of the infrared, Raman, and 2D-IR photon echo spectra of water in nanoscale silica pores

DOE PAGES

Burris, Paul C.; Laage, Damien; Thompson, Ward H.

2016-05-20

Vibrational spectroscopy is frequently used to characterize nanoconfined liquids and probe the effect of the confining framework on the liquid structure and dynamics relative to the corresponding bulk fluid. However, it is still unclear what molecular-level information can be obtained from such measurements. In this Paper, we address this question by using molecular dynamics (MD) simulations to reproduce the linear infrared (IR), Raman, and two-dimensional IR (2D-IR) photon echo spectra for water confined within hydrophilic (hydroxyl-terminated) silica mesopores. To simplify the spectra the OH stretching region of isotopically dilute HOD in D 2O is considered. An empirical mapping approach ismore » used to obtain the OH vibrational frequencies, transition dipoles, and transition polarizabilities from the MD simulations. The simulated linear IR and Raman spectra are in good general agreement with measured spectra of water in mesoporous silica reported in the literature. The key effect of confinement on the water spectrum is a vibrational blueshift for OH groups that are closest to the pore interface. The blueshift can be attributed to the weaker hydrogen bonds (H-bonds) formed between the OH groups and silica oxygen acceptors. Non-Condon effects greatly diminish the contribution of these OH moieties to the linear IR spectrum, but these weaker H-bonds are readily apparent in the Raman spectrum. The 2D-IR spectra have not yet been measured and thus the present results represent a prediction. Lastly, the simulated spectra indicate that it should be possible to probe the slower spectral diffusion of confined water compared to the bulk liquid by analysis of the 2D-IR spectra.« less

Simulations of the infrared, Raman, and 2D-IR photon echo spectra of water in nanoscale silica pores.

PubMed

Burris, Paul C; Laage, Damien; Thompson, Ward H

2016-05-21

Vibrational spectroscopy is frequently used to characterize nanoconfined liquids and probe the effect of the confining framework on the liquid structure and dynamics relative to the corresponding bulk fluid. However, it is still unclear what molecular-level information can be obtained from such measurements. In this paper, we address this question by using molecular dynamics (MD) simulations to reproduce the linear infrared (IR), Raman, and two-dimensional IR (2D-IR) photon echo spectra for water confined within hydrophilic (hydroxyl-terminated) silica mesopores. To simplify the spectra the OH stretching region of isotopically dilute HOD in D2O is considered. An empirical mapping approach is used to obtain the OH vibrational frequencies, transition dipoles, and transition polarizabilities from the MD simulations. The simulated linear IR and Raman spectra are in good general agreement with measured spectra of water in mesoporous silica reported in the literature. The key effect of confinement on the water spectrum is a vibrational blueshift for OH groups that are closest to the pore interface. The blueshift can be attributed to the weaker hydrogen bonds (H-bonds) formed between the OH groups and silica oxygen acceptors. Non-Condon effects greatly diminish the contribution of these OH moieties to the linear IR spectrum, but these weaker H-bonds are readily apparent in the Raman spectrum. The 2D-IR spectra have not yet been measured and thus the present results represent a prediction. The simulated spectra indicates that it should be possible to probe the slower spectral diffusion of confined water compared to the bulk liquid by analysis of the 2D-IR spectra.

Simulations of the infrared, Raman, and 2D-IR photon echo spectra of water in nanoscale silica pores

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burris, Paul C.; Thompson, Ward H., E-mail: wthompson@ku.edu; Laage, Damien, E-mail: damien.laage@ens.fr

2016-05-21

Vibrational spectroscopy is frequently used to characterize nanoconfined liquids and probe the effect of the confining framework on the liquid structure and dynamics relative to the corresponding bulk fluid. However, it is still unclear what molecular-level information can be obtained from such measurements. In this paper, we address this question by using molecular dynamics (MD) simulations to reproduce the linear infrared (IR), Raman, and two-dimensional IR (2D-IR) photon echo spectra for water confined within hydrophilic (hydroxyl-terminated) silica mesopores. To simplify the spectra the OH stretching region of isotopically dilute HOD in D{sub 2}O is considered. An empirical mapping approach ismore » used to obtain the OH vibrational frequencies, transition dipoles, and transition polarizabilities from the MD simulations. The simulated linear IR and Raman spectra are in good general agreement with measured spectra of water in mesoporous silica reported in the literature. The key effect of confinement on the water spectrum is a vibrational blueshift for OH groups that are closest to the pore interface. The blueshift can be attributed to the weaker hydrogen bonds (H-bonds) formed between the OH groups and silica oxygen acceptors. Non-Condon effects greatly diminish the contribution of these OH moieties to the linear IR spectrum, but these weaker H-bonds are readily apparent in the Raman spectrum. The 2D-IR spectra have not yet been measured and thus the present results represent a prediction. The simulated spectra indicates that it should be possible to probe the slower spectral diffusion of confined water compared to the bulk liquid by analysis of the 2D-IR spectra.« less

Adsorption of 1- and 2-butylimidazoles at the copper/air and steel/air interfaces studied by sum frequency generation vibrational spectroscopy.

PubMed

Casford, Michael T L; Davies, Paul B

2012-07-24

The structure of thin films of 1- and 2-butylimidazoles adsorbed on copper and steel surfaces under air was examined using sum frequency generation (SFG) vibrational spectroscopy in the ppp and ssp polarizations. Additionally, the SFG spectra of both isomers were recorded at 55 °C at the liquid imidazole/air interface for reference. Complementary bulk infrared, reflection-absorption infrared spectroscopy (RAIRS), and Raman spectra of both imidazoles were recorded for assignment purposes. The SFG spectra in the C-H stretching region at the liquid/air interface are dominated by resonances from the methyl end group of the butyl side chain of the imidazoles, indicating that they are aligned parallel or closely parallel to the surface normal. These are also the most prominent features in the SFG spectra on copper and steel. In addition, both the ppp and ssp spectra on copper show resonances from the C-H stretching modes of the imidazole ring for both isomers. The ring C-H resonances are completely absent from the spectra on steel and at the liquid/air interface. The relative intensities of the SFG spectra can be interpreted as showing that, on copper, under air, both butylimidazoles are adsorbed with their butyl side chains perpendicular to the interface and with the ring significantly inclined away from the surface plane and toward the surface normal. The SFG spectra of both imidazoles on steel indicate an orientation where the imidazole rings are parallel or nearly parallel to the surface. The weak C-H resonances from the ring at the liquid/air interface suggest that the tilt angle of the ring from the surface normal at this interface is significantly greater than it is on copper.

Understanding reliability and some limitations of the images and spectra reconstructed from a multi-monochromatic x-ray imager

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagayama, T.; Mancini, R. C.; Mayes, D.

2015-11-15

Temperature and density asymmetry diagnosis is critical to advance inertial confinement fusion (ICF) science. A multi-monochromatic x-ray imager (MMI) is an attractive diagnostic for this purpose. The MMI records the spectral signature from an ICF implosion core with time resolution, 2-D space resolution, and spectral resolution. While narrow-band images and 2-D space-resolved spectra from the MMI data constrain temperature and density spatial structure of the core, the accuracy of the images and spectra depends not only on the quality of the MMI data but also on the reliability of the post-processing tools. Here, we synthetically quantify the accuracy of imagesmore » and spectra reconstructed from MMI data. Errors in the reconstructed images are less than a few percent when the space-resolution effect is applied to the modeled images. The errors in the reconstructed 2-D space-resolved spectra are also less than a few percent except those for the peripheral regions. Spectra reconstructed for the peripheral regions have slightly but systematically lower intensities by ∼6% due to the instrumental spatial-resolution effects. However, this does not alter the relative line ratios and widths and thus does not affect the temperature and density diagnostics. We also investigate the impact of the pinhole size variation on the extracted images and spectra. A 10% pinhole size variation could introduce spatial bias to the images and spectra of ∼10%. A correction algorithm is developed, and it successfully reduces the errors to a few percent. It is desirable to perform similar synthetic investigations to fully understand the reliability and limitations of each MMI application.« less

Understanding reliability and some limitations of the images and spectra reconstructed from a multi-monochromatic x-ray imager.

PubMed

Nagayama, T; Mancini, R C; Mayes, D; Tommasini, R; Florido, R

2015-11-01

Temperature and density asymmetry diagnosis is critical to advance inertial confinement fusion (ICF) science. A multi-monochromatic x-ray imager (MMI) is an attractive diagnostic for this purpose. The MMI records the spectral signature from an ICF implosion core with time resolution, 2-D space resolution, and spectral resolution. While narrow-band images and 2-D space-resolved spectra from the MMI data constrain temperature and density spatial structure of the core, the accuracy of the images and spectra depends not only on the quality of the MMI data but also on the reliability of the post-processing tools. Here, we synthetically quantify the accuracy of images and spectra reconstructed from MMI data. Errors in the reconstructed images are less than a few percent when the space-resolution effect is applied to the modeled images. The errors in the reconstructed 2-D space-resolved spectra are also less than a few percent except those for the peripheral regions. Spectra reconstructed for the peripheral regions have slightly but systematically lower intensities by ∼6% due to the instrumental spatial-resolution effects. However, this does not alter the relative line ratios and widths and thus does not affect the temperature and density diagnostics. We also investigate the impact of the pinhole size variation on the extracted images and spectra. A 10% pinhole size variation could introduce spatial bias to the images and spectra of ∼10%. A correction algorithm is developed, and it successfully reduces the errors to a few percent. It is desirable to perform similar synthetic investigations to fully understand the reliability and limitations of each MMI application.

Compound annotation in liquid chromatography/high-resolution mass spectrometry based metabolomics: robust adduct ion determination as a prerequisite to structure prediction in electrospray ionization mass spectra.

PubMed

Jaeger, Carsten; Méret, Michaël; Schmitt, Clemens A; Lisec, Jan

2017-08-15

A bottleneck in metabolic profiling of complex biological extracts is confident, non-supervised annotation of ideally all contained, chemically highly diverse small molecules. Recent computational strategies combining sum formula prediction with in silico fragmentation achieve confident de novo annotation, once the correct neutral mass of a compound is known. Current software solutions for automated adduct ion assignment, however, are either publicly unavailable or have been validated against only few experimental electrospray ionization (ESI) mass spectra. We here present findMAIN (find Main Adduct IoN), a new heuristic approach for interpreting ESI mass spectra. findMAIN scores MS 1 spectra based on explained intensity, mass accuracy and isotope charge agreement of adducts and related ionization products and annotates peaks of the (de)protonated molecule and adduct ions. The approach was validated against 1141 ESI positive mode spectra of chemically diverse standard compounds acquired on different high-resolution mass spectrometric instruments (Orbitrap and time-of-flight). Robustness against impure spectra was evaluated. Correct adduct ion assignment was achieved for up to 83% of the spectra. Performance was independent of compound class and mass spectrometric platform. The algorithm proved highly tolerant against spectral contamination as demonstrated exemplarily for co-eluting compounds as well as systematically by pairwise mixing of spectra. When used in conjunction with MS-FINDER, a state-of-the-art sum formula tool, correct sum formulas were obtained for 77% of spectra. It outperformed both 'brute force' approaches and current state-of-the-art annotation packages tested as potential alternatives. Limitations of the heuristic pertained to poorly ionizing compounds and cationic compounds forming [M] + ions. A new, validated approach for interpreting ESI mass spectra is presented, filling a gap in the nontargeted metabolomics workflow. It is freely available in the latest version of R package InterpretMSSpectrum. Copyright © 2017 John Wiley & Sons, Ltd.

Similarities and Differences between RNA and DNA Double-Helical Structures in Circular Dichroism Spectroscopy: A SAC-CI Study.

PubMed

Miyahara, Tomoo; Nakatsuji, Hiroshi; Sugiyama, Hiroshi

2016-11-17

The helical structures of DNA and RNA are investigated experimentally using circular dichroism (CD) spectroscopy. The signs and the shapes of the CD spectra are much different between the right- and left-handed structures as well as between DNA and RNA. The main difference lies in the sign at around 295 nm of the CD spectra: it is positive for the right-handed B-DNA and the left-handed Z-RNA but is negative for the left-handed Z-DNA and the right-handed A-RNA. We calculated the SAC-CI CD spectra of DNA and RNA using the tetramer models, which include both hydrogen-bonding and stacking interactions that are important in both DNA and RNA. The SAC-CI results reproduced the features at around 295 nm of the experimental CD spectra of each DNA and RNA, and elucidated that the strong stacking interaction between the two base pairs is the origin of the negative peaks at 295 nm of the CD spectra for both DNA and RNA. On the basis of these facts, we discuss the similarities and differences between RNA and DNA double-helical structures in the CD spectroscopy based on the ChiraSac methodology.

Carbon X-ray absorption spectra of fluoroethenes and acetone: A study at the coupled cluster, density functional, and static-exchange levels of theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fransson, Thomas; Norman, Patrick; Coriani, Sonia

2013-03-28

Near carbon K-edge X-ray absorption fine structure spectra of a series of fluorine-substituted ethenes and acetone have been studied using coupled cluster and density functional theory (DFT) polarization propagator methods, as well as the static-exchange (STEX) approach. With the complex polarization propagator (CPP) implemented in coupled cluster theory, relaxation effects following the excitation of core electrons are accounted for in terms of electron correlation, enabling a systematic convergence of these effects with respect to electron excitations in the cluster operator. Coupled cluster results have been used as benchmarks for the assessment of propagator methods in DFT as well as themore » state-specific static-exchange approach. Calculations on ethene and 1,1-difluoroethene illustrate the possibility of using nonrelativistic coupled cluster singles and doubles (CCSD) with additional effects of electron correlation and relativity added as scalar shifts in energetics. It has been demonstrated that CPP spectra obtained with coupled cluster singles and approximate doubles (CC2), CCSD, and DFT (with a Coulomb attenuated exchange-correlation functional) yield excellent predictions of chemical shifts for vinylfluoride, 1,1-difluoroethene, trifluoroethene, as well as good spectral features for acetone in the case of CCSD and DFT. Following this, CPP-DFT is considered to be a viable option for the calculation of X-ray absorption spectra of larger {pi}-conjugated systems, and CC2 is deemed applicable for chemical shifts but not for studies of fine structure features. The CCSD method as well as the more approximate CC2 method are shown to yield spectral features relating to {pi}*-resonances in good agreement with experiment, not only for the aforementioned molecules but also for ethene, cis-1,2-difluoroethene, and tetrafluoroethene. The STEX approach is shown to underestimate {pi}*-peak separations due to spectral compressions, a characteristic which is inherent to this method.« less

Carbon X-ray absorption spectra of fluoroethenes and acetone: a study at the coupled cluster, density functional, and static-exchange levels of theory.

PubMed

Fransson, Thomas; Coriani, Sonia; Christiansen, Ove; Norman, Patrick

2013-03-28

Near carbon K-edge X-ray absorption fine structure spectra of a series of fluorine-substituted ethenes and acetone have been studied using coupled cluster and density functional theory (DFT) polarization propagator methods, as well as the static-exchange (STEX) approach. With the complex polarization propagator (CPP) implemented in coupled cluster theory, relaxation effects following the excitation of core electrons are accounted for in terms of electron correlation, enabling a systematic convergence of these effects with respect to electron excitations in the cluster operator. Coupled cluster results have been used as benchmarks for the assessment of propagator methods in DFT as well as the state-specific static-exchange approach. Calculations on ethene and 1,1-difluoroethene illustrate the possibility of using nonrelativistic coupled cluster singles and doubles (CCSD) with additional effects of electron correlation and relativity added as scalar shifts in energetics. It has been demonstrated that CPP spectra obtained with coupled cluster singles and approximate doubles (CC2), CCSD, and DFT (with a Coulomb attenuated exchange-correlation functional) yield excellent predictions of chemical shifts for vinylfluoride, 1,1-difluoroethene, trifluoroethene, as well as good spectral features for acetone in the case of CCSD and DFT. Following this, CPP-DFT is considered to be a viable option for the calculation of X-ray absorption spectra of larger π-conjugated systems, and CC2 is deemed applicable for chemical shifts but not for studies of fine structure features. The CCSD method as well as the more approximate CC2 method are shown to yield spectral features relating to π∗-resonances in good agreement with experiment, not only for the aforementioned molecules but also for ethene, cis-1,2-difluoroethene, and tetrafluoroethene. The STEX approach is shown to underestimate π∗-peak separations due to spectral compressions, a characteristic which is inherent to this method.

Theoretical and experimental NMR studies on muscimol from fly agaric mushroom (Amanita muscaria)

NASA Astrophysics Data System (ADS)

Kupka, Teobald; Wieczorek, Piotr P.

2016-01-01

In this article we report results of combined theoretical and experimental NMR studies on muscimol, the bioactive alkaloid from fly agaric mushroom (Amanita muscaria). The assignment of 1H and 13C NMR spectra of muscimol in DMSO-d6 was supported by additional two-dimensional heteronuclear correlated spectra (2D NMR) and gauge independent atomic orbital (GIAO) NMR calculations using density functional theory (DFT). The effect of solvent in theoretical calculations was included via polarized continuum model (PCM) and the hybrid three-parameter B3LYP density functional in combination with 6-311++G(3df,2pd) basis set enabled calculation of reliable structures of non-ionized (neutral) molecule and its NH and zwitterionic forms in the gas phase, chloroform, DMSO and water. GIAO NMR calculations, using equilibrium and rovibrationally averaged geometry, at B3LYP/6-31G* and B3LYP/aug-cc-pVTZ-J levels of theory provided muscimol nuclear magnetic shieldings. The theoretical proton and carbon chemical shifts were critically compared with experimental NMR spectra measured in DMSO. Our results provide useful information on its structure in solution. We believe that such data could improve the understanding of basic features of muscimol at atomistic level and provide another tool in studies related to GABA analogs.

Comparative studies on molecular structure, vibrational spectra and hyperpolarizabilies of NLO chromophore Ethyl 4-Dimethylaminobenzoate

NASA Astrophysics Data System (ADS)

Amalanathan, M.; Jasmine, G. Femina; Roy, S. Dawn Dharma

2017-08-01

The molecular structure, vibrational spectra and polarizabilities of Ethyl 4-Dimethylaminobenzoate (EDAB) was investigated by density functional theory employing Becke's three parameter hybrid exchange functional with Lee-Yang-Parr (B3LYP) co-relational functional involving 6-311++G(d,p) basis set and compared with some other levels. A detailed interpretation of the IR and Raman spectra of EDBA have been reported and analyzed. Complete vibrational assignments of the vibrational modes have been done on the basis of the potential energy distribution (TED) using VEDA software. The molecular electrostatic potential mapped onto total density surface has been obtained. A study on the electronic properties, such as absorption wavelength, and frontier molecular orbitals energy, was performed using DFT approach. The stability of the molecule arising from hyper conjugative interactions and accompanying charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The natural and Mulliken charge also calculated and compared with different level of calculation. The dipole moment, polarizability and first, second order hyperpolarizabilities of the title molecule were calculated and compared with the experimental values. The energy gap between frontier orbitals has been used along with electric moments and first order hyperpolarizability, to understand the non linear optical (NLO) activity of the molecule. The NLO activity of molecule was confirmed by SHG analysis.

Dielectric characterization of high-performance spaceflight materials

NASA Astrophysics Data System (ADS)

Kleppe, Nathan Alan

As commercial space travel increases, the need for reliable structural health monitoring to predict possible weaknesses or failures of structural materials also increases. Monitoring of polymer-based materials may be achieved through the use of dielectric spectroscopy by comparing permittivity or conductivity measurements performed on a sample in use to that of a pristine sample. Changes in these measured values or of the relaxation frequencies, if present, can indicate chemical or physical changes occurring within the material and the possible need for maintenance/replacement. In this work, we established indicative trends that occur in the dielectric spectra during accelerated aging of various high-performance polymeric materials (EVOH, PEEK, PPS, and UHMWPE). Uses for these materials range from electrical insulation and protective coatings to windows and air- or space-craft parts that may be subject to environmental damage over long-term operation. Accelerated thermal aging and ultraviolet/water-spray cyclic aging were performed in order to investigate the degradation of the aforementioned material. The Havriliak-Negami model was used in the analysis of the measured dielectric spectra in order to obtain the characteristic fit parameters from which aging-related trends were identified. With reference to the literature and from measured FTIR spectra, observations were connected to the underlying mechanisms causing the dielectric relaxations.

Tannin fingerprinting in vegetable tanned leather by solid state NMR spectroscopy and comparison with leathers tanned by other processes.

PubMed

Romer, Frederik H; Underwood, Andrew P; Senekal, Nadine D; Bonnet, Susan L; Duer, Melinda J; Reid, David G; van der Westhuizen, Jan H

2011-01-28

Solid state ¹³C-NMR spectra of pure tannin powders from four different sources--mimosa, quebracho, chestnut and tara--are readily distinguishable from each other, both in pure commercial powder form, and in leather which they have been used to tan. Groups of signals indicative of the source, and type (condensed vs. hydrolyzable) of tannin used in the manufacture are well resolved in the spectra of the finished leathers. These fingerprints are compared with those arising from leathers tanned with other common tanning agents. Paramagnetic chromium (III) tanning causes widespread but selective disappearance of signals from the spectrum of leather collagen, including resonances from acidic aspartyl and glutamyl residues, likely bound to Cr (III) structures. Aluminium (III) and glutaraldehyde tanning both cause considerable leather collagen signal sharpening suggesting some increase in molecular structural ordering. The ²⁷Al-NMR signal from the former material is consistent with an octahedral coordination by oxygen ligands. Solid state NMR thus provides easily recognisable reagent specific spectral fingerprints of the products of vegetable and some other common tanning processes. Because spectra are related to molecular properties, NMR is potentially a powerful tool in leather process enhancement and quality or provenance assurance.

Conformational analysis, spectroscopic, structure-activity relations and quantum chemical simulation studies of 4-(trifluoromethyl)benzylamine

NASA Astrophysics Data System (ADS)

Arjunan, V.; Devi, L.; Mohan, S.

2018-05-01

The FT-IR and FT-Raman spectra of 4-trifluoromethylbenzylamine (TFMBA) have been recorded in the range 4000-450 and 4000-100 cm-1 respectively. The conformational analysis of the compound has been carried out to attain stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers obtained theoretically from the B3LYP gradient calculations employing the standard high level 6-311++G** and cc-pVTZ basis sets for the optimised geometry of the compound. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The 1H (400 MHz; CDCl3) and 13C (100 MHz; CDCl3) nuclear magnetic resonance (NMR) spectra were also recorded. The electronic properties, highest occupied molecular orbital and lowest unoccupied molecular orbital energies are measured by DFT approach. The charges of the atoms by natural bond orbital (NBO) analysis are determined by B3LYP/cc-pVTZ method. The structure-chemical reactivity relations of the compound are determined through chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods.

Influence of the hydrogen bond quantum nature in liquid water and heavy water on stimulated Raman scattering

NASA Astrophysics Data System (ADS)

Li, Fabing; Li, Zhanlong; Li, Shuo; Fang, Wenhui; Sun, Chenglin; Men, Zhiwei

2018-06-01

Stimulated Raman scattering (SRS) of liquid water and heavy water have been investigated using Nd:YAG laser. The SRS spectra of liquid heavy water indicate that ice-VII and ice-VIII structures are formed by shock-induced compression (SIC) in forward and backward directions, respectively. Simultaneously, the SRS spectra reveal of liquid water that only ice-VII structure is formed in the backward direction. The difference in ice structures formed by SIC in liquid water and heavy water could be attributed to the effect of the hydrogen bond quantum nature with H+. SRS spectra of 2 M NaOH water solution with ice-VII and ice-VIII structures have been successfully obtained in forward and backward, respectively, as OH- greatly reduce the quantum nature of hydrogen bonds by neutralizing H+ in water. The hydrogen bond quantum nature is important for understanding isotope calibration test structure and isotopic effect.

Chemical Principles Revisited. Proton Magnetic Resonance Spectroscopy.

ERIC Educational Resources Information Center

McQuarrie, Donald A.

1988-01-01

Discusses how to interpret nuclear magnetic resonance (NMR) spectra and how to use them to determine molecular structures. This discussion is limited to spectra that are a result of observation of only the protons in a molecule. This type is called proton magnetic resonance (PMR) spectra. (CW)

Correlating the Structure, Optical Spectra, and Electrodynamics of Single Silver Nanocubes

DTIC Science & Technology

2009-01-27

Correlating the Structure, Optical Spectra, and Electrodynamics of Single Silver Nanocubes Jeffrey M. McMahon,†,‡ Yingmin Wang,§ Leif J. Sherry...response and detailed structural information for a single nanoparticle, using a silver (Ag) nanocube as the example. By carefully incorporating the HRTEM...this work is to describe the relationship between the optical response, morphology, and dielectric environment of a single silver (Ag) cubic

Spectral and time-resolved studies on ocular structures

NASA Astrophysics Data System (ADS)

Schweitzer, D.; Jentsch, S.; Schenke, S.; Hammer, M.; Biskup, C.; Gaillard, E.

2007-07-01

Measurements of endogeous fluorophores open the possibility for evaluation of metabolic state at the eye. For interpretation of 2-dimensional measurements of time-resolved auto fluorescence in 2 separate spectral ranges at the human eye, comparing measurements were performed on porcine eyes. Determining excitation and emission spectra, attention was drawn of proof of coenzymes NADH and FAD in isolated anatomical structures cornea, aqueous humor, lens, vitreous, neuronal retina, retinal pigment epithelium (RPE), choroid, and sclera. All these structures exhibit auto fluorescence, highest in lens. Excitation at 350 nm results in local fluorescence maxima at 460 nm, corresponding to NADH, in all structures. This short-wave excitation allows metabolic studies only at the anterior eye, because of the limited transmission of the ocular media. During excitation at 446 nm the existence of FAD is expressed by local fluorescence maxima at 530 nm. The composition fluorescence spectra allow no discrimination between single ocular structures. Approximating the dynamic fluorescence by a double exponential function, the shortest lifetimes were detected in RPE and neuronal retina. The histograms of mean lifetime t M cover each other on lens with cornea and also on sclera with choroid. Despite the lifetimes are close between RPE and neuronal retina, the relative contributions Q I are wide different. The gradient of trend lines in cluster diagrams of amplitudes α II vs. α I allows a discrimination of ocular structures.

Simulation of Thin-Film Damping and Thermal Mechanical Noise Spectra for Advanced Micromachined Microphone Structures.

PubMed

Hall, Neal A; Okandan, Murat; Littrell, Robert; Bicen, Baris; Degertekin, F Levent

2008-06-01

In many micromachined sensors the thin (2-10 μm thick) air film between a compliant diaphragm and backplate electrode plays a dominant role in shaping both the dynamic and thermal noise characteristics of the device. Silicon microphone structures used in grating-based optical-interference microphones have recently been introduced that employ backplates with minimal area to achieve low damping and low thermal noise levels. Finite-element based modeling procedures based on 2-D discretization of the governing Reynolds equation are ideally suited for studying thin-film dynamics in such structures which utilize relatively complex backplate geometries. In this paper, the dynamic properties of both the diaphragm and thin air film are studied using a modal projection procedure in a commonly used finite element software and the results are used to simulate the dynamic frequency response of the coupled structure to internally generated electrostatic actuation pressure. The model is also extended to simulate thermal mechanical noise spectra of these advanced sensing structures. In all cases simulations are compared with measured data and show excellent agreement-demonstrating 0.8 pN/√Hz and 1.8 μPa/√Hz thermal force and thermal pressure noise levels, respectively, for the 1.5 mm diameter structures under study which have a fundamental diaphragm resonance-limited bandwidth near 20 kHz.

Tunable alumina 2D photonic-crystal structures via biomineralization of peacock tail feathers

NASA Astrophysics Data System (ADS)

Jiang, Yonggang; Wang, Rui; Feng, Lin; Li, Jian; An, Zhonglie; Zhang, Deyuan

2018-04-01

Peacock tail feathers with subtle periodic nanostructures exhibit diverse striking brilliancy, which can be applied as natural templates to fabricate artificial photonic crystals (PhCs) via a biomineralization method. Alumina photonic-crystal structures are successfully synthesized via an immersion and two-step calcination process. The lattice constants of the artificial PhCs are greatly reduced compared to their natural matrices. The lattice constants are tunable by modifying the final annealing conditions in the biomineralization process. The reflection spectra of the alumina photonic-crystal structures are measured, which is related to their material and structural parameters. This work suggests a facile fabrication process to construct alumina PhCs with a high-temperature resistance.

Two-photon absorption spectra of carotenoids compounds

NASA Astrophysics Data System (ADS)

Vivas, Marcelo Gonçalves; Silva, Daniel Luiz; Boni, Leonardo de; Zalesny, Robert; Bartkowiak, Wojciech; Mendonca, Cleber Renato

2011-05-01

Carotenoids are biosynthetic organic pigments that constitute an important class of one-dimensional π-conjugated organic molecules with enormous potential for application in biophotonic devices. In this context, we studied the degenerate two-photon absorption (2PA) cross-section spectra of two carotenoid compounds (β-carotene and β-apo-8'-carotenal) employing the conventional and white-light-continuum Z-scan techniques and quantum chemistry calculations. Because carotenoids coexist at room temperature as a mixture of isomers, the 2PA spectra reported here are due to samples containing a distribution of isomers, presenting distinct conjugation length and conformation. We show that these compounds present a defined structure on the 2PA spectra, that peaks at 650 nm with an absorption cross-section of approximately 5000 GM, for both compounds. In addition, we observed a 2PA band at 990 nm for β-apo-8'-carotenal, which was attributed to a overlapping of 11Bu+-like and 21Ag--like states, which are strongly one- and two-photon allowed, respectively. Spectroscopic parameters of the electronic transitions to singlet-excited states, which are directly related to photophysical properties of these compounds, were obtained by fitting the 2PA spectra using the sum-over-states approach. The analysis and interpretations of the 2PA spectra of the investigated carotenoids were supported by theoretical predictions of one- and two-photon transitions carried out using the response functions formalism within the density functional theory framework, using the long-range corrected CAM-B3LYP functional.

Power Spectra and Eddy Dissipation Rate Measured by the Coyote Unmanned Aircraft System in Hurricane Edouard (2014)

NASA Astrophysics Data System (ADS)

Kalina, E.; Cione, J.; Bryan, G. H.; Lenschow, D. H.; Fairall, C. W.

2016-12-01

Open-ocean measurements of turbulence variables in the tropical cyclone (TC) boundary layer are rare, given the dangers posed by convective downdrafts, high waves, and sea spray to manned hurricane reconnaissance aircraft. The Coyote Unmanned Aircraft System (UAS) represents an opportunity to mitigate the risk to personnel while simultaneously collecting low-altitude measurements of air pressure, temperature, humidity, and wind in TCs. In 2014, the Coyote UAS flew at a height of h = 760 m in Hurricane Edouard for 45 min. The resulting wind velocity measurements were used to estimate the turbulent eddy dissipation rate (ɛ) along the Coyote flight track, using power spectra and the second-order velocity structure function. Power spectra of both the longitudinal (Suu) and transverse wind components (Svv) exhibited well-defined inertial subranges with five-thirds scaling, as expected from Kolmogorov (1941). The ratio Svv:Suu was 4:3, in agreement with theory. Under the moderate wind speeds (15-25 m s-1) sampled by the Coyote, estimates of ɛ from the power spectra and structure function ranged from 2-3.5×10-4 m2 s-3. An idealized TC simulation with Cloud Model version 1 (CM1) and a horizontal grid spacing of dx = 20 m was then used to support the observed estimates of ɛ. Along the mock Coyote flight path, the model domain-averaged value of ɛ was 3.0×10-4 m2 s-3, which is within the range of the observationally-based estimates. This agreement was achieved despite the relatively slow sampling rate (1 Hz) of the Coyote sensors and occasional missing data. Therefore, a 1-Hz sampling rate may be adequate for estimating ɛ, and time series with missing samples may still contain the necessary information to estimate the power spectra and structure functions, and thus ɛ. These findings are motivating subsequent Coyote flights into high-wind regions of TCs to collect turbulence measurements that will be used to evaluate subgrid turbulence schemes for numerical models. Future flights in the surface layer (h < 100 m) will also be used to measure the surface drag coefficient at hurricane-force wind speeds.

ULg Spectra: An Interactive Software Tool to Improve Undergraduate Students' Structural Analysis Skills

ERIC Educational Resources Information Center

Agnello, Armelinda; Carre, Cyril; Billen, Roland; Leyh, Bernard; De Pauw, Edwin; Damblon, Christian

2018-01-01

The analysis of spectroscopic data to solve chemical structures requires practical skills and drills. In this context, we have developed ULg Spectra, a computer-based tool designed to improve the ability of learners to perform complex reasoning. The identification of organic chemical compounds involves gathering and interpreting complementary…

The structure of an integral membrane peptide: a deuterium NMR study of gramicidin.

PubMed Central

Prosser, R S; Daleman, S I; Davis, J H

1994-01-01

Solid state deuterium NMR was employed on oriented multilamellar dispersions consisting of 1,2-dilauryl-sn-glycero-3-phosphatidylcholine and deuterium (2H) exchange-labeled gramicidin D, at a lipid to protein molar ratio (L/P) of 15:1, in order to study the dynamic structure of the channel conformation of gramicidin in a liquid crystalline phase. The corresponding spectra were used to discriminate between several structural models for the channel structure of gramicidin (based on the left- and right-handed beta 6.3 LD helix) and other models based on a structure obtained from high resolution NMR. The oriented spectrum is complicated by the fact that many of the doublets, corresponding to the 20 exchangeable sites, partially overlap. Furthermore, the asymmetry parameter, eta, of the electric field gradient tensor of the amide deuterons is large (approximately 0.2) and many of the amide groups are involved in hydrogen bonding, which is known to affect the quadrupole coupling constant. In order to account for these complications in simulating the spectra in the fast motional regime, an ab initio program called Gaussian 90 was employed, which permitted us to calculate, by quantum mechanical means, the complete electric field gradient tensor for each residue in gramicidin (using two structural models). Our results indicated that the left-handed helical models were inconsistent with our observed spectra, whereas a model based on the high-resolution structure derived by Arseniev and coworkers, but relaxed by a simple energy minimization procedure, was consistent with our observed spectra. The molecular order parameter was then estimated from the motional narrowing assuming the relaxed (right-handed) Arseniev structure. Our resultant order parameter of SZZ = 0.91 translates into an rms angle of 14 degrees, formed by the helix axis and the local bilayer normal. The strong resemblance between our spectra (and also those reported for gramicidin in 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) multilayers) and the spectra of the same peptide incorporated in a lyotropic nematic phase, suggests that the lyotropic nematic phase simulates the local environment of the lipid bilayer. PMID:7520293

Spectroscopic and structural study of the newly synthesized heteroligand complex of copper with creatinine and urea.

PubMed

Gangopadhyay, Debraj; Singh, Sachin Kumar; Sharma, Poornima; Mishra, Hirdyesh; Unnikrishnan, V K; Singh, Bachcha; Singh, Ranjan K

2016-02-05

Study of copper complex of creatinine and urea is very important in life science and medicine. In this paper, spectroscopic and structural study of a newly synthesized heteroligand complex of copper with creatinine and urea has been discussed. Structural studies have been carried out using DFT calculations and spectroscopic analyses were carried out by FT-IR, Raman, UV-vis absorption and fluorescence techniques. The copper complex of creatinine and the heteroligand complex were found to have much increased water solubility as compared to pure creatinine. The analysis of FT-IR and Raman spectra helps to understand the coordination properties of the two ligands and to determine the probable structure of the heteroligand complex. The LIBS spectra of the heteroligand complex reveal that the complex is free from other metal impurities. UV-visible absorption spectra and the fluorescence emission spectra of the aqueous solution of Cu-Crn-urea heteroligand complex at different solute concentrations have been analyzed and the complex is found to be rigid and stable in its monomeric form at very low concentrations. Copyright © 2015 Elsevier B.V. All rights reserved.

Theoretical studies on the structural and spectra properties of two C74 fullerenes and the chlorinated species C74Cl10

NASA Astrophysics Data System (ADS)

Zheng, Mei; Song, Xitong; Li, Xiaoqi; Qi, Jiayuan

2018-07-01

The geometrical/electronic structures, X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure spectroscopy of two especially C74 fullerenes (D3h-C74 and C1-C74) and the chlorinated species C1-C74Cl10, which are newly isolated in the experiment, have been calculated by means of the density functional theory (DFT) method. Effective changes in the electronic structure and simulated X-ray spectra have been observed after chlorination. Strong isomer dependence has been found in both spectra, thus the 'fingerprints' in the spectra can be employed as a tool to identify the isomers. The ultraviolet-visible (UV-vis) absorption spectrum of C1-C74Cl10 has been performed by using the time-dependent DFT method. The generated UV-vis spectrum coincides with the previous experimental counterpart. The results of this work can provide useful information especially for isomer identification and further study on fullerenes by means of the aforementioned spectroscopy techniques.

The molecular structure and vibrational, 1H and 13C NMR spectra of lidocaine hydrochloride monohydrate

NASA Astrophysics Data System (ADS)

Badawi, Hassan M.; Förner, Wolfgang; Ali, Shaikh A.

2016-01-01

The structure, vibrational and NMR spectra of the local anesthetic drug lidocaine hydrochloride monohydrate salt were investigated by B3LYP/6-311G∗∗ calculations. The lidocaine·HCl·H2O salt is predicted to have the gauche structure as the predominant form at ambient temperature with NCCN and CNCC torsional angles of 110° and -123° as compared to 10° and -64°, respectively in the base lidocaine. The repulsive interaction between the two N-H bonds destabilized the gauche structure of lidocaine·HCl·H2O salt. The analysis of the observed vibrational spectra is consistent with the presence of the lidocaine salt in only one gauche conformation at room temperature. The 1H and 13C NMR spectra of lidocaine·HCl·H2O were interpreted by experimental and DFT calculated chemical shifts of the lidocaine salt. The RMSD between experimental and theoretical 1H and 13C chemical shifts for lidocaine·HCl·H2O is 2.32 and 8.21 ppm, respectively.

Raman Spectral Signatures as Conformational Probes of Biomolecules

NASA Astrophysics Data System (ADS)

Golan, Amir; Mayorkas, Nitzan; Rosenwaks, Salman; Bar, Ilana

2009-06-01

A first application of ionization-loss stimulated Raman spectroscopy (ILSRS) for monitoring the spectral features of four conformers of a gas phase neurotransmitter (2-phenylethylamine) is reported. The Raman spectra of the conformers show bands that uniquely identify the conformational structure of the molecule and are well matched by density functional theory calculations. The measurement of spectral signatures by ILSRS in an extended spectral range, with a relatively convenient laser source, is extremely important, allowing enhanced accessibility to intra- and inter-molecular forces, which are significant in biological structure and activity.

Raman Spectral Signatures as Conformational Probes of Biomolecules

NASA Astrophysics Data System (ADS)

Bar, Ilana; Golan, Amir; Mayorkas, Nitzan; Rosenwaks, Salman

2009-03-01

A first application of ionization-loss stimulated Raman spectroscopy (ILSRS) monitoring the spectral features of four conformers of a gas phase neurotransmitter (2-phenylethylamine) is reported. The Raman spectra of the conformers show bands that uniquely identify the conformational structure of the molecule and are well matched by density functional theory calculations. The measurement of spectral signatures by ILSRS in an extended spectral range, with a relatively convenient laser source, is extremely important, allowing enhanced accessibility to intra- and inter-molecular forces, which are significant in biological structure and activity.

Isolation and structure elucidation of the nucleoside antibiotic strepturidin from Streptomyces albus DSM 40763.

PubMed

Pesic, Alexander; Steinhaus, Britta; Kemper, Sebastian; Nachtigall, Jonny; Kutzner, Hans Jürgen; Höfle, Gerhard; Süssmuth, Roderich D

2014-06-01

The antibiotic strepturidin (1) was isolated from the microorganism Streptomyces albus DSM 40763, and its structure elucidated by spectroscopic methods and chemical degradation studies. The determination of the relative and absolute stereocenters was partially achieved using chiral GC/EI-MS analysis and microderivatization by acetal ring formation and subsequent 2D-NMR analysis of key (1)H,(1)H-NOESY NMR correlations and extraction of (1)H,(13)C coupling constants from (1)H,(13)C-HMBC NMR spectra. Based on these results, a biosynthesis model was proposed.

The structure elucidation of mequindox and 1,4-bisdesoxymequindox: NMR analyses, FT-IR spectra, DFT calculations and thermochemical studies

NASA Astrophysics Data System (ADS)

Zhang, Jiaheng; He, Xin; Gao, Haixiang

2011-10-01

In the current work, we report a combined experimental and theoretical study on the molecular conformation, vibrational spectra, and nuclear magnetic resonance (NMR) spectra of mequindox (MEQ) and 1,4-bisdesoxymequindox (1,4-BDM). The geometric structure and vibrational frequencies of MEQ and 1,4-BDM have been calculated by density functional theory employing the B3LYP functional and 6-311++G(d,p) basis set. The 1H and 13C NMR chemical shifts have been calculated by gauge-including atomic orbital method with B3LYP 6-311++G(2df,2pd) approach. The calculation results have been applied to simulate the infrared and NMR spectra of the compounds. The theoretical results agree well with the observed spectra. The bond dissociation enthalpy of MEQ and the heat of formation of MEQ and 1,4-BDM have also been computed.

Structure of the two-dimensional relaxation spectra seen within the eigenmode perturbation theory and the two-site exchange model.

PubMed

Bytchenkoff, Dimitri; Rodts, Stéphane

2011-01-01

The form of the two-dimensional (2D) NMR-relaxation spectra--which allow to study interstitial fluid dynamics in diffusive systems by correlating spin-lattice (T(1)) and spin-spin (T(2)) relaxation times--has given rise to numerous conjectures. Herein we find analytically a number of fundamental structural properties of the spectra: within the eigen-modes formalism, we establish relationships between the signs and intensities of the diagonal and cross-peaks in spectra obtained by various 1 and 2D NMR-relaxation techniques, reveal symmetries of the spectra and uncover interdependence between them. We investigate more specifically a practically important case of porous system that has sets of T(1)- and T(2)-eigenmodes and eigentimes similar to each other by applying the perturbation theory. Furthermore we provide a comparative analysis of the application of the, mathematically more rigorous, eigen-modes formalism and the, rather more phenomenological, first-order two-site exchange model to diffusive systems. Finally we put the results that we could formulate analytically to the test by comparing them with computer-simulations for 2D porous model systems. The structural properties, in general, are to provide useful clues for assignment and analysis of relaxation spectra. The most striking of them--the presence of negative peaks--underlines an urgent need for improvement of the current 2D Inverse Laplace Transform (ILT) algorithm used for calculation of relaxation spectra from NMR raw data. Copyright © 2010 Elsevier Inc. All rights reserved.

Biological tissue component evaluation by measuring photoacoustic spectrum

NASA Astrophysics Data System (ADS)

Namita, Takeshi; Murata, Yuya; Tokuyama, Junji; Kondo, Kengo; Yamakawa, Makoto; Shiina, Tsuyoshi

2017-03-01

Photoacoustic imaging has garnered constant attention as a non-invasive modality for visualizing details of the neovascularization structure of tumors, or the distribution of oxygen saturation, which is related to the tumor grade. However, photoacoustic imaging is applicable not only for vascular imaging but also for diagnosing properties of various tissues such as skin or muscle diseases, fat related to arteriosclerosis or fatty liver, cartilage related to arthritis, and fibrous tissues related to hepatitis. The photoacoustic signal intensity is wavelength-dependent and proportional to the absorption coefficient and thermal acoustic conversion efficiency (i.e. Grüneisen parameter) of the target biological tissue. To ascertain the appropriate wavelength range for biological tissue imaging and to evaluate tissue properties, photoacoustic spectra of various tissues (e.g., skin, muscle, and adipose tissue) were measured using a hydrophone (9 mm diameter) at 680-1600 nm wavelengths. Results confirmed that respective tissues have unique photoacoustic spectra. However, almost all samples have peaks around 1200 nm and 1400-1500 nm for wavelengths where the light absorbance of lipid or water is high. The main components of biological tissues are water, protein, and lipid. Results confirmed that photoacoustic spectra reflect the tissue components well. To evaluate the feasibility of the tissue characterization using photoacoustic methods, the photoacoustic signal intensity ratio between two wavelength regions was calculated as described above. Signal intensity ratios agreed well with the composition ratio between water and lipid in samples. These analyses verified the feasibility of evaluating tissue properties using photoacoustic methods.

Fabrication and photoluminescence properties of graphite fiber/ZnO nanorod core-shell structures.

PubMed

Liu, Xianbin; Du, Hejun; Liu, Bo; Wang, Jianxiong; Sun, Xiao Wei; Sun, Handong

2011-08-01

Graphite fiber/ZnO nanorod core-shell structures were synthesized by thermal evaporation process. The core-shell hybrid architectures were comprised of ZnO nanorods grown on the surface of graphite fiber. In addition, Hollow ZnO hierarchical structure can be obtained by oxidizing the graphite fiber. Room temperature photoluminescence (PL) of the as-made graphite fiber/ZnO nanorod structures shows two UV peaks at around 3.274 eV and 3.181 eV. The temperature-dependent photoluminescence spectra demonstrate the two UV emissions are attributed to the intrinsic optical transitions and extrinsic defect-related emissions in ZnO. These hybrid structures may be used as the building block for fabrication of nanodevices.

Surface proton transport of fully protonated poly(aspartic acid) thin films on quartz substrates

NASA Astrophysics Data System (ADS)

Nagao, Yuki; Kubo, Takahiro

2014-12-01

Thin film structure and the proton transport property of fully protonated poly(aspartic acid) (P-Asp100) have been investigated. An earlier study assessed partially protonated poly(aspartic acid), highly oriented thin film structure and enhancement of the internal proton transport. In this study of P-Asp100, IR p-polarized multiple-angle incidence resolution (P-MAIR) spectra were measured to investigate the thin film structure. The obtained thin films, with thicknesses of 120-670 nm, had no oriented structure. Relative humidity dependence of the resistance, proton conductivity, and normalized resistance were examined to ascertain the proton transport property of P-Asp100 thin films. The obtained data showed that the proton transport of P-Asp100 thin films might occur on the surface, not inside of the thin film. This phenomenon might be related with the proton transport of the biological system.

Comparison of red blood cells from gastric cancer patients and healthy persons using FTIR spectroscopy

NASA Astrophysics Data System (ADS)

Liu, Hui; Su, Qinglong; Sheng, Daping; Zheng, Wei; Wang, Xin

2017-02-01

In this paper, FTIR spectroscopy was used to compare gastric cancer patients' red blood cells (RBCs) with healthy persons' RBCs. IR spectra were acquired with high resolution. The A1653/A1543 (the protein secondary structures), A1543/A2958 (the relative content of proteins and lipids), A1106/A1166 (the structure and content changes of sugars) and A1543/A1106 (the relative content of proteins and sugars) ratios of gastric cancer patients' RBCs were significantly different from those of healthy persons' RBCs. Curve fitting results showed that the protein secondary structures and sugars' structures had differences between gastric cancer patients' and healthy persons' RBCs. Additionally, FTIR spectroscopy could obtain 95% sensitivity, 70% specificity, 84.2% accuracy and 80.9% positive predictive value in combination with canconical discriminant analysis. The above results indicate FTIR spectroscopy may be useful for diagnosing gastric cancer.

The affects of doping Eu 3+ on structures and morphology of ZrO 2 nanocrystals

NASA Astrophysics Data System (ADS)

Yu, Lixin; Liu, Hai; Nogami, Masayuki

2010-07-01

The ZrO 2 and ZrO 2:Eu 3+ nanocrystals (NCs) were prepared by a hydrothermal method. The samples were sintered at different temperatures (500, 800 and 1100 °C). The results indicate that the Eu 3+ ions affect not only the structures of hosts (ZrO 2), but also the morphology of hosts. The shape of ZrO 2:Eu 3+ NCs heated at 1100 °C is the one-dimensional nanorod, while is the zero-dimensional nanoparticle for pure ZrO 2 samples sintered at the same temperature. The excitation and emission spectra of ZrO 2:Eu 3+ NCs were studied. In excitation spectra, the charge transfer band of Eu 3+ in ZrO 2 NCs heated at 1100 °C evidently blue-shifts in comparison with the NCs calcined at 500 and 800 °C. The relative intensity of 5D-7F transitions of Eu 3+ ions and color chromaticity for nanorods are increased in comparison with the nanoparticles.

Polarization Dependent Bulk-sensitive Valence Band Photoemission Spectroscopy and Density Functional Theory Calculations: Part I. 3d Transition Metals

NASA Astrophysics Data System (ADS)

Ueda, Shigenori; Hamada, Ikutaro

2017-12-01

The X-ray polarization dependent valence band HAXPES spectra of 3d transition metals (TMs) of Ti-Zn were measured to investigate the orbital resolved electronic structures by utilizing that the fact the photoionization cross-section of the atomic orbitals strongly depends on the experimental geometry. We have calculated the HAXPES spectra, which correspond to the cross-section weighted densities of states (CSW-DOSs), where the DOSs were obtained by the density functional theory calculations, and we have determined the relative photoionization cross-sections of the 4s and 4p orbitals to the 3d orbital in the 3d TMs. The experimentally obtained bulk-sensitive 3d and 4s DOSs were good agreement with the calculated DOSs in Ti, V, Cr, and Cu. In contrast, the deviations between the experimental and calculated 3d DOSs for Mn, Fe, Co, Ni were found, suggesting that the electron correlation plays an important role in the electronic structures for these materials.

Structural phase transitions in niobium oxide nanocrystals

NASA Astrophysics Data System (ADS)

Yuvakkumar, R.; Hong, Sun Ig

2015-09-01

Niobium oxide nanocrystals were successfully synthesized employing the green synthesis method. Phase formation, microstructure and compositional properties of 1, 4 and 7 days incubation treated samples after calcinations at 450 °C were examined using X-ray diffraction, Raman, photoluminescence (PL), infrared, X-ray photoelectron spectra and transmission electron microscopic characterizations. It was observed that phase formation of Nb2O5 nanocrystals was dependent upon the incubation period required to form stable metal oxides. The characteristic results clearly revealed that with increasing incubation and aging, the transformation of cubic, orthorhombic and monoclinic phases were observed. The uniform heating at room temperature (32 °C) and the ligation of niobium atoms due to higher phenolic constituents of utilized rambutan during aging processing plays a vital role in structural phase transitions in niobium oxide nanocrystals. The defects over a period of incubation and the intensities of the PL spectra changing over a period of aging were related to the amount of the defects induced by the phase transition.

Influence of silver nanoparticles on food components in wheat

NASA Astrophysics Data System (ADS)

Nawrocka, A.; Cieśla, J.

2013-01-01

During storage, grain might be affected by bacterial and fungal infections. Pathogens diminish the grain quality through contamination with excrements and second metabolites. It is very important to prevent grain from infections. Due to their antimicrobial properties, silver nanoparticles can play the role of an effective protector. The influence of nanoparticles on wheat quality was studied. The gluten parameters and falling number did not change after covering the grain with silver nanoparticles stabilized by sodium citrate. Changes in the structure of starch and gluten were investigated using Fourier-transform infrared spectroscopy. Infrared spectra of the whole meal and starch have shown a slight shift (from 1 000 to 995cm-1) of the band connected with the C-O-H bending. This displacement is probably related to the changes in sample moisture. Significant differences, corresponding to changes in the protein secondary structure, have appeared in the gluten spectra after covering.A decrease of absorbance in the amide and CH and OH regions has been observed regardless of the covering time.

Molecular spectroscopy of CH Cygni in the 1998-2000 active phas

NASA Astrophysics Data System (ADS)

Kotnik-Karuza, D.; Jurdana-Sepic, R.; Majlinger, Z.

The subject of this study is the very peculiar symbiotic binary CH Cygni, in particular the physical conditions in the photosphere of its cool component. The latter has been classified as an M late type giant due to its spectral appearance in the optical and near IR spectral region during quiescent and active phases. Several consecutive spectra obtained with different exposure times covering the region lambda 4800-9000 A were obtained on 24/25 November 1999 which means that they belong to the 1998-2000 active phase. We have concentrated our investigations on the TiO absorption bands which are the most outstanding feature in these spectra. The bands, some of which give evidence of a partly resolved rotational structure, have been identified as members of the alpha, gamma, gamma prim, beta, delta, phi and epsilon band systems. Measurement of the band head relative intensities and some other features in their structure have led to determination of temperatures of the coolest layers in the red giant's photosphere.

Turbulence and Coherent Structure in the Atmospheric Boundary Layer near the Eyewall of Hurricane Hugo (1989)

NASA Astrophysics Data System (ADS)

Zhang, J. A.; Marks, F. D.; Montgomery, M. T.; Black, P. G.

2008-12-01

In this talk we present an analysis of observational data collected from NOAA'S WP-3D research aircraft during the eyewall penetration of category five Hurricane Hugo (1989). The 1 Hz flight level data near 450m above the sea surface comprising wind velocity, temperature, pressure and relative humidity are used to estimate the turbulence intensity and fluxes. In the turbulent flux calculation, the universal shape spectra and co-spectra derived using the 40 Hz data collected during the Coupled Boundary Layer Air-sea Transfer (CBLAST) Hurricane experiment are applied to correct the high frequency part of the data collected in Hurricane Hugo. Since the stationarity assumption required for standard eddy correlations is not always satisfied, different methods are summarized for computing the turbulence parameters. In addition, a wavelet analysis is conducted to investigate the time and special scales of roll vortices or coherent structures that are believed important elements of the eye/eyewall mixing processes that support intense storms.

Non-destructive evaluation of nano-sized structure of thin film devices by using small angle neutron scattering.

PubMed

Shin, E J; Seong, B S; Choi, Y; Lee, J K

2011-01-01

Nano-sized multi-layers copper-doped SrZrO3, platinum (Pt) and silicon oxide (SiO2) on silicon substrates were prepared by dense plasma focus (DPF) device with the high purity copper anode tip and analyzed by using small angle neutron scattering (SANS) to establish a reliable method for the non-destructive evaluation of the under-layer structure. Thin film was well formed at the time-to-dip of 5 microsec with stable plasma of DPF. Several smooth intensity peaks were periodically observed when neutron beam penetrates the thin film with multi-layers perpendicularly. The platinum layer is dominant to intensity peaks, where the copper-doped SrZnO3 layer next to the platinum layer causes peak broadening. The silicon oxide layer has less effect on the SANS spectra due to its relative thick thickness. The SANS spectra shows thicknesses of platinum and copper-doped SrZnO3 layers as 53 and 25 nm, respectively, which are well agreement with microstructure observation.

An investigation on physical properties of SiOx nanowires deposited by chemical vapor deposition method: The effect of substrate to boat distance

NASA Astrophysics Data System (ADS)

Heidaryan, Narges; Eshghi, Hosein

2017-09-01

Large-scale silicon oxide nanowires (SiOx NWs) with a diameter about 250 nm on silicon wafers were synthesized by thermal evaporation of silicon monoxide (SiO) powder. In order to investigate the role of distance on the physical properties of SiOx NWs, Si substrates were positioned at 5 cm and 10 cm apart from the boat position set at 1150∘C. The local temperatues of the samples were 1100∘C and 1050∘C, respectively. The SEM images and EDS spectra showed interweaved networks of SiOx NWs with x = 0.62 and 0.65 in these layers. The XRD patterns showed S1 has a polycrystalline structure (cristobalite), while S2 has amorphous nature. The PL spectra showed an intense blue peak at 468 nm in S1, and a violet peak at 427 nm in S2 that could be related to the differences in the crystallite structures and oxygen vacancies in these samples.

Various physical properties of Mn_1-xFex alloy films

NASA Astrophysics Data System (ADS)

Kim, J. B.; Cho, K. H.; Nahm, T.-U.; Lee, Y. P.; Kim, K. W.; Kudryavtsev, Y. V.; Gontarz, R.; Szymanski, B.

2003-03-01

The structural dependences of the magneto-optical, the optical and the magnetic properties of Mn_1-xFex alloy films have been investigated. It was revealed that the EKE (equatorial Kerr effect) signal at 293 K for the Mn_1-xFex alloy films can be observed only for x > 0.50. All the EKE spectra have nearly the same spectral shape (Fe-like) and differ from each other only in the intensity. The observed experimental EKE spectra for the Fe-rich Mn_1-xFex alloy films can be nicely described by the simulated ones made in the framework of the effective medium approximation. The optical properties such as optical conductivity of all the investigated alloys can be separated into three groups which are related to the different crystalline structures of alloys: predominance of the α-Fe (0.8 < x < 0.97), the γ-Mn-Fe (0.2 < x < 0.6) and the α-Mn (0.02 < x < 0.23) phases, respectively.

The pressure-induced structural response of rare earth hafnate and stannate pyrochlore from 0.1-50 GPa

NASA Astrophysics Data System (ADS)

Turner, K. M.; Rittman, D.; Heymach, R.; Turner, M.; Tracy, C.; Mao, W. L.; Ewing, R. C.

2017-12-01

Complex oxides with the pyrochlore (A2B2O7) and defect-fluorite ((A,B)4O7) structure-types undergo structural transformations under high-pressure. These compounds are under consideration for applications including as a proposed waste-form for actinides generated in the nuclear fuel cycle. High-pressure transformations in rare earth hafnates (A2Hf2O7, A=Sm, Eu, Gd, Dy, Y, Yb) and stannates (A2Sn2O7, A=Nd, Gd, Er) were investigated to 50 GPa by in situ Raman spectroscopy and synchrotron x-ray diffraction (XRD). Rare-earth hafnates form the pyrochlore structure for A=La-Tb and the defect-fluorite structure for A=Dy-Lu. Lanthanide stannates form the pyrochlore structure. Raman spectra revealed that at ambient pressure all compositions have pyrochlore-type short-range order. Stannate compositions show a larger degree of pyrochlore-type short-range ordering relative to hafnates. In situ high-pressure synchrotron XRD showed that rare earth hafnates and stannates underwent a pressure-induced phase transition to a cotunnite-like (Pnma) structure that begins between 18-25 GPa in hafnates and between 30-33 GPa in stannates. The phase transition is not complete at 50 GPa, and upon decompression, XRD indicates that all compositions transform to defect-fluorite with an amorphous component. In situ Raman spectroscopy showed that disordering in stannates and hafnates occurs gradually upon compression. Pyrochlore-structured hafnates retain short-range order to a higher pressure (30 GPa vs. <10 GPa) than defect-fluorite-structured hafnates. Hafnates and stannates decompressed from 50 GPa show Raman spectra consistent with weberite-type structures, also reported in irradiated stannates. The second-order Birch-Murnaghan equation of state fit gives a bulk modulus of 250 GPa for hafnate compositions with the pyrochlore structure, and 400 GPa for hafnate compositions with the defect-fluorite structure. Stannates have a lower bulk modulus relative to hafnates (between 80-150 GPa). Stannate and hafnate pyrochlore compositions taken to high pressure show structural transformations consistent with irradiated pyrochlore, and compositionally disordered pyrochlore: a long-range structure best described by defect-fluorite, and a short-range structure best described by weberite.

Coherent manipulation of spontaneous emission spectra in coupled semiconductor quantum well structures.

PubMed

Chen, Aixi

2014-11-03

In triple coupled semiconductor quantum well structures (SQWs) interacting with a coherent driving filed, a coherent coupling field and a weak probe field, spontaneous emission spectra are investigated. Our studies show emission spectra can easily be manipulated through changing the intensity of the driving and coupling field, detuning of the driving field. Some interesting physical phenomena such as spectral-line enhancement/suppression, spectral-line narrowing and spontaneous emission quenching may be obtained in our system. The theoretical studies of spontaneous emission spectra in SQWS have potential application in high-precision spectroscopy. Our studies are based on the real physical system [Appl. Phys. Lett.86(20), 201112 (2005)], and this scheme might be realizable with presently available techniques.

Luminescence spectra of a cholesteric photonic crystal

NASA Astrophysics Data System (ADS)

Dolganov, P. V.

2017-05-01

The transmission and luminescence spectra of a cholesteric photonic crystal doped with an organic dye are measured. The density of photon states is calculated using the material parameters obtained from the comparison of the experimental and theoretical spectra. The shape of the luminescence spectra is modified with respect to the density of photon states owing to the difference in the structure of the normal modes of the photonic crystal near the short-wavelength and long-wavelength edges of the photonic quasi-band gap upon the "pushing" of the photon states from the gap and to the nonvanishing orientation ordering of the luminescent molecules. The luminescence spectrum calculated taking into account the chiral structure of the photonic crystal agrees with the experimental spectrum.

Trident: A Universal Tool for Generating Synthetic Absorption Spectra from Astrophysical Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hummels, Cameron B.; Smith, Britton D.; Silvia, Devin W.

Hydrodynamical simulations are increasingly able to accurately model physical systems on stellar, galactic, and cosmological scales; however, the utility of these simulations is often limited by our ability to directly compare them with the data sets produced by observers: spectra, photometry, etc. To address this problem, we have created trident, a Python-based open-source tool for post-processing hydrodynamical simulations to produce synthetic absorption spectra and related data. trident can (i) create absorption-line spectra for any trajectory through a simulated data set mimicking both background quasar and down-the-barrel configurations; (ii) reproduce the spectral characteristics of common instruments like the Cosmic Origins Spectrograph;more » (iii) operate across the ultraviolet, optical, and infrared using customizable absorption-line lists; (iv) trace simulated physical structures directly to spectral features; (v) approximate the presence of ion species absent from the simulation outputs; (vi) generate column density maps for any ion; and (vii) provide support for all major astrophysical hydrodynamical codes. trident was originally developed to aid in the interpretation of observations of the circumgalactic medium and intergalactic medium, but it remains a general tool applicable in other contexts.« less

Identification and Structural Characterization of Naturally-Occurring Broad-Spectrum Cyclic Antibiotics Isolated from Paenibacillus

NASA Astrophysics Data System (ADS)

Knolhoff, Ann M.; Zheng, Jie; McFarland, Melinda A.; Luo, Yan; Callahan, John H.; Brown, Eric W.; Croley, Timothy R.

2015-08-01

The rise of antimicrobial resistance necessitates the discovery and/or production of novel antibiotics. Isolated strains of Paenibacillus alvei were previously shown to exhibit antimicrobial activity against a number of pathogens, such as E. coli, Salmonella, and methicillin-resistant Staphylococcus aureus (MRSA). The responsible antimicrobial compounds were isolated from these Paenibacillus strains and a combination of low and high resolution mass spectrometry with multiple-stage tandem mass spectrometry was used for identification. A group of closely related cyclic lipopeptides was identified, differing primarily by fatty acid chain length and one of two possible amino acid substitutions. Variation in the fatty acid length resulted in mass differences of 14 Da and yielded groups of related MSn spectra. Despite the inherent complexity of MS/MS spectra of cyclic compounds, straightforward analysis of these spectra was accomplished by determining differences in complementary product ion series between compounds that differ in molecular weight by 14 Da. The primary peptide sequence assignment was confirmed through genome mining; the combination of these analytical tools represents a workflow that can be used for the identification of complex antibiotics. The compounds also share amino acid sequence similarity to a previously identified broad-spectrum antibiotic isolated from Paenibacillus. The presence of such a wide distribution of related compounds produced by the same organism represents a novel class of broad-spectrum antibiotic compounds.

Atmospheric Modeling of Cool Giant and Supergiant Stars

NASA Astrophysics Data System (ADS)

Linsky, Jeffrey L.

1984-07-01

We propose to continue our collaborative program of obtaining and analysing high dispersion SWP spectra of cool stars. We request high dispersion, short wavelength IUE spectra of the stars alpha Tau (K5III), gamma Cru (M3III), epsilon Peg (K2Ib) and beta Cam (G0Ib) with exposure times of 16 hours or more. These spectra will provide measurements of line profiles, widths and Doppler shifts in addition to density-sensitive and opacity-sensitive line ratios. Models of chromospheric and transition region (where present) structure will be calculated by a combination of emission measure analysis, line opacity/probability of escape methods and model atmosphere calculations for optically thick resonance lines such as MgII h and k, including partial redistribution radiative transfer. These models will be used to investigate the atmospheric energy balance and the nature of energy transport and nonradiative energy deposition processes. The results will be considered in relation to stellar evolution and compared with the chromospheric properties of other stars previously studied by the authors and their collaborators.

Energy spectra of vibron and cluster models in molecular and nuclear systems

NASA Astrophysics Data System (ADS)

Jalili Majarshin, A.; Sabri, H.; Jafarizadeh, M. A.

2018-03-01

The relation of the algebraic cluster model, i.e., of the vibron model and its extension, to the collective structure, is discussed. In the first section of the paper, we study the energy spectra of vibron model, for diatomic molecule then we derive the rotation-vibration spectrum of 2α, 3α and 4α configuration in the low-lying spectrum of 8Be, 12C and 16O nuclei. All vibrational and rotational states with ground and excited A, E and F states appear to have been observed, moreover the transitional descriptions of the vibron model and α-cluster model were considered by using an infinite-dimensional algebraic method based on the affine \\widehat{SU(1,1)} Lie algebra. The calculated energy spectra are compared with experimental data. Applications to the rotation-vibration spectrum for the diatomic molecule and many-body nuclear clusters indicate that there are solvable models and they can be approximated very well using the transitional theory.

How diverse is the asteroid belt?

NASA Technical Reports Server (NTRS)

Burbine, Thomas H.; Bell, Jeffrey F.

1993-01-01

For approximately twenty years, many different asteroid taxonomies, which used many different observational data sets, have been developed to try to group asteroids into classes that contain members with similar spectral characteristics. However, to understand the structure of the asteroid belt, the resulting classes are only useful if they are grouping together asteroids with somewhat similar mineralogies and thermal histories. Until recently, these taxonomies have focused on spectral reflectance data from 0.3 to 1.1 microns and visual albedo. But in the last five years, observational data sets (e.g., 0.8 to 2.5 microns spectra, CCD spectra, 3 microns spectra, and radar albedos) for a small number of asteroids were compiled that can give a better mineralogical interpretation, but whose use in asteroid taxonomy was relatively limited. Analyses of these 'supplementary' data sets show that most asteroid classes contain members with different compositions and/or thermal histories. To understand the diversity of the asteroid belt, the number of objects with these observations must be expanded and used in the next generation of taxonomies.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, and trimethylgermyl derivatives of 3,3-dimethyl cyclopropene V. 3,3-Dimethyl-1-(trimethylgermyl)cyclopropene

NASA Astrophysics Data System (ADS)

De Maré, G. R.; Panchenko, Yu. N.; Abramenkov, A. V.; Baird, M. S.; Tverezovsky, V. V.; Nizovtsev, A. V.; Bolesov, I. G.

2004-02-01

3,3-Dimethyl-1-(trimethylgermyl)cyclopropene ( I) was synthesised using a standard procedure. The IR and Raman spectra of I in the liquid phase were measured. The molecular geometry of I was optimised completely at the HF/6-31G* level. The HF/6-31G*//HF/6-31G* force field was calculated and scaled using the set of scale factors transferred from those determined previously for scaling the theoretical force fields of 3,3-dimethylbutene-1 and 1-methyl-, 1,2-dimethyl-, and 3,3-dimethylcyclopropene. The assignments of the observed vibrational bands were performed using the theoretical frequencies calculated from the scaled HF/6-31G*//HF/6-31G* force field and the ab initio values of the IR intensities, Raman cross-sections and depolarisation ratios. The theoretical spectra are given. The completely optimised structural parameters of I and its vibrational frequencies are compared with corresponding data of related molecules.

Phase transitions and proton ordering in hemimorphite: new insights from single-crystal EPR experiments and DFT calculations

NASA Astrophysics Data System (ADS)

Mao, Mao; Li, Zucheng; Pan, Yuanming

2013-02-01

Single-crystal electron paramagnetic resonance spectra of gamma-ray-irradiated hemimorphite (Mapimi, Durango, Mexico) after storage at room temperature for 3 months, measured from 4 to 275 K, reveal a hydroperoxy radical HO2 derived from the water molecule in the channel. The EPR spectra of the HO2 radical confirm that hemimorphite undergoes two reversible phase transitions at ~98 and ~21 K and allow determinations of its spin Hamiltonian parameters, including superhyperfine coupling constants of two more-distant protons from the neighboring hydroxyl groups, at 110, 85, 40 and 7 K. These EPR results show that the HO2 radical changes in site symmetry from monoclinic to triclinic related to the ordering and rotation of its precursor water molecule in the channel at <98 K. The monoclinic structure of hemimorphite with completely ordered O-H systems at low temperature has been evaluated by both the EPR spectra of the HO2 radical at <21 K and periodic density functional theory calculations.

Studies of molecular diffusion in single-supported bilayer lipid membranes at high hydration by quasielastic neutron scattering

NASA Astrophysics Data System (ADS)

Bai, M.; Miskowiec, A.; Wang, S.-K.; Taub, H.; Hansen, F. Y.; Jenkins, T.; Tyagi, M.; Neumann, D. A.; Diallo, S. O.; Mamontov, E.; Herwig, K. W.

2011-03-01

Bilayer lipid membranes supported on a solid surface are attractive model systems for understanding the structure and dynamics of more complex biological membranes that form the outer boundary of living cells. We have recently obtained quasielastic neutron spectra from single-supported bilayer lipid membranes using the backscattering spectrometer BASIS at the Spallation Neutron Source. Protonated DMPC membranes were deposited onto Si O2 -coated Si(100) substrates and characterized by AFM. Analysis of their neutron spectra shows evidence of a relatively broad Lorentzian component that we associate with bulk-like water above a freezing temperature of ~ 267 K. At lower temperatures, the spectra differ qualitatively from that of bulk supercooled water, a behavior that we attribute to water bound to the membrane. We also find evidence of a narrow Lorentzian component that we tentatively identify with a slower motion (time scale ~ 1 ns) associated with conformational changes of the alkyl tails of the lipid molecules. Supported by NSF Grant No. DMR-0705974.

Spectral fitting inversion of low-frequency normal modes with self-coupling and cross-coupling of toroidal and spheroidal multiplets: numerical experiments to estimate the isotropic and anisotropic velocity structures

NASA Astrophysics Data System (ADS)

Oda, Hitoshi

2016-06-01

The aspherical structure of the Earth is described in terms of lateral heterogeneity and anisotropy of the P- and S-wave velocities, density heterogeneity, ellipticity and rotation of the Earth and undulation of the discontinuity interfaces of the seismic wave velocities. Its structure significantly influences the normal mode spectra of the Earth's free oscillation in the form of cross-coupling between toroidal and spheroidal multiplets and self-coupling between the singlets forming them. Thus, the aspherical structure must be conversely estimated from the free oscillation spectra influenced by the cross-coupling and self-coupling. In the present study, we improve a spectral fitting inversion algorithm which was developed in a previous study to retrieve the global structures of the isotropic and anisotropic velocities of the P and S waves from the free oscillation spectra. The main improvement is that the geographical distribution of the intensity of the S-wave azimuthal anisotropy is represented by a nonlinear combination of structure coefficients for the anisotropic velocity structure, whereas in the previous study it was expanded into a generalized spherical harmonic series. Consequently, the improved inversion algorithm reduces the number of unknown parameters that must be determined compared to the previous inversion algorithm and employs a one-step inversion method by which the structure coefficients for the isotropic and anisotropic velocities are directly estimated from the fee oscillation spectra. The applicability of the improved inversion is examined by several numerical experiments using synthetic spectral data, which are produced by supposing a variety of isotropic and anisotropic velocity structures, earthquake source parameters and station-event pairs. Furthermore, the robustness of the inversion algorithm is investigated with respect to the back-ground noise contaminating the spectral data as well as truncating the series expansions by finite terms to represent the three-dimensional velocity structures. As a result, it is shown that the improved inversion can estimate not only the isotropic and anisotropic velocity structures but also the depth extent of the anisotropic regions in the Earth. In particular, the cross-coupling modes are essential to correctly estimate the isotropic and anisotropic velocity structures from the normal mode spectra. In addition, we argue that the effect of the seismic anisotropy is not negligible when estimating only the isotropic velocity structure from the spheroidal mode spectra.

Electrical, thermal, catalytic and magnetic properties of nano-structured materials and their applications

NASA Astrophysics Data System (ADS)

Liu, Zuwei

Nanotechnology is a subject that studies the fabrication, properties, and applications of materials on the nanometer-scale. Top-down and bottom-up approaches are commonly used in nano-structure fabrication. The top-down approach is used to fabricate nano-structures from bulk materials by lithography, etching, and polishing etc. It is commonly used in mechanical, electronic, and photonic devices. Bottom-up approaches fabricate nano-structures from atoms or molecules by chemical synthesis, self-assembly, and deposition, such as sol-gel processing, molecular beam epitaxy (MBE), focused ion beam (FIB) milling/deposition, chemical vapor deposition (CVD), and electro-deposition etc. Nano-structures can have several different dimensionalities, including zero-dimensional nano-structures, such as fullerenes, nano-particles, quantum dots, nano-sized clusters; one-dimensional nano-structures, such as carbon nanotubes, metallic and semiconducting nanowires; two-dimensional nano-structures, such as graphene, super lattice, thin films; and three-dimensional nano-structures, such as photonic structures, anodic aluminum oxide, and molecular sieves. These nano-structured materials exhibit unique electrical, thermal, optical, mechanical, chemical, and magnetic properties in the quantum mechanical regime. Various techniques can be used to study these properties, such as scanning probe microscopy (SPM), scanning/transmission electron microscopy (SEM/TEM), micro Raman spectroscopy, etc. These unique properties have important applications in modern technologies, such as random access memories, display, solar energy conversion, chemical sensing, and bio-medical devices. This thesis includes four main topics in the broad area of nanoscience: magnetic properties of ferro-magnetic cobalt nanowires, plasmonic properties of metallic nano-particles, photocatalytic properties of titanium dioxide nanotubes, and electro-thermal-optical properties of carbon nanotubes. These materials and their properties are briefly reviewed in Chapter One, including the concepts of ferro-magnetism, plasmonics, photocatalysis, thermal emission, and Raman spectra of carbon nanotubes. In Chapter Two, we focus on the magnetic properties of ferro-magnetic cobalt nanowires with high crystalline quality synthesized via a low voltage electro-deposition method. The crystal structure of these Co nanowires is characterized by high resolution transmission electron microscopy and X-ray diffraction. The magnetic properties of individual nanowires and nanowire arrays are investigated by magnetic force microscope (MFM) and superconducting quantum interference device (SQUID) measurements. A theoretical model is developed to explain these experimental observations. In Chapter Three, we exploit the strong plasmon resonance of gold nanoparticles. We also demonstrate a new method for patterning SERS (surface enhanced Raman spectroscopy) aggregates of gold nanoparticles by using a focused laser beam to optically trap the nanoparticles in a water suspension. Raman spectroscopy is used to estimate the temperature in the laser spot during the in-situ aggregation, by measuring the Raman peak of the hydroxyl bond of water. In Chapter Four, we demonstrate plasmonic enhancement of photocatalytic water splitting under visible illumination by integrating strongly plasmonic Au nanoparticles with strongly catalytic TiO2. Electromagnetic simulations indicate that the near-field optical enhancement increases the electron-hole pair generation rate at the surface of the TiO2, thus increasing the amount of photo-generated charge contributing to catalysis. Our results suggest that enhancement factors many times larger than this are possible if this mechanism can be optimized. In Chapter Five, we study the Raman spectra and thermal emission spectra of individual suspended carbon nanotubes induced by electrical heating. Semiconducting and metallic devices exhibit different spectra, based on their distinctive band structures. Raman spectra and the blackbody emission background are used to fit the device temperature. In addition to the blackbody emission background, polarized peaks along the nanotube direction are observed in different ranges of the thermal emission spectra for metallic and semiconducting devices. These peaks are attributed to the transitions between Van Hove singularities that are thermally driven under these high applied bias voltages. A theoretical model is developed to calculate the thermal emission spectra based on this conclusion. In Chapter Six, we present some data of single crystal zinc oxide (ZnO) nanowires synthesized by the CVD method, including magneto-resistance measurements, optical-resistance measurements, and scanning-gate measurements. In Chapter Seven, we discuss some future work related to photocatalysis and carbon nanotubes.

Investigation on the neutral and anionic BxAlyH2 (x + y = 7, 8, 9) clusters using density functional theory combined with photoelectron spectroscopy.

PubMed

Ding, Li-Ping; Shao, Peng; Lu, Cheng; Zhang, Fang-Hui; Ding, Lei; Yuan, Tao Li

2016-08-17

The structure and bonding nature of neutral and negatively charged BxAlyH2 (x + y = 7, 8, 9) clusters are investigated with the aid of previously published experimental photoelectron spectra combined with the present density functional theory calculations. The comparison between the experimental photoelectron spectra and theoretical simulated spectra helps to identify the ground state structures. The accuracy of the obtained ground state structures is further verified by calculating their adiabatic electron affinities and vertical detachment energies and comparing them against available experimental data. The results show that the structures of BxAlyH2 transform from three-dimensional to planar structures as the number of boron atoms increases. Moreover, boron atoms tend to bind together forming Bn units. The hydrogen atoms prefer to bind with boron atoms rather than aluminum atoms. The analyses of the molecular orbital on the ground state structures further support the abovementioned results.

Structure assignment, electronic properties, and magnetism quenching of endohedrally doped neutral silicon clusters, Si(n)Co (n = 10-12).

PubMed

Li, Yejun; Tam, Nguyen Minh; Claes, Pieterjan; Woodham, Alex P; Lyon, Jonathan T; Ngan, Vu Thi; Nguyen, Minh Tho; Lievens, Peter; Fielicke, André; Janssens, Ewald

2014-09-18

The structures of neutral cobalt-doped silicon clusters have been assigned by a combined experimental and theoretical study. Size-selective infrared spectra of neutral Si(n)Co (n = 10-12) clusters are measured using a tunable IR-UV two-color ionization scheme. The experimental infrared spectra are compared with calculated spectra of low-energy structures predicted at the B3P86 level of theory. It is shown that the Si(n)Co (n = 10-12) clusters have endohedral caged structures, where the silicon frameworks prefer double-layered structures encapsulating the Co atom. Electronic structure analysis indicates that the clusters are stabilized by an ionic interaction between the Co dopant atom and the silicon cage due to the charge transfer from the silicon valence sp orbitals to the cobalt 3d orbitals. Strong hybridization between the Co dopant atom and the silicon host quenches the local magnetic moment on the encapsulated Co atom.

Unravelling electronic and structural requisites of triplet-triplet energy transfer by advanced electron paramagnetic resonance and density functional theory

NASA Astrophysics Data System (ADS)

Di Valentin, M.; Salvadori, E.; Barone, V.; Carbonera, D.

2013-10-01

Advanced electron paramagnetic resonance (EPR) techniques, in combination with Density Functional theory (DFT), have been applied to the comparative study of carotenoid triplet states in two major photosynthetic antenna complexes, the Peridinin-chlorophyll a-protein of dinoflagellates and the light-harvesting complex II of higher plants. Carotenoid triplet states are populated by triplet-triplet energy transfer (TTET) from chlorophyll molecules to photoprotect the system from singlet oxygen formation under light-stress conditions. The TTET process is strongly dependent on the relative arrangement and on the electronic properties of the triplet states involved. The proposed spectroscopic approach exploits the concept of spin conservation during TTET, which leads to recognisable spin polarisation effects in the time-resolved and field-swept echo-detected EPR spectra. The electron spin polarisation produced at the carotenoid acceptor site depends on the initial polarisation of the chlorophyll donor and on the relative geometrical arrangement of the donor-acceptor zero-field splitting axes. We have demonstrated that a proper analysis of the spectra in the framework of spin angular momentum conservation allows to derive the pathways of TTET and to gain insight into the structural requirements of this mechanism for those antenna complexes, whose X-ray structure is available. We have further proved that this method, developed for natural antenna complexes of known X-ray structure, can be extended to systems lacking structural information in order to derive the relative arrangement of the partners in the energy transfer process. The structural requirements for efficient TTET, obtained from time-resolved and pulse EPR, have been complemented by a detailed description of the electronic structure of the carotenoid triplet state, provided by pulse Electron-Nuclear DOuble Resonance (ENDOR) experiments. Triplet-state hyperfine couplings of the α- and β-protons of the carotenoid conjugated chain have been assigned with the aid of quantum chemical calculation. DFT predictions of the electronic structure of the carotenoid triplet state, in terms of spin density distribution, frontier orbital description and orbital excitation represent suitable building blocks toward a deeper understanding of electronic requirements for efficient TTET.

Characterization of chitin extracted from fish scales of marine fish species purchased from local markets in North Sulawesi, Indonesia

NASA Astrophysics Data System (ADS)

Rumengan, I. F. M.; Suptijah, P.; Wullur, S.; Talumepa, A.

2017-10-01

Chitin is a biodegradable biopolymer with a variety of commercial applications, including in the food food-supplement industries as a marine-derived nutraceutical. The purpose of this study was to characterize the molecular structure of chitin extracted from fish scales of important marine fish purchased from local markets in North Sulawesi. Chitin compound material was obtained from a specific fish scale, and then sequentially carrying out a boiling treatment to separate it from a complex with collagen. From the scales of two fish species, parrotfish (Chlorurus sordidus) and red snapper (Lutjanus argentimaculatus), the rendemen of chitin obtained were 45 % and 33%, respectively. Structural characteristics of the chitin were discussed by FTIR (Fourier Transform Infrared) analysis data. FTIR analysis was done using infrared spectroscopy, which is the resulting spectrum represents the molecular absorption and transmission, creating a molecular fingerprint of the sample. The molecular structure of chitin, C18H26N2O10, where the hydroxyl group on the second carbon replaced by acetyl amide, was shown by the infrared spectra. In the infrared spectra, chitin from parrot fish scales indicated the amide band at 1627.13 cm-1, and chitin from red snapper fish scales the amide band at 1648.09 cm-1 which are a typical one for marine chitin. The hydroxyl and amino bands at the ranged spectra up to 3500 cm-1. The yields of chitin isolated from fish scale were relatively huge. Some treatments are necessary to confirm the molecular conformation and deacetylation behavior. All products from the extraction of fish scales could be more accessible for structural modifications to develop biocompatible materials for pharmaceutical purposes.

a Chiral Tagging Strategy for Determining Absolute Configuration and Enantiomeric Excess by Molecular Rotational Spectroscopy

NASA Astrophysics Data System (ADS)

Evangelisti, Luca; Caminati, Walther; Patterson, David; Thomas, Javix; Xu, Yunjie; West, Channing; Pate, Brooks

2017-06-01

The introduction of three wave mixing rotational spectroscopy by Patterson, Schnell, and Doyle [1,2] has expanded applications of molecular rotational spectroscopy into the field of chiral analysis. Chiral analysis of a molecule is the quantitative measurement of the relative abundances of all stereoisomers of the molecule and these include both diastereomers (with distinct molecular rotational spectra) and enantiomers (with equivalent molecular rotational spectra). This work adapts a common strategy in chiral analysis of enantiomers to molecular rotational spectroscopy. A "chiral tag" is attached to the molecule of interest by making a weakly bound complex in a pulsed jet expansion. When this tag molecule is enantiopure, it will create diastereomeric complexes with the two enantiomers of the molecule being analyzed and these can be differentiated by molecule rotational spectroscopy. Identifying the structure of this complex, with knowledge of the absolute configuration of the tag, establishes the absolute configuration of the molecule of interest. Furthermore, the diastereomer complex spectra can be used to determine the enantiomeric excess of the sample. The ability to perform chiral analysis will be illustrated by a study of solketal using propylene oxide as the tag. The possibility of using current methods of quantum chemistry to assign a specific structure to the chiral tag complex will be discussed. Finally, chiral tag rotational spectroscopy offers a "gold standard" method for determining the absolute configuration of the molecule through determination of the substitution structure of the complex. When this measurement is possible, rotational spectroscopy can deliver a quantitative three dimensional structure of the molecule with correct stereochemistry as the analysis output. [1] David Patterson, Melanie Schnell, John M. Doyle, Nature 497, 475 (2013). [2] David Patterson, John M. Doyle, Phys. Rev. Lett. 111, 023008 (2013).

Structure, Elastic Constants and XRD Spectra of Extended Solids under High Pressure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Batyrev, I. G.; Coleman, S. P.; Ciezak-Jenkins, J. A.

We present results of evolutionary simulations based on density functional calculations of a potentially new type of energetic materials called extended solids: P-N and N-H. High-density structures with covalent bonds generated using variable and fixed concentration methods were analysed in terms of thermo-dynamical stability and agreement with experimental X-ray diffraction (XRD) spectra. X-ray diffraction spectra were calculated using a virtual diffraction algorithm that computes kinematic diffraction intensity in three-dimensional reciprocal space before being reduced to a two-theta line profile. Calculated XRD patterns were used to search for the structure of extended solids present at experimental pressures by optimizing data accordingmore » to experimental XRD peak position, peak intensity and theoretically calculated enthalpy. Elastic constants has been calculated for thermodynamically stable structures of P-N system.« less

Exotic phases of frustrated antiferromagnet LiCu2O2

NASA Astrophysics Data System (ADS)

Bush, A. A.; Büttgen, N.; Gippius, A. A.; Horvatić, M.; Jeong, M.; Kraetschmer, W.; Marchenko, V. I.; Sakhratov, Yu. A.; Svistov, L. E.

2018-02-01

7Li NMR spectra were measured in a magnetic field up to 17 T at temperatures 5-30 K on single crystalline LiCu2O2 . Earlier reported anomalies on magnetization curves correspond to magnetic field values where we observe changes of the NMR spectral shape. For the interpretation of the field and temperature evolutions of our NMR spectra, the magnetic structures were analyzed in the frame of the phenomenological theoretical approach of the Dzyaloshinskii-Landau theory. A set of possible planar and collinear structures was obtained. Most of these structures have an unusual configuration; they are characterized by a two-component order parameter and their magnetic moments vary harmonically not only in direction, but also in size. From the modeling of the observed spectra, a possible scenario of magnetic structure transformations is obtained.

Advances in structure elucidation of small molecules using mass spectrometry

PubMed Central

Fiehn, Oliver

2010-01-01

The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules. Electronic supplementary material The online version of this article (doi:10.1007/s12566-010-0015-9) contains supplementary material, which is available to authorized users. PMID:21289855

Evaluation of the Molecular Structural Parameters of Normal Rice Starch and Their Relationships with Its Thermal and Digestion Properties.

PubMed

Lin, Lingshang; Zhang, Qing; Zhang, Long; Wei, Cunxu

2017-09-12

The molecular structural parameters of six normal rice starches with different amylose contents were investigated through their iodine absorption spectra and gel permeation chromatography of fully branched and debranched starches. The thermal and digestion properties of starches were also determined and their relationships with molecular structural parameters were analyzed. Results showed that the molecular structural parameters of maximum absorption wavelength, blue value (BV), optical density 620 nm/550 nm (OD 620/550), amylose, intermediate component, and amylopectin, including its short branch-chains, long branch-chains, and branching degree, had high correlation in different determining methods. The intermediate component of starch was significantly positively related to amylose and negatively related to amylopectin, and the amylopectin branching degree was significantly positively related to amylopectin content and negatively related to amylose content. The gelatinization temperatures and enthalpy of native starch were significantly positively related to BV, OD 620/550, and amylose content and negatively related to amylopectin short branch-chains. The gelatinization temperatures and enthalpy of retrograded starch were significantly negatively related to amylopectin branching degree. The digestions of gelatinized and retrograded starches were significantly negatively related to the BV, OD 620/550, amylose, and intermediate component and positively related to amylopectin and its short branch-chains and branching degree.

Site-directed mutagenesis of firefly luciferase: implication of conserved residue(s) in bioluminescence emission spectra among firefly luciferases.

PubMed

Tafreshi, Narges Kh; Sadeghizadeh, Majid; Emamzadeh, Rahman; Ranjbar, Bijan; Naderi-Manesh, Hossein; Hosseinkhani, Saman

2008-05-15

The bioluminescence colours of firefly luciferases are determined by assay conditions and luciferase structure. Owing to red light having lower energy than green light and being less absorbed by biological tissues, red-emitting luciferases have been considered as useful reporters in imaging technology. A set of red-emitting mutants of Lampyris turkestanicus (Iranian firefly) luciferase has been made by site-directed mutagenesis. Among different beetle luciferases, those from Phrixothrix (railroad worm) emit either green or red bioluminescence colours naturally. By substitution of three specific amino acids using site-specific mutagenesis in a green-emitting luciferase (from L. turkestanicus), the colour of emitted light was changed to red concomitant with decreasing decay rate. Different specific mutations (H245N, S284T and H431Y) led to changes in the bioluminescence colour. Meanwhile, the luciferase reaction took place with relative retention of its basic kinetic properties such as K(m) and relative activity. Structural comparison of the native and mutant luciferases using intrinsic fluorescence, far-UV CD spectra and homology modelling revealed a significant conformational change in mutant forms. A change in the colour of emitted light indicates the critical role of these conserved residues in bioluminescence colour determination among firefly luciferases. Relatively high specific activity and emission of red light might make these mutants suitable as reporters for the study of gene expression and bioluminescence imaging.

Modeling and measurements of XRD spectra of extended solids under high pressure

NASA Astrophysics Data System (ADS)

Batyrev, I. G.; Coleman, S. P.; Stavrou, E.; Zaug, J. M.; Ciezak-Jenkins, J. A.

2017-06-01

We present results of evolutionary simulations based on density functional calculations of various extended solids: N-Si and N-H using variable and fixed concentration methods of USPEX. Predicted from the evolutionary simulations structures were analyzed in terms of thermo-dynamical stability and agreement with experimental X-ray diffraction spectra. Stability of the predicted system was estimated from convex-hull plots. X-ray diffraction spectra were calculated using a virtual diffraction algorithm which computes kinematic diffraction intensity in three-dimensional reciprocal space before being reduced to a two-theta line profile. Calculations of thousands of XRD spectra were used to search for a structure of extended solids at certain pressures with best fits to experimental data according to experimental XRD peak position, peak intensity and theoretically calculated enthalpy. Comparison of Raman and IR spectra calculated for best fitted structures with available experimental data shows reasonable agreement for certain vibration modes. Part of this work was performed by LLNL, Contract DE-AC52-07NA27344. We thank the Joint DoD / DOE Munitions Technology Development Program, the HE C-II research program at LLNL and Advanced Light Source, supported by BES DOE, Contract No. DE-AC02-05CH112.

Vibrational spectra and structures of neutral Si(m)C(n) clusters (m + n = 6): sequential doping of silicon clusters with carbon atoms.

PubMed

Savoca, Marco; Lagutschenkov, Anita; Langer, Judith; Harding, Dan J; Fielicke, André; Dopfer, Otto

2013-02-14

Vibrational spectra of mixed silicon carbide clusters Si(m)C(n) with m + n = 6 in the gas phase are obtained by resonant infrared-vacuum-ultraviolet two-color ionization (IR-UV2CI for n ≤ 2) and density functional theory (DFT) calculations. Si(m)C(n) clusters are produced in a laser vaporization source, in which the silicon plasma reacts with methane. Subsequently, they are irradiated with tunable IR light from an IR free electron laser before they are ionized with UV photons from an F(2) laser. Resonant absorption of one or more IR photons leads to an enhanced ionization efficiency for Si(m)C(n) and provides the size-specific IR spectra. IR spectra measured for Si(6), Si(5)C, and Si(4)C(2) are assigned to their most stable isomers by comparison with calculated linear absorption spectra. The preferred Si(m)C(n) structures with m + n = 6 illustrate the systematic transition from chain-like geometries for bare C(6) to three-dimensional structures for bare Si(6). In contrast to bulk SiC, carbon atom segregation is observed already for the smallest n (n = 2).

Dynamic molecular structure retrieval from low-energy laser-induced electron diffraction spectra

NASA Astrophysics Data System (ADS)

Vu, Dinh-Duy T.; Phan, Ngoc-Loan T.; Hoang, Van-Hung; Le, Van-Hoang

2017-12-01

A recently developed quantitative rescattering theory showed that a laser-free elastic cross section can be separated from laser-induced electron diffraction (LIED) spectra. Based upon this idea, Blaga et al investigated the possibility of reconstructing molecular structure from LIED spectra (2012 Nature 483 7388). In the above study, an independent atoms model (IAM) was used to interpret high-energy electron-molecule collisions induced by a mid-infrared laser. Our research aims to extend the application range of this structural retrieval method to low-energy spectra induced by more common near-infrared laser sources. The IAM is insufficient in this case, so we switch to a more comprehensive model—the multiple scattering (MS) theory. From the original version concerning only neutral targets, we upgrade the model so that it is compatible with electron-ion collisions at low energy. With available LIED experiment data of CO2 and O2, the upgraded MS is shown to be greatly effective as a tool for molecular imaging from spectra induced by a near-infrared laser. The captured image is at about 2 fs after the ionization, shorter than the period 4-6 fs by using the mid-infrared laser in Blaga’s experiment.

Conformational and Structural Studies of Isopropylamine from Temperature Dependent Raman Spectra of Xenon Solutions and {AB INITIO} Calculations

NASA Astrophysics Data System (ADS)

Klaassen, Joshua J.; Darkhalil, Ikhlas D.; Durig, James R.

2012-06-01

The Raman and infrared spectra (4000 to 50 cm-1) of the gas, liquid or solution, and solid have been recorded of isopropylamine, (CH3)2CHNH2. Variable temperature (-50 to -100oC) studies of the Raman spectra (3500 to 100 cm-1) dissolved in liquid xenon have been carried out. From these data, both the {trans} and {gauche} conformers have been identified and their relative stability obtained. The enthalpy difference has been determined from 20 band pairs at 6 temperatures to be 113 +/- 11 cm-1 (1.35 +/- 0.13 kJ mol-1) with the {trans} conformer the more stable form. The percentage of the {gauche} conformer is estimated to be 54 +/- 1 percent at ambient temperature. The conformational stabilities have been predicted from {ab initio} calculations utilizing several different basis sets up to aug-cc-pVTZ from both MP2(full) and density functional theory calculations by the B3LYP method. By utilizing previously reported microwave rotational constants along with {ab initio} MP2(full)/6-311+G(d,p) predicted structural values, adjusted r0 parameters have been obtained for the {trans} conformer. The determined heavy atom and NH2 distances in angstroms are C-C = 1.530(3), C-N = 1.465(3), N-H = 1.019(3) and angles in degrees NCC = 108.9(5), CCC = 111.0(5), HNC = 110.3(5). The structural parameters for the {gauche} conformer were estimated by using the same adjustment differences to the {gauche} form as those obtained for the corresponding {trans} parameters. Vibrational assignments have been provided for the observed bands for both conformers which are supported by MP2(full)/6-31G(d) {ab initio} calculations to predict harmonic force constants, wavenumbers, infrared intensities, Raman activities and depolarization ratios for both conformers. The results are discussed and compared to the corresponding properties of some related molecules.

A generalized modal shock spectra method for spacecraft loads analysis. [internal loads in a spacecraft structure subjected to a dynamic launch environment

NASA Technical Reports Server (NTRS)

Trubert, M.; Salama, M.

1979-01-01

Unlike an earlier shock spectra approach, generalization permits an accurate elastic interaction between the spacecraft and launch vehicle to obtain accurate bounds on the spacecraft response and structural loads. In addition, the modal response from a previous launch vehicle transient analysis with or without a dummy spacecraft - is exploited to define a modal impulse as a simple idealization of the actual forcing function. The idealized modal forcing function is then used to derive explicit expressions for an estimate of the bound on the spacecraft structural response and forces. Greater accuracy is achieved with the present method over the earlier shock spectra, while saving much computational effort over the transient analysis.

Acoustic band gaps of the woodpile sonic crystal with the simple cubic lattice

NASA Astrophysics Data System (ADS)

Wu, Liang-Yu; Chen, Lien-Wen

2011-02-01

This study theoretically and experimentally investigates the acoustic band gap of a three-dimensional woodpile sonic crystal. Such crystals are built by blocks or rods that are orthogonally stacked together. The adjacent layers are perpendicular to each other. The woodpile structure is embedded in air background. Their band structures and transmission spectra are calculated using the finite element method with a periodic boundary condition. The dependence of the band gap on the width of the stacked rods is discussed. The deaf bands in the band structure are observed by comparing with the calculated transmission spectra. The experimental transmission spectra for the Γ-X and Γ-X' directions are also presented. The calculated results are compared with the experimental results.

Heat capacity and magnetic properties of fluoride CsFe{sup 2+}Fe{sup 3+}F{sub 6} with defect pyrochlore structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gorev, M.V., E-mail: gorev@iph.krasn.ru; Institute of Engineering Physics and Radio Electronics, Siberian State University, 660074 Krasnoyarsk; Flerov, I.N.

2016-05-15

Heat capacity, Mössbauer and Raman spectra as well as magnetic properties of fluoride CsFe{sub 2}F{sub 6} with defect pyrochlore structure were studied. In addition to recently found above room temperature three successive structural transformations Pnma-Imma-I4{sub 1}amd-Fd-3m, phase transition of antiferromagnetic nature with the 13.7 K Neel temperature and a broad heat capacity anomaly with a maximum at about 30 K were observed. The room temperature symmetry Pnma is unchanged at least down to 7 K. Simple model of indirect bond used to estimate the exchange interactions and to propose a magnetic structure model. - Graphical abstract: The ordered arrangement ofmore » Fe{sup 2+} and Fe{sup 3+} ions in high-spin states as well as antiferromagnetic phase transition followed by significant magnetic frustrations were found in pyrocholore-related CsFe{sup 2+}Fe{sup 3+}F{sub 6}. A magnetic structure was proposed using a simple model of indirect bonds. - Highlights: • The Pnma structure in pyrocholore CsFe{sub 2}F{sub 6} is stable down to helium temperature. • Mössbauer spectra confirmed the ordering of Fe{sup 2+} and Fe{sup 3+} ions. • Antiferromagnetic transformation and significant magnetic frustrations are found. • Experimental magnetic entropy agrees with entropy for Fe ions in high-spin state. • Superexchange interactions were calculated and a magnetic structure was proposed.« less

Structure-spectrophotometric selectivity relationship in interactions of quercetin related flavonoids with double stranded and single stranded RNA

NASA Astrophysics Data System (ADS)

Piantanida, Ivo; Mašić, Lozika; Rusak, Gordana

2009-04-01

Interactions of five flavonoids with dsRNA and single stranded ssRNA were studied by UV/vis titrations. The results obtained supported the intercalative binding mode as a dominant interaction of studied flavonoids with dsRNA as well as major interaction with ssRNA. Furthermore, changes of the UV/vis spectra of flavonoids induced by addition of poly G or poly C, respectively, are significantly stronger than changes induced by double stranded poly G-poly C, pointing to essential role of the free poly G or poly C sequence (not hydrogen bonded in double helix). Exclusively poly G caused significant batochromic shift of the UV/vis maxima of all studied flavonoids, whereby the intensity of batochromic shift is nicely correlated to the number of OH groups of flavonoid. Unlikely to poly G, addition of poly A and poly U induced measurable changes only in the UV/vis spectra of flavonoids characterised by no OH (galangin) or three OH groups (myricetin) on the phenyl part of the molecule. Consequently, flavonoids with one- or two-OH groups on the phenyl part of the molecule (luteolin, fisetin, kaempferol) specifically differentiate between poly A, poly U (negligible changes in the UV/Vis spectra) and poly G (strong changes in the UV/Vis spectra) as well as poly C (moderate changes in the UV/Vis spectra).

Microhydrated dihydrogen phosphate clusters probed by gas phase vibrational spectroscopy and first principles calculations

DOE PAGES

Sun, Shou -Tian; Jiang, Ling; Liu, J. W.; ...

2015-06-05

We report infrared multiple photon dissociation (IRMPD) spectra of cryogenically-cooled H 2PO 4 -(H 2O) n anions (n = 2–12) in the spectral range of the stretching and bending modes of the solute anion (600–1800 cm-1). The spectra cannot be fully understood using the standard technique of comparison to harmonic spectra of minimum-energy structures; a satisfactory assignment requires considering anharmonic effects as well as entropy-driven hydrogen bond network fluctuations. Aided by finite temperature ab initio molecular dynamics simulations, the observed changes in the position, width and intensity of the IRMPD bands with cluster size are related to the sequence ofmore » microsolvation. Due to stronger hydrogen bonding to the two terminal P=O groups, these are hydrated before the two P–OH groups. By n = 6, all four end groups are involved in the hydrogen bond network and by n = 12, the cluster spectra show similarities to the condensed phase spectrum of H 2PO 4 -(aq). Our results reveal some of the microscopic details concerning the formation of the aqueous solvation environment around H 2PO 4 -, provide ample testing grounds for the design of model solvation potentials for this biologically relevant anion, and support a new paradigm for the interpretation of IRMPD spectra of microhydrated ions.« less

Modeling the CH Stretch Vibrational Spectroscopy of M(+)[Cyclohexane] (M = Li, Na, and K) Ions.

PubMed

Sibert, Edwin L; Tabor, Daniel P; Lisy, James M

2015-10-15

The CH stretch vibrations of M(+)[cyclohexane][Ar] (M = Li, Na, and K) cluster ions were theoretically modeled. Results were compared to the corresponding infrared photodissociation spectra of Patwari and Lisy [ J. Chem. Phys A 2007 , 111 , 7585 ]. The experimental spectra feature a substantial spread in CH stretch vibration frequencies due to the alkali metal cation binding to select hydrogens of cyclohexane. This spread was observed to increase with decreasing metal ion size. Exploring the potential energy landscape revealed the presence of three conformers whose energy minima lie within ∼1 kcal of each other. It was determined that in all conformers the metal ion interacts with three hydrogen atoms; these hydrogen atoms can be either equatorial or axial. The corresponding spectra for these conformers were obtained with a theoretical model Hamiltonian [ J. Chem. Phys. 2013 , 138 , 064308 ] that consists of local mode CH stretches bilinearly coupled to each other and Fermi coupled to lower frequency modes. Frequencies and coupling parameters were obtained from electronic structure calculations that were subsequently scaled on the basis of previous studies. Theoretical spectra of a single low energy conformer were found to match well with the experimental spectra. The relative frequency shifts with changing metal ion size were accurately modeled with parameters generated by using ωB97X-D/6-311++(2d,p) calculations.

Vapor-phase infrared spectroscopy on solid organic compounds with a pulsed resonant photoacoustic detection scheme

NASA Astrophysics Data System (ADS)

Bartlome, Richard; Fischer, Cornelia; Sigrist, Markus W.

2005-08-01

There is a great need for a low cost and sensitive method to measure infrared spectra of solid organic compounds in the gas phase. To record such spectra, we propose an optical parametric generator-based photoacoustic spectrometer, which emits in the mid-infrared fingerprint region between 3 and 4 microns. In this system, the sample is heated in a vessel before entering a home built photoacoustic cell, where the gaseous molecules are excited by a tunable laser source with a frequency repetition rate that matches the first longitudinal resonance frequency of the photocaoustic cell. In a first phase, we have focused on low-melting point stimulants such as Nikethamide, Mephentermine sulfate, Methylephedrine, Ephedrine and Pseudoephedrine. The vapor-phase spectra of these doping substances were measured between 2800 and 3100 cm-1, where fundamental C-H stretching vibrations take place. Our spectra show notable differences with commercially available condensed phase spectra. Our scheme enables to measure very low vapor pressures of low-melting point (<160 °C) solid organic compounds. Furthermore, the optical resolution of 8 cm-1 is good enough to distinguish closely related chemical structures such as the Ephedra alkaloids Ephedrine and Methylephedrine, but doesn't allow to differentiate diastereoisomeric pairs such as Ephedrine and Pseudoephedrine, two important neurotransmitters which reveal different biological activities. Therefore, higher resolution and a system capable of measuring organic compounds with higher melting points are required.

Adsorption geometry and core excitation spectra of three phenylpropene isomers on Cu(111)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolczewski, C.; Williams, F. J.; Cropley, R. L.

Theoretical C 1s near edge x-ray absorption fine structure (NEXAFS) spectra for the C{sub 9}H{sub 10} isomers trans-methylstyrene, {alpha}-methylstyrene, and allylbenzene in gas phase and adsorbed at Cu(111) surfaces have been obtained from density functional theory calculations where adsorbate geometries were determined by corresponding total energy optimizations. The three species show characteristic differences in widths and peak shapes of the lowest C 1s{yields}{pi}* transitions which are explained by different coupling of the {pi}-electron system of the C{sub 6} ring with that of the side chain in the molecules as well as by the existence of nonequivalent carbon centers. The adsorbedmore » molecules bind only weakly with the substrate which makes the use of theoretical NEXAFS spectra of the oriented free molecules meaningful for an interpretation of experimental angle-resolved NEXAFS spectra of the adsorbate systems obtained in this work. However, a detailed quantitative account of relative peak intensities requires theoretical angle-resolved NEXAFS spectra of the complete adsorbate systems which have been evaluated within the surface cluster approach. The comparison with experiment yields almost perfect agreement and confirms the reliability of the calculated equilibrium geometries of the adsorbates. This can help to explain observed differences in the catalytic epoxidation of the three molecules on Cu(111) based on purely geometric considerations.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reddy, N.R.S.; Kolaczkowski, S.V.; Small, G.J.

Reddy et al. (Science, accepted) have reported persistent, nonphotochemical hole-burned (NPHB) spectra for the Q[sub y] states of the reaction center of Rhodopseudomonas viridis. The photoinduced structural transformation was shown to be highly localized on the special pair. This transformation leads to a red shift of the special pair's lowest-energy absorption band, P960, of 150 cm[sup [minus]1] and a comparable blue shift for a state at 850 nm, which, as a consequence, could be assigned as being most closely associated with the upper dimer component. Additional experimental results are presented here together with a theoretical analysis of the extent tomore » which the NPHB spectra provide information on the contribution from the bacteriochlorophyll monomers of the special pair to the Q[sub y] states that absorb higher in energy than P960. Structured photochemical hole-burned (PHB) spectra of P960 are also presented that underscore the importance of strong electron-phonon coupling from a broad distribution of modes with a mean frequency of 30 cm[sup [minus]1] for an understanding of the P960 absorption profile. These spectra also identify the zero-phonon hole of the strongly damped special pair marker mode (145 cm[sup [minus]1]) and its associated phonon sideband structure. Calculated spectra are presented which are in good agreement with the experimental PHB spectra. 30 refs., 6 figs., 4 tabs.« less

High-resolution soft X-ray spectra of Scorpius X-1 - The structure of circumsource accreting material

NASA Technical Reports Server (NTRS)

Kahn, S. M.; Seward, F. D.; Chlebowski, T.

1984-01-01

Four observations of Scorpius X-1 with the Objective Grating Spectrometer of the Einstein Observatory have provided high-resolution spectra (lambda/Delta lambda = approximately 20-50) in the wavelength range 7-46 A. The spectra reveal the presence of absorption structure due to oxygen, nitrogen, and iron, and variable emission structure associated with ionized iron and nitrogen. The strengths of these features suggest that the N/O abundance ratio in the absorbing and line emitting gas is anomalously high, which might indicate that these spectral components are associated with processed material, probably accreting matter transferred from the surface of an evolved companion. Constraints on the inclination of the system, however, imply that this cool, dense, accreting material must be well out of the plane of the binary system. Possible models for the origin and nature of this circumsource medium are discussed. An extensive discussion of the calibration of the Objective Grating Spectrometer and of the analysis of spectra acquired by that instrument is also provided.

Impact of Site-Directed Mutant Luciferase on Quantitative Green and Orange/Red Emission Intensities in Firefly Bioluminescence

NASA Astrophysics Data System (ADS)

Wang, Yu; Akiyama, Hidefumi; Terakado, Kanako; Nakatsu, Toru

2013-08-01

Firefly bioluminescence has attracted great interest because of its high quantum yield and intriguing modifiable colours. Modifications to the structure of the enzyme luciferase can change the emission colour of firefly bioluminescence, and the mechanism of the colour change has been intensively studied by biochemists, structural biologists, optical physicists, and quantum-chemistry theorists. Here, we report on the quantitative spectra of firefly bioluminescence catalysed by wild-type and four site-directed mutant luciferases. While the mutation caused different emission spectra, the spectra differed only in the intensity of the green component (λmax ~ 560 nm). In contrast, the orange (λmax ~ 610 nm) and red (λmax ~ 650 nm) components present in all the spectra were almost unaffected by the modifications to the luciferases and changes in pH. Our results reveal that the intensity of the green component is the unique factor that is influenced by the luciferase structure and other reaction conditions.

Expert System for Analysis of Spectra in Nuclear Metrology

NASA Astrophysics Data System (ADS)

Petrović, Ivan; Petrović, V.; Krstić, D.; Nikezić, D.; Bočvarski, V.

In this paper is described an expert system (ES) developed in order to enable the analysis of emission spectra, which are obtained by measurements of activities of radioactive elements, i.e., isotopes, actually cesium. In the structure of those spectra exists two parts: first on lower energies, which originates from the Compton effect, and second on higher energies, which contains the photopeak. The aforementioned ES is made to perform analysis of spectra in whole range of energies. Analysis of those spectra is very interesting because of the problem of environmental contamination by radio nuclides.

Effect of annealing temperature on the structural and optical properties of CeO{sub 2}:Ni thin films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murugan, R.; Vijayaprasath, G.; Sakthivel, P.

2016-05-06

High quality Ni-doped CeO{sub 2} (CeO{sub 2}:Ni) thin films were deposited on glass substrates at room temperature by using radio frequency magnetron sputtering. The effect of annealing temperature on structural and optical properties of the CeO{sub 2}:Ni films was investigated. The structural, optical and vibrational properties of the films were determined using X-ray diffraction (XRD), photoluminescence spectrometer (PL) and Raman spectrometer. It was found that the as-deposited film has a fluorite cubic structure. By increasing annealing temperature from 100°C to 300°C, the crystalline quality of the thin films could be improved. The UV and visible band emissions were observed inmore » the photoluminescence spectra, due to exciton, defect related emissions respectively. The micro-Raman results show the characteristic peak of CeO{sub 2} F{sub 2g} at 465 cm{sup −1} and 2L0 at 1142 cm{sup −1}. Defect peaks like D and 0 bands were observed at 641 cm{sup −1} and 548 cm{sup −1} respectively. It is found from the spectra that the peak intensity of the films increased with increase of annealing temperature.« less

High Resolution Direct Frequency Comb Spectroscopy of Vinyl Bromide (C_2H_3Br) and Nitromethane (CH_3NO_2) in the CH Stretch Region

NASA Astrophysics Data System (ADS)

Changala, Bryan; Spaun, Ben; Patterson, David; Ye, Jun

2016-06-01

We present high resolution rovibrational spectra of buffer gas cooled vinyl bromide (C_2H_3Br) and nitromethane (CH_3NO_2) in the 3 μm CH stretch region, acquired via cavity-enhanced direct frequency comb absorption spectroscopy. The ˜10 K translational and rotational temperatures of the molecular gas, as well as the narrow linewidth of the frequency comb, yield well resolved rotational structure, isotope shifts, and nuclear hyperfine splittings. Given the wide bandwidth of the light source and the long path length of the enhancement cavity, we measure entire vibrational bands in a single shot with high signal-to-noise ratios. We discuss spectra of the entire fundamental CH stretch manifolds of both C_2H_3Br and CH_3NO_2, which provide contrasting examples of rovibrational structure of rigid and non-rigid systems. C_2H_3Br is a relatively normal asymmetric top, exhibiting local perturbations to its rotational structure. Conversely, CH_3NO_2 contains an essentially unhindered methyl rotor. Of particular interest are its quasi-degenerate asymmetric CH stretch modes. Here, one must consider multiple couplings between torsional, rotational, and vibrational angular momentum, leading to qualitatively new level patterns and structure.

FT-IR SOLUTION SPECTRA OF PROPYL SULFIDE, PROPYL SULFOXIDE, AND PROPYL SULFONE

EPA Science Inventory

FT-IR spectra were obtained of 0.5% volumetric solutions of propyl sulfide, propyl sulfoxide, and propyl sulfone in hexane, CCl4, CS2, and CHCl3 to assist in the assignment of FT-IR-PAS spectra of propyl sulfoxide sorbed within the structure of several peats and onto cellulose. T...

Morphological, structural, and spectral characteristics of amorphous iron sulfates

PubMed Central

Sklute, E. C.; Jensen, H. B.; Rogers, A. D.; Reeder, R. J.

2018-01-01

Current or past brine hydrologic activity on Mars may provide suitable conditions for the formation of amorphous ferric sulfates. Once formed, these phases would likely be stable under current Martian conditions, particularly at low- to mid-latitudes. Therefore, we consider amorphous iron sulfates (AIS) as possible components of Martian surface materials. Laboratory AIS were created through multiple synthesis routes and characterized with total X-ray scattering, thermogravimetric analysis, scanning electron microscopy, visible/near-infrared (VNIR), thermal infrared (TIR), and Mössbauer techniques. We synthesized amorphous ferric sulfates (Fe(III)2(SO4)3 · ~ 6–8H2O) from sulfate-saturated fluids via vacuum dehydration or exposure to low relative humidity (<11%). Amorphous ferrous sulfate (Fe(II)SO4 · ~1H2O) was synthesized via vacuum dehydration of melanterite. All AIS lack structural order beyond 11 Å. The short-range (<5 Å) structural characteristics of amorphous ferric sulfates resemble all crystalline reference compounds; structural characteristics for the amorphous ferrous sulfate are similar to but distinct from both rozenite and szomolnokite. VNIR and TIR spectral data for all AIS display broad, muted features consistent with structural disorder and are spectrally distinct from all crystalline sulfates considered for comparison. Mössbauer spectra are also distinct from crystalline phase spectra available for comparison. AIS should be distinguishable from crystalline sulfates based on the position of their Fe-related absorptions in the visible range and their spectral characteristics in the TIR. In the NIR, bands associated with hydration at ~1.4 and 1.9 μm are significantly broadened, which greatly reduces their detectability in soil mixtures. AIS may contribute to the amorphous fraction of soils measured by the Curiosity rover. PMID:29675340

Simulation of electron energy loss spectra of nanomaterials with linear-scaling density functional theory

DOE PAGES

Tait, E. W.; Ratcliff, L. E.; Payne, M. C.; ...

2016-04-20

Experimental techniques for electron energy loss spectroscopy (EELS) combine high energy resolution with high spatial resolution. They are therefore powerful tools for investigating the local electronic structure of complex systems such as nanostructures, interfaces and even individual defects. Interpretation of experimental electron energy loss spectra is often challenging and can require theoretical modelling of candidate structures, which themselves may be large and complex, beyond the capabilities of traditional cubic-scaling density functional theory. In this work, we present functionality to compute electron energy loss spectra within the onetep linear-scaling density functional theory code. We first demonstrate that simulated spectra agree withmore » those computed using conventional plane wave pseudopotential methods to a high degree of precision. The ability of onetep to tackle large problems is then exploited to investigate convergence of spectra with respect to supercell size. As a result, we apply the novel functionality to a study of the electron energy loss spectra of defects on the (1 0 1) surface of an anatase slab and determine concentrations of defects which might be experimentally detectable.« less

Characterization of the Solid-Phase Behavior of n-Nonylammonium Tetrachlorocuprate by Fourier Transform Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Ning, Guo

1995-06-01

The solid-phase behavior of [n-C9H19NH3]2CuCl4 was investigated by infrared spectroscopy. The nature of the three solid phases (phase I, phase II, and phase III) is discussed. A temperature-dependent study of infrared spectra provides evidence for the occurrence of structural phase transitions related to the dynamics of the alkyl chains and -NH3 polar heads. The phase transition at Tc1 (22°C) arises from variation in the interaction and packing structure of the chain. The phase transition at Tc2 (34°C) is related to variation in partial conformational order-disorder at the intramolecular level. The GTG or GTG‧ and small concentration of TG structures near the CH3 group are generated in phase III (above 38°C).

How Noniridescent Colors Are Generated by Quasi-ordered Structures of Bird Feathers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noh, Heeso; Liew, Seng Fatt; Saranathan, Vinodkumar

2012-03-26

We investigate the mechanism of structural coloration by quasi-ordered nanostructures in bird feather barbs. Small-angle X-ray scattering (SAXS) data reveal the structures are isotropic and have short-range order on length scales comparable to optical wavelengths. We perform angle-resolved reflection and scattering spectrometry to fully characterize the colors under directional and omni-directional illumination of white light. Under directional lighting, the colors change with the angle between the directions of illumination and observation. The angular dispersion of the primary peaks in the scattering/reflection spectra can be well explained by constructive interference of light that is scattered only once in the quasi-ordered structures.more » Using the Fourier power spectra of structure from the SAXS data we calculate optical scattering spectra and explain why the light scattering peak is the highest in the backscattering direction. Under omni-directional lighting, colors from the quasi-ordered structures are invariant with the viewing angle. The non-iridescent coloration results from the isotropic nature of structures instead of strong backscattering.« less

Low-energy collision induced dissociation (low-energy CID), collision induced dissociation (CID) and higher-energy collision dissociation (HCD) mass spectrometry for structural elucidation of saccharides and clarification of their dissolution mechanism in DMAc/LiCl.

PubMed

Bayat, Parisa; Lesage, Denis; Cole, Richard B

2018-05-29

The dissolution mechanism of oligosaccharides in N,N-dimethylacetamide/lithium chloride (DMAc/LiCl), a solvent used for cellulose dissolution, and the capabilities of low-energy collision induced dissociation (low-energy CID), collision induced dissociation (CID) and higher-energy collision dissociation (HCD) for structural analysis of carbohydrates were investigated. Comparing the spectra obtained using three techniques shows that, generally, when working with mono-lithiated sugars, CID spectra provide more structurally informative fragments, and glycosidic bond cleavage is the main pathway. However, when working with di-lithiated sugars, HCD spectra can be more informative providing predominately cross-ring cleavage fragments. This is because HCD is a non-resonant activation technique and it allows a higher amount of energy to be deposited in a short time, giving access to more endothermic decomposition pathways as well as consecutive fragmentations. The difference in preferred dissociation pathways of mono-lithiated and di-lithiated sugars indicates that the presence of the second lithium strongly influences the relative rate constants for cross-ring cleavages (rearrangement) vs. direct glycosidic bond cleavages, and disfavors the latter. Regarding the dissolution mechanism of sugars in DMAc/LiCl, CID and HCD experiments on di-lithiated and tri-lithiated sugars reveal that intensities of product ions containing two Li + or three Li + , respectively, are higher than those bearing only one Li + . In addition, comparing the fragmentation spectra (both HCD and CID) of LiCl adducted lithiated sugar and NaCl adducted sodiated sugar shows that while, in the latter case, loss of NaCl is dominant, in the former case, loss of HCl occurs preferentially. The compiled evidence implies that there is a strong and direct interaction between lithium and the saccharide during the dissolution process in the DMAc/LiCl solvent system. This article is protected by copyright. All rights reserved.

SiSeRHMap v1.0: a simulator for mapped seismic response using a hybrid model

NASA Astrophysics Data System (ADS)

Grelle, Gerardo; Bonito, Laura; Lampasi, Alessandro; Revellino, Paola; Guerriero, Luigi; Sappa, Giuseppe; Guadagno, Francesco Maria

2016-04-01

The SiSeRHMap (simulator for mapped seismic response using a hybrid model) is a computerized methodology capable of elaborating prediction maps of seismic response in terms of acceleration spectra. It was realized on the basis of a hybrid model which combines different approaches and models in a new and non-conventional way. These approaches and models are organized in a code architecture composed of five interdependent modules. A GIS (geographic information system) cubic model (GCM), which is a layered computational structure based on the concept of lithodynamic units and zones, aims at reproducing a parameterized layered subsoil model. A meta-modelling process confers a hybrid nature to the methodology. In this process, the one-dimensional (1-D) linear equivalent analysis produces acceleration response spectra for a specified number of site profiles using one or more input motions. The shear wave velocity-thickness profiles, defined as trainers, are randomly selected in each zone. Subsequently, a numerical adaptive simulation model (Emul-spectra) is optimized on the above trainer acceleration response spectra by means of a dedicated evolutionary algorithm (EA) and the Levenberg-Marquardt algorithm (LMA) as the final optimizer. In the final step, the GCM maps executor module produces a serial map set of a stratigraphic seismic response at different periods, grid solving the calibrated Emul-spectra model. In addition, the spectra topographic amplification is also computed by means of a 3-D validated numerical prediction model. This model is built to match the results of the numerical simulations related to isolate reliefs using GIS morphometric data. In this way, different sets of seismic response maps are developed on which maps of design acceleration response spectra are also defined by means of an enveloping technique.

Applying Tandem Mass Spectral Libraries for Solving the Critical Assessment of Small Molecule Identification (CASMI) LC/MS Challenge 2012

PubMed Central

Oberacher, Herbert

2013-01-01

The “Critical Assessment of Small Molecule Identification” (CASMI) contest was aimed in testing strategies for small molecule identification that are currently available in the experimental and computational mass spectrometry community. We have applied tandem mass spectral library search to solve Category 2 of the CASMI Challenge 2012 (best identification for high resolution LC/MS data). More than 230,000 tandem mass spectra part of four well established libraries (MassBank, the collection of tandem mass spectra of the “NIST/NIH/EPA Mass Spectral Library 2012”, METLIN, and the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’) were searched. The sample spectra acquired in positive ion mode were processed. Seven out of 12 challenges did not produce putative positive matches, simply because reference spectra were not available for the compounds searched. This suggests that to some extent the limited coverage of chemical space with high-quality reference spectra is still a problem encountered in tandem mass spectral library search. Solutions were submitted for five challenges. Three compounds were correctly identified (kanamycin A, benzyldiphenylphosphine oxide, and 1-isopropyl-5-methyl-1H-indole-2,3-dione). In the absence of any reference spectrum, a false positive identification was obtained for 1-aminoanthraquinone by matching the corresponding sample spectrum to the structurally related compounds N-phenylphthalimide and 2-aminoanthraquinone. Another false positive result was submitted for 1H-benz[g]indole; for the 1H-benz[g]indole-specific sample spectra provided, carbazole was listed as the best matching compound. In this case, the quality of the available 1H-benz[g]indole-specific reference spectra was found to hamper unequivocal identification. PMID:24957994

Benzo(a)pyrene-7,8-dihydrodiol 9,10-oxide adenosine and deoxyadenosine adducts: structure and stereochemistry.

PubMed

Jeffrey, A M; Grzeskowiak, K; Weinstein, I B; Nakanishi, K; Roller, P; Harvey, R G

1979-12-14

The structure and absolute stereoconfigurations of four adenosine adducts with (+/-)-7 alpha,8 beta-dihydroxy-9 beta, 10 beta-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene (BPDE) and their deoxyadenosine analogs have been determined. They result from both cis and trans addition of the N6 amino group of ademine to the 10 position of both enantiomers of BDPE. This was determined from studies of the nuclear magnetic resonance spectra, mass spectra, and circular dichroism spectra, as well as from their pKa values and chemical reactivities.

Macromolecular structure of coals. 6. Mass spectroscopic analysis of coal-derived liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hooker, D.T.; Lucht, L.M.; Peppas, N.A.

1986-02-01

The macromolecular structure of coal networks was analyzed by depolymerizing coal samples using the Sternberg reductive alkylation and the Miyake alkylation techniques. Electron impact mass spectra showed peaks of greater abundance of 125-132, 252-260, 383-391, and 511-520 m/z ratios. Based on analysis of the patterns of the spectra, the cluster size of the cross-linked structure of bituminous coals was determined as 126-130. Various chemical species were identified.

[Monitoring of Crack Propagation in Repaired Structures Based on Characteristics of FBG Sensors Reflecting Spectra].

PubMed

Yuan, Shen-fang; Jin, Xin; Qiu, Lei; Huang, Hong-mei

2015-03-01

In order to improve the security of aircraft repaired structures, a method of crack propagation monitoring in repaired structures is put forward basing on characteristics of Fiber Bragg Grating (FBG) reflecting spectra in this article. With the cyclic loading effecting on repaired structure, cracks propagate, while non-uniform strain field appears nearby the tip of crack which leads to the FBG sensors' reflecting spectra deformations. The crack propagating can be monitored by extracting the characteristics of FBG sensors' reflecting spectral deformations. A finite element model (FEM) of the specimen is established. Meanwhile, the distributions of strains which are under the action of cracks of different angles and lengths are obtained. The characteristics, such as main peak wavelength shift, area of reflecting spectra, second and third peak value and so on, are extracted from the FBGs' reflecting spectral which are calculated by transfer matrix algorithm. An artificial neural network is built to act as the model between the characteristics of the reflecting spectral and the propagation of crack. As a result, the crack propagation of repaired structures is monitored accurately and the error of crack length is less than 0.5 mm, the error of crack angle is less than 5 degree. The accurately monitoring problem of crack propagation of repaired structures is solved by taking use of this method. It has important significance in aircrafts safety improvement and maintenance cost reducing.

Comprehensive identification and structural characterization of target components from Gelsemium elegans by high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry based on accurate mass databases combined with MS/MS spectra.

PubMed

Liu, Yan-Chun; Xiao, Sa; Yang, Kun; Ling, Li; Sun, Zhi-Liang; Liu, Zhao-Ying

2017-06-01

This study reports an applicable analytical strategy of comprehensive identification and structure characterization of target components from Gelsemium elegans by using high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QqTOF MS) based on the use of accurate mass databases combined with MS/MS spectra. The databases created included accurate masses and elemental compositions of 204 components from Gelsemium and their structural data. The accurate MS and MS/MS spectra were acquired through data-dependent auto MS/MS mode followed by an extraction of the potential compounds from the LC-QqTOF MS raw data of the sample. The same was matched using the databases to search for targeted components in the sample. The structures for detected components were tentatively characterized by manually interpreting the accurate MS/MS spectra for the first time. A total of 57 components have been successfully detected and structurally characterized from the crude extracts of G. elegans, but has failed to differentiate some isomers. This analytical strategy is generic and efficient, avoids isolation and purification procedures, enables a comprehensive structure characterization of target components of Gelsemium and would be widely applicable for complicated mixtures that are derived from Gelsemium preparations. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Raman Spectra of High-κ Dielectric Layers Investigated with Micro-Raman Spectroscopy Comparison with Silicon Dioxide

PubMed Central

Borowicz, P.; Taube, A.; Rzodkiewicz, W.; Latek, M.; Gierałtowska, S.

2013-01-01

Three samples with dielectric layers from high-κ dielectrics, hafnium oxide, gadolinium-silicon oxide, and lanthanum-lutetium oxide on silicon substrate were studied by Raman spectroscopy. The results obtained for high-κ dielectrics were compared with spectra recorded for silicon dioxide. Raman spectra suggest the similarity of gadolinium-silicon oxide and lanthanum-lutetium oxide to the bulk nondensified silicon dioxide. The temperature treatment of hafnium oxide shows the evolution of the structure of this material. Raman spectra recorded for as-deposited hafnium oxide are similar to the results obtained for silicon dioxide layer. After thermal treatment especially at higher temperatures (600°C and above), the structure of hafnium oxide becomes similar to the bulk non-densified silicon dioxide. PMID:24072982

REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform

PubMed Central

Marsella, Luca; Sirocco, Francesco; Trovato, Antonio; Seno, Flavio; Tosatto, Silvio C.E.

2009-01-01

Motivation: Proteins with solenoid repeats evolve more quickly than non-repetitive ones and their periodicity may be rapidly hidden at sequence level, while still evident in structure. In order to identify these repeats, we propose here a novel method based on a metric characterizing amino-acid properties (polarity, secondary structure, molecular volume, codon diversity, electric charge) using five previously derived numerical functions. Results: The five spectra of the candidate sequences coding for structural repeats, obtained by Discrete Fourier Transform (DFT), show common features allowing determination of repeat periodicity with excellent results. Moreover it is possible to introduce a phase space parameterized by two quantities related to the Fourier spectra which allow for a clear distinction between a non-homologous set of globular proteins and proteins with solenoid repeats. The DFT method is shown to be competitive with other state of the art methods in the detection of solenoid structures, while improving its performance especially in the identification of periodicities, since it is able to recognize the actual repeat length in most cases. Moreover it highlights the relevance of local structural propensities in determining solenoid repeats. Availability: A web tool implementing the algorithm presented in the article (REPETITA) is available with additional details on the data sets at the URL: http://protein.bio.unipd.it/repetita/. Contact: silvio.tosatto@unipd.it PMID:19478001

FTIR spectra of the solid solutions (Na0.88K0.12)VO3, (Na0.5K0.5)VO3, and Na(V0.66P0.34)O3

NASA Astrophysics Data System (ADS)

de Waal, D.; Heyns, A. M.

1992-03-01

It is known that three different solid solutions, (Na0.88K0.12)VO3, (Na0.5K0.5)VO3 and Na(V0.66P0.34)O3, form in the (Na,K)(V,P)O3 system. These compounds all have monoclinic crystal structures similar to the pure alkali metal metavanadates containing small cations, e.g. Li+ and Na+ (Space group C2/c). Metavanadates with large cations like K+, Rb+, C+s and NH+4 form orthorhombic crystals, space group Pbcm. All those are structurally related to the silicate pyroxenes. Na(V0.66P0.34)O3 and (Na0.88K0.12)VO3 have the same modified diopside structure as (alpha) - NaVO3 while (Na0.5K0.5)VO3 adopts the true diopside structure. The infrared spectra of the three solid solutions are reported here in comparison with those of (alpha) -NaVO3 and KVO3. The results are also correlated with those obtained in two independent high pressure Raman studies of NH4VO3 and RbVO3 as the introduction of a larger cation like K+ should increase the pressure in the structure.

Microwave spectra and molecular structures of (Z)-pent-2-en-4-ynenitrile and maleonitrile.

PubMed

Halter, R J; Fimmen, R L; McMahon, R J; Peebles, S A; Kuczkowski, R L; Stanton, J F

2001-12-12

Accurate equilibrium structures have been determined for (Z)-pent-2-en-4-ynenitrile (8) and maleonitrile (9) by combining microwave spectroscopy data and ab initio quantum chemistry calculations. The microwave spectra of 10 isotopomers of 8 and 5 isotopomers of 9 were obtained using a pulsed nozzle Fourier transform microwave spectrometer. The ground-state rotational constants were adjusted for vibration-rotation interaction effects calculated from force fields obtained from ab initio calculations. The resultant equilibrium rotational constants were used to determine structures that are in very good agreement with those obtained from high-level ab initio calculations (CCSD(T)/cc-pVTZ). The geometric parameters in 8 and 9 are very similar; they also do not differ significantly from the all-carbon analogue, (Z)-hex-3-ene-1,5-diyne (7), the parent molecule for the Bergman cyclization. A small deviation from linearity about the alkyne and cyano linkages is observed for 7-9 and several related species where accurate equilibrium parameters are available. The data on 7-9 should be of interest to radioastronomy and may provide insights on the formation and interstellar chemistry of unsaturated species such as the cyanopolyynes.

Luminescence studies of HgCdTe- and InAsSb-based quantum-well structures

NASA Astrophysics Data System (ADS)

Izhnin, I. I.; Izhnin, A. I.; Fitsych, O. I.; Voitsekhovskii, A. V.; Gorn, D. I.; Semakova, A. A.; Bazhenov, N. L.; Mynbaev, K. D.; Zegrya, G. G.

2018-04-01

Results of photoluminescence studies of single-quantum-well HgCdTe-based structures and electroluminescence studies of multiple-quantum-well InAsSb-based structures are reported. HgCdTe structures were grown with molecular beam epitaxy on GaAs substrates. InAsSb-based structures were grown with metal-organic chemical vapor deposition on InAs substrates. The common feature of luminescence spectra of all the structures was the presence of peaks with the energy much larger than that of calculated optical transitions between the first quantization levels for electrons and heavy holes. Possibility of observation of optical transitions between the quantization levels of electrons and first and/or second heavy and light hole levels is discussed in the paper in relation to the specifics of the electronic structure of the materials under consideration.

A vibrational spectroscopic study of hydrated Fe(3+) hydroxyl-sulfates; polymorphic minerals butlerite and parabutlerite.

PubMed

Cejka, Jiří; Sejkora, Jiří; Plášil, Jakub; Bahfenne, Silmarilly; Palmer, Sara J; Frost, Ray L

2011-09-01

Raman and infrared spectra of two polymorphous minerals with the chemical formula Fe3+(SO4)(OH)·2H2O, monoclinic butlerite and orthorhombic parabutlerite, are studied and the spectra assigned. Observed bands are attributed to the (SO4)2- stretching and bending vibrations, hydrogen bonded water molecules, stretching and bending vibrations of hydroxyl ions, water librational modes, Fe-O and Fe-OH stretching vibrations, Fe-OH bending vibrations and lattice vibrations. The O-H⋯O hydrogen bond lengths in the structures of both minerals are calculated from the wavenumbers of the stretching vibrations. One symmetrically distinct (SO4)2- unit in the structure of butlerite and two symmetrically distinct (SO4)2- units in the structure of parabutlerite are inferred from the Raman and infrared spectra. This conclusion agrees with the published crystal structures of both mineral phases. Copyright © 2011 Elsevier B.V. All rights reserved.

Characterization of a Structural Transformation of Carbon Nanotube Materials by Raman Spectroscopy

NASA Technical Reports Server (NTRS)

Cui, Y.; Burger, A.; Zhu, S.; Su, C.-H.; Lehoczky, S. L.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Raman spectra of carbon nanotubes and carbon microstructure materials synthesized on Si substrates by pulsed laser vaporization have been measured in the range of 50/cm to 4500/cm with the excitation of He-Ne laser. It is found that the formation of nanotubes depends strongly on the growth temperatures and high quality multi-wall and single-wall nanotubes were produced at 700 and 990 C, respectively. The Raman spectra of one sample grown at 700 C were found to be dependent on the excitation intensity. The spectra of the sample suggest that the structure is similar to that of multi-wall nanotubes at low excitation intensity (2.5 kW/sq cm) and it converts to the structure of single-wall nanotubes at higher intensity (25 kW/sq cm). Measurements taken while cycling the light intensity indicate a reversible structural transition.

Structures and interactions in N-methylacetamide-water mixtures studied by IR spectra and density functional theory

NASA Astrophysics Data System (ADS)

Zhang, Rong; Li, Haoran; Lei, Yi; Han, Shijun

2004-05-01

IR spectra have been performed to study the structures and interactions in N-methylacetamide and water mixtures. Because of the competitions of acceptor and donor of the strong hydrogen bonds, some interesting phenomena of red shifts and blue shifts are observed in νCO and νN-H. It is due to the blue-shifting C-H⋯O hydrogen bond, the νC-H blue shifts more obviously. Then some representative cluster structures are suggested and further investigated by density functional theory method. The changes in bond length and frequency shift of the structures give good reasons for the red shift and blue shift, which represents excellent agreement with the IR experiment. The investigations of IR spectra and DFT calculations reveal that the weak C-H⋯O interactions play different roles compared with the classical strong hydrogen bonds in the NMA-water mixtures.

A study on micro-structural and optical parameters of InxSe1-x thin film

NASA Astrophysics Data System (ADS)

Patel, P. B.; Desai, H. N.; Dhimmar, J. M.; Modi, B. P.

2018-04-01

Thin film of Indium Selenide (InSe) has been deposited by thermal evaporation technique onto pre cleaned glass substrate under high vacuum condition. The micro-structural and optical properties of InxSe1-x (x = 0.6, 1-x = 0.4) thin film have been characterized by X-ray diffractrometer (XRD) and UV-Visible spectrophotometer. The XRD spectra showed that InSe thin film has single phase hexagonal structure with preferred orientation along (1 1 0) direction. The micro-structural parameters (crystallite size, lattice strain, dislocation density, domain population) for InSe thin film have been calculated using XRD spectra. The optical parameters (absorption, transmittance, reflectance, energy band gap, Urbach energy) of InSe thin film have been evaluated from absorption spectra. The direct energy band gap and Urbach energy of InSe thin film is found to be 1.90 eV and 235 meV respectively.

Automated Lipid A Structure Assignment from Hierarchical Tandem Mass Spectrometry Data

NASA Astrophysics Data System (ADS)

Ting, Ying S.; Shaffer, Scott A.; Jones, Jace W.; Ng, Wailap V.; Ernst, Robert K.; Goodlett, David R.

2011-05-01

Infusion-based electrospray ionization (ESI) coupled to multiple-stage tandem mass spectrometry (MS n ) is a standard methodology for investigating lipid A structural diversity (Shaffer et al. J. Am. Soc. Mass. Spectrom. 18(6), 1080-1092, 2007). Annotation of these MS n spectra, however, has remained a manual, expert-driven process. In order to keep up with the data acquisition rates of modern instruments, we devised a computational method to annotate lipid A MS n spectra rapidly and automatically, which we refer to as hierarchical tandem mass spectrometry (HiTMS) algorithm. As a first-pass tool, HiTMS aids expert interpretation of lipid A MS n data by providing the analyst with a set of candidate structures that may then be confirmed or rejected. HiTMS deciphers the signature ions (e.g., A-, Y-, and Z-type ions) and neutral losses of MS n spectra using a species-specific library based on general prior structural knowledge of the given lipid A species under investigation. Candidates are selected by calculating the correlation between theoretical and acquired MS n spectra. At a false discovery rate of less than 0.01, HiTMS correctly assigned 85% of the structures in a library of 133 manually annotated Francisella tularensis subspecies novicida lipid A structures. Additionally, HiTMS correctly assigned 85% of the structures in a smaller library of lipid A species from Yersinia pestis demonstrating that it may be used across species.

Deficiency of water molecules in the crystallographic structure of vauxite

NASA Astrophysics Data System (ADS)

Van Alboom, A.; da Costa, G. M.; De Grave, E.

2017-07-01

A vauxite mineral sample from Huanuni, Bolivia, was studied by XRD, TGA and Mössbauer spectroscopy. The XRD revealed the sample as having the typical triclinic structure of vauxite. The chemical formula was determined as (Fe0.88Mn0.01)Al1.99(PO4)2(OH)1.75(H2O)5.31, implying some Fe2+, OH- and H2O deficiencies. The TGA curve showed ca. 27% loss of weight over a temperature range from 80 to 400 °C, supposedly due to the loss of water and hydroxyl groups. For the first time, Mössbauer spectra for vauxite were collected over a wide temperature range between 9 and 310 K. No magnetic ordering was detected. The spectra could be successfully and consistently analyzed by a superposition of four doublet subspectra. On the basis of the relation between the center shift and the mean Fe-ligand distance on the one hand and the center shift values for the various doublets on the other hand, one doublet was assigned to Fe(2). For the other doublets, it is proposed that, as a result of the H2O deficiency in the structure of the present vauxite sample, vacancies are present in the second coordination spheres of some Fe(1) and that these vacancies affect the quadrupole splitting of the corresponding Fe(1) cations, thus causing three Fe(1) doublet components in the Mössbauer spectra. The temperature variations of center shift and quadrupole splitting of the various doublet contributions are presented and discussed.

Changes in the dielectric properties of medaka fish embryos during development, studied by electrorotation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shirakashi, Ryo, E-mail: aa21150@iis.u-tokyo.ac.jp; Mischke, Miriam; Fischer, Peter

2012-11-09

Highlights: Black-Right-Pointing-Pointer Electrorotation offers a non-invasive tool for dielectric analysis of fish embryos. Black-Right-Pointing-Pointer The three-shell dielectric model matches the rotation spectra of medaka eggs. Black-Right-Pointing-Pointer The capacitance value suggests a double-membrane structure of yolk envelope. -- Abstract: The Japanese medaka fish, Oryzias latipes, has become a powerful vertebrate model organism in developmental biology and genetics. The present study explores the dielectric properties of medaka embryos during pre-hatching development by means of the electrorotation (ROT) technique. Due to their layered structure, medaka eggs exhibited up to three ROT peaks in the kHz-MHz frequency range. During development from blastula to earlymore » somite stage, ROT spectra varied only slightly. But as the embryo progressed to the late-somite stage, the ROT peaks underwent significant changes in frequency and amplitude. Using morphological data obtained by light and electron microscopy, we analyzed the ROT spectra with a three-shell dielectric model that accounted for the major embryonic compartments. The analysis yielded a very high value for the ionic conductivity of the egg shell (chorion), which was confirmed by independent osmotic experiments. A relatively low capacitance of the yolk envelope was consistent with its double-membrane structure revealed by transmission electron microscopy. Yolk-free dead eggs exhibited only one co-field ROT peak, shifted markedly to lower frequencies with respect to the corresponding peak of live embryos. The dielectric data may be useful for monitoring the development and changes in fish embryos' viability/conditions in basic research and industrial aquaculture.« less

Evidence of conformational exchange averaging in the thermal rotational spectrum of ethyl cyanoformate.

PubMed

True, Nancy S

2006-06-15

The Stark modulated low resolution microwave spectrum of ethyl cyanoformate between 21.5 and 24.0 GHz at 210, 300, and 358 K, which shows the J + 1 <-- J = 8 <-- 7 bands of three species, is compared to simulations based on electronic structure calculations at the MP2/6-311++G theory level. Calculations at this theory level reproduce the relative energies of the syn-anti and syn-gauche conformers, obtained in a previous study, and indicate that the barrier to conformer exchange is approximately 360 cm(-1) higher in energy than the syn-anti minimum. Simulated spectra of the eigenstates of the calculated O-ethyl torsional potential function reproduce the relative intensities and shapes of the lower and higher frequency bands which correspond to transitions of the syn-anti and syn-gauche conformers, respectively, but fail to reproduce the intense center band in the experimental spectra. A model incorporating exchange averaging reproduces the intensity of the center band and its temperature dependence. These simulations indicate that a large fraction of the thermal population at all three temperatures undergoes conformational exchange with an average energy specific rate constant, , of approximately 25 GHz. This model can explain anomalies present in rotational spectra of many other compounds composed of mixtures of conformers.

GC-MS and GC-IRD studies on the ring isomers of N-methyl-2-methoxyphenyl-3-butanamines (MPBA) related to 3,4-MDMA.

PubMed

Awad, Tamer; Maher, Hadir M; DeRuiter, Jack; Clark, C Randall

2011-05-01

The mass spectra of the controlled substance 3,4-MDMA and its regioisomer 2,3-MDMA are characterized by an imine fragment base peak at m/z 58 and additional fragments at m/z 135/136 for the methylenedioxybenzyl cation and radical cation, respectively. Three positional ring methoxy isomers of N-methyl-2-(methoxyphenyl)-3-butanamine (MPBA) have an isobaric relationship to 2,3- and 3,4-MDMA. All five compounds have the same molecular weight and produce similar EI mass spectra. This lack of mass spectral specificity for the isomers in addition to the possibility of chromatographic co-elution could result in misidentification. The lack of reference materials for the potential imposter molecules constitutes a significant analytical challenge. Perfluoroacylation of the amine group reduced the nitrogen basicity and provided individual fragmentation pathways for discrimination among these compounds based on unique fragment ions and the relative abundance of common ions. Studies using gas chromatography with infrared detection provided additional structure-IR spectra relationships. The underivatized amines and the perfluoroacylated derivatives (PFPA and HFBA) were resolved by capillary gas chromatography on a 100% dimethylpolysiloxane stationary phase. The perfluoroacylated derivatives showed better resolution on a cyclodextrin modified stationary phase.

Automated generation and ensemble-learned matching of X-ray absorption spectra

NASA Astrophysics Data System (ADS)

Zheng, Chen; Mathew, Kiran; Chen, Chi; Chen, Yiming; Tang, Hanmei; Dozier, Alan; Kas, Joshua J.; Vila, Fernando D.; Rehr, John J.; Piper, Louis F. J.; Persson, Kristin A.; Ong, Shyue Ping

2018-12-01

X-ray absorption spectroscopy (XAS) is a widely used materials characterization technique to determine oxidation states, coordination environment, and other local atomic structure information. Analysis of XAS relies on comparison of measured spectra to reliable reference spectra. However, existing databases of XAS spectra are highly limited both in terms of the number of reference spectra available as well as the breadth of chemistry coverage. In this work, we report the development of XASdb, a large database of computed reference XAS, and an Ensemble-Learned Spectra IdEntification (ELSIE) algorithm for the matching of spectra. XASdb currently hosts more than 800,000 K-edge X-ray absorption near-edge spectra (XANES) for over 40,000 materials from the open-science Materials Project database. We discuss a high-throughput automation framework for FEFF calculations, built on robust, rigorously benchmarked parameters. FEFF is a computer program uses a real-space Green's function approach to calculate X-ray absorption spectra. We will demonstrate that the ELSIE algorithm, which combines 33 weak "learners" comprising a set of preprocessing steps and a similarity metric, can achieve up to 84.2% accuracy in identifying the correct oxidation state and coordination environment of a test set of 19 K-edge XANES spectra encompassing a diverse range of chemistries and crystal structures. The XASdb with the ELSIE algorithm has been integrated into a web application in the Materials Project, providing an important new public resource for the analysis of XAS to all materials researchers. Finally, the ELSIE algorithm itself has been made available as part of veidt, an open source machine-learning library for materials science.

Organic Spectroscopy Laboratory: Utilizing IR and NMR in the Identification of an Unknown Substance

ERIC Educational Resources Information Center

Glagovich, Neil M.; Shine, Timothy D.

2005-01-01

A laboratory experiment that emphasizes the interpretation of both infrared (IR) and nuclear magnetic resonance (NMR) spectra in the elucidation of the structure of an unknown compound was developed. The method helps students determine [to the first power]H- and [to the thirteenth power]C-NMR spectra from the structures of compounds and to…

Strategy for the elucidation of elemental compositions of trace analytes based on a mass resolution of 100,000 full width at half maximum.

PubMed

Kaufmann, Anton

2010-07-30

Elemental compositions (ECs) can be elucidated by evaluating the high-resolution mass spectra of unknown or suspected unfragmented analyte ions. Classical approaches utilize the exact mass of the monoisotopic peak (M + 0) and the relative abundance of isotope peaks (M + 1 and M + 2). The availability of high-resolution instruments like the Orbitrap currently permits mass resolutions up to 100,000 full width at half maximum. This not only allows the determination of relative isotopic abundances (RIAs), but also the extraction of other diagnostic information from the spectra, such as fully resolved signals originating from (34)S isotopes and fully or partially resolved signals related to (15)N isotopes (isotopic fine structure). Fully and partially resolved peaks can be evaluated by visual inspection of the measured peak profiles. This approach is shown to be capable of correctly discarding many of the EC candidates which were proposed by commercial EC calculating algorithms. Using this intuitive strategy significantly extends the upper mass range for the successful elucidation of ECs. Copyright 2010 John Wiley & Sons, Ltd.

Synthesis, crystal structure, Hirshfeld surfaces analysis and anti-ischemic activity of cinnamide derivatives

NASA Astrophysics Data System (ADS)

Zhong, Jian-gang; Han, Jia-pei; Li, Xiao-feng; Xu, Yi; Zhong, Yan; Wu, Bin

2018-02-01

Two cinnamide derivatives, namely, (E)-1-(4-(bis(4-methylphenyl)- methyl)piperazin-1-yl)-3-(3,4-diethoxyphenyl)prop-2-en-1-one (5) and (E)-1-(4-(bis- (4-fluorophenyl)methyl)piperazin-1-yl)-3-(4-methoxyphenyl)prop-2-en-1-one (6), have been synthesized and characterized by IR spectra, High resolution mass spectra, 1H NMR spectra, 13C NMR spectra. The compound 5 is a novel compound and has never been reported in the literature. Their crystal structures were studied by single-crystal X-ray diffraction. They all crystallize in the monoclinic system. The single-crystal X-ray revealed that compound 5 has infinite X-shaped 1-D polymeric chains structure and compound 6 has a layered 3-D structure by intermolecular interactions. Hirshfeld surface analysis demonstrated the presence of H⋯H, O⋯H, C⋯H, F⋯H, Csbnd H⋯π and π⋯π intermolecular interactions. In addition, the MTT assay results indicated that the compounds 5 and 6 display effective activities against neurotoxicity which is induced by glutamine in PC12 cells. The in vivo experiment indicated that the compound 6 has a good protective effect on cerebral infarction.

X-ray absorption investigation of the electronic structure of the CuI@SWCNT nanocomposite

NASA Astrophysics Data System (ADS)

Generalov, A. V.; Brzhezinskaya, M. M.; Vinogradov, A. S.; Püttner, R.; Chernysheva, M. V.; Lukashin, A. V.; Eliseev, A. A.

2011-03-01

The Cu 2 p, I 3 d, and C 1 sX-ray absorption spectra of the CuI@SWCNT nanocomposite prepared by filling single-walled carbon nanotubes (SWCNTs) with the CuI melt by the capillary technique have been measured with a high-energy resolution using the equipment of the Russian-German beamline at the BESSY electron storage ring. In order to characterize the electronic structure of the nanocomposite and possible changes in the atomic and electronic structures of CuI and SWCNTs in the CuI@SWCNT nanocomposite, the spectra obtained have been analyzed in the framework of the quasi-molecular approach by comparing with the spectra of the pristine (CuI and SWCNT) and reference (CuO) systems. It has been revealed that the encapsulation of the CuI compound inside SWCNTs is accompanied by changes in the electronic structure of CuI and SWCNTs due to the chemical interaction between the filler and carbon nanotubes and the change in the atomic structure of CuI.

Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

PubMed

Courtney, Joseph M; Ye, Qing; Nesbitt, Anna E; Tang, Ming; Tuttle, Marcus D; Watt, Eric D; Nuzzio, Kristin M; Sperling, Lindsay J; Comellas, Gemma; Peterson, Joseph R; Morrissey, James H; Rienstra, Chad M

2015-10-06

Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation efforts. Here we present a qualitatively distinct and novel approach, called Comparative, Objective Measurement of Protein Architectures by Scoring Shifts (COMPASS), which identifies the best structures from a set of structural models by numerical comparison with a single, unassigned 2D (13)C-(13)C NMR spectrum containing backbone and side-chain aliphatic signals. COMPASS does not require resonance assignments. It is particularly well suited for interpretation of magic-angle spinning solid-state NMR spectra, but also applicable to solution NMR spectra. We demonstrate COMPASS with experimental data from four proteins--GB1, ubiquitin, DsbA, and the extracellular domain of human tissue factor--and with reconstructed spectra from 11 additional proteins. For all these proteins, with molecular mass up to 25 kDa, COMPASS distinguished the correct fold, most often within 1.5 Å root-mean-square deviation of the reference structure. Copyright © 2015 Elsevier Ltd. All rights reserved.

Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum

PubMed Central

Courtney, Joseph M.; Ye, Qing; Nesbitt, Anna E.; Tang, Ming; Tuttle, Marcus D.; Watt, Eric D.; Nuzzio, Kristin M.; Sperling, Lindsay J.; Comellas, Gemma; Peterson, Joseph R.; Morrissey, James H.; Rienstra, Chad M.

2016-01-01

Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation efforts. Here we present a qualitatively distinct and novel approach, called Comparative, Objective Measurement of Protein Architectures by Scoring Shifts (COMPASS), which identifies the best structures from a set of structural models by numerical comparison with a single, unassigned 2D 13C-13C NMR spectrum containing backbone and side-chain aliphatic signals. COMPASS does not require resonance assignments. It is particularly well suited for interpretation of magic-angle spinning solid-state NMR spectra, but also applicable to solution NMR spectra. We demonstrate COMPASS with experimental data from four proteins—GB1, ubiquitin, DsbA, and the extracellular domain of human tissue factor—and with reconstructed spectra from 11 additional proteins. For all these proteins, with molecular mass up to 25 kDa, COMPASS distinguished the correct fold, most often within 1.5 Å root-mean-square deviation of the reference structure. PMID:26365800

The Azimuth Structure of Nuclear Collisions — I

NASA Astrophysics Data System (ADS)

Trainor, Thomas A.; Kettler, David T.

We describe azimuth structure commonly associated with elliptic and directed flow in the context of 2D angular autocorrelations for the purpose of precise separation of so-called nonflow (mainly minijets) from flow. We extend the Fourier-transform description of azimuth structure to include power spectra and autocorrelations related by the Wiener-Khintchine theorem. We analyze several examples of conventional flow analysis in that context and question the relevance of reaction plane estimation to flow analysis. We introduce the 2D angular autocorrelation with examples from data analysis and describe a simulation exercise which demonstrates precise separation of flow and nonflow using the 2D autocorrelation method. We show that an alternative correlation measure based on Pearson's normalized covariance provides a more intuitive measure of azimuth structure.

Electronic structure of α-SrB4O7: experiment and theory

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Kesler, V. G.; Zaitsev, A. I.; Molokeev, M. S.; Aleksandrovsky, A. S.; Kuzubov, A. A.; Ignatova, N. Y.

2013-02-01

The investigation of valence band structure and electronic parameters of constituent element core levels of α-SrB4O7 has been carried out with x-ray photoemission spectroscopy. Optical-quality crystal α-SrB4O7 has been grown by the Czochralski method. Detailed photoemission spectra of the element core levels have been recorded from the powder sample under excitation by nonmonochromatic Al Kα radiation (1486.6 eV). The band structure of α-SrB4O7 has been calculated by ab initio methods and compared to XPS measurements. It has been found that the band structure of α-SrB4O7 is weakly dependent on the Sr-related states.

Advanced spectroscopic analysis of 0.8-1.0-MA Mo x pinches and the influence of plasma electron beams on L-shell spectra of Mo ions.

PubMed

Shlyaptseva, A S; Hansen, S B; Kantsyrev, V L; Fedin, D A; Ouart, N; Fournier, K B; Safronova, U I

2003-02-01

This paper presents a detailed investigation of the temporal, spatial, and spectroscopic properties of L-shell radiation from 0.8 to 1.0 MA Mo x pinches. Time-resolved measurements of x-ray radiation and both time-gated and time-integrated spectra and pinhole images are presented and analyzed. High-current x pinches are found to have complex spatial and temporal structures. A collisional-radiative kinetic model has been developed and used to interpret L-shell Mo spectra. The model includes the ground state of every ionization stage of Mo and detailed structure for the O-, F-, Ne-, Na-, and Mg-like ionization stages. Hot electron beams generated by current-carrying electrons in the x pinch are modeled by a non-Maxwellian electron distribution function and have significant influence on L-shell spectra. The results of 20 Mo x-pinch shots with wire diameters from 24 to 62 microm have been modeled. Overall, the modeled spectra fit the experimental spectra well and indicate for time-integrated spectra electron densities between 2 x 10(21) and 2 x 10(22) cm(-3), electron temperatures between 700 and 850 eV, and hot electron fractions between 3% and 7%. Time-gated spectra exhibit wide variations in temperature and density of plasma hot spots during the same discharge.

Investigations of interhydrogen bond dynamical coupling effects in the polarized IR spectra of acetanilide crystals.

PubMed

Flakus, Henryk T; Michta, Anna

2010-02-04

This Article presents the investigation results of the polarized IR spectra of the hydrogen bond in acetanilide (ACN) crystals measured in the frequency range of the proton and deuteron stretching vibration bands, nu(N-H) and nu(N-D). The basic spectral properties of the crystals were interpreted quantitatively in terms of the "strong-coupling" theory. The model of the centrosymmetric dimer of hydrogen bonds postulated by us facilitated the explanation of the well-developed, two-branch structure of the nu(N-H) and nu(N-D) bands as well as the isotopic dilution effects in the spectra. On the basis of the linear dichroic and temperature effects in the polarized IR spectra of ACN crystals, the H/D isotopic "self-organization" effects were revealed. A nonrandom distribution of hydrogen isotope atoms (H or D) in the lattice was deduced from the spectra of isotopically diluted ACN crystals. It was also determined that identical hydrogen isotope atoms occupy both hydrogen bonds in the dimeric systems, where each hydrogen bond belongs to a different chain. A more complex fine structure pattern of nu(N-H) and nu(N-D) bands in ACN spectra in comparison with the spectra of other secondary amides (e.g., N-methylacetamide) can be explained in terms of the "relaxation" theory of the IR spectra of hydrogen-bonded systems.

Evaporation of Particle-Stabilized Emulsion Sunscreen Films.

PubMed

Binks, Bernard P; Fletcher, Paul D I; Johnson, Andrew J; Marinopoulos, Ioannis; Crowther, Jonathan M; Thompson, Michael A

2016-08-24

We recently showed (Binks et al., ACS Appl. Mater. Interfaces, 2016, DOI: 10.1021/acsami.6b02696) how evaporation of sunscreen films consisting of solutions of molecular UV filters leads to loss of UV light absorption and derived sun protection factor (SPF). In the present work, we investigate evaporation-induced effects for sunscreen films consisting of particle-stabilized emulsions containing a dissolved UV filter. The emulsions contained either droplets of propylene glycol (PG) in squalane (SQ), droplets of SQ in PG or droplets of decane in PG. In these different emulsion types, the SQ is involatile and shows no evaporation, the PG is volatile and evaporates relatively slowly, whereas the decane is relatively very volatile and evaporates quickly. We have measured the film mass and area, optical micrographs of the film structure, and the UV absorbance spectra during evaporation. For emulsion films containing the involatile SQ, evaporation of the PG causes collapse of the emulsion structure with some loss of specular UV absorbance due to light scattering. However, for these emulsions with droplets much larger than the wavelength of light, the light is scattered only at small forward angles so does not contribute to the diffuse absorbance and the film SPF. The UV filter remains soluble throughout the evaporation and thus the UV absorption by the filter and the SPF remain approximately constant. Both PG-in-SQ and SQ-in-PG films behave similarly and do not show area shrinkage by dewetting. In contrast, the decane-in-PG film shows rapid evaporative loss of the decane, followed by slower loss of the PG resulting in precipitation of the UV filter and film area shrinkage by dewetting which cause the UV absorbance and derived SPF to decrease. Measured UV spectra during evaporation are in reasonable agreement with spectra calculated using models discussed here.

Study of hydrogen bond polarized IR spectra of cinnamic acid crystals

NASA Astrophysics Data System (ADS)

Flakus, Henryk T.; Jabłońska, Magdalena

2004-11-01

This paper presents the results of investigation of the polarized IR spectra of cinnamic acid and of its deuterium derivative crystals. The spectra were measured by a transmission method, using polarized light, at the room temperature and at 77 K, for two different crystalline faces. Theoretical analysis of the results concerned linear dichroic effects, H/D isotopic and temperature effects, observed in the spectra of the hydrogen and of the deuterium bonds in cinnamic acid crystals, at the frequency ranges of the νO-H and the νO-D bands. The basic crystal spectral properties could be satisfactorily interpreted in a quantitative way for a centrosymmetric cyclic hydrogen bond dimer model. Such a model explains not only a two-branch structure of the νO-H and νO-D bands in crystalline spectra, but also some essential linear dichroic effects in the band frequency ranges, measured for isotopically diluted crystals. Model calculations, performed within the limits of the 'strong-coupling' model, allowed for quantitative interpretation and for understanding of the basic properties of the hydrogen bond IR spectra of cinnamic acid crystals, H/D isotopic, temperature and dichroic effects included. In the scope of our studies the mechanism of H/D isotopic 'self-organization' processes, taking place in the crystal hydrogen bond lattices, was also recognized. It was proved that for isotopically diluted crystalline samples of cinnamic acid, a non-random distribution of protons and deuterons occurs exclusively in the hydrogen bond dimers. Nevertheless, these co-operative interactions between the hydrogen bonds do not involve the adjacent hydrogen bond dimers in each unit cell. The two-branch fine structure pattern of the νO-H and νO-D bands was ascribed to the vibronic mechanism of vibrational dipole selection rule breaking in centrosymmetric hydrogen bond dimers. The observed in the spectra very high intensity of the forbidden transition sub-band in the analyzed νO-H and νO-D bands is a manifestation of an extremely effective symmetry rule breaking mechanism. It correlates with a relatively large excess electron charge on the cinnamic aid dimer carboxyl groups. This effect is a result of a partial withdrawal of the electron charge, from the conjugated π-bond systems of the styryl substituents, by the carboxyl groups. This statement has been supported by ab initio calculations.

SiSeRHMap v1.0: a simulator for mapped seismic response using a hybrid model

NASA Astrophysics Data System (ADS)

Grelle, G.; Bonito, L.; Lampasi, A.; Revellino, P.; Guerriero, L.; Sappa, G.; Guadagno, F. M.

2015-06-01

SiSeRHMap is a computerized methodology capable of drawing up prediction maps of seismic response. It was realized on the basis of a hybrid model which combines different approaches and models in a new and non-conventional way. These approaches and models are organized in a code-architecture composed of five interdependent modules. A GIS (Geographic Information System) Cubic Model (GCM), which is a layered computational structure based on the concept of lithodynamic units and zones, aims at reproducing a parameterized layered subsoil model. A metamodeling process confers a hybrid nature to the methodology. In this process, the one-dimensional linear equivalent analysis produces acceleration response spectra of shear wave velocity-thickness profiles, defined as trainers, which are randomly selected in each zone. Subsequently, a numerical adaptive simulation model (Spectra) is optimized on the above trainer acceleration response spectra by means of a dedicated Evolutionary Algorithm (EA) and the Levenberg-Marquardt Algorithm (LMA) as the final optimizer. In the final step, the GCM Maps Executor module produces a serial map-set of a stratigraphic seismic response at different periods, grid-solving the calibrated Spectra model. In addition, the spectra topographic amplification is also computed by means of a numerical prediction model. This latter is built to match the results of the numerical simulations related to isolate reliefs using GIS topographic attributes. In this way, different sets of seismic response maps are developed, on which, also maps of seismic design response spectra are defined by means of an enveloping technique.

Evaluation of the performance of a tandem mass spectral library with mass spectral data extracted from literature.

PubMed

Würtinger, Philipp; Oberacher, Herbert

2012-01-01

MSforID represents a database of tandem mass spectral data obtained from (quasi-)molecular ions produced by atmospheric pressure ionization methods. At the current stage of development the library contains 12 122 spectra of 1208 small (bio-)organic molecules. The present work was aimed to evaluate the performance of the MSforID library in terms of accuracy and transferability with a collection of fragment ion mass spectra from various compounds acquired on multiple instruments. A literature survey was conducted to collect the set of sample spectra. A total number of 554 spectra covering 291 compounds were extracted from 109 publications. The majority of spectra originated from publications on applications of LC/MS/MS in drug monitoring, pharmacokinetics, environmental analysis, forensic analysis as well as food analysis. Almost all types of tandem mass spectrometric instruments distributed by the five most important instrument vendors were included in the study. The overall sensitivity of library search was found to be 96.4%, which clearly proves that the MSforID library can successfully handle data from a huge variety of mass spectrometric instruments to allow accurate compound identification. Only for spectra containing three or more fragment ions, however, the rate of classified matches (= matches with a relative average match probability (ramp) score > 40.0) was 95%. Ambiguous or unclassified results were mainly obtained for searches with single precursor-to-fragment ion transitions due to the insufficient specificity of such a low amount of structural information to unequivocally define a single compound. Copyright © 2011 John Wiley & Sons, Ltd.

Complete structure of the polysaccharide from Streptococcus sanguis J22

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abeygunawardana, C.; Bush, C.A.; Cisar, J.O.

1990-01-09

The cell wall polysaccharides of certain oral streptococci such as Streptococcus sanguis strains 34 and J22, although immunologically distinct, act as receptors for the fimbrial lectins of Actinomyces viscosus T14V. The authors report the complete covalent structure of the polysaccharide from S. sanguis J22 which is composed of a heptasaccharide subunit linked by phosphodiester bonds. The repeating subunit, which contains {alpha}-GalNAc, {alpha}-rhamnose, {beta}-rhamnose, {beta}-glucose, and {beta}-galactose all in the pyranoside form and {beta}-galactofuranose, is compared with the previously published structure of the polysaccharide from strain 34. The structure has been determined almost exclusively by high-resolution nuclear magnetic resonance methods. Themore » {sup 1}H and {sup 13}C NMR spectra of the polysaccharides from both strains 34 and J22 have been completely assigned. The stereochemistry of pyranosides was assigned from J{sub H-H} values determined from phase-sensitive COSY spectra, and acetamido sugars were assigned by correlation of the resonances of the amide {sup 1}H with the sugar ring protons. The {sup 13}C spectra were assigned by {sup 1}H-detected multiple-quantum correlation (HMQC) spectra, and the assignments were confirmed by {sup 1}H-detected multiple-bond correlation (HMBC) spectra. The positions of the glycosidic linkages were assigned by detection of three-bond {sup 1}H-{sup 13}C correlation across the glycosidic linkage in the HMBC spectra. The positions of the phosphodiester linkages were determined by splittings observed in the {sup 13}C resonances due to {sup 31}P coupling and also by {sup 1}H-detected {sup 31}P correlation spectroscopy.« less

NIR Raman spectroscopy in medicine and biology: results and aspects

NASA Astrophysics Data System (ADS)

Schrader, B.; Dippel, B.; Erb, I.; Keller, S.; Löchte, T.; Schulz, H.; Tatsch, E.; Wessel, S.

1999-05-01

Analyses of biomaterial by 'classical' Raman spectroscopy with excitation in the visible range has not been possible since the fluorescence of many essential constituents of all animal and plant cells and tissues overlays the Raman spectra completely. Fluorescence, however, is virtually avoided, when Raman spectra are excited with the Nd : YAG laser line at 1064 nm. Within seven dissertations we explored different fields of potential applications to medical diagnostics. Identification and qualification of tissues and cells is possible. Tumors show small but significant differences to normal tissues; in order to develop a reliable tool for tumor diagnostics more research is necessary, especially a collection of reference spectra in a data bank is needed. Raman spectra of biomineralization structures in teeth and bones show pathological tissues as well as the development of new mineralized structures. NIR Raman spectra of flowers, leaves, and fruit show, without special preparation, their constituents: alkaloids, the essential oils, natural dyes, flavors, spices and drugs. They allow application to taxonomy, optimizing plant breeding and control of food.

FT-IR and FT-Raman characterization of non-cellulosic polysaccharides fractions isolated from plant cell wall.

PubMed

Chylińska, Monika; Szymańska-Chargot, Monika; Zdunek, Artur

2016-12-10

The purpose of this work was to reveal the structural changes of cell wall polysaccharides' fractions during tomato fruit development by analysis of spectral data. Mature green and red ripe tomato fruit were taken into consideration. The FT-IR spectra of water soluble pectin (WSP), imidazole soluble pectin (ISP) and diluted alkali soluble pectin (DASP) contained bands typical for pectins. Whereas for KOH fraction spectra bands typical for hemicelluloses were present. The FT-IR spectra showed the drop down of esterification degree of WSP and ISP polysaccharides during maturation. The changes in polysaccharides structure revealed by spectra were the most visible in the case of pectic polysaccharides. The WSP and DASP fraction pectins molecules length were shortened during tomato maturation and ripening. Whereas the ISP fraction spectra analysis showed that this fraction contained rhamnogalacturonan I, but also for red ripe was rich in pectic galactan comparing with ISP fraction from mature green. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structural elucidation of direct analysis in real time ionized nerve agent simulants with infrared multiple photon dissociation spectroscopy.

PubMed

Rummel, Julia L; Steill, Jeffrey D; Oomens, Jos; Contreras, Cesar S; Pearson, Wright L; Szczepanski, Jan; Powell, David H; Eyler, John R

2011-06-01

Infrared multiple photon dissociation (IRMPD) was used to generate vibrational spectra of ions produced with a direct analysis in real time (DART) ionization source coupled to a 4.7 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The location of protonation on the nerve agent simulants diisopropyl methylphosphonate (DIMP) and dimethyl methylphosphonate (DMMP) was studied while solutions of the compounds were introduced for extended periods of time with a syringe pump. Theoretical vibrational spectra were generated with density functional theory calculations. Visual comparison of experimental mid-IR IRMPD spectra and theoretical spectra could not establish definitively if a single structure or a mixture of conformations was present for the protonated parent of each compound. However, theoretical calculations, near-ir IRMPD spectra, and frequency-to-frequency and statistical comparisons indicated that the protonation site for both DIMP and DMMP was predominantly, if not exclusively, the phosphonyl oxygen instead of one of the oxygen atoms with only single bonds.

Nonlinear optical spectra having characteristics of Fano interferences in coherently coupled lowest exciton biexciton states in semiconductor quantum dots

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gotoh, Hideki, E-mail: gotoh.hideki@lab.ntt.co.jp; Sanada, Haruki; Yamaguchi, Hiroshi

2014-10-15

Optical nonlinear effects are examined using a two-color micro-photoluminescence (micro-PL) method in a coherently coupled exciton-biexciton system in a single quantum dot (QD). PL and photoluminescence excitation spectroscopy (PLE) are employed to measure the absorption spectra of the exciton and biexciton states. PLE for Stokes and anti-Stokes PL enables us to clarify the nonlinear optical absorption properties in the lowest exciton and biexciton states. The nonlinear absorption spectra for excitons exhibit asymmetric shapes with peak and dip structures, and provide a distinct contrast to the symmetric dip structures of conventional nonlinear spectra. Theoretical analyses with a density matrix method indicatemore » that the nonlinear spectra are caused not by a simple coherent interaction between the exciton and biexciton states but by coupling effects among exciton, biexciton and continuum states. These results indicate that Fano quantum interference effects appear in exciton-biexciton systems at QDs and offer important insights into their physics.« less

Sequencing BPS spectra

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar

In this article, we provide both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explainmore » from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincar e polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (re fined) modular S-matrix. This leads to the identi fication of modular transformations in Chern-Simons theory and 3d N = 2 theory via the 3d/3d correspondence. In conclusion, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.« less

Luminescence Mechanism of Carbon Dots by Tailoring Functional Groups for Sensing Fe3+ Ions

PubMed Central

Yu, Jingjing; Liu, Chang; Yuan, Kang; Lu, Zunming; Cheng, Yahui; Li, Lanlan; Jin, Peng; Meng, Fanbin; Liu, Hui

2018-01-01

In this paper, spherical carbon dots (CDs) with distinct compositions and surface states have been successfully synthesized by a facile microwave method. From the fluorescence spectra, several characteristic luminescence features have been observed: surface amino groups are dominant in the whole emission spectra centering at 445 nm, and the fingerprint emissions relevant to the impurity levels formed by some groups related to C and N elements, including C-C/C=C (intrinsic C), C-N (graphitic N), N-containing heterocycles (pyridine N) and C=O groups, are located around 305 nm, 355 nm, 410 nm, and 500 nm, respectively. Those fine luminescence features could be ascribed to the electron transition among various trapping states within the band structure caused by different chemical bonds in carbon cores, or functional groups attached to the CDs’ surfaces. According to the theoretical calculations and experimental results, a scheme of the band structure has been proposed to describe the positions of those trapping states within the band gap. Additionally, it has also been observed that the emission of CDs is sensitive to the concentration of Fe3+ ions with a linear relation in the range of Fe3+ concentration from 12.5 to 250 μM. PMID:29649110

Sequencing BPS spectra

DOE PAGES

Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; ...

2016-03-02

In this article, we provide both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explainmore » from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincar e polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (re fined) modular S-matrix. This leads to the identi fication of modular transformations in Chern-Simons theory and 3d N = 2 theory via the 3d/3d correspondence. In conclusion, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.« less

Ne matrix spectra of the sym-C6Br3F3+ radical cation

USGS Publications Warehouse

Bondybey, V.E.; Sears, T.J.; Miller, T.A.; Vaughn, C.; English, J.H.; Shiley, R.S.

1981-01-01

The electronic absorption and laser excited, wavelength resolved fluorescence spectra of the title cation have been observed in solid Ne matrix and vibrationally analysed. The vibrational structure of the excited B2A2??? state shows close similarity to the parent compound. The X2E??? ground state structure is strongly perturbed and irregular owing to a large Jahn-Teller distortion. The data are analysed in terms of a recently developed, sophisticated multimode Jahn-Teller theoretical model. We have generated the sym-C6Br3F3+ cations in solid Ne matrix and obtained their wavelength resolved emission and absorption spectra. T ground electronic X2E??? state exhibits an irregular and strongly perturbed vibrational structure, which can be successfully modeled using sophisticated multimode Jahn-Teller theory. ?? 1981.

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

NASA Astrophysics Data System (ADS)

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

2014-10-01

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

Molecular structure and vibrational spectra of Irinotecan: a density functional theoretical study.

PubMed

Chinna Babu, P; Sundaraganesan, N; Sudha, S; Aroulmoji, V; Murano, E

2012-12-01

The solid phase FTIR and FT-Raman spectra of Irinotecan have been recorded in the regions 400-4000 and 50-4000 cm(-1), respectively. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by density functional theory (DFT) using B3LYP method with 6-31G(d) as basis set. The vibrational frequencies were calculated for Irinotecan by DFT method and were compared with the experimental frequencies, which yield good agreement between observed and calculated frequencies. The infrared spectrum was also simulated from the calculated intensities. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis were investigated using theoretical calculations. Copyright © 2012 Elsevier B.V. All rights reserved.

[Absorption Characteristics and Simulation of LLM-105 in the Terahertz Range].

PubMed

Meng, Zeng-rui; Shang, Li-ping; Du, Yu; Deng, Hu

2015-07-01

2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105), a novel explosive with high energy and low sensibility. In order to study the molecular structure characteristics of the explosive, the absorption spectra of LLM-105 in the frequency range of 0.2-2.4 THz were detected by terahertz time-domain spectroscopy (THz-TDS). The results showed that a number of characteristic absorption peaks with different intensity located at 1.27, 1.59, 2.00, 2.08, 2.20, 2.29 THz. The article also simulated the absorption spectra of LLM-105 molecular crystal within 0.2-2.5 THz region by using Materials Studio 6.0 software based on density functional theory (DFT), and the simulated results agreed well with the experimental data except for the peak at 2.29 THz, which verified theoretically the accuracy of the experimental data. In addition, the vibrational modes of the characteristic peaks in the experimental absorption spectra were analyzed and identified, the results showed that the forming of the characteristic absorption peaks and the molecular vibration were closely related, which further provided important laboratory and technology support for the study of the transformation of molecule structure of LLM-105. There was no simulated frequency agreed with the experimental absorption peak at 2.29 THz, which may be caused by the vibration of the crystal lattice or other reasons.

H/D isotopic recognition and temperature effects in IR spectra of hydrogen-bonded cyclic dimers in crystals: 3-Methylcinnamic acid and 4-phenylbutyric acid

NASA Astrophysics Data System (ADS)

Hachuła, Barbara; Jabłońska-Czapla, Magdalena; Flakus, Henryk T.; Nowak, Maria; Kusz, Joachim

2015-01-01

In the present work, the experimental and theoretical study of the nature of the inter-hydrogen bond interactions in two different carboxylic acids, 3-methylcinnamic acid (3MCA) and 4-phenylbutyric acid (4PBA), were reported. The polarized IR spectra of 3MCA and 4PBA crystals were recorded at the frequency ranges of the νOsbnd H and νOsbnd D bands. The spectral properties of 3MCA and 4PBA interpreted with the aid of the calculations based on the "strong-coupling" model. The differences in the spectral properties of the two different dimeric systems in the crystals provide a valuable information about the existence of a direct relationship between the crystal spectral properties in IR and the electronic structure of the molecular systems. In 3MCA crystals strong vibrational exciton interactions favor a "tail-to-head" (TH)-type Davydov coupling widespread via the π-electrons, whereas in 4PBA crystals a weak "through-space" (SS) exciton coupling is responsible for a "side-to-side"-type coupling. The relative contribution of each individual exciton coupling mechanism in IR spectra generation strongly depends on temperature and molecular electronic structure. The H/D isotopic recognition effect, depending on a non-random distribution of protons and deuterons in the crystal hydrogen bridges, was also analyzed.

H/D isotopic recognition and temperature effects in IR spectra of hydrogen-bonded cyclic dimers in crystals: 3-methylcinnamic acid and 4-phenylbutyric acid.

PubMed

Hachuła, Barbara; Jabłońska-Czapla, Magdalena; Flakus, Henryk T; Nowak, Maria; Kusz, Joachim

2015-01-05

In the present work, the experimental and theoretical study of the nature of the inter-hydrogen bond interactions in two different carboxylic acids, 3-methylcinnamic acid (3MCA) and 4-phenylbutyric acid (4PBA), were reported. The polarized IR spectra of 3MCA and 4PBA crystals were recorded at the frequency ranges of the νO-H and νO-D bands. The spectral properties of 3MCA and 4PBA interpreted with the aid of the calculations based on the "strong-coupling" model. The differences in the spectral properties of the two different dimeric systems in the crystals provide a valuable information about the existence of a direct relationship between the crystal spectral properties in IR and the electronic structure of the molecular systems. In 3MCA crystals strong vibrational exciton interactions favor a "tail-to-head" (TH)-type Davydov coupling widespread via the π-electrons, whereas in 4PBA crystals a weak "through-space" (SS) exciton coupling is responsible for a "side-to-side"-type coupling. The relative contribution of each individual exciton coupling mechanism in IR spectra generation strongly depends on temperature and molecular electronic structure. The H/D isotopic recognition effect, depending on a non-random distribution of protons and deuterons in the crystal hydrogen bridges, was also analyzed. Copyright © 2014 Elsevier B.V. All rights reserved.

Measurement of neutron spectra in the experimental reactor LR-0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prenosil, Vaclav; Mravec, Filip; Veskrna, Martin

2015-07-01

The measurement of fast neutron fluxes is important in many areas of nuclear technology. It affects the stability of the reactor structural components, performance of fuel, and also the fuel manner. The experiments performed at the LR-0 reactor were in the past focused on the measurement of neutron field far from the core, in reactor pressure vessel simulator or in biological shielding simulator. In the present the measurement in closer regions to core became more important, especially measurements in structural components like reactor baffle. This importance increases with both reactor power increase and also long term operation. Other important taskmore » is an increasing need for the measurement close to the fuel. The spectra near the fuel are aimed due to the planned measurements with the FLIBE salt, in FHR / MSR research, where one of the task is the measurement of the neutron spectra in it. In both types of experiments there is strong demand for high working count rate. The high count rate is caused mainly by high gamma background and by high fluxes. The fluxes in core or in its vicinity are relatively high to ensure safe reactor operation. This request is met in the digital spectroscopic apparatus. All experiments were realized in the LR-0 reactor. It is an extremely flexible light water zero-power research reactor, operated by the Research Center Rez (Czech Republic). (authors)« less

Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

PubMed

Ivanciuc, Ovidiu

2013-06-01

Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance.

Digital Speckle Photography of Subpixel Displacements of Speckle Structures Based on Analysis of Their Spatial Spectra

NASA Astrophysics Data System (ADS)

Maksimova, L. A.; Ryabukho, P. V.; Mysina, N. Yu.; Lyakin, D. V.; Ryabukho, V. P.

2018-04-01

We have investigated the capabilities of the method of digital speckle interferometry for determining subpixel displacements of a speckle structure formed by a displaceable or deformable object with a scattering surface. An analysis of spatial spectra of speckle structures makes it possible to perform measurements with a subpixel accuracy and to extend the lower boundary of the range of measurements of displacements of speckle structures to the range of subpixel values. The method is realized on the basis of digital recording of the images of undisplaced and displaced speckle structures, their spatial frequency analysis using numerically specified constant phase shifts, and correlation analysis of spatial spectra of speckle structures. Transformation into the frequency range makes it possible to obtain quantities to be measured with a subpixel accuracy from the shift of the interference-pattern minimum in the diffraction halo by introducing an additional phase shift into the complex spatial spectrum of the speckle structure or from the slope of the linear plot of the function of accumulated phase difference in the field of the complex spatial spectrum of the displaced speckle structure. The capabilities of the method have been investigated in natural experiment.

Structures of the dehydrogenation products of methane activation by 5d transition metal cations revisited: Deuterium labeling and rotational contours

NASA Astrophysics Data System (ADS)

Owen, Cameron J.; Boles, Georgia C.; Chernyy, Valeriy; Bakker, Joost M.; Armentrout, P. B.

2018-01-01

A previous infrared multiple photon dissociation (IRMPD) action spectroscopy and density functional theory (DFT) study explored the structures of the [M,C,2H]+ products formed by dehydrogenation of methane by four, gas-phase 5d transition metal cations (M+ = Ta+, W+, Ir+, and Pt+). Complicating the analysis of these spectra for Ir and Pt was observation of an extra band in both spectra, not readily identified as a fundamental vibration. In an attempt to validate the assignment of these additional peaks, the present work examines the gas phase [M,C,2D]+ products of the same four metal ions formed by reaction with perdeuterated methane (CD4). As before, metal cations are formed in a laser ablation source and react with methane pulsed into a reaction channel downstream, and the resulting products are spectroscopically characterized through photofragmentation using the free-electron laser for intracavity experiments in the 350-1800 cm-1 range. Photofragmentation was monitored by the loss of D for [Ta,C,2D]+ and [W,C,2D]+ and of D2 in the case of [Pt,C,2D]+ and [Ir,C,2D]+. Comparison of the experimental spectra and DFT calculated spectra leads to structural assignments for all [M,C,2H/2D]+ systems that are consistent with previous identifications and allows a full description of the systematic spectroscopic shifts observed for deuterium labeling of these complexes, some of the smallest systems to be studied using IRMPD action spectroscopy. Further, full rotational contours are simulated for each vibrational band and explain several observations in the present spectra, such as doublet structures in several bands as well as the observed linewidths. The prominent extra bands in the [Pt,C,2D/2H]+ spectra appear to be most consistent with an overtone of the out-of-plane bending vibration of the metal carbene cation structure.

XAS Characterization of the Zn Site of Non-structural Protein 3 (NS3) from Hepatitis C Virus

NASA Astrophysics Data System (ADS)

Ascone, I.; Nobili, G.; Benfatto, M.; Congiu-Castellano, A.

2007-02-01

XANES spectra of non structural protein 3 (NS3) have been calculated using 4 Zn coordination models from three crystallographic structures in the Protein Data Base (PDB): 1DY9, subunit B, 1CU1 subunit A and B, and 1JXP subunit B. Results indicate that XANES is an appropriate tool to distinguish among them. Experimental XANES spectra have been simulated refining crystallographic data. The model obtained by XAS is compared with the PDB models.

Electronic Structure of the Ferryl Intermediate in the α-Ketoglutarate Dependent Non-Heme Iron Halogenase SyrB2: Contributions to H Atom Abstraction Reactivity.

PubMed

Srnec, Martin; Wong, Shaun D; Matthews, Megan L; Krebs, Carsten; Bollinger, J Martin; Solomon, Edward I

2016-04-20

Low temperature magnetic circular dichroism (LT MCD) spectroscopy in combination with quantum-chemical calculations are used to define the electronic structure associated with the geometric structure of the Fe(IV)═O intermediate in SyrB2 that was previously determined by nuclear resonance vibrational spectroscopy. These studies elucidate key frontier molecular orbitals (FMOs) and their contribution to H atom abstraction reactivity. The VT MCD spectra of the enzymatic S = 2 Fe(IV)═O intermediate with Br(-) ligation contain information-rich features that largely parallel the corresponding spectra of the S = 2 model complex (TMG3tren)Fe(IV)═O (Srnec, M.; Wong, S. D.; England, J; Que, L; Solomon, E. I. Proc. Natl. Acad. Sci. USA 2012, 109, 14326-14331). However, quantitative differences are observed that correlate with π-anisotropy and oxo donor strength that perturb FMOs and affect reactivity. Due to π-anisotropy, the Fe(IV)═O active site exhibits enhanced reactivity in the direction of the substrate cavity that proceeds through a π-channel that is controlled by perpendicular orientation of the substrate C-H bond relative to the halide-Fe(IV)═O plane. Also, the increased intrinsic reactivity of the SyrB2 intermediate relative to the ferryl model complex is correlated to a higher oxyl character of the Fe(IV)═O at the transition states resulting from the weaker ligand field of the halogenase.

Visible and Near-IR Reflectance Spectra of Smectite Acquired Under Dry Conditions for Interpretation of Martian Surface Mineralogy

NASA Technical Reports Server (NTRS)

Morris, Richard V.; Achilles, Cherie N; Archer, Paul D.; Graff, Trevor G.; Agresti, David G.; Ming, Douglas W; Golden, Dadi C.; Mertzman, Stanley A.

2011-01-01

Visible and near-IR (VNIR) spectra from the MEx OMEGA and the MRO CRISM hyper-spectral imaging instruments have spectral features associated with the H2O molecule and M OH functional groups (M = Mg, Fe, Al, and Si). Mineralogical assignments of martian spectral features are made on the basis of laboratory VNIR spectra, which were often acquired under ambient (humid) conditions. Smectites like nontronite, saponite, and montmorillionite have interlayer H2O that is exchangeable with their environment, and we have acquired smectite reflectance spectra under dry environmental conditions for interpretation of martian surface mineralogy. We also obtained chemical, Moessbauer (MB), powder X-ray diffraction (XRD), and thermogravimetric (TG) data to understand variations in spectral properties. VNIR spectra were recorded in humid lab air at 25-35C, in a dynamic dry N2 atmosphere (50-150 ppmv H2O) after exposing the smectite samples (5 nontronites, 3 montmorillionites, and 1 saponite) to that atmosphere for up to approximately l000 hr each at 25-35C, approximately 105C, and approximately 215C, and after re-exposure to humid lab air. Heating at 105C and 215C for approximately 1000 hr is taken as a surrogate for geologic time scales at lower temperatures. Upon exposure to dry N2, the position and intensity of spectral features associated with M-OH were relatively insensitive to the dry environment, and the spectral features associated with H2O (e.g., approximately 1.90 micrometers) decreased in intensity and are sometimes not detectable by the end of the 215C heating step. The position and intensity of H2O spectral features recovered upon re-exposure to lab air. XRD data show interlayer collapse for the nontronites and Namontmorillionites, with the interlayer remaining collapsed for the latter after re-exposure to lab air. The interlayer did not collapse for the saponite and Ca-montmorillionite. TG data show that the concentration of H2O derived from structural OH was invariant to the dry N2 treatment for saponite and the montmorillionites, but the nontronites had additional structural OH after treatment. Upon exposure to dry N2, the VNIR spectra also acquired a red slope with decreasing albedo between approximately 0.4 and approximately 2.0 micrometers. The magnitude of the effects covaries with exposure time to dry N2 and heating temperature. Upon re-exposure to lab air, the slope and albedo do not completely recover to pre-exposure values. MB data show that these effects do not result from partial reduction of ferric to ferrous iron, and TG data show they do not result from loss of structural OH. Possible explanations include formation of small clusters of (superparamagnetic) ferric oxide and reduced smectite crystallinity. The difference in spectral properties between spectra acquired in humid lab air and under dry conditions are consequential for interpretation of CRISM and OMEGA spectra. For example, nontronite by itself and not nontronite plus ferrihydrite can account for the red spectral slope in martian spectra where nontronite is indicated by the Fe-OH spectral features.

Energetic particles in the pre-dawn magnetotail of Jupiter

NASA Technical Reports Server (NTRS)

Schardt, A. W.; Mcdonald, F. B.; Trainor, J. H.

1980-01-01

A detailed account is given of the energetic electron and proton populations as observed with Voyagers 1 and 2 during their passes through the dawn magnetotail of Jupiter. The region between 20 and 150 R sub J is dominated by a thin plasma sheet, where trapped energetic electron and proton fluxes reach their maximum. Proton spectra can be represented by an exponential in rigidity with a characteristic energy of approximately 50 keV. Proton anisotropies were consistent with corotation even at 100 R sub J. A major proton acceleration event as well as several cases of field aligned proton streaming were observed. The flux of 0.4 MeV protons decreases by three orders of magnitude between 30 and 90 R sub J and then remains relatively constant to the magnetopause. Fine structure in the data indicate longitudinal asymmetries with respect to the dipole orientation. Electron spectra in the magnetosheath and interplanetary space are modulated by the Jovian longitude relative to the subsolar point.

Continued development of thallium bromide and related compounds for gamma-ray spectrometers

NASA Astrophysics Data System (ADS)

Kim, H.; Churilov, A.; Ciampi, G.; Cirignano, L.; Higgins, W.; Kim, S.; O'Dougherty, P.; Olschner, F.; Shah, Kanai

2011-02-01

Thallium bromide (TlBr) and related ternary compounds, TlBrI and TlBrCl, have been under development for room temperature gamma-ray spectroscopy due to high density, high Z and wide bandgap of the material. Low melting point and cubic crystal structure of selected compositions of these compounds facilitate crystal growth by melt techniques. Recent advances in material purification, crystal growth, and device processing have led to mobility-lifetime products of electrons in the mid 10 -3 cm 2/V range enabling working detectors of greater than 15 mm thickness to be fabricated. In this paper we report on our recent progress on TlBr detector development and first results from TlBr xCl 1- x devices. Pulse height spectra will be presented from TlBr arrays as thick as 18 mm. Depth corrected spectra will also be presented. For a 5 mm thick TlBr array, energy resolution of less than 1% (FWHM at 662 keV) was obtained after depth correction.

Outbursts by low-mass white dwarfs in symbiotic variables

NASA Technical Reports Server (NTRS)

Sion, Edward M.; Ready, Christian J.

1992-01-01

The high-resolution IUE spectra of the symbiotic variables BF Cygni and EG Andromedae are studied in order to describe the P Cygni-like features of these objects. The 10 high-dispersion IUE spectra are examined for orbital phase-dependent variations in the C IV resonance doublet in terms of velocity and/or structure. One image is found to have a strong He-II absorption feature that coincides in velocity with the C-IV absorption component in P Cygni. The absorbing material for both lines is related to outflow and P Cygni self-absorption near the hot component. The P Cygni profiles do not appear to be related to a red-giant wind nor an expanding circumbinary shell in the in both BF Cyg and EG And. Quasi-static evolutionary model calculations demonstrate an unexpected outburst behavior in response to the assumed accretion. These data are shown to be important for the study of symbiotic systems that contain low-mass white dwarfs.

Electron Cyclotron Radiation, Related Power Loss, and Passive Current Drive in Tokamaks: A Review

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fidone, Ignazio; Giruzzi, Gerardo; Granata, Giovanni

2001-01-15

A critical review on emission of weakly damped, high-harmonics electron cyclotron radiation, the related synchrotron power loss, and passive current drive in tokamaks with a fish-scale first wall is presented. First, the properties of overlapping harmonics are discussed using general analytical formulas and numerical applications. Next, the radiation power loss and efficiency of passive current drive in tokamak reactors are derived for the asymmetric fish-scale first wall. The radiation power loss is determined by the direction-averaged reflection coefficient {sigma}{sub 0} and the passive current drive by the differential reflectivity {delta}{sigma}/(1 - {sigma}{sub 0}). Finally, the problem of experimental investigations ofmore » the high harmonics radiation spectra, of {sigma}{sub 0} and {delta}{sigma}/(1 - {sigma}{sub 0}) in existing and next-step tokamaks, is discussed. Accurate measurements of the radiation spectra and the fish-scale reflectivity can be performed at arbitrary electron temperature using a partial fish-scale structure located near the tokamak equatorial plane.« less

Gritty Surface Sample Holder Invented To Obtain Correct X-ray Absorption Fine Structure Spectra for Concentrated Materials by Fluorescence Yield.

PubMed

Abe, Hitoshi; Niwa, Yasuhiro; Kimura, Masao; Murakami, Youichi; Yokoyama, Toshiharu; Hosono, Hideo

2016-04-05

A gritty surface sample holder has been invented to obtain correct XAFS spectra for concentrated samples by fluorescence yield (FY). Materials are usually mixed with boron nitride (BN) to prepare proper concentrations to measure XAFS spectra. Some materials, however, could not be mixed with BN and would be measured in too concentrated conditions to obtain correct XAFS spectra. Consequently, XAFS spectra will be incorrect typically with decreased intensities of the peaks. We have invented the gritty surface sample holders to obtain correct XAFS spectra even for concentrated materials for FY measurements. Pure Cu and CuO powders were measured mounted on the sample holders, and the same spectra were obtained as transmission spectra of properly prepared samples. This sample holder is useful to measure XAFS for any concentrated materials.

Theoretical study of the potential energy surfaces and dynamics of CaNC/CaCN

NASA Astrophysics Data System (ADS)

Nanbu, Shinkoh; Minamino, Satoshi; Aoyagi, Mutsumi

1997-05-01

Potential energy surfaces for the ground and two low-lying electronically excited states of CaNC/CaCN, are calculated using the ab initio molecular orbital (MO) configuration interaction (CI) method. The absorption and emission spectra of the system are computed by performing time-dependent quantum dynamical calculations on these surfaces. The most stable geometries for the two lowest lying 12Σ+ and 12Π electronic states correspond to the calcium isocyanide (CaNC) structure. These two states are characterized by ionic bonding and the potential energy curves along the bending coordinate are relatively isotropic. The result of our wave packet dynamics shows that the characteristics of the experimental spectra observed by the laser-induced fluorescence spectroscopy can be explained by the Renner-Teller splitting.

Characteristics of propeller noise on an aircraft fuselage related to interior noise transmission

NASA Technical Reports Server (NTRS)

Mixson, J. S.; Barton, C. K.; Piersol, A. G.; Wilby, J. F.

1979-01-01

Exterior noise was measured on the fuselage of a twin-engine, light aircraft at four values of engine rpm in ground static tests and at forward speeds up to 36 m/s in taxi tests. Propeller noise levels, spectra, and correlations were determined using a horizontal array of seven flush-mounted microphones and a vertical array of four flush-mounted microphones in the propeller plane. The measured levels and spectra are compared with predictions based on empirical and analytical methods for static and taxi conditions. Trace wavelengths of the propeller noise field, obtained from point-to-point correlations, are compared with the aircraft sidewall structural dimensions, and some analytical results are presented that suggest the sensitivity of interior noise transmission to variations of the propeller noise characteristics.

Carbonate stability in the earth's mantle - A vibrational spectroscopic study of aragonite and dolomite at high pressures and temperatures

NASA Technical Reports Server (NTRS)

Kraft, Susan; Knittle, Elise; Williams, Quentin

1991-01-01

The structural changes of aragonite and dolomite taking place at high pressures and temperatures were investigated by measuring the Raman spectra of these materials to pressures of 23 and 28 GPa (generated in a diamond anvil cell), respectively; in addition, the IR spectra of aragonite were measured to 40 GPa. The spectroscopic data demonstrated that, at 300 K, dolomite and aragonite samples were stable to pressures of 28 and 41 GPa, respectively. No phase transitions were observed following heating of aragonite and dolomite to temperatures of 2000 K and 800 K, respectively. The mode Grueneisen parameters indicate that the carbonate group in these two minerals is relatively insensitive to pressure, with the dominant compaction mechanism being the compression of the Ca and Mg polyhedra.

Selectivity of similar compounds' identification using IR spectrometry: β-Lactam antibiotics

NASA Astrophysics Data System (ADS)

Sadlej-Sosnowska, Nina; Ocios, Agnieszka; Fuks, Leon

2006-07-01

The study aims to develop a reliable, quantitative method for positive identification or discrimination of a substance, when it is compared to a set of similar ones. In the course of the study a group of structurally related compounds, namely a set of β-lactam antimicrobial agents has been explored. Identification of a substance was based on the comparison of its spectrum with that of a reference material by using two functional algorithms. The algorithm based on the calculation of correlation coefficient between the first derivatives of the spectra has been proved more powerful than that using the original spectra. Then the results in a few spectral regions were likened. Limiting values were proposed for correlation coefficients that allow for qualification of a substance as identical to the reference one.

Analysis of Picosecond Pulsed Laser Melted Graphite

DOE R&D Accomplishments Database

Steinbeck, J.; Braunstein, G.; Speck, J.; Dresselhaus, M. S.; Huang, C. Y.; Malvezzi, A. M.; Bloembergen, N.

1986-12-01

A Raman microprobe and high resolution TEM have been used to analyze the resolidified region of liquid carbon generated by picosecond pulse laser radiation. From the relative intensities of the zone center Raman-allowed mode for graphite at 1582 cm{sup -1} and the disorder-induced mode at 1360 cm{sup -1}, the average graphite crystallite size in the resolidified region is determined as a function of position. By comparison with Rutherford backscattering spectra and Raman spectra from nanosecond pulsed laser melting experiments, the disorder depth for picosecond pulsed laser melted graphite is determined as a function of irradiating energy density. Comparisons of TEM micrographs for nanosecond and picosecond pulsed laser melting experiments show that the structure of the laser disordered regions in graphite are similar and exhibit similar behavior with increasing laser pulse fluence.

Part 1: Synthesis and visible absorption spectra of some new monoazo dyes derived from ethyl 2-amino-4-(4";-substitutedphenyl)thiophenes

NASA Astrophysics Data System (ADS)

Babür, Banu; Ertan, Nermin

2014-10-01

Series of monoazo dyes from some ethyl 2-amino-4-(4";-substitutedphenyl) thiophenes were prepared and characterized. The structure of the substances was confirmed by FT-IR, 1H NMR and mass spectroscopic techniques. The relationship among the structure of the dyes, their absorption characteristics and the solvatochromic and halochromic behaviors of the dyes were investigated. Introduction of electron-accepting substituent into the diazo moiety results in large bathochromic shifts in all solvents used. The dyes exhibited positive solvatochromism and their solvatochromic properties were discussed in relation to tautomerism.