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Sample records for spectra molecular structure

  1. Rotational structure in molecular infrared spectra

    CERN Document Server

    di Lauro, Carlo

    2013-01-01

    Recent advances in infrared molecular spectroscopy have resulted in sophisticated theoretical and laboratory methods that are difficult to grasp without a solid understanding of the basic principles and underlying theory of vibration-rotation absorption spectroscopy. Rotational Structure in Molecular Infrared Spectra fills the gap between these recent, complex topics and the most elementary methods in the field of rotational structure in the infrared spectra of gaseous molecules. There is an increasing need for people with the skills and knowledge to interpret vibration-rotation spectra in many scientific disciplines, including applications in atmospheric and planetary research. Consequently, the basic principles of vibration-rotation absorption spectroscopy are addressed for contemporary applications. In addition to covering operational quantum mechanical methods, spherical tensor algebra, and group theoretical methods applied to molecular symmetry, attention is also given to phase conventions and their effe...

  2. Ab initio molecular crystal structures, spectra, and phase diagrams.

    Science.gov (United States)

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

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

    Science.gov (United States)

    2017-05-05

    Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6390--17-9724 Equilibrium Structures and Absorption Spectra for SixOy Molecular Clusters...TELEPHONE NUMBER (include area code) b. ABSTRACT c. THIS PAGE 18. NUMBER OF PAGES 17. LIMITATION OF ABSTRACT Equilibrium Structures and Absorption...and electronic excited-state absorption spectra for eqilibrium structures of SixOy molecular clusters using density function theory (DFT) and time

  4. The structure of quasi-molecular KX-ray spectra from heavy ion collisions

    International Nuclear Information System (INIS)

    Kaun, K.-N.; Frank, W.; Manfrass, P.

    1976-01-01

    In the experiments with Ge, Nb, Kr and La ions continuum X-ray spectra having a two-component structure have been observed. Both components atr interpreted as quasi-molecular X-radiation caused by transitions to the 2psigma and 1ssigma states in the quasimolecule

  5. Molecular structure and vibrational spectra of Bis(melaminium) terephthalate dihydrate: A DFT computational study

    Science.gov (United States)

    Tanak, Hasan; Marchewka, Mariusz K.; Drozd, Marek

    2013-03-01

    The experimental and theoretical vibrational spectra of Bis(melaminium) terephthalate dihydrate were studied. The Fourier transform infrared (FT-IR) spectra of the Bis(melaminium) terephthalate dihydrate and its deuterated analogue were recorded in the solid phase. The molecular geometry and vibrational frequencies of Bis(melaminium) terephthalate dihydrate in the ground state have been calculated by using the density functional method (B3LYP) with 6-31++G(d,p) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The molecule contains the weak hydrogen bonds of Nsbnd H⋯O, Nsbnd H⋯N and Osbnd H⋯O types, and those bonds are calculated with DFT method. In addition, molecular electrostatic potential, frontier molecular orbitals and natural bond orbital analysis of the title compound were investigated by theoretical calculations. The lack of the second harmonic generation (SHG) confirms the presence of macroscopic center of inversion.

  6. Comparative studies on molecular structure, vibrational spectra and hyperpolarizabilies of NLO chromophore Ethyl 4-Dimethylaminobenzoate

    Science.gov (United States)

    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.

  7. Cooperativity in Molecular Dynamics Structural Models and the Dielectric Spectra of 1,2-Ethanediol

    Science.gov (United States)

    Usacheva, T. M.

    2018-05-01

    Linear relationships are established between the experimental equilibrium correlation factor and the molecular dynamics (MD) mean value of the O-H···O bond angle and the longitudinal component of the unit vector of the mean statistical dipole moment of the cluster in liquid 1,2-ethanediol (12ED). The achievements of modern MD models in describing the experimental dispersion of the permittivity of 12ED by both continuous and discrete relaxation time spectra are analyzed. The advantage computer MD experiments have over dielectric spectroscopy for calculating relaxation time and determining the molecular diffusion mechanisms of the rearrangement of the network 12ED structure, which is more complex than water, is demonstrated.

  8. Microwave measurements of the spectra and molecular structure for phthalic anhydride

    Science.gov (United States)

    Pejlovas, Aaron M.; Sun, Ming; Kukolich, Stephen G.

    2014-05-01

    The microwave rotational spectrum for phthalic anhydride (PhA) has been measured in the 4-14 GHz microwave region using a pulsed-beam Fourier transform (PBFT) Flygare-Balle type microwave spectrometer. Initially, the molecular structure was calculated using Gaussian 09 suite with mp2/6-311++G** basis and the calculations were used in predicting spectra for the measured isotopologues. The experimental rotational transition frequencies were measured and used to calculate the rotational and centrifugal distortion constants. The rotational constants for the normal isotopologue, four unique 13C substituted isotopologues and two 18O isotologues, were used in a least squares fit to determine nearly all structural parameters for this molecule. Since no substitutions were made at hydrogen sites, the calculated positions of the hydrogen atoms relative to the bonded carbon atoms were used in the structure determination. The rotational constants for the parent isotopologue were determined to be A = 1801.7622(9) MHz, B = 1191.71816(26) MHz, C = 717.44614(28) MHz. Small values for the centrifugal distortion constants were obtained; DJ = 0.0127 kHz, DJK = 0.0652 kHz, and DK = -0.099 kHz, indicating a fairly rigid structure. The structure of PhA is planar with a negative inertial defect of Δ = -0.154 amu Å2. Structural parameters from the mp2 and DFT calculations are in quite good agreement with measured parameters.

  9. Spectroscopic study on deuterated benzenes. I. Microwave spectra and molecular structure in the ground state

    Energy Technology Data Exchange (ETDEWEB)

    Kunishige, Sachi; Katori, Toshiharu; Baba, Masaaki, E-mail: baba@kuchem.kyoto-u.ac.jp [Division of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Nakajima, Masakazu; Endo, Yasuki [Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902 (Japan)

    2015-12-28

    We observed microwave absorption spectra of some deuterated benzenes and accurately determined the rotational constants of all H/D isotopomers in the ground vibrational state. Using synthetic analysis assuming that all bond angles are 120°, the mean bond lengths were obtained to be r{sub 0}(C–C) = 1.3971 Å and r{sub 0}(C–H) = r{sub 0}(C–D) = 1.0805 Å. It has been concluded that the effect of deuterium substitution on the molecular structure is negligibly small and that the mean bond lengths of C–H and C–D are identical unlike small aliphatic hydrocarbons, in which r{sub 0}(C–D) is about 5 mÅ shorter than r{sub 0}(C–H). It is considered that anharmonicity is very small in the C–H stretching vibration of aromatic hydrocarbons.

  10. Dielectric relaxation spectra of liquid crystals in relation to molecular structure

    International Nuclear Information System (INIS)

    Wrobel, S.

    1986-07-01

    The dielectric spectra obtained for some members of two homologous series, i.e. for di-alkoxyazoxybenzenes and penthyl-alkoxythiobenzoates, are discussed qualitatively on the basis of the Nordio-Rigatti-Segre diffusion model. It is additionally assumed that the molecular reorientations take place about the principal axes of the inertia tensor. The distribution of correlation times, which is strongly temperature dependent in the vicinity of the clearing point, is interpreted as being caused by fluctuations of the principal axes frame which are due to conformation changes inside the end chains. The Bauer equation is used to describe both principal molecular reorientations, i.e. the reorientations about the long and short axis, observed in liquid crystalline structure by means of dielectric relaxation methods. The energies and entropies of activation have been computed for both principal reorientations. The differences between the high frequency limit of the dielectric permittivity and the refractive index squared of liquid crystals are explained in terms of two librational motions of the molecules observed by other experimental techniques, viz. far infra-red, Raman and inelastic neutron scattering spectroscopies, and found in this work on the basis of dielectrically measured energy barriers. It has been shown qualitatively that intramolecular libratory motions greatly effect the high frequency dielectric spectrum. Finally, molecular motions in liquid crystals are divided into two types: coherent and incoherent. 127 refs., 56 figs., 17 tabs. (author)

  11. Theoretical Studies Of Molecular Structure And Vibrational Spectra Of 5-Aminolevulinic Acid Hexyl Ester

    International Nuclear Information System (INIS)

    Comert, H.

    2010-01-01

    The molecular geometry and vibrational frequencies of The 5-Aminolevulinic acid's hexyl ester (ALA-H) in the ground state have been calculated using Hartree-Fock (HF) and Density functional method (B3LYP) with 6-31++G(d) basis set. The calculated vibrational spectra and geometric parameters of title compound were compered with experimental ones.

  12. Molecular structure, vibrational spectra and photochemistry of 5-mercapto-1-methyltetrazole

    Science.gov (United States)

    Gómez-Zavaglia, A.; Reva, I. D.; Frija, L.; Cristiano, M. L.; Fausto, R.

    2006-04-01

    In this work, 5-mercapto-1-methyltetrazole was studied by low temperature matrix-isolation and solid-state infrared spectroscopy, DFT(B3LYP)/6-311++G(d,p) calculations and photochemical methods. In the low temperature neat solid phase and isolated in an argon matrix, the compound was found to exist in the 1-methyl-1,4-dihydro-5 H-tetrazole-5-thione tautomeric form. The infrared spectra of the compound were fully assigned and correlated with structural properties. In situ UV-irradiation ( λ>235 nm) of the matrix-isolated monomer is shown to induce different photochemical processes, all of them involving cleavage of the tetrazole ring: e.g. (1) molecular nitrogen expulsion, with production of 1-methyl-1 H-diazirene-3-thiol, which is produced in two different conformers; (2) ring cleavage leading to production of methyl isothiocyanate and azide; (3) simultaneous elimination of nitrogen and sulphur with production of N-methylcarbodiimide. Following these photoprocesses, subsequent reactions occur, leading to production of methyl diazene, carbon monosulphide and nitrogen hydride. Spectroscopic evidence of the production of the above-mentioned chemical species is provided.

  13. Studies on molecular structure, vibrational spectra and molecular docking analysis of 3-Methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl 4-aminobenzoate

    Science.gov (United States)

    Suresh, D. M.; Amalanathan, M.; Hubert Joe, I.; Bena Jothy, V.; Diao, Yun-Peng

    2014-09-01

    The molecular structure, vibrational analysis and molecular docking analysis of the 3-Methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl 4-aminobenzoate (MDDNAB) molecule have been carried out using FT-IR and FT-Raman spectroscopic techniques and DFT method. The equilibrium geometry, harmonic vibrational wave numbers, various bonding features have been computed using density functional method. The calculated molecular geometry has been compared with experimental data. The detailed interpretation of the vibrational spectra has been carried out by using VEDA program. The hyper-conjugative interactions and charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The simulated FT-IR and FT-Raman spectra satisfactorily coincide with the experimental spectra. The PES and charge analysis have been made. The molecular docking was done to identify the binding energy and the Hydrogen bonding with the cancer protein molecule.

  14. Molecular complex of lumiflavin and 2-aminobenzoic acid: crystal structure, crystal spectra, and solution properties.

    Science.gov (United States)

    Shieh, H S; Ghisla, S; Hanson, L K; Ludwig, M L; Nordman, C E

    1981-08-04

    The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N4O2.C7H7NO2.H2O) crystallizes from from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 A, c = 7.045 A, alpha = 95.44 degrees , beta = 95.86 degrees, and gamma = 105.66 degrees . The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating lumiflavin adn un-ionized (neutral) 2-aminobenzoic acid molecules. Two different modes of stacking interaction are observed. In one, 2-aminobenzoic acid overlaps all three of the isoalloxazine rings, at a mean distance of 3.36 A; in the other, 2-aminobenzoic acid interacts distance of 3.36 A; in the other, 2-aminobenzoic acid interacts with the pyrazine and dimethylbenzene moieties, at a distance of 3.42 A. Perpendicular to the stacking direction, the molecules form a continuous sheet. Each flavin is hydrogen bonded via O(2) and NH(3) to two symmetrically related aminobenzoates; the water of crystallization forms three hydrogen bonds, bridging two flavins, via O(4) and N(5), and one aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid. The red color of the crystals results from a charge-transfer transition involving stacked flavin and 2-aminobenzoic acid molecules. Measurements of the polarized optical absorption spectra of crystals show that the transition moment direction for the long wavelength absorbance (beyond 530 nm) contains an out-of-plane component which can only arise from a charge-transfer interaction. Since the amino N does not make exceptionally close interactions with isoalloxazine atoms in either stacking mode (minimum interatomic distance 3.52 A), the charge transfer is presumed to involve pi orbitals of the 2-aminobenzoic acid donor.

  15. Analysis of molecular structure and vibrational spectra of hexadecyl (cetyl) trimethylammonium brode (CTAB)

    International Nuclear Information System (INIS)

    Goekce, H.; Bahceli, S.

    2010-01-01

    FT-IR and Raman spectra of CTAB [C 1 6H 3 3N(CH 3 ) 3 ] + Br - have been experimentally recorded in the region 550-4000 cm - 1 and 400-3100 cm - 1, respectively. The molecular geometry and vibrational frequencies of CTAB in the ground state have been calculated by using ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) methods with the 6-31+G(d,p) basis set. The obtained optimized geometric parameters (bond lengths and bond angles) and vibrational frequencies were in very good agreement with the experimental data. The comparisons of the observed fundamental vibrational frequencies and calculated results for the fundamental vibrational frequencies of CTAB shows that the scaled B3LYP method is superior compared to the scaled HF method.

  16. Crystal structure and vibrational spectra of piperazinium bis(4-hydroxybenzenesulphonate) molecular-ionic crystal

    Science.gov (United States)

    Marchewka, M. K.; Pietraszko, A.

    2008-02-01

    The piperazinium bis(4-hydroxybenzenesulphonate) crystallizes from water solution at room temperature in P2 1/ c space group of monoclinic system. The crystals are built up of doubly protonated piperazinium cations and ionized 4-hydroxybenzenesulphonate anions that interact through weak hydrogen bonds of O-H⋯O and N-H⋯O type. Mutual orientation of anions is determined by non-conventional hydrogen bonds of C-H⋯π type. Room temperature powder FT IR and FT Raman measurements were carried out. The vibrational spectra are in full agreement with the structure obtained from X-ray crystallography. The big single crystals of the title salt can be grown.

  17. Microwave spectra, molecular structure, and aromatic character of 4a,8a-azaboranaphthalene

    Energy Technology Data Exchange (ETDEWEB)

    Pejlovas, Aaron M.; Daly, Adam M.; Kukolich, Stephen G. [Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721 (United States); Ashe, Arthur J. [Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055 (United States)

    2016-03-21

    The microwave spectra for seven unique isotopologues of 4a,8a-azaboranaphthalene [hereafter referred to as BN-naphthalene] were measured using a pulsed-beam Fourier transform microwave spectrometer. Spectra were obtained for the normal isotopologues with {sup 10}B, {sup 11}B, and all unique single {sup 13}C and the {sup 15}N isotopologue (with {sup 11}B), in natural abundance. The rotational, centrifugal distortion and quadrupole coupling constants determined for the {sup 11}B{sup 14}N isotopologue are A = 3042.712 75(43) MHz, B = 1202.706 57(35) MHz, C = 862.220 13(35) MHz, D{sub J} = 0.06(1) kHz, 1.5χ{sub aa} ({sup 14}N) = 2.5781(61) MHz, 0.25(χ{sub bb} − χ{sub cc}) ({sup 14}N) = − 0.1185(17) MHz, 1.5χ{sub aa} (11B) = − 3.9221(75) MHz, and 0.25(χ{sub bb} − χ{sub cc}) ({sup 11}B) = − 0.9069(24) MHz. The experimental inertial defect is Δ = − 0.159 amu Å{sup 2}, which is consistent with a planar structure for the molecule. The B—N bond length from the experimentally determined structure is 1.47 Å, which indicates π-bonding character between the B and N. The measured quadrupole coupling strengths provide important and useful information about the bonding, orbital occupancy, and aromatic character for this aromatic molecule. Extended Townes-Dailey analyses were used to determine the B and N electron sp{sup 2}-hybridized and p-orbital occupations. These results are compared with electron orbital occupations from the natural bond orbital option in theoretical calculations. From the analyses, it was determined that BN-naphthalene has aromatic character similar to that of other N-containing aromatics. The results are compared with similar results for B—N bonding in 1,2-dihydro-1,2-azaborine and BN-cyclohexene. Accurate and precise structural parameters were obtained from the microwave measurements on seven isotopologues and from high-level G09 calculations.

  18. Microwave spectra and molecular structures of (Z)-pent-2-en-4-ynenitrile and maleonitrile.

    Science.gov (United States)

    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.

  19. Molecular Complex of Lumiflavin and 2-Aminobenzoic Acid : Crystal Structure, Crystal Spectra, and Solution Properties

    OpenAIRE

    Shieh, Huey-Sheng; Ghisla, Sandro; Hanson, Louise Karle; Ludwig, Martha L.; Nordman, Christer E.

    1981-01-01

    The molecular complex lumiflavin-2-aminobenzoic acid monohydrate (C13H12N402●C7H7N02●H2O)crystallizes from aqueous solution as red triclinic prisms. The space group is P1 with cell dimensions a = 9.660 A, b = 14.866 Å, c = 7.045 Å, α = 95.44°, β = 95.86°, and γ = 105.66°. The crystal structure was solved by direct methods and refined by block-diagonal least-squares procedures to an R value of 0.050 on the basis of 1338 observed reflections. The structure is composed of stacks of alternating l...

  20. Molecular structure, vibrational spectra and DFT computational studies of melaminium N-acetylglycinate dihydrate

    Science.gov (United States)

    Tanak, H.; Pawlus, K.; Marchewka, M. K.

    2016-10-01

    Melaminium N-acetylglycinate dihydrate, an organic material has been synthesized and characterized by X-ray diffraction, FT-IR, and FT-Raman spectroscopies for the protiated and deuteriated crystals. The title complex crystallizes in the triclinic system, and the space group is P-1 with a = 5.642(1) Å, b = 7.773(2) Å, c = 15.775(3) Å, α = 77.28(1)°, β = 84.00(1)°, γ = 73.43(1)° and Z = 2. The molecular geometry, vibrational frequencies and intensity of the vibrational bands have been interpreted with the aid of structure optimization based on density functional method (B3LYP) with the 6-311++G(d,p) basis set. The obtained vibrational wavenumbers and optimized geometric parameters were seen to be in good agreement with the experimental data. The intermolecular hydrogen bonding interactions of the title compound have been investigated using the natural bonding orbital analysis. It reveals that the O-H···O, N-H···N and N-H···O intermolecular interactions significantly influence crystal packing of this molecule. The non-linear optical properties are also addressed theoretically. The predicted NLO properties of the title compound are much greater than ones of urea. In addition, DFT calculations of the title compound, molecular electrostatic potential, thermodynamic properties, frontier orbitals and chemical reactivity descriptors were also performed at 6-311++G(d,p) level of theory.

  1. Theoretical Investigation on the Molecular Structure, Vibrational and NMR Spectra of N, N, 4-Tri chlorobenzenesulfonamide

    International Nuclear Information System (INIS)

    Cinar, M.

    2008-01-01

    In the present study, the structural properties of N,N,4-Tri chlorobenzenesulfonamide have been studied extensively using Density Functional Theory (DFT) employing B3LYP exchange correlation. The geometry of the molecule was fully optimized, vibrational spectrum was calculated and fundamental vibrations were assigned based on the scaled theoretical wavenumbers. The 1 H and 13 C nuclear magnetic resonance (NMR) chemical shifts of the compound were calculated using the Gauge-Invariant Atomic Orbital (GIAO) method. To investigate the basis set effects, calculations were performed at the 6-31G(d,p), 6-311G(d,p), 6-31++G(d,p) and 6-311++G(d,p) levels. Finally, geometric parameters, vibrational bands and isotropic chemical shifts were compared with available experimental data of compound. The fully optimized geometry of the molecule was found to be consistent with the X-ray crystal structure. The observed and calculated frequencies and chemical shifts were found to be in very good agreement. The computed results appear that the basis set has slight effect on the molecular geometry of N,N,4-Tri chlorobenzenesulfonamide

  2. X-ray photoelectron spectra structure of actinide compounds stipulated by electrons of the inner valence molecular orbitals (IVMO)

    International Nuclear Information System (INIS)

    Teterin, Yu. A.; Ivanov, K. E.

    1997-01-01

    Development of precise X-ray photoelectron spectroscopy using X-ray radiation hν< 1.5 KeV allowed to carry out immediate investigations of fine spectra structure of both weakly bond and deep electrons. Based on the experiments and the obtained results it may be concluded: 1. Under favourable conditions the inner valence molecular orbitals (IVMO) may form in all actinide compounds. 2. The XPS spectra fine structure stipulated by IVMO electrons allows to judge upon the degree of participation of the filled AO electrons in the chemical bond, on the structure o considered atom close environment and the bond lengths in compounds. For amorphous compounds the obtaining of such data based on X-ray structure analysis is restricted. 3. The summary contribution of IVMO electrons to the absolute value of the chemical bonding is comparable with the corresponding value of OMO electrons contribution to the atomic bonding. This fact is very important and new in chemistry. (author)

  3. Comparison of various molecular forms of bovine trypsin: Correlation of infrared spectra with X-ray crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Prestrelski, S.J. (Mount Sinai School of Medicine of the City Univ. of New York (USA)); Byler, D.M. (U.S. Department of Agriculture, Philadelphia, PA (USA)); Liebman, M.N. (AMOCO Technology Corporation, Naperville, IL (USA))

    1991-01-01

    Fourier-transform infrared spectroscopy is a valuable method for the study of protein conformation in solution primarily because of the sensitivity to conformation of the amide I band (1700-1620 cm{sup {minus}1}) which arises from the backbone C{double bond}O stretching vibration. Combined with resolution-enhancement techniques such as derivative spectroscopy and self-deconvolution, plus the application of iterative curve-fitting techniques, this method provides a wealth of information concerning protein secondary structure. Further extraction of conformational information from the amide I band is dependent upon discerning the correlations between specific conformation types and component bands in the amide I region. In this paper the authors report spectra-structure correlations derived from conformational perturbations in bovine trypsin which arise from autolytic processing, zymogen activation, and active-site inhibition. IR spectra were collected for the single-chain ({beta}-trypsin) and once-cleaved, double-chain ({alpha}-trypsin) forms as well as at various times during the course of autolysis and also for zymogen, trypsinogen, and {beta}-trypsin inhibited with diisopropyl fluorophosphate. Spectral differences among the various molecular forms were interpreted in light of previous biochemical studies of autolysis and the known three-dimensional structures of the zymogen, the active enzyme, and the DIP-inhibited form. The spectroscopic results from these proteins in D{sub 2}O imply that certain loop structures may absorb in the region of 1655 cm{sup {minus}1}. They estimate that this approach to data analysis and interpretation is sensitive to changes of 0.01 unit or less in the relative integrated intensities of component bands in spectra whose peaks are well resolved.

  4. Molecular structure and vibrational spectra of 6-methylquinoline and 8-methylquinoline molecules by quantum mechanical methods

    International Nuclear Information System (INIS)

    Kurt, M.

    2005-01-01

    The molecular geometry and vibrational frequencies of 6-methylquinoline(6MQ) and 8-methylquinolines(8MQ) in the ground state have been calculated by using the Hartree-Fock and density functional methods (B3LYP and BLYP) with 6-31G (d) as the basis set. The optimized geometric bond lengths obtained by using B3LYP and bond angles obtained by BLYP were given corresponding experimental values of similar molecule. Comparison of the observed fundamental vibrational frequencies of these molecules and calculated results by density functional B3LYP, BLYP and Hartree-Fock methods indicates that B3LYP is superior to the scaled Hartree- Fock and BLYP approach for molecular vibrational problems

  5. Study on structure, vibrational analysis and molecular characteristics of some halogen substituted azido-phenylethanones using FTIR spectra and DFT

    Science.gov (United States)

    Prashanth, J.; Reddy, Byru Venkatram

    2018-03-01

    The Fourier transform infrared (FTIR) spectra of organic compounds 4-fluoro-2-azido-1-phenylethanone (FAP), 4-chloro-2-azido-1-phenylethanone (CAP) and 4-bromo-2-azido-1-phenylethanone (BAP) have been recorded in the region 4000-400 cm-1. The optimized molecular structure for global minimum energy of the titled molecules is determined by evaluating torsional potentials as a function of rotation angle about free rotation bonds among the substituent groups subjecting them to DFT employing B3LYP functional with 6-311++G (d,p) basis set. The vibrational frequencies along with infrared intensities are computed by SQM procedure. The rms error between observed and calculated frequencies is found to be 9.27, 8.17 and 7.95 cm-1 for FAP, CAP and BAP, respectively which shows good agreement between experimental and scaled values of calculated frequencies obtained by DFT. The vibrational assignments of all the fundamental bands of each molecule are made unambiguously using PED and eigen vectors obtained in the computations. The computed values of dipole moment, polarizability and hyperpolarizability indicate that the titled molecules exhibit NLO behaviour and hence may be considered for potential applicants for the development of NLO materials. HOMO and LUMO energies evaluated in the study demonstrate chemical stability of the molecules. NBO analysis is made to study the stability of the molecules arising from hyper conjugative interactions and charge delocalization. The molecular electrostatic surface potential (MESP) and thermodynamic parameters are also evaluated.

  6. Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of Gallic acid imprinted polymers

    Science.gov (United States)

    Pardeshi, Sushma; Dhodapkar, Rita; Kumar, Anupama

    2013-12-01

    Gallic acid (GA) is known by its antioxidant, anticarcinogenic properties and scavenger activity against several types of harmful free radicals. Molecularly imprinted polymers (MIPs) are used in separation of a pure compound from complex matrices. A stable template-monomer complex generates the MIPs with the highest affinity and selectivity for the template. The quantum chemical computations based on density functional theory (DFT) was used on the template Gallic acid (GA), monomer acrylic acid (AA) and GA-AA complex to study the nature of interactions involved in the GA-AA complex. B3LYP/6-31+G(2d,2p) model chemistry was used to optimize their structures and frequency calculations. The effect of porogen acetonitrile (ACN) on complex formation was included by using polarizable continuum model (PCM). The results demonstrated the formation of a stable GA-AA complex through the intermolecular hydrogen bonding between carboxylic acid groups of GA and AA. The Mulliken atomic charge analysis and simulated vibrational spectra also supported the stable hydrogen bonding interaction between the carboxylic acid groups of GA and AA with minimal interference of porogen ACN. Further, simulations on GA-AA mole ratio revealed that 1:4 GA-AA was optimum for synthesis of MIP for GA.

  7. Atomic and molecular effects in the VUV spectra of solids

    International Nuclear Information System (INIS)

    Sonntag, B.

    1977-10-01

    The VUV spectra of solids are often dominated by atomic or molecular effects, which clearly manifest themselves in the gross features of the spectra and the fine structure at inner shell excitation thresholds. Evidence for the influence of atomic and molecular matrix elements, multiplet-splitting and correlation is presented. Special emphasis is given to the direct experimental verification based on the comparison of atomic and solid state spectra. (orig.) [de

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

    Science.gov (United States)

    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.

  9. Imprints of the Molecular Electronic Structure in the Photoelectron Spectra of Strong-Field Ionized Asymmetric Triatomic Model Molecules

    Science.gov (United States)

    Paul, Matthias; Yue, Lun; Gräfe, Stefanie

    2018-06-01

    We examine the circular dichroism in the angular distribution of photoelectrons of triatomic model systems ionized by strong-field ionization. Following our recent work on this effect [Paul, Yue, and Gräfe, J. Mod. Opt. 64, 1104 (2017), 10.1080/09500340.2017.1299883], we demonstrate how the symmetry and electronic structure of the system is imprinted into the photoelectron momentum distribution. We use classical trajectories to reveal the origin of the threefolded pattern in the photoelectron momentum distribution, and show how an asymmetric nuclear configuration of the triatomic system effects the photoelectron spectra.

  10. Astrophysical interpretation of molecular spectra

    International Nuclear Information System (INIS)

    Scoville, N.Z.

    1984-01-01

    As sensitive, high resolution spectrometers are developed throughout the infrared great progress is anticipated in understanding not only the young-stellar objects but also the active galaxy nuclei so luminous in the far-infrared. In the infrared the variety of atomic and molecular spectroscopic transitions is capable of probing conditions ranging from hot circumstellar HII regions, molecular envelopes, and shock fronts at > 2000 K down to cold, low density interstellar gas at < 10 K. The ability to measure both physical conditions and kinematics aids in the separation of the physical regimes and in the building of a coherent dynamic/evolutionary model. The author briefly reviews the characteristics of some of the observed molecular transitions and theoretical considerations important for understanding their excitation. (Auth.)

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

    Science.gov (United States)

    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.

  12. Comparison of the performance of different DFT methods in the calculations of the molecular structure and vibration spectra of serotonin (5-hydroxytryptamine, 5-HT)

    Science.gov (United States)

    Yang, Yue; Gao, Hongwei

    2012-04-01

    Serotonin (5-hydroxytryptamine, 5-HT) is a monoamine neurotransmitter which plays an important role in treating acute or clinical stress. The comparative performance of different density functional theory (DFT) methods at various basis sets in predicting the molecular structure and vibration spectra of serotonin was reported. The calculation results of different methods including mPW1PW91, HCTH, SVWN, PBEPBE, B3PW91 and B3LYP with various basis sets including LANL2DZ, SDD, LANL2MB, 6-31G, 6-311++G and 6-311+G* were compared with the experimental data. It is remarkable that the SVWN/6-311++G and SVWN/6-311+G* levels afford the best quality to predict the structure of serotonin. The results also indicate that PBEPBE/LANL2DZ level show better performance in the vibration spectra prediction of serotonin than other DFT methods.

  13. Molecular structure, vibrational spectra and quantum chemical MP2/DFT studies toward the rational design of hydroxyurea imprinted polymer

    Science.gov (United States)

    Prasad, Bhim Bali; Rai, Garima

    2013-03-01

    In this study, both experimental and theoretical vibrational spectra of template (hydroxyurea, HU), monomer (N-(4,6-bisacryloyl amino-[1,3,5] triazine-2-yl-)-acryl amide, TAT), and HU-TAT complexes were compared and these were respectively found to be in good agreement. Binding energies of HU, when complexed with different monomers, were computed using second order Moller Plesset theory (MP2) at 6-311++G(d,p) level both in the gas as well as solution phases. HU is an antineoplastic agent extensively being used in the treatment of polycythaemia Vera and thrombocythemia. It is also used to reduce the frequency of painful attacks in sickle cell anemia. It has antiretroviral property in disease like AIDS. All spectral characterizations were made using Density Functional Theory (DFT) at B3LYP employing 6-31+g(2d, 2p) basis set. The theoretical values for 13C and 1H NMR chemical shifts were found to be in accordance with the corresponding experimental values. Of all different monomers studied for the synthesis of molecularly imprinted polymer (MIP) systems, the monomer TAT (2 mol) was typically found to have a best binding score requisite for complexation with HU (1 mol) at the ground state.

  14. Two-dimensional 1H and 31P NMR spectra and restrained molecular dynamics structure of an oligodeoxyribonucleotide duplex refined via a hybrid relaxation matrix procedure

    International Nuclear Information System (INIS)

    Powers, R.; Jones, C.R.; Gorenstein, D.G.

    1990-01-01

    Assignment of the 1H and 31P resonances of a decamer DNA duplex, d(CGCTTAAGCG)2 was determined by two-dimensional COSY, NOESY and 1H-31P Pure Absorption phase Constant time (PAC) heteronuclear correlation spectroscopy. The solution structure of the decamer was calculated by an iterative hybrid relaxation matrix method combined with NOESY-distance restrained molecular dynamics. The distances from the 2D NOESY spectra were calculated from the relaxation rate matrix which were evaluated from a hybrid NOESY volume matrix comprising elements from the experiment and those calculated from an initial structure. The hybrid matrix-derived distances were then used in a restrained molecular dynamics procedure to obtain a new structure that better approximates the NOESY spectra. The resulting partially refined structure was then used to calculate an improved theoretical NOESY volume matrix which is once again merged with the experimental matrix until refinement is complete. JH3'-P coupling constants for each of the phosphates of the decamer were obtained from 1H-31P J-resolved selective proton flip 2D spectra. By using a modified Karplus relationship the C4'-C3'-O3'-P torsional angles were obtained. Comparison of the 31P chemical shifts and JH3'-P coupling constants of this sequence has allowed a greater insight into the various factors responsible for 31P chemical shift variations in oligonucleotides. It also provides an important probe of the sequence-dependent structural variation of the deoxyribose phosphate backbone of DNA in solution. These correlations are consistent with the hypothesis that changes in local helical structure perturb the deoxyribose phosphate backbone. The variation of the 31P chemical shift, and the degree of this variation from one base step to the next is proposed as a potential probe of local helical conformation within the DNA double helix

  15. L-lysine-L-tartaric acid: New molecular complex with nonlinear optical properties. Structure, vibrational spectra and phase transitions

    International Nuclear Information System (INIS)

    Debrus, S.; Marchewka, M.K.; Baran, J.; Drozd, M.; Czopnik, R.; Pietraszko, A.; Ratajczak, H.

    2005-01-01

    The first X-ray diffraction and vibrational spectroscopic analysis of a novel complex between L-lysine and L-tartaric acid is reported. The structure was solved in two temperatures (320 and 260 K) showing incommensurate phase between them. Room-temperature powder infrared and Raman measurements for the L-lysine-L-tartaric acid molecular complex (1:1) were carried out. DSC measurements on powder samples indicate two phase transitions points at about 295, 300 and 293, 300 K, for heating and cooling, respectively, with noticeable temperature interval between them. Second harmonic generation efficiency d eff =0.35 d eff (KDP)

  16. 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

    Science.gov (United States)

    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 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

  17. The structure of BPS spectra

    Science.gov (United States)

    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

  18. Crystal and molecular structure of N-(4-nitrophenyl)-β-alanine—Its vibrational spectra and theoretical calculations

    Science.gov (United States)

    Marchewka, M. K.; Drozd, M.; Janczak, J.

    2011-08-01

    The N-(4-nitrophenyl)-β-alanine in crystalline form directly by the addition of 4-nitroaniline to the acrylic acid in aqueous solution has been obtained. The title β-alanine derivative crystallizes in the P2 1/ c space group of monoclinic system with four molecules per unit cell. The X-ray geometry of β-alanine derivative molecule has been compared with those obtained by molecular orbital calculations corresponding to the gas phase. In the crystal the molecules related by an inversion center interact via symmetrically equivalent O-H⋯O hydrogen bonds with O⋯O distance of 2.656(2) Å forming a dimeric structure. The dimers of β-alanine derivative weakly interact via N-H⋯O hydrogen bonds between the H atom of β-amine groups and one of O atom of nitro groups. The room temperature powder vibrational (infrared and Raman) measurements are in accordance with the X-ray analysis. In aqueous solution of 4-nitroaniline and acrylic acid, the double C dbnd C bond of vinyl group of acrylic acid breaks as result of 4-nitroaniline addition.

  19. A theoretical study of the molecular structures and vibrational spectra of the N 2O⋯(HF) 2

    Science.gov (United States)

    de Lima, Nathália B.; Ramos, Mozart N.

    2012-01-01

    Theoretical calculations using both the MP2 and B3LYP levels of calculation with a 6-311++G(3df,3pd) basis set have been performed to determine stable structures and molecular properties for the H-bonded complexes involving nitrous oxide (N 2O) and two HF molecules. Five complex have been characterized as minima since no imaginary frequency was found. Three complex are predicted to be relatively more stable with binding energies varying from 14 kJ mol -1 to 23 kJ mol -1 after BSSE and ZPE corrections. Our calculations have revealed that the second complexation with HF preferably occurs with the first complexed HF molecule, i.e., forming the X⋯H sbnd F⋯H sbnd F skeleton with X = O or N instead the F sbnd H⋯N sbnd N sbnd O⋯H sbnd F one. As expected, the H sbnd F chemical bonds are increased after complexation due to intermolecular charge transfer from "n" isolated pair of the X atom (X = N, O or F) to the σ ∗ anti-bonding orbital of HF. For the strongly bounded complex, the doubly complexed HF molecule acts as a bridge between the two end molecules while transferring electrons from N 2O to HF. Both possess the same amount of residual charge but with opposite signs. The H sbnd F stretching frequency of the monoprotic acid is shifted downward after complexation whereas its IR intensity is much enhanced. This increase has been adequately interpreted in terms of equilibrium hydrogen charge and charge-flux associated to the H sbnd F stretching using the CCFOM model for infrared intensities. This procedure has also allowed to analyze the new vibrational modes arising upon H-bond formation, especially those associated with the out-of-plane and in-plane HF bending modes, which are pure rotations in the HF isolated molecule.

  20. Energetics of the rearrangement of neutral and ionized perfluorocyclopropane to perfluoropropylene. Use of infrared multiphoton dissociation spectra to identify structural isomers of molecular ions

    International Nuclear Information System (INIS)

    Bomse, D.S.; Berman, D.W.; Beauchamp, J.L.

    1981-01-01

    Infrared photodissociation spectroscopy is used to compare the structure of gas-phase C 3 F 6 + ions obtained by electron-impact ionization of two isomeric precursors: perfluoropropylene and perfluorocyclopropane. Photodissociation spectra are obtained by observing the extent of multiphoton dissociation as the CO 2 laser is tuned across the 925 to 1080 cm -1 wavelength range. Ions are formed, stored, and detected with the use of techniques of ion cyclotron resonance spectroscopy. Infrared multiphoton excitation is effected by using low-power, continuous-wave laser radiation. The fingerprint spectrum of the molecular ion of perfluorocyclopropane is identical with that obtained from perfluoropropylene, indicating rearrangement of the former to the latter. Photodissociation kinetics indicate that the entire perfluorocyclopropane molecular ion population isomerizes to the more stable perfluoropropylene structure. Thermochemistry of C 3 F 6 and C 3 F 6 + isomers is discussed. Comparisons are made with the analogous C 3 H 6 system. Photoionization mass spectroscopy results yield ΔH/sub f/(c-C 3 F 6 ) = -233.8 kcal/mol. 4 figures

  1. Theoretical investigation of molecular structure and vibrational spectra of 4,5-bis-(2-isopropyl-5- methylphenoxy) phthalonitrile molecule

    International Nuclear Information System (INIS)

    Avci, D.

    2005-01-01

    The molecular geometry and vibrational frequencies of 4,5-bis-(2-isopropyl-5- methylphenoxy) phthalonitrile in the ground state have been calculated using the Hartree- Fock (HF) and density functional method (B3LYP) with 6-31G(d) basis set. The optimized geometric bond lengths and bond angles obtained by using HF and DFT (B3LYP) show the best agreement with the experimental data. Comparison of the observed fundamental vibrational frequencies of 4,5-bis-(2-isopropyl-5-methylphenoxy) phthalonitrile with calculated results by density functional B3LYP and Hartree-Fock methods indicate that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems

  2. Process and apparatus for determining molecular spectra

    International Nuclear Information System (INIS)

    Boesl, U.; Neusser, H.J.; Schlag, E.W.

    1984-01-01

    A process for determining molecular spectra in unseparated mixtures, in particular unseparated isotopic mixtures, which comprises allowing said mixture to successively flow through a photoreactor which is irradiated by an adjustable-wavelength laser and then through a mass spectrometer wherein the concentration of particles of specified mass is determined by variation of the wavelength of the laser or variation of the mass setting of the mass spectrometer in such a manner that a two-dimensional spectrum results having the parameters of wavelength and mass

  3. The molecular structure and vibrational spectra of N-(2,2-diphenylacetyl)- N'-(naphthalen-1yl)-thiourea by Hartree-Fock and density functional methods

    Science.gov (United States)

    Arslan, Hakan; Mansuroglu, Demet Sezgin; VanDerveer, Don; Binzet, Gun

    2009-04-01

    N-(2,2-Diphenylacetyl)- N'-(naphthalen-1yl)-thiourea (PANT) has been synthesized and characterized by elemental analysis, IR spectroscopy and 1H NMR spectroscopy. The crystal and molecular structure of the title compound has been determined from single crystal X-ray diffraction data. It crystallizes in the triclinic space group P-1, Z = 2 with a = 10.284(2) Å, b = 10.790(2) Å, c = 11.305(2) Å, α = 64.92(3)°, β = 89.88(3)°, γ = 62.99(3)°, V = 983.7(3) Å 3 and Dcalc = 1.339 Mg/m 3. The molecular structure, vibrational frequencies and infrared intensities of PANT were calculated by the Hartree-Fock and density functional theory methods (BLYP and B3LYP) using the 6-31G* basis set. The calculated geometric parameters were compared to the corresponding X-ray structure of the title compound. We obtained 22 stable conformers for the title compound; however Conformer 1 is approximately 9.53 kcal/mol more stable than Conformer 22. The comparison of the theoretical and experimental geometry of the title compound shows that the X-ray parameters fairly well reproduce the geometry of Conformer 17. The harmonic vibrations computed for this compound by the B3LYP/6-31G* method are in good agreement with the observed IR spectral data. Theoretical vibrational spectra of the title compound were interpreted by means of PEDs using the VEDA 4 program. A general better performance of the investigated methods was calculated by PAVF 1.0 program.

  4. Dynamical analysis of highly excited molecular spectra

    Energy Technology Data Exchange (ETDEWEB)

    Kellman, M.E. [Univ. of Oregon, Eugene (United States)

    1993-12-01

    The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.

  5. Machine learning molecular dynamics for the simulation of infrared spectra.

    Science.gov (United States)

    Gastegger, Michael; Behler, Jörg; Marquetand, Philipp

    2017-10-01

    Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated. To this end, we develop a molecular dipole moment model based on environment dependent neural network charges and combine it with the neural network potential approach of Behler and Parrinello. Contrary to the prevalent big data philosophy, we are able to obtain very accurate machine learning models for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points. This is made possible through the use of molecular forces during neural network potential training and the introduction of a fully automated sampling scheme. We demonstrate the power of our machine learning approach by applying it to model the infrared spectra of a methanol molecule, n -alkanes containing up to 200 atoms and the protonated alanine tripeptide, which at the same time represents the first application of machine learning techniques to simulate the dynamics of a peptide. In all of these case studies we find an excellent agreement between the infrared spectra predicted via machine learning models and the respective theoretical and experimental spectra.

  6. Two-dimensional 1H and 31P NMR spectra and restrained molecular dynamics structure of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex

    International Nuclear Information System (INIS)

    Nikonowicz, E.; Roongta, V.; Jones, C.R.; Gorenstein, D.G.

    1989-01-01

    Assignment of the 1H and 31P NMR spectra of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex, d(CGCAGAATTCGCG)2, has been made by two-dimensional 1H-1H and heteronuclear 31P-1H correlated spectroscopy. The downfield 31P resonance previously noted by Patel et al. (1982) has been assigned by both 17O labeling of the phosphate as well as a pure absorption phase constant-time heteronuclear 31P-1H correlated spectrum and has been associated with the phosphate on the 3' side of the extrahelical adenosine. JH3'-P coupling constants for each of the phosphates of the tridecamer were obtained from the 1H-31P J-resolved selective proton-flip 2D spectrum. By use of a modified Karplus relationship the C4-C3'-O3-P torsional angles (epsilon) were obtained. There exists a good linear correlation between 31P chemical shifts and the epsilon torsional angle. The 31P chemical shifts and epsilon torsional angles follow the general observation that the more internal the phosphate is located within the oligonucleotide sequence, the more upfield the 31P resonance occurs. Because the extrahelical adenosine significantly distorts the deoxyribose phosphate backbone conformation even several bases distant from the extrahelical adenosine, 31P chemical shifts show complex site- and sequence-specific variations. Modeling and NOESY distance-restrained energy minimization and restrained molecular dynamics suggest that the extrahelical adenosine stacks into the duplex. However, a minor conformation is also observed in the 1H NMR, which could be associated with a structure in which the extrahelical adenosine loops out into solution

  7. Molecular structure and vibrational spectra of MHal3 (M = Sc, Y, La, Lu; Hal = F, Cl, Br, I): ab initio calculations by the CISD+Q method

    International Nuclear Information System (INIS)

    Solomonik, V.G.; Marochko, O.Yu.

    2000-01-01

    Structure and vibrational spectra of MHal 3 molecules (M = Sc, Y, La, Lu; Hal = F, Cl, Br, I) are studied by the CISD+Q method. It is ascertained that equilibrium configuration of nuclei in all the molecules, except LaF 3 , is plane (D 3h symmetry), while that of LaF 3 molecule - pyramidal (C 3c symmetry). Results of the calculations are compared with previously published experimental data. Band reference in IR spectra of ScBr 3 , YF 3 and YCl 3 molecules has been corrected [ru

  8. Structure of high-resolution NMR spectra

    CERN Document Server

    Corio, PL

    2012-01-01

    Structure of High-Resolution NMR Spectra provides the principles, theories, and mathematical and physical concepts of high-resolution nuclear magnetic resonance spectra.The book presents the elementary theory of magnetic resonance; the quantum mechanical theory of angular momentum; the general theory of steady state spectra; and multiple quantum transitions, double resonance and spin echo experiments.Physicists, chemists, and researchers will find the book a valuable reference text.

  9. Molecular Structure, Vibrational Spectra, Quantum Chemical Calculations and Photochemistry of Picolinamide and Isonicotinamide Isolated in Cryogenic Inert Matrixes and in the Neat Low-Temperature Solid Phases

    OpenAIRE

    Borba, Ana; Gómez-Zavaglia, Andrea; Fausto, R.

    2007-01-01

    Picolinamide (PA) and isonicotinamide (INA), two structural isomers of pyridinecarboxamide, have been investigated by matrix isolation and low-temperature solid-state infrared spectroscopy, combined with UV (λ > 235 nm) photoexcitation and density functional theory and ab initio (MP2) theoretical studies. In consonance with the theoretical data, both PA and INA were found to exist in a single conformation in cryogenic rare gas matrixes. Comparison between the experimental spectra of the matri...

  10. Theoretical investigations of molecular wires: Electronic spectra and electron transport

    Science.gov (United States)

    Palma, Julio Leopoldo

    The results of theoretical and computational research are presented for two promising molecular wires, the Nanostar dendrimer, and a series of substituted azobenzene derivatives connected to aluminum electrodes. The electronic absorption spectra of the Nanostar (a phenylene-ethynylene dendrimer attached to an ethynylperylene chromophore) were calculated using a sequential Molecular Dynamics/Quantum Mechanics (MD/QM) method to perform an analysis of the temperature dependence of the electronic absorption process. We modeled the Nanostar as a series of connected units, and performed MD simulations for each chromophore at 10 K and 300 K to study how the temperature affected the structures and, consequently, the spectra. The absorption spectra of the Nanostar were computed using an ensemble of 8000 structures for each chromophore. Quantum Mechanical (QM) ZINDO/S calculations were performed for each conformation in the ensemble, including 16 excited states, for a total of 128,000 excitation energies. The spectral intensity was then scaled linearly with the number of conjugated units. Our calculations for both the individual chromophores and the Nanostar, are in good agreement with experiments. We explain in detail the effects of temperature and the consequences for the absorption process. The second part of this thesis presents a study of the effects of chemical substituents on the electron transport properties of the azobenzene molecule, which has been proposed recently as a component of a light-driven molecular switch. This molecule has two stable conformations (cis and trans) in its electronic ground state, with considerable differences in their conductance. The electron transport properties were calculated using first-principles methods combining non-equilibrium Green's function (NEGF) techniques with density functional theory (DFT). For the azobenzene studies, we included electron-donating groups and electron-withdrawing groups in meta- and ortho-positions with

  11. Hydration of amino acids: FTIR spectra and molecular dynamics studies.

    Science.gov (United States)

    Panuszko, Aneta; Adamczak, Beata; Czub, Jacek; Gojło, Emilia; Stangret, Janusz

    2015-11-01

    The hydration of selected amino acids, alanine, glycine, proline, valine, isoleucine and phenylalanine, has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure and the chemometric method have been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To support interpretation of obtained spectral results, molecular dynamics simulations of amino acids were performed. The structural-energetic characteristic of these solute-affected water molecules shows that, on average, water affected by amino acids forms stronger and shorter H-bonds than those in pure water. Differences in the influence of amino acids on water structure have been noticed. The effect of the hydrophobic side chain of an amino acid on the solvent interactions seems to be enhanced because of the specific cooperative coupling of water strong H-bond chain, connecting the carboxyl and amino groups, with the clathrate-like H-bond network surrounding the hydrocarbon side chain. The parameter derived from the spectral data, which corresponds to the contributions of the population of weak hydrogen bonds of water molecules which have been substituted by the stronger ones in the hydration sphere of amino acids, correlated well with the amino acid hydrophobicity indexes.

  12. Optical spectra and lattice dynamics of molecular crystals

    CERN Document Server

    Zhizhin, GN

    1995-01-01

    The current volume is a single topic volume on the optical spectra and lattice dynamics of molecular crystals. The book is divided into two parts. Part I covers both the theoretical and experimental investigations of organic crystals. Part II deals with the investigation of the structure, phase transitions and reorientational motion of molecules in organic crystals. In addition appendices are given which provide the parameters for the calculation of the lattice dynamics of molecular crystals, procedures for the calculation of frequency eigenvectors of utilizing computers, and the frequencies and eigenvectors of lattice modes for several organic crystals. Quite a large amount of Russian literature is cited, some of which has previously not been available to scientists in the West.

  13. Decoding Pure Rotational Molecular Spectra for Asymmetric Molecules

    Directory of Open Access Journals (Sweden)

    S. A. Cooke

    2013-01-01

    Full Text Available Rotational spectroscopy can provide insights of unparalleled precision with respect to the wavefunctions of molecular systems that have relevance in fields as diverse as astronomy and biology. In this paper, we demonstrate how asymmetric molecular pure rotational spectra may be analyzed “pictorially” and with simple formulae. It is shown that the interpretation of such spectra relies heavily upon pattern recognition. The presentation of some common spectral line positions in near-prolate asymmetric rotational spectra provides a means by which spectral assignment, and approximate rotational constant determination, may be usefully explored. To aid in this endeavor we have created a supporting, free, web page and mobile web page.

  14. Molecular geometry in the ultraviolet absorption spectra

    International Nuclear Information System (INIS)

    Albuquerque, S.F. de; Monteiro, L.S.; Adamis, L.M.B.; Baltar, M.C.P.; Silva, R.M. da

    1977-01-01

    The ultraviolet absorption spectra may be sensibly affected by steric effects. These effects can cause a lot of difficulties and unexpected changes in spectrum. The most general source of such difficulties is steric inhibition of resonance. In addition to this, ultraviolet epectra may be markedly changed by steric factors which change the positions of dipoles in the molecule with respect to each other and by the interaction of nonconjugated chromophores suitably located in space. We have studied in detail each of these effects presenting a lot of usual and importants examples in Organic Chemistry. Others relevants subjects were not considerated in this present work [pt

  15. An experimental and theoretical study of molecular structure and vibrational spectra of 2-methylphenyl boronic acid by density functional theory calculations

    Science.gov (United States)

    Hiremath, Sudhir M.; Hiremath, C. S.; Khemalapure, S. S.; Patil, N. R.

    2018-05-01

    This paper reports the experimental and theoretical study on the structure and vibrations of 2-Methylphenyl boronic acid (2MPBA). The different spectroscopic techniques such as FT-IR (4000-400 cm-1) and FT-Raman (4000-50 cm-1) of the title molecule in the solid phase were recorded. The geometry of the molecule was fully optimized using density functional theory (DFT) (B3LYP) with 6-311++G(d, p) basis set calculations. The vibrational wavenumbers were also corrected with scale factor to take better results for the calculated data. Vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the potential energy distribution (PED) of the vibrational modes obtained from VEDA 4 program. The calculated wavenumbers showed the best agreement with the experimental results. Whereas, it is observed that, the theoretical frequencies are more than the experimental one for O-H stretching vibration modes of the title molecule.

  16. Vibrational spectra, molecular structure, NBO, HOMO-LUMO and first order hyperpoalarizability analysis of 1,4-bis(4-formylphenyl)anthraquinone by density functional theory

    Science.gov (United States)

    Renjith, R.; Mary, Y. Sheena; Varghese, Hema Tresa; Panicker, C. Yohannan; Thiemann, Thies; Van Alsenoy, Christian

    2014-10-01

    Anthraquinone derivatives are most important class of a system that absorb in the visible region. Infrared and Raman spectroscopic analyses were carried out on 1,4-bis(4-formylphenyl)anthraquinone. The interpretation of the spectra was aided by DFT calculations of the molecule. The vibrational wavenumbers were examined theoretically using the Gaussian09 set of quantum chemistry codes, and the normal modes were assigned by potential energy distribution (PED) calculations. A computation of the first hyperpolarizability of the compound indicates that this class of substituted anthraquinones may be a good candidate as a NLO material. Optimized geometrical parameters of the compound are in agreement with similar reported structures. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis.

  17. Vibrational spectra, molecular structure, natural bond orbital, first order hyperpolarizability, thermodynamic analysis and normal coordinate analysis of Salicylaldehyde p-methylphenylthiosemicarbazone by density functional method

    Science.gov (United States)

    Porchelvi, E. Elamurugu; Muthu, S.

    2015-01-01

    The thiosemicarbazone compound, Salicylaldehyde p-methylphenylthiosemicarbazone (abbreviated as SMPTSC) was synthesized and characterized by FTIR, FT-Raman and UV. Density functional (DFT) calculations have been carried out for the title compound by performing DFT level of theory using B3LYP/6-31++G(d,p) basis set. The molecular geometry and vibrational frequencies were calculated and compared with the experimental data. The detailed interpretation of the vibrational spectra has been carried out with aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology. The electronic dipole moment (μD) and the first hyperpolarizability (βtot) values of the investigated molecule were computed using density functional theory (DFT/B3LYP) with 6-311++G(d,p) basis set. The stability and charge delocalization of the molecule was studied by natural bond orbital (NBO) analysis. Thearomaticities of the phenyl rings were studied using the standard harmonic oscillator model of aromaticity (HOMA) index. Mulliken population analysis on atomic charges is also calculated. The molecule orbital contributions are studied by density of energy states (DOSs).

  18. Structures, energetics, vibrational spectra of NH4+ (H2O)(n=4,6) clusters: Ab initio calculations and first principles molecular dynamics simulations.

    Science.gov (United States)

    Karthikeyan, S; Singh, Jiten N; Park, Mina; Kumar, Rajesh; Kim, Kwang S

    2008-06-28

    Important structural isomers of NH(4) (+)(H(2)O)(n=4,6) have been studied by using density functional theory, Moller-Plesset second order perturbation theory, and coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The zero-point energy (ZPE) correction to the complete basis set limit of the CCSD(T) binding energies and free energies is necessary to identify the low energy structures for NH(4) (+)(H(2)O)(n=4,6) because otherwise wrong structures could be assigned for the most probable structures. For NH(4) (+)(H(2)O)(6), the cage-type structure, which is more stable than the previously reported open structure before the ZPE correction, turns out to be less stable after the ZPE correction. In first principles Car-Parrinello molecular dynamics simulations around 100 K, the combined power spectrum of three lowest energy isomers of NH(4) (+)(H(2)O)(4) and two lowest energy isomers of NH(4) (+)(H(2)O)(6) explains each experimental IR spectrum.

  19. Infrared spectra of small molecular ions trapped in solid neon

    Energy Technology Data Exchange (ETDEWEB)

    Jacox, Marilyn E. [Optical Technology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899 (United States)

    2015-01-22

    The infrared spectrum of a molecular ion provides a unique signature for that species, gives information on its structure, and is amenable to remote sensing. It also serves as a comparison standard for refining ab initio calculations. Experiments in this laboratory trap molecular ions in dilute solid solution in neon at 4.2 K in sufficient concentration for observation of their infrared spectra between 450 and 4000 cm{sup !1}. Discharge-excited neon atoms produce cations by photoionization and/or Penning ionization of the parent molecule. The resulting electrons are captured by other molecules, yielding anions which provide for overall charge neutrality of the deposit. Recent observations of ions produced from C{sub 2}H{sub 4} and BF{sub 3} will be discussed. Because of their relatively large possibility of having low-lying excited electronic states, small, symmetric molecular cations are especially vulnerable to breakdown of the Born-Oppenheimer approximation. Some phenomena which can result from this breakdown will be discussed. Ion-molecule reaction rates are sufficiently high that in some systems absorptions of dimer cations and anions are also observed. When H{sub 2} is introduced into the system, the initially-formed ion may react with it. Among the species resulting from such ion-molecule reactions that have recently been studied are O{sub 4}{sup +}, NH{sub 4}{sup +}, HOCO{sup +}, and HCO{sub 2}{sup !}.

  20. Structure and spectra of a confined HeH molecule

    International Nuclear Information System (INIS)

    Lo, J M H; Klobukowski, M; Bielinska-Wacz, D; Schreiner, E W S; Diercksen, G H F

    2006-01-01

    The influence of spatial confinement on the structure and spectra of the Rydberg HeH molecule is analysed at the level of the variational full configuration interaction approach. The confining potential is assumed to have cylindrical symmetry, with the symmetry axis of the potential overlapping with the molecular bond. In the direction perpendicular to the axis quadratic dependence of the potential on the electron coordinates is assumed. The influence of the confining potential on the form of the potential energy curves (in particular on the bond lengths), on the electronic spectra and on the ionization due to the confinement is studied in detail

  1. Electron energy-loss spectra in molecular fluorine

    Science.gov (United States)

    Nishimura, H.; Cartwright, D. C.; Trajmar, S.

    1979-01-01

    Electron energy-loss spectra in molecular fluorine, for energy losses from 0 to 17.0 eV, have been taken at incident electron energies of 30, 50, and 90 eV and scattering angles from 5 to 140 deg. Features in the spectra above 11.5 eV energy loss agree well with the assignments recently made from optical spectroscopy. Excitations of many of the eleven repulsive valence excited electronic states are observed and their location correlates reasonably well with recent theoretical results. Several of these excitations have been observed for the first time and four features, for which there are no identifications, appear in the spectra.

  2. Study on Properties of Energy Spectra of the Molecular Crystals

    Science.gov (United States)

    Pang, Xiao-Feng; Chen, Xiang-Rong

    The energy-spectra of nonlinear vibration of molecular crystals such as acetanilide have been calculated by using discrete nonlinear Schrödinger equation appropriate to the systems, containing various interactions. The energy levels including higher excited states are basically consistent with experimental values obtained by infrared absorption and Raman scattering in acetanilide. We further give the features of distribution of the energy-spectra for the acetanilide. Using the energy spectra we also explained well experimental results obtained by Careri et al..

  3. Molecular structure and infrared spectra of the monomeric 3-(methoxy)-1,2-benzisothiazole 1,1-dioxide (methyl pseudosaccharyl ether)

    Science.gov (United States)

    Kaczor, Agnieszka; Almeida, Rui; Gómez-Zavaglia, Andrea; Cristiano, Maria de Lurdes S.; Fausto, Rui

    2008-03-01

    The computational description of saccharin (1,2-benzisothiazol-3(2 H)-one-1,1-dioxide) and its derivatives is difficult due to the presence of hypervalent S dbnd O bonds in their structures. Therefore, in this investigation, the HF, DFT/B3LYP and MP2 methods were used to predict the geometry and the infrared spectrum of the saccharyl derivative 3-(methoxy)-1,2-benzisothiazole 1,1-dioxide (MBID). Their relative predictive capabilities were then evaluated by comparing the obtained results with experimentally available data, namely the newly obtained IR spectra of MBID isolated in low-temperature inert matrices. For each method, different basis sets [6-31++G(d,p), 6-31++G(3df,3pd), 6-311++G(d,p), 6-311++G(2df,2pd), 6-311++G(3df,3pd), aug-cc-pVDZ and aug-cc-pVTZ] were considered. The best overall agreement has been achieved at the B3LYP/6-311++G(3df,3pd) and B3LYP/6-31++G(3df,3pd) levels of theory, showing the adequacy of the B3LYP functional to describe the investigated properties in this type of compounds and stressing the relevance of including high-order polarization functions in the basis set. The chosen level of theory [B3LYP/6-311++G(3df,3pd)] was applied to analyze the vibrational spectra and the geometry of the title molecule. In agreement with the experiment, the C sbnd O sbnd C linkage in MBID is predicted by these calculations to exhibit considerably short (1.320 Å) and long (1.442 Å) (N dbnd )C sbnd O and (H 3)C sbnd O bonds, respectively, and a hybridization of the central oxygen atom close to sp 2 (the C sbnd O sbnd C angle is predicted to be ca. 117°). This C sbnd O sbnd C bonding pattern fits the well-known high reactivity of MBID upon thermal rearrangement, which has been shown to result in easy selective [1,3']-isomerization of the compound.

  4. Classical and quantum molecular dynamics in NMR spectra

    CERN Document Server

    Szymański, Sławomir

    2018-01-01

    The book provides a detailed account of how condensed-phase molecular dynamics are reflected in the line shapes of NMR spectra. The theories establishing connections between random, time-dependent molecular processes and lineshape effects are exposed in depth. Special emphasis is placed on the theoretical aspects, involving in particular intermolecular processes in solution, and molecular symmetry issues. The Liouville super-operator formalism is briefly introduced and used wherever it is beneficial for the transparency of presentation. The proposed formal descriptions of the discussed problems are sufficiently detailed to be implemented on a computer. Practical applications of the theory in solid- and liquid-phase studies are illustrated with appropriate experimental examples, exposing the potential of the lineshape method in elucidating molecular dynamics NMR-observable molecular phenomena where quantization of the spatial nuclear degrees of freedom is crucial are addressed in the last part of the book. As ...

  5. Conformation of the azo bond and its influence on the molecular and crystal structures, IR and Raman spectra, and electron properties of 6-methyl-3,5-dinitro-2-[(E)-phenyldiazenyl]pyridine - Quantum chemical DFT calculations

    Science.gov (United States)

    Michalski, J.; Bryndal, I.; Lorenc, J.; Hermanowicz, K.; Janczak, J.; Hanuza, J.

    2018-02-01

    The crystal and molecular structures of 6-methyl-3,5-dinitro-2-[(E)-phenyldiazenyl]pyridine have been determined by X-ray diffraction and quantum chemical DFT calculations. The crystal is monoclinic, space group Cc (No. 9) with Z = 4 with the unit cell parameters: a = 12.083(7), b = 12.881(6), c = 8.134(3) Å and β = 97.09(5)°. The azo-bridge appears in the trans conformation in which C2-N2-N2‧-C1‧ torsion angle takes a value - 178.6(3)°, whereas the dihedral angle between the planes of the phenyl and pyridine rings is 3.5(2)°. The IR and Raman spectra measured in the temperature range 80-350 K and quantum chemical calculations with the use of B3LYP/6-311G(2d,2p) approach confirmed the trans configuration of the azo-bridge as the most stable energetically and allowed determination of the energy other virtual structures. The observed effects were used in the discussion of vibrational dynamics of the studied compound. The energy gap between cis and trans conformers equals to 1.054 eV (0.03873 Hartree). The electron absorption and emission spectra have been measured and analyzed on the basis of DFT calculations. The life time of the excited state is 12 μs and the Stokes shift is close to 5470 cm- 1.

  6. Probing molecular chirality by coherent optical absorption spectra

    Energy Technology Data Exchange (ETDEWEB)

    Jia, W. Z. [Quantum Optoelectronics Laboratory, School of Physics and Technology, Southwest Jiaotong University, Chengdu 610031 (China); Wei, L. F. [Quantum Optoelectronics Laboratory, School of Physics and Technology, Southwest Jiaotong University, Chengdu 610031 (China); State Key Laboratory of Optoelectronic Materials and Technologies, School of Physics and Engineering, Sun Yat-Sen University, Guangzhou 510275 (China)

    2011-11-15

    We propose an approach to sensitively probe the chirality of molecules by measuring their coherent optical-absorption spectra. It is shown that quantum dynamics of the cyclic three-level chiral molecules driven by appropriately designed external fields is total-phase dependent. This will result in chirality-dependent absorption spectra for the probe field. As a consequence, the charality-dependent information in the spectra (such as the locations and relative heights of the characteristic absorption peaks) can be utilized to identify molecular chirality and determinate enantiomer excess (i.e., the percentages of different enantiomers). The feasibility of the proposal with chiral molecules confined in hollow-core photonic crystal fiber is also discussed.

  7. Valency and molecular structure

    CERN Document Server

    Cartmell, E

    1977-01-01

    Valency and Molecular Structure, Fourth Edition provides a comprehensive historical background and experimental foundations of theories and methods relating to valency and molecular structures. In this edition, the chapter on Bohr theory has been removed while some sections, such as structures of crystalline solids, have been expanded. Details of structures have also been revised and extended using the best available values for bond lengths and bond angles. Recent developments are mostly noted in the chapter on complex compounds, while a new chapter has been added to serve as an introduction t

  8. Molecular structure, vibrational spectra, MEP, HOMO-LUMO and NBO analysis of Hf(SeO3)(SeO4)(H2O)4

    Science.gov (United States)

    Yankova, Rumyana; Genieva, Svetlana; Halachev, Nenko; Dimitrova, Ginka

    2016-02-01

    Hf(SeO3)(SeO4)(H2O)4 was obtained with the hydrothermal synthesis. The geometry optimization of this molecule was done by Density Functional Theory (DFT/B3LYP) method with 6-31G(d) basis set and LANL2DZ for Hf. The experimental infrared spectrum was compared with calculated and complete vibrational assignment was provided. The bond orders and the electronic properties of the molecule were calculated. The natural bond orbital analysis (NBO) was performed in order to study the intramolecular bonding interactions among bonds and delocalization of unpaired electrons. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap were presented. The electrostatic potential was calculated in order to investigate the reaction properties of the molecule. The thermodynamic properties of the studied compound at different temperatures were calculated.

  9. The Vibrational Spectra of the Boron Halides and their Molecular ...

    African Journals Online (AJOL)

    The structures, interaction energies and vibrational spectra of the van derWaals complexes formed between boron trifluoride, as Lewis acid, and water and hydrogen sulphide, as Lewis bases, have been determined by means of ab initio calculations at the second-order level of Møller-Plesset perturbation theory, using a ...

  10. Molecular dynamics simulation and TDDFT study of the structures and UV-vis absorption spectra of MCT-β-CD and its inclusion complexes.

    Science.gov (United States)

    Lu, Huijuan; Wang, Yujiao; Xie, Xiaomei; Chen, Feifei; Li, Wei

    2015-01-01

    In this research, the inclusion ratios and inclusion constants of MCT-β-CD/PERM and MCT-β-CD/CYPERM inclusion complexes were measured by UV-vis and fluorescence spectroscopy. The inclusion ratios are both 1:1, and the inclusion constants are 60 and 342.5 for MCT-β-CD/PERM and MCT-β-CD/CYPERM, respectively. The stabilities of inclusion complexes were investigated by MD simulation. MD shows that VDW energy plays a vital role in the stability of inclusion complex, and the destruction of inclusion complex is due to the increasing temperature. The UV-vis absorption spectra of MCT-β-CD and its inclusion complexes were studied by time-dependent density functional theory (TDDFT) method employing BLYP-D3, B3LYP-D3 and M06-2X-D3 functionals. BLYP-D3 well reproduces the UV-vis absorption spectrum and reveals that the absorption bands of MCT-β-CD mainly arise from n→π(∗) and n→σ(∗) transition, and those of inclusion complexes mainly arise from intramolecular charge transfer (ICT). ICT results in the shift of main absorption bands of MCT-β-CD. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Photoionization and molecular structure

    International Nuclear Information System (INIS)

    Palma, A.

    1983-01-01

    A presentation is here given of the theoretical work on photoionization and molecular structure carried out by the author and coworkers. The implications of the photoionization process on the molecular geometry are emphasized. In particular, the ionization effect on deep orbitals is considered and it is shown that, contrary to traditional thinking, these orbitals have relevant effects on the molecular geometry. The problem of calculating photoionization relative intensities for the full spectrum is also considered, and the results of the present model are compared with experimental and other theoretical results. (author)

  12. ExoCross: Spectra from molecular line lists

    Science.gov (United States)

    Yurchenko, Sergei N.; Al-Refaie, Ahmed; Tennyson, Jonathan

    2018-03-01

    ExoCross generates spectra and thermodynamic properties from molecular line lists in ExoMol, HITRAN, or several other formats. The code is parallelized and also shows a high degree of vectorization; it works with line profiles such as Doppler, Lorentzian and Voigt and supports several broadening schemes. ExoCross is also capable of working with the recently proposed method of super-lines. It supports calculations of lifetimes, cooling functions, specific heats and other properties. ExoCross converts between different formats, such as HITRAN, ExoMol and Phoenix, and simulates non-LTE spectra using a simple two-temperature approach. Different electronic, vibronic or vibrational bands can be simulated separately using an efficient filtering scheme based on the quantum numbers.

  13. Crystal and molecular structure and Raman and 127I Moessbauer spectra of iodine(III) bis(fluorosulfate) iodide, I(OSO2F)2I

    International Nuclear Information System (INIS)

    Birchall, T.; Denes, G.; Faggiani, R.; Frampton, C.S.; Gillespie, R.J.; Kapoor, R.; Vekris, J.E.

    1990-01-01

    Iodine is oxidized by peroxodisulfuryl difluoride, S 2 O 6 F 2 , to give I(OSO 2 F) 2 I. The crystal structure of the orthorhombic type crystal is reported. The structure was solved by means of Patterson functions and refined by least squares to final agreement indices of R 1 = 0.0353 and R 2 = 0.0374 for 1,600 independent reflections. There are three primary bonds to the central iodine, I(1), (I(1)-OSO 2 F = 2.086 (7) and 2.258 (7) angstrom; I(1)-I(2) = 2.676 (1) angstrom), which create a distorted T=shaped AX 3 E 2 geometry. The second iodine, I(2), has a primary bond to I(1) and a strong intermolecular secondary I(2)-O bond of length 2.655 (8) angstrom to one of the fluorosulfate groups that is colinear with the primary bond, giving an AXYE 3 geometry about I(2). The Raman spectrum of the solid and the 127 I Moessbauer spectrum are in full agreement with the structure found. 30 refs., 3 figs., 4 tabs

  14. Uranyl oxalate hydrates: structures and IR spectra

    International Nuclear Information System (INIS)

    Giesting, P.A.; Porter, N.J.; Burns, P.C.

    2006-01-01

    The novel compound (UO 2 ) 2 C 2 O 4 (OH) 2 (H 2 O) 2 (UrOx2A) and the previously studied compound UO 2 C 2 O 4 (H 2 O) 3 (UrOx3) have been synthesized by mild hydrothermal methods. Single crystal diffraction data collected at 125 K using MoK α radiation and a CCD-based area detector were used to solve and refine the crystal structures by full-matrix least-squares techniques to agreement indices (UrOx2A, UrOx3) wR 2 = 0.037, 0.049 for all data, and R1 0.015, 0.024 calculated for 1285, 2194 unique reflections respectively. The compound UrOx2A is triclinic, space group P1, Z = 1, a = 5.5353(4), b 6.0866(4), c = 7.7686(6) Aa, α = 85.6410(10) , β = 89.7740(10) , γ = 82.5090(10) , V = 258.74(3) Aa 3 . The compound UrOx3 is monoclinic, space group P2 1 /c, Z = 4, a = 5.5921(4), b = 16.9931(13), c = 9.3594(7) Aa, β = 99.5330(10) , V = 877.11(11) Aa 3 . The structures consist of chains of uranyl pentagonal bipyramids connected by oxalate groups and, in UrOx2A, hydroxyl groups; UrOx2A is also notable for its high (2:1) ratio of uranyl to oxalate groups, higher than any observed in other published structures of uranyl oxalates. The structure determined for UrOx3, previously studied by Jayadevan and Chackraburtty (1972); Mikhailov et al. (1999) is in agreement with the previous results; however, the increased precision of the present low-temperature structure refinement allows for the assignment of H atom positions based on the difference Fourier map of electron density. The infrared spectra of these two materials collected at room temperature are also presented and compared with previous work on uranyl oxalate systems. (orig.)

  15. Understanding molecular structure from molecular mechanics.

    Science.gov (United States)

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  16. Synthesis, structural, spectroscopic, anti-cancer and molecular docking studies on novel 2-[(Anthracene-9-ylmethylene)amino]-2-methylpropane-1,3-diol using XRD, FTIR, NMR, UV-Vis spectra and DFT

    Science.gov (United States)

    Pavitha, P.; Prashanth, J.; Ramu, G.; Ramesh, G.; Mamatha, K.; Venkatram Reddy, Byru

    2017-11-01

    The novel titled compound 2-[(Anthracene-9-ylmethylene)amino]-2-methylpropane-1,3-diol (AMD) has been synthesized by slow evaporation technique from mixed solvent system of methanol with anthracene-9-carbaldehyde and 2-amino-2-methylpropane-1,3-diol. The synthesized molecule AMD was characterized experimentally by single crystal XRD, FTIR, NMR and UV-Vis spectra and density functional theory (DFT) computations. The structure of the crystal has been determined as orthorhombic system with space group P 21 21 21 and the cell parameters are obtained using XRD data. The optimized ground state geometry of the molecule is determined by evaluating torsional potentials as a function of angle of free rotation around Csbnd C bonds of functional groups by DFT method employing B3LYP functional with 6-311++G(d,p) basis set. All the fundamental vibrations of the molecule are assigned unambiguously using potential energy distribution (PED) obtained in the DFT computations. The rms error between the observed and scaled frequencies is 6.20 cm-1. The values of dipole moment, polarizability and hyperpolarizability are evaluated to study the NLO behavior of the molecule. The HOMO-LUMO energies and thermodynamic parameters are also determined. The molecular electrostatic surface potential (MESP) is mapped to obtain the charge density distribution. The 1H and 13C NMR chemical shifts of the molecule are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. UV-visible spectrum of the compound is also recorded in the region 200-800 nm to know the type of electronic transitions involved. The anti-cancer activity of AMD is determined against human breast cancer cell line MCF-7 and human prostate cancer cell line PC-3 and correlated the results with study of molecular docking against pharmacological protein IDO-1 receptor.

  17. Analysis of the Alkali Metal Diatomic Spectra; Using molecular beams and ultracold molecules

    Science.gov (United States)

    Kim, Jin-Tae

    2014-12-01

    This ebook illustrates the complementarity of molecular beam (MB) spectra and ultracold molecule (UM) spectra in unraveling the complex electronic spectra of diatomic alkali metal molecules, using KRb as a prime example. Researchers interested in molecular spectroscopy, whether physicist, chemist, or engineer, may find this ebook helpful and may be able to apply similar ideas to their molecules of interest.

  18. Algebraic descriptions of nuclear and molecular rotation-vibration spectra

    International Nuclear Information System (INIS)

    Roosmalen, O.S. van.

    1982-01-01

    The application of algebraic models to the description of rotational and vibrational degrees of freedom of nuclei and molecules are discussed. Simple model Hamiltonians are shown to give good agreement with the energy spectra of diatomic molecules and nuclei. Some formal aspects of path integral methods for many-boson systems are treated. The two representations for the quantum mechanical propagator are compared and appear to be identical in leading order in 1/N (N is the number of bosons). Approximations for both are static and dynamic problems are discussed. Applications of mean field techniques are also treated. A description of tri- and tetra-atomic molecules in terms of a U(4)xU(4) and U(4)xU(4)xU(4) group structure is given. Linear molecules appear to correspond with symmetries of O(4) type. S-matrix elements are calculated to test mean field methods, and the results compared with exact calculations. (Auth.)

  19. Molecular Structure of Nucleic Acids

    Indian Academy of Sciences (India)

    Molecular Structure of Nucleic Acids. A Structure for Deoxyribose Nucleic Acid. J. D. Watson and F. H. C. Crick. Medical Research Council Unit for the Study of the Molecular Structure of Biological. Systems, Cavendish Laboratory, Cambridge. April 2. We wish to suggest a structure for the salt of deoxyribose nucleic acid ...

  20. Molecular Geometry And Vibrational Spectra of 2'-chloroacetanilide

    International Nuclear Information System (INIS)

    Gokce, H.

    2008-01-01

    The molecular structure, vibrational frequencies and the corresponding vibrational assingments of 2'-chloroacetanilide in the ground state have been calculated by using Hartree-Fock (HF) and Density Functional Theory (DFT/B3LYP) methods with 6-311++G(d,p) basis set. The obtained vibrational frequencies and optimized geometric parameters (bond lenghts and angles) are in very good agreement with the experimental data. The comparison of the observed and calculated vibrational frequencies assignments of 2'-chloroacetanilide exhibit that the scaled DFT/B3LYP method is superior to be scaled HF method. Furthermore the calculated Infrared and Raman intensities are also reported

  1. Structural Molecular Biology 2017 | SSRL

    Science.gov (United States)

    Highlights Training Workshops & Summer Schools Summer Students Structural Molecular Biology Illuminating experimental driver for structural biology research, serving the needs of a large number of academic and — Our Mission The SSRL Structural Molecular Biology program operates as an integrated resource and has

  2. Influence of soil-structure interaction on floor response spectra

    International Nuclear Information System (INIS)

    Costantino, C.J.; Miller, C.A.; Curreri, J.R.

    1985-01-01

    A study was undertaken to investigate the influence of soil-structure interaction on floor response spectra developed in typical nuclear power plant structures. A horizontal earthquake time history, whose spectra envelops the Reg. Guide 1.60 criteria and is scaled to a 1 g peak acceleration, was used as input to structural models. Two different structural stick models were used, representing typical BWR and PWR facilities. By varying the structural and soil stiffness parameters, a wide range of system behaviors were investigated. Floor response spectra, required to assess equipment qualification, were of primary interest. It was found from a variation of parameter study that the interaction soil parameters, particularly radiation damping, greatly affect the nature of the calculated responses. (orig.)

  3. Influence of soil-structure interaction on floor response spectra

    International Nuclear Information System (INIS)

    Costantino, C.J.; Miller, C.A.; Curreri, J.R.

    1985-01-01

    A study was undertaken to investigate the influence of soil-structure interaction on floor response spectra developed in typical nuclear power plant structures. A horizontal earthquake time history, whose spectra envelops the Regulatory Guide 1.60 criteria and is scaled to a log peak acceleration, was used as input to structural models. Two different structural stick models were used, representing typical BWR and PWR facilities. By varying the structural and soil stiffness parameters, a wide range of system behaviors were investigated. Floor response spectra, required to assess equipment qualification, were of primary interest. It was found from a variation of parameter study that the interaction soil parameters, particularly radiation damping, greatly affect the nature of the calculated responses. 2 refs., 2 figs., 2 tabs

  4. Core-level spectra and molecular deformation in adsorption: V-shaped pentacene on Al(001)

    Science.gov (United States)

    Lin, He; Brivio, Gian Paolo; Floreano, Luca; Fratesi, Guido

    2015-01-01

    Summary By first-principle simulations we study the effects of molecular deformation on the electronic and spectroscopic properties as it occurs for pentacene adsorbed on the most stable site of Al(001). The rationale for the particular V-shaped deformed structure is discussed and understood. The molecule–surface bond is made evident by mapping the charge redistribution. Upon X-ray photoelectron spectroscopy (XPS) from the molecule, the bond with the surface is destabilized by the electron density rearrangement to screen the core hole. This destabilization depends on the ionized carbon atom, inducing a narrowing of the XPS spectrum with respect to the molecules adsorbed hypothetically undistorted, in full agreement to experiments. When looking instead at the near-edge X-ray absorption fine structure (NEXAFS) spectra, individual contributions from the non-equivalent C atoms provide evidence of the molecular orbital filling, hybridization, and interchange induced by distortion. The alteration of the C–C bond lengths due to the V-shaped bending decreases by a factor of two the azimuthal dichroism of NEXAFS spectra, i.e., the energy splitting of the sigma resonances measured along the two in-plane molecular axes. PMID:26734516

  5. Core-level spectra and molecular deformation in adsorption: V-shaped pentacene on Al(001

    Directory of Open Access Journals (Sweden)

    Anu Baby

    2015-11-01

    Full Text Available By first-principle simulations we study the effects of molecular deformation on the electronic and spectroscopic properties as it occurs for pentacene adsorbed on the most stable site of Al(001. The rationale for the particular V-shaped deformed structure is discussed and understood. The molecule–surface bond is made evident by mapping the charge redistribution. Upon X-ray photoelectron spectroscopy (XPS from the molecule, the bond with the surface is destabilized by the electron density rearrangement to screen the core hole. This destabilization depends on the ionized carbon atom, inducing a narrowing of the XPS spectrum with respect to the molecules adsorbed hypothetically undistorted, in full agreement to experiments. When looking instead at the near-edge X-ray absorption fine structure (NEXAFS spectra, individual contributions from the non-equivalent C atoms provide evidence of the molecular orbital filling, hybridization, and interchange induced by distortion. The alteration of the C–C bond lengths due to the V-shaped bending decreases by a factor of two the azimuthal dichroism of NEXAFS spectra, i.e., the energy splitting of the sigma resonances measured along the two in-plane molecular axes.

  6. On the geometry dependence of molecular dimer spectra with an application to aggregates of perylene bisimide

    International Nuclear Information System (INIS)

    Seibt, J.; Marquetand, P.; Engel, Volker; Chen, Z.; Dehm, V.; Wuerthner, F.

    2006-01-01

    We study spectroscopic properties of molecular dimers coupled by dipole-dipole interactions within the framework of time-dependent quantum mechanics. A systematic variation of the dimer geometry allows to establish relationships between the latter and structures in the absorption spectrum. The theoretical model is constructed with the purpose to characterize the changes in absorption and emission properties arising upon aggregation of perylene bisimides. Measured and calculated spectra are compared, thereby addressing the question if a simple exciton model is capable to describe excited state properties of nanoaggregates of these molecules

  7. Floor response spectra of buildings with uncertain structural properties

    International Nuclear Information System (INIS)

    Chen, P.C.

    1975-01-01

    All Category I equipment, such as reactors, vessels, and major piping systems of nuclear power plants, is required to withstand earthquake loadings in order to minimize risk of seismic damage. The equipment is designed by using response spectra of the floor on which the equipment is mounted. The floor response spectra are constructed usually from the floor response time histories which are obtained through a deterministic dynamic analysis. This analysis assumes that all structural parameters, such as mass, stiffness, and damping have been calculated precisely, and that the earthquakes are known. However, structural parameters are usually difficult to determine precisely if the structures are massive and/or irregular, such as nuclear containments and its internal structures with foundation soil incorporated into the analysis. Faced with these uncertainties, it has been the practice to broaden the floor response spectra peaks by +-10 percent of the peak frequencies on the basis of conservatism. This approach is based on engineering judgement and does not have an analytical basis to provide a sufficient level of confidence in using these spectra for equipment design. To insure reliable design, it is necessary to know structural response variations due to variations in structural properties. This consideration leads to the treatment of structural properties as random variables and the use of probabilistic methods to predict structural response more accurately. New results on floor response spectra of buildings with uncertain structural properties obtained by determining the probabilistic dynamic response from the deterministic dynamic response and its standard deviation are presented. The resulting probabilistic floor response spectra are compared with those obtained deterministically, and are shown to provide a more reliable method for determining seismic forces

  8. Generate floor response spectra, Part 2: Response spectra for equipment-structure resonance

    International Nuclear Information System (INIS)

    Li, Bo; Jiang, Wei; Xie, Wei-Chau; Pandey, Mahesh D.

    2015-01-01

    Highlights: • The concept of tRS is proposed to deal with tuning of equipment and structures. • Established statistical approaches for estimating tRS corresponding to given GRS. • Derived a new modal combination rule from the theory of random vibration. • Developed efficient and accurate direct method for generating floor response spectra. - Abstract: When generating floor response spectra (FRS) using the direct spectra-to-spectra method developed in the companion paper, probability distribution of t-response spectrum (tRS), which deals with equipment-structure resonance or tuning, corresponding to a specified ground response spectrum (GRS) is required. In this paper, simulation results using a large number of horizontal and vertical ground motions are employed to establish statistical relationships between tRS and GRS. It is observed that the influence of site conditions on horizontal statistical relationships is negligible, whereas the effect of site conditions on vertical statistical relationships cannot be ignored. Considering the influence of site conditions, horizontal statistical relationship suitable for all site conditions and vertical statistical relationships suitable for hard sites and soft sites, respectively, are established. The horizontal and vertical statistical relationships are suitable to estimate tRS for design spectra in USNRC R.G. 1.60 and NUREG/CR-0098, Uniform Hazard Spectra (UHS) in Western North America (WNA), or any GRS falling inside the valid coverage of the statistical relationship. For UHS with significant high frequency spectral accelerations, such as UHS in Central and Eastern North America (CENA), an amplification ratio method is proposed to estimate tRS. Numerical examples demonstrate that the statistical relationships and the amplification ratio method are acceptable to estimate tRS for given GRS and to generate FRS using the direct method in different practical situations.

  9. Generate floor response spectra, Part 2: Response spectra for equipment-structure resonance

    Energy Technology Data Exchange (ETDEWEB)

    Li, Bo, E-mail: b68li@uwaterloo.ca; Jiang, Wei, E-mail: w46jiang@uwaterloo.ca; Xie, Wei-Chau, E-mail: xie@uwaterloo.ca; Pandey, Mahesh D., E-mail: mdpandey@uwaterloo.ca

    2015-11-15

    Highlights: • The concept of tRS is proposed to deal with tuning of equipment and structures. • Established statistical approaches for estimating tRS corresponding to given GRS. • Derived a new modal combination rule from the theory of random vibration. • Developed efficient and accurate direct method for generating floor response spectra. - Abstract: When generating floor response spectra (FRS) using the direct spectra-to-spectra method developed in the companion paper, probability distribution of t-response spectrum (tRS), which deals with equipment-structure resonance or tuning, corresponding to a specified ground response spectrum (GRS) is required. In this paper, simulation results using a large number of horizontal and vertical ground motions are employed to establish statistical relationships between tRS and GRS. It is observed that the influence of site conditions on horizontal statistical relationships is negligible, whereas the effect of site conditions on vertical statistical relationships cannot be ignored. Considering the influence of site conditions, horizontal statistical relationship suitable for all site conditions and vertical statistical relationships suitable for hard sites and soft sites, respectively, are established. The horizontal and vertical statistical relationships are suitable to estimate tRS for design spectra in USNRC R.G. 1.60 and NUREG/CR-0098, Uniform Hazard Spectra (UHS) in Western North America (WNA), or any GRS falling inside the valid coverage of the statistical relationship. For UHS with significant high frequency spectral accelerations, such as UHS in Central and Eastern North America (CENA), an amplification ratio method is proposed to estimate tRS. Numerical examples demonstrate that the statistical relationships and the amplification ratio method are acceptable to estimate tRS for given GRS and to generate FRS using the direct method in different practical situations.

  10. Electronic spectra and structures of some biologically important xanthines

    Science.gov (United States)

    Shukla, M. K.; Mishra, P. C.

    1994-08-01

    Electronic absorption and fluorescence spectra of aqueous solutions of xanthine, caffeine, theophylline and theobromine have been studied at different pH. The observed spectra have been interpreted in terms of neutral and ionic forms of the molecules with the help of molecular orbital calculations. At neutral and acidic pH, the spectra can be assigned to the corresponding most stable neutral forms, with the exception that the fluorescence of xanthine at acidic pH appears to originate from the lowest singlet excited state of a cation of the molecule. At alkaline pH, xanthine and theophylline exist mainly as their monoanions. In xanthine and theophylline at alkaline pH, fluorescence originates from the lowest singlet excited state of the corresponding anion. However, in caffeine and theobromine, even at alkaline pH, fluorescence belongs to the neutral species. On the whole, the properties of xanthine are quite different from those of the methyl xanthines.

  11. Photoelectron spectra and electronic structure of some spiroborate complexes

    Energy Technology Data Exchange (ETDEWEB)

    Vovna, V.I.; Tikhonov, S.A.; Lvov, I.B., E-mail: lvov.ib@dvfu.ru; Osmushko, I.S.; Svistunova, I.V.; Shcheka, O.L.

    2014-12-15

    Highlights: • The electronic structure of three spiroborate complexes—boron 1,2-dioxyphenylene β-diketonates has been investigated. • UV and X-ray photoelectron spectra have been interpreted. • DFT calculations have been used for interpretation of spectral bands. • The binding energy of nonequivalent carbon and oxygen atoms were measured. • The structure of X-ray photoelectron spectra of the valence electrons is in good agreement with the energies and composition of Kohn–Sham orbitals. - Abstract: The electronic structure of the valence and core levels of three spiroborate complexes – boron 1,2-dioxyphenylene β-diketonates – has been investigated by methods of UV and X-ray photoelectron spectroscopy and quantum chemical density functional theory. The ionization energy of π- and n-orbitals of the dioxyphenylene fragment and β-diketonate ligand were measured from UV photoelectron spectra. This made it possible to determine the effect of substitution of one or two methyl groups by the phenyl in diketone on the electronic structure of complexes. The binding energy of nonequivalent carbon and oxygen atoms were measured from X-ray photoelectron spectra. The results of calculations of the energy of the valence orbitals of complexes allowed us to refer bands observed in the spectra of the valence electrons to the 2s-type levels of carbon and oxygen.

  12. Computer simulation of molecular absorption spectra for asymmetric top molecules

    International Nuclear Information System (INIS)

    Bende, A.; Tosa, V.; Cosma, V.

    2001-01-01

    The effective Hamiltonian formalism has been used to develop a model for infrared multiple-photon absorption (IRMPA) process in asymmetric top molecules. Assuming a collisionless regime, the interaction between the molecule and laser field can be described by the time-dependent Schroedinger equation. By using the rotating wave approximation and Laplace transformation, the time-dependent problem reduces to a time-independent eigen problem for an effective Hamiltonian which can be solved only numerically for a real vibrational-rotational structure of polyatomic molecule. The vibrational-rotational structure is assumed to be an anharmonic oscillator coupled to an asymmetric rigid rotor. The main assumptions taken into account for this model are the following: (1) the excitation is coherent, i.e. the collision (if present during the laser pulse) does not influence the excitation; (2) the excitation starts from the ground state and is near resonant to a normal mode, thus, the rotating wave approximation can be applied; (3) after absorbing N photons the vibrational energy of the excited mode leak into a quasicontinuum; (4) the thermal population of the ground state is given by the Maxwell-Boltzmann distribution law. The energy levels of the asymmetric top molecules cannot be represented by an explicit formula analogous to that for the symmetric top, according to quantum mechanics, but we can consider it a deviation from the prolate or oblate case of the symmetric top, and we can find in the same manner the selection rules of the asymmetric case using the selection rules for the symmetric case. The infrared bands of asymmetric top molecules are not resolved, but if the dispersion used is not too small, so that the envelopes of the bands can be distinguished from simple maxima, it is possible to draw conclusions as to the type of the bands. In this case, the simulation of the absorption spectra can give us some important information about the types of these bands. In

  13. Biomolecular Structure Information from High-Speed Quantum Mechanical Electronic Spectra Calculation.

    Science.gov (United States)

    Seibert, Jakob; Bannwarth, Christoph; Grimme, Stefan

    2017-08-30

    A fully quantum mechanical (QM) treatment to calculate electronic absorption (UV-vis) and circular dichroism (CD) spectra of typical biomolecules with thousands of atoms is presented. With our highly efficient sTDA-xTB method, spectra averaged along structures from molecular dynamics (MD) simulations can be computed in a reasonable time frame on standard desktop computers. This way, nonequilibrium structure and conformational, as well as purely quantum mechanical effects like charge-transfer or exciton-coupling, are included. Different from other contemporary approaches, the entire system is treated quantum mechanically and neither fragmentation nor system-specific adjustment is necessary. Among the systems considered are a large DNA fragment, oligopeptides, and even entire proteins in an implicit solvent. We propose the method in tandem with experimental spectroscopy or X-ray studies for the elucidation of complex (bio)molecular structures including metallo-proteins like myoglobin.

  14. Study of atomic and molecular emission spectra of Sr by laser induced breakdown spectroscopy (LIBS).

    Science.gov (United States)

    Bhatt, Chet R; Alfarraj, Bader; Ayyalasomayajula, Krishna K; Ghany, Charles; Yueh, Fang Y; Singh, Jagdish P

    2015-12-01

    Laser Induced Breakdown Spectroscopy (LIBS) is an ideal analytical technique for in situ analysis of elemental composition. We have performed a comparative study of the quantitative and qualitative analysis of atomic and molecular emission from LIBS spectra. In our experiments, a mixture of SrCl2 and Al2O3 in powder form was used as a sample. The atomic emission from Sr and molecular emission from SrCl and SrO observed in LIBS spectra were analyzed. The optimum laser energies, gate delays, and gate widths for selected atomic lines and molecular bands were determined from spectra recorded at various experimental parameters. These optimum experimental conditions were used to collect calibration data, and the calibration curves were used to predict the Sr concentration. Limits of detection (LODs) for selected atomic and molecular emission spectra were determined.

  15. Using Molecular Modeling in Teaching Group Theory Analysis of the Infrared Spectra of Organometallic Compounds

    Science.gov (United States)

    Wang, Lihua

    2012-01-01

    A new method is introduced for teaching group theory analysis of the infrared spectra of organometallic compounds using molecular modeling. The main focus of this method is to enhance student understanding of the symmetry properties of vibrational modes and of the group theory analysis of infrared (IR) spectra by using visual aids provided by…

  16. Equipment response spectra for base-isolated shear beam structures

    International Nuclear Information System (INIS)

    Ahmadi, G.; Su, L.

    1992-01-01

    Equipment response spectra in base-isolated structure under seismic ground excitations are studied. The equipment is treated as a single-degree-of-freedom system attached to a nonuniform elastic beam structural model. Several leading base isolation systems, including the laminated rubber bearing, the resilient-friction base isolator with and without a sliding upper plate, and the EDF system are considered. Deflection and acceleration response spectra for the equipment and the shear beam structure subject to a sinusoidal and the accelerogram of the N00W component of El Centro 1940 earthquake are evaluated. Primary-secondary interaction effects are included in the analysis. Several numerical parametric studies are carried out and the effectiveness of different base isolation systems in protecting the nonstructural components is studied. It is shown that use of properly designed base isolation systems provides considerable protection for secondary systems, as well as, the structure against severe seismic loadings. (orig.)

  17. Molecular vibration-rotation spectra starting from the Fues potential

    International Nuclear Information System (INIS)

    Ley Koo, E.

    1976-01-01

    The solution of Schroedinger's equation for the Fues potential is analyzed and compared with the corresponding problems for the Coulomb, harmonic oscillator and molecular potentials. These comparisons allow us to emphasize certain pedagogical, conceptual and computational advantages of the Fues potential which make it a favorable alternative as the starting point in the analysis of molecular vibration-rotation and in the determination of potential energy curves. (author)

  18. Evolution of complex organic molecules in hot molecular cores. Synthetic spectra at (sub-)mm wavebands

    Science.gov (United States)

    Choudhury, R.; Schilke, P.; Stéphan, G.; Bergin, E.; Möller, T.; Schmiedeke, A.; Zernickel, A.

    2015-03-01

    Context. Hot molecular cores (HMCs) are intermediate stages of high-mass star formation and are also known for their rich chemical reservoirs and emission line spectra at (sub-)mm wavebands. Complex organic molecules (COMs) such as methanol (CH3OH), ethanol (C2H5OH), dimethyl ether (CH3OCH3), and methyl formate (HCOOCH3) produce most of these observed lines. The observed spectral feature of HMCs such as total number of emission lines and associated line intensities are also found to vary with evolutionary stages. Aims: We aim to investigate the spectral evolution of these COMs to explore the initial evolutionary stages of high-mass star formation including HMCs. Methods: We developed various 3D models for HMCs guided by the evolutionary scenarios proposed by recent empirical and modeling studies. We then investigated the spatio-temporal variation of temperature and molecular abundances in HMCs by consistently coupling gas-grain chemical evolution with radiative transfer calculations. We explored the effects of varying physical conditions on molecular abundances including density distribution and luminosity evolution of the central protostar(s) among other parameters. Finally, we simulated the synthetic spectra for these models at different evolutionary timescales to compare with observations. Results: Temperature has a profound effect on the formation of COMs through the depletion and diffusion on grain surface to desorption and further gas-phase processing. The time-dependent temperature structure of the hot core models provides a realistic framework for investigating the spatial variation of ice mantle evaporation as a function of evolutionary timescales. We find that a slightly higher value (15 K) than the canonical dark cloud temperature (10 K) provides a more productive environment for COM formation on grain surface. With increasing protostellar luminosity, the water ice evaporation font (~100 K) expands and the spatial distribution of gas phase abundances of

  19. Theoretical investigation on the molecular structure, Infrared, Raman and NMR spectra of para-halogen benzenesulfonamides, 4-X-C 6H 4SO 2NH 2 (X = Cl, Br or F)

    Science.gov (United States)

    Karabacak, Mehmet; Çınar, Mehmet; Çoruh, Ali; Kurt, Mustafa

    2009-02-01

    In the present study, the structural properties of para-halogen benzenesulfonamides, 4-XC 6H 4SO 2NH 2 (4-chlorobenzenesulfonamide (I), 4-bromobenzenesulfonamide (II) and 4-fluorobenzenesulfonamide (III)) have been studied extensively utilizing ab initio Hartree-Fock (HF) and density functional theory (DFT) employing B3LYP exchange correlation. The vibrational frequencies were calculated and scaled values were compared with experimental values. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The effects of the halogen substituent on the characteristic benzenesulfonamides bands in the spectra are discussed. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecules were calculated using the Gauge-Invariant Atomic Orbital (GIAO) method. Finally, geometric parameters, vibrational bands and chemical shifts were compared with available experimental data of the molecules. The fully optimized geometries of the molecules were found to be consistent with the X-ray crystal structures. The observed and calculated frequencies and chemical shifts were found to be in very good agreement.

  20. α-spectra hyperfine structure resolution by silicon planar detectors

    International Nuclear Information System (INIS)

    Eremin, V.K.; Verbitskaya, E.M.; Strokan, N.B.; Sukhanov, V.L.; Malyarenko, A.M.

    1986-01-01

    The lines with 13 keV step from the main one is α-spectra of nuclei with an odd number of nucleons take place. Silicon planar detectors n-Si with the operation surface of 10 mm 2 are developed for resolution of this hyperfine structure. The mechanism of losses in detectors for short-range-path particles is analyzed. The results of measurements from detectors with 10 keV resolution are presented

  1. cap alpha. -spectra hyperfine structure resolution by silicon planar detectors

    Energy Technology Data Exchange (ETDEWEB)

    Eremin, V K; Verbitskaya, E M; Strokan, N B; Sukhanov, V L; Malyarenko, A M

    1986-10-01

    The lines with 13 keV step from the main one is ..cap alpha..-spectra of nuclei with an odd number of nucleons take place. Silicon planar detectors n-Si with the operation surface of 10 mm/sup 2/ are developed for resolution of this hyperfine structure. The mechanism of losses in detectors for short-range-path particles is analyzed. The results of measurements from detectors with 10 keV resolution are presented.

  2. The Electronic Structure and Spectra of Triphenylamines Functionalized by Phenylethynyl Groups

    Science.gov (United States)

    Baryshnikov, G. V.; Minaeva, V. A.; Minaev, B. F.; Grigoras, M.

    2018-01-01

    We study the features of the electronic structure and the IR, UV, and visible spectra of a series of triphenylamines substituted with phenylethynyl groups. The analysis is performed at the level of the density functional theory (DFT) and its nonstationary version in comparison with the experimental data of IR and electron spectroscopy. It is shown that, in the excited state, there is a change in the alternation of single, double, and triple bonds in accordance with the character of bonding and antibonding in the lowest vacant molecular orbital. The gradual introduction of additional phenylethynyl groups does not cause frequency shifts in the IR spectra of the molecules under study, but significantly affects the intensity of the corresponding IR bands. A similar effect is also observed in the electronic-absorption spectra of these compounds. This can be used for optical tuning of triphenylamines as promising materials for organic light-emitting diodes and solar cells.

  3. QCD's Partner Needed for Mass Spectra and Parton Structure Functions

    International Nuclear Information System (INIS)

    Kim, Y.S.

    2009-01-01

    as in the case of the hydrogen atom, bound-state wave functions are needed to generate hadronic spectra. For this purpose, in 1971, Feynman and his students wrote down a Lorentz-invariant harmonic oscillator equation. This differential equation has one set of solutions satisfying the Lorentz-covariant boundary condition. This covariant set generates Lorentz-invariant mass spectra with their degeneracies. Furthermore, the Lorentz-covariant wave functions allow us to calculate the valence parton distribution by Lorentz-boosting the quark-model wave function from the hadronic rest frame. However, this boosted wave function does not give an accurate parton distribution. The wave function needs QCD corrections to make a contact with the real world. Likewise, QCD needs the wave function as a starting point for calculating the parton structure function. (author)

  4. Molecular absorption spectra of beryllium, cerium, lanthanum, iron, and platinum salts

    International Nuclear Information System (INIS)

    Daidoji, Hidehiro

    1980-01-01

    The absorption spectra of some salts of beryllium, cerium, lanthanum, iron and platinum in air-acetylene flame were measured in the wavelength range from 200 to 400 nm. A Hitachi 207 type atomic absorption spectrophotometer was used. A deuterium lamp, a home-made continuous radiation lamp and some hollow cathode lamps were used as light sources. The new molecular absorption spectra of cerium, lanthanum and platinum and the absorption spectra due to Be(OH) 2 , LaO, PtH, FeO and FeCl in 200-400 nm region were obtained. Emission spectra of CeO, LaO and FeOH were also obtained. These molecular absorption bands were estimated as absorption errors of maximum 15 times to the sensitivity of each elements in atomic absorption spectrometry. In addition, spectral line interferences of iron were observed in atomic absorption spectrometry of Zn, Cd, Ni, Cu and Cr. (author)

  5. Orbital momentum profiles and binding energy spectra for the complete valence shell of molecular fluorine

    International Nuclear Information System (INIS)

    Zheng, Y.; Brion, C.E.; Brunger, M.J.; Zhao, K.; Grisogono, A.M.; Braidwood, S.; Weigold, E.; Chakravorty, S.J.; Davidson, E.R.; Sgamellotti, A.; von Niessen, W.

    1996-01-01

    The first electronic structural study of the complete valence shell binding energy spectrum of molecular fluorine, encompassing both the outer and inner valence regions, is reported. These binding energy spectra as well as the individual orbital momentum profiles have been measured using an energy dispersive multichannel electron momentum spectrometer at a total energy of 1500 eV, with an energy resolution of 1.5 eV and a momentum resolution of 0.1 a.u. The measured binding energy spectra in the energy range of 14-60 eV are compared with the results of ADC(4) many-body Green's function and also direct-Configuration Interaction (CI) and MRSD-CI calculations. The experimental orbital electron momentum profiles are compared with SCF theoretical profiles calculated using the target Hartree-Fock approximation with a range of basis sets and with Density Functional Theory predictions in the target Kohn-Sham approximation with non-local potentials. The truncated (aug-cc-pv5z) Dunning basis sets were used for the Density Functional Theory calculations which also include some treatment of correlation via the exchange and correlation potentials. Comparisons are also made with the full ion-neutral overlap amplitude calculated with MRSD-CI wave functions. Large, saturated basis sets (199-GTO) were employed for both the high level SCF near Hartree-Fock limit and MRSD-CI calculations to investigate the effects of electron correlation and relaxation. 66 refs., 9 tabs., 9 figs

  6. Molecular Structure of Membrane Tethers

    NARCIS (Netherlands)

    Baoukina, Svetlana; Marrink, Siewert J.; Tieleman, D. Peter

    2012-01-01

    Membrane tethers are nanotubes formed by a lipid bilayer. They play important functional roles in cell biology and provide an experimental window on lipid properties. Tethers have been studied extensively in experiments and described by theoretical models, but their molecular structure remains

  7. Modeling of A-DLTS Spectra of MOS Structures

    Directory of Open Access Journals (Sweden)

    Peter Hockicko

    2008-01-01

    Full Text Available Acquisition of basic characteristic of defects has become possible through a wide class of measurement techniqueswhich probe the interface, the near interface, as well as the bulk of semiconductor. Results presented here are basedessentially on the acoustic version of Deep Level Transient Spectroscopy (A-DLTS measurements. This method is based onthe acoustoelectric response effect observed at the interface. The A-DLTS uses the acoustoelectric response signal (ARSproduced by MOS structure interface when a longitudal acoustic wave propagates through a structure. The ARS is extremelysensitive to external conditions of the structure and reflects any changes in the charge distribution connected with chargedtraps. The temperature dependence of ARS after bias voltage step application is investigated and the activation energies andsome other parameters of traps at the insulator – semiconductor interface are determined. The results obtained formArrhenius plots of A-DLTS spectra of selected MOS structures are compared with results obtained from modeling of ADLTS spectra using theoretical model.

  8. Influence of cross-section structure on unfolded neutron spectra

    International Nuclear Information System (INIS)

    Ertek, C.; Vlasov, M.F.; Cross, B.; Smith, P.M.

    1979-01-01

    The influence of cross-section structure on neutron spectra unfolded by multiple foil activation technique, SAND-II case, has been studied. For three reactions with evident structure in neutron cross-section above threshold: 27Al(n,α)24Na, 31P(n,p)31Si and 32S(n,p)32P, two remarkably different sets of evaluated data were selected from the available evaluations; one set of data was ''smooth'', the structure having been averaged over by a smooth curve; the other set was ''sharp'' with structure given in detail. These data were used in unfolding procedure together with other reactions, the same in both cases (as well as input spectra and measured reaction rates). It was found that during unfolding calculations less iteration steps were needed to unfold the neutron flux spectrum with the set of ''sharp'' data. In case of ''smooth'' data it was difficult to obtain an agreement between measured and calculated activity values even by increasing the number of iteration steps. Contrary to expectations, considerable deformation of unfolded neutron flux spectrum has been observed in the case of the ''smooth'' data set. (author)

  9. Properties of Energy Spectra of Molecular Crystals Investigated by Nonlinear Theory

    Science.gov (United States)

    Pang, Xiao-Feng; Zhang, Huai-Wu

    We calculate the quantum energy spectra of molecular crystals, such as acetanilide, by using discrete nonlinear Schrodinger equation, containing various interactions, appropriate to the systems. The energy spectra consist of many energy bands, in each energy band there are a lot of energy levels including some higher excited states. The result of energy spectrum is basically consistent with experimental values obtained by infrared absorption and Raman scattering in acetanilide and can also explain some experimental results obtained by Careri et al. Finally, we further discuss the influences of variously characteristic parameters on the energy spectra of the systems.

  10. Spatial structure of directional wave spectra in hurricanes

    Science.gov (United States)

    Esquivel-Trava, Bernardo; Ocampo-Torres, Francisco J.; Osuna, Pedro

    2015-01-01

    The spatial structure of the wave field during hurricane conditions is studied using the National Data Buoy Center directional wave buoy data set from the Caribbean Sea and the Gulf of Mexico. The buoy information, comprising the directional wave spectra during the passage of several hurricanes, was referenced to the center of the hurricane using the path of the hurricane, the propagation velocity, and the radius of the maximum winds. The directional wave spectra were partitioned into their main components to quantify the energy corresponding to the observed wave systems and to distinguish between wind-sea and swell. The findings are consistent with those found using remote sensing data (e.g., Scanning Radar Altimeter data). Based on the previous work, the highest waves are found in the right forward quadrant of the hurricane, where the spectral shape tends to become uni-modal, in the vicinity of the region of maximum winds. More complex spectral shapes are observed in distant regions at the front of and in the rear quadrants of the hurricane, where there is a tendency of the spectra to become bi- and tri-modal. The dominant waves generally propagate at significant angles to the wind direction, except in the regions next to the maximum winds of the right quadrants. Evidence of waves generated by concentric eyewalls associated with secondary maximum winds was also found. The frequency spectra display some of the characteristics of the JONSWAP spectrum adjusted by Young (J Geophys Res 111:8020, 2006); however, at the spectral peak, the similarity with the Pierson-Moskowitz spectrum is clear. These results establish the basis for the use in assessing the ability of numerical models to simulate the wave field in hurricanes.

  11. Prediction of molecular crystal structures

    International Nuclear Information System (INIS)

    Beyer, Theresa

    2001-01-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol -1 of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  12. Prediction of molecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Beyer, Theresa

    2001-07-01

    The ab initio prediction of molecular crystal structures is a scientific challenge. Reliability of first-principle prediction calculations would show a fundamental understanding of crystallisation. Crystal structure prediction is also of considerable practical importance as different crystalline arrangements of the same molecule in the solid state (polymorphs)are likely to have different physical properties. A method of crystal structure prediction based on lattice energy minimisation has been developed in this work. The choice of the intermolecular potential and of the molecular model is crucial for the results of such studies and both of these criteria have been investigated. An empirical atom-atom repulsion-dispersion potential for carboxylic acids has been derived and applied in a crystal structure prediction study of formic, benzoic and the polymorphic system of tetrolic acid. As many experimental crystal structure determinations at different temperatures are available for the polymorphic system of paracetamol (acetaminophen), the influence of the variations of the molecular model on the crystal structure lattice energy minima, has also been studied. The general problem of prediction methods based on the assumption that the experimental thermodynamically stable polymorph corresponds to the global lattice energy minimum, is that more hypothetical low lattice energy structures are found within a few kJ mol{sup -1} of the global minimum than are likely to be experimentally observed polymorphs. This is illustrated by the results for molecule I, 3-oxabicyclo(3.2.0)hepta-1,4-diene, studied for the first international blindtest for small organic crystal structures organised by the Cambridge Crystallographic Data Centre (CCDC) in May 1999. To reduce the number of predicted polymorphs, additional factors to thermodynamic criteria have to be considered. Therefore the elastic constants and vapour growth morphologies have been calculated for the lowest lattice energy

  13. Electronic structure and photoelectron spectra of boron beta-diketonates

    International Nuclear Information System (INIS)

    Borisenko, A.V.; Vovna, V.I.

    1990-01-01

    Photoelectron spectra and data of semiempirical (MNDO, CNDO/2, CNDO/S, INDO) and nonempirical (with STO-3G basis) methods of calculation were obtained to analyse the electronic structure of boron-containing diketonate cycle and the influence of substitution effect (aromatic substituents in particular) on it. The sequence and the character of upper occupied MO were determined; the nature of bond of the fragment X 2 B + and AA was established; charges of six-membered ion and influence of substituents on their values were determined. 13 refs.; 5 figs.; 4 tabs

  14. Electronic structure and UV spectra of N-arylthio-1,4-benzoquinone imines

    International Nuclear Information System (INIS)

    Pirozhenko, V.V.; Boldeskul, I.E.; Kolesnikov, V.T.; Vid, L.V.; Kuz'menko, L.O.

    1986-01-01

    The electronic structure of N-arylthio-1,4-benzoquinone imines (II) was studied by quantum-chemical methods (CNDO/2). It was shown that the special characteristics of the reactivity of the compounds in reaction with chlorine compared with sulfenylketimines R 2 C=N-S-Ar not containing a quinonoid ring may be due to the different nature of the lowest unoccupied molecular orbitals (LUMO). The UV spectra of compounds (II) were investigated. In the visible region the spectra of all the compounds contain strong absorption (R 1 = R 2 = R 3 = R 4 = R 5 = H, λ/sub m/ = 433 nm, epsilon/sub m/ = 2.12 x 10 4 liters/mole x cm), due to intramolecular charge transfer from the sulfur atom to the quinonoid fragment of the molecule. It was established that there is a linear relation between the energy of the transition and the σ + constants of the substituents in the aryl fragment. The assignment of the transitions was confirmed by calculations of the UV spectra of N-arylthio-1,4-benzoquinone imines by the PPP method. Comparison of the UV spectra of these compounds with the UV spectra of N-arylsulfonyl-1,4-benzoquinone imines makes it possible to conclude that the sulfur atom of the SO 2 group, unlike the divalent sulfur atom, is not capable of transmitting the electronic effects of the substituents from one part of the molecule to the other

  15. X-ray photoelectron spectra structure and chemical bonding in AmO2

    Directory of Open Access Journals (Sweden)

    Teterin Yury A.

    2015-01-01

    Full Text Available Quantitative analysis was done of the X-ray photoelectron spectra structure in the binding energy range of 0 eV to ~35 eV for americium dioxide (AmO2 valence electrons. The binding energies and structure of the core electronic shells (~35 eV-1250 eV, as well as the relativistic discrete variation calculation results for the Am63O216 and AmO8 (D4h cluster reflecting Am close environment in AmO2 were taken into account. The experimental data show that the many-body effects and the multiplet splitting contribute to the spectral structure much less than the effects of formation of the outer (0-~15 eV binding energy and the inner (~15 eV-~35 eV binding energy valence molecular orbitals. The filled Am 5f electronic states were shown to form in the AmO2 valence band. The Am 6p electrons participate in formation of both the inner and the outer valence molecular orbitals (bands. The filled Am 6p3/2 and the O 2s electronic shells were found to make the largest contributions to the formation of the inner valence molecular orbitals. Contributions of electrons from different molecular orbitals to the chemical bond in the AmO8 cluster were evaluated. Composition and sequence order of molecular orbitals in the binding energy range 0-~35 eV in AmO2 were established. The experimental and theoretical data allowed a quantitative scheme of molecular orbitals for AmO2, which is fundamental for both understanding the chemical bond nature in americium dioxide and the interpretation of other X-ray spectra of AmO2.

  16. Vibrational infrared and Raman spectra of polypeptides: Fragments-in-fragments within molecular tailoring approach

    Energy Technology Data Exchange (ETDEWEB)

    Sahu, Nityananda; Gadre, Shridhar R., E-mail: gadre@iitk.ac.in [Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016 (India)

    2016-03-21

    The present work reports the calculation of vibrational infrared (IR) and Raman spectra of large molecular systems employing molecular tailoring approach (MTA). Further, it extends the grafting procedure for the accurate evaluation of IR and Raman spectra of large molecular systems, employing a new methodology termed as Fragments-in-Fragments (FIF), within MTA. Unlike the previous MTA-based studies, the accurate estimation of the requisite molecular properties is achieved without performing any full calculations (FC). The basic idea of the grafting procedure is implemented by invoking the nearly basis-set-independent nature of the MTA-based error vis-à-vis the respective FCs. FIF has been tested out for the estimation of the above molecular properties for three isomers, viz., β-strand, 3{sub 10}- and α-helix of acetyl(alanine){sub n}NH{sub 2} (n = 10, 15) polypeptides, three conformers of doubly protonated gramicidin S decapeptide and trpzip2 protein (PDB id: 1LE1), respectively, employing BP86/TZVP, M06/6-311G**, and M05-2X/6-31G** levels of theory. For most of the cases, a maximum difference of 3 cm{sup −1} is achieved between the grafted-MTA frequencies and the corresponding FC values. Further, a comparison of the BP86/TZVP level IR and Raman spectra of α-helical (alanine){sub 20} and its N-deuterated derivative shows an excellent agreement with the existing experimental spectra. In view of the requirement of only MTA-based calculations and the ability of FIF to work at any level of theory, the current methodology provides a cost-effective solution for obtaining accurate spectra of large molecular systems.

  17. On the effects of transforming the vibrational spectra of molecular systems under microwave radiation

    International Nuclear Information System (INIS)

    Serikov, A.A.

    1993-01-01

    This problem is analyzed within the quantum-classical theory of molecular spectra. It is shown that the above-mentioned spectrum transformation could be, in principle, realized in macromolecular systems with strong interaction, and attention is drawn to the resonance character of the effect. (author). 19 refs., 1 fig

  18. Research Investigation Directed Toward Extending the Useful Range of the Electromagnetic Spectrum. [atomic spectra and electronic structure of alkali metals

    Science.gov (United States)

    Hartmann, S. R.; Happer, W.

    1974-01-01

    The report discusses completed and proposed research in atomic and molecular physics conducted at the Columbia Radiation Laboratory from July 1972 to June 1973. Central topics described include the atomic spectra and electronic structure of alkali metals and helium, molecular microwave spectroscopy, the resonance physics of photon echoes in some solid state systems (including Raman echoes, superradiance, and two photon absorption), and liquid helium superfluidity.

  19. Orbital momentum profiles and binding energy spectra for the complete valence shell of molecular fluorine

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Y.; Brion, C.E. [British Columbia Univ., Vancouver, BC (Canada). Dept. of Chemistry; Brunger, M.J.; Zhao, K.; Grisogono, A.M.; Braidwood, S.; Weigold, E. [Flinders Univ. of South Australia, Adelaide, SA (Australia). Electronic Structure of Materials Centre; Chakravorty, S.J.; Davidson, E.R. [Indiana Univ., Bloomington, IN (United States). Dept. of Chemistry; Sgamellotti, A. [Univ di Perugia (Italy). Dipartimento di Chimica; von Niessen, W. [Technische Univ. Braunschweig (Germany). Inst fuer Physikalische

    1996-01-01

    The first electronic structural study of the complete valence shell binding energy spectrum of molecular fluorine, encompassing both the outer and inner valence regions, is reported. These binding energy spectra as well as the individual orbital momentum profiles have been measured using an energy dispersive multichannel electron momentum spectrometer at a total energy of 1500 eV, with an energy resolution of 1.5 eV and a momentum resolution of 0.1 a.u. The measured binding energy spectra in the energy range of 14-60 eV are compared with the results of ADC(4) many-body Green`s function and also direct-Configuration Interaction (CI) and MRSD-CI calculations. The experimental orbital electron momentum profiles are compared with SCF theoretical profiles calculated using the target Hartree-Fock approximation with a range of basis sets and with Density Functional Theory predictions in the target Kohn-Sham approximation with non-local potentials. The truncated (aug-cc-pv5z) Dunning basis sets were used for the Density Functional Theory calculations which also include some treatment of correlation via the exchange and correlation potentials. Comparisons are also made with the full ion-neutral overlap amplitude calculated with MRSD-CI wave functions. Large, saturated basis sets (199-GTO) were employed for both the high level SCF near Hartree-Fock limit and MRSD-CI calculations to investigate the effects of electron correlation and relaxation. 66 refs., 9 tabs., 9 figs.

  20. Regio-Regular Oligo and Poly(3-hexyl thiophene): Precise Structural Markers from the Vibrational Spectra of Oligomer Single Crystals.

    KAUST Repository

    Brambilla, Luigi

    2014-10-14

    © 2014 American Chemical Society. In this work, we report a comparative analysis of the infrared and Raman spectra of octa(3-hexylthiophene) (3HT)8, trideca(3-hexylthiophene) (3HT)13, and poly(3-hexylthiophene) P3HT recorded in various phases, namely, amorphous, semicrystalline, polycrystalline and single crystal. We have based our analysis on the spectra of the (3HT)8 single crystal (whose structure has been determined by selected area electron diffraction) taken as reference and on the results of DFT calculations and molecular vibrational dynamics. New and precise spectroscopic markers of the molecular structures show the existence of three phases, namely: hairy (phase 1), ordered (phase 2), and disordered/amorphous (phase 3). Conceptually, the identified markers can be used for the molecular structure analysis of other similar systems.

  1. Ab initio and DFT studies of the structure and vibrational spectra of anhydrous caffeine

    Science.gov (United States)

    Srivastava, Santosh K.; Singh, Vipin B.

    2013-11-01

    Vibrational spectra and molecular structure of anhydrous caffeine have been systematically investigated by second order Moller-Plesset (MP2) perturbation theory and density functional theory (DFT) calculations. Vibrational assignments have been made and many previous ambiguous assignments in IR and Raman spectra are amended. The calculated DFT frequencies and intensities at B3LYP/6-311++G(2d,2p) level, were found to be in better agreement with the experimental values. It was found that DFT with B3LYP functional predicts harmonic vibrational wave numbers more close to experimentally observed value when it was performed on MP2 optimized geometry rather than DFT geometry. The calculated TD-DFT vertical excitation electronic energies of the valence excited states of anhydrous caffeine are found to be in consonance to the experimental absorption peaks.

  2. Photoelectron spectra and electronic structure of β-diketonates of p- and d-elements

    International Nuclear Information System (INIS)

    Vovna, V.I.; Andreev, V.A.; Cherednichenko, A.I.

    1990-01-01

    Consideration is given to results of studying electronic structure of β-diketonates of metals and β-diketones by the method of gas-phase photoelectron spectroscopy. Manifestation of covalence of metal-ligand bonds in PE spectra and change of covalence in series and groups of d-elements of the periodic table are analysed. It is shown that ionization energy of outer valence electrons doesn't reflect in all cases effective charges of ligands, due to the influence of molecular potential. 35 refs.; 7 figs.; 12 tabs

  3. Vibronic-structure tracking: A shortcut for vibrationally resolved UV/Vis-spectra calculations

    Energy Technology Data Exchange (ETDEWEB)

    Barton, Dennis; König, Carolin; Neugebauer, Johannes, E-mail: j.neugebauer@uni-muenster.de [Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster (Germany)

    2014-10-28

    The vibrational coarse structure and the band shapes of electronic absorption spectra are often dominated by just a few molecular vibrations. By contrast, the simulation of the vibronic structure even in the simplest theoretical models usually requires the calculation of the entire set of normal modes of vibration. Here, we exploit the idea of the mode-tracking protocol [M. Reiher and J. Neugebauer, J. Chem. Phys. 118, 1634 (2003)] in order to directly target and selectively calculate those normal modes which have the largest effect on the vibronic band shape for a certain electronic excitation. This is achieved by defining a criterion for the importance of a normal mode to the vibrational progressions in the absorption band within the so-called “independent mode, displaced harmonic oscillator” (IMDHO) model. We use this approach for a vibronic-structure investigation for several small test molecules as well as for a comparison of the vibronic absorption spectra of a truncated chlorophyll a model and the full chlorophyll a molecule. We show that the method allows to go beyond the often-used strategy to simulate absorption spectra based on broadened vertical excitation peaks with just a minimum of computational effort, which in case of chlorophyll a corresponds to about 10% of the cost for a full simulation within the IMDHO approach.

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

    International Nuclear Information System (INIS)

    Pentlehner, D.; Slenczka, A.

    2015-01-01

    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 broad (Δν > 100 cm −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

  5. Effects of phonon broadening on x-ray near-edge spectra in molecular crystals

    Science.gov (United States)

    Vinson, John; Jach, Terrence; Elam, Tim; Denlinger, Jonathon

    2014-03-01

    Calculations of near-edge x-ray spectra are often carried out using the average atomic coordinates from x-ray or neutron scattering experiments or from density functional theory (DFT) energy minimization. This neglects disorder from thermal and zero-point vibrations. Here we look at the nitrogen K-edge of ammonium chloride and ammonium nitrate, comparing Bethe-Salpeter calculations of absorption and fluorescence to experiment. We find that intra-molecular vibrational effects lead to significant, non-uniform broadening of the spectra, and that for some features zero-point motion is the primary source of the observed shape.

  6. The geometric content of the interacting boson model for molecular spectra

    International Nuclear Information System (INIS)

    Levit, S.; Smilansky, U.

    1981-12-01

    The recently proposed algebraic model for collective spectra of diatomic molecules is analysed in terms of conventional geometrical degrees of freedom. We present a mapping of the algebraic Hamiltonian onto an exactly solvable geometrical Hamiltonian with the Morse potential. This mapping explains the success of the algebraic model in reproducing the low lying part of molecular spectra. At the same time the mapping shows that the expression for the dipole transition operator in terms of boson operators differs from the simplest IBM expression and in general must include many-body boson terms. The study also provides an insight into the problem of possible interpretations of the bosons in the nuclear IBM. (author)

  7. CSMB | Center For Structural Molecular Biology

    Data.gov (United States)

    Federal Laboratory Consortium — The Center for Structural Molecular Biologyat ORNL is dedicated to developing instrumentation and methods for determining the 3-dimensional structures of proteins,...

  8. Uncertainties of Molecular Structural Parameters

    International Nuclear Information System (INIS)

    Császár, Attila G.

    2014-01-01

    performed. Simply, there are significant disagreements between the same bond lengths measured by different techniques. These disagreements are, however, systematic and can be computed via techniques of quantum chemistry which deal not only with the motions of the electrons (electronic structure theory) but also with the often large amplitude motions of the nuclei. As to the relevant quantum chemical computations, since about 1970 electronic structure theory has become able to make quantitative predictions and thus challenge (or even overrule) many experiments. Nevertheless, quantitative agreement of quantum chemical results with experiment can only be expected when the motions of the atoms are also considered. In the fourth age of quantum chemistry we are living in an era where one can bridge quantitatively the gap between ‘effective’, experimental and ‘equilibrium’, computed structures at even elevated temperatures of interest thus minimizing any real uncertainties of structural parameters. The connections mentioned are extremely important as they help to understand the true uncertainty of measured structural parameters. Traditionally it is microwave (MW) and millimeterwave (MMW) spectroscopy, as well as gas-phase electron diffraction (GED), which yielded the most accurate structural parameters of molecules. The accuracy of the MW and GED experiments approached about 0.001Å and 0.1º under ideal circumstances, worse, sometimes considerably worse, in less than ideal and much more often encountered situations. Quantum chemistry can define both highly accurate equilibrium (so-called Born-Oppenheimer, r_e"B"O, and semiexperimental, r_e"S"E) structures and, via detailed investigation of molecular motions, accurate temperature-dependent rovibrationally averaged structures. Determining structures is still a rich field for research, understanding the measured or computed uncertainties of structures and structural parameters is still a challenge but there are firm and well

  9. Restricted active space calculations of L-edge X-ray absorption spectra: from molecular orbitals to multiplet states.

    Science.gov (United States)

    Pinjari, Rahul V; Delcey, Mickaël G; Guo, Meiyuan; Odelius, Michael; Lundberg, Marcus

    2014-09-28

    The metal L-edge (2p → 3d) X-ray absorption spectra are affected by a number of different interactions: electron-electron repulsion, spin-orbit coupling, and charge transfer between metal and ligands, which makes the simulation of spectra challenging. The core restricted active space (RAS) method is an accurate and flexible approach that can be used to calculate X-ray spectra of a wide range of medium-sized systems without any symmetry constraints. Here, the applicability of the method is tested in detail by simulating three ferric (3d(5)) model systems with well-known electronic structure, viz., atomic Fe(3+), high-spin [FeCl6](3-) with ligand donor bonding, and low-spin [Fe(CN)6](3-) that also has metal backbonding. For these systems, the performance of the core RAS method, which does not require any system-dependent parameters, is comparable to that of the commonly used semi-empirical charge-transfer multiplet model. It handles orbitally degenerate ground states, accurately describes metal-ligand interactions, and includes both single and multiple excitations. The results are sensitive to the choice of orbitals in the active space and this sensitivity can be used to assign spectral features. A method has also been developed to analyze the calculated X-ray spectra using a chemically intuitive molecular orbital picture.

  10. Capturing molecular multimode relaxation processes in excitable gases based on decomposition of acoustic relaxation spectra

    Science.gov (United States)

    Zhu, Ming; Liu, Tingting; Wang, Shu; Zhang, Kesheng

    2017-08-01

    Existing two-frequency reconstructive methods can only capture primary (single) molecular relaxation processes in excitable gases. In this paper, we present a reconstructive method based on the novel decomposition of frequency-dependent acoustic relaxation spectra to capture the entire molecular multimode relaxation process. This decomposition of acoustic relaxation spectra is developed from the frequency-dependent effective specific heat, indicating that a multi-relaxation process is the sum of the interior single-relaxation processes. Based on this decomposition, we can reconstruct the entire multi-relaxation process by capturing the relaxation times and relaxation strengths of N interior single-relaxation processes, using the measurements of acoustic absorption and sound speed at 2N frequencies. Experimental data for the gas mixtures CO2-N2 and CO2-O2 validate our decomposition and reconstruction approach.

  11. An analytic approach to 2D electronic PE spectra of molecular systems

    International Nuclear Information System (INIS)

    Szoecs, V.

    2011-01-01

    Graphical abstract: The three-pulse photon echo (3P-PE) spectra of finite molecular systems using direct calculation from electronic Hamiltonians allows peak classification from 3P-PE spectra dynamics. Display Omitted Highlights: → RWA approach to electronic photon echo. → A straightforward calculation of 2D electronic spectrograms in finite molecular systems. → Importance of population time dynamics in relation to inter-site coherent coupling. - Abstract: The three-pulse photon echo (3P-PE) spectra of finite molecular systems and simplified line broadening models is presented. The Fourier picture of a heterodyne detected three-pulse rephasing PE signal in the δ-pulse limit of the external field is derived in analytic form. The method includes contributions of one and two-excitonic states and allows direct calculation of Fourier PE spectrogram from corresponding Hamiltonian. As an illustration, the proposed treatment is applied to simple systems, e.g. 2-site two-level system (TLS) and n-site TLS model of photosynthetic unit. The importance of relation between Fourier picture of 3P-PE dynamics (corresponding to nonzero population time, T) and coherent inter-state coupling is emphasized.

  12. Vulnerability and floor spectra of seismically isolated structures

    International Nuclear Information System (INIS)

    Pham, K.H.

    2010-09-01

    This thesis was motivated by issues that arise regarding the use of the method of seismic isolation in the nuclear industry. Despite the research conducted during the last decades in the field of seismic isolation, many questions about the behavior of isolated structures remain. These questions concern, on the one hand, the vulnerability of these structures, due to an excursion (unexpected) in the post-linear domain, and on the other hand, phenomena that can lead to a significant excitation of none isolated modes. Furthermore, unlike previous work studying the seismic behavior of buildings, an important part of this thesis is devoted to the behavior of equipment through the study of floor spectra. Firstly, the probability of failure, in the case of nonlinear response of the superstructure, was studied with simple models, for different laws of nonlinear behavior and different types of support. Then, the effects of heavy damping were investigated and the mechanism of amplification of the response of non-isolated modes has been explained. To resolve the amplification problem of none isolated modes, the mixed isolated systems, combining passive isolation with semi-active devices, have been considered. The numerical analyses confirm the effectiveness of this approach. Finally, a series of shaking table tests on a simple model with two degrees of freedom was conducted. The model is equipped with a magneto-rheological damper which is controlled as a semi-active device. The comparison of the experimental results with those of numerical simulations shows that the models developed are able to represent satisfactorily the essential physical phenomena. (author)

  13. Molecular structure and vibrational spectroscopy of isoproturon

    Science.gov (United States)

    Vrielynck, L.; Dupuy, N.; Kister, J.; Nowogrocki, G.

    2006-05-01

    The crystal structure of isoproturon [ N-(4-isopropylphenyl)- N', N'-dimethylurea] has been determined: the compound crystallizes in the space group Pbca with unit cell parameters a=10.186(2) Å, b=11.030(2) Å, c=20.981(4) Å. The structure was solved and refined down to R1=0.0508 and ωR2=0.12470 for 3056 reflections. The crystalline molecular network of this pesticide is stabilized, as for many molecules of the same family, by π-π interactions but especially by a medium-strong N-H⋯C dbnd6 O intermolecular hydrogen bond (2.14 Å). The X-ray parameters were then compared with the results of DFT quantum chemical calculation computed with the GAUSSIAN 94 package. A tentative assignment of the ATR-FT-IR and Raman spectra was proposed supported by vibrational mode calculation and spectroscopic data on benzenic and urea derivatives available in the literature. The presence of a tight band around 3300 cm -1, which can be assigned to the NH bond stretching mode as well as the low frequency position of the amide I band at 1640 cm -1, sensitive to solvent polarity, confirms the existence of a quite strong intermolecular hydrogen bond between neighboring molecules in the crystal of isoproturon.

  14. Crystal structure, vibrational spectra and DFT studies of hydrogen bonded 1,2,4-triazolium hydrogenselenate

    Science.gov (United States)

    Arjunan, V.; Thirunarayanan, S.; Marchewka, M. K.; Mohan, S.

    2017-10-01

    The new hydrogen bonded molecular complex 1,2,4-triazolium hydrogenselenate (THS) is prepared by the reaction of 1H-1,2,4-triazole and selenic acid. This complex is stabilised by N-H⋯O and C-H⋯O hydrogen bonding and electrostatic attractive forces between 1H and 1,2,4-triazolium cations and hydrogen selenate anions. The XRD studies revealed that intermolecular proton transfer occur from selenic acid to 1H-1,2,4-triazole molecule, results in the formation of 1,2,4-triazolium hydrogenselenate which contains 1,2,4-triazolium cations and hydrogenselenate anions. The molecular structure of THS crystal has also been optimised by using Density Functional Theory (DFT) using B3LYP/cc-pVTZ and B3LYP/6-311++G** methods in order to find the whole characteristics of the molecular complex. The theoretical structural parameters such as bond length, bond angle and dihedral angle determined by DFT methods are well agreed with the XRD parameters. The atomic charges and thermodynamic properties are also calculated and analysed. The energies of frontier molecular orbitals HOMO, LUMO, HOMO-1, LUMO+1 and LUMO-HUMO energy gap are calculated to understand the kinetic stability and chemical reactivity of the molecular complex. The natural bond orbital analysis (NBO) has been performed in order to study the intramolecular bonding interactions and delocalisation of electrons. These intra molecular charge transfer may induce biological activities such as antimicrobials, antiinflammatory, antifungal etc. The complete vibrational assignments of THS have been performed by using FT-IR and FT-Raman spectra.

  15. Application of the generalized multi structural (GMS) wave function to photoelectron spectra and electron scattering processes

    International Nuclear Information System (INIS)

    Nascimento, M.A.C. do

    1992-01-01

    A Generalized Multi Structural (GMS) wave function is presented which combines the advantages of the SCF-MO and VB models, preserving the classical chemical structures but optimizing the orbitals in a self-consistent way. This wave function is particularly suitable to treat situations where the description of the molecular state requires localized wave functions. It also provides a very convenient way of treating the electron correlation problem, avoiding large CI expansions. The final wave functions are much more compact and easier to interpret than the ones obtained by the conventional methods, using orthogonal orbitals. Applications of the GMS wave function to the study of the photoelectron spectra of the trans-glyoxal molecule and to electron impact excitation processes in the nitrogen molecule are presented as an illustration of the method. (author)

  16. Theoretically predicted soft x-ray emission and absorption spectra of graphitic-structured BC2N

    Science.gov (United States)

    Muramatsu, Yasuji

    Theoretical B K, C K and N K x-ray emission/absorption spectra of three possible graphitic-structured BC2N clusters are predicted based on the B2p-, C2p-, and N2p- density-of-states (DOS) calculated by discrete variational (DV)-X[alpha] molecular orbital calculations. Several prominent differences in DOS spectral features among BC2Ns, h-BN, and graphite are confirmed from comparison of calculated B2p-, C2p-, and N2p-DOS spectra. These variations in the spectra allow BC2N structures to be positively identified by high-resolution x-ray emission/absorption spectroscopy in the B K, C K, and N K regions.

  17. The effects of soil-structure interaction modeling techniques on in-structure response spectra

    International Nuclear Information System (INIS)

    Johnson, J.J.; Wesley, D.A.; Almajan, I.T.

    1977-01-01

    The structure considered for this investigation consisted of the reactor containment building (RCB) and prestressed concrete reactor vessel (PCRV) for a HTGR plant. A conventional lumped-mass dynamic model in three dimensions was used in the study. The horizontal and vertical response, which are uncoupled due to the symmetry of the structure, were determined for horizontal and vertical excitation. Five different site conditions ranging from competent rock to a soft soil site were considered. The simplified approach to the overall plant analysis utilized stiffness proportional composite damping with a limited amount of soil damping consistent with US NRC regulatory guidelines. Selected cases were also analyzed assuming a soil damping value approximating the theoretical value. The results from the simplified approach were compared to those determined by rigorously coupling the structure to a frequency independent half-space representation of the soil. Finally, equivalent modal damping ratios were found by matching the frequency response at a point within the coupled soil-structure system determined by solution of the coupled and uncoupled equations of motion. The basis for comparison of the aforementioned techniques was the response spectra at selected locations within the soil-structure system. Each of the five site conditions was analyzed and in-structure response spectra were generated. The response spectra were combined to form a design envelope which encompasses the entire range of site parameters. Both the design envelopes and the site-by-site results were compared

  18. FTIR and FT-Raman spectra and density functional computations of the vibrational spectra, molecular geometry and atomic charges of the biomolecule: 5-bromouracil

    Czech Academy of Sciences Publication Activity Database

    Rastogi, V.K.; Palafox, M. A.; Mittal, L.; Peica, N.; Keifer, W.; Lang, Kamil; Ojha, S.P.

    2007-01-01

    Roč. 38, č. 10 (2007), s. 1227-1241 ISSN 0377-0486 Institutional research plan: CEZ:AV0Z40320502 Keywords : FTIR and FT-Raman spectra * density functional computations * molecular geometry Subject RIV: CA - Inorganic Chemistry Impact factor: 3.514, year: 2007

  19. Structures in semiclassical spectra: a question of scale

    International Nuclear Information System (INIS)

    Berry, M.V.

    1984-01-01

    Theories of semiclassical bound state spectra for systems with N freedoms are reviewed, emphasizing the different features occurring on successively finer scales of energy E, measured in terms of h/2π, and attempting to correlate these with whether the underlying classical motion is regular or irregular. (Auth.)

  20. Hydrostatic pressure and temperature effect on the Raman spectra of the molecular crystal 2-amine-1,3,4-thiadiazole

    Science.gov (United States)

    de Toledo, T. A.; da Costa, R. C.; Bento, R. R. F.; Pizani, P. S.

    2018-03-01

    The structural, thermal and vibrational properties of the molecular crystal 2-amine-1,3,4-thiadiazole (ATD) were investigated combining X-ray diffraction, infrared spectroscopy, Raman scattering (in solid and in solution) and thermal analysis as experimental techniques and first principle calculations based on density functional theory using PZ, BLYP in condensed-phase and B3LYP/cc-pVTZ in isolated molecule methods. The structural stability and phonon anharmonicity were also studied using Raman spectroscopy at different temperatures and hydrostatic pressures. A reasonable agreement was obtained between calculated and experimental results. The main difference between experimental and computed structural and vibrational spectra occurred in the intermolecular bond distance Nsbnd H⋯N and stretching modes of NH2. The vibrational spectra were interpreted and assigned based on group theory and functional group analysis assisted by theoretical results, which led to a more comprehensive knowledge about external and internal modes at different thermodynamic conditions. As temperature increases, it was observed the line-width increases and red-shifts, indicating a phonon anharmonicity without a temperature-induced phase transition in the range 10-413 K. However, ATD crystal undergoes a phase transition in the temperature range 413-475 K, as indicated by thermal analysis curve and Raman spectra. Furthermore, increasing pressure from ambient to 3.1 GPa, it was observed the splitting of the external Raman bands centered at 122 cm-1 (at 0.2 GPa), 112 cm-1 (1.1 GPa), 93 cm-1 (2.4 GPa) in two components as well as the appearance of new band near 50 cm-1 at 1.1 GPa, indicating a possible phase-transition. The blue-shift of the Raman bands was associated to anharmonicity of the interatomic potential caused by unit cell contraction.

  1. VizieR Online Data Catalog: Sgr B2 los molecular absorption line spectra (Corby+, 2018)

    Science.gov (United States)

    Corby, J. F.; McGuire, B. A.; Herbst, E.; Remijan, A. J.

    2017-11-01

    Spectra covering transitions of c-C3H2, c-H1 SO, CCS, H2CS, HCS+, OH, SiO, 29SiO, H2CO, H2(13C)O, l-C3H, and l-C3H+ with line-of-sight absorption observed in the 1-50 GHz data from the PRebiotic Interstellar MOlecular Survey (PRIMOS) taken with the Robert C. Byrd Green Bank Telescope (GBT). Data were observed between 2001 and 2014, with the majority of the data obtained in 2007 in GBT Key Science project ID GBT07A-051. Spectra have been baseline-subtracted using best fit polynomials as described in the paper, and normalized by the continuum, so that the y-axis represents (T/TC-1). Data are provided in the FITS format; each FITS file contains all lines of a single molecule that are observed to have foreground absorption. Please refer to Table 1 of the paper to obtain molecular transition rest frequencies, energies, GBT beam sizes, and transition quantum numbers. (2 data files).

  2. Qualitative features of the rearrangement of molecular energy spectra from a “wall-crossing” perspective

    Energy Technology Data Exchange (ETDEWEB)

    Iwai, T., E-mail: iwai@amp.i.kyoto-u.ac.jp [Kyoto University, Kyoto (Japan); Zhilinskii, B., E-mail: zhilin@univ-littoral.fr [Université du Littoral Côte d' Opale, 59140 Dunkerque (France)

    2013-11-15

    Qualitatively different systems of molecular energy bands are studied on example of a parametric family of effective Hamiltonians describing rotational structure of triply degenerate vibrational state of a cubic symmetry molecule. The modification of band structure under variation of control parameters is associated with a topological invariant “delta-Chern”. This invariant is evaluated by using a local Hamiltonian for the control parameter values assigned at the boundary between adjacent parameter domains which correspond to qualitatively different band structures.

  3. Experimental and theoretical study on the structure and vibrational spectra of β-2-aminopyridinium dihydrogenphosphate

    Science.gov (United States)

    Çırak, Çağrı; Demir, Selçuk; Ucun, Fatih; Çubuk, Osman

    2011-08-01

    Experimental and theoretical vibrational spectra of β-2-aminopyridinium dihydrogenphosphate (β-2APDP) have been investigated. The FT-IR spectrum of β-2APDP was recorded in the region 4000-400 cm -1. The optimized molecular structure and theoretical vibrational frequencies of β-2APDP have been investigated using ab initio Hartree-Fock (HF) and density functional B3LYP method with 6-311++G(d,p) basis set. The optimized geometric parameters (bond lengths and bond angles) and theoretical frequencies have been compared with the corresponding experimental data and it is found that they agree well with each other. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program. Furthermore, the used scale factors were obtained from the ratio of the frequency values of the strongest peaks in the experimental and theoretical IR spectra. From the results it was concluded that the B3LYP method is superior to the HF method for the vibrational frequencies.

  4. MOLECULAR STRUCTURE AND VIBRATIONAL FREQUENCIES OF

    Directory of Open Access Journals (Sweden)

    Fatih UCUN

    2009-02-01

    Full Text Available Abstract: The molecular structure, vibrational frequencies and the corresponding assignments of N-aminophthalimide (NAPH in the ground state have been calculated using the Hartree-Fock (HF and density functional methods (B3LYP with 6-31G (d, p basis set. The calculations were utilized in the CS symmetry of NAPH. The obtained vibrational frequencies and optimized geometric parameters (bond lengths and bond angles were seen to be in good agreement with the experimental data. The comparison of the observed and calculated results showed that B3LYP is superior to the scaled HF method. Theoretical infrared intensities and Raman activities were also reported. Key words: N-aminophthalimide; vibrations; IR spectra; Raman spectra; HF; DFT N-AMİNOFİTALOMİD'İN MOLEKÜLER YAPISI VE TİTREŞİM FREKANSLARI Özet: Temel haldeki N-aminofitalamidin (NAPH moleküler yapısı, titreşim frekansları ve uygun mod tanımlamaları, 6-31 G (d, p temel setli Hartree-Fock (HF ve yoğunluk fonksiyonu metodları (B3LYP kullanılarak hesaplandı. Hesaplamalar, NAPH'ın CS simetrisine uyarlandı. Elde edilen titreşim frekansları ve optimize geometrik parametreleri (bağ uzunlukları ve bağ açıları, deneysel değerlerle iyi bir uyum içinde olduğu görüldü. Deneysel ve teorik sonuçların karşılaştırılması, B3LYP'nin HF metodundan daha üstün olduğunu gösterdi. Ayrıca teorik infrared şiddetleri ve Raman aktiviteleri verildi. Anahtar Kelimeler: N-aminofitalamidin; titreşimler; IR spektrumu; Raman Spektrumu; HF; DFT

  5. Simulation of the energy spectra of original versus recombined H2+ molecular ions transmitted through thin foils

    International Nuclear Information System (INIS)

    Barriga-Carrasco, Manuel D.; Garcia-Molina, Rafael

    2004-01-01

    This work presents the results of computer simulations for the energy spectra of original versus recombined H 2 + molecular ions transmitted through thin amorphous carbon foils, for a broad range of incident energies. A detailed description of the projectile motion through the target has been done, including nuclear scattering and Coulomb repulsion as well as electronic self-retarding and wake forces; the two latter are calculated in the dielectric formalism framework. Differences in the energy spectra of recombined and original transmitted H 2 + molecular ions clearly appear in the simulations, in agreement with the available experimental data. Our simulation code also differentiates the contributions due to original and to recombined H 2 + molecular ions when the energy spectra contain both contributions, a feature that could be used for experimental purposes in estimating the ratio between the number of original and recombined H 2 + molecular ions transmitted through thin foils

  6. Synthesis, molecular structure, spectroscopic investigations and ...

    Indian Academy of Sciences (India)

    MS received 29 December 2015; revised 9 April 2016; accepted 25 May 2016 ... B, open form blue. Scheme 1. Structures and Photochromic reaction of the title compound. 2. Experimental. 2.1 Materials and measurements. The mid-IR spectra were obtained in the ... segment is put between two parallel Au(111) surfaces,.

  7. Vibrational spectra of solid solution series with ordered perovskite structure

    NARCIS (Netherlands)

    Blasse, G.

    I.R. and Raman spectra are reported for the following three systems: Ba2CaMo1−xTexO6, Ba2−xSrxMgWO6 and Ba2Ca1−xMgxWO6. In the first series the internal vibrations of the M6+O6 octahedra do not influence each other. The intensity of ν1 (MoO6) is five times that of ν1 (TeO6). In the second system

  8. Emission spectra of gaseous avalanches and their time structure

    International Nuclear Information System (INIS)

    Fraga, M.M.; Lima, E.P. de; Marques, R.F.; Policarpo, A.J.P.L.; Alves, M.A.F.; Salete, M.; Leite, S.C.P.

    1993-01-01

    Following previous measurements in argon/methane mixtures, the authors now report on the emission spectra of argon/ethane and methane/ethane mixtures, in the region from 120 to 450 nm, for a single wire chamber working in the proportional and/or self-quenching streamer modes. Identification of radicals and fragments is attempted. The time evolution of VUV light, relevant to photon feedback processes, is presented for the CI lines at 156.1 and 165.7nm in argon/methane, argon/ethane and methane/ethane mixtures

  9. Crystal structures and photoelectron spectra of some trimethanoanthracenes, tetramethanonaphthacenes, and pentamethanopentacenes. Experimental evidence for laticyclic hyperconjugation

    DEFF Research Database (Denmark)

    Paddon-Row, Michael N.; Englehardt, Lutz M.; Skelton, Brian W.

    1987-01-01

    Photoelectron (p.e.) spectra of the series of dienes (), (), ()-(), and crystal structures for the dodecachlorodienes()-() are reported. The spectra revealed large [small pi]-splitting energies of 0.32 and 0.52 eV for () and () respectively. The value of () is attributed to the presence of orbita...

  10. Spectral Barcoding of Quantum Dots: Deciphering Structural Motifs from the Excitonic Spectra

    International Nuclear Information System (INIS)

    Mlinar, V.; Zunger, A.

    2009-01-01

    Self-assembled semiconductor quantum dots (QDs) show in high-resolution single-dot spectra a multitude of sharp lines, resembling a barcode, due to various neutral and charged exciton complexes. Here we propose the 'spectral barcoding' method that deciphers structural motifs of dots by using such barcode as input to an artificial-intelligence learning system. Thus, we invert the common practice of deducing spectra from structure by deducing structure from spectra. This approach (i) lays the foundation for building a much needed structure-spectra understanding for large nanostructures and (ii) can guide future design of desired optical features of QDs by controlling during growth only those structural motifs that decide given optical features.

  11. A hysteresis phenomenon in NMR spectra of molecular nanomagnets Fe8: a resonant quantum tunneling system

    Science.gov (United States)

    Yamasaki, Tomoaki; Ueda, Miki; Maegawa, Satoru

    2003-05-01

    A molecular nanomagnet Fe8 with a total spin S=10 in the ground state attracts much attention as a substance which exhibits the quantum tunneling of magnetization below 300 mK. We performed 1H NMR measurements for a single crystal of Fe8 in temperature range between 20 and 800 mK. The spectra below 300 mK strongly depend on the sequence of the applied field and those in the positive and negative fields are not symmetric about zero field, while they are symmetric above 300 mK. We discuss the origin of this hysteresis phenomenon, relating to the initial spin state of molecules, the resonant quantum tunneling and the nuclear spin relaxation process.

  12. A hysteresis phenomenon in NMR spectra of molecular nanomagnets Fe8: a resonant quantum tunneling system

    International Nuclear Information System (INIS)

    Yamasaki, Tomoaki; Ueda, Miki; Maegawa, Satoru

    2003-01-01

    A molecular nanomagnet Fe8 with a total spin S=10 in the ground state attracts much attention as a substance which exhibits the quantum tunneling of magnetization below 300 mK. We performed 1 H NMR measurements for a single crystal of Fe8 in temperature range between 20 and 800 mK. The spectra below 300 mK strongly depend on the sequence of the applied field and those in the positive and negative fields are not symmetric about zero field, while they are symmetric above 300 mK. We discuss the origin of this hysteresis phenomenon, relating to the initial spin state of molecules, the resonant quantum tunneling and the nuclear spin relaxation process

  13. Communications: On artificial frequency shifts in infrared spectra obtained from centroid molecular dynamics: Quantum liquid water

    Science.gov (United States)

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

    2010-01-01

    Centroid molecular dynamics (CMD) is a popular method to extract approximate quantum dynamics from path integral simulations. Very recently we have shown that CMD gas phase infrared spectra exhibit significant artificial redshifts of stretching peaks, due to the so-called "curvature problem" imprinted by the effective centroid potential. Here we provide evidence that for condensed phases, and in particular for liquid water, CMD produces pronounced artificial redshifts for high-frequency vibrations such as the OH stretching band. This peculiar behavior intrinsic to the CMD method explains part of the unexpectedly large quantum redshifts of the stretching band of liquid water compared to classical frequencies, which is improved after applying a simple and rough "harmonic curvature correction."

  14. kspectrum: an open-source code for high-resolution molecular absorption spectra production

    International Nuclear Information System (INIS)

    Eymet, V.; Coustet, C.; Piaud, B.

    2016-01-01

    We present the kspectrum, scientific code that produces high-resolution synthetic absorption spectra from public molecular transition parameters databases. This code was originally required by the atmospheric and astrophysics communities, and its evolution is now driven by new scientific projects among the user community. Since it was designed without any optimization that would be specific to any particular application field, its use could also be extended to other domains. kspectrum produces spectral data that can subsequently be used either for high-resolution radiative transfer simulations, or for producing statistic spectral model parameters using additional tools. This is a open project that aims at providing an up-to-date tool that takes advantage of modern computational hardware and recent parallelization libraries. It is currently provided by Méso-Star (http://www.meso-star.com) under the CeCILL license, and benefits from regular updates and improvements. (paper)

  15. Sharp Absorption Peaks in THz Spectra Valuable for Crystal Quality Evaluation of Middle Molecular Weight Pharmaceuticals

    Science.gov (United States)

    Sasaki, Tetsuo; Sakamoto, Tomoaki; Otsuka, Makoto

    2018-05-01

    Middle molecular weight (MMW) pharmaceuticals (MW 400 4000) are attracting attention for their possible use in new medications. Sharp absorption peaks were observed in MMW pharmaceuticals at low temperatures by measuring with a high-resolution terahertz (THz) spectrometer. As examples, high-resolution THz spectra for amoxicillin trihydrate, atorvastatin calcium trihydrate, probucol, and α,β,γ,δ-tetrakis(1-methylpyridinium-4-yl)porphyrin p-toluenesulfonate (TMPyP) were obtained at 10 K. Typically observed as peaks with full width at half-height (FWHM) values as low as 5.639 GHz at 0.96492 THz in amoxicillin trihydrate and 8.857 GHz at 1.07974 THz for probucol, many sharp peaks of MMW pharmaceuticals could be observed. Such narrow absorption peaks enable evaluation of the crystal quality of MMW pharmaceuticals and afford sensitive detection of impurities.

  16. Crystal structure and vibrational spectra of melaminium arsenate

    Science.gov (United States)

    Anbalagan, G.; Marchewka, M. K.; Pawlus, K.; Kanagathara, N.

    2015-01-01

    The crystals of the new melaminium arsenate (MAS) [C3H7N6+ṡH2AsO4-] were obtained by the slow evaporation of an aqueous solution at room temperature. Single crystal X-ray diffraction analysis reveals that the crystal belongs to triclinic system with centro symmetric space group P-1. The crystals are built up from single protonated melaminium residues and single dissociated arsenate H2AsO4- anions. The protonated melaminium ring is almost planar. A combination of ionic and donor-acceptor hydrogen-bond interactions linking together the melaminium and arsenate residues forms a three-dimensional network. Vibrational spectroscopic analysis is reported on the basis of FT-IR and FT-Raman spectra recorded at room temperature. Hydrogen bonded network present in the crystal gives notable vibrational effect. DSC has also been performed for the crystal shows no phase transition in the studied temperature range (113-293 K).

  17. Large Molecule Structures by Broadband Fourier Transform Molecular Rotational Spectroscopy

    Science.gov (United States)

    Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

    2016-06-01

    Fourier transform molecular rotational resonance spectroscopy (FT-MRR) using pulsed jet molecular beam sources is a high-resolution spectroscopy technique that can be used for chiral analysis of molecules with multiple chiral centers. The sensitivity of the molecular rotational spectrum pattern to small changes in the three dimensional structure makes it possible to identify diastereomers without prior chemical separation. For larger molecules, there is the additional challenge that different conformations of each diastereomer may be present and these need to be differentiated from the diastereomers in the spectral analysis. Broadband rotational spectra of several larger molecules have been measured using a chirped-pulse FT-MRR spectrometer. Measurements of nootkatone (C15H22O), cedrol (C15H26O), ambroxide (C16H28O) and sclareolide (C16H26O2) are presented. These spectra are measured with high sensitivity (signal-to-noise ratio near 1,000:1) and permit structure determination of the most populated isomers using isotopic analysis of the 13C and 18O isotopologues in natural abundance. The accuracy of quantum chemistry calculations to identify diastereomers and conformers and to predict the dipole moment properties needed for three wave mixing measurements is examined.

  18. Molecular Structure of Nucleic Acids

    Indian Academy of Sciences (India)

    chain, that is, after 34 A. The distance of a phosphorus atom from the fibre axis is 10. A. As the phosphates are on the outside, cations have easy access to them. The structure is an open one, and its water content is rather high. At lower water contents we would expect the bases to tilt so that the structure could become more.

  19. Linear optical absorption spectra of mesoscopic structures in intense THz fields: Free-particle properties

    DEFF Research Database (Denmark)

    Johnsen, Kristinn; Jauho, Antti-Pekka

    1998-01-01

    We theoretically study the effect of THz radiation on the linear optical absorption spectra of semiconductor structures. A general theoretical framework, based on nonequilibrium Green functions, is formulated and applied to the calculation of linear optical absorption spectrum for several...

  20. Exploring RNA structure by integrative molecular modelling

    DEFF Research Database (Denmark)

    Masquida, Benoît; Beckert, Bertrand; Jossinet, Fabrice

    2010-01-01

    RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With new structured RNAs constituting a central class of cellular regulators discovered every year, the need for swift and reliable modelling methods is more crucial than ever. The pragmatic method based...... on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded...

  1. Molecular Origin of the Vibrational Structure of Ice Ih.

    Science.gov (United States)

    Moberg, Daniel R; Straight, Shelby C; Knight, Christopher; Paesani, Francesco

    2017-06-15

    An unambiguous assignment of the vibrational spectra of ice I h remains a matter of debate. This study demonstrates that an accurate representation of many-body interactions between water molecules, combined with an explicit treatment of nuclear quantum effects through many-body molecular dynamics (MB-MD), leads to a unified interpretation of the vibrational spectra of ice I h in terms of the structure and dynamics of the underlying hydrogen-bond network. All features of the infrared and Raman spectra in the OH stretching region can be unambiguously assigned by taking into account both the symmetry and the delocalized nature of the lattice vibrations as well as the local electrostatic environment experienced by each water molecule within the crystal. The high level of agreement with experiment raises prospects for predictive MB-MD simulations that, complementing analogous measurements, will provide molecular-level insights into fundamental processes taking place in bulk ice and on ice surfaces under different thermodynamic conditions.

  2. The Molecular Structure of Penicillin

    Science.gov (United States)

    Bentley, Ronald

    2004-01-01

    Overviews of the observations that constitute a structure proof for penicillin, specifically aimed at the general student population, are presented. Melting points and boiling points were criteria of purity and a crucial tool was microanalysis leading to empirical formulas.

  3. Green synthesis, structure and fluorescence spectra of new azacyanine dyes

    Science.gov (United States)

    Enchev, Venelin; Gadjev, Nikolai; Angelov, Ivan; Minkovska, Stela; Kurutos, Atanas; Markova, Nadezhda; Deligeorgiev, Todor

    2017-11-01

    A series of symmetric and unsymmetric monomethine azacyanine dyes (monomethine azacyanine and merocyanine sulfobetaines) were synthesized with moderate to high yields via a novel method using microwave irradiation. The compounds are derived from a condensation reaction between 2-thiomethylbenzotiazolium salts and 2-imino-3-methylbenzothiazolines proceeded under microwave irradiation. The synthetic approach involves the use of green solvent and absence of basic reagent. TD-DFT calculations were performed to simulate absorption and fluorescent spectra of synthesized dyes. Absorption maxima, λmax, of the studied dyes were found in the range 364-394 nm. Molar absorbtivities were evaluated in between 40300 and 59200 mol-1 dm3 cm-1. Fluorescence maxima, λfl, were registered around 418-448 nm upon excitation at 350 nm. A slight displacements of theoretically estimated absorption maxima according to experimental ones is observed. The differences are most probably due to the fact that the DFT calculations were carried out without taking into account the solvent effect. In addition, the merocyanine sulfobetaines also fluorescence in blue optical range (420-480 nm) at excitation in red range (630-650 nm).

  4. STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

    Energy Technology Data Exchange (ETDEWEB)

    Sawada, Tsuyoshi [Joint ALMA Office, Alonso de Cordova 3107, Vitacura, Santiago 763-0355 (Chile); Hasegawa, Tetsuo [NAOJ Chile Observatory, Joaquin Montero 3000 Oficina 702, Vitacura, Santiago 763-0409 (Chile); Koda, Jin, E-mail: sawada.tsuyoshi@nao.ac.jp [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800 (United States)

    2012-11-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory {sup 13}CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  5. Classical electron ionization mass spectra in gas chromatography/mass spectrometry with supersonic molecular beams.

    Science.gov (United States)

    Gordin, Alexander; Fialkov, Alexander B; Amirav, Aviv

    2008-09-01

    A major benefit of gas chromatography/mass spectrometry (GC/MS) with a supersonic molecular beam (SMB) interface and its fly-through ion source is the ability to obtain electron ionization of vibrationally cold molecules (cold EI), which show enhanced molecular ions. However, GC/MS with an SMB also has the flexibility to perform 'classical EI' mode of operation which provides mass spectra to mimic those in commercial 70 eV electron ionization MS libraries. Classical EI in SMB is obtained through simple reduction of the helium make-up gas flow rate, which reduces the SMB cooling efficiency; hence the vibrational temperatures of the molecules are similar to those in traditional EI ion sources. In classical EI-SMB mode, the relative abundance of the molecular ion can be tuned and, as a result, excellent identification probabilities and very good matching factors to the NIST MS library are obtained. Classical EI-SMB with the fly-through dual cage ion source has analyte sensitivity similar to that of the standard EI ion source of a basic GC/MS system. The fly-through EI ion source in combination with the SMB interface can serve for cold EI, classical EI-SMB, and cluster chemical ionization (CCI) modes of operation, all easily exchangeable through a simple and quick change (not involving hardware). Furthermore, the fly-through ion source eliminates sample scattering from the walls of the ion source, and thus it offers full sample inertness, tailing-free operation, and no ion-molecule reaction interferences. It is also robust and enables increased column flow rate capability without affecting the sensitivity.

  6. On The Design of Gravity Structures using Wave Spectra

    DEFF Research Database (Denmark)

    Burcharth, Hans F.; Brorsen, Michael

    Although most structures are subjected to dynamic, stochastic loads, it is in fact seldom that these loads are considered in the design, Normally the design is based on an equivalent static load, establishing naturally with due consideration to the true conditions, This method is often called det...... deterministic, the loading being described as a specified function of time....

  7. Neutron spectra and cross sections for ice and clathrate generated from the synthetic spectrum and synthetic model for molecular solids

    International Nuclear Information System (INIS)

    Petriw, S; Cantargi, F; Granada, R

    2006-01-01

    We present here a Synthetic Model for Molecular Solids, aimed at the description of the interaction of thermal neutrons with this kind of systems.Simple representations of the molecular dynamical modes are used, in order to produce a fair description of neutron scattering kernels and cross sections with a minimum set of input data. Using those spectra, we have generated thermal libraries for M C N P [es

  8. Energy spectra of vibron and cluster models in molecular and nuclear systems

    Science.gov (United States)

    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.

  9. Structural properties of maize hybrids established by infrared spectra

    Directory of Open Access Journals (Sweden)

    Radenović Čedomir N.

    2015-01-01

    Full Text Available This paper discusses the application of the infrared (IR spectroscopy method for determination of structural properties of maize hybrid grains. The IR spectrum of maize grain has been registered in the following hybrids: ZP 341, ZP 434 and ZP 505. The existence of spectral bands varying in both number and intensity, as well as their shape, frequency and kinetics have been determined. They have been determined by valence oscillations and deformation oscillations of the following organic compounds: alkanes, alkenes, alkynes, amides, alcohols, ethers, carboxylic acids, esters and aldehydes and ketones, characteristic for biogenic compounds such as carbohydrates, proteins and lipids. In this way, possible changes in the grain structure of observed maize hybrids could be detected.

  10. Structures of conserved currents and mass spectra for scalar fields

    International Nuclear Information System (INIS)

    Shintani, Meiun.

    1979-05-01

    Considering the commutators between a scalar field and a conserved current, we shall clarify the connection between the mass spectrum for a scalar field and the structures of a current. For a special form of currents involving c-number functions, non-invariance of the vacuum under the corresponding transformation entails the existence of a massive mode. It is shown that once a type of currents is specified, the pole structures for sub(o) depend only on c-number parts of J sub(μ)(x). We shall show that non-vanishing Goldstone commutator does not automatically imply the degeneracy of the vacuum state, and discuss the applicability of the Goldstone theorem. (author)

  11. Theory vs. experiment for molecular clusters: Spectra of OCS trimers and tetramers

    Energy Technology Data Exchange (ETDEWEB)

    Evangelisti, Luca [Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904 (United States); Dipartimento di Chimica “G. Ciamician,” University of Bologna, Via Selmi 2, Bologna 40126 (Italy); Perez, Cristobal; Seifert, Nathan A.; Pate, Brooks H. [Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904 (United States); Dehghany, M.; Moazzen-Ahmadi, N. [Department of Physics and Astronomy, University of Calgary, 2500 University Drive North West, Calgary, Alberta T2N 1N4 (Canada); McKellar, A. R. W. [National Research Council of Canada, Ottawa, Ontario K1A 0R6 (Canada)

    2015-03-14

    All singly substituted {sup 13}C, {sup 18}O, and {sup 34}S isotopomers of the previously known OCS trimer are observed in natural abundance in a broad-band spectrum measured with a chirped-pulse Fourier transform microwave spectrometer. The complete substitution structure thus obtained critically tests (and confirms) the common assumption that monomers tend to retain their free structure in a weakly bound cluster. A new OCS trimer isomer is also observed, and its structure is determined to be barrel-shaped but with the monomers all approximately aligned, in contrast to the original trimer which is barrel-shaped with two monomers aligned and one anti-aligned. An OCS tetramer spectrum is assigned for the first time, and the tetramer structure resembles an original trimer with an OCS monomer added at the end with two sulfur atoms. Infrared spectra observed in the region of the OCS ν{sub 1} fundamental (≈2060 cm{sup −1}) are assigned to the same OCS tetramer, and another infrared band is tentatively assigned to a different tetramer isomer. The experimental results are compared and contrasted with theoretical predictions from the literature and from new cluster calculations which use an accurate OCS pair potential and assume pairwise additivity.

  12. Asymptotic behaviour of optimal fraction-rational series of the perturbation theory at description of molecular rotational spectra

    International Nuclear Information System (INIS)

    Burenin, A.V.

    1994-01-01

    A possibility is shown of substantial expansion of the choice of asymptotic behaviour of optimal fraction-rational series of the perturbation theory on description of molecular rotational spectra. The expansion permits to hope for substantial improvement of results of using the conception of effective rotational hamiltonian in a fraction-rational form on the description of highly perturbed vibrational states

  13. Vibronic Boson Sampling: Generalized Gaussian Boson Sampling for Molecular Vibronic Spectra at Finite Temperature.

    Science.gov (United States)

    Huh, Joonsuk; Yung, Man-Hong

    2017-08-07

    Molecular vibroic spectroscopy, where the transitions involve non-trivial Bosonic correlation due to the Duschinsky Rotation, is strongly believed to be in a similar complexity class as Boson Sampling. At finite temperature, the problem is represented as a Boson Sampling experiment with correlated Gaussian input states. This molecular problem with temperature effect is intimately related to the various versions of Boson Sampling sharing the similar computational complexity. Here we provide a full description to this relation in the context of Gaussian Boson Sampling. We find a hierarchical structure, which illustrates the relationship among various Boson Sampling schemes. Specifically, we show that every instance of Gaussian Boson Sampling with an initial correlation can be simulated by an instance of Gaussian Boson Sampling without initial correlation, with only a polynomial overhead. Since every Gaussian state is associated with a thermal state, our result implies that every sampling problem in molecular vibronic transitions, at any temperature, can be simulated by Gaussian Boson Sampling associated with a product of vacuum modes. We refer such a generalized Gaussian Boson Sampling motivated by the molecular sampling problem as Vibronic Boson Sampling.

  14. Heat-induced changes to lipid molecular structure in Vimy flaxseed: Spectral intensity and molecular clustering

    Science.gov (United States)

    Yu, Peiqiang; Damiran, Daalkhaijav

    2011-06-01

    Autoclaving was used to manipulate nutrient utilization and availability. The objectives of this study were to characterize any changes of the functional groups mainly associated with lipid structure in flaxseed ( Linum usitatissimum, cv. Vimy), that occurred on a molecular level during the treatment process using infrared Fourier transform molecular spectroscopy. The parameters included lipid CH 3 asymmetric (ca. 2959 cm -1), CH 2 asymmetric (ca. 2928 cm -1), CH 3 symmetric (ca. 2871 cm -1) and CH 2 symmetric (ca. 2954 cm -1) functional groups, lipid carbonyl C dbnd O ester group (ca. 1745 cm -1), lipid unsaturation group (CH attached to C dbnd C) (ca. 3010 cm -1) as well as their ratios. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were conducted to identify molecular spectral differences. Flaxseed samples were kept raw for the control or autoclaved in batches at 120 °C for 20, 40 or 60 min for treatments 1, 2 and 3, respectively. Molecular spectral analysis of lipid functional group ratios showed a significant decrease ( P 0.05) on lipid carbonyl C dbnd O ester group and lipid unsaturation group (CH attached to C dbnd C) (with average spectral peak area intensities of 138.3 and 68.8 IR intensity units, respectively). Multivariate molecular spectral analyses, CLA and PCA, were unable to make distinctions between the different treatment original spectra at the CH 3 and CH 2 asymmetric and symmetric region (ca. 2988-2790 cm -1). The results indicated that autoclaving had an impact to the mid-infrared molecular spectrum of flaxseed to identify heat-induced changes in lipid conformation. A future study is needed to quantify the relationship between lipid molecular structure changes and functionality/availability.

  15. Bumping structure of initial energy density distributions and peculiarities of pion spectra in A + A collisions

    International Nuclear Information System (INIS)

    Borysova, M.S.

    2012-01-01

    The effect of a fluctuating bumping structure of the initial conditions on spectra and the collective evolution of matter created in heavy-ion collisions in the frameworks of the Hydro-Kinetic Model is investigated. As motivated by the glasma-flux-tube scenario, the initial conditions are modeled by the set of four high energy-density tube-like fluctuations with longitudinally homogeneous structure within some space-rapidity region in a boost-invariant 2D geometry. It was found that the presence of transversally bumping tube-like fluctuations in initial conditions strongly affects the hydrodynamic evolution and leads to emergence of conspicuous structures in the calculated pion spectra. It was observed that the 4 tube initial configuration generates a four-peak structure in the final azimuthal distributions of one-particle spectra.

  16. Structure, spectra and stability of solid bismuth carbonates

    International Nuclear Information System (INIS)

    Taylor, Peter; Sunder, S.; Lopata, V.J.

    1984-01-01

    A previously unreported basic bismuth carbonate, (BiO)sub(4)(OH)sub(2)COsub(3), has been identified as an intermediate product in the interconversion of α-Bisub(2)Osub(3) and synthetic bismutite, (BiO)sub(2)COsub(3), in aqueous carbonate solutions. It has a narrow stability field between COsub(2) partial pressures of 10sup(-5.5+-1.0) Pa, in the presence of dilute aqueous solution at 25 degrees C. Gibbs energies of formation, calculated from these partial pressures, are Δsub(f)Gsup(0)((BiO)sub(4)(OH)sub(2)COsub(3),s,298.15 K)-1678 +- 9 kJ molsup(-1) and Δsub(f)Gsup(0)((BiO)sub(2)COsub(3),s,298.15 K)=-945 +- 7 kJ molsup(-1). The two carbonates have been compared by thermogravimetric analysis, X-ray powder diffractometry, and infrared and Raman spectroscopy. The unit cell of (BiO)sub(4)(OH)sub(2)COsub(3) is dimensionally orthorhombic, with a=10.772(1), b=5.4898(5), c=14.757(1)angstrom,Z=4, but its true symmetry is probably triclinic. A structural model for (BiO)sub(4)(OH)sub(2)COsub(3), and two modified models for (BiO)sub(2)COsub(3), are proposed. The possible natural occurrence of (BiO)sub(4)(OH)sub(2)COsub(3) is discussed

  17. Learning surface molecular structures via machine vision

    Science.gov (United States)

    Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

    2017-08-01

    Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

  18. Molecular Structure of Human-Liver Glycogen.

    Directory of Open Access Journals (Sweden)

    Bin Deng

    Full Text Available Glycogen is a highly branched glucose polymer which is involved in maintaining blood-sugar homeostasis. Liver glycogen contains large composite α particles made up of linked β particles. Previous studies have shown that the binding which links β particles into α particles is impaired in diabetic mice. The present study reports the first molecular structural characterization of human-liver glycogen from non-diabetic patients, using transmission electron microscopy for morphology and size-exclusion chromatography for the molecular size distribution; the latter is also studied as a function of time during acid hydrolysis in vitro, which is sensitive to certain structural features, particularly glycosidic vs. proteinaceous linkages. The results are compared with those seen in mice and pigs. The molecular structural change during acid hydrolysis is similar in each case, and indicates that the linkage of β into α particles is not glycosidic. This result, and the similar morphology in each case, together imply that human liver glycogen has similar molecular structure to those of mice and pigs. This knowledge will be useful for future diabetes drug targets.

  19. Collisional effects on molecular spectra laboratory experiments and models, consequences for applications

    CERN Document Server

    Hartmann, Jean-Michel; Robert, Daniel

    2008-01-01

    Gas phase molecular spectroscopy is a powerful tool for obtaining information on the geometry and internal structure of isolated molecules as well as on the interactions that they undergo. It enables the study of fundamental parameters and processes and is also used for the sounding of gas media through optical techniques. It has been facing always renewed challenges, due to the considerable improvement of experimental techniques and the increasing demand for accuracy and scope of remote sensing applications. In practice, the radiating molecule is usually not isolated but diluted in a mixture

  20. Synthesis IR spectra and crystal structure of N-(4-bromophenyl)-1,1,1-trifluoroacetyl-acetonimine HN(C6H4Br)xC(Me)xCHxC(CF3)xO(HL) and its molecular complex with tungstene(4) oxotetrachloride WOCl4xHL

    International Nuclear Information System (INIS)

    Sergienko, V.S.; Ilyukhin, A.B.; Abramenko, V.L.

    1997-01-01

    Synthesis, IR spectroscopic and X-ray diffraction studies of compound HN(C 6 H 4 Br)xC(Me)xCHxC(CF 3 )xO(HL) (1) and of molecular complex WOCl 4 xHL(2) have been conducted. In 1 and 2 HL molecule exists in ketoamine tautomeric form (acid proton is localized at nitrogen atom). The results of 1 and 2 study are compared with literature data on structures of HL type molecules and Mo(6) molecular complexes with β-enaminevinylketone, as well as with the structure of chelate compound WOCl 3 L 1 , where L 1 - anion of N-phenylacetylacetonimine

  1. Molecular Eigensolution Symmetry Analysis and Fine Structure

    Directory of Open Access Journals (Sweden)

    William G. Harter

    2013-01-01

    Full Text Available 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.

  2. Ionization probes of molecular structure and chemistry

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, P.M. [State Univ. of New York, Stony Brook (United States)

    1993-12-01

    Various photoionization processes provide very sensitive probes for the detection and understanding of the spectra of molecules relevant to combustion processes. The detection of ionization can be selective by using resonant multiphoton ionization or by exploiting the fact that different molecules have different sets of ionization potentials. Therefore, the structure and dynamics of individual molecules can be studied even in a mixed sample. The authors are continuing to develop methods for the selective spectroscopic detection of molecules by ionization, and to use these methods for the study of some molecules of combustion interest.

  3. Similarity of High-Resolution Tandem Mass Spectrometry Spectra of Structurally Related Micropollutants and Transformation Products

    Science.gov (United States)

    Schollée, Jennifer E.; Schymanski, Emma L.; Stravs, Michael A.; Gulde, Rebekka; Thomaidis, Nikolaos S.; Hollender, Juliane

    2017-12-01

    High-resolution tandem mass spectrometry (HRMS2) with electrospray ionization is frequently applied to study polar organic molecules such as micropollutants. Fragmentation provides structural information to confirm structures of known compounds or propose structures of unknown compounds. Similarity of HRMS2 spectra between structurally related compounds has been suggested to facilitate identification of unknown compounds. To test this hypothesis, the similarity of reference standard HRMS2 spectra was calculated for 243 pairs of micropollutants and their structurally related transformation products (TPs); for comparison, spectral similarity was also calculated for 219 pairs of unrelated compounds. Spectra were measured on Orbitrap and QTOF mass spectrometers and similarity was calculated with the dot product. The influence of different factors on spectral similarity [e.g., normalized collision energy (NCE), merging fragments from all NCEs, and shifting fragments by the mass difference of the pair] was considered. Spectral similarity increased at higher NCEs and highest similarity scores for related pairs were obtained with merged spectra including measured fragments and shifted fragments. Removal of the monoisotopic peak was critical to reduce false positives. Using a spectral similarity score threshold of 0.52, 40% of related pairs and 0% of unrelated pairs were above this value. Structural similarity was estimated with the Tanimoto coefficient and pairs with higher structural similarity generally had higher spectral similarity. Pairs where one or both compounds contained heteroatoms such as sulfur often resulted in dissimilar spectra. This work demonstrates that HRMS2 spectral similarity may indicate structural similarity and that spectral similarity can be used in the future to screen complex samples for related compounds such as micropollutants and TPs, assisting in the prioritization of non-target compounds. [Figure not available: see fulltext.

  4. Multi-phase Turbulence Density Power Spectra in the Perseus Molecular Cloud

    Science.gov (United States)

    Pingel, N. M.; Lee, Min-Young; Burkhart, Blakesley; Stanimirović, Snežana

    2018-04-01

    We derive two-dimensional spatial power spectra of four distinct interstellar medium tracers, H I, 12CO(J = 1–0), 13CO(J = 1–0), and dust, in the Perseus molecular cloud, covering linear scales ranging from ∼0.1 pc to ∼90 pc. Among the four tracers, we find the steepest slopes of ‑3.23 ± 0.05 and ‑3.22 ± 0.05 for the uncorrected and opacity-corrected H I column density images. This result suggests that the H I in and around Perseus traces a non-gravitating, transonic medium on average, with a negligible effect from opacity. On the other hand, we measure the shallowest slope of ‑2.72 ± 0.12 for the 2MASS dust extinction data and interpret this as the signature of a self-gravitating, supersonic medium. Possible variations in the dust-to-gas ratio likely do not alter our conclusion. Finally, we derive slopes of ‑3.08 ± 0.08 and ‑2.88 ± 0.07 for the 12CO(1–0) and 13CO(1–0) integrated intensity images. Based on theoretical predictions for an optically thick medium, we interpret these slopes of roughly ‑3 as implying that both CO lines are susceptible to the opacity effect. While simple tests for the impact of CO formation and depletion indicate that the measured slopes of 12CO(1–0) and 13CO(1–0) are not likely affected by these chemical effects, our results generally suggest that chemically more complex and/or fully optically thick media may not be a reliable observational tracer for characterizing turbulence.

  5. N-acetylglutamate synthase deficiency: Novel mutation associated with neonatal presentation and literature review of molecular and phenotypic spectra

    Directory of Open Access Journals (Sweden)

    Eiman H. Al Kaabi

    2016-09-01

    Full Text Available The urea cycle is the main pathway for the disposal of excess nitrogen. Carbamoylphosphate synthetase 1 (CPS1, the first and rate-limiting enzyme of urea cycle, is activated by N-acetylglutamate (NAG, and thus N-acetylglutamate synthase (NAGS is an essential part of the urea cycle. Although NAGS deficiency is the rarest urea cycle disorder, it is the only one that can be specifically and effectively treated by a drug, N-carbamylglutamate, a stable structural analogous of NAG that activates CPS1. Here we report an infant with NAGS deficiency who presented with neonatal hyperammonemia. She was found to have a novel homozygous splice-site mutation, c.1097-2A>T, in the NAGS gene. We describe the clinical course of this infant, who had rapid response to N-carbamylglutamate treatment. In addition, we reviewed the clinical and molecular spectra of previously reported individuals with NAGS deficiency, which presents in most cases with neonatal hyperammonemia, and in some cases the presentation is later, with a broad spectrum of ages and manifestations. With this broad later-onset phenotypic spectrum, maintaining a high index of suspicion is needed for the early diagnosis of this treatable disease.

  6. Characteristics studies of molecular structures in drugs

    Directory of Open Access Journals (Sweden)

    Wei Gao

    2017-05-01

    Full Text Available In theoretical medicine, topological indices are defined to test the medicine and pharmacy characteristics, such as melting point, boiling point, toxicity and other biological activities. As basic molecular structures, hexagonal jagged-rectangle and distance-regular structure are widely appeared in medicine, pharmacy and biology engineering. In this paper, we study the chemical properties of hexagonal jagged-rectangle from the mathematical point of view. Several vertex distance-based indices are determined. Furthermore, the Wiener related indices of distance-regular structure are also considered.

  7. Response spectra for nuclear structures on rock sites considering the near-fault directivity effect

    Institute of Scientific and Technical Information of China (English)

    Xu Longiun; Yang Shengchao; Xie Lili

    2010-01-01

    Near-fault ground motions, potentially with large amplitude and typical velocity pulses, may significantly impact the performance of a wide range of structures. The current study is aimed at evaluating the safety implications of the near-fault effect on nuclear power plant facilities designed according to the Chinese code. To this end, a set of near-fault ground motions at rock sites with typical forward-directivity effect is examined with special emphasis on several key parameters and response spectra. Spectral comparison of the selected records with the Chinese and other code design spectra was conducted. The bi-normalized response spectra in terms of different comer periods are utilized to derive nuclear design spectra. It is concluded that nuclear design spectra on rock sites derived from typical rupture directivity records are significantly influenced both by the earthquake magnitude and the rupture distance. The nuclear design spectra specified in the code needs to be adjusted to reflect the near-fault directivity effect of large earthquakes.

  8. Generation of floor response spectra for a model structure of nuclear power plant

    International Nuclear Information System (INIS)

    Vaidyanathan, C.V.; Kamatchi, P.; Ravichandran, R.; Lakshmanan, N.

    2003-01-01

    The importance of Nuclear power plants and the consequences of a nuclear accident require that the nuclear structures be designed for the most severe environmental conditions. Earthquakes constitutes major design consideration for the system, structures and equipment of a nuclear power plant. The design of structures on ground is based on the ground response spectra. Many important parts of a nuclear power plant facility are attached to the principal parts of the structure and respond in a manner determined by the structural response rather than by the general ground motion to which the structure is supported. Hence the seismic response of equipment is generally based on the response spectrum of the floor on which it is mounted. In this paper such floor response spectra have been generated at different nodes of a chosen model structure of a nuclear power plant. In the present study a detailed nonlinear time history analysis has been carried out on the mathematical model of the chosen Nuclear Power Plant model structure with the spectrum compatible time history. The acceleration response results of the time history analysis has been used in the spectral analysis and the response spectra are generated. Further peak broadening has been done to account for uncertainties in the material properties and soil characteristics. (author)

  9. The study of crystal structures and vibrational spectra of inorganicsalts of 2,4-diaminopyrimidine

    Czech Academy of Sciences Publication Activity Database

    Matulková, I.; Mathauserová, J.; Císařová, I.; Němec, I.; Fábry, Jan

    2016-01-01

    Roč. 1103, Jan (2016), s. 82-93 ISSN 0022-2860 R&D Projects: GA ČR GA14-05506S Institutional support: RVO:68378271 Keywords : salts of 2,4-diaminopyrimidine * single crystal X-ray structural analysis * vibrational spectra Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.753, year: 2016

  10. Vibrational Spectra of β″-Type BEDT-TTF Salts: Relationship between Conducting Property, Time-Averaged Site Charge and Inter-Molecular Distance

    Directory of Open Access Journals (Sweden)

    Takashi Yamamoto

    2012-07-01

    Full Text Available The relationship between the conducting behavior and the degree of charge fluctuation in the β″-type BEDT-TTF salts is reviewed from the standpoints of vibrational spectroscopy and crystal structure. A group of β″-type ET salts demonstrates the best model compounds for achieving the above relationship because the two-dimensional structure is simple and great diversity in conducting behavior is realized under ambient pressure. After describing the requirement for the model compound, the methodology for analyzing the results of the vibrational spectra is presented. Vibrational spectroscopy provides the time-averaged molecular charge, the charge distribution in the two-dimensional layer, and the inter-molecular interactions, etc. The experimental results applied to 2/3-filled and 3/4-filled β″-type ET salts are reported. These experimental results suggest that the conducting property, the difference in the time-averaged molecular charges between the ionic and neutral-like sites, the alternation in the inter-molecular distances and the energy levels in the charge distributions are relevant to one another. The difference in the time-averaged molecular charges, ∆ρ, is a useful criterion for indicating conducting behavior. All superconductors presented in this review are characterized as small but finite ∆ρ.

  11. Marine Biotoxins: Laboratory Culture and Molecular Structure

    Science.gov (United States)

    1991-01-21

    ciguateric carnivorous fishes in concentrations ranging from I to 10 ppb. Its molecular structure has been elucidated. It has been isolated from toxic...American Chemical Society, Washington, DC, 1984, pp 217-329. 6. Med. J. Australia 1986, 145 (11/12), 558; 584-5M). 7. "Toxic Plants and Animals A Guide...isolated and grown in the laboratory. Lethality of crude acetone and methanol extracts were assa~ed by ip injection into mice. In vitro cytotoxicity and

  12. Computation of diatomic molecular spectra for selected transitions of aluminum monoxide, cyanide, diatomic carbon, and titanium monoxide

    Energy Technology Data Exchange (ETDEWEB)

    Parigger, Christian G., E-mail: cparigge@tennessee.edu [The University of Tennessee/University of Tennessee Space Institute, Center for Laser Applications, 411 B.H. Goethert Parkway, Tullahoma, TN 37388-9700 (United States); Woods, Alexander C.; Surmick, David M.; Gautam, Ghaneshwar; Witte, Michael J. [The University of Tennessee/University of Tennessee Space Institute, Center for Laser Applications, 411 B.H. Goethert Parkway, Tullahoma, TN 37388-9700 (United States); Hornkohl, James O. [Hornkohl Consulting, Tullahoma, TN 37388 (United States)

    2015-05-01

    Laser ablation studies with laser-induced breakdown spectroscopy (LIBS) typically emphasize atomic species yet fingerprints from molecular species can occur subsequently or concurrently. In this work, selected molecular transitions of aluminum monixide (AlO), diatomic carbon (C{sub 2}), cyanide (CN), and titanium monoxide (TiO) are accurately computed. Line strength tables are used to describe the radiative transitions of diatomic molecules primarily in the visible, optical region. Details are elaborated of the computational procedure that allows one to utilize diatomic spectra as a predictive and as a diagnostic tool. In order to create a computed spectrum, the procedure requires information regarding the temperature of the diatomic transitions along with other input such as the spectral resolution. When combined with a fitting algorithm to optimize such parameters, this procedure is used to infer information from an experimentally obtained spectrum. Furthermore, the programs and data files are provided for LIBS investigations that also reveal AlO, C{sub 2}, CN, and TiO diatomic spectra. - Highlights: • We present a program for fitting of molecular spectra. • This includes data base for AlO, C{sub 2}, CN, and TiO. • We discuss the details of the program including fitting. • We show computed examples and reference current work.

  13. Electronic structure and spectroscopy of nucleic acid bases: Ionization energies, ionization-induced structural changes, and photoelectron spectra

    Energy Technology Data Exchange (ETDEWEB)

    Bravaya, Ksenia B.; Kostko, Oleg; Dolgikh, Stanislav; Landau, Arie; Ahmed, Musahid; Krylov, Anna I.

    2010-08-02

    We report high-level ab initio calculations and single-photon ionization mass spectrometry study of ionization of adenine (A), thymine (T), cytosine (C) and guanine (G). For thymine and adenine, only the lowest-energy tautomers were considered, whereas for cytosine and guanine we characterized five lowest-energy tautomeric forms. The first adiabatic and several vertical ionization energies were computed using equation-of-motion coupled-cluster method for ionization potentials with single and double substitutions. Equilibrium structures of the cationic ground states were characterized by DFT with the {omega}B97X-D functional. The ionization-induced geometry changes of the bases are consistent with the shapes of the corresponding molecular orbitals. For the lowest-energy tautomers, the magnitude of the structural relaxation decreases in the following series G > C > A > T, the respective relaxation energies being 0.41, 0.32, 0.25 and 0.20 eV. The computed adiabatic ionization energies (8.13, 8.89, 8.51-8.67 and 7.75-7.87 eV for A,T,C and G, respectively) agree well with the onsets of the photoionization efficiency (PIE) curves (8.20 {+-} 0.05, 8.95 {+-} 0.05, 8.60 {+-} 0.05 and 7.75 {+-} 0.05 eV). Vibrational progressions for the S{sub 0}-D{sub 0} vibronic bands computed within double-harmonic approximation with Duschinsky rotations are compared with previously reported experimental photoelectron spectra.

  14. Host material induced hyperfine structure of F{sup +} centres EPR spectra in CaS

    Energy Technology Data Exchange (ETDEWEB)

    Seeman, Viktor, E-mail: viktor.seeman@ut.ee; Dolgov, Sergei; Maaroos, Aarne

    2017-05-15

    The hyperfine structure (HFS) of F{sup +} centres in CaS single crystals due to the interaction with {sup 33}S and {sup 43}Ca nuclei was observed in EPR spectra for the first time. Angular variations of the HFS were measured for rotation of magnetic field in {100} and {110} crystallographic planes. Using measured orientation-dependent EPR spectra and the EPR NMR program, the parameters of the spin Hamiltonian were determined. In case of {sup 33}S nucleus there is a strong dependence of the F{sup +} centre EPR spectrum on the quadrupole term whereas for {sup 43}Ca nucleus this dependence is insignificant.

  15. Assignment of near-edge x-ray absorption fine structure spectra of metalloporphyrins by means of time-dependent density-functional calculations

    International Nuclear Information System (INIS)

    Schmidt, Norman; Fink, Rainer; Hieringer, Wolfgang

    2010-01-01

    The C 1s and N 1s near-edge x-ray absorption fine structure (NEXAFS) spectra of three prototype tetraphenyl porphyrin (TPP) molecules are discussed in the framework of a combined experimental and theoretical study. We employ time-dependent density-functional theory (TDDFT) to compute the NEXAFS spectra of the open- and closed-shell metalloporphyrins CoTPP and ZnTPP as well as the free-base 2HTPP in realistic nonplanar conformations. Using Becke's well-known half-and-half hybrid functional, the computed core excitation spectra are mostly in good agreement with the experimental data in the low-energy region below the appropriate ionization threshold. To make these calculations feasible, we apply a new, simple scheme based on TDDFT using a modified single-particle input spectrum. This scheme is very easy to implement in standard codes and allows one to compute core excitation spectra at a similar cost as ordinary UV/vis spectra even for larger molecules. We employ these calculations for a detailed assignment of the NEXAFS spectra including subtle shifts in certain peaks of the N 1s spectra, which depend on the central coordination of the TPP ligand. We furthermore assign the observed NEXAFS resonances to the individual molecular subunits of the investigated TPP molecules.

  16. DFT studies for three Cu(II) coordination polymers: Geometrical and electronic structures, g factors and UV-visible spectra

    Science.gov (United States)

    Ding, Chang-Chun; Wu, Shao-Yi; Xu, Yong-Qiang; Wu, Li-Na; Zhang, Li-Juan

    2018-05-01

    This work presents a systematic density functional theory (DFT) study for geometrical and electronic structures, g factors and UV-vis spectra of three Cu(II) coordination polymers (CPs) [Cu(XL)(NO3)2]n (1), {[Cu(XL)(4,4‧-bpy)(NO3)2]•CH3CN}n (2) and {[Cu(XL)3](NO3)2·3.5H2O}n (3) based on the ligand N,N‧-bicyclo[2.2.2]oct-7-ene-2,3,5,6-tetracarboxdiimide bi(1,2,4-triazole) (XL) with the linker triazole coordinated with copper to construct the CPs. For three CPs with distinct ligands, the optimized molecular structures with PBE0 hybrid functional and the 6-311g basis set agree well with the corresponding XRD data. Meanwhile, the electronic properties are also analyzed for all the systems. The calculated g factors are found sensitive to the (Hartree-Fock) HF character due to the significant hybridization between copper and ligand orbitals. The calculated UV-visible spectra reveal that the main electronic transitions for CP 1 contain d-d and CT transitions, while those for CPs 2 and 3 largely belong to CT ones. The present CPs seem difficult to adsorb small molecules, e.g., CP 1 with H2O and NO2 exhibit unfavorable adsorption and deformation structures near the Cu2+ site.

  17. Coherent manipulation of spontaneous emission spectra in coupled semiconductor quantum well structures.

    Science.gov (United States)

    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.

  18. The spectra of type IIB flux compactifications at large complex structure

    International Nuclear Information System (INIS)

    Brodie, Callum; Marsh, M.C. David

    2016-01-01

    We compute the spectra of the Hessian matrix, H, and the matrix M that governs the critical point equation of the low-energy effective supergravity, as a function of the complex structure and axio-dilaton moduli space in type IIB flux compactifications at large complex structure. We find both spectra analytically in an h − 1,2 +3 real-dimensional subspace of the moduli space, and show that they exhibit a universal structure with highly degenerate eigenvalues, independently of the choice of flux, the details of the compactification geometry, and the number of complex structure moduli. In this subspace, the spectrum of the Hessian matrix contains no tachyons, but there are also no critical points. We show numerically that the spectra of H and M remain highly peaked over a large fraction of the sampled moduli space of explicit Calabi-Yau compactifications with 2 to 5 complex structure moduli. In these models, the scale of the supersymmetric contribution to the scalar masses is strongly linearly correlated with the value of the superpotential over almost the entire moduli space, with particularly strong correlations arising for g s <1. We contrast these results with the expectations from the much-used continuous flux approximation, and comment on the applicability of Random Matrix Theory to the statistical modelling of the string theory landscape.

  19. [Monitoring of Crack Propagation in Repaired Structures Based on Characteristics of FBG Sensors Reflecting Spectra].

    Science.gov (United States)

    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.

  20. The Born-Oppenheimer molecular simulations of infrared spectra of crystalline poly-(R)-3-hydroxybutyrate with analysis of weak Csbnd H⋯Odbnd C hydrogen bonds

    Science.gov (United States)

    Brela, Mateusz Z.; Boczar, Marek; Wójcik, Marek J.; Sato, Harumi; Nakajima, Takahito; Ozaki, Yukihiro

    2017-06-01

    In this letter we present results of study of weak Csbnd H⋯Odbnd C hydrogen bonds of crystalline poly-(R)-3-hydroxybutyrate (PHB) by using Born-Oppenheimer molecular dynamics. The polymeric structure and IR spectra of PHB result from the presence of the weak hydrogen bonds. We applied the post-molecular dynamics analysis to consider a Cdbnd O motion as indirectly involved in the hydrogen bonds. Quantization of the nuclear motion of the oxygens was done to perform detailed analysis of the strength and properties of the Cdbnd O bands involved in the weak hydrogen bonds. We have also shown the dynamic character of the weak hydrogen bond interactions.

  1. Molecular structure of the lecithin ripple phase

    Science.gov (United States)

    de Vries, Alex H.; Yefimov, Serge; Mark, Alan E.; Marrink, Siewert J.

    2005-04-01

    Molecular dynamics simulations of lecithin lipid bilayers in water as they are cooled from the liquid crystalline phase show the spontaneous formation of rippled bilayers. The ripple consists of two domains of different length and orientation, connected by a kink. The organization of the lipids in one domain of the ripple is found to be that of a splayed gel; in the other domain the lipids are gel-like and fully interdigitated. In the concave part of the kink region between the domains the lipids are disordered. The results are consistent with the experimental information available and provide an atomic-level model that may be tested by further experiments. molecular dynamics simulation | structural model

  2. Interrelationship of crystal structure, infrared spectra and physicochemical properties of perovskites

    Energy Technology Data Exchange (ETDEWEB)

    Bazuev, G V; Shveikin, G P [AN SSSR, Sverdlovsk. Inst. Khimii

    1975-12-01

    In the range 400-800 cm/sup -1/ a study has been made of infrared absorption spectra of perowskites ABO/sub 3/, where A is a rare-earth element or yttrium, B is Ti or V. A common feature of the infrared absorption spectra of perowskites ABO/sub 3/ is the presence of two intensive wide bands in the range 400-700 cm/sup -1/ one of which (low-frequency) is splitted into two or three components. The spectrum of LaTiO/sub 3/ is distinguished from spectra of other compounds. In the range measured this compound is non-transparent for electromagnetic radiation. On the basis of determination of temperature dependences of the electric resistance it is found that LaTiO/sub 3/ has metallic conductivity unlike other perowskites studied which are semiconductors. The spectrum of EuTiO/sub 3/ also differs from other spectra. It is close in its structure and position of bands to the spectrum of cubic perowskite, SrTiO/sub 3/. The splitting of the low-frequency band into two and in the case of TbVO/sub 3/ into three components is caused by deformation of crystal structures of these compounds. A direct dependence between the value of splitting and the deformation degree is observed.

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

    International Nuclear Information System (INIS)

    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

  4. A series of sheet-structured alkali metal uranyl oxalate hydrates: structures and IR spectra

    International Nuclear Information System (INIS)

    Giesting, P.A.; Porter, N.J.; Burns, P.C.

    2006-01-01

    The novel compounds K[(UO 2 ) 2 (C 2 O 4 ) 2 OH] . 2 H 2 O (KUrO x ), Rb[(UO 2 ) 2 (C 2 O 4 ) 2 OH] . 2 H 2 O (RbUrO x ), and Cs[(UO 2 ) 2 (C 2 O 4 ) 2 OH] . H 2 O (CsUrO x ) have been synthesized by mild hydrothermal methods. Single crystal diffraction data collected at 125 K using MoK α radiation and a CCD-based area detector were used to solve and refine the crystal structures by full-matrix least-squares techniques to agreement indices (KUrO x , RbUrO x , CsUrO x ) wR 2 = 0.045, 0.062, 0.042 for all data, and R1 = 0.023, 0.030, 0.022 calculated for 1834, 1863, 1821 unique reflections respectively. The compounds KUrO x , RbUrO x , and CsUrO x are all monoclinic, space group P2 1 /m, Z = 2. The unit cell of KUrO x has the dimensions a = 5.6427(4), b = 13.7123(9), c = 9.2669(6) Aa, β = 98.7490(10) , V = 708.68(8) Aa 3 . The unit cell of RbUrO x has the dimensions a = 5.6225(4), b = 13.8339(9), c = 9.3308(6) Aa, β = 98.1590(10) , V = 718.41(8) Aa 3 . The unit cell of CsUrO x has the dimensions a = 5.4688(3), b = 13.5710(8), c = 9.5408(5) Aa, β = 97.5830(10) , V = 701.90(7) Aa 3 . The structures consist of chains of uranyl pentagonal bipyramids connected by oxalate groups and hydroxyl groups, and are isotypic with the compound NR 4 [(UO 2 ) 2 (C 2 O 4 ) 2 OH] . 2 H 2 O studied by Artem'eva et al. (2003); all four of these compounds are structurally composed of sheets made by polymerizing the chains of UO 2 C 2 O 4 (H 2 O) . 2 H 2 O (Jayadevan and Chackraburtty, 1972; Mikhailov et al., (1999)), this being achieved by removing a H atom from an H 2 O group in the coordination sphere of the uranyl ion to form a hydroxyl vertex that is shared by two uranyl ions. Compensating positive charges are provided by the inclusion of large monovalent cations in channels that run through the sheets; these channels also contain hydrogen-bound H 2 O groups. The positions of the cations and H 2 O groups change in relation to the uranyl oxalate sheets and to each other through the

  5. IR spectra and structure of uranyl pivaloyltrifluoroacetylacetonate isolated in argon matrix

    International Nuclear Information System (INIS)

    Belyaeva, A.A.; Dushin, R.B.; Sidorenko, G.V.; Suglobov, D.N.

    1985-01-01

    When studying IR absorption spectra of a number of isotopomers of uranyl pivaloyl trifluoroacetonate (UPTFA), isolated in the matrix of argon and dissolved in benzene, and comparing them with the spectra of uranyl hexafluoroacetylacetonate (UHFA) vapours, it has been ascertained, that UPTFA vapours consist of monomers and dimers, and UPTFA solution in benzene - of dimers.It is shown, that the dimers have T-shaped structure, at that, the bond inside the dimer is realized by yl-atom of oxygen of an uranyl ion, included in the equatorial coordination sphere of another uranyl ion. Proofs of the dimer T-like structure distortion in gaseous or matrix-isolated state, as a result of which the difference of the angles between uranyl axes from 90 deg is observed, are given. In the framework of approximated model of isolated uranyl-ion the force constants for all the compounds investigated are calaculted

  6. Ab initio Hartree-Fock and density functional theory investigations on the conformational stability, molecular structure and vibrational spectra of 5-chloro-3-(2-(4-methylpiperazin-1-yl)-2-oxoethyl)benzo[d]thiazol-2(3H)-one drug molecule.

    Science.gov (United States)

    Taşal, Erol; Kumalar, Mustafa

    2012-09-01

    In this work, the experimental and theoretical spectra of 5-chloro-3-(2-(4-methylpiperazin-1-yl)-2-oxoethyl)benzo[d]thiazol-2(3H)-one molecule (abbreviated as 5CMOT) are studied. The molecular geometry and vibrational frequencies are calculated in the ground state of molecule using ab initio Hartree-Fock (HF) and Density Function Theory (DFT) methods with 6-311++G(d,p), 6-31G++(d,p), 6-31G(d,p), 6-31G(d) and 6-31G basis sets. Three staggered stable conformers were observed on the torsional potential energy surfaces. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes calculated. The comparison of the theoretical and experimental geometries of the title compound indicated that the X-ray parameters fairly well agree with the theoretically obtained values for the most stable conformer. The theoretical results showed an excellent agreement with the experimental values. The calculated HOMO and LUMO energies show that the charge transfer occurs within the molecule. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Secondary electronic processes and the structure of X-ray photoelectron spectra of lanthanides in oxygen-containing compounds

    International Nuclear Information System (INIS)

    Teterin, Yu.A.; Teterin, A.Yu.; Lebedev, A.M.; Ivanov, K.E.

    2004-01-01

    X-ray photoelectron spectra of lanthanide compounds in the binding energy range 0-1250 eV beside the spin-orbitally split doublets exhibit fine structure. In particular, in the low-energy spectral range 0-50 eV such structure appears most likely due to the formation of the inner (IVMO) and outer (OVMO) valence molecular orbitals. The many-body perturbation shows up in the spectra of all the studied electronic shells but with different probabilities, while the multiplet splitting and dynamic effect in the spectra of just some inner shells. The present work studies the X-ray photoelectron spectral structure of lanthanide (La-Lu except for Pm) oxides and orthoniobates due to the secondary electronic processes accompanying the photoemission from the inner shells: many-body perturbation and dynamic effect. As a result, for example, the relative intensity of the line due to the many-body perturbation (shake-up process) with ΔE sat ∼4 eV for LaNbO 4 was found to decrease with decreasing of the binding energy of the inner electrons from 0.72 (E b for La 3d 5/2 =834.8 eV) to 0.28 (E b for La 4d 5/2 =102.9 eV). The full-width at half-maximum of the Ln 3d 5/2 line of lanthanide oxides and orthoniobates decreases as the atomic number Z of lanthanide grows in the range 58≤Z≤67 to the middle of the lanthanide row, and then increases. This agrees with the fact that for the beginning of the lanthanide row the Ln 3d 5/2 photoemission is accompanied by the shake-up process, while for the second half of the row--by the shake-down. It is important to note that it is connected with the Ln 4f binding energy change relative to the OVMO in compounds. The present work also confirms experimentally that the dynamic effect due to the gigantic Coster-Kronig transitions observed in the Ln 4p spectra takes place within the inner Ln 4p, 4d and outer Ln 4f shells with formation of the additional two-hole final state Ln 4p 6 4d 8 4f n+1 . The influence of the chemical environment on the Ln 4

  8. Peak-Broadening of Floor Response Spectra for Base Isolated Nuclear Structures

    International Nuclear Information System (INIS)

    Ju, Heekun; Choun, Young-Sun; Kim, Min-Kyu

    2015-01-01

    In this paper, uncertainties in developing FRS are explained first. Then FDRS of a fixed structure is computed using a conventional method as an example. Lastly FRS of a base-isolated structure is computed and suitability of current peak-broadening method is examined. Uncertainties in the material property of structure influence FRS of fixed structures significantly, but their effect on FRS of base-isolated structures is negligible. Nuclear structures should be designed to ensure the safety of equipment and components mounted on their floors. However, coupled analysis of a structure and components is complex, so equipment is separately analyzed using floor response spectra (FRS). FRS calculated from dynamic analysis of structural model should be modified to create floor design response spectra (FDRS), the input for seismic design of equipment. For nuclear structures, smoothing and broadening peaks of FRS is required to account for uncertainties owing to material properties of structures, soil, modeling techniques, and others. The peak broadening method proposed for fixed based structures may not be appropriate for base-isolated structures because of additional uncertainties in the property of isolation bearings. For base-isolated structures, mechanical property of isolator plays a dominant role on the change of FRS. As base-isolated nuclear plants should meet the ASCE provisions, uncertainty in the isolation system would be around 10%. For the base isolated 3-storied beam model with 2.5-sec isolation period, 6.9% of broadening ratio was enough for development of FDRS at the required variation condition. Also for the models with various isolation periods, less than 10% of broadening ratio was sufficient

  9. New solar carbon abundance based on non-LTE CN molecular spectra

    International Nuclear Information System (INIS)

    Mount, G.H.; Linsky, J.L.

    1975-01-01

    A detailed non-LTE analysis of solar CN spectra strongly suggests a revised carbon abundance for the Sun. A value of log A/subc/=8.35plus-or-minus0.15 which is significantly lower than the presently accepted value of log A/subc/=8.55 is suggested. This revision may have important consequences in astrophysics

  10. Diffraction structures in delta electron spectra emitted in heavy-ion atom collisions

    International Nuclear Information System (INIS)

    Liao, C.; Bhalla, C.; Shingal, R.; Schmidt-Boecking, H.; Shinpaugh, J.; Wolf, W.; Wolf, H.

    1992-01-01

    We have measured doubly differential cross sections DDCS for projectiles between F and Au and find evidence for strong diffraction structure in the Binary Encounter region of the emitted electron spectra for Au(Z=79), I(Z=53) and Cu(Z=29) projectiles, however not for F projectiles in the collision energy range between 0.2 and 0.5 MeV/u. (orig.)

  11. Search for resonance structures in inclusive charged pion spectra from p-barp annihilation at rest

    International Nuclear Information System (INIS)

    Angelopoulos, A.; Apostolakis, A.; Papaelias, P.

    1985-01-01

    The charged pion momentum spectra from p-barp annihilation at rest have been measured with high statistics. A search for structures finds four narrow lines which are identified with the absorption and decay processes of kaons stopping in the target. Limits of 1-6 x 10 -4 /p-bar (90% C.L.) are placed on the yield of a narrow state in the mass range 1000--1660 MeV

  12. Synthesis, crystal structure, vibrational spectra and theoretical calculations of quantum chemistry of a potential antimicrobial Meldrum's acid derivative

    Science.gov (United States)

    Campelo, M. J. M.; Freire, P. T. C.; Mendes Filho, J.; de Toledo, T. A.; Teixeira, A. M. R.; da Silva, L. E.; Bento, R. R. F.; Faria, J. L. B.; Pizani, P. S.; Gusmão, G. O. M.; Coutinho, H. D. M.; Oliveira, M. T. A.

    2017-10-01

    A new derivative of Meldrum's acid 5-((5-chloropyridin-2-ylamino)methylene)-2,2-dimethyl-1,3-dioxane-4,6-dione (CYMM) of molecular formula C12H11ClN2O4 was synthesized and structurally characterized using single crystal X-ray diffraction technique. The vibrational properties of the crystal were studied by Fourier Transform infrared (FT-IR), Fourier Transform Raman (FT-Raman) techniques and theoretical calculations of quantum chemistry using Density functional theory (DFT) and Density functional perturbation theory (DFPT). A comparison with experimental spectra allowed the assignment of all the normal modes. The descriptions of the normal modes were carried by means of potential energy distribution (PED). Additionally, analysis of the antimicrobial activity and antibiotic resistance modulatory activity was carried out to evaluate the antibacterial potential of the CYMM.

  13. Digital Speckle Photography of Subpixel Displacements of Speckle Structures Based on Analysis of Their Spatial Spectra

    Science.gov (United States)

    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.

  14. SSI response of a typical shear wall structure. Appendix B. In-structure response spectra comparisons. Volume 2

    International Nuclear Information System (INIS)

    Johnson, J.J.; Schewe, E.C.; Maslenikov, O.R.

    1984-04-01

    The objectives of this study were two-fold: (1) develop building response calibration factors, i.e., factors which relate best estimate or median level response to responses calculated by selected design procedures. Soil-structure interaction was the phenomenon of interest because significant simplifications are frequently introduced in its treatment; and (2) the second objective can be viewed in the context of a question: what effect does placing an identical structure on different sites and with different foundation conditions have on structure response. The structure selected for this study is a part of the Zion AFT complex. Only the auxiliary, fuel-handling, and diesel generator buildings were studied. This structure is a connected group of shear-wall buildings constructed of reinforced concrete, typical of nuclear power plant structures. The bases of comparison for this study were structure responses: peak in-structure accelerations (27 components), and peak wall forces and moments (111 components). In-structure response spectra were also considered. This appendix contains in-structure response spectra comparisons in detail

  15. Molecular Models of Genetic and Organismic Structures

    CERN Document Server

    Baianu, I C

    2004-01-01

    In recent studies we showed that the earlier relational theories of organismic sets (Rashevsky,1967), Metabolic-Replication (M,R)-systems (Rosen,1958)and molecular sets (Bartholomay,1968) share a joint foundation that can be studied within a unified categorical framework of functional organismic structures (Baianu,1980. This is possible because all relational theories have a biomolecular basis, that is, complex structures such as genomes, cells,organs and biological organisms are mathematically represented in terms of biomolecular properties and entities,(that are often implicit in their representation axioms. The definition of organismic sets, for example, requires that certain essential quantities be determined from experiment: these are specified by special sets of values of general observables that are derived from physicochemical measurements(Baianu,1970; Baianu,1980; Baianu et al, 2004a.)Such observables are context-dependent and lead directly to natural transformations in categories and Topoi, that are...

  16. Effect of molecular weight on the vibronic structure of a diketopyrrolopyrrole polymer

    KAUST Repository

    Hayes, Sophia C.

    2016-09-27

    Resonance Raman Spectroscopy (RRS) is employed in this study to examine the influence of molecular weight on the optical response of a diketopyrrolopyrrole polymer (DPP-TT-T) in solution. The vibronic structure observed for the ground state absorption of this polymer is found to vary with molecular weight and solvent. Resonance Raman Intensity Analysis (RRIA) revealed that the absorption spectra can be described by at least two dipole-allowed transitions and the vibronic structure variation is due to differing contributions from linear and curved segments of the polymer.

  17. Effect of molecular weight on the vibronic structure of a diketopyrrolopyrrole polymer

    KAUST Repository

    Hayes, Sophia C.; Pieridou, Galatia; Vezie, Michelle; Few, Sheridan; Bronstein, Hugo; Meager, Iain; McCulloch, Iain; Nelson, Jenny

    2016-01-01

    Resonance Raman Spectroscopy (RRS) is employed in this study to examine the influence of molecular weight on the optical response of a diketopyrrolopyrrole polymer (DPP-TT-T) in solution. The vibronic structure observed for the ground state absorption of this polymer is found to vary with molecular weight and solvent. Resonance Raman Intensity Analysis (RRIA) revealed that the absorption spectra can be described by at least two dipole-allowed transitions and the vibronic structure variation is due to differing contributions from linear and curved segments of the polymer.

  18. ATR-FTIR and density functional theory study of the structures, energetics, and vibrational spectra of phosphate adsorbed onto goethite.

    Science.gov (United States)

    Kubicki, James D; Paul, Kristian W; Kabalan, Lara; Zhu, Qing; Mrozik, Michael K; Aryanpour, Masoud; Pierre-Louis, Andro-Marc; Strongin, Daniel R

    2012-10-16

    Periodic plane-wave density functional theory (DFT) and molecular cluster hybrid molecular orbital-DFT (MO-DFT) calculations were performed on models of phosphate surface complexes on the (100), (010), (001), (101), and (210) surfaces of α-FeOOH (goethite). Binding energies of monodentate and bidentate HPO(4)(2-) surface complexes were compared to H(2)PO(4)(-) outer-sphere complexes. Both the average potential energies from DFT molecular dynamics (DFT-MD) simulations and energy minimizations were used to estimate adsorption energies for each configuration. Molecular clusters were extracted from the energy-minimized structures of the periodic systems and subjected to energy reminimization and frequency analysis with MO-DFT. The modeled P-O and P---Fe distances were consistent with EXAFS data for the arsenate oxyanion that is an analog of phosphate, and the interatomic distances predicted by the clusters were similar to those of the periodic models. Calculated vibrational frequencies from these clusters were then correlated with observed infrared bands. Configurations that resulted in favorable adsorption energies were also found to produce theoretical vibrational frequencies that correlated well with experiment. The relative stability of monodentate versus bidentate configurations was a function of the goethite surface under consideration. Overall, our results show that phosphate adsorption onto goethite occurs as a variety of surface complexes depending on the habit of the mineral (i.e., surfaces present) and solution pH. Previous IR spectroscopic studies may have been difficult to interpret because the observed spectra averaged the structural properties of three or more configurations on any given sample with multiple surfaces.

  19. 2D IR spectra of cyanide in water investigated by molecular dynamics simulations

    Science.gov (United States)

    Lee, Myung Won; Carr, Joshua K.; Göllner, Michael; Hamm, Peter; Meuwly, Markus

    2013-01-01

    Using classical molecular dynamics simulations, the 2D infrared (IR) spectroscopy of CN− solvated in D2O is investigated. Depending on the force field parametrizations, most of which are based on multipolar interactions for the CN− molecule, the frequency-frequency correlation function and observables computed from it differ. Most notably, models based on multipoles for CN− and TIP3P for water yield quantitatively correct results when compared with experiments. Furthermore, the recent finding that T 1 times are sensitive to the van der Waals ranges on the CN− is confirmed in the present study. For the linear IR spectrum, the best model reproduces the full widths at half maximum almost quantitatively (13.0 cm−1 vs. 14.9 cm−1) if the rotational contribution to the linewidth is included. Without the rotational contribution, the lines are too narrow by about a factor of two, which agrees with Raman and IR experiments. The computed and experimental tilt angles (or nodal slopes) α as a function of the 2D IR waiting time compare favorably with the measured ones and the frequency fluctuation correlation function is invariably found to contain three time scales: a sub-ps, 1 ps, and one on the 10-ps time scale. These time scales are discussed in terms of the structural dynamics of the surrounding solvent and it is found that the longest time scale (≈10 ps) most likely corresponds to solvent exchange between the first and second solvation shell, in agreement with interpretations from nuclear magnetic resonance measurements.

  20. Introductory group theory and its application to molecular structure

    CERN Document Server

    Ferraro, John R

    1975-01-01

    The success of the first edition of this book has encouraged us to revise and update it. In the second edition we have attempted to further clarify por­ tions of the text in reference to point symmetry, keeping certain sections and removing others. The ever-expanding interest in solids necessitates some discussion on space symmetry. In this edition we have expanded the discus­ sion on point symmetry to include space symmetry. The selection rules in­ clude space group selection rules (for k = 0). Numerous examples are pro­ vided to acquaint the reader with the procedure necessary to accomplish this. Recent examples from the literature are given to illustrate the use of group theory in the interpretation of molecular spectra and in the determination of molecular structure. The text is intended for scientists and students with only a limited theoretical background in spectroscopy. For this reason we have presented detailed procedures for carrying out the selection rules and normal coor­ dinate treatment of ...

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

    Science.gov (United States)

    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.

  2. Trajectory resolved analysis of LEIS energy spectra: Neutralization and surface structure

    International Nuclear Information System (INIS)

    Beikler, Robert; Taglauer, Edmund

    2001-01-01

    For a quantitative evaluation of low-energy ion scattering (LEIS) data with respect to surface composition and structure a detailed analysis of the energy spectra is required. This includes the identification of multiple scattering processes and the determination of ion survival probabilities. We analyzed scattered ion energy spectra by using the computer code MARLOWE for which we developed a new analysis routine that allows to record energy distributions in dependence of the number of projectile-target atom collisions, in dependence of the distance of closest approach, or in dependence of the scattering crystalline layer. This procedure also permits the determination of ion survival probabilities by applying simple collision-dependent neutralization models. Experimental energy spectra for various projectile (He + , Ne + , Na + ) and target (transition metals, oxides) combinations are well reproduced and quantitative results for ion survival probabilities are obtained. These are largely in agreement with results obtained for bimetallic crystal surfaces obtained in a different way. Such MARLOWE calculations are also useful for the identification of structure relevant processes. This is shown exemplarily for the reconstructed Au(1 1 0) surface including a possibility to determine the (1x2)→(1x1) transition temperature

  3. Photoelectron spectra and electronic structure of nitrogen analogues of boron β-diketonates with aromatic substituents

    Energy Technology Data Exchange (ETDEWEB)

    Tikhonov, Sergey A., E-mail: allser@bk.ru [Far Eastern Federal University, 8 Sukhanova St., Vladivostok, 690950 (Russian Federation); Vovna, Vitaliy I. [Far Eastern Federal University, 8 Sukhanova St., Vladivostok, 690950 (Russian Federation); Borisenko, Aleksandr V. [Vladivostok Branch of Russian Customs Academy, 16v Strelkovaya St., Vladivostok, 690034 (Russian Federation)

    2016-11-15

    Highlights: • The electronic structures of three nitrogen analogues of boron β-diketonates have been investigated. • UV photoelectron spectra have been interpreted. • The structure of the UV photoelectron spectra is in good agreement with the energies and compositions of Kohn-Sham orbitals. - Abstract: The electronic structure of three nitrogen analogoues of boron β-diketonates containing aromatic substituents was studied by the ultraviolet photoelectron spectroscopy and within the density functional theory. In order to determine effects of heteroatom substitution in the chelate ligand, a comparative analysis was carried out for the electronic structure of three model compounds. In a range of model compounds, the HOMO's nature was revealed to be the same. The HOMO-1 orbital of nitrogen containing compounds is determined by the presence of lone electron pairs of nitrogen. In a range of the complexes under study, the influence of aromatic substituents on the electronic structure was defined. In the imidoylamidinate complex, in contrast to formazanates and β-diketonates, it was found the absence of any noticeable mixing of π-orbitals of the chelate and benzene rings. It was shown that within energy range to 11 eV, the calculated results reproduce well the energy differences between the ionized states of complexes.

  4. Relation between molecular electronic structure and nuclear spin-induced circular dichroism

    DEFF Research Database (Denmark)

    Štěpánek, Petr; Coriani, Sonia; Sundholm, Dage

    2017-01-01

    with spatially localized, high-resolution information. To survey the factors relating the molecular and electronic structure to the NSCD signal, we theoretically investigate NSCD of twenty structures of the four most common nucleic acid bases (adenine, guanine, thymine, cytosine). The NSCD signal correlates...... with the spatial distribution of the excited states and couplings between them, reflecting changes in molecular structure and conformation. This constitutes a marked difference to the nuclear magnetic resonance (NMR) chemical shift, which only reflects the local molecular structure in the ground electronic state....... The calculated NSCD spectra are rationalized by means of changes in the electronic density and by a sum-over-states approach, which allows to identify the contributions of the individual excited states. Two separate contributions to NSCD are identified and their physical origins and relative magnitudes...

  5. Effects of the molecular rotational dynamics on dielectric and far-infra-red spectra of anisotropic liquids

    International Nuclear Information System (INIS)

    Nordio, P.L.; Segre, U.

    1981-01-01

    Dielectric and far-infra-red spectra of uniaxial liquid-crystal phase are analysed in terms of correlation functions calculated by a memory function formalism. SAIL (strong anisotropic interaction limit) conditions are always found to apply, resulting in diffusional regime at low working frequencies. Dipole friction has been also included in the calculations to consider many-particle interactions, its effect being analogous to the introduction of slowly relaxing local structures. (author)

  6. Quantum-mechanical study of energies, structures, and vibrational spectra of the H(D)Cl complexed with dimethyl ether

    Energy Technology Data Exchange (ETDEWEB)

    Boda, Łukasz, E-mail: lboda@chemia.uj.edu.pl; Boczar, Marek; Gług, Maciej; Wójcik, Marek J. [Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków (Poland)

    2015-11-28

    Interaction energies, molecular structure and vibrational frequencies of the binary complex formed between H(D)Cl and dimethyl ether have been obtained using quantum-chemical methods. Equilibrium and vibrationally averaged structures, harmonic and anharmonic wavenumbers of the complex and its deuterated isotopomer were calculated using harmonic and anharmonic second-order perturbation theory procedures with Density Functional Theory B3LYP and B2PLYP-D and ab initio Møller-Plesset second-order methods, and a 6-311++G(3d,3p) basis set. A phenomenological model describing anharmonic-type vibrational couplings within hydrogen bonds was developed to explain the unique broadening and fine structure, as well as the isotope effect of the Cl–H and Cl–D stretching IR absorption bands in the gaseous complexes with dimethyl ether, as an effect of hydrogen bond formation. Simulations of the rovibrational structure of the Cl–H and Cl–D stretching bands were performed and the results were compared with experimental spectra.

  7. Projected quasiparticle theory for molecular electronic structure

    Science.gov (United States)

    Scuseria, Gustavo E.; Jiménez-Hoyos, Carlos A.; Henderson, Thomas M.; Samanta, Kousik; Ellis, Jason K.

    2011-09-01

    We derive and implement symmetry-projected Hartree-Fock-Bogoliubov (HFB) equations and apply them to the molecular electronic structure problem. All symmetries (particle number, spin, spatial, and complex conjugation) are deliberately broken and restored in a self-consistent variation-after-projection approach. We show that the resulting method yields a comprehensive black-box treatment of static correlations with effective one-electron (mean-field) computational cost. The ensuing wave function is of multireference character and permeates the entire Hilbert space of the problem. The energy expression is different from regular HFB theory but remains a functional of an independent quasiparticle density matrix. All reduced density matrices are expressible as an integration of transition density matrices over a gauge grid. We present several proof-of-principle examples demonstrating the compelling power of projected quasiparticle theory for quantum chemistry.

  8. Molecular motion and structure in plastics

    International Nuclear Information System (INIS)

    Doolan, K.R.; Baxter, M.

    2000-01-01

    Full text: When molten thermoplastics solidify, the polymeric chains form a completely amorphous structure or a mixture of crystalline and amorphous regions. Measurement of Nuclear Magnetic Resonance (NMR) relaxation times provides information about the configuration and molecular motion of polymeric chains in solid plastics. We are currently measuring the NMR relaxation times T 1 , T 2 , T 2 and T 1p as a function of temperature using a Bruker High Power pulsed NMR Spectrometer for several different classes of thermoplastics containing varying concentrations of inorganic filler materials. We present data here for T 1 , and T 2 obtained for polyethylenes, polypropylenes, polystyrenes and acrylics in the temperature range 100 K to 450 K. At temperatures below 320 K, all of the polyethylenes and polypropylenes and some of the polystyrenes and acrylics produced NMR signals after a single radio frequency (RF) pulse with rapidly and slowly decaying components corresponding to the rigid and flexible regions within the plastic. From these results we have estimated using Mathematica the amount of crystallinity within the polyethylenes and polypropylenes. For the impact modified polystyrenes and acrylics studied we have estimated the amounts of elastomeric phases present. We find that the initial rapid decay signal produced by polyethylenes and polypropylenes is Gaussian while the long tail is Lorentzian. All of the signal components from the polystyrenes and the acrylics were fitted using Lorentzian functions indicating their structures are highly amorphous. Addition of CaCO 3 filler to polypropylene resins appears to reduce the crystallinity of the material. We also present data for the activation energy of the molecular motion inducing longitudinal relaxation, from T 1 measurements

  9. Soil-structure interaction effects on containment fragilities and floor response spectra statistics

    International Nuclear Information System (INIS)

    Pires, J.; Reich, M.; Chokshi, N.C.

    1987-01-01

    The probability-based method for the reliability evaluation of nuclear structures developed at Brookhaven National Laboratory (BNL) is extended to include soil-structure interaction effects. A reinforced concrete containment is analyzed in order to investigate the soil-structure interaction effects on: structural fragilities; floor response spectra statistics and acceleration response correlations. To include the effect of soil flexibility on the reliability assessment the following two step approach is used. In the first step, the lumped parameter method for soil-structure interaction analysis is used together with a stick model representation of the structure in order to obtain the motions of the foundation plate. These motions, which include both translations and rotations of the foundation plate, are expressed in terms of the power-spectral density of the free-field ground excitation and the transfer function of the total acceleration response of the foundation. The second step involves a detailed finite element model of the structure subjected to the interaction motions computed from step one. Making use of the structural model and interaction motion the reliability analysis method yields the limit stat probabilities and fragility data for the structure

  10. Molecular structure input on the web

    Directory of Open Access Journals (Sweden)

    Ertl Peter

    2010-02-01

    Full Text Available Abstract A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential. The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

  11. Ab initio Molecular Orbital Studies of the Vibrational Spectra of some ...

    African Journals Online (AJOL)

    NJD

    2004-06-15

    Jun 15, 2004 ... molecular complexes containing the family of Lewis acids carbon dioxide ..... cating a successively weaker interaction along the series. For. SO2. ..... Schleyer, H.F. Schaefer III, P.R. Scheiner, W.L. Jorgensen, W. Thiel and.

  12. Some aspects of floor spectra of 1DOF nonlinear primary structures

    International Nuclear Information System (INIS)

    Politopoulos, I.; Feau, C.

    2007-01-01

    In this paper the influence of the nonlinear behaviour of the primary structure on floor spectra is investigated by means of simple models. The general trends of floor spectra for different types of nonlinear behaviour of one degree of freedom (1DOF) primary structure are shown and we point out their common futures and their differences. A special attention is given to the cases of elastoplastic and nonlinear elastic behaviours and methods to determine an equivalent linear oscillator are proposed. The properties (frequency and damping) of this equivalent linear oscillator are quite different from the properties of equivalent linear oscillators commonly considered in practice. In particular, in the case of elastoplastic behaviour, there is no frequency shift and damping is smaller than assumed by other methods commonly used. In the case of nonlinear elastic behaviour, the concept of an equivalent frequency which is a random variable is used. Finally, a design floor spectrum of primary structures, exhibiting energy dissipating nonlinear behaviour is proposed. (authors)

  13. Structure, spectra and phase transition in p-nitroanilinium perchlorate crystal

    Energy Technology Data Exchange (ETDEWEB)

    Marchewka, M.K.; Drozd, M.; Pietraszko, A

    2003-07-25

    The first X-ray diffraction and vibrational spectroscopic analysis of a novel complex between p-nitroaniline and perchloric acid is reported. The structure was solved in 295 K. Room temperature powder infrared and Raman measurements for the p-nitroanilinium perchlorate (1:1) crystals were carried out. The vibrational spectra in the region of internal vibrations of ions corroborates the X-ray data which show that p-nitroaniline molecule is monoprotonated. DSC measurements on powder sample indicate the phase transition point at about 213 and 208 K for heating and cooling, respectively. No detectable signal was observed during powder test for second harmonic generation.

  14. Interplay of intra-atomic and interatomic effects: An investigation of the 2p core level spectra of atomic Fe and molecular FeCl2

    International Nuclear Information System (INIS)

    Richter, T.; Wolff, T.; Zimmermann, P.; Godehusen, K.; Martins, M.

    2004-01-01

    The 2p photoabsorption and photoelectron spectra of atomic Fe and molecular FeCl 2 were studied by photoion and photoelectron spectroscopy using monochromatized synchrotron radiation and atomic or molecular beam technique. The atomic spectra were analyzed with configuration interaction calculations yielding excellent agreement between experiment and theory. For the analysis of the molecular photoelectron spectrum which shows pronounced interatomic effects, a charge transfer model was used, introducing an additional 3d 7 configuration. The resulting good agreement between the experimental and theoretical spectrum and the remarkable similarity of the molecular with the corresponding spectrum in the solid phase opens a way to a better understanding of the interplay of the interatomic and intra-atomic interactions in the 2p core level spectra of the 3d metal compounds

  15. Phosphorescent Molecularly Doped Light-Emitting Diodes with Blended Polymer Host and Wide Emission Spectra

    Directory of Open Access Journals (Sweden)

    Jun Wang

    2013-01-01

    Full Text Available Stable green light emission and high efficiency organic devices with three polymer layers were fabricated using bis[2-(4′-tert-butylphenyl-1-phenyl-1H-benzoimidazole-N,C2′] iridium(III (acetylacetonate doped in blended host materials. The 1 wt% doping concentration showed maximum luminance of 7841 cd/cm2 at 25.6 V and maximum current efficiency of 9.95 cd/A at 17.2 V. The electroluminescence spectra of devices indicated two main peaks at 522 nm and 554 nm coming from phosphor dye and a full width at half maximum (FWHM of 116 nm. The characteristics of using blended host, doping iridium complex, emission spectrum, and power efficiency of organic devices were investigated.

  16. Regio-Regular Oligo and Poly(3-hexyl thiophene): Precise Structural Markers from the Vibrational Spectra of Oligomer Single Crystals.

    KAUST Repository

    Brambilla, Luigi; Tommasini, Matteo; Botiz, Ioan; Rahimi, Khosrow; Agumba, John O.; Stingelin, Natalie; Zerbi, Giuseppe

    2014-01-01

    , namely, amorphous, semicrystalline, polycrystalline and single crystal. We have based our analysis on the spectra of the (3HT)8 single crystal (whose structure has been determined by selected area electron diffraction) taken as reference

  17. The general atomic and molecular electronic structure system HONDO: Version 7.0

    International Nuclear Information System (INIS)

    Dupuis, M.; Watts, J.D.; Villar, H.O.; Hurst, G.J.B.

    1989-01-01

    We describe a computer program for ab initio quantum mechanical calculations of atomic and molecular wavefunctions and energies. Capabilities for the calculation of energy gradients and second derivatives with respect to nuclear coordinates are provided for several types of wavefunctions. Calculations of many molecular properties based on the electron density are possible. The program contains automated algorithms for the determination of equilibrium structures, saddle points, reaction pathways, vibrational spectra including infrared and Raman intensities. We illustrate the capabilities of the program by highlighting research problems recently investigated with the present program. (orig.)

  18. Theoretical Study of Copper Complexes: Molecular Structure, Properties, and Its Application to Solar Cells

    Directory of Open Access Journals (Sweden)

    Jesus Baldenebro-Lopez

    2013-01-01

    Full Text Available We present a theoretical investigation of copper complexes with potential applications as sensitizers for solar cells. The density functional theory (DFT and time-dependent DFT were utilized, using the M06 hybrid meta-GGA functional with the LANL2DZ (D95V on first row and DZVP basis sets. This level of calculation was used to find the optimized molecular structure, the absorption spectra, the molecular orbitals energies, and the chemical reactivity parameters that arise from conceptual DFT. Solvent effects have been taken into account by an implicit approach, namely, the polarizable continuum model (PCM, using the nonequilibrium version of the IEF-PCM model.

  19. Response spectra for differential motion of structures supports during earthquakes in Egypt

    Directory of Open Access Journals (Sweden)

    Mohamed I.S. Elmasry

    2012-12-01

    Full Text Available Differential motions of ground supports of stiff structures with large plan dimensions and separate foundations under earthquakes were studied by researchers during the last few decades. Such a type of structural response was previously underestimated. The importance of studying such a response comes up from the fact that usually the structures affected are of strategic importance such as bridges. During their expected life, structures may experience vibrations excited by ground waves of short wavelengths during near-source earthquakes, or during amplified earthquake signals, during explosions, or during vibrations induced from nearby strong vibration sources. This is the case when the differential motion of supports becomes considerable. This paper aims to review the effects of seismic signal variations along the structures dimensions with emphasis on Egypt as a case study. The paper shows some patterns of the damage imposed by such differential motion. A replication of the differential motion in the longitudinal direction is applied on a frame bridge model. The resulting straining actions show the necessity for considering the differential motion of supports in the design of special structures in Egypt. Finally, response spectra for the differential motion of supports, based on the available data from previous earthquakes in Egypt, is derived and proposed for designers to include in the design procedure when accounting for such type of structural response, and especially in long-span bridges.

  20. The cyclopropene radical cation: Rovibrational level structure at low energies from high-resolution photoelectron spectra

    Energy Technology Data Exchange (ETDEWEB)

    Vasilatou, K.; Michaud, J. M.; Baykusheva, D.; Grassi, G.; Merkt, F. [Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093 Zurich (Switzerland)

    2014-08-14

    The cyclopropene radical cation (c-C{sub 3}H{sub 4}{sup +}) is an important but poorly characterized three-membered-ring hydrocarbon. We report on a measurement of the high-resolution photoelectron and photoionization spectra of cyclopropene and several deuterated isotopomers, from which we have determined the rovibrational energy level structure of the X{sup ~+} {sup 2}B{sub 2} ground electronic state of c-C{sub 3}H{sub 4}{sup +} at low energies for the first time. The synthesis of the partially deuterated isotopomers always resulted in mixtures of several isotopomers, differing in their number of D atoms and in the location of these atoms, so that the photoelectron spectra of deuterated samples are superpositions of the spectra of several isotopomers. The rotationally resolved spectra indicate a C{sub 2v}-symmetric R{sub 0} structure for the ground electronic state of c-C{sub 3}H{sub 4}{sup +}. Two vibrational modes of c-C{sub 3}H{sub 4}{sup +} are found to have vibrational wave numbers below 300 cm{sup −1}, which is surprising for such a small cyclic hydrocarbon. The analysis of the isotopic shifts of the vibrational levels enabled the assignment of the lowest-frequency mode (fundamental wave number of ≈110 cm{sup −1} in c-C{sub 3}H{sub 4}{sup +}) to the CH{sub 2} torsional mode (ν{sub 8}{sup +}, A{sub 2} symmetry) and of the second-lowest-frequency mode (≈210 cm{sup −1} in c-C{sub 3}H{sub 4}{sup +}) to a mode combining a CH out-of-plane with a CH{sub 2} rocking motion (ν{sub 15}{sup +}, B{sub 2} symmetry). The potential energy along the CH{sub 2} torsional coordinate is flat near the equilibrium structure and leads to a pronounced anharmonicity.

  1. Reconstruction of structural damage based on reflection intensity spectra of fiber Bragg gratings

    International Nuclear Information System (INIS)

    Huang, Guojun; Wei, Changben; Chen, Shiyuan; Yang, Guowei

    2014-01-01

    We present an approach for structural damage reconstruction based on the reflection intensity spectra of fiber Bragg gratings (FBGs). Our approach incorporates the finite element method, transfer matrix (T-matrix), and genetic algorithm to solve the inverse photo-elastic problem of damage reconstruction, i.e. to identify the location, size, and shape of a defect. By introducing a parameterized characterization of the damage information, the inverse photo-elastic problem is reduced to an optimization problem, and a relevant computational scheme was developed. The scheme iteratively searches for the solution to the corresponding direct photo-elastic problem until the simulated and measured (or target) reflection intensity spectra of the FBGs near the defect coincide within a prescribed error. Proof-of-concept validations of our approach were performed numerically and experimentally using both holed and cracked plate samples as typical cases of plane-stress problems. The damage identifiability was simulated by changing the deployment of the FBG sensors, including the total number of sensors and their distance to the defect. Both the numerical and experimental results demonstrate that our approach is effective and promising. It provides us with a photo-elastic method for developing a remote, automatic damage-imaging technique that substantially improves damage identification for structural health monitoring. (paper)

  2. Oxygen infrared spectra of oxyhemoglobins and oxymyoglobins. Evidence of two major liganded O2 structures

    International Nuclear Information System (INIS)

    Potter, W.T.; Tucker, M.P.; Houtchens, R.A.; Caughey, W.S.

    1987-01-01

    The dioxygen stretch bands in infrared spectra for solutions of oxy species of human hemoglobin A and its separated subunits, human mutant hemoglobin Zurich (β63His to Arg), rabbit hemoglobin, lamprey, hemoglobin, sperm whale myoglobin, bovine myoglobin, and a sea worm chlorocruorin are examined. Each protein exhibits multiple isotope-sensitive bands between 1160 and 1060 cm -1 for the liganded 16 O 2 , 17 O 2 , and 18 O 2 . The O-O stretch bands for each of the mammalian myoglobins and hemoglobins are similar, with frequencies that differ between proteins by only 3-5 cm -1 . The spectra for the lamprey and sea worm hemoglobins exhibit greater diversity. For all proteins an O-O stretch band expected to occur near 1125 cm -1 for 16 O 2 and 17 O 2 , but not 18 O 2 , appears split by ∼25 cm -1 due to an unidentified perturbation. The spectrum for each dioxygen isotope, if unperturbed, would contain two strong bands for the mammalian myoglobins (1150 and 1120 cm -1 ) and hemoglobins (1155 and 1125 cm -1 ). Two strong bands separated by ∼30 cm -1 for each oxy heme protein subunit indicate that two major protein conformations (structure) that differ substantially in O 2 bonding are present. The two dioxygen structures can result from a combination of dynamic distal and proximal effects upon the O 2 ligand bound in a bent-end-on stereochemistry

  3. Molecular structures and intramolecular dynamics of pentahalides

    Science.gov (United States)

    Ischenko, A. A.

    2017-03-01

    This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

  4. Mass Spectra-Based Framework for Automated Structural Elucidation of Metabolome Data to Explore Phytochemical Diversity

    Science.gov (United States)

    Matsuda, Fumio; Nakabayashi, Ryo; Sawada, Yuji; Suzuki, Makoto; Hirai, Masami Y.; Kanaya, Shigehiko; Saito, Kazuki

    2011-01-01

    A novel framework for automated elucidation of metabolite structures in liquid chromatography–mass spectrometer metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method. PMID:22645535

  5. Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity

    Directory of Open Access Journals (Sweden)

    Fumio eMatsuda

    2011-08-01

    Full Text Available A novel framework for automated elucidation of metabolite structures in liquid chromatography-mass spectrometer (LC-MS metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method.

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

    Science.gov (United States)

    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.

  7. Structure and luminescence spectra of lutetium and yttrium borates synthesized from ammonium nitrate melt

    International Nuclear Information System (INIS)

    Klassen, Nikolay V.; Shmurak, Semion Z.; Shmyt'ko, Ivan M.; Strukova, Galina K.; Derenzo, Stephen E.; Weber, Marvin J.

    2005-01-01

    Lutetium and yttrium borates doped with europium, terbium, gadolinium, etc. have been synthesized by dissolving initial oxides and nitrates in ammonium nitrate melt and thermal decomposition of the solvent. Annealings in the range of 500-1100 deg. C modified the dimensions of the grains from 2 to 3 nm to more than 100 nm. Significant dependence of the structure of lutetium borate on slight doping with rare earth ions has been found: terbium makes high-temperature vaterite phase preferential at room temperature, whereas europium stabilizes low-temperature calcite phase. Influence of the structure of the borates on the pattern of the luminescence spectra of europium dopant was observed. Possibilities for manufacturing of scintillating lutetium borate ceramics by means of this method of synthesis are discussed

  8. Structure and luminescence spectra of lutetium and yttrium borates synthesized from ammonium nitrate melt

    Science.gov (United States)

    Klassen, Nikolay V.; Shmurak, Semion Z.; Shmyt'ko, Ivan M.; Strukova, Galina K.; Derenzo, Stephen E.; Weber, Marvin J.

    2005-01-01

    Lutetium and yttrium borates doped with europium, terbium, gadolinium, etc. have been synthesized by dissolving initial oxides and nitrates in ammonium nitrate melt and thermal decomposition of the solvent. Annealings in the range of 500-1100°C modified the dimensions of the grains from 2 to 3 nm to more than 100 nm. Significant dependence of the structure of lutetium borate on slight doping with rare earth ions has been found: terbium makes high-temperature vaterite phase preferential at room temperature, whereas europium stabilizes low-temperature calcite phase. Influence of the structure of the borates on the pattern of the luminescence spectra of europium dopant was observed. Possibilities for manufacturing of scintillating lutetium borate ceramics by means of this method of synthesis are discussed.

  9. Electronic Structures of Purple Bronze KMo6O17 Studied by X-Ray Photoemission Spectra

    Science.gov (United States)

    Qin, Xiaokui; Wei, Junyin; Shi, Jing; Tian, Mingliang; Chen, Hong; Tian, Decheng

    X-ray photoemission spectroscopy study has been performed for the purple bronze KMo6O17. The structures of conduction band and valence band are analogous to the results of ultraviolet photoemission spectra and are also consistent with the model of Travaglini et al., but the gap between conduction and valence band is insignificant. The shape of asymmetric and broadening line of O-1s is due to unresolved contributions from the many inequivalent oxygen sites in this crystal structure. Mo 3d core-level spectrum reveals that there are two kinds of valence states of Molybdenum (Mo+5 and Mo+6). The calculated average valence state is about +5.6, which is consistent with the expectation value from the composition of this material. The tail of Mo-3d spectrum toward higher binding energy is the consequence of the excitation of electron-hole pairs with singularity index of 0.21.

  10. Spectral scalability and optical spectra of fractal multilayer structures: FDTD analysis

    Science.gov (United States)

    Simsek, Sevket; Palaz, Selami; Mamedov, Amirullah M.; Ozbay, Ekmel

    2017-01-01

    An investigation of the optical properties and band structures for the conventional and Fibonacci photonic crystals (PCs) based on SrTiO3 and Sb2Te3 is made in the present research. Here, we use one-dimensional SrTiO3- and Sb2Te3-based layers. We have theoretically calculated the photonic band structure and transmission spectra of SrTiO3- and Sb2Te3-based PC superlattices. The position of minima in the transmission spectrum correlates with the gaps obtained in the calculation. The intensity of the transmission depths is more intense in the case of higher refractive index contrast between the layers.

  11. The effects of pseudo magnetic fields in molecular spectra and scattering

    International Nuclear Information System (INIS)

    Kendrick, B.K.

    1996-01-01

    Pseudo magnetic fields appear in the Born-Oppenheimer method for molecules when conical intersections or electronic angular momenta are taken into account. These fields are not real magnetic fields but they have the same mathematical properties and can lead to real observable effects in the dynamics of molecules. A general vector potential (gauge theory) approach for including these field effects in the Born-Oppenheimer method is introduced and applied to H + O 2 scattering and the vibrational spectrum of Na 3 (X) for zero total angular momentum (J = 0). The scattering results for HO 2 show significant shifts in the resonance energies and lifetimes due to a magnetic solenoid type field originating from the C 2v conical intersection in HO 2 . Significant changes in the state-to-state transition probabilities are also observed. The non-degenerate A 1 and A 2 vibrational spectra of Na 3 (X) show significant shifts in the energy levels due to a magnetic solenoid type field originating from the D 3h conical intersection in Na 3 . These two examples show that the effects of pseudo magnetic fields can be significant and in many cases they must be included in order to obtain agreement between theory and experiment. The newly developed gauge theory techniques for treating pseudo magnetic fields are also relevant for including the effects of real magnetic fields

  12. Quantitative analysis of satellite structures in XPS spectra of gold and silver

    Energy Technology Data Exchange (ETDEWEB)

    Pauly, N., E-mail: nipauly@ulb.ac.be [Université libre de Bruxelles, Service de Métrologie Nucléaire (CP 165/84), 50 av. F. D. Roosevelt, B-1050 Brussels (Belgium); Yubero, F. [Instituto de Ciencia de Materiales de Sevilla, Univ. Sevilla – CSIC, av. Américo Vespucio 49, E-41092 Sevilla (Spain); Tougaard, S. [Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M (Denmark)

    2016-10-15

    Highlights: • Accurate determination of the energy loss functions for Au and Ag. • Calculation of effective inelastic electron scattering cross sections for Au and Ag. • Convolution of these cross sections with varying model primary spectra F(E). • Variation of F(E) until a good agreement with experimental XPS spectra is reached. • Quantitative determination of Au 4f and Ag 3d characteristics. - Abstract: Identification of specific chemical states and local electronic environments at surfaces by X-ray photoelectron spectroscopy (XPS) is often difficult because it is not straightforward to quantitatively interpret the shape and intensity of shake-up structures that originate from the photoexcitation process. Indeed the shape and intensity of measured XPS structures are strongly affected by both extrinsic excitations due to electron transport out of the surface and intrinsic excitations induced by the sudden creation of the static core hole. These processes must be taken into account to quantitatively extract, from experimental XPS, the primary excitation spectrum of the considered transition which includes all effects that are part of the initial photo-excitation process, i.e. lifetime broadening, spin–orbit coupling, and multiplet splitting. It was previously shown [N. Pauly, S. Tougaard, F. Yubero, Surf. Sci. 620 (2014) 17] that both extrinsic and intrinsic excitations could be included in an effective energy-differential inelastic electron scattering cross section for XPS which is then convoluted with the primary excitation spectrum to model the full XPS spectrum. This method can thus be applied to determine the primary excitation spectrum from any XPS spectrum. We use this approach in the present paper to determine the Au 4f and Ag 3d photoemission spectra from pure metals. We observe that characteristic energy loss features of the XPS spectra are not only due to photoelectron energy losses. We thus prove the existence of a double shake-up process

  13. Understanding the interface between silicon-based materials and water: Molecular-dynamics exploration of infrared spectra

    Directory of Open Access Journals (Sweden)

    José A. Martinez-Gonzalez

    2017-11-01

    Full Text Available Molecular-dynamics simulations for silicon, hydrogen- and hydroxyl-terminated silicon in contact with liquid water, at 220 and 300 K, display water-density ‘ordering’ along the laboratory z-axis, emphasising the hydrophobicity of the different systems and the position of this first adsorbed layer. Density of states (DOS of the oxygen and proton velocity correlation functions (VACFs and infrared (IR spectra of the first monolayer of adsorbed water, calculated via Fourier transformation, indicate similarities to more confined, ice-like dynamical behaviour (redolent of ice. It was observed that good qualitative agreement is obtained between the DOS for this first layer in all systems. The DOS for the lower-frequency zone indicates that for the interface studied (i.e., the first layer near the surface, the water molecules try to organise in a similar form, and that this form is intermediate between liquid water and ice. For IR spectra, scrutiny of the position of the highest-intensity peaks for the stretching and bending bands indicate that such water molecules in the first solvating layer are organised in an intermediate fashion between ice and liquid water.

  14. Molecular structure, vibrational spectroscopic studies and natural

    Indian Academy of Sciences (India)

    The entropy of the title compound was also performed at HF using the hybrid functional BLYP and B3LYP with 6-31 G(d,p) as basis set levels of theory. Natural bond orbital (NBO) analysis of the title molecule is also carried out. The theoretical spectrogram for FTIR spectra of the title molecule has been constructed.

  15. ExoMol molecular line lists - XXVII: spectra of C2H4

    Science.gov (United States)

    Mant, Barry P.; Yachmenev, Andrey; Yurchenko, Jonathan Tennyson Sergei N.

    2018-05-01

    A new line list for ethylene, 12C21H4 is presented. The line list is based on high level ab initiopotential energy and dipole moment surfaces. The potential energy surface is refined by fitting to experimental energies. The line list covers the range up to 7000 cm-1(1.43 μm) with all ro-vibrational transitions (50 billion) with the lower state below 5000 cm-1included and thus should be applicable for temperatures up to 700 K. A technique for computing molecular opacities from vibrational band intensities is proposed and used to provide temperature dependent cross sections of ethylene for shorter wavelength and higher temperatures. When combined with realistic band profiles (such as the proposed three-band model), the vibrational intensity technique offers a cheap but reasonably accurate alternative to the full ro-vibrational calculations at high temperatures and should be reliable for representing molecular opacities. The C2H4 line list, which is called MaYTY, is rmade available in electronic form from the CDS (http://cdsarc.u-strasbg.fr) and ExoMol (www.exomol.com) databases.

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

    Science.gov (United States)

    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.

  17. Synthesis, spectra, and the crystal structure of α-(3,3-dimethyl-3,4-dihydroisoquinolyl-1)-hydroxyiminoacetamide

    International Nuclear Information System (INIS)

    Sokol, V.I.; Davydov, V.V.; Kartashova, I.V.; Zaitsev, B.E.; Shklyaev, Yu.V.; Ryabov, M.A.; Sergienko, V.S.

    1996-01-01

    α-(3,3-Dimethyl-3,4-dihydroisoquinolyl-1)-hydroxyiminoacetamide (I) was synthesized, and its x-ray structure analysis was performed (Enraf-Nonius CAD-4 diffractometer; MoKα radiation; graphite monochromator; θ/2θ scan; 2θmax=56 deg. ; 2496 reflections with I≥2σ(I); and R=0.038). Crystals of I are monoclinic; a=11.67(1), b=8.365(3), and c=15.22(2) A; β=107.7(1) deg.; V=1415.2(2) A 3; ρ(calc)=1.236 g/cm3; Z=4; and sp. gr. P21/n. I crystallizes as a monohydrate, and its formula is C13H15N3O2·H2O. In a crystal, I exists in a azomethineoxime tautomeric form. The planes of amideoxime and dihydroisoquinoline moieties are nearly orthogonal to each other. According to IR and electronic spectra, when passing from crystal to solution the conformation of I changes only slightly. An effect of water molecules on the molecular structure of I is discussed

  18. ExoMol molecular line lists - XXVI: spectra of SH and NS

    Science.gov (United States)

    Yurchenko, Sergei N.; Bond, Wesley; Gorman, Maire N.; Lodi, Lorenzo; McKemmish, Laura K.; Nunn, William; Shah, Rohan; Tennyson, Jonathan

    2018-07-01

    Line lists for the sulphur-containing molecules SH (the mercapto radical) and NS are computed as part of the ExoMol project. These line lists consider transitions within the X2Π ground state for 32SH, 33SH, 34SH,36SH and, 32SD, and 14N32S, 14N33S, 14N34S, 14N36S, and 15N32S. Ab initio potential energy (PEC) and spin-orbit coupling (SOC) curves are computed and then improved by fitting to experimentally observed transitions. Fully ab initio dipole moment curves (DMCs) computed at high level of theory are used to produce the final line lists. For SH, our fit gives a root-mean-square (rms) error of 0.03 cm-1 between the observed (vmax = 4, Jmax = 34.5) and calculated transitions wavenumbers; this is extrapolated such that all X2Π rotational-vibrational-electronic (rovibronic) bound states are considered. For 32SH the resulting line list contains about 81 000 transitions and 2300 rovibronic states, considering levels up to vmax = 14 and Jmax = 60.5. For NS the refinement used a combination of experimentally determined frequencies and energy levels and led to an rms-fitting error of 0.002 cm-1. Each NS-calculated line list includes around 2.8 million transitions and 31 000 rovibronic states with a vibrational range up to v = 53 and rotational range up to J = 235.5, which covers up to 23 000 cm-1. Both line lists should be complete for temperatures up to 5000 K. Example spectra simulated using this line list are shown and comparisons made to the existing data in the CDMS data base. The line lists are available from the CDS (http://cdsarc.u-strasbg.fr) and ExoMol (www.exomol.com) data bases.

  19. ExoMol molecular line lists - XXIII. Spectra of PO and PS

    Science.gov (United States)

    Prajapat, Laxmi; Jagoda, Pawel; Lodi, Lorenzo; Gorman, Maire N.; Yurchenko, Sergei N.; Tennyson, Jonathan

    2017-12-01

    Comprehensive line lists for phosphorus monoxide (31P16O) and phosphorus monosulphide (31P32S) in their X 2Π electronic ground state are presented. The line lists are based on new ab initio potential energy (PEC), spin-orbit (SOC) and dipole moment (DMC) curves computed using the MRCI+Q-r method with aug-cc-pwCV5Z and aug-cc-pV5Z basis sets. The nuclear motion equations (i.e. the rovibronic Schrödinger equations for each molecule) are solved using the program DUO. The PECs and SOCs are refined in least-squares fits to available experimental data. Partition functions, Q(T), are computed up to T = 5000 K, the range of validity of the line lists. These line lists are the most comprehensive available for either molecule. The characteristically sharp peak of the Q-branches from the spin-orbit split components gives useful diagnostics for both PO and PS in spectra at infrared wavelengths. These line lists should prove useful for analysing observations and setting up models of environments such as brown dwarfs, low-mass stars, O-rich circumstellar regions and potentially for exoplanetary retrievals. Since PS is yet to be detected in space, the role of the two lowest excited electronic states (a 4Π and B 2Π) are also considered. An approximate line list for the PS X-B electronic transition, which predicts a number of sharp vibrational bands in the near ultraviolet, is also presented. The line lists are available from the CDS (http://cdsarc.u-strasbg.fr) and ExoMol (www.exomol.com) data bases.

  20. ExoMol molecular line lists - XXVI: spectra of SH and NS

    Science.gov (United States)

    Yurchenko, Sergei N.; Bond, Wesley; Gorman, Maire N.; Lodi, Lorenzo; McKemmish, Laura K.; Nunn, William; Shah, Rohan; Tennyson, Jonathan

    2018-04-01

    Line lists for the sulphur-containing molecules SH (the mercapto radical) and NS are computed as part of the ExoMol project. These line lists consider transitions within the X 2Π ground state for 32SH, 33SH, 34SH and 32SD, and 14N32S, 14N33S, 14N34S, 14N36S and 15N32S. Ab initio potential energy (PEC) and spin-orbit coupling (SOC) curves are computed and then improved by fitting to experimentally observed transitions. Fully ab initio dipole moment curves (DMCs) computed at high level of theory are used to produce the final line lists. For SH, our fit gives a root-mean-square (rms) error of 0.03 cm-1 between the observed (vmax = 4, Jmax = 34.5) and calculated transitions wavenumbers; this is extrapolated such that all X 2Π rotational-vibrational-electronic (rovibronic) bound states are considered. For 32SH the resulting line list contains about 81 000 transitions and 2 300 rovibronic states, considering levels up to vmax = 14 and Jmax = 60.5. For NS the refinement used a combination of experimentally determined frequencies and energy levels and led to an rms fitting error of 0.002 cm-1. Each NS calculated line list includes around 2.8 million transitions and 31 000 rovibronic states with a vibrational range up to v = 53 and rotational range to J = 235.5, which covers up to 23 000 cm-1. Both line lists should be complete for temperatures up to 5000 K. Example spectra simulated using this line list are shown and comparisons made to the existing data in the CDMS database. The line lists are available from the CDS (http://cdsarc.u-strasbg.fr) and ExoMol (www.exomol.com) data bases.

  1. Synthesis, crystal structure, and spectra of 3,3- dimethyl-1-N-(1'-phenyl-2',3'-dimethyl-5'-oxo-3'- pyrazolin-4'-yl)imino-1,2,3,4-tetrahydroisoquinoline

    International Nuclear Information System (INIS)

    Sokol, V.I.; Ryabov, M.A.; Merkur'eva, N.Yu.; Davydov, V.V.; Zaitsev, B.E.; Shklyaev, Yu.V.; Sergienko, V.S.; Zaitsev, B.E.

    1996-01-01

    The synthesis and the crystal and molecular structure of 3,3-dimethyl-1-N-(1'-phenyl-2',3'- dimethyl-5'-oxo-3'-pyrazolin-4'-yl)imino-1,2,3,4-tetrahydroisoquinoline are reported. As is evidenced by the 1H NMR, IR, and electron spectra, the tautomeric form of the compounds observed in the crystal is also retained in solutions

  2. Analysis of fine structure of X-ray spectra from laser-irradiated gold dot

    International Nuclear Information System (INIS)

    Yang Guohong; Zhang Jiyan; Zhang Baohan; Zhou Yuqing; Li Jun

    2000-01-01

    The X-ray emission spectra from highly stripped plasma of gold has been observed by focusing a Nd-glass frequency tripled laser beam onto the surface of the gold dot at the XINGGUANG II laser facilities. The spectra of gold ions in the range of 0.0003 nm-0.0004 nm was recorded using the plate PET (2d = 0.8742 nm) crystal spectrometer. The code of average energy of relativistic sub-arrays was built on the basis of the code MCDF (Multi-Configuration-Dirac-Fock). Using the spin-orbit-split-arrays (SOSA) formalism, mean wavelengths and full widths at half height of isolated peaks of sub-arrays of lower charged gold ions, isoelectronic with Cu, Zn, Ga and Ge, was calculated. Twenty-six lines are interpreted, they pertain mainly to transitions of 3d-nf (n = 5,6,7) of gold ions from Ni-like to As-like. These results of experiment and calculation have important application in plasma diagnostics and examination of high Z elemental atomic structure calculation

  3. Electronic structure of SnS deduced from photoelectron spectra and band-structure calculations

    NARCIS (Netherlands)

    Ettema, A.R.H.F.; Groot, R.A. de; Haas, C.; Turner, T.S.

    1992-01-01

    SnS is a layer compound with a phase transition from a high-temperature β phase to a low-temperature α phase with a lower symmetry. Ab initio band-structure calculations are presented for both phases. The calculations show that the charge distributions in the two phases are very similar. However,

  4. Molecular structure and motion in zero field magnetic resonance

    International Nuclear Information System (INIS)

    Jarvie, T.P.

    1989-10-01

    Zero field magnetic resonance is well suited for the determination of molecular structure and the study of motion in disordered materials. Experiments performed in zero applied magnetic field avoid the anisotropic broadening in high field nuclear magnetic resonance (NMR) experiments. As a result, molecular structure and subtle effects of motion are more readily observed

  5. Pyrimidine and halogenated pyrimidines near edge x-ray absorption fine structure spectra at C and N K-edges: experiment and theory

    International Nuclear Information System (INIS)

    Bolognesi, P.; O'Keeffe, P.; Ovcharenko, Y.; Coreno, M.; Avaldi, L.; Feyer, V.; Plekan, O.; Prince, K. C.; Zhang, W.; Carravetta, V.

    2010-01-01

    The inner shell excitation of pyrimidine and some halogenated pyrimidines near the C and N K-edges has been investigated experimentally by near edge x-ray absorption fine structure spectroscopy and theoretically by density functional theory calculations. The selected targets, 5-Br-pyrimidine, 2-Br-pyrimidine, 2-Cl-pyrimidine, and 5-Br-2-Cl-pyrimidine, allow the effects of the functionalization of the pyrimidine ring to be studied either as a function of different halogen atoms bound to the same molecular site or as a function of the same halogen atom bound to different molecular sites. The results show that the individual characteristics of the different spectra of the substituted pyrimidines can be rationalized in terms of variations in electronic and geometrical structures of the molecule depending on the localization and the electronegativity of the substituent.

  6. Diagnosis of lubricating oil by evaluating cyanide and carbon molecular emission lines in laser induced breakdown spectra

    Science.gov (United States)

    Elnasharty, I. Y.; Kassem, A. K.; Sabsabi, M.; Harith, M. A.

    2011-08-01

    To prevent engine failure it is essential to change lubricating oil regularly before it loses its protective properties. It is also necessary to monitor the physical and chemical conditions of the oil to reliably determine the optimum oil-change intervals. The present work focuses on studying evolution of the cyanide (CN) and carbon (C 2) molecular spectral emission lines in the laser induced breakdown spectra of lubricating oil as a function of its consumption. The intensities of these molecular bands have been taken as indicator of engine oil degradation at certain mileage. Furthermore, the percentage of decay of CN and C 2 integral intensity values at the corresponding mileage was calculated in order to relate it to the degree of consumption of the motor oil. Such percentage decay of the CN and C 2 integral intensities have been found to increase gradually with increasing mileage which is accompanied with increasing depletion of engine oil. The results of using LIBS technique in the present measurements proved that it is possible to have a direct, straightforward and easy method for prediction of lubricating oil degree of consumption. This may facilitate scheduling the proper time and/or mileage intervals for changing the oil to avoid any possibility of engine failure.

  7. Diagnosis of lubricating oil by evaluating cyanide and carbon molecular emission lines in laser induced breakdown spectra

    Energy Technology Data Exchange (ETDEWEB)

    Elnasharty, I.Y.; Kassem, A.K. [National Institute of Laser Enhanced Science, Cairo University (Egypt); Sabsabi, M. [National Research Council, Industrial Material Institute, Quebec (Canada); Harith, M.A., E-mail: mharithm@niles.edu.eg [National Institute of Laser Enhanced Science, Cairo University (Egypt)

    2011-08-15

    To prevent engine failure it is essential to change lubricating oil regularly before it loses its protective properties. It is also necessary to monitor the physical and chemical conditions of the oil to reliably determine the optimum oil-change intervals. The present work focuses on studying evolution of the cyanide (CN) and carbon (C{sub 2}) molecular spectral emission lines in the laser induced breakdown spectra of lubricating oil as a function of its consumption. The intensities of these molecular bands have been taken as indicator of engine oil degradation at certain mileage. Furthermore, the percentage of decay of CN and C{sub 2} integral intensity values at the corresponding mileage was calculated in order to relate it to the degree of consumption of the motor oil. Such percentage decay of the CN and C{sub 2} integral intensities have been found to increase gradually with increasing mileage which is accompanied with increasing depletion of engine oil. The results of using LIBS technique in the present measurements proved that it is possible to have a direct, straightforward and easy method for prediction of lubricating oil degree of consumption. This may facilitate scheduling the proper time and/or mileage intervals for changing the oil to avoid any possibility of engine failure.

  8. Diagnosis of lubricating oil by evaluating cyanide and carbon molecular emission lines in laser induced breakdown spectra

    International Nuclear Information System (INIS)

    Elnasharty, I.Y.; Kassem, A.K.; Sabsabi, M.; Harith, M.A.

    2011-01-01

    To prevent engine failure it is essential to change lubricating oil regularly before it loses its protective properties. It is also necessary to monitor the physical and chemical conditions of the oil to reliably determine the optimum oil-change intervals. The present work focuses on studying evolution of the cyanide (CN) and carbon (C 2 ) molecular spectral emission lines in the laser induced breakdown spectra of lubricating oil as a function of its consumption. The intensities of these molecular bands have been taken as indicator of engine oil degradation at certain mileage. Furthermore, the percentage of decay of CN and C 2 integral intensity values at the corresponding mileage was calculated in order to relate it to the degree of consumption of the motor oil. Such percentage decay of the CN and C 2 integral intensities have been found to increase gradually with increasing mileage which is accompanied with increasing depletion of engine oil. The results of using LIBS technique in the present measurements proved that it is possible to have a direct, straightforward and easy method for prediction of lubricating oil degree of consumption. This may facilitate scheduling the proper time and/or mileage intervals for changing the oil to avoid any possibility of engine failure.

  9. Perspective: Tipping the scales: Search for drifting constants from molecular spectra

    International Nuclear Information System (INIS)

    Jansen, Paul; Bethlem, Hendrick L.; Ubachs, Wim

    2014-01-01

    Transitions in atoms and molecules provide an ideal test ground for constraining or detecting a possible variation of the fundamental constants of nature. In this perspective, we review molecular species that are of specific interest in the search for a drifting proton-to-electron mass ratio μ. In particular, we outline the procedures that are used to calculate the sensitivity coefficients for transitions in these molecules and discuss current searches. These methods have led to a rate of change in μ bounded to 6 × 10 −14 /yr from a laboratory experiment performed in the present epoch. On a cosmological time scale, the variation is limited to |Δμ/μ| −5 for look-back times of 10–12× 10 9 years and to |Δμ/μ| −7 for look-back times of 7× 10 9 years. The last result, obtained from high-redshift observation of methanol, translates into μ . /μ=(1.4±1.4)×10 −17 /yr if a linear rate of change is assumed

  10. Molecular cytogenetic analysis of human blastocysts andcytotrophoblasts by multi-color FISH and Spectra Imaging analyses

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Jingly F.; Ferlatte, Christy; Baumgartner, Adolf; Jung,Christine J.; Nguyen, Ha-Nam; Chu, Lisa W.; Pedersen, Roger A.; Fisher,Susan J.; Weier, Heinz-Ulrich G.

    2006-02-08

    Numerical chromosome aberrations in gametes typically lead to failed fertilization, spontaneous abortion or a chromosomally abnormal fetus. By means of preimplantation genetic diagnosis (PGD), we now can screen human embryos in vitro for aneuploidy before transferring the embryos to the uterus. PGD allows us to select unaffected embryos for transfer and increases the implantation rate in in vitro fertilization programs. Molecular cytogenetic analyses using multi-color fluorescence in situ hybridization (FISH) of blastomeres have become the major tool for preimplantation genetic screening of aneuploidy. However, current FISH technology can test for only a small number of chromosome abnormalities and hitherto failed to increase the pregnancy rates as expected. We are in the process of developing technologies to score all 24 chromosomes in single cells within a 3 day time limit, which we believe is vital to the clinical setting. Also, human placental cytotrophoblasts (CTBs) at the fetal-maternal interface acquire aneuploidies as they differentiate to an invasive phenotype. About 20-50% of invasive CTB cells from uncomplicated pregnancies were found aneuploidy, suggesting that the acquisition of aneuploidy is an important component of normal placentation, perhaps limiting the proliferative and invasive potential of CTBs. Since most invasive CTBs are interphase cells and possess extreme heterogeneity, we applied multi-color FISH and repeated hybridizations to investigate individual CTBs. In summary, this study demonstrates the strength of Spectral Imaging analysis and repeated hybridizations, which provides a basis for full karyotype analysis of single interphase cells.

  11. Molecular clouds and galactic spiral structure

    International Nuclear Information System (INIS)

    Dame, T.M.

    1984-02-01

    Galactic CO line emission at 115 GHz was surveyed in order to study the distribution of molecular clouds in the inner galaxy. Comparison of this survey with similar H1 data reveals a detailed correlation with the most intense 21 cm features. To each of the classical 21 cm H1 spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is devised for the galactic distribution of molecular clouds. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide

  12. Molecular catalysts structure and functional design

    CERN Document Server

    Gade, Lutz H

    2014-01-01

    Highlighting the key aspects and latest advances in the rapidly developing field of molecular catalysis, this book covers new strategies to investigate reaction mechanisms, the enhancement of the catalysts' selectivity and efficiency, as well as the rational design of well-defined molecular catalysts. The interdisciplinary author team with an excellent reputation within the community discusses experimental and theoretical studies, along with examples of improved catalysts, and their application in organic synthesis, biocatalysis, and supported organometallic catalysis. As a result, readers wil

  13. Floor Response Spectra of Nuclear Containment Building with Soil-Structure Interaction

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Choon Gyo; Ryu, Jeong Soo [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2008-10-15

    This paper presents a seismic analysis technique for a 3D soil-structure interaction(SSI) system in frequency domain, based on the finite element formulation incorporating frequency-dependent dynamic infinite elements for the far field soil region. Earthquake input motions are regarded as traveling SV-wave which is vertically incident from a far-field soil region. In which, the equivalent earthquake forces in the frequency domain are calculated using the exterior rigid boundary method and the free field response analysis. For the application, floor response spectra analyses for nuclear containment building on a soil medium is carried out, the obtained results are compared with the free field response by other solution.

  14. Yield Frequency Spectra and seismic design of code-compatible RC structures: an illustrative example

    DEFF Research Database (Denmark)

    Katsanos, Evangelos; Vamvatsikos, Dimitrios

    2017-01-01

    with given yield displacement and capacity curve shape. For the 8-story case study building, deformation checking is the governing limit state. A conventional code-based design was performed using seismic intensities tied to the desired MAF for safety checking. Then, the YFS-based approach was employed......The seismic design of an 8-story reinforced concrete space frame building is undertaken using a Yield Frequency Spectra (YFS) performance-based approach. YFS offer a visual representation of the entire range of a system’s performance in terms of the mean annual frequency (MAF) of exceeding...... to redesign the resulting structure working backwards from the desired MAF of response (rather than intensity) to estimate an appropriate value of seismic intensity for use within a typical engineering design process. For this high-seismicity and high-importance midrise building, a stiffer system with higher...

  15. Selected aspects in the structure of beta-delayed particle spectra

    International Nuclear Information System (INIS)

    Honkanen, J.; Aeystoe, J.; Eskola, K.

    1986-01-01

    Some weak beta-delayed particle emitters in the T z =-3/2, -1, -1/2, +1/2 and +5/2 series are reviewed. Selected features of the delayed particle emission are discussed in terms of experimental delayed particle data and (p,γ), (p,p') and (p,n) reaction data. Experimental beta transition strengths are compared with the existing complete shell-model calculations for the sd-shell nuclei. The effect of the Gamow-Teller giant resonance on the structure of the delayed particle spectra is considered. The correlation between the widths of two decay channels, protons and alpha particles, and the preceeding beta decay is studied in the case of the 40 Sc decay. (orig.)

  16. Double photoionisation spectra of molecules

    CERN Document Server

    Eland, John

    2017-01-01

    This book contains spectra of the doubly charged positive ions (dications) of some 75 molecules, including the major constituents of terrestrial and planetary atmospheres and prototypes of major chemical groups. It is intended to be a new resource for research in all areas of molecular spectroscopy involving high energy environments, both terrestrial and extra-terrestrial. All the spectra have been produced by photoionisation using laboratory lamps or synchrotron radiation and have been measured using the magnetic bottle time-of-flight technique by coincidence detection of correlated electron pairs. Full references to published work on the same species are given, though for several molecules these are the first published spectra. Double ionisation energies are listed and discussed in relation to the molecular electronic structure of the molecules. A full introduction to the field of molecular double ionisation is included and the mechanisms by which double photoionisation can occur are examined in detail. A p...

  17. First-principles simulation of Raman spectra and structural properties of quartz up to 5 GPa

    International Nuclear Information System (INIS)

    Liu Lei; Lv Chao-Jia; Yi Li; Liu Hong; Du Jian-Guo; Zhuang Chun-Qiang

    2015-01-01

    The crystal structure and Raman spectra of quartz are calculated by using first-principles method in a pressure range from 0 to 5 GPa. The results show that the lattice constants (a, c, and V) decrease with increasing pressure and the a-axis is more compressible than the c axis. The Si–O bond distance decreases with increasing pressure, which is in contrast to experimental results reported by Hazen et al. [Hazen R M, Finger L W, Hemley R J and Mao H K 1989 Solid State Communications 725 507–511], and Glinnemann et al. [Glinnemann J, King H E Jr, Schulz H, Hahn T, La Placa S J and Dacol F 1992 Z. Kristallogr. 198 177–212]. The most striking changes are of inter-tetrahedral O–O distances and Si–O–Si angles. The volume of the tetrahedron decreased by 0.9% (from 0 to 5 GPa), which suggests that it is relatively rigid. Vibrational models of the quartz modes are identified by visualizing the associated atomic motions. Raman vibrations are mainly controlled by the deformation of the tetrahedron and the changes in the Si–O–Si bonds. Vibrational directions and intensities of atoms in all Raman modes just show little deviations when pressure increases from 0 to 5 GPa. The pressure derivatives (dν i /dP) of the 12 Raman frequencies are obtained at 0 GPa–5 GPa. The calculated results show that first-principles methods can well describe the high-pressure structural properties and Raman spectra of quartz. The combination of first-principles simulations of the Raman frequencies of minerals and Raman spectroscopy experiments is a useful tool for exploring the stress conditions within the Earth. (paper)

  18. Influence of hurricane wind field in the structure of directional wave spectra

    Science.gov (United States)

    Esquivel-Trava, Bernardo; Ocampo-Torres, Francisco J.; Osuna, Pedro

    2015-04-01

    Extensive field measurements of wind waves in deep waters in the Gulf of Mexico and Caribbean Sea, have been analyzed to describe the spatial structure of directional wave spectra during hurricane conditions. Following Esquivel-Trava et al. (2015) this analysis was made for minor hurricanes (categories 1 and 2) and major hurricanes (categories 3, 4 and 5). In both cases the directionality of the energy wave spectrum is similar in all quadrants. Some differences are observed however, and they are associated with the presence and the shape of swell energy in each quadrant. Three numerical experiments using the spectral wave prediction model SWAN were carried out to gain insight into the mechanism that controls the directional and frequency distributions of hurricane wave energy. The aim of the experiments is to evaluate the effect of the translation speed of the hurricane and the presence of concentric eye walls, on both the wave growth process and the shape of the directional wave spectrum. The HRD wind field of Hurricane Dean on August 20 at 7:30 was propagated at two different velocities (5 and 10 m/s). An idealized concentric eye wall (a Gaussian function that evolve in time along a path in the form of an Archimedean spiral) was imposed to the wind field. The white-capping formulation of Westhuysen et al. (2007) was selected. The wave model represents fairly well the directionality of the energy and the shape of the directional spectra in the hurricane domain. The model results indicate that the forward movement of the storm influences the development of the waves, consistent with field observations. This work has been supported by CONACYT scholarship 164510 and projects RugDisMar (155793), CB-2011-01-168173 and the Department of Physical Oceanography of CICESE. References Esquivel-Trava, B., Ocampo-Torres, F. J., & Osuna, P. (2015). Spatial structure of directional wave spectra in hurricanes. Ocean Dynam., 65(1), 65-76. doi:10.1007/s10236-014-0791-9 Van der

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

    Science.gov (United States)

    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.

  20. Theoretical study on molecular packing and electronic structure of bi-1,3,4-oxadiazole derivatives

    KAUST Repository

    Wang, Haitao; Bai, Fuquan; Jia, Xiaoshi; Cao, Di; Ravva, Mahesh Kumar; Bredas, Jean-Luc; Qu, Songnan; Bai, Binglian; Zhang, Hongxing; Li, Min

    2014-01-01

    The molecular aggregation structure of 5,5′-bis(naphthalen-2-yl)-2,2′-bi(1,3,4-oxadiazole) (BOXD-NP) was studied by computing the intermolecular interaction potential energy surface (PES) at density functional theory level based on a dimer model. All B3LYP, CAM-B3LYP and M062x functionals can yield a reliable isolated molecular geometry. The conformation of BOXD-NP obtained with all methods is perfectly planar, indicating good conjugation ability between oxadiazole and naphthalene rings. The vibrational frequencies of BOXD-NP were also calculated using the B3LYP/6-311+G∗∗ method, which showed great consistency with the experimental observations and makes the assignments of the IR spectra more solid. It was revealed that the lowest excited state of BOXD-NP should be assigned as a highly allowed π-π∗ state by TD-DFT calculation. Considering the non-covalent interactions in molecular aggregates, the M062x functional was applied in the construction of the PES. Besides the packing structure found in the crystals, PES also predicted several stable structures, indicating that PES has great ability in guiding molecular self-assembly. Symmetry Adapted Perturbation Theory (SAPT) analysis on these energy-minimum molecular stacking structures revealed that London dispersion forces are the strongest attractive component in the binding. This journal is

  1. X-ray photoelectron spectra and electronic structure of quasi-one-dimensional SbSeI crystals

    Directory of Open Access Journals (Sweden)

    J.Grigas

    2007-01-01

    Full Text Available The paper presents the X-ray photoelectron spectra (XPS of the valence band (VB and of the principal core levels from the (110 and (001 crystal surfaces for the quasi-one-dimensional high permittivity SbSeI single crystal isostructural to ferroelectric SbSI. The XPS were measured with monochromatized Al Ka radiation in the energy range of 0-1400 eV at room temperature. The VB is located from 1.6 to 20 eV below the Fermi level. Experimental energies of the VB and core levels are compared with the results of theoretical ab initio calculations of the molecular model of the SbSeI crystal. The electronic structure of the VB is revealed. Shifts in the core-level binding energies of surface atoms relative to bulk ones, which show a dependency on surface crystallography, have been observed. The chemical shifts of the core levels (CL in the SbSeI crystal for the Sb, I and Se states are obtained.

  2. Automated assignment and 3D structure calculations using combinations of 2D homonuclear and 3D heteronuclear NOESY spectra

    International Nuclear Information System (INIS)

    Oezguen, Numan; Adamian, Larisa; Xu Yuan; Rajarathnam, Krishna; Braun, Werner

    2002-01-01

    The NOAH/DIAMOD suite uses feedback filtering and self-correcting distance geometry to generate 3D structures from unassigned NOESY spectra. In this study we determined the minimum set of experiments needed to generate a high quality structure bundle. Different combinations of 3D 15 N-edited, 13 C-edited HSQC-NOESY and 2D homonuclear 1 H- 1 H NOESY spectra of the 77 amino acid protein, myeloid progenitor inhibitory factor-1 (MPIF-1) were used as input for NOAH/DIAMOD calculations. The quality of the assignments of NOESY cross peaks and the accuracy of the automatically generated 3D structures were compared to those obtained with a conventional manual procedure. Combining data from two types of experiments synergistically increased the number of peaks assigned unambiguously in both individual spectra. As a general trend for the accuracy of the structures we observed structural variations in the backbone fold of the final structures of about 2 A for single spectral data, of 1 A to 1.5 A for double spectral data, and of 0.6 A for triple spectral data sets. The quality of the assignments and 3D structures from the optimal data using all three spectra were similar to those obtained from traditional assignment methods with structural variations within the bundle of 0.6 A and 1.3 A for backbone and heavy atoms, respectively. Almost all constraints (97%) of the automatic NOESY cross peak assignments were cross compatible with the structures from the conventional manual assignment procedure, and an even larger proportion (99%) of the manually derived constraints were compatible with the automatically determined 3D structures. The two mean structures determined by both methods differed only by 1.3 A rmsd for the backbone atoms in the well-defined regions of the protein. Thus NOAD/DIAMOD analysis of spectra from labeled proteins provides a reliable method for high throughput analysis of genomic targets

  3. Conformational states of N-acylalanine dithio esters: correlation of resonance Raman spectra with structures

    International Nuclear Information System (INIS)

    Lee, H.; Angus, R.H.; Storer, A.C.; Varughese, K.I.; Carey, P.R.

    1988-01-01

    The conformational states of N-acylalanine dithio esters, involving rotational isomers about the RC(=O)NH-CH(CH 3 ) and NHCH(CH 3 )-C(=S) bonds, are defined and compared to those of N-acylglycine dithio esters. The structure of N-(p-nitrobenzoyl)-DL-alanine ethyl dithio ester has been determined by X-ray crystallographic analysis; it is a B-type conformer with the amide N atom cis to the thiol sulfur. Raman and resonance Raman (RR) measurements on this compound and for the B conformers of solid N-benzoyl-DL-alanine ethyl dithio ester and N-(β-phenylpropionyl)-DL-alanine ethyl dithio ester and its NHCH(CD 3 )C(=S) and NHCH(CH 3 ) 13 C(=S) analogues are used to set up a library of RR data for alanine-based dithio esters in a B-conformer state. RR data for this solid material in its isotopically unsubstituted and CH(C-D 3 )C(=S) and CH(CH 3 ) 13 C(=S) forms provide information on the RR signatures of alanine dithio esters in A-like conformations. RR spectra are compared for the solid compounds, for N-(p-nitrobenzoyl)-DL-alanine, N-(β-phenylpropionyl)-DL-alanine, and (methyloxycarbonyl)-L-phenylalanyl-DL-alanine ethyl dithio ester, and for several 13 C=S- and CD 3 -substituted analogues in CCl 4 or aqueous solutions. The RR data demonstrate that the alanine-based dithio esters take up A, B, and C 5 conformations in solution. The RR spectra of these conformers are clearly distinguishable from those for the same conformers of N-acylglycine dithio esters. However, the crystallographic and spectroscopic results show that the results show that the conformational properties of N-acylglycine and N-acylalanine dithio esters are very similar

  4. Molecular structure of the lecithin ripple phase

    NARCIS (Netherlands)

    de Vries, AH; Yefimov, S; Mark, AE; Marrink, SJ

    2005-01-01

    Molecular dynamics simulations of lecithin lipid bilayers in water as they are cooled from the liquid crystalline phase show the spontaneous formation of rippled bilayers. The ripple consists of two domains of different length and orientation, connected by a kink. The organization of the lipids in

  5. Theoretical Investigation of the Effect of the Rare Gas Matrices on the Vibrational Spectra of Solvated Molecular Ions: Cu+CO

    Czech Academy of Sciences Publication Activity Database

    Bludský, Ota; Šilhan, Martin; Nachtigall, Petr

    2002-01-01

    Roč. 117, č. 20 (2002), s. 9298-9305 ISSN 0021-9606 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : vibrational spectra * solvated molecular ions Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.998, year: 2002

  6. Study of the structural characteristics of a group of natural silicates by means of their Kβ emission spectra

    International Nuclear Information System (INIS)

    Torres Deluigi, Maria Torres; Strasser, Edgardo N.; Vasconcellos, Marcos A.Z.; Riveros, Jose A.

    2006-01-01

    In this work, the Si Kβ and Al Kβ emission spectra of a group of natural silicates typical of a region in San Luis (Argentina) are described qualitatively within the frame of the Molecular Orbital (MO) theory. Since these spectra come from electron transitions from valence orbitals, they offer information on the chemical bonds that are present and on the molecular orbitals involved. The spectra were obtained by means of an electron microprobe. The energies, intensities and full-width at half-maximum (FWHM) of the lines that conform the silicon and aluminium Kβ spectra were quantified. It was observed that an increase in the number of oxygen ions shared by the tetrahedra (SiO 4 ) 4- caused a lineal increase in the FWHM of the Si Kβ 1,3 and Al Kβ 1,3 lines. This behavior is caused by the increase of the covalent character of the Si-O and Al-O bonds with the quantity of oxygen ions shared by the adjacent tetrahedra

  7. Nuclear molecular structure in heavy mass systems

    International Nuclear Information System (INIS)

    Arctaedius, T.; Bargholtz, C.

    1989-04-01

    A study is made of nuclear molecular configurations involving one heavy mass partner. The stability of these configurations to mass flow and to fission is investigated as well as their population in fusion reactions. It is concluded that shell effects in combination with the effects of angular momentum may be important in stabilizing certain configurations. A possible relation of these configurations to the so called superdeformed states is pointed out. The spectrum of rotational and vibrational trasitions within molecular configurations is investigated. For sufficiently mass-asymmetric systems the engergies of vibrational transitions are comparable to the neutron separation energy. Gamma radiation from such transitions may then be observable above the background of statistical transitions. The gamma spectrum and the directional distribution of the radioation following fusion reactions with 12 C and 16 O are calculated. (authors)

  8. The hierarchical structure of molecular clouds

    International Nuclear Information System (INIS)

    Chieze, J.P.

    1987-01-01

    The mass-radius-velocity dispersion relations observed among the members of cool molecular complexes is interpreted in terms of fragmentation at the gravitational instability threshold in a roughly constant pressure environment. The mass range of the self-similar fragmentation hierarchy is governed by the thermal instability thresholds. Using a realistic equation of state, the gravitational stability of thermally stable clumps is analysed as a function of both the local gas pressure and extinction of the mean interstellar radiation field

  9. Molecular structure and DFT investigations on new cobalt(II ...

    Indian Academy of Sciences (India)

    tion process was demonstrated.9 Late-transition metals, especially Ni, Pd ..... in table S2 (Supplementary Information). Most of the ... to molecular system because of atomic charges affect ... structure, acidity–basicity behavior and other proper-.

  10. The Role of Molecular Structure and Conformation in Polymer Electronics

    NARCIS (Netherlands)

    von Hauff, Elizabeth

    2011-01-01

    ABSTRACT Conjugated polymers have unique material properties that make them promising for a wide range of applications. The potential lies in the virtually infinite possibilities for creating new materials for specific applications by simply chemically tuning the molecular structure. Conjugated

  11. Crystal structure and pair potentials: A molecular-dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Parrinello, M.; Rahman, A.

    1980-10-06

    With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

  12. Adaptation of high viscous dampers (HVD) for essential decreasing of in-structure floor response spectra

    International Nuclear Information System (INIS)

    Kostarev, V.V.; Petrenko, A.V.; Vasilyev, P.S.; Reinsch, K.-H.

    2005-01-01

    This paper concerns a further development of High Viscous Damper (HVD) approach for essential decreasing of structure's floor response spectra. Usually restraining of components and pipelines by HVD is used for significant decreasing of operational vibration and seismic loads. A new approach consists of dampers installation for essential upgrading of a whole system's damping that is much more efficient in both technical and economical points of view than restraining of each component of the system. In that way using of HVD means high energy dissipation for whole dynamic system 'Building-Components' subjected to the base seismic or other extreme load excitation. The specific feature of each NPP site is an existing of a few closely spaced buildings: reactor building, turbine hall and so on. As the rule such buildings play sufficiently different roles in NPP operation and therefore have sufficiently different design, natural frequencies (periods) and distortion of floors and different rocking modes on a soil. The main idea explained in the paper is an interconnection of buildings by HVD. Then differences in their mechanical properties provide their out-of-phase relative motions during an earthquake and therefore effective dissipative work provided by HVD devices. At the same time implementation of HVD approach allows to eliminate possible interactions and collisions in the gaps between building structures that wears potential threat of building failure. The detailed 3D finite element models of reactor building, turbine hall and special building were developed for NPP with VVER-1000 MWt reactor type. Performed analysis has shown high efficiency of suggested approach for protection of buildings, structures, systems and components against seismic and other impacts. (authors)

  13. Structural and spectroscopic properties of the second generation phosphorus-viologen "molecular asterisk".

    Science.gov (United States)

    Furer, V L; Vandukov, A E; Katir, N; Majoral, J P; El Kadib, A; Caminade, A M; Bousmina, M; Kovalenko, V I

    2013-11-01

    The FTIR and FT Raman spectra of the second generation phosphorus-viologen "molecular asterisk" G2 built from cyclotriphosphazene core with 12 viologen units and 6 terminal phosphonate groups have been recorded and analyzed. The experimental X-ray data of 1,1-bis(4-formylbenzyl)-4,4'-bipyridinium bis(hexaflurophosphate) was used in molecular modeling studies. The optimization of isolated 1,1-bis(4-formylbenzyl)-4,4'-bipyridinium (BFBP) molecule without counter ions PF6(-) does not lead to significant changes of dihedral angles, thus the molecular conformation does not depend on interactions with the counter ions. The structural optimization and normal mode analysis were performed for G2 on the basis of the density functional theory (DFT). The calculated geometrical parameters and harmonic vibrational frequencies are predicted in a good agreement with the experimental data. It was found that G2 has a kind of "egg timer" structure with planar OC6H4CHNN(CH3) fragments and slightly non-planar cyclotriphosphazene core. The experimental IR and Raman spectra of G2 were interpreted by means of potential energy distribution. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. CASD-NMR 2: robust and accurate unsupervised analysis of raw NOESY spectra and protein structure determination with UNIO

    International Nuclear Information System (INIS)

    Guerry, Paul; Duong, Viet Dung; Herrmann, Torsten

    2015-01-01

    UNIO is a comprehensive software suite for protein NMR structure determination that enables full automation of all NMR data analysis steps involved—including signal identification in NMR spectra, sequence-specific backbone and side-chain resonance assignment, NOE assignment and structure calculation. Within the framework of the second round of the community-wide stringent blind NMR structure determination challenge (CASD-NMR 2), we participated in two categories of CASD-NMR 2, namely using either raw NMR spectra or unrefined NOE peak lists as input. A total of 15 resulting NMR structure bundles were submitted for 9 out of 10 blind protein targets. All submitted UNIO structures accurately coincided with the corresponding blind targets as documented by an average backbone root mean-square deviation to the reference proteins of only 1.2 Å. Also, the precision of the UNIO structure bundles was virtually identical to the ensemble of reference structures. By assessing the quality of all UNIO structures submitted to the two categories, we find throughout that only the UNIO–ATNOS/CANDID approach using raw NMR spectra consistently yielded structure bundles of high quality for direct deposition in the Protein Data Bank. In conclusion, the results obtained in CASD-NMR 2 are another vital proof for robust, accurate and unsupervised NMR data analysis by UNIO for real-world applications

  15. Invisible structures in the X-ray absorption spectra of actinides

    NARCIS (Netherlands)

    Kvashnina, Kristina O.; De Groot, Frank M F

    The X-ray absorption spectra of actinides are discussed with an emphasis on the fundamental effects that influence their spectral shape, including atomic multiplet theory, charge transfer theory and crystal field theory. Many actinide spectra consist of a single peak and it is shown that the use of

  16. FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular conformational analysis of 2,5-di-tert-butyl-hydroquinone

    Science.gov (United States)

    Subramanian, N.; Sundaraganesan, N.; Dereli, Ö.; Türkkan, E.

    2011-12-01

    The purpose of finding conformer among six different possible conformers of 2,5-di-tert-butyl-hydroquinone (DTBHQ), its equilibrium geometry and harmonic wavenumbers were calculated by the B3LYP/6-31G(d,p) method. The infrared and Raman spectra of DTBHQ were recorded in the region 400-4000 cm -1 and 50-3500 cm -1, respectively. In addition, the IR spectra in CCl 4 at various concentrations of DTBHQ are also recorded. The computed vibrational wavenumbers were compared with the IR and Raman experimental data. Computational calculations at B3LYP level with two different basis sets 6-31G(d,p) and 6-311++G(d,p) are also employed in the study of the possible conformer of DTBHQ. The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated using VEDA 4 program. The general agreement between the observed and calculated frequencies was established.

  17. Molecular clouds and galactic spiral structure

    International Nuclear Information System (INIS)

    Dame, T.M.

    1983-01-01

    Galactic CO line emission at 115 GHz has been surveyed in the region 12 0 less than or equal to l less than or equal to 60 0 and -1 0 less than or equal to b less than or equal to 1 0 in order to study the distribution of molecular clouds in the inner galaxy; an inner strip 0 0 .5 wide has been sampled every beamwidth (0 0 .125), the rest every two beamwidths. Comparison of the survey with similar HI data reveals a detailed correlation with the most intense 21-cm features, implying that the CO and HI trace the same galactic features and have the same large-scale kinematics. To each of the classical 21-cm (HI) spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is developed in which all of the CO emission from the inner galaxy arises from spiral arms. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide. A variety of methods are employed to estimate distances and masses for the largest clouds detected by the inner-galaxy survey and a catalogue is compiled. The catalogued clouds, the largest of which have masses of several 10 6 M/sub sunmass/ and linear dimensions in excess of 100 pc, are found to be excellent spiral-arm tracers. One of the nearest of the clouds, that associated with the supernova remnant W44, is fully mapped in both CO and 13 CO and is discussed in detail

  18. Measurements and calculations of integral capture cross-sections of structural materials in fast reactor spectra

    International Nuclear Information System (INIS)

    Seth, S.; Brunson, G.; Gmuer, K.; Jermann, M.; McCombie, C.; Richmond, R.; Schmocker, U.

    1979-01-01

    This paper relates the checking of integral data of steel and iron in fast reactor lattices. The fully-rodded GCFR benchmark lattice of the zero-energy reactor PROTEUS was successively modified by replacing the PuO 2 -UO 2 fuel rods by steel-18/8 or steel-37 (iron) rods. The neutron spectra of the modified lattices in fact have median energies close to that of a typical LMFBR. The replacement of fuel by the structural material of interest was such that in each case the value of k(infinity) was reduced to near-unity. This allowed the measurement of the lattice-k(infinity) by the null-reactivity technique. In addition, the principal reaction rates (namely U238 capture and fission, relative to Pu239 fission) and the neutron spectrum were measured. These directly measured integral data which are particularly sensitive to the steel cross-sections can be used for the checking and systematic adjustment of data sets. The results may also be analysed so as to derive specific values for the integral capture cross-sections of steel and iron. Neutron balance equations were set-up for each of the lattices using the measured k(infinity) and reaction rates

  19. Crystal structures and Moessbauer spectra of spin-crossover iron(III) complexes of quinquedentate ligands

    International Nuclear Information System (INIS)

    Maeda, Yonezo; Noda, Yosuke; Oshio, Hiroki; Takashima, Yoshimasa; Matsumoto, Naohide

    1994-01-01

    Magnetic properties, Moessbauer spectra and crystal structures of spin-crossover iron(III) complexes with a quinquedentate ligand [FeLX]BPh 4 are reported. X and L denote a unidentate ligand and a quinquedentate ligand, respectively. [Fe(mbpN)(im)]BPh 4 shows spin-crossover behavior in an appropriate organic solvent, and [Fe(mbpN)(lut)]BPh 4 , [Fe(bpN)(py)]BPh 4 and [Fe(salten)X]BPh 4 (X = 4me-py or 2me-im) show spin-crossover behavior in a solid and in an organic solvent. It was found that the ligand field strength of salten was stronger than that of mbpN. The rates of spin-state interexchange in the complexes are as fast as the inverse of the lifetime (1 x 10 -7 s) of the Moessbauer nuclear level. The Moessbauer spectroscopic behavior of [Fe(mbpN)(lut)]BPh 4 and [Fe(bpN)(py)]BPh 4 is different to that of [Fe(salten)X]BPh 4 (X = 4me-py or 2me-im). The difference was ascribed to the different geometrical positions of the corresponding anions. (orig.)

  20. Instructional Approach to Molecular Electronic Structure Theory

    Science.gov (United States)

    Dykstra, Clifford E.; Schaefer, Henry F.

    1977-01-01

    Describes a graduate quantum mechanics projects in which students write a computer program that performs ab initio calculations on the electronic structure of a simple molecule. Theoretical potential energy curves are produced. (MLH)

  1. From structure to spectra. Tight-binding theory of InGaAs quantum dots

    International Nuclear Information System (INIS)

    Goldmann, Elias

    2014-01-01

    Self-assembled semiconductor quantum dots have raised considerable interest in the last decades due to a multitude of possible applications ranging from carrier storage to light emitters, lasers and future quantum communication devices. Quantum dots offer unique electronic and photonic properties due to the three-dimensional confinement of charge carriers and the coupling to a quasi-continuum of wetting layer and barrier states. In this work we investigate the electronic structure of In x Ga 1-x As quantum dots embedded in GaAs, considering realistic quantum dot geometries and Indium concentrations. We utilize a next-neighbour sp 3 s * tight-binding model for the calculation of electronic single-particle energies and wave functions bound in the nanostructure and account for strain arising from lattice mismatch of the constituent materials atomistically. With the calculated single-particle wave functions we derive Coulomb matrix elements and include them into a configuration interaction treatment, yielding many-particle states and energies of the interacting many-carrier system. Also from the tight-binding single-particle wave functions we derive dipole transition strengths to obtain optical quantum dot emission and absorption spectra with Fermi's golden rule. Excitonic fine-structure splittings are obtained, which play an important role for future quantum cryptography and quantum communication devices for entanglement swapping or quantum repeating. For light emission suited for long-range quantum-crypted fiber communication InAs quantum dots are embedded in an In x Ga 1-x As strain-reducing layer, shifting the emission wavelength into telecom low-absorption windows. We investigate the influence of the strain-reducing layer Indium concentration on the excitonic finestructure splitting. The fine-structure splitting is found to saturate and, in some cases, even reduce with strain-reducing layer Indium concentration, a result being counterintuitively. Our result

  2. From structure to spectra. Tight-binding theory of InGaAs quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Goldmann, Elias

    2014-07-23

    Self-assembled semiconductor quantum dots have raised considerable interest in the last decades due to a multitude of possible applications ranging from carrier storage to light emitters, lasers and future quantum communication devices. Quantum dots offer unique electronic and photonic properties due to the three-dimensional confinement of charge carriers and the coupling to a quasi-continuum of wetting layer and barrier states. In this work we investigate the electronic structure of In{sub x}Ga{sub 1-x}As quantum dots embedded in GaAs, considering realistic quantum dot geometries and Indium concentrations. We utilize a next-neighbour sp{sup 3}s{sup *} tight-binding model for the calculation of electronic single-particle energies and wave functions bound in the nanostructure and account for strain arising from lattice mismatch of the constituent materials atomistically. With the calculated single-particle wave functions we derive Coulomb matrix elements and include them into a configuration interaction treatment, yielding many-particle states and energies of the interacting many-carrier system. Also from the tight-binding single-particle wave functions we derive dipole transition strengths to obtain optical quantum dot emission and absorption spectra with Fermi's golden rule. Excitonic fine-structure splittings are obtained, which play an important role for future quantum cryptography and quantum communication devices for entanglement swapping or quantum repeating. For light emission suited for long-range quantum-crypted fiber communication InAs quantum dots are embedded in an In{sub x}Ga{sub 1-x}As strain-reducing layer, shifting the emission wavelength into telecom low-absorption windows. We investigate the influence of the strain-reducing layer Indium concentration on the excitonic finestructure splitting. The fine-structure splitting is found to saturate and, in some cases, even reduce with strain-reducing layer Indium concentration, a result being

  3. Systematic analysis of crystal and molecular structures

    Czech Academy of Sciences Publication Activity Database

    Hašek, Jindřich; Dohnálek, Jan

    2012-01-01

    Roč. 19, č. 2 (2012), s. 86-87 ISSN 1211-5894. [Struktura 2012. Kolokvium Krystalografické společnosti. 11.06.2012-14.06.2012, Klatovy] R&D Projects: GA ČR GA310/09/1407 Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : structure databases * structure-function relations * organic and inorganic materials Subject RIV: EE - Microbiology, Virology

  4. Theoretical investigations of the structures and electronic spectra of 8-hydroxylquinoline derivatives

    Science.gov (United States)

    Ning, Pan; Ren, Tiegang; Zhang, Yanxin; Zhang, Jinglai

    2013-11-01

    The spectroscopic properties of 8-hydroxyquinoline derivatives are theoretically investigated by means of density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. The target molecules are divided into two groups: group (I): (E)-2-(2-(3,5-dimethyl-1-phenyl-1H-pyrazol-4-yl)vinyl)quinolin-8-ol (A), together with corresponding potential reaction products of A with acetic acid, i.e., (E)-2-(2-(3,5-dimethyl-1-phenyl-1H-pyrazol-4-yl)vinyl)quinolin-8-yl acetate (AR1), and (E)-2-(2-(3,5-dimethyl-1-phenyl-1H-pyrazol-4-yl)vinyl)-8-hydroxyquinolinium (AR2); group (II): (E)-2-(2-(1-(4-chlorophenyl)-3,5-dimethyl-1H-pyrazol-4-yl)vinyl)quinolin-8-ol (B), as well as potential reaction products of B with acetic acid, i.e., (E)-2-(2-(1-(4-chlorophenyl)-3,5-dimethyl-1H-pyrazol-4-yl)vinyl)quinolin-8-yl acetate (BR1), and (E)-2-(2-(1-(4-chlorophenyl)-3,5-dimethyl-1H-pyrazol-4-yl)vinyl)-8-hydroxyquinolinium (BR2). The geometries are optimized by B3LYP and M06 methods. The results indicate that product molecules tend to be effectively planar compared with reactants. Subsequently, UV absorption spectra are simulated through TD-DFT method with PCM model to further confirm the reasonable products of two reactions. AR2 and BR2 are identified as the target molecules through the experimental spectra for the real products. It is worth noting that the maximum absorption wavelengths of compounds AR2 and BR2 present prominent red shift compared the initial reactants A and B, respectively, which should be ascribed to the enhancive planarity of products that mentioned above and the decreased HOMO-LUMO energy gap. Geometric structures and optical properties for corresponding compounds are discussed in detail.

  5. Li{sub 4}Ba[BN{sub 2}]{sub 2} - structure and vibrational spectra

    Energy Technology Data Exchange (ETDEWEB)

    Seidel, Stefan; Rodewald, Ute C.; Poettgen, Rainer [Institut fuer Anorganische und Analytische Chemie, Universitaet Muenster (Germany); Somer, Mehmet; Kiraz, Kamil [Chemistry Department, Koc University, Sariyer-Istanbul (Turkey)

    2017-12-13

    The nitridoborate Li{sub 4}Ba[BN{sub 2}]{sub 2} was synthesized from a 4:1 molar ratio of Li{sub 3}[BN]{sub 2} and Ba{sub 3}[BN{sub 2}]{sub 2} in an arc-welded niobium ampoule at a maximum annealing temperature of 1173 K. The structure was refined from single-crystal X-ray diffractometer data: new type, P1, a = 533.9(2), b = 585.0(3), c = 860.6(4) pm, α = 80.72(3), β = 73.84(6), γ = 89.87(4) , wR{sub 2} = 0.1196, 1429 F{sup 2} values, 50 variables. The Li{sub 4}Ba[BN{sub 2}]{sub 2} structure contains two crystallographically independent [BN{sub 2}]{sup 3-} units with 134 pm B-N distance, which are slightly bent: 178 for N2-B1-N1 and 175 for N4-B2-N3. Due to the high lithium content both [BN{sub 2}]{sup 3-} units have a strongly distorted coordination by 8Li{sup +} + 3Ba{sup 2+}. The four crystallographically independent lithium cations show distorted tetrahedral coordination by [BN{sub 2}]{sup 3-} units with Li-N distances ranging from 195 to 247 pm. IR and Raman spectra show the typical vibrations of the [BN{sub 2}] unit along with a well-resolved splitting of the ν({sup 10}B) and ν({sup 11}B) frequencies. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  6. Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

    Science.gov (United States)

    Sumner, Isaiah; Iyengar, Srinivasan S

    2007-10-18

    We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

  7. Structure of X-ray photoelectron spectra of low-energy and core electrons of Ln(C6H4OCH3COO-3

    Directory of Open Access Journals (Sweden)

    Teterin Yury A.

    2005-01-01

    Full Text Available This paper deals with the results of an X-ray photo electron spectroscopy of lanthanide ortho-metoxybenzoates Ln(C6H4OCH3COO-3, where Ln represents lanthanides La through Lu except for Pm and C6H4OCH3COO- - residuum of ortho-metoxybenzoic acid. The core and outer electron X-ray photo electron spectroscopy spectra in the binding energy range of 0-1250 eV were shown to exhibit a complex, fine structure. The said structure was established due to the outer (0-15 eV binding energy and inner (15-50 eV binding energy valence molecular orbital from the filled Ln5p and O2s atomic shells multiple splitting, many-body perturbation, dynamic effect, etc. The mechanisms of such a fine structure formation were shown to manifest different probabilities in the spectrum of a certain electronic shell. There fore, the fine X-ray photo electron spectroscopy spectral structure resulting from a certain mechanism can be interpreted and its quantitative parameters related to the physical and chemical properties of the studied com pounds (degree of delocalization and participation of Ln4f electrons in the chemical bond, electronic configuration and oxidation states, density of uncoupled electrons on paramagnetic ions, degree of participation of the low binding energy filled electronic shells of lanthanide and ligands information of the outer and in nervalence molecular orbitals, lanthanide close environment structure in amorphous materials, etc.

  8. Quantum Mechanical Study on the Structure and Vibrational Spectra of Cyclobutanone and 1,2-Cyclobutanedione

    Directory of Open Access Journals (Sweden)

    Anoop kumar Pandey

    2013-01-01

    Full Text Available For 1,2-cyclobutanedione and cyclobutanone, we have carried out a comparative study of different methods like B3LYP, LSDA, and B3PW91 of DFT using 6-31G (d, p basis set and MP2 method. On comparing these methods we find that B3PW91 method is closer to the experimental one. So by using B3PW91 method, we have made a comparative study of their structures, normal mode analysis, and other properties of the two derivatives of cyclobutane. The molecular HOMO, LUMO composition, their respective energy gaps, and MESP contours/surfaces have also been drawn to explain the activity of 1,2-cyclobutanedione and cyclobutanone.

  9. Ab initio molecular orbital studies of the vibrational spectra of the van der Waals complexes of boron trifluoride with the noble gases.

    Science.gov (United States)

    Ford, Thomas A

    2005-05-01

    The molecular structures, interaction energies, charge transfer properties and vibrational spectra of the van der Waals complexes formed between boron trifluoride and the noble gases neon, argon, krypton and xenon have been computed using second and fourth order Møller-Plesset perturbation theory and the Los Alamos National Laboratory LANL2DZ basis set. The complexes are all symmetric tops, with the noble gas atom acting as a sigma electron donor along the C3 axis of the BF3 molecule. The interaction energies are all vanishingly small, and the amount of charge transferred in each case is of the order of 0.01e. The directions of the wavenumber shifts of the symmetric bending (nu2) and antisymmetric stretching (nu3) modes of the BF3 fragment confirm those determined experimentally, and the shifts are shown to correlate well with the polarizability of the noble gas atom and the inverse sixth power of the intermonomer separation. The nu2 mode is substantially more sensitive to complexation than the nu3 vibration.

  10. Molecular and structural aspects of oocyte maturation

    NARCIS (Netherlands)

    Hölzenspies, J.J.

    2009-01-01

    In the mammalian ovary, oocytes are contained within follicles, specialized structures that facilitate oocyte growth and development. During the reproductive cycle, several follicles are recruited into growth, and through a process of selection, one (human, cow) or several (mouse, pig) of these

  11. Synthesis, Crystal Structure, Density Function Theory, Molecular ...

    African Journals Online (AJOL)

    Tropical Journal of Pharmaceutical Research ... Purpose: To determine the exact structure and antimicrobial activity of 2-(3-(4 phenylpiperazin-1-yl) ... Besides HOMO– LUMO energy gap was performed at B3LYP/6-31G (d,p) level of theory.

  12. Neutron irradiation effects in fusion or spallation structural materials: Some recent insights related to neutron spectra

    International Nuclear Information System (INIS)

    Garner, F.A.; Greenwood, L.R.

    1998-01-01

    A review is presented of recent insights on the role of transmutation in the development of radiation-induced changes in dimension or radiation-induced changes in physical or mechanical properties. It is shown that, in some materials and some neutron spectra, transmutation can significantly affect or even dominate a given property change process. When the process under study is also sensitive to displacement rate, and especially if it involves radiation-induced segregation and precipitation, it becomes much more difficult to separate the transmutation and displacement rate dependencies. This complicates the application of data derived from 'surrogate' spectra to predictions in other flux-spectra environments. It is also shown in this paper that one must be sensitive to the impact of previously -ignored 'small' variations in neutron spectra within a given reactor. In some materials these small variations have major consequences. (author)

  13. Experimental determination of neutron capture cross sections of fast reactor structure materials integrated in intermediate energy spectra. Vol. 2: description of experimental structure

    International Nuclear Information System (INIS)

    Tassan, S.

    1978-01-01

    A selection of technical documents is given concerning the experimental determination of the neutron capture cross-sections of fast reactor structural materials (Fe, Cr, Ni...) integrated over the intermediate energy spectra. The experimental structure project and modifications of the reactor RB2 for this experiment, together with criticality and safety calculations, are presented

  14. Comparisons of experimental beta-ray spectra important to decay heat predictions with ENSDF [Evaluated Nuclear Structure Data File] evaluations

    International Nuclear Information System (INIS)

    Dickens, J.K.

    1990-03-01

    Graphical comparisons of recently obtained experimental beta-ray spectra with predicted beta-ray spectra based on the Evaluated Nuclear Structure Data File are exhibited for 77 fission products having masses 79--99 and 130--146 and lifetimes between 0.17 and 23650 sec. The comparisons range from very poor to excellent. For beta decay of 47 nuclides, estimates are made of ground-state transition intensities. For 14 cases the value in ENSDF gives results in very good agreement with the experimental data. 12 refs., 77 figs., 1 tab

  15. Molecular dynamics of the structure and thermodynamics of dusty ...

    African Journals Online (AJOL)

    The static structure and thermodynamic properties of two-dimensional dusty plasma are analyzed for some typical values of coupling and screening parameters using classical molecular dynamics. Radial distribution function and static structure factor are computed. The radial distribution functions display the typical ...

  16. Molecular dynamic analysis of the structure of dendrimers

    Energy Technology Data Exchange (ETDEWEB)

    Canetta, E.; Maino, G. E-mail: maino@bologna.enea.it

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.

  17. Molecular dynamic analysis of the structure of dendrimers

    International Nuclear Information System (INIS)

    Canetta, E.; Maino, G.

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques

  18. Electronic structure and intersubband magnetoabsorption spectra of CdSe/CdS core-shell nanowires

    Science.gov (United States)

    Xiong, Wen

    2016-10-01

    The electronic structures of CdSe/CdS core-shell nanowires are calculated based on the effective-mass theory, and it is found that the hole states in CdSe/CdS core-shell nanowires are strongly mixed, which are very different from the hole states in CdSe or CdS nanowires. In addition, we find the three highest hole states at the Γ point are almost localized in the CdSe core and the energies of the hole states in CdSe/CdS core-shell nanowires can be enhanced greatly when the core radius Rc increases and the total radius R is fixed. The degenerate hole states are split by the magnetic field, and the split energies will increase when |Jh | increases from 1/2 to 7/2, while they are almost not influenced by the change of the core radius Rc. The absorption spectra of CdSe/CdS core-shell nanowires at the Γ point are also studied in the magnetic field when the temperature T is considered, and we find there are only two peaks will arise if the core radius Rc and the temperature T increase. The intensity of each optical absorption can be considerably enhanced by increasing the core radius Rc when the temperature T is fixed, it is due to the increase of their optical transition matrix element. Meanwhile, the intensity of each optical absorption can be decreased when the temperature T increases and the core radius Rc is fixed, and this is because the Fermi-Dirac distribution function of the corresponding hole states will increase as the increase of the temperature T.

  19. Radiation damage of variscite in historic crafts: Solarization, decolouration, structural changes and spectra from ionoluminescence

    International Nuclear Information System (INIS)

    Garcia-Guinea, J.; Correcher, V.; Sanchez-Munoz, L.; Lopez-Arce, P.; Townsend, P.D.; Hole, D.E.

    2008-01-01

    X-ray diffraction measurements, during halogen lamp illumination to simulate sunlight, (TXRD) show a phase transition from variscite (AlPO 4 .H 2 O) Messbach to variscite Lucin and a loss of the dark green colour. The differential-thermal and thermo-gravimetric (DTA-TG) analyses and thermoluminescence (TL) peaks all depict this first-order phase transition which takes place under sunlight. From the water vaporization temperature up to circa 650 deg. C, a second-order phase transition progressively occurs from variscite to berlinite (AlPO 4 ) by loss of a second unit of water with hydrogen bonded to the lattice. The ion beam luminescence (IBL) spectra of the Zamora variscite display a spectral band from 500 to 570 nm attributed to [UO 2 ] 2+ in phosphates, and another spectral band from 670 to 740 nm is linked with Cr(VI) 3+ defects situated in octahedral Al(VI) 3+ positions. In the hydrous variscite lattice, the Al-O and P-O chemical bonds are mainly covalent; with the degree of covalency of the P-O chemical bond significantly larger than of Al-O. This open structure of variscite, which has a crystal field of reduced strength, involves small shifts of the absorption bands which intensify the blue-green transmission producing the characteristic emerald colour of the dark green variscite of Zamora. These data provide a valuable basis for detection of solarization damage in historic crafts with inlaid variscite in the Museo del Prado (Madrid, Spain)

  20. Efficient "on-the-fly" calculation of Raman spectra from ab-initio molecular dynamics: Application to hydrophobic/hydrophilic solutes in bulk water.

    Science.gov (United States)

    Partovi-Azar, Pouya; Kühne, Thomas D

    2015-11-05

    We present a novel computational method to accurately calculate Raman spectra from first principles. Together with an extension of the second-generation Car-Parrinello method of Kühne et al. (Phys. Rev. Lett. 2007, 98, 066401) to propagate maximally localized Wannier functions together with the nuclei, a speed-up of one order of magnitude can be observed. This scheme thus allows to routinely calculate finite-temperature Raman spectra "on-the-fly" by means of ab-initio molecular dynamics simulations. To demonstrate the predictive power of this approach we investigate the effect of hydrophobic and hydrophilic solutes in water solution on the infrared and Raman spectra. © 2015 Wiley Periodicals, Inc.

  1. Structures of Life: The Role of Molecular Structures in Scientists' Work

    NARCIS (Netherlands)

    Vyas, Dhaval; Kulyk, Olga Anatoliyivna; van der Vet, P.E.; Nijholt, Antinus; van der Veer, Gerrit C.; Jorge, J

    2008-01-01

    The visual and multidimensional representations like images and graphical structures related to biology provide great insights into understanding the complexities of different organisms. Especially, life scientists use different representations of molecular structures to answer biological questions

  2. Response spectra by blind faults for design purpose of stiff structures on rock site

    International Nuclear Information System (INIS)

    Hiroyuki Mizutani; Kenichi Kato; Masayuki Takemura; Kazuhiko Yashiro; Kazuo Dan

    2005-01-01

    The goal of this paper is to propose the response spectra by blind faults for seismic design of nuclear power facilities. It is impossible to evaluate earthquake ground motions from blind faults, because the size and the location of blind fault cannot be identified even if the detailed geological surveys are conducted. From the viewpoint of seismic design, it is crucial to investigate the upper level of earthquake ground motions due to blind faults. In this paper, 41 earthquakes that occurred in the upper crust in Japan and California are selected and classified into the active and the blind fault types. On the basis of near-source strong motion records observed on rock sites, upper level of response spectra by blind faults is examined. The estimated upper level is as follows: the peak ground acceleration is 450 cm/s 2 , the flat level of the acceleration response spectra is 1200 cm/s 2 , and the flat level of the velocity response spectra is 100 cm/s on rock sites with shear wave velocity Vs of about 700 m/s. The upper level can envelop the observed response spectra in near-source region on rock sites. (authors)

  3. Crystal and molecular structure of 2-thiouridine

    Energy Technology Data Exchange (ETDEWEB)

    Hawkinson, S W

    1977-01-01

    The ''minor'' nucleoside 2-thiouridine, C/sub 9/H/sub 12/O/sub 5/N/sub 2/S, crystallizes in a monoclinic cell, space group P2/sub 1/ with a = 5.049 (2), b = 7.526 (2), c = 14.050 (3) A, ..beta.. = 90.17 (2)/sup 0/, and d = 1.619 g cm/sup -3/ (for Z = 2) at 22 +- 2/sup 0/C. The structure was derived from 1334 unique intensities measured with an Oak Ridge computer-controlled diffractometer to a limit of sin theta/lambda = 0.65 A/sup -1/ with Nb-filtered Mo K..cap alpha.. radiation. Atomic parameters were obtained by a combination of Patterson and Fourier techniques and refined by full-matrix least squares to a final R(F) value of 0.023 for all data. The bond lengths and angles in the molecule agree well with those of other thiopyrimidines (C(2) - S = 1.677 A). The conformation of the sugar ring relative to the base is anti with a torsion angle chi(O(1')--C(1') ..-->.. N(1)--C(6)) of 17/sup 0/. The sugar exists in the 3'-endo conformation. The O(5')--C(5') bond is gauche to C(4) - O(1') and trans to C(4')--C(3') (torsion angles of 74 and -169/sup 0/ respectively). The molecules are linked together in the crystal by hydrogen bonds in an intricate network which is identical to that inferred by Kojic-Prodic, Liminga, Sljukic and Ruzic-Toros (Acta Cryst. (1974), B30, 1550-1555) for the crystal structure of 5,6-dihydro-2-thiouridine. 2 figures; 6 tables.

  4. Exciton spectra and energy band structure of Cu{sub 2}ZnSiSe{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Guc, M., E-mail: gmax@phys.asm.md [Institute of Applied Physics, Academy of Sciences of Moldova, Academiei Str. 5, Chisinau MD 2028, Republic of Moldova (Moldova, Republic of); Levcenko, S. [Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner-Platz 1, D-14109 Berlin (Germany); Dermenji, L. [Institute of Applied Physics, Academy of Sciences of Moldova, Academiei Str. 5, Chisinau MD 2028, Republic of Moldova (Moldova, Republic of); Gurieva, G. [Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner-Platz 1, D-14109 Berlin (Germany); Schorr, S. [Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner-Platz 1, D-14109 Berlin (Germany); Free University Berlin, Institute of Geological Sciences, Malteserstr. 74-100, Berlin (Germany); Syrbu, N.N. [Technical University of Moldova, Chisinau MD-2004, Republic of Moldova (Moldova, Republic of); Arushanov, E. [Institute of Applied Physics, Academy of Sciences of Moldova, Academiei Str. 5, Chisinau MD 2028, Republic of Moldova (Moldova, Republic of)

    2014-02-25

    Highlights: • Reflection spectra of Cu{sub 2}ZnSiSe{sub 4} were studied for E ⊥ c and E || c light polarizations. • Four excitonic series are revealed in the reflection spectra at 10 K. • Model of exciton dispersion and the presence of a dead-layer. • Exciton Rydberg energies and free carriers effective masses were calculated. • Reflectivity for E ⊥ c and E || c were analyzed in the region 3–6 eV at 300 K. -- Abstract: Exciton spectra are studied in Cu{sub 2}ZnSiSe{sub 4} single crystals at 10 and 300 K by means of reflection spectroscopy. The exciton parameters, dielectric constant and free carriers effective masses are deduced from experimental spectra by calculations in the framework of a model taking into account the spatial dispersion and the presence of a dead-layer. The structure found in the reflectivity was analyzed and related to the theoretical electronic band structure of close related Cu{sub 2}ZnSiS{sub 4} semiconductor.

  5. Effect of low-temperature argon matrices on IR spectra and structure of flexible N-acetylglycine molecules

    International Nuclear Information System (INIS)

    Stepan'yan, S.G.; Ivanov, A.Yu.; Adamowicz, L.

    2016-01-01

    The influence of the matrix environment on structure and IR spectra of the N-acetylglycine conformers was studied. Based on the FTIR spectra of N-acetyl-glycine isolated in low temperature argon matrices we determined its conformational composition. The spectra bands of main and two minor conformers of N-acetylglycine were identified in the FTIR spectra. The structure of the observed conformers was stabilized by different intramolecular hydrogen bonds. The Gibbs free energies of the conformers (CCSD(T)/CBS method) were performed and population of the con-formers at 360 K were determined. They were 85.3% for the main conformer and 9.6 and 5.1% for the mi-nor N-acetylglycine conformers. We also determined size and shape of the cavities which were formed by embedding of the N-acetylglycine conformers in argon matrices during deposition. It was found that for the planar main conformer the most energetically preferred cavity was formed by substituting of 7 argon atoms. At the same time, bulky minor conformers were embedded in a cavity formed by substituting of 8 argon atoms. Complexation energies as well as the deformation energies of the argon crystal and conformers of N-acetylglycine were calculated. Also we determined values of the matrix shifts of vibrational frequencies of N-acetylglycine conformers.

  6. Vibrational spectra (FT-IR, FT-Raman), frontier molecular orbital, first hyperpolarizability, NBO analysis and thermodynamics properties of Piroxicam by HF and DFT methods

    Science.gov (United States)

    Suresh, S.; Gunasekaran, S.; Srinivasan, S.

    2015-03-01

    The solid phase FT-IR and FT-Raman spectra of 4-Hydroxy-2-methyl-N-(2-pyridinyl)-2H-1,2-benzothiazine-3-carboxamide-1,1-dioxide (Piroxicam) have been recorded in the region 4000-400 and 4000-100 cm-1 respectively. The molecular geometry, harmonic vibrational frequencies and bonding features of piroxicam in the ground state have been calculated by Hartree-Fock (HF) and density functional theory (DFT) methods using 6-311++G(d,p) basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimental obtained by FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of the title compound has been made on the basis of the calculated potential energy distribution (PED). The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) are also performed. The linear polarizability (α) and the first order hyper polarizability (β) values of the title compound have been computed. The molecular stability arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

  7. Metal alkyls programmed to generate metal alkylidenes by α-H abstraction: prognosis from NMR chemical shift† †Electronic supplementary information (ESI) available: Experimental and computational details, NMR spectra, results of NMR calculations and NCS analysis, graphical representation of shielding tensors, molecular orbital diagrams of selected compounds, optimized structures for all calculated species. See DOI: 10.1039/c7sc05039a

    Science.gov (United States)

    Gordon, Christopher P.; Yamamoto, Keishi; Searles, Keith; Shirase, Satoru

    2018-01-01

    Metal alkylidenes, which are key organometallic intermediates in reactions such as olefination or alkene and alkane metathesis, are typically generated from metal dialkyl compounds [M](CH2R)2 that show distinctively deshielded chemical shifts for their α-carbons. Experimental solid-state NMR measurements combined with DFT/ZORA calculations and a chemical shift tensor analysis reveal that this remarkable deshielding originates from an empty metal d-orbital oriented in the M–Cα–Cα′ plane, interacting with the Cα p-orbital lying in the same plane. This π-type interaction inscribes some alkylidene character into Cα that favors alkylidene generation via α-H abstraction. The extent of the deshielding and the anisotropy of the alkyl chemical shift tensors distinguishes [M](CH2R)2 compounds that form alkylidenes from those that do not, relating the reactivity to molecular orbitals of the respective molecules. The α-carbon chemical shifts and tensor orientations thus predict the reactivity of metal alkyl compounds towards alkylidene generation. PMID:29675237

  8. RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

    Science.gov (United States)

    Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng

    2011-09-01

    Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. qnhu@whu.edu.cn.

  9. Electronic structure of molecular Rydberg states of some small molecules and molecular ion

    International Nuclear Information System (INIS)

    Sun Biao; Li Jiaming

    1993-01-01

    Based on an independent-particle-approximation (i.e. the multiple scattering self-consistent-field theory), the electronic structures of Rydberg states of the small diatomic molecules H 2 , He 2 and the He 2 + molecular ion were studied. The principal quantum number of the first state of the Rydberg series is determined from a convention of the limit of the molecular electronic configuration. The dynamics of the excited molecules and molecular ion has been elucidated. The theoretical results are in fair agreement with the existing experimental measurements, thus they can serve as a reliable basis for future refined treatment such as the configuration interaction calculation

  10. Quark-gluon structure of the pomeron and the rise of inclusive spectra at high energies

    International Nuclear Information System (INIS)

    Kaidalov, A.V.

    1982-01-01

    The topological expansion and the nodel of a colour tube are used for the calculation of inclusive hadronic spectra in the central region. The higher-order terms of the 1/Nsub(f)-expansion, which correspond to the contribution of the poliperipheral diagrams are taken into account. It is shown that the intrinsic motion of quarks inside colliding hadrons leads to the rise of inclusive spectra with energy in the central region. The model gives a good quantitative description of the effects observed recently at the CERN SPS Collider

  11. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

    Directory of Open Access Journals (Sweden)

    Rong Shen

    2015-10-01

    Full Text Available The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels, each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good

  12. Monte Carlo Simulations of Electron Energy-Loss Spectra with the Addition of Fine Structure from Density Functional Theory Calculations.

    Science.gov (United States)

    Attarian Shandiz, Mohammad; Guinel, Maxime J-F; Ahmadi, Majid; Gauvin, Raynald

    2016-02-01

    A new approach is presented to introduce the fine structure of core-loss excitations into the electron energy-loss spectra of ionization edges by Monte Carlo simulations based on an optical oscillator model. The optical oscillator strength is refined using the calculated electron energy-loss near-edge structure by density functional theory calculations. This approach can predict the effects of multiple scattering and thickness on the fine structure of ionization edges. In addition, effects of the fitting range for background removal and the integration range under the ionization edge on signal-to-noise ratio are investigated.

  13. Molecular structure of dextran sulphate sodium in aqueous environment

    Science.gov (United States)

    Yu, Miao; Every, Hayley A.; Jiskoot, Wim; Witkamp, Geert-Jan; Buijs, Wim

    2018-03-01

    Here we propose a 3D-molecular structural model for dextran sulphate sodium (DSS) in a neutral aqueous environment based on the results of a molecular modelling study. The DSS structure is dominated by the stereochemistry of the 1,6-linked α-glucose units and the presence of two sulphate groups on each α-glucose unit. The structure of DSS can be best described as a helix with various patterns of di-sulphate substitution on the glucose rings. The presence of a side chain does not alter the 3D-structure of the linear main chain much, but affects the overall spatial dimension of the polymer. The simulated polymers have a diameter similar to or in some cases even larger than model α-hemolysin nano-pores for macromolecule transport in many biological processes, indicating a size-limited translocation through such pores. All results of the molecular modelling study are in line with previously reported experimental data. This study establishes the three-dimensional structure of DSS and summarizes the spatial dimension of the polymer, serving as the basis for a better understanding on the molecular level of DSS-involved electrostatic interaction processes with biological components like proteins and cell pores.

  14. Seismic analysis of a PWR 900 reactor: study of reactor building with soil-structure interaction and evaluation of floor spectra

    International Nuclear Information System (INIS)

    Gantenbein, F.; Aguilar, J.

    1983-08-01

    The purpose of this paper is the evaluation of seismic response and floor spectra for a typical PWR 900 reactor building with respect to soil-structure interaction for soil stiffness). The typical PWR 900 reactor building consists of a concrete cylindrical external building and roof dome, a concrete internal structure (internals) on a common foundation mat as illustrated. The seismic response is obtained by SRSS method and floor spectra directly from ground spectrum and modal properties of the structure. Seismic responses and floor spectra computation is performed in the case of two different ground spectra: EDF spectrum (mean of oscillator spectra obtained from 8 californian records) normalized to 0.2 g, and DSN spectrum (typical of shallow seism) normalized to 0.3 g. The first section is devoted to internals' modelisation, the second one to the axisymmetric model of the reactor, the third one to the seismic response, the fourth one to floor spectra

  15. Nanohashtag structures based on carbon nanotubes and molecular linkers

    Science.gov (United States)

    Frye, Connor W.; Rybolt, Thomas R.

    2018-03-01

    Molecular mechanics was used to study the noncovalent interactions between single-walled carbon nanotubes and molecular linkers. Groups of nanotubes have the tendency to form tight, parallel bundles (||||). Molecular linkers were introduced into our models to stabilize nanostructures with carbon nanotubes held in perpendicular orientations. Molecular mechanics makes it possible to estimate the strength of noncovalent interactions holding these structures together and to calculate the overall binding energy of the structures. A set of linkers were designed and built around a 1,3,5,7-cyclooctatetraene tether with two corannulene containing pincers that extend in opposite directions from the central cyclooctatetraene portion. Each pincer consists of a pairs of "arms." These molecular linkers were modified so that the "hand" portions of each pair of "arms" could close together to grab and hold two carbon nanotubes in a perpendicular arrangement. To illustrate the possibility of more complicated and open perpendicular CNTs structures, our primary goal was to create a model of a nanohashtag (#) CNT conformation that is more stable than any parallel CNT arrangements with bound linker molecules forming clumps of CNTs and linkers in non-hashtag arrangements. This goal was achieved using a molecular linker (C280H96) that utilizes van der Waals interactions to two perpendicular oriented CNTs. Hydrogen bonding was then added between linker molecules to augment the stability of the hashtag structure. In the hashtag structure with hydrogen bonding, four (5,5) CNTs of length 4.46 nm (18 rings) and four linkers (C276H92N8O8) stabilized the hashtag so that the average binding energy per pincer was 118 kcal/mol.

  16. DFT study of structure, IR and Raman spectra of the fluorescent "Janus" dendron built from cyclotriphosphazene core

    Science.gov (United States)

    Furer, V. L.; Vandyukova, I. I.; Vandyukov, A. E.; Fuchs, S.; Majoral, J. P.; Caminade, A. M.; Kovalenko, V. I.

    2011-11-01

    The FTIR and FT-Raman spectra of the zero generation dendron, possessing five fluorescent dansyl terminal groups, cyclotriphosphazene core, and one carbamate function G0v were studied. The structural optimization and normal mode analysis were performed for G0v dendron on the basis of the density functional theory (DFT). The calculated geometrical parameters and harmonic vibrational frequencies are predicted in a good agreement with the experimental data. It was found that dendron molecule G0v has a concave lens structure with slightly non-planar cyclotriphosphazene core. The experimental IR and Raman spectra of G0v dendron were interpreted by means of potential energy distributions. Relying on DFT calculations a complete vibrational assignment is proposed. The frequency of ν(N-H) band in the IR spectrum reveal the presence of H-bonds in the G0v dendron.

  17. Molecular structure and spectroscopic properties of 4-nitrocatechol at different pH: UV-visible, Raman, DFT and TD-DFT calculations

    International Nuclear Information System (INIS)

    Cornard, Jean-Paul; Rasmiwetti; Merlin, Jean-Claude

    2005-01-01

    We investigated theoretically, by density functional theoretical calculations and by vibrational and electronic spectroscopies, the structure and the molecular spectroscopic properties of the 4-nitrocatechol molecule with varying pH. The lower energy stable structures of the neutral, monoanion and dianion forms were compared, and influence of water solvation was examined. The Raman and UV-visible spectra of 4-nitrocatechol and of its singly deprotonated form were recorded by varying the pH from 2 to 9. A calculation of the vibrational frequencies has allowed a complete assignment of the Raman spectra of the two forms of 4-nitrocatechol, and has permitted to investigate the evolution of vibrational normal modes upon deprotonation. Based on the molecular orbital analysis and the time dependent DFT (TD-DFT) calculations, we discussed the electronic structure and the assignment of the absorption bands in the electronic spectra of 4-nitrocatechol and mono-deprotonated 4-nitrocatechol

  18. Influence of changes in the valence electronic configuration on the structure of L-X-ray spectra of molybdenum

    International Nuclear Information System (INIS)

    Polasik, M; Koziol, K; Slabkowska, K; Czarnota, M; Pajek, M

    2009-01-01

    Extensive multiconfiguration Dirac-Fock (MCDF) calculations with the inclusion of the transverse (Breit) interaction and QED corrections have been carried out on molybdenum to explain the dependence of the structure of Lα 1,2 and Lβ 1 lines on the changes in configurations of the valence electrons belonging to two different configuration types: three open-shell 4d 6-r 5s r (r = 2,1,0) configurations and one closed-shell 4d 4 3/2 5s 2 configuration. It has been found that the MCDF predictions for open-shell valence configurations (4d 4 5s 2 , 4d 5 5s 1 , 4d 6 5s 0 ) much better reproduce observed structure of Lα 1,2 lines in X-ray spectra of molybdenum than closed-shell 4d 4 3/2 5s 2 valence configuration. The influence of changes in the valence electronic configuration on the structure of L-X-ray spectra of molybdenum is noticeable. Moreover, the observation of the shapes of L-X-ray spectra seems to be very good method to investigate the changes of the valence electronic configuration caused by the chemical environment.

  19. [Molecular structure and luminescent property of bis(2-(4-methyl-2-hydroxyphenyl)benzothiazolate) zinc].

    Science.gov (United States)

    Xu, Hui-Xia; Chen, Liu-Qing; Wang, Hua; Hao, Yu-Ying; Xu, Bing-She

    2011-02-01

    Bis(2-(4-methyl-2-hydroxyphenyl)benzothiazolate) zinc(Zn(4-MeBTZ)2) was synthesized. Its molecular structure was confirmed by single-crystal x-ray diffraction. Single-crystal data are as follows: space group triclinic, P-1; a = 8.989 9(11) angstroms, b =12.161 7 (15) angstroms, c = 12.871 9 (16) angstroms, alpha = 63.492 (2) degrees, beta = 84.825 (2) degrees, gamma =71.187 (2) degrees. The steric hindrance provided by introduction methyl groups on phenoxide ring prohibited effectively the formation of pentacoordinate complex. There is distinct intermolecular pi-pi interaction between molecules. The dihedral angle between the phenol and benzothiazolate rings of Zn(4-MeBTZ)2 is 2.166 degrees. The HOMO energy, LUMO energy and optical gap are -5.84, -3.46 and 2.37 eV, respectively. The maximum wavelength peak of PL spectra located at 470 nm. The double-layer devices were employed using Zn(4-MeBTZ)2 as emitter and NPB as hole-transport material. The EL spectra split into two peaks located at 501 and 544 nm respectively. The broadened EL spectra were demonstrated to be originated from the exciplexes formed at the interface between NPB and Zn(4-MeBTZ)2.

  20. Introductory group theory and its application to molecular structure

    CERN Document Server

    Ferraro, John R

    1969-01-01

    This volume is a consequence of a series of seminars presented by the authors at the Infrared Spectroscopy Institute, Canisius College, Buffalo, New York, over the last nine years. Many participants on an intermediate level lacked a sufficient background in mathematics and quantum mechan­ ics, and it became evident that a non mathematical or nearly nonmathe­ matical approach would be necessary. The lectures were designed to fill this need and proved very successful. As a result of the interest that was developed in this approach, it was decided to write this book. The text is intended for scientists and students with only limited theore­ tical background in spectroscopy, but who are sincerely interested in the interpretation of molecular spectra. The book develops the detailed selection rules for fundamentals, combinations, and overtones for molecules in several point groups. Detailed procedures used in carrying out the normal coordinate treatment for several molecules are also presented. Numerous examples...

  1. Learning Molecular Structures in a Tangible Augmented Reality Environment

    Science.gov (United States)

    Asai, Kikuo; Takase, Norio

    2011-01-01

    This article presents the characteristics of using a tangible table top environment produced by augmented reality (AR), aimed at improving the environment in which learners observe three-dimensional molecular structures. The authors perform two evaluation experiments. A performance test for a user interface demonstrates that learners with a…

  2. Molecular epidemiology and population structure of bovine Streptococcus uberis

    DEFF Research Database (Denmark)

    Rato, M G; Bexiga, R; Nunes, S F

    2008-01-01

    The molecular epidemiology and population structure of 30 bovine subclinical mastitis field isolates of Streptococcus uberis, collected from 6 Portuguese herds (among 12 farms screened) during 2002 and 2003, were examined by using pulsed-field gel electrophoresis (PFGE) for clustering of the isol...

  3. Structure of hydrogenated amorphous silicon from ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Buda, F. (Department of Physics, The Ohio State University, 174 West 18th Avenue, Columbus, Ohio (USA)); Chiarotti, G.L. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Laboratorio Tecnologie Avanzate Superfici e Catalisi del Consorzio Interuniversitario Nazionale di Fisica della Materia, Padriciano 99, I-34012 Trieste (Italy)); Car, R. (International School for Advanced Studies, Strada Costiera 11, I-34014 Trieste (Italy) Institut Romard de Recherche Numerique en Physique des Materiaux, CH-1015 Lausanne, Switzerland Department of Condensed Matter Physics, University of Geneva, CH-1211 Geneva (Switzerland)); Parrinello, M. (IBM Research Division, Zurich Research Laboratory, CH-8803 Rueschlikon (Switzerland))

    1991-09-15

    We have generated a model of hydrogenated amorphous silicon by first-principles molecular dynamics. Our results are in good agreement with the available experimental data and provide new insight into the microscopic structure of this material. The calculation lends support to models in which monohydride complexes are prevalent, and indicates a strong tendency of hydrogen to form small clusters.

  4. Structural changes in polytetrafluoroethylene molecular chains upon sliding against steel

    NARCIS (Netherlands)

    Shen, J.T.; Pei, Y.T.; Hosson, J.Th.M. De

    In this work, the influence of dry sliding between a steel counterpart ball and polytetrafluoroethylene (PTFE) plate sample on the transformation of PTFE molecular structure is investigated. With X-ray diffraction, differential scanning calorimetry, Fourier transform infrared (FT-IR) spectroscopy

  5. Molecular and vibrational structure of 2,2'-dihydroxybenzophenone

    DEFF Research Database (Denmark)

    Birklund Andersen, Kristine; Langgård, M.; Spanget-Larsen, Jens

    1999-01-01

    2,2'-dihydroxybenzophenone (DHBP) contains similar bifold intramolecular H-bonding as the psoriatic drug anthralin, but because of steric interference the phenolic rings are twisted in a propeller-like manner, resulting in a molecular structure of C2 symmetry. In contrast to the case of C2v...

  6. Variational cellular model of the molecular and crystal electronic structure

    International Nuclear Information System (INIS)

    Ferreira, L.G.; Leite, J.R.

    1977-12-01

    A variational version of the cellular method is developed to calculate the electronic structure of molecules and crystals. Due to the simplicity of the secular equation, the method is easy to be implemented. Preliminary calculations on the hydrogen molecular ion suggest that it is also accurate and of fast convergence [pt

  7. Molecular and vibrational structure of 2,2'-dihydroxybenzophenone

    DEFF Research Database (Denmark)

    Birklund Andersen, Kristine; Langgård, M.; Spanget-Larsen, Jens

    1999-01-01

    2,2'-dihydroxybenzophenone (DHBP) contains similar bifold intramolecular H-bonding as the psoriatic drug anthralin, but because of steric interference the phenolic rings are twisted in a propeller-like manner, resulting in a molecular structure of C2 symmetry. In contrast to the case of C2v anthr...

  8. Microwave, infrared and Raman spectra, adjusted r{sub 0} structural parameters, conformational stability, and vibrational assignment of cyclopropylfluorosilane

    Energy Technology Data Exchange (ETDEWEB)

    Panikar, Savitha S. [Department of Chemistry, University of Missouri-Kansas City, Kansas City, MO 64110 (United States); Guirgis, Gamil A.; Eddens, Matthew T.; Dukes, Horace W. [Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424 (United States); Conrad, Andrew R.; Tubergen, Michael J. [Department of Chemistry, Kent State University, Kent, OH 44242 (United States); Gounev, Todor K. [Department of Chemistry, University of Missouri-Kansas City, Kansas City, MO 64110 (United States); Durig, James R., E-mail: durigj@umkc.edu [Department of Chemistry, University of Missouri-Kansas City, Kansas City, MO 64110 (United States)

    2013-03-29

    Highlights: ► The most stable gauche conformer has been identified from microwave spectra. ► Enthalpy difference has been determined between the two forms. ► Adjusted r{sub 0} structures were obtained for the gauche form. ► Ab initio calculations were performed for the two conformers. - Abstract: FT-microwave, infrared spectra of gas and Raman spectra of liquid for cyclopropylfluorosilane, c-C{sub 3}H{sub 5}SiH{sub 2}F have been recorded. 51 transitions for the {sup 28}Si, {sup 29}Si, and {sup 30}Si isotopomers have been assigned for the gauche conformer. Enthalpy differences in xenon solution by variable temperature infrared spectra between the more stable gauche and lesser stable cis form gave 109 ± 9 cm{sup −1}. From the microwave rotational constants for the three isotopomers ({sup 28}Si, {sup 29}Si, {sup 30}Si) combined with structural parameters predicted from MP2(full)/6-311+G(d, p) calculations, adjusted r{sub 0} structural parameters were obtained for the gauche conformer. The heavy atom distances (Å): Si–C{sub 2} = 1.836(3); C{sub 2}–C{sub 4} = 1.525(3); C{sub 2}–C{sub 5} = 1.519(3); C{sub 4}–C{sub 5} = 1.494(3); Si–F = 1.594(3) and angles (°): ∠CSiF = 111.2(5); ∠SiC{sub 2}C{sub 4} = 117.5(5); ∠SiC{sub 2}C{sub 5} = 119.2(5). To support the vibrational assignments, MP2(full)/6-31G(d) calculations were carried out. Results are discussed and compared to the corresponding properties of some similar molecules.

  9. Computing UV/vis spectra using a combined molecular dynamics and quantum chemistry approach: bis-triazin-pyridine (BTP) ligands studied in solution.

    Science.gov (United States)

    Höfener, Sebastian; Trumm, Michael; Koke, Carsten; Heuser, Johannes; Ekström, Ulf; Skerencak-Frech, Andrej; Schimmelpfennig, Bernd; Panak, Petra J

    2016-03-21

    We report a combined computational and experimental study to investigate the UV/vis spectra of 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine (BTP) ligands in solution. In order to study molecules in solution using theoretical methods, force-field parameters for the ligand-water interaction are adjusted to ab initio quantum chemical calculations. Based on these parameters, molecular dynamics (MD) simulations are carried out from which snapshots are extracted as input to quantum chemical excitation-energy calculations to obtain UV/vis spectra of BTP ligands in solution using time-dependent density functional theory (TDDFT) employing the Tamm-Dancoff approximation (TDA). The range-separated CAM-B3LYP functional is used to avoid large errors for charge-transfer states occurring in the electronic spectra. In order to study environment effects with theoretical methods, the frozen-density embedding scheme is applied. This computational procedure allows to obtain electronic spectra calculated at the (range-separated) DFT level of theory in solution, revealing solvatochromic shifts upon solvation of up to about 0.6 eV. Comparison to experimental data shows a significantly improved agreement compared to vacuum calculations and enables the analysis of relevant excitations for the line shape in solution.

  10. Physiochemical Characteristics and Molecular Structures for Digestible Carbohydrates of Silages.

    Science.gov (United States)

    Refat, Basim; Prates, Luciana L; Khan, Nazir A; Lei, Yaogeng; Christensen, David A; McKinnon, John J; Yu, Peiqiang

    2017-10-18

    The main objectives of this study were (1) to assess the magnitude of differences among new barley silage varieties (BS) selected for varying rates of in vitro neutral detergent fiber (NDF) digestibility (ivNDFD; Cowboy BS with higher ivNDFD, Copeland BS with intermediate ivNDFD, and Xena BS with lower ivNDFD) with regard to their carbohydrate (CHO) molecular makeup, CHO chemical fractions, and rumen degradability in dairy cows in comparison with a new corn silage hybrid (Pioneer 7213R) and (2) to quantify the strength and pattern of association between the molecular structures and digestibility of carbohydrates. The carbohydrate-related molecular structure spectral data was measured using advanced vibrational molecular spectroscopy (FT/IR). In comparison to BS, corn silage showed a significantly (P carbohydrates were significantly (P carbohydrate content of the silages. In conclusion, the univariate approach with only one-factor consideration (ivNDFD) might not be a satisfactory method for evaluating and ranking BS quality. FT/IR molecular spectroscopy can be used to evaluate silage quality rapidly, particularly the digestible fiber content.

  11. Structure of the X-ray photoelectron spectra of fluorides and oxides of lanthanides connected with the dynamic effect

    International Nuclear Information System (INIS)

    Teterin, Yu.A.; Teterin, A.Yu.; Lebedev, A.M.; Utkin, I.O.; Nikitin, A.S.

    1998-01-01

    Impact of dynamic effect on the fine structure of the X-ray electron spectra of the lanthanide oxides and fluorides is considered. Significant complication of the Ln4p-electrons occurs due to interaction of configurations of the basic single-hole and additional two-hole finite states of the 4p 5 4d 10 4f n ↔ 4p 6 4d 8 4f n+1 type. Impact of the atoms nature of the nearest surrounding of the lanthanides ions on the parameters of such fine structure is evaluated [ru

  12. Experimental search of structures in missing mass spectra of B=2, T=1 system: possible evidence for narrow states

    International Nuclear Information System (INIS)

    Tatischeff, B.; Combes, M.P.; Didelez, J.P.

    1984-01-01

    The missing mass spectra for the transfer reaction p( 3 He,d)X (B=2, T=1) have been measured at Tsub( 3 He) = 2.7 GeV. The data show: 1) a narrow structure lying on top of an important continuum, with a mass M = 2.240+-0.005 GeV and a width GAMMAsub(1/2) = .016 +- .003 GeV; 2) a large structure with centroid location close to Msub(x) approximately equal to 2.170 +- .005 GeV and width GAMMAsub(1/2) approximately .100 +- .005 Gev

  13. Intercomparison of ion beam analysis software for the simulation of backscattering spectra from two-dimensional structures

    Energy Technology Data Exchange (ETDEWEB)

    Mayer, M., E-mail: matej.mayer@ipp.mpg.de [Max-Planck-Institut für Plasmaphysik, Boltzmannstr. 2, 85748 Garching (Germany); Malinský, P. [Nuclear Physics Institute of the Czech Academy of Sciences v.v.i., 250 68 Rez (Czech Republic); Department of Physics, Faculty of Science, J.E. Purkinje University, Ceske mladeze 8, 400 96 Usti nad Labem (Czech Republic); Schiettekatte, F. [Regroupement Québécois sur les Matériaux de Pointe (RQMP), Département de Physique, Université de Montréal, Montréal, QC (Canada); Zolnai, Z. [Centre for Energy Research, Institute of Technical Physics and Materials Science (MFA), Konkoly-Thege M. út 29-33, H-1121 Budapest (Hungary)

    2016-10-15

    The codes RBS-MAST, STRUCTNRA, F95-Rough and CORTEO are simulation codes for ion beam analysis spectra from two- or three-dimensional sample structures. The codes were intercompared in a code-code comparison using an idealized grating structure and by comparison to experimental data from a silicon grating on tantalum interlayer. All codes are in excellent agreement at higher incident energies and not too large energy losses. At lower incident energies, grazing angles of incidence and/or larger energy losses plural scattering effects play an increasing role. Simulation codes with plural scattering capabilities offer higher accuracy and better agreement to experimental results in this regime.

  14. MID-INFRARED ATOMIC FINE-STRUCTURE EMISSION-LINE SPECTRA OF LUMINOUS INFRARED GALAXIES: SPITZER/IRS SPECTRA OF THE GOALS SAMPLE

    Energy Technology Data Exchange (ETDEWEB)

    Inami, H. [National Optical Astronomy Observatory, Tucson, AZ 85719 (United States); Armus, L.; Stierwalt, S.; Díaz-Santos, T.; Surace, J.; Howell, J.; Marshall, J. [Spitzer Science Center, California Institute of Technology, CA 91125 (United States); Charmandaris, V. [Department of Physics and Institute of Theoretical and Computational Physics, University of Crete, GR-71003 Heraklion (Greece); Groves, B. [Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg (Germany); Kewley, L. [Research School of Astronomy and Astrophysics, The Australian National University, Cotter Road, Weston Creek, ACT 2611 (Australia); Petric, A. [Department of Astronomy, California Institute of Technology, MS 320-47, Pasadena, CA 91125 (United States); Rich, J. [The Observatories, Carnegie Institute of Washington, 813 Santa Barbara Street, Pasadena, CA 91101 (United States); Haan, S. [CSIRO Astronomy and Space Science, Marsfield, NSW 2122 (Australia); Evans, A. S. [Department of Astronomy, University of Virginia, P.O. Box 400325, Charlottesville, VA 22904 (United States); Mazzarella, J.; Lord, S. [Infrared Processing and Analysis Center, MS 100-22, California Institute of Technology, Pasadena, CA 91125 (United States); Appleton, P. [NASA Herschel Science Center, 770 South Wilson Avenue, Pasadena, CA 91125 (United States); Spoon, H. [Astronomy Department, Cornell University, Ithaca, NY 14853 (United States); Frayer, D. [National Radio Astronomy Observatory, P.O. Box 2, Green Bank, WV 24944 (United States); Matsuhara, H., E-mail: inami@noao.edu [Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (Japan); and others

    2013-11-10

    We present the data and our analysis of mid-infrared atomic fine-structure emission lines detected in Spitzer/Infrared Spectrograph high-resolution spectra of 202 local Luminous Infrared Galaxies (LIRGs) observed as part of the Great Observatories All-sky LIRG Survey (GOALS). We readily detect emission lines of [S IV], [Ne II], [Ne V], [Ne III], [S III]{sub 18.7{sub μm}}, [O IV], [Fe II], [S III]{sub 33.5{sub μm}}, and [Si II]. More than 75% of these galaxies are classified as starburst-dominated sources in the mid-infrared, based on the [Ne V]/[Ne II] line flux ratios and equivalent width of the 6.2 μm polycyclic aromatic hydrocarbon feature. We compare ratios of the emission-line fluxes to those predicted from stellar photo-ionization and shock-ionization models to constrain the physical and chemical properties of the gas in the starburst LIRG nuclei. Comparing the [S IV]/[Ne II] and [Ne III]/[Ne II] line ratios to the Starburst99-Mappings III models with an instantaneous burst history, the emission-line ratios suggest that the nuclear starbursts in our LIRGs have ages of 1-4.5 Myr, metallicities of 1-2 Z{sub ☉}, and ionization parameters of 2-8 × 10{sup 7} cm s{sup –1}. Based on the [S III]{sub 33.5{sub μm}}/[S III]{sub 18.7{sub μm}} ratios, the electron density in LIRG nuclei is typically one to a few hundred cm{sup –3}, with a median electron density of ∼300 cm{sup –3}, for those sources above the low density limit for these lines. We also find that strong shocks are likely present in 10 starburst-dominated sources of our sample. A significant fraction of the GOALS sources (80) have resolved neon emission-line profiles (FWHM ≥600 km s{sup –1}) and five show clear differences in the velocities of the [Ne III] or [Ne V] emission lines, relative to [Ne II], of more than 200 km s{sup –1}. Furthermore, six starburst and five active galactic nucleus dominated LIRGs show a clear trend of increasing line width with ionization potential

  15. Hydration effects on the molecular structure of silica-supported vanadium oxide catalysts: A combined IR, Raman, UV–vis and EXAFS study

    NARCIS (Netherlands)

    Keller, D.E.; Visser, T.; Soulimani, F.; Koningsberger, D.C.; Weckhuysen, B.M.

    2007-01-01

    The effect of hydration on the molecular structure of silica-supported vanadium oxide catalysts with loadings of 1–16 wt.% V has been systematically investigated by infrared, Raman, UV–vis and EXAFS spectroscopy. IR and Raman spectra recorded during hydration revealed the formation of V–OH groups,

  16. Molecular orientation and electronic structure at organic heterojunction interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Zhong, Shu [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Zhong, Jian Qiang; Wee, Andrew T.S. [Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); Chen, Wei, E-mail: phycw@nus.edu.sg [Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543 Singapore (Singapore); Department of Physics, National University of Singapore, 2 Science Drive 3, 117542 Singapore (Singapore); National University of Singapore (Suzhou) Research Institute, Suzhou (China)

    2015-10-01

    Highlights: • Molecular orientation at the organic heterojunction interfaces. • Energy level alignments at the organic heterojunction interfaces. • Gap-states mediated interfacial energy level alignment. - Abstract: Due to the highly anisotropic nature of π-conjugated molecules, the molecular orientation in organic thin films can significantly affect light absorption, charge transport, energy level alignment (ELA) and hence device performance. Synchrotron-based near-edge X-ray absorption fine structure (NEXAFS) spectroscopy represents a powerful technique for probing molecular orientation. The aim of this review paper is to provide a balanced assessment on the investigation of molecular orientation at the organic–organic heterojunction (OOH) interface by NEXAFS, as well as the gap-states mediated orientation dependent energy level alignment at OOH interfaces. We highlight recent progress in elucidating molecular orientation at OOH interfaces dominated by various interfacial interactions, gap-states controlled orientation dependent energy level alignments at OOH interfaces, and the manipulations of molecular orientation and ELA in OOH.

  17. Modification of erbium photoluminescence excitation spectra for the emission wavelength 1.54 μm in mesoscopic structures

    International Nuclear Information System (INIS)

    Gaponenko, N.V.; Unuchak, D.M.; Mudryi, A.V.; Malyarevich, G.K.; Gusev, O.B.; Stepikhova, M.V.; Krasilnikova, L.V.; Stupak, A.P.; Kleshcheva, S.M.; Samoilovich, M.I.; Tsvetkov, M.Yu.

    2006-01-01

    Photoluminescence excitation (PLE) spectra for the emission wavelength 1.54 μm were studied for erbium-doped xerogels embedded in artificial opals and porous anodic alumina films. Opals were chosen with photonic stop-band in green spectral range, where excitation of 1.54 μm occurs most efficiently. In comparison to the structure erbium-doped titania xerogel/porous anodic alumina/silicon the photoluminescence excitation spectra for 1.54 μm emission wavelength significantly changes for the same xerogels embedded in artificial opals. Enhancement of erbium-related 1.54 μm emission was observed from the structure Fe 2 O 3 xerogel/porous anodic alumina fabricated on silicon, having some incompletely anodized aluminium, under excitation with either the lasing source at 532 nm or xenon lamp. Evident difference in PLE spectra for erbium doped TiO 2 and Fe 2 O 3 xerogels in porous anodic alumina is observed

  18. Novel push-pull fluorescent dyes - 7-(diethylamino)furo- and thieno[3,2-c]coumarins derivatives: structure, electronic spectra and TD-DFT study

    Science.gov (United States)

    Akchurin, Igor O.; Yakhutina, Anna I.; Bochkov, Andrei Y.; Solovjova, Natalya P.; Medvedev, Michael G.; Traven, Valerii F.

    2018-05-01

    Novel push-pull fluorescent dyes - 7-(diethylamino)furo- and 7-(diethylamino)thieno[3,2-c]coumarins derivatives have been synthesized using formyl derivatives of furo- and thieno[3,2-c]coumarins as starting materials. Electron absorption and fluorescent spectra of the dyes have been recorded in different solvents. Structure and solvent effects on the dyes spectral characteristics were analyzed. The fusion of five-membered heterocycle to coumarin provides a definite increase of Stokes shifts in all solvents and results in higher quantum yields of fluorescence. The absorption and emission bands of thieno[3,2-c] coumarin derivatives are definitely shifted to the red region (3-30 nm) compared to similar derivatives of furo[3,2-c]coumarin. TD-DFT calculations of some of the studied compounds have shown that hybrid DFT functionals and adequate representation of molecular environment are essential for obtaining accurate UV-Vis absorption spectra for the dyes with extended π-system. The longest-wave electron transitions in the studied compounds were computationally shown to be of push-pull nature.

  19. A new tridentate Schiff base Cu(II) complex: synthesis, experimental and theoretical studies on its crystal structure, FT-IR and UV-Visible spectra.

    Science.gov (United States)

    Saheb, Vahid; Sheikhshoaie, Iran; Setoodeh, Nasim; Rudbari, Hadi Amiri; Bruno, Giuseppe

    2013-06-01

    A new Cu(II) complex [Cu(L)(NCS)] has been synthesized, using 1-(N-salicylideneimino)-2-(N,N-methyl)-aminoethane as tridentate ONN donor Schiff base ligand (HL). The dark green crystals of the compound are used for single-crystal X-ray analysis and measuring Fourier Transform Infrared (FT-IR) and UV-Visible spectra. Electronic structure calculations at the B3LYP and MP2 levels of theory are performed to optimize the molecular geometry and to calculate the UV-Visible and FT-IR spectra of the compound. Vibrational assignments and analysis of the fundamental modes of the compound are performed. Time-dependent density functional theory (TD-DFT) method is used to calculate the electronic transitions of the complex. A scaling factor of 1.015 is obtained for vibrational frequencies computed at the B3LYP level using basis sets 6-311G(d,p). It is found that solvent has a profound effect on the electronic absorption spectrum. The UV-Visible spectrum of the complex recorded in DMSO and DMF solution can be correctly predicted by a model in which DMSO and DMF molecules are coordinated to the central Cu atom via their oxygen atoms. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. Design of Carborane Molecular Architectures via Electronic Structure Computations

    International Nuclear Information System (INIS)

    Oliva, J.M.; Serrano-Andres, L.; Klein, D.J.; Schleyer, P.V.R.; Mich, J.

    2009-01-01

    Quantum-mechanical electronic structure computations were employed to explore initial steps towards a comprehensive design of poly carborane architectures through assembly of molecular units. Aspects considered were (i) the striking modification of geometrical parameters through substitution, (ii) endohedral carboranes and proposed ejection mechanisms for energy/ion/atom/energy storage/transport, (iii) the excited state character in single and dimeric molecular units, and (iv) higher architectural constructs. A goal of this work is to find optimal architectures where atom/ion/energy/spin transport within carborane superclusters is feasible in order to modernize and improve future photo energy processes.

  1. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron.

    Science.gov (United States)

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

    2016-01-01

    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons.

  2. New Diethyl Ammonium Salt of Thiobarbituric Acid Derivative: Synthesis, Molecular Structure Investigations and Docking Studies

    Directory of Open Access Journals (Sweden)

    Assem Barakat

    2015-11-01

    Full Text Available The synthesis of the new diethyl ammonium salt of diethylammonium(E-5-(1,5-bis(4-fluorophenyl-3-oxopent-4-en-1-yl-1,3-diethyl-4,6-dioxo-2-thioxohexaydropyrimidin-5-ide 3 via a regioselective Michael addition of N,N-diethylthiobarbituric acid 1 to dienone 2 is described. In 3, the carboanion of the thiobarbituric moiety is stabilized by the strong intramolecular electron delocalization with the adjacent carbonyl groups and so the reaction proceeds without any cyclization. The molecular structure investigations of 3 were determined by single-crystal X-ray diffraction as well as DFT computations. The theoretically calculated (DFT/B3LYP geometry agrees well with the crystallographic data. The effect of fluorine replacement by chlorine atoms on the molecular structure aspects were investigated using DFT methods. Calculated electronic spectra showed a bathochromic shift of the π-π* transition when fluorine is replaced by chlorine. Charge decomposition analyses were performed to study possible interaction between the different fragments in the studied systems. Molecular docking simulations examining the inhibitory nature of the compound show an anti-diabetic activity with Pa (probability of activity value of 0.229.

  3. Building bridges between cellular and molecular structural biology.

    Science.gov (United States)

    Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J; Collinson, Lucy; Gault, David; Grünewald, Kay; Hecksel, Corey; Huiskonen, Juha T; Iudin, Andrii; Jones, Martin L; Korir, Paul K; Koster, Abraham J; Lagerstedt, Ingvar; Lawson, Catherine L; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B; Saalfeld, Stephan; Saibil, Helen R; Sarntivijai, Sirarat; Solanes Valero, Irene; Subramaniam, Sriram; Swedlow, Jason R; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J

    2017-07-06

    The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

  4. Lipid Dynamics Studied by Calculation of 31P Solid-State NMR Spectra Using Ensembles from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Hansen, Sara Krogh; Vestergaard, Mikkel; Thøgersen, Lea

    2014-01-01

    , for example, order parameters. Therefore, valuable insight into the dynamics of biomolecules may be achieved by the present method. We have applied this method to study the dynamics of lipid bilayers containing the antimicrobial peptide alamethicin, and we show that the calculated 31P spectra obtained...

  5. Spectra-structure correlations in NIR region: Spectroscopic and anharmonic DFT study of n-hexanol, cyclohexanol and phenol

    Science.gov (United States)

    Beć, Krzysztof B.; Grabska, Justyna; Czarnecki, Mirosław A.

    2018-05-01

    We investigated near-infrared (7500-4000 cm-1) spectra of n-hexanol, cyclohexanol and phenol in CCl4 (0.2 M) by using anharmonic quantum calculations. These molecules represent three major kinds of alcohols; linear and cyclic aliphatic, and aromatic ones. Vibrational second-order perturbation theory (VPT2) was employed to calculate the first overtones and binary combination modes and to reproduce the experimental NIR spectra. The level of conformational flexibility of these three alcohols varies from one stable conformer of phenol through four conformers of cyclohexanol to few hundreds conformers in the case of n-hexanol. To take into account the most relevant conformational population of n-hexanol, a systematic conformational search was performed. Accurate reproduction of the experimental NIR spectra was achieved and detailed spectra-structure correlations were obtained for these three alcohols. VPT2 approach provides less reliable description of highly anharmonic modes, i.e. OH stretching. In the present work this limitation was manifested in erroneous results yielded by VPT2 for 2νOH mode of cyclohexanol. To study the anharmonicity of this mode we solved the corresponding time-independent Schrödinger equation based on a dense-grid probing of the relevant vibrational potential. These results allowed for significant improvement of the agreement between the calculated and experimental 2νOH band of cyclohexanol. Various important biomolecules include similar structural units to the systems investigated here. A detailed knowledge on spectral properties of these three types of alcohols is therefore essential for advancing our understanding of NIR spectroscopy of biomolecules.

  6. Prediction of EPR Spectra of Lyotropic Liquid Crystals using a Combination of Molecular Dynamics Simulations and the Model-Free Approach.

    Science.gov (United States)

    Prior, Christopher; Oganesyan, Vasily S

    2017-09-21

    We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional electron paramagnetic resonance (EPR) spectra of lyotropic liquid crystals in different aggregation states doped with a paramagnetic spin probe. The purpose of this study is twofold. First, given that EPR spectra are highly sensitive to the motions and order of the spin probes doped within lyotropic aggregates, simulation of EPR line shapes from the results of MD modelling provides an ultimate test bed for the force fields currently employed to model such systems. Second, the EPR line shapes are simulated using the motional parameters extracted from MD trajectories using the Model-Free (MF) approach. Thus a combined MD-EPR methodology allowed us to test directly the validity of the application of the MF approach to systems with multi-component molecular motions. All-atom MD simulations using the General AMBER Force Field (GAFF) have been performed on sodium dodecyl sulfate (SDS) and dodecyltrimethylammonium chloride (DTAC) liquid crystals. The resulting MD trajectories were used to predict and interpret the EPR spectra of pre-micellar, micellar, rod and lamellar aggregates. The predicted EPR spectra demonstrate good agreement with most of experimental line shapes thus confirming the validity of both the force fields employed and the MF approach for the studied systems. At the same time simulation results confirm that GAFF tends to overestimate the packing and the order of the carbonyl chains of the surfactant molecules. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. IR spectra and structure of glasses in the BaO-WO3-P2O5 system

    International Nuclear Information System (INIS)

    Miroshnichenko, O.Ya.; Mombelli, V.V.

    1979-01-01

    Studied are IR absorption spectra and determined are the main structural characteristics of tungstophosphate glasses of the BaO-WO 3 -P 2 O 5 system in all the area of glass formation. It is shown that the main structural components of their anion network are phosphate chains consisting of PO 4 tetrahedrons and tungstate chains consisting of WO 4 tetrahedrons and of WO 6 octahedrons. These chains are connected by P-O-W bridges into three-dimentional tungstophosphate network, where the ratio of phosphate and tungstate structural units and their polymerization degree change without limits depending on the glass composition. Analysis of concentration frequency dependence and spectral band intensity permit to clarify the effect of each component on the glass structure in all the area of glass formation of the triple system

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

    Energy Technology Data Exchange (ETDEWEB)

    Ikeya, Teppei [Goethe University Frankfurt am Main, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (Germany); Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune [Tokyo Metropolitan University, Graduate School of Science (Japan)], E-mail: kainosho@nmr.chem.metro-u.ac.jp; Guentert, Peter [Goethe University Frankfurt am Main, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (Germany)], E-mail: guentert@em.uni-frankfurt.de

    2009-08-15

    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 {sup 13}C/{sup 15}N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional 'through-bond' spectrum (and 2D HSQC spectra) in addition to the {sup 13}C-edited and {sup 15}N-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.

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

    International Nuclear Information System (INIS)

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

    2009-01-01

    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 13 C/ 15 N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional 'through-bond' spectrum (and 2D HSQC spectra) in addition to the 13 C-edited and 15 N-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

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

    Science.gov (United States)

    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.

  11. DFT Calculation of IR Absorption Spectra for PCE-nH2O, TCE-nH2O, DCE-nH2O, VC-nH2O for Small and Water-Dominated Molecular Clusters

    Science.gov (United States)

    2017-10-31

    VC-nH2O for Small and Water-Dominated Molecular Clusters October 31, 2017 Approved for public release; distribution is unlimited. L. Huang S.g...Calculation of IR Absorption Spectra for PCE-nH2O, TCE-nH2O, DCE-nH2O, VC-nH2O for Small and Water-Dominated Molecular Clusters L. Huang,1 S.G...nH2O molecular clusters using density function theory (DFT). DFT can provide interpretation of absorption spectra with respect to molecular

  12. Molecular Cloud Structures and Massive Star Formation in N159

    Science.gov (United States)

    Nayak, O.; Meixner, M.; Fukui, Y.; Tachihara, K.; Onishi, T.; Saigo, K.; Tokuda, K.; Harada, R.

    2018-02-01

    The N159 star-forming region is one of the most massive giant molecular clouds (GMCs) in the Large Magellanic Cloud (LMC). We show the 12CO, 13CO, CS molecular gas lines observed with ALMA in N159 west (N159W) and N159 east (N159E). We relate the structure of the gas clumps to the properties of 24 massive young stellar objects (YSOs) that include 10 newly identified YSOs based on our search. We use dendrogram analysis to identify properties of the molecular clumps, such as flux, mass, linewidth, size, and virial parameter. We relate the YSO properties to the molecular gas properties. We find that the CS gas clumps have a steeper size–linewidth relation than the 12CO or 13CO gas clumps. This larger slope could potentially occur if the CS gas is tracing shocks. The virial parameters of the 13CO gas clumps in N159W and N159E are low (<1). The threshold for massive star formation in N159W is 501 M ⊙ pc‑2, and the threshold for massive star formation in N159E is 794 M ⊙ pc‑2. We find that 13CO is more photodissociated in N159E than N159W. The most massive YSO in N159E has cleared out a molecular gas hole in its vicinity. All the massive YSO candidates in N159E have a more evolved spectral energy distribution type in comparison to the YSO candidates in N159W. These differences lead us to conclude that the giant molecular cloud complex in N159E is more evolved than the giant molecular cloud complex in N159W.

  13. Structural and Molecular Modeling Features of P2X Receptors

    Directory of Open Access Journals (Sweden)

    Luiz Anastacio Alves

    2014-03-01

    Full Text Available Currently, adenosine 5'-triphosphate (ATP is recognized as the extracellular messenger that acts through P2 receptors. P2 receptors are divided into two subtypes: P2Y metabotropic receptors and P2X ionotropic receptors, both of which are found in virtually all mammalian cell types studied. Due to the difficulty in studying membrane protein structures by X-ray crystallography or NMR techniques, there is little information about these structures available in the literature. Two structures of the P2X4 receptor in truncated form have been solved by crystallography. Molecular modeling has proven to be an excellent tool for studying ionotropic receptors. Recently, modeling studies carried out on P2X receptors have advanced our knowledge of the P2X receptor structure-function relationships. This review presents a brief history of ion channel structural studies and shows how modeling approaches can be used to address relevant questions about P2X receptors.

  14. Spatial structure of kinetic energy spectra in LES simulations of flow in an offshore wind farm

    Science.gov (United States)

    Fruh, Wolf-Gerrit; Creech, Angus

    2017-04-01

    The evolution of wind turbine and wind farm wakes was investigated numerically for the case of Lillgrund wind farm consisting of a tightly packed array of 48 turbines. The simulations for a number of wind directions at a free wind speed of just under the rated wind speed in a neutrally stable atmosphere were carried out using Large-Eddy Simulations with the adaptive Finite-Element CFD solver Fluidity. The results were interpolated from the irregularly spaced mesh nodes onto a regular grid with comparable spatial resolution at horizontal slices at various heights. To investigate the development of the wake as the flow evolves through the array, spectra of the kinetic energy in sections perpendicular to the wind directions within the wake and to the sides of the array were calculated. This paper will present the key features and spectral slopes of the flow as a function of downstream distance from the front turbine through and beyond the array. The main focus will be on the modification of the spectra as the flow crosses a row of turbines followed by its decay in the run-up to the next row, but we will also present to wake decay of the wind farm wake downstream of the array.

  15. Molecular structure and interactions of nucleic acid components in nanoparticles: ab initio calculations

    International Nuclear Information System (INIS)

    Rubin, Yu.V.; Belous, L.F.

    2012-01-01

    Self-associates of nucleic acid components (stacking trimers and tetramers of the base pairs of nucleic acids) and short fragments of nucleic acids are nanoparticles (linear sizes of these particles are more than 10 A). Modern quantum-mechanical methods and softwares allow one to perform ab initio calculations of the systems consisting of 150-200 atoms with enough large basis sets (for example, 6-31G * ). The aim of this work is to reveal the peculiarities of molecular and electronic structures, as well as the energy features of nanoparticles of nucleic acid components. We had carried out ab initio calculations of the molecular structure and interactions in the stacking dimer, trimer, and tetramer of nucleic base pairs and in the stacking (TpG)(ApC) dimer and (TpGpC) (ApCpG) trimer of nucleotides, which are small DNA fragments. The performed calculations of molecular structures of dimers and trimers of nucleotide pairs showed that the interplanar distance in the structures studied is equal to 3.2 A on average, and the helical angle in a trimer is approximately equal to 30 o : The distance between phosphor atoms in neighboring chains is 13.1 A. For dimers and trimers under study, we calculated the horizontal interaction energies. The analysis of interplanar distances and angles between nucleic bases and their pairs in the calculated short oligomers of nucleic acid base pairs (stacking dimer, trimer, and tetramer) has been carried out. Studies of interactions in the calculated short oligomers showed a considerable role of the cross interaction in the stabilization of the structures. The contribution of cross interactions to the horizontal interactions grows with the length of an oligomer. Nanoparticle components get electric charges in nanoparticles. Longwave low-intensity bands can appear in the electron spectra of nanoparticles.

  16. Molecular modeling of nucleic Acid structure: electrostatics and solvation.

    Science.gov (United States)

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

    2014-12-19

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. Copyright © 2014 John Wiley & Sons, Inc.

  17. FT-IR, FT-Raman, NMR spectra, density functional computations of the vibrational assignments (for monomer and dimer) and molecular geometry of anticancer drug 7-amino-2-methylchromone

    Science.gov (United States)

    Mariappan, G.; Sundaraganesan, N.

    2014-04-01

    Vibrational assignments for the 7-amino-2-methylchromone (abbreviated as 7A2MC) molecule using a combination of experimental vibrational spectroscopic measurements and ab initio computational methods are reported. The optimized geometry, intermolecular hydrogen bonding, first order hyperpolarizability and harmonic vibrational wavenumbers of 7A2MC have been investigated with the help of B3LYP density functional theory method. The calculated molecular geometry parameters, the theoretically computed vibrational frequencies for monomer and dimer and relative peak intensities were compared with experimental data. DFT calculations using the B3LYP method and 6-31 + G(d,p) basis set were found to yield results that are very comparable to experimental IR and Raman spectra. Detailed vibrational assignments were performed with DFT calculations and the potential energy distribution (PED) obtained from the Vibrational Energy Distribution Analysis (VEDA) program. Natural Bond Orbital (NBO) study revealed the characteristics of the electronic delocalization of the molecular structure. 13C and 1H NMR spectra have been recorded and 13C and 1H nuclear magnetic resonance chemical shifts of the molecule have been calculated using the gauge independent atomic orbital (GIAO) method. Furthermore, All the possible calculated values are analyzed using correlation coefficients linear fitting equation and are shown strong correlation with the experimental data.

  18. Calculation on uranium carbon oxygen system molecular structure by DFT

    International Nuclear Information System (INIS)

    Zhang Guangfeng; Wang Xiaolin; Zou Lexi; Sun Ying; Xue Weidong; Zhu Zhenghe; Wang Hongyan

    2001-01-01

    The authors study on the possible molecular structures U-C-O, U-O-C, C-U-O (angular structure C a nd linear structure C ∞υ ) of carbon monoxide interacting on uranium metal surface by Density functional theory (DFT). The uranium atom is used RECP (Relativistic Effective Core Potential) and contracted valence basis sets (6s5p2d4f)/[3s3p2d2f], and for carbon and oxygen atoms all are 6-311G basis sets. The author presents the results of energy optimum which shows that triple and quintuple state are more stable. The authors get the electronic state, geometry structure, energy, harmonic frequency, mechanical property, etc. of these twelve triple and quintuple state relative stable structures. The normal vibrational analytical figure of angular structure (C s ) and linear structure (C ∞υ ) is given at the same time. It is indicated that angular structure has lower energy than linear structure, moreover the angular structure of U-C-O( 3 A ) has the lowest energy. The bond strength between uranium atom and carbon monoxide is weak and between uranium atom and oxygen atom is slightly stronger than between uranium atom and carbon atom which the authors can know by superposition population and bond energy analysis among atoms

  19. The effect of nonlocal dielectric response on the surface-enhanced Raman and fluorescence spectra of molecular systems

    Science.gov (United States)

    Wei, Yong; Pei, Huan; Li, Li; Zhu, Yanying

    2018-06-01

    We present a theoretical study on the influence of the nonlocal dielectric response on surface-enhanced resonant Raman scattering (SERRS) and fluorescence (SEF) spectra of a model molecule confined in the center of a Ag nanoparticle (NP) dimer. In the simulations, the nonlocal dielectric response caused by the electron–hole pair generation in Ag NPs was computed with the d-parameter theory, and the scattering spectra of a model molecule representing the commonly used fluorescent dye rhodamine 6G (R6G) were obtained by density-matrix calculations. The influence of the separation between Ag NP dimers on the damping rate and scattering spectra with and without the nonlocal response were systematically analyzed. The results show that the nonlocal dielectric response is very sensitive to the gap distance of the NP dimers, and it undergoes much faster decay with the increase of the separation than the radiative and energy transfer rates. The Raman and fluorescence peaks as simulated with the nonlocal dielectric response are relative weaker than that without the nonlocal effect for smaller NP separations because the extra decay rates of the nonlocal effect could reduce both the population of the excited state and the interband coherence between the ground and excited states. Our result also indicates that the nonlocal effect is more prominent on the SEF process than the SERRS process.

  20. Exponential Repulsion Improves Structural Predictability of Molecular Docking

    Czech Academy of Sciences Publication Activity Database

    Bazgier, Václav; Berka, K.; Otyepka, M.; Banáš, P.

    2016-01-01

    Roč. 37, č. 28 (2016), s. 2485-2494 ISSN 0192-8651 Institutional support: RVO:61389030 Keywords : cyclin-dependent kinases * structure-based design * scoring functions * cdk2 inhibitors * force-field * ligand interactions * drug discovery * purine * potent * protein-kinase-2 * molecular docking * dock 6.6 * drug design * cyclin-dependent kinase 2 * directory of decoys Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.229, year: 2016

  1. Invariant molecular-dynamics approach to structural phase transitions

    International Nuclear Information System (INIS)

    Wentzcovitch, R.M.

    1991-01-01

    Two fictitious Lagrangians to be used in molecular-dynamics simulations with variable cell shape and suitable to study problems like structural phase transitions are introduced. Because they are invariant with respect to the choice of the simulation cell edges and eliminate symmetry breaking associated with the fictitious part of the dynamics, they improve the physical content of numerical simulations that up to now have been done by using Parrinello-Rahman dynamics

  2. VPAC receptors: structure, molecular pharmacology and interaction with accessory proteins.

    Science.gov (United States)

    Couvineau, Alain; Laburthe, Marc

    2012-05-01

    The vasoactive intestinal peptide (VIP) is a neuropeptide with wide distribution in both central and peripheral nervous systems, where it plays important regulatory role in many physiological processes. VIP displays a large biological functions including regulation of exocrine secretions, hormone release, fetal development, immune responses, etc. VIP appears to exert beneficial effect in neuro-degenerative and inflammatory diseases. The mechanism of action of VIP implicates two subtypes of receptors (VPAC1 and VPAC2), which are members of class B receptors belonging to the super-family of GPCR. This article reviews the current knowledge regarding the structure and molecular pharmacology of VPAC receptors. The structure-function relationship of VPAC1 receptor has been extensively studied, allowing to understand the molecular basis for receptor affinity, specificity, desensitization and coupling to adenylyl cyclase. Those studies have clearly demonstrated the crucial role of the N-terminal ectodomain (N-ted) of VPAC1 receptor in VIP recognition. By using different approaches including directed mutagenesis, photoaffinity labelling, NMR, molecular modelling and molecular dynamic simulation, it has been shown that the VIP molecule interacts with the N-ted of VPAC1 receptor, which is itself structured as a 'Sushi' domain. VPAC1 receptor also interacts with a few accessory proteins that play a role in cell signalling of receptors. Recent advances in the structural characterization of VPAC receptor and more generally of class B GPCRs will lead to the design of new molecules, which could have considerable interest for the treatment of inflammatory and neuro-degenerative diseases. © 2011 The Authors. British Journal of Pharmacology © 2011 The British Pharmacological Society.

  3. The past and the future of Alzheimer’s disease CSF biomarkers – a journey towards validated biochemical tests covering the whole spectra of molecular events

    Directory of Open Access Journals (Sweden)

    Kaj eBlennow

    2015-09-01

    Full Text Available This paper gives a short review on cerebrospinal fluid (CSF biomarkers for Alzheimer’s disease (AD, from early developments to high-precision validated assays on fully automated lab analyzers. We also discuss developments on novel biomarkers, such as synaptic proteins and Aβ oligomers. Our vision for the future is that assaying a set of biomarkers in a single CSF tube can monitor the whole spectra of AD molecular pathogenic events. CSF biomarkers will have a central position not only for clinical diagnosis, but also for the understanding of the sequence of molecular events in the pathogenic process underlying AD and as tools to monitor the effects of novel drug candidates targeting these different mechanisms.

  4. Structural characterization of tellurite glasses doped with transition metal oxides using Raman spectra and ab initio calculations.

    Science.gov (United States)

    Mohamed, Tarek A; Shaltout, I; Al Yahyaei, K M

    2006-05-01

    Systems of iron tellurite glasses were prepared by melt quenching with compositions of [85%TeO2+5%Fe2O3+10%TMO], where transition metal oxides (TMO) are TiO2, V2O5, MnO, CoO, NiO and CuO. Furthermore, the main structural units of these samples have been characterized by means of Raman spectra (150-1200 cm(-1)) as well as wavenumber predictions by means of Gaussian 98 ab initio calculations for the proposed site symmetries of TeO4(4-) triagonal bipyramid (C2v) and Te2O7(6-) bridged tetrahedra (Cs and C1). Aided by normal coordinate analysis, calculated vibrational frequencies, Raman scattering activities, force constants in internal coordinates and potential energy distributions (PEDs), revised vibrational assignments for the fundamental modes have been proposed. The main structural features are correlated to the dominant units of triagonal bipyramid (tbp) or bridged tetrahedral (TeO3+1 binds to TeO3 through TeOTe bridge; corner sharing). Moreover, the Raman spectra of the investigated tellurites reflect a structural change from tbp (coordination number is four) to triagonal pyramidal (coordination number is three).

  5. On the origin of fine structure in the photoluminescence spectra of the β-sialon:Eu2+ green phosphor

    Directory of Open Access Journals (Sweden)

    Kohsei Takahashi, Ken-ichi Yoshimura, Masamichi Harada, Yoshitaka Tomomura, Takashi Takeda, Rong-Jun Xie and Naoto Hirosaki

    2012-01-01

    Full Text Available The photoluminescence (PL and PL excitation (PLE spectra of Si6−zAlzOzN8−z (β-sialon:Eu2+ phosphors with small z values (z=0.025–0.24 were studied at room temperature and 6 K. The PL and PLE spectra exhibit fine structure with the PL lines being as sharp as 45–55 nm even at room temperature; this fine structure was enhanced by decreasing the z value. These results can be used for expanding the color gamut of liquid crystal displays, particularly in the blue–green region. From low-temperature measurements, the fine PLE structure was ascribed to discrete energy levels of 7FJ states. The 4f65d excited states of Eu2+ are considered to be localized near the 4f orbital. This is because the bonding of Eu2+ with surrounding atoms is ionic rather than covalent. Lattice phonon absorptions were also observed in the PLE spectrum, revealing that the optically active Eu2+ ions are located in the β-sialon crystal. The PL spectrum of the sample with the smallest z value (0.025 consists of a sharp zero-phonon line and lattice phonon replicas, which results in a sharp and asymmetric spectral shape.

  6. Quantum chemical analysis of the electronic structure and Moessbauer spectra parameters for low spin cyanide- and pyridine-hemichromes

    International Nuclear Information System (INIS)

    Khleskov, V.I.; Kolpakov, E.V.; Smirnov, A.B.

    1992-01-01

    The work contains results of quantum-chemical calculations of electronic structure and Moessbauer spectra parameters for low spin S=1/2 hexa-coordinated ferri-porphyrin complexes with cyanide (CN) and pyridine (Py) as axial ligands. Theoretical results made it possible to explain experimentally observed regularity of anomalous quadrupole splitting decrease after substitution of Py-ligands by CN. Comparison of theoretical and experimental data indicated that 2 E g must be the ground state of investigated hemichromes. In this state unpaired electron symmetrically occupies d π -orbitals of Fe-ion. (orig.)

  7. Isotope chemistry and molecular structure. The WINIMAX weighting factor

    International Nuclear Information System (INIS)

    Lee, M.W.; Bigeleisen, J.

    1979-01-01

    The modulating coefficients for the finite polynomial expansion of the logarithm of the reduced partition function, lnb (u), of a harmonic oscillator have been obtained for the range of 0 6 . It is shown that this weighting function is near optimum to insure minimum amplitudes of oscillation in the expansion of lnb (u) as a function of the order of the expansion and to include most of the important molecular structure information contained in the moments of the eigenvalues. Beyond Σu/sub i/ 6 , there is little new structural information

  8. Fine structure of spectra of a bound exciton in tetragonal zinc diphosphide

    International Nuclear Information System (INIS)

    Syrbu, N.N.; Morozova, V.I.; Stratan, G.I.

    1989-01-01

    Investigation into the low-temperature luminescence spectra recorded in different crystal geometry relative to the direction of incident radiation wave vector, has demonstrated the existence of saddle-shaped valent zone ceiling near k=0 in zinc tetragonal diphosphide monocrystals. Binding energies of free (2.2085 eV) and bound (A(2.1943eV)B(2.1765eV), C(2.1447eV)) excitons as well as the phonon energy value are determined by investigations into absorption spectrum and radiative recombination. Phonon-free lines of bound A 0 and C 0 excitons are splitted into 2.2 and 0.3 MeV respectively. The band exciton singlet-triplet state splittings in a magnetic field and their field dependences are obtained. The spectroscopic splitting factor g=1.9 is determined

  9. X-ray spectra and electronic structure of the Ca3Ga2Ge3О12 compound

    Science.gov (United States)

    Shcherba, I. D.; Kostyk, L. V.; Noga, H.; Bekenov, L. V.; Uskokovich, D.; Jatsyk, B. M.

    2017-09-01

    The band structure of Ca3Ga2Ge3О12 with the garnet structure has been determined for the first time by X-ray emission and photoelectron spectroscopy. It has been established that the bottom of the valence band is formed by Ge d states, which are not dominant in the chemical bonding. Strong hybridization of oxygen 2s states with 4p states of Ga and Ge revealed by the presence of an extra structure in the X-ray emission spectra has been found. The middle of the valence band has been demonstrated to be occupied by d states of Ga, while Ga and Ge 4рstates with a considerable admixture of oxygen 2p states form the top of the valence band.

  10. Correlation of vapor phase infrared spectra and regioisomeric structure in synthetic cannabinoids

    Science.gov (United States)

    Smith, Lewis W.; Thaxton-Weissenfluh, Amber; Abiedalla, Younis; DeRuiter, Jack; Smith, Forrest; Clark, C. Randall

    2018-05-01

    The twelve 1-n-pentyl-2-, 3-, 4-, 5-, 6- and 7-(1- and 2-naphthoyl)-indoles each have the same substituents attached to the indole ring, identical elemental composition (C24H23NO) yielding identical nominal and accurate masses. These twelve isomers cover all possible positions of carbonyl bridge substitution for both indole (positons 2-7) and naphthalene rings (positions 1 and 2). Regioisomeric compounds can represent significant challenges for mass based analytical methods however, infrared spectroscopy is a powerful tool for the identification of positional isomers in organic compounds. The vapor phase infrared spectra of these twelve uniquely similar compounds were evaluated in GC-IR experiments. These spectra show the bridge position on the indole ring is a dominating influence over the carbonyl absorption frequency observed for these compounds. Substitution on the pyrrole moiety of the indole ring yields the lowest Cdbnd O frequency values for position 2 and 3 giving a narrow range from 1656 to 1654 cm-1. Carbonyl absorption frequencies are higher when the naphthoyl group is attached to the benzene portion of the indole ring yielding absorption values from 1674 to 1671 cm-1. The aliphatic stretching bands in the 2900 cm-1 region yield a consistent triplet pattern because the N-alkyl substituent tail group remains unchanged for all twelve regioisomers. The asymmetric CH2 stretch is the most intense of these three bands. Changes in positional bonding for both the indole and naphthalene ring systems results in unique patterns within the 700 wavenumber out-of-plane region and these absorption bands are different for all 12 regioisomers.

  11. Using photoelectron diffraction to determine complex molecular adsorption structures

    International Nuclear Information System (INIS)

    Woodruff, D P

    2010-01-01

    Backscattering photoelectron diffraction, particularly in the energy-scan mode, is now an established technique for determining in a quantitative fashion the local structure of adsorbates on surfaces, and has been used successfully for ∼100 adsorbate phases. The elemental and chemical-state specificity afforded by the characteristic core level photoelectron binding energies means that it has particular advantages for molecular adsorbates, as the local geometry of inequivalent atoms in the molecule can be determined in a largely independent fashion. On the other hand, polyatomic molecules present a general problem for all methods of surface structure determination in that a mismatch of intramolecular distances with interatomic distances on the substrate surface means that the atoms in the adsorbed molecule are generally in low-symmetry sites. The quantities measured experimentally then represent an incoherent sum of the properties of each structural domain that is inequivalent with respect to the substrate point group symmetry. This typically leads to greater ambiguity or precision in the structural solutions. The basic principles of the method are described and illustrated with a simple example involving molecule/substrate bonding through only one constituent atom (TiO 2 -(110)/H 2 O). This example demonstrates the importance of obtaining quantitative local structural information. Further examples illustrate both the successes and the problems of this approach when applied to somewhat more complex molecular adsorbates.

  12. Comparison of molecular structure of alkali metal o-, m- and p-nitrobenzoates

    Science.gov (United States)

    Regulska, E.; Świsłocka, R.; Samsonowicz, M.; Lewandowski, W.

    2008-09-01

    The influence of nitro-substituent in ortho, meta and para positions as well as lithium, sodium, potassium, rubidium and cesium on the electronic system of aromatic ring and the distribution of electronic charge in carboxylic group of the nitrobenzoates were estimated. Optimized geometrical structures were calculated (B3LYP/6-311++G ∗∗). To make quantitative evaluation of aromaticity of studied molecules the geometric (A J, BAC, I 6 and HOMA) as well as magnetic (NICS) aromaticity indices were calculated. Electronic charge distribution was also examined by molecular spectroscopic study, which may be the source of quality criterion for aromaticity. Experimental and theoretical FT-IR, FT-Raman and NMR ( 1H and 13C) spectra of the title compounds were analyzed. The calculated parameters were compared to experimental characteristics of these molecules.

  13. Molecular and structural properties of polymer composites filled with activated charcoal particles

    Energy Technology Data Exchange (ETDEWEB)

    Tahir, Dahlang, E-mail: dtahir@fmipa.unhas.ac.id; Bakri, Fahrul [Department of Physics, Hasanuddin University, Makassar 90245 Indonesia (Indonesia); Liong, Syarifuddin [Department of Chemistry, Hasanuddin University, Makassar 90245 Indonesia (Indonesia)

    2016-03-11

    We have studied the molecular properties, structural properties, and chemical composition of composites by Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD) spectroscopy, and X-ray fluorescence (XRF) spectroscopy, respectively. FTIR spectra shows absorption band of hydroxyl group (-OH), methyl group (-CH{sub 3}) and aromatic group (C-C). The absorption band for aromatic group (C-C) shows the formation of carbonaceous in composites. XRF shows chemical composition of composites, which the main chemicals are SO{sub 3}, Cl, and ZnO. The loss on ignition value (LOI) of activated charcoal indicates high carbonaceous matter. The crystallite size for diffraction pattern from hydrogel polymer is about 17 nm and for activated charcoal are about 19 nm. The crystallite size of the polymer is lower than that of activated charcoal, which make possible of the particle from filler in contact with each other to form continuous conducting polymer through polymer matrix.

  14. An Observation of Diamond-Shaped Particle Structure in a Soya Phosphatidylcohline and Bacteriorhodopsin Composite Langmuir Blodgett Film Fabricated by Multilayer Molecular Thin Film Method

    Science.gov (United States)

    Tsujiuchi, Y.; Makino, Y.

    A composite film of soya phosphatidylcohline (soya PC) and bacteriorhodopsin (BR) was fabricated by the multilayer molecular thin film method using fatty acid and lipid on a quartz substrate. Direct Force Microscopy (DFM), UV absorption spectra and IR absorption spectra of the film were characterized on the detail of surface structure of the film. The DFM data revealed that many rhombus (diamond-shaped) particles were observed in the film. The spectroscopic data exhibited the yield of M-intermediate of BR in the film. On our modelling of molecular configuration indicate that the coexistence of the strong inter-molecular interaction and the strong inter-molecular interaction between BR trimmers attributed to form the particles.

  15. Molecular tailoring approach for exploring structures, energetics and ...

    Indian Academy of Sciences (India)

    Administrator

    Keywords. Molecular clusters; linear scaling methods; molecular tailoring approach (MTA); Hartree– ..... energy decomposition analysis also performed and which clearly ... through molecular dynamics simulation furnished by. Takeguchi,. 46.

  16. Molecular conformational analysis, vibrational spectra and normal coordinate analysis of trans-1,2-bis(3,5-dimethoxy phenyl)-ethene based on density functional theory calculations.

    Science.gov (United States)

    Joseph, Lynnette; Sajan, D; Chaitanya, K; Isac, Jayakumary

    2014-03-25

    The conformational behavior and structural stability of trans-1,2-bis(3,5-dimethoxy phenyl)-ethene (TDBE) were investigated by using density functional theory (DFT) method with the B3LYP/6-311++G(d,p) basis set combination. The vibrational wavenumbers of TDBE were computed at DFT level and complete vibrational assignments were made on the basis of normal coordinate analysis calculations (NCA). The DFT force field transformed to natural internal coordinates was corrected by a well-established set of scale factors that were found to be transferable to the title compound. The infrared and Raman spectra were also predicted from the calculated intensities. The observed Fourier transform infrared (FTIR) and Fourier transform (FT) Raman vibrational wavenumbers were analyzed and compared with the theoretically predicted vibrational spectra. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecules has been obtained by mapping electron density isosurface with electrostatic potential surfaces (ESP). Copyright © 2013 Elsevier B.V. All rights reserved.

  17. Tunneling and resonant conductance in one-dimensional molecular structures

    International Nuclear Information System (INIS)

    Kozhushner, M.A.; Posvyanskii, V.S.; Oleynik, I.I.

    2005-01-01

    We present a theory of tunneling and resonant transitions in one-dimensional molecular systems which is based on Green's function theory of electron sub-barrier scattering off the structural units (or functional groups) of a molecular chain. We show that the many-electron effects are of paramount importance in electron transport and they are effectively treated using a formalism of sub-barrier scattering operators. The method which calculates the total scattering amplitude of the bridge molecule not only predicts the enhancement of the amplitude of tunneling transitions in course of tunneling electron transfer through onedimensional molecular structures but also allows us to interpret conductance mechanisms by calculating the bound energy spectrum of the tunneling electron, the energies being obtained as poles of the total scattering amplitude of the bridge molecule. We found that the resonant tunneling via bound states of the tunneling electron is the major mechanism of electron conductivity in relatively long organic molecules. The sub-barrier scattering technique naturally includes a description of tunneling in applied electric fields which allows us to calculate I-V curves at finite bias. The developed theory is applied to explain experimental findings such as bridge effect due to tunneling through organic molecules, and threshold versus Ohmic behavior of the conductance due to resonant electron transfer

  18. Hydrophobic radical influence on structure and vibration spectra of zwitter-ionic forms of glycine and alanine in condensed state

    International Nuclear Information System (INIS)

    Ten, G.N.; Kadrov, D.M.; Baranov, V.I.

    2014-01-01

    Structure and vibrational spectra of the zwitter-ionic forms of glycine and alanine in water solution and solid state have been calculated in the B3LYP/6-311++G(d,p) approximation. The environment influence has been taken into account by two methods: the self-consistent reaction field (SCRF) method and one of modeling the glycine and alanine complexes with molecules of water. The structure, energy and spectral properties have been determined which allow establishing an influence of the hydrophobic radical on the glycine and alanine ability to form the hydrogen bonds. It is shown by comparison with experiment that for the calculation of vibrational (IR and Raman) spectra of the zwitter-ionic forms of glycine and alanine in the condensed states they must be surrounded with three molecules of water, one of which is located between the N + H 3 and COO - ionic groups. The value of energy necessary to form the Ala complexes with water compared to Gly ones is 56.47 and 12.55 kcal/mol higher in the case of the complex formation with 1and 3 molecules of water, respectively, located between bipolar groups. (authors)

  19. Electronic structure and optical spectra of semiconducting carbon nanotubes functionalized by diazonium salts

    Science.gov (United States)

    Ramirez, Jessica; Mayo, Michael L.; Kilina, Svetlana; Tretiak, Sergei

    2013-02-01

    We report density functional (DFT) calculations on finite-length semiconducting carbon nanotubes covalently and non-covalently functionalized by aryl diazonium moieties and their chlorinated derivatives. For these systems, we investigate (i) an accuracy of different functionals and basis sets, (ii) a solvent effect, and (iii) the impact of the chemical functionalization on optical properties of nanotubes. In contrast to B3LYP, only long-range-corrected functionals, such as CAM-B3LYP and wB97XD, properly describe the ground and excited state properties of physisorbed molecules. We found that physisorbed cation insignificantly perturbs the optical spectra of nanotubes. In contrast, covalently bound complexes demonstrate strong redshifts and brightening of the lowest exciton that is optically dark in pristine nanotubes. However, the energy and oscillator strength of the lowest state are dictated by the position of the molecule on the nanotube. Thus, if controllable and selective chemical functionalization is realized, the PL of nanotubes could be improved.

  20. New structures of power density spectra for four Kepler active galactic nuclei

    Science.gov (United States)

    Dobrotka, A.; Antonuccio-Delogu, V.; Bajčičáková, I.

    2017-09-01

    Many nearby active galactic nuclei display a significant short-term variability. In this work, we reanalyse photometric data of four active galactic nuclei observed by Kepler in order to study the flickering activity, with our main goal to search for multiple components in the power density spectra. We find that all four objects have similar characteristics, with two break frequencies at approximately log( f /Hz) = -5.2 and -4.7. We consider some physical phenomena whose characteristic time-scales are consistent with those observed, in particular mass accretion fluctuations in the inner geometrically thick disc (hot X-ray corona) and unstable relativistic Rayleigh-Taylor modes. The former is supported by detection of the same break frequencies in the Swift X-ray data of ZW229-15. We also discuss rms-flux relations, and we detect a possible typical linear trend at lower flux levels. Our findings support the hypothesis of a multiplicative character of variability, in agreement with the propagating accretion fluctuation model.

  1. High-resolution spectroscopy in superfluid helium droplets. Investigation of vibrational fine structures in electronic spectra of phthalocyanine and porphyrin derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Riechers, Ricarda Eva Friederike Elisabeth

    2011-03-22

    Since a considerably large variety of substituted compounds is commercially available and the electronic excitation spectra fit well into the spectral range covered by the continuous wave dye laser used for this study several porphyrin and phthalocyanine derivatives substituted with different types and numbers of alkyl and aryl groups were chosen as molecular probes. Recording fluorescence excitation and dispersed emission spectra revealed exclusively sharp transitions for all species. A change of the molecule's electrostatic moments, primarily and most effectively, a change of the molecular dipole moment regarding both magnitude and orientation, was identified as the main contribution for line broadening effects. Apart from the sharp lines presented in their fluorescence excitation spectra, the phthalocyanine derivatives investigated for this study, namely chloro-aluminium-phthalocyanine (AlClPc) and tetra-tertbutyl-phthalocyanine (TTBPc), exhibited more than one emission spectrum.

  2. High-resolution spectroscopy in superfluid helium droplets. Investigation of vibrational fine structures in electronic spectra of phthalocyanine and porphyrin derivatives

    International Nuclear Information System (INIS)

    Riechers, Ricarda Eva Friederike Elisabeth

    2011-01-01

    Since a considerably large variety of substituted compounds is commercially available and the electronic excitation spectra fit well into the spectral range covered by the continuous wave dye laser used for this study several porphyrin and phthalocyanine derivatives substituted with different types and numbers of alkyl and aryl groups were chosen as molecular probes. Recording fluorescence excitation and dispersed emission spectra revealed exclusively sharp transitions for all species. A change of the molecule's electrostatic moments, primarily and most effectively, a change of the molecular dipole moment regarding both magnitude and orientation, was identified as the main contribution for line broadening effects. Apart from the sharp lines presented in their fluorescence excitation spectra, the phthalocyanine derivatives investigated for this study, namely chloro-aluminium-phthalocyanine (AlClPc) and tetra-tertbutyl-phthalocyanine (TTBPc), exhibited more than one emission spectrum.

  3. Molecular structure, vibrational, HOMO-LUMO, MEP and NBO analysis of hafnium selenite

    Science.gov (United States)

    Yankova, Rumyana; Genieva, Svetlana; Dimitrova, Ginka

    2017-08-01

    In hydrothermal condition hafnium selenite with estimated chemical composition Hf(SeO3)2·n(H2O) was obtained and characterized by powder X-Ray diffraction, IR spectroscopy and thermogravimetrical analysis. The composition of the obtained crystalline phase was established as dihydrate of tetraaqua complex of the hafnium selenite [Hf(SeO3)2(H2O)4]·2H2O. The results of the thermogravimetrical analysis are shown that the two hydrated water molecules are released in the temperature interval 80-110°C, while the four coordinated water molecules - at 210-300°C. By DFT method, with Becke's three parameter exchange-functional combined with gradient-corrected correlation functional of Lee, Yang and Parr and 6-31G(d), 6-311 + G(d,p) basis sets and LANL2DZ for Hf atom were calculated the molecular structure, vibrational frequencies and thermodynamic properties of the structure. The UV-Vis spectra and electronic properties are presented. The energy and oscillator strength calculated by time-dependent density functional theory corresponds well with the experimental ones. Molecular electrostatic potential (MEP) was performed. Mulliken population analysis on atomic charges was also calculated. The stability and intramolecular interactions are interpreted by NBO analysis.

  4. The effect of SNR structure on non-equilibrium X-ray spectra

    International Nuclear Information System (INIS)

    Hamilton, A.J.S.; Sarazin, C.L.

    1983-01-01

    A technique is presented for characterizing the ionization structure and consequent thermal X-ray emission of a SNR when non-equilibrium ionization effects are important. The technique allows different theoretical SNR models to be compared and contrasted rapidly in advance of detailed numerical computations. In particular it is shown that the spectrum of a Sedov remnant can probably be applied satisfactorily in a variety of SNR structures, including the reverse shock model advocated by Chevalier (1982) for Type I SN, the isothermal similarity solution of Solinger, Rappaport and Buff (1975), and various inhomogenous or 'messy' structures. (Auth.)

  5. Molecular Diagnostics of the Internal Structure of Starspots and Sunspots

    Science.gov (United States)

    Afram, N.; Berdyugina, S. V.; Fluri, D. M.; Solanki, S. K.; Lagg, A.; Petit, P.; Arnaud, J.

    2006-12-01

    We have analyzed the usefulness of molecules as a diagnostic tool for studying solar and stellar magnetism with the molecular Zeeman and Paschen-Back effects. In the first part we concentrate on molecules that are observed in sunspots such as MgH and TiO. We present calculated molecular line profiles obtained by assuming magnetic fields of 2-3 kG and compare these synthetic Stokes profiles with spectro-polarimetric observations in sunspots. The good agreement between the theory and observations allows us to turn our attention in the second part to starspots to gain insight into their internal structure. We investigate the temperature range in which the selected molecules can serve as indicators for magnetic fields on highly active cool stars and compare synthetic Stokes profiles with our recent observations.

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

    Science.gov (United States)

    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.

  7. Towards structural models of molecular recognition in olfactory receptors.

    Science.gov (United States)

    Afshar, M; Hubbard, R E; Demaille, J

    1998-02-01

    The G protein coupled receptors (GPCR) are an important class of proteins that act as signal transducers through the cytoplasmic membrane. Understanding the structure and activation mechanism of these proteins is crucial for understanding many different aspects of cellular signalling. The olfactory receptors correspond to the largest family of GPCRs. Very little is known about how the structures of the receptors govern the specificity of interaction which enables identification of particular odorant molecules. In this paper, we review recent developments in two areas of molecular modelling: methods for modelling the configuration of trans-membrane helices and methods for automatic docking of ligands into receptor structures. We then show how a subset of these methods can be combined to construct a model of a rat odorant receptor interacting with lyral for which experimental data are available. This modelling can help us make progress towards elucidating the specificity of interactions between receptors and odorant molecules.

  8. Structure of a molecular liquid GeI4

    International Nuclear Information System (INIS)

    Fuchizaki, Kazuhiro; Sakagami, Takahiro; Kohara, Shinji; Mizuno, Akitoshi; Asano, Yuta; Hamaya, Nozomu

    2016-01-01

    A molecular liquid GeI 4 is a candidate that undergoes a pressure-induced liquid-to-liquid phase transition. This study establishes the reference structure of the low-pressure liquid phase. Synchrotron x-ray diffraction measurements were carried out at several temperatures between the melting and the boiling points under ambient pressure. The molecule has regular tetrahedral symmetry, and the intramolecular Ge–I length of 2.51 Å is almost temperature-independent within the measured range. A reverse Monte Carlo (RMC) analysis is employed to find that the distribution of molecular centers remains self-similar against heating, and thus justifying the length-scaling method adopted in determining the density. The RMC analysis also reveals that the vertex-to-face orientation of the nearest molecules are not straightly aligned, but are inclined at about 20 degrees, thereby making the closest intermolecular I–I distance definitely shorter than the intramolecular one. The prepeak observed at  ∼1 Å −1 in the structural factor slightly shifts and increases in height with increasing temperature. The origin of the prepeak is clearly identified to be traces of the 111 diffraction peak in the crystalline state. The prepeak, assuming the residual spatial correlation between germanium sites in the densest direction, thus shifts toward lower wavenumbers with thermal expansion. The aspect that a relative reduction in molecular size associated with the volume expansion is responsible for the increase in the prepeak’s height is confirmed by a simulation, in which the molecular size is changed. (paper)

  9. Volume and surface photoemission from tungsten. I. Calculation of band structure and emission spectra

    DEFF Research Database (Denmark)

    Christensen, N. Egede; Feuerbacher, B.

    1974-01-01

    is obtained from an ad hoc potential based on a Dirac-Slater atomic calculation for the ground-state configuration and with full Slater exchange in the atomic as well as in the crystal potential. The selection of this best potential is justified by comparing the calculated band structure to Fermi...... of states. The present work includes a crude estimate of this surface density of states, which is derived from the bulk band structure by narrowing the d bands according to an effective number of neighbors per surface atom. Estimates of surface relaxation effects are also included.......The electronic energy-band structure of tungsten has been calculated by means of the relativistic-augmented-plane-wave method. A series of mutually related potentials are constructed by varying the electronic configuration and the amount of Slater exchange included. The best band structure...

  10. Inelastic spectra to predict period elongation of structures under earthquake loading

    DEFF Research Database (Denmark)

    Katsanos, Evangelos; Sextos, A.G.

    2015-01-01

    Period lengthening, exhibited by structures when subjected to strong ground motions, constitutes an implicit proxy of structural inelasticity and associated damage. However, the reliable prediction of the inelastic period is tedious and a multi-parametric task, which is related to both epistemic ...... for period lengthening as a function of Ry and Tel. These equations may be used in the framework of the earthquake record selection and scaling....

  11. Solvated electrons at elevated temperatures in different alcohols: Temperature and molecular structure effects

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Yu [Department of Nuclear Engineering and Management, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656 (Japan); Lin, Mingzhang [Nuclear Science and Engineering Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Naka, Ibaraki 319-1195 (Japan); Katsumura, Yosuke, E-mail: katsu@n.t.u-tokyo.ac.j [Department of Nuclear Engineering and Management, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656 (Japan); Nuclear Professional School, Graduate School of Engineering, University of Tokyo, 2-22 Shirakata-Shirane, Tokai, Naka, Ibaraki 319-1188 (Japan); Fu, Haiying; Muroya, Yusa [Nuclear Professional School, Graduate School of Engineering, University of Tokyo, 2-22 Shirakata-Shirane, Tokai, Naka, Ibaraki 319-1188 (Japan)

    2010-12-15

    The absorption spectra of solvated electrons in pentanol, hexanol and octanol are measured from 22 to 200, 22 to 175 and 50 to150 {sup o}C, respectively, at a fixed pressure of 15 MPa, using nanosecond pulse radiolysis technique. The results show that the peak positions of the absorption spectra have a red-shift (shift to longer wavelengths) as temperature increases, similar to water and other alcohols. Including the above mentioned data, a compilation of currently available experimental data on the energy of absorption maximum (E{sub max}) of solvated electrons changed with temperature in monohydric alcohols, diols and triol is presented. E{sub max} of solvated electron is larger in those alcohols that have more OH groups at all the temperatures. The molecular structure effect, including OH numbers, OH position and carbon chain length, is investigated. For the primary alcohols with same OH group number and position, the temperature coefficient increases with increase in chain length. For the alcohols with same chain length and OH numbers, temperature coefficient is larger for the symmetric alcohols than the asymmetric ones.

  12. III - V semiconductor structures for biosensor and molecular electronics applications

    Energy Technology Data Exchange (ETDEWEB)

    Luber, S M

    2007-01-15

    The present work reports on the employment of III-V semiconductor structures to biosensor and molecular electronics applications. In the first part a sensor based on a surface-near two dimensional electron gas for a use in biological environment is studied. Such a two dimensional electron gas inherently forms in a molecular beam epitaxy (MBE) grown, doped aluminum gallium arsenide - gallium arsenide (AlGaAs-GaAs) heterostructure. Due to the intrinsic instability of GaAs in aqueous solutions the device is passivated by deposition of a monolayer of 4'-substituted mercaptobiphenyl molecules. The influence of these molecules which bind to the GaAs via a sulfur group is investigated by Kelvin probe measurements in air. They reveal a dependence of GaAs electron affinity on the intrinsic molecular dipole moment of the mercaptobiphenyls. Furthermore, transient surface photovoltage measurements are presented which demonstrate an additional influence of mercaptobiphenyl chemisorption on surface carrier recombination rates. As a next step, the influence of pH-value and salt concentration upon the sensor device is discussed based on the results obtained from sensor conductance measurements in physiological solutions. A dependence of the device surface potential on both parameters due to surface charging is deduced. Model calculations applying Poisson-Boltzmann theory reveal as possible surface charging mechanisms either the adsorption of OH- ions on the surface, or the dissociation of OH groups in surface oxides. A comparison between simulation settings and physical device properties indicate the OH- adsorption as the most probable mechanism. In the second part of the present study the suitability of MBE grown III-V semiconductor structures for molecular electronics applications is examined. In doing so, a method to fabricate nanometer separated, coplanar, metallic electrodes based on the cleavage of a supporting AlGaAs-GaAs heterostructure is presented. This is followed by a

  13. III - V semiconductor structures for biosensor and molecular electronics applications

    Energy Technology Data Exchange (ETDEWEB)

    Luber, S.M.

    2007-01-15

    The present work reports on the employment of III-V semiconductor structures to biosensor and molecular electronics applications. In the first part a sensor based on a surface-near two dimensional electron gas for a use in biological environment is studied. Such a two dimensional electron gas inherently forms in a molecular beam epitaxy (MBE) grown, doped aluminum gallium arsenide - gallium arsenide (AlGaAs-GaAs) heterostructure. Due to the intrinsic instability of GaAs in aqueous solutions the device is passivated by deposition of a monolayer of 4'-substituted mercaptobiphenyl molecules. The influence of these molecules which bind to the GaAs via a sulfur group is investigated by Kelvin probe measurements in air. They reveal a dependence of GaAs electron affinity on the intrinsic molecular dipole moment of the mercaptobiphenyls. Furthermore, transient surface photovoltage measurements are presented which demonstrate an additional influence of mercaptobiphenyl chemisorption on surface carrier recombination rates. As a next step, the influence of pH-value and salt concentration upon the sensor device is discussed based on the results obtained from sensor conductance measurements in physiological solutions. A dependence of the device surface potential on both parameters due to surface charging is deduced. Model calculations applying Poisson-Boltzmann theory reveal as possible surface charging mechanisms either the adsorption of OH- ions on the surface, or the dissociation of OH groups in surface oxides. A comparison between simulation settings and physical device properties indicate the OH- adsorption as the most probable mechanism. In the second part of the present study the suitability of MBE grown III-V semiconductor structures for molecular electronics applications is examined. In doing so, a method to fabricate nanometer separated, coplanar, metallic electrodes based on the cleavage of a supporting AlGaAs-GaAs heterostructure is presented. This is followed

  14. DFT/TD-semiempirical study on the structural and electronic properties and absorption spectra of supramolecular fullerene-porphyrine-metalloporphyrine triads based dye-sensitized solar cells

    Science.gov (United States)

    Rezvani, M.; Darvish Ganji, M.; Jameh-Bozorghi, S.; Niazi, A.

    2018-04-01

    In the present work density functional theory (DFT) and time-dependent semiempirical ZNIDO/S (TD-ZNIDO/S) methods have been used to investigate the ground state geometries, electronic structures and excited state properties of triad systems. The influences of the type of metal in the porphyrin ring, change in bridge position and porphyrine-ZnP duplicate on the energies of frontier molecular orbital and UV-Vis spectra has been studied. Geometry optimization, the energy levels and electron density of the Highest Occupied Molecular Orbital (HOMO) and the Lowest Unoccupied Molecular Orbital (LUMO), chemical hardness (η), electrophilicity index (ω), electron accepting power (ω+) were calculated using ZINDO/S method to predict which molecule is the most efficient with a great capability to be used as a triad molecule in solar industry. Moreover the light harvesting efficiency (LHE) was calculated by means of the oscillator strengths which are obtained by TD-ZINDO/S calculation. Theoretical studies of the electronic spectra by ZINDO/S method were helpful in interpreting the observed electronic transitions. This aspect was systematically explored in a series of C60-Porphyrine-Metalloporphyrine (C60-P-Mp) triad system with M being Fe, Co, Ni, Ti, and Zn. Generally, transition metal coordination compounds are used as effective sensitizers, due to their intense charge-transfer absorption over the whole visible range and highly efficient metal-to-ligand charge transfer. We aim to optimize the performance of the title solar cells by altering the frontier orbital energy gaps. The results reveal that cell efficiency can be enhanced by metal functionalization of the free base porphyrin. Ti-porphyrin was found to be the most efficient dye sensitizer for dye sensitized solar cells (DSSCs) based on C60-P-Mptriad system due to C60-Por-TiP complex has lower chemical hardness, gap energy and chemical potential as well as higher electron accepting power among other complexes. In

  15. Influence of hurricane wind field in the structure of directional wave spectra.

    Science.gov (United States)

    Esquivel-Trava, Bernardo; García-Nava, Hector; Osuna, Pedro; Ocampo-Torres, Francisco J.

    2017-04-01

    Three numerical experiments using the spectral wave prediction model SWAN were carried out to gain insight into the mechanism that controls the directional and frequency distributions of hurricane wave energy. One particular objective is to evaluate the effect of the translation speed of the hurricane and the presence of concentric eye walls, on both the wave growth process and the shape of the directional wave spectrum. The HRD wind field of Hurricane Dean on August 20 at 7:30 was propagated at two different velocities (5 and 10 m/s). An idealized concentric eye wall (a Gaussian function that evolve in time along a path in the form of an Archimedean spiral) was imposed to the wind field. The white-capping formulation of Westhuysen et al. (2007) was selected. The wave model represents fairly well the directionality of the energy and the shape of the directional spectra in the hurricane domain. The model results indicate that the forward movement of the storm influences the development of the waves, consistent with field observations. Additionally the same experiments were carried out using the Wave Watch III model with the source terms formulation proposed by Ardhuin et al., 2010, with the aim of making comparisons between the physical processes that represent each formulation, and the latest results will be addressed. References Ardhuin, F., Rogers, E., Babanin, A. V., Filipot, J.-F., Magne, R., Roland, A., van der Westhuysen, A., et al. (2010). Semiempirical Dissipation Source Functions for Ocean Waves. Part I: Definition, Calibration, and Validation. Journal of Physical Oceanography, 40(9), 1917-1941. doi:10.1175/2010JPO4324.1 Van der Westhuysen, A. J., Zijlema, M., & Battjes, J. A. (2007). Nonlinear saturation-based whitecapping dissipation in SWAN for deep and shallow water. Coast. Eng., 54(2), 151-170. doi:10.1016/j.coastaleng.2006.08.006

  16. The interface of protein structure, protein biophysics, and molecular evolution

    Science.gov (United States)

    Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

    2012-01-01

    Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

  17. Contributions to advances in blend pellet products (BPP) research on molecular structure and molecular nutrition interaction by advanced synchrotron and globar molecular (Micro)spectroscopy.

    Science.gov (United States)

    Guevara-Oquendo, Víctor H; Zhang, Huihua; Yu, Peiqiang

    2018-04-13

    To date, advanced synchrotron-based and globar-sourced techniques are almost unknown to food and feed scientists. There has been little application of these advanced techniques to study blend pellet products at a molecular level. This article aims to provide recent research on advanced synchrotron and globar vibrational molecular spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction. How processing induced molecular structure changes in relation to nutrient availability and utilization of the blend pellet products. The study reviews Utilization of co-product components for blend pellet product in North America; Utilization and benefits of inclusion of pulse screenings; Utilization of additives in blend pellet products; Application of pellet processing in blend pellet products; Conventional evaluation techniques and methods for blend pellet products. The study focus on recent applications of cutting-edge vibrational molecular spectroscopy for molecular structure and molecular structure association with nutrient utilization in blend pellet products. The information described in this article gives better insight on how advanced molecular (micro)spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction.

  18. Structural, vibrational and theoretical studies of anilinium trichloroacetate: New hydrogen bonded molecular crystal with nonlinear optical properties

    Science.gov (United States)

    Tanak, H.; Pawlus, K.; Marchewka, M. K.; Pietraszko, A.

    2014-01-01

    In this work, we report a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of the potential nonlinear optical (NLO) material anilinium trichloroacetate. The FT-IR and FT-Raman spectra of the compound have been recorded together between 4000-80 cm-1 and 3600-80 cm-1 regions, respectively. The compound crystallizes in the noncentrosymmetric space group of monoclinic system. The optimized molecular structure, vibrational wavenumbers, IR intensities and Raman activities have been calculated by using density functional method (B3LYP) with 6-311++G(d,p) as higher basis set. The obtained vibrational wavenumbers and optimized geometric parameters were seen to be in good agreement with the experimental data. DSC measurements on powder samples do not indicate clearly on the occurrence of phase transitions in the temperature 113-293 K. The Kurtz and Perry powder reflection technique appeared to be very effective in studies of second-order nonlinear optical properties of the molecule. The non-linear optical properties are also addressed theoretically. The predicted NLO properties of the title compound are much greater than ones of urea. In addition, DFT calculations of the title compound, molecular electrostatic potential, frontier orbitals and thermodynamic properties were also performed at 6-311++G(d,p) level of theory. For title crystal the SHG efficiency was estimated by Kurtz-Perry method to be deff = 0.70 deff (KDP).

  19. Synthesis, properties, and molecular structure of a trivalent organouranium diphosphine hydride

    International Nuclear Information System (INIS)

    Duttera, M.R.; Fagan, P.J.; Marks, T.J.; Day, V.W.

    1982-01-01

    Hydrogenolysis of U[(CH 3 ) 5 C 5 ] 2 R 2 , [R = CH 3 Ch 2 Si(CH 3 ) 3 ], proceeds at -20 0 C in the presence of excess bis(2 dimethylphosphino)ethane(dmpe) according to this reaction: U[(CH 3 ) 3 C 5 ] 2 R 2 + 1.5H 2 + dmpe → (toluene, 18h) U[(CH 3 ) 5 C 5 ] 2 (dmpe) H + 2RH. Black microcrystals can be purified by vacuum Soxhlet extraction with toluene. All processes involving this compound must be performed under argon or helium atmospheres, since it reacts with nitrogen. The structure was studied by NMR, ir spectra. The molar magnetic suceptibility was measured at 295 K, 5120 x 10 -4 emu and is consistent with a U (III) formulation. Crystals are orthorhombic. X-ray diffraction data were collected. Structural parameters were refined to convergence. X-ray structural analysis reveals monocrystals of discrete mononuclear U[eta 5 -(CH 3 ) 5 C 5 ] 2 (dmpe)H molecules. The molecular structure is evaluated. 1 figure

  20. Free radicals. High-resolution spectroscopy and molecular structure

    International Nuclear Information System (INIS)

    Hirota, E.

    1983-01-01

    High-resolution, high-sensitivity spectroscopy using CW laser and microwave sources has been applied to free radicals and transient molecules to establish their existence and to explore their properties in detail. The radicals studied were mainly generated by discharge-induced reactions. A few molecules are used as typical examples to illustrate the results so far obtained. The molecular and electronic structures of free radicals, intramolecular motions of large amplitudes in some labile molecules, and metastable electronic states of carbenes are given special emphasis. The significance of the present spectroscopic results in other related fields such as astronomy and atmospheric chemistry is stressed. 4 figures, 3 tables

  1. Coalescence of silver unidimensional structures by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Perez A, M.; Gutierrez W, C.E.; Mondragon, G.; Arenas, J.

    2007-01-01

    The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)

  2. Nonlinear excitations in two-dimensional molecular structures with impurities

    DEFF Research Database (Denmark)

    Gaididei, Yuri Borisovich; Rasmussen, Kim; Christiansen, Peter Leth

    1995-01-01

    We study the nonlinear dynamics of electronic excitations interacting with acoustic phonons in two-dimensional molecular structures with impurities. We show that the problem is reduced to the nonlinear Schrodinger equation with a varying coefficient. The latter represents the influence...... of the impurity. Transforming the equation to the noninertial frame of reference coupled with the center of mass we investigate the soliton behavior in the close vicinity of the impurity. With the help of the lens transformation we show that the soliton width is governed by an Ermakov-Pinney equation. We also...... excitations. Analytical results are in good agreement with numerical simulations of the nonlinear Schrodinger equation....

  3. The structure of molecular liquids. Neutron diffraction and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Bianchi, L.

    2000-05-01

    Neutron diffraction (ND) measurements on liquid methanol (CD 3 OD, CD 3 O(H/D), CD 3 OH) under ambient conditions were performed to obtain the distinct (intra- + inter-molecular), G dist (r) and inter-molecular, G inter (r) radial distribution functions (rdfs) for the three samples. The H/D substitution on hydroxyl-hydrogen (Ho) has been used to extract the partial distribution functions, G XHo (r) (X=C, O, and H - a methyl hydrogen) and G XX (r) at both the distinct and inter-molecular levels from the difference techniques of ND. The O-Ho bond length, which has been the subject of controversy in the past, is found purely from the distinct partial distribution function, G XHo (r) to be 0.98 ± 0.01 A. The C-H distance obtained from the distinct G XX (r) partial is 1.08 ± 0.01 A. These distances determined by fitting an intra-molecular model to the total distinct structure functions are 0.961 ± 0.001 A and 1.096 ± 0.001 A, respectively. The inter-molecular G XX (r) function, dominated by contributions from the methyl groups, apart from showing broad oscillations extending up to ∼14 A is featureless, mainly because of cancellation effects from six contributing pairs. The Ho-Ho partial pair distribution function (pdf), g HoHo (r), determined from the second order difference, shows that only one other Ho atom can be found within a mean Ho-Ho separation of 2.36 A. The average position of the O-Ho hydrogen bond determined for the first time purely from experimental inter-molecular G XHo (r) partial distribution function is found to be at 1.75 ± 0.03 A. The experimental structural results at the partial distribution level are compared with those obtained from molecular dynamics (MD) simulations performed in NVE ensemble by using both 3- and 6-site force field models for the first time in this study. The MD simulations with both the models reproduce the ND rdfs rather well. However, discrepancies begin to appear between the simulated and the experimental partial

  4. Simultaneous analysis of rotational and vibrational-rotational spectra of DF and HF to obtain irreducible molecular constants for HF

    International Nuclear Information System (INIS)

    Horiai, Koui; Uehara, Hiromichi

    2011-01-01

    Graphical abstract: Available rotational and vibrational-rotational spectral lines of DF and HF are analyzed simultaneously using a non-Born-Oppenheimer effective Hamiltonian. Research highlights: → Simultaneous analysis of DF and HF spectral data. → Application of a non-Born-Oppenheimer effective Hamiltonian. → Twenty irreducible molecular constants for HF have been determined. - Abstract: Analytic expressions of corrections for the breakdown of the Born-Oppenheimer approximation to Dunham's Y ij with optimal parameters, i.e., determinable clusters of expansion coefficients, are applied to a data analysis of the rotational and vibrational-rotational transitions of HF reported in the literature. All the available spectral lines of the two isotopologues, DF and HF, are simultaneously fitted to a single set of molecular parameters of HF within experimental errors. Fitting of a data set of 595 spectral transitions for DF and HF has generated only 20 minimal independent parameter values, i.e., 'irreducible' molecular constants of HF, that are sufficient to precisely generate 82 Y ij coefficients and 144 band constants in total: 41 Y ij and 72 band constants each for DF and HF.

  5. Structure and vibrational spectra of melaminium bis(trifluoroacetate) trihydrate: FT-IR, FT-Raman and quantum chemical calculations

    Science.gov (United States)

    Sangeetha, V.; Govindarajan, M.; Kanagathara, N.; Marchewka, M. K.; Gunasekaran, S.; Anbalagan, G.

    Melaminium bis(trifluoroacetate) trihydrate (MTFA), an organic material has been synthesized and single crystals of MTFA have been grown by the slow solvent evaporation method at room temperature. X-ray powder diffraction analysis confirms that MTFA crystal belongs to the monoclinic system with space group P2/c. The molecular geometry, vibrational frequencies and intensity of the vibrational bands have been interpreted with the aid of structure optimization based on density functional theory (DFT) B3LYP method with 6-311G(d,p) and 6-311++G(d,p) basis sets. The X-ray diffraction data have been compared with the data of optimized molecular structure. The theoretical results show that the crystal structure can be reproduced by optimized geometry and the vibrational frequencies show good agreement with the experimental values. The nuclear magnetic resonance (NMR) chemical shift of the molecule has been calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. HOMO-LUMO, and other related molecular and electronic properties are calculated. The Mulliken and NBO charges have also been calculated and interpreted.

  6. Electronic structure, photoemission spectra, and vacuum-ultraviolet optical spectra of CsPbCl3 and CsPbBr3

    Science.gov (United States)

    Heidrich, K.; Schäfer, W.; Schreiber, M.; Söchtig, J.; Trendel, G.; Treusch, J.; Grandke, T.; Stolz, H. J.

    1981-11-01

    Optical spectra of CsPbCl3 and CsPbBr3 have been measured in the range from 2 to 10 eV and have been combined with ultraviolet-photoemission-spectroscopy (UPS)-measurements at 21.1 and 40.8 eV. A quantitative band calculation is presented, which takes into account anion-anion interaction as well as electronic states of the Cs+ ion. The prominent features of earlier band models and measurements are reestablished through our measurements and calculations, namely that the valence band consists of anionic p functions and Pb 6s functions, the lowest conduction band being Pb 6p type, and the lowest gap occuring at the R point of the Brillouin zone. Inclusion of a further (Cs 6s-type) conduction band, however, is necessary to bring the calculated joint density of states into agreement with vacuum-ultraviolet optical spectra. The calculated densities of states of the valence bands are in quantitative agreement with those deduced from our UPS measurements.

  7. Molecular simulations of hydrated proton exchange membranes. The structure

    Energy Technology Data Exchange (ETDEWEB)

    Marcharnd, Gabriel [Duisburg-Essen Univ., Essen (Germany). Lehrstuhl fuer Theoretische Chemie; Bordeaux Univ., Talence (France). Dept. of Chemistry; Bopp, Philippe A. [Bordeaux Univ., Talence (France). Dept. of Chemistry; Spohr, Eckhard [Duisburg-Essen Univ., Essen (Germany). Lehrstuhl fuer Theoretische Chemie

    2013-01-15

    The structure of two hydrated proton exchange membranes for fuel cells (PEMFC), Nafion {sup registered} (Dupont) and Hyflon {sup registered} (Solvay), is studied by all-atom molecular dynamics (MD) computer simulations. Since the characteristic times of these systems are long compared to the times for which they can be simulated, several different, but equivalent, initial configurations with a large degree of randomness are generated for different water contents and then equilibrated and simulated in parallel. A more constrained structure, analog to the newest model proposed in the literature based on scattering experiments, is investigated in the same way. One might speculate that a limited degree of entanglement of the polymer chains is a key feature of the structures showing the best agreement with experiment. Nevertheless, the overall conclusion remains that the scattering experiments cannot distinguish between the several, in our view equally plausible, structural models. We thus find that the characteristic features of experimental scattering curves are, after equilibration, fairly well reproduced by all systems prepared with our method. We thus study in more detail some structural details. We attempt to characterize the spatial and size distribution of the water rich domains, which is where the proton diffusion mostly takes place, using several clustering algorithms. (orig.)

  8. Rich structure in the correlation matrix spectra in non-equilibrium steady states.

    Science.gov (United States)

    Biswas, Soham; Leyvraz, Francois; Monroy Castillero, Paulino; Seligman, Thomas H

    2017-01-17

    It has been shown that, if a model displays long-range (power-law) spatial correlations, its equal-time correlation matrix will also have a power law tail in the distribution of its high-lying eigenvalues. The purpose of this paper is to show that the converse is generally incorrect: a power-law tail in the high-lying eigenvalues of the correlation matrix may exist even in the absence of equal-time power law correlations in the initial model. We may therefore view the study of the eigenvalue distribution of the correlation matrix as a more powerful tool than the study of spatial Correlations, one which may in fact uncover structure, that would otherwise not be apparent. Specifically, we show that in the Totally Asymmetric Simple Exclusion Process, whereas there are no clearly visible correlations in the steady state, the eigenvalues of its correlation matrix exhibit a rich structure which we describe in detail.

  9. Modeling the structure and vibrational spectra for oxouranium dichloride monomer and dimer

    Science.gov (United States)

    Umreiko, D. S.; Shundalau, M. B.; Trubina, O. V.

    2010-11-01

    Structural models are designed and spectral characteristics are computed for the monomer and dimer of the oxouranium dichloride (UOCl2) molecule based on ab initio calculations. The calculations were carried out in the LANL2DZ effective core potential approximation for the uranium atom and all-electron basis sets using DFT methods for oxygen and chlorine atoms (B3LYP/cc-pVDZ). A close-to-planar Y-shaped equilibrium configuration with Cs symmetry is obtained for the UOCl2 monomer. The formation of the dimer is accompanied by both significant changes in the structure of the monomeric fragments and the actual loss of their identities. The obtained spectral characteristics are analyzed and compared with experimental data. The adequacy of the proposed models and qualitative agreement between calculation and experiment are demonstrated.

  10. CRYSTAL AND MOLECULAR STRUCTURE OF 5-NITROPIRIDINE PIPERIDINE-SULFENAMIDE

    OpenAIRE

    Brito, Iván; León, Yasna; Arias, Mauricio; Vargas, Danitza; Carmona, Francisco; Ramírez, Eduardo; Restovic, Ambrosio; Cárdenas, Alejandro; Wittke, Oscar; López-Rodríguez, Matías

    2002-01-01

    The crystal and molecular structure of 5-nitropiridine piperidine-sulfenamide, C10H13N3O2 S is described and compared with other sulfenamides and with other similar compounds. This structure belongs to a type of divalent sulphur compound and crystallizes in the orthorhombic space group Pnma with a= 27.810(4), b=6.797(1), c=6.110(1)Å, and Dx =1.376 g cm-3 with Z=4. The S-N bond distance of 1.699(4) Å is shorter than a single S-N bond [1.74 Å]. The NO2-(C6H3N)-S-N(C 5H10) molecule lies on a cry...

  11. Chemical structure and properties of low-molecular furin inhibitors

    Directory of Open Access Journals (Sweden)

    T. V. Osadchuk

    2016-12-01

    Full Text Available The review is devoted to the analysis of the relationship between a chemical structure and properties of low-molecular weight inhibitors of furin, the most studied proprotein convertase, which is involved in the development of some pathologies, such as oncologic diseases, viral and bacterial infections, etc. The latest data concerning the influence of peptides, pseudo-peptides, aromatic and heterocyclic compounds, some natural ones such as flavonoids, coumarins, and others on enzyme inactivation are considered. The power of furin inhibition is shown to rise with the increasing number of positively charged groups in the structure of these compounds. Peptidomimetics (Ki = 5-8 pM are shown to be the most effective furin inhibitors. The synthesized substances, however, have not been used in practical application yet. Nowadays it is very important to find more selective inhibitors, improve their stability, bioavailability and safety for the human organism.

  12. Surfaces of Microparticles in Colloids: Structure and Molecular Adsorption Kinetics

    Science.gov (United States)

    Dai, Hai-Lung

    2002-03-01

    Surfaces of micron and sub-micron size particles in liquid solution are probed by second harmonic generation (SHG) facilitated with femtosecond laser pulses. The particles probed include inorganic objects such as carbon black and color pigments, polymeric species like polystyrene beads, and biological systems such as blood cells and ecoli. In the experiments, dye molecules are first adsorbed onto the particle surface to allow generation of second harmonics upon light irradiation. Competition for adsorption between these surface dye molecules and the molecules of interest in the solution is then monitored by the SHG signal to reveal the molecular adsorption kinetics and surface structure. Specifically, surfactant adsorption on polymer surfaces, the structure of carbon black surface, and protein adsorption on biological surfaces, monitored by this technique, will be discussed.

  13. Relation of high harmonic spectra to electronic structure in N2

    International Nuclear Information System (INIS)

    Farrell, J.P.; McFarland, B.K.; Guehr, M.; Bucksbaum, P.H.

    2009-01-01

    High harmonics of N 2 exhibit a number of features that are related to the electronic structure and sub-femtosecond dynamics of the molecule. Through measurements and simulations, we show how the harmonic spectral shape, spectral phase, alignment angle dependence, and intensity dependence can be related to the strong-field ionization and recombination dynamics of the HOMO and HOMO-1 electron orbitals. A field-free static model of the molecule is insufficient to explain the observations.

  14. Thiobarbiturate and barbiturate salts of pefloxacin drug: Growth, structure, thermal stability and IR-spectra

    Science.gov (United States)

    Golovnev, Nicolay N.; Molokeev, Maxim S.; Lesnikov, Maxim K.; Sterkhova, Irina V.; Atuchin, Victor V.

    2017-12-01

    Three new salts of pefloxacin (PefH) with thiobarbituric (H2tba) and barbituric (H2ba) acids, pefloxacinium 2-thiobarbiturate trihydrate, PefH2(Htba)·3H2O (1), pefloxacinium 2-thiobarbiturate, PefH2(Htba) (2) and bis(pefloxacinium barbiturate) hydrate, (PefH2)2(Hba)2·2.56H2O (3) are synthesized and structurally characterized by the X-ray single-crystal diffraction. The structures of 1-3 contain intramolecular hydrogen bonds Csbnd H⋯F, Osbnd H⋯O. Intermolecular hydrogen bonds Nsbnd H⋯O and Osbnd H⋯O form a 2D plane network in 1. In 2 and 3, intermolecular hydrogen bonds Nsbnd H⋯O form the infinite chains. In 1-3, the Htba- and Hba- ions are connected with PefH2+ only by one intermolecular hydrogen bond Nsbnd H⋯O. In 2 and 3, two Htba- and Hba- ions are connected by two hydrogen bonds Nsbnd H⋯O. These pairs form infinite chains. All three structures are stabilized by the π-π interactions of the head-to-tail type between PefH2+ ions. Compounds 2 and 3 are characterized by powder XRD, TG-DSC and FT-IR.

  15. Structures and physicochemical properties of molecular aggregates of lipids

    International Nuclear Information System (INIS)

    Iwahashi, Makio

    2005-01-01

    Structures and physicochemical properties of lipids such as fatty acids, alcohols, acylglycerols and steroids in their two- or three-dimensional states were studied through the measurements of surface pressure (π), surface-molecular area (A), vapor-pressure osmosis, radioactivity (R), self-diffusion coefficient (D), density, viscosity, near-infrared spectroscopy (NIR), 13 C-NMR spin-lattice relaxation time (T 1 ), ESR, SEM, DSC, X-ray diffraction and small-angle neutron scattering (SANS). Following results are obtained: (1) π-A and R-A relationships indicate that the explanation, being widely believed, of the reaction occurred in the oleic acid or the trioleylglycerol monolayer on the aqueous KMnO 4 solution is incorrect. (2) By using the LB film of 3 H-labelled fatty acid, the upper limit of the neutrino mass was determined. In addition, by using the LB film of 14 C-labelled fatty acid, a new type of crystal-transformation process was found, in which fatty-acid crystal transforms from its unstable state to its stable one by the transfer of the fatty acid molecules through the vapor phase. (3) Fatty acids always exist as their dimers in their liquid state and mostly in non-polar solvents; the dimers are the units of the molecular movements in the molten liquid and in solvents. T 1 results clearly showed the internal molecular movements of the dimers. In addition, D and SANS results indicated that two different kinds of fatty acids in their binary mixture make only each homodimers. (4) Furthermore, the study on the liquid structure of fatty acids such as cis-6-, cis-9-, cis-11-, trans-9-octadecenoic acids and stearic acid indicated that these fatty-acid dimers construct the clusters resemble to the smectic-liquid crystal in the liquid state. The clusters determine the physicochemical properties of the liquid of the fatty acid. (author)

  16. Micro structure processing on plastics by accelerated hydrogen molecular ions

    Science.gov (United States)

    Hayashi, H.; Hayakawa, S.; Nishikawa, H.

    2017-08-01

    A proton has 1836 times the mass of an electron and is the lightest nucleus to be used for accelerator in material modification. We can setup accelerator with the lowest acceleration voltage. It is preferable characteristics of Proton Beam Writer (PBW) for industrial applications. On the contrary ;proton; has the lowest charge among all nuclei and the potential impact to material is lowest. The object of this research is to improve productivity of the PBW for industry application focusing on hydrogen molecular ions. These ions are generated in the same ion source by ionizing hydrogen molecule. There is no specific ion source requested and it is suitable for industrial use. We demonstrated three dimensional (3D) multilevel micro structures on polyester base FPC (Flexible Printed Circuits) using proton, H2+ and H3+. The reactivity of hydrogen molecular ions is much higher than that of proton and coincident with the level of expectation. We can apply this result to make micro devices of 3D multilevel structures on FPC.

  17. Arrangement of Fibril Side Chains Studied by Molecular Dynamics and Simulated Infrared and Vibrational Circular Dichroism Spectra

    Czech Academy of Sciences Publication Activity Database

    Kessler, Jiří; Kiederling, T. A.; Bouř, Petr

    2014-01-01

    Roč. 118, č. 24 (2014), s. 6937-6945 ISSN 1520-6106 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant - others:MŠMT(CZ) LM2010005; AV ČR(CZ) M200550902; MŠMT(CZ) ED3.2.00/08.0144 Institutional support: RVO:61388963 Keywords : insulin amyloid superstructures * DFT * VCD * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.302, year: 2014

  18. Molecular structure, vibrational, UV, NMR, HOMO-LUMO, MEP, NLO, NBO analysis of 3,5 di tert butyl 4 hydroxy benzoic acid

    Science.gov (United States)

    Mathammal, R.; Sangeetha, K.; Sangeetha, M.; Mekala, R.; Gadheeja, S.

    2016-09-01

    In this study, we report a combined experimental and theoretical study on molecular structure and vibrational spectra of 3,5 di tert butyl 4 hydroxy benzoic acid. The properties of title compound have been evaluated by quantum chemical calculation (DFT) using B3LYP functional and 6-31 + G (d, p) as basis set. IR Spectra has been recorded using Fourier transform infrared spectroscopy (FT-IR) in the region 4000-400 cm-1. The vibrational assignment of the calculated normal modes has been made on the basis set. The isotropic chemical shifts computed by 13C and 1H NMR (Nuclear Magnetic Resonance) analyses also show good agreement with experimental observations. The theoretical UV-Vis spectrum of the compound are used to study the visible absorption maxima (λ max). The structure activity relationship have been interpreted by mapping electrostatic potential surface (MEP), which is valuable information for the quality control of medicines and drug receptor interactions. The Mullikan charges, HOMO (Highest Occupied Molecular Orbital) - LUMO (Lowest Unoccupied Molecular Orbital) energy are analyzed. HOMO-LUMO energy gap and other related molecular properties are also calculated. The Natural Bond Orbital (NBO) analysis is carried out to investigate the various intra and inter molecular interactions of molecular system. The Non-linear optical properties such as dipole moment (μ), polarizability (αtot) and molecular first order hyperpolarizability (β) of the title compound are computed with B3LYP/6-31 + G (d,p) level of theory.

  19. PGOPHER: A program for simulating rotational, vibrational and electronic spectra

    International Nuclear Information System (INIS)

    Western, Colin M.

    2017-01-01

    The PGOPHER program is a general purpose program for simulating and fitting molecular spectra, particularly the rotational structure. The current version can handle linear molecules, symmetric tops and asymmetric tops and many possible transitions, both allowed and forbidden, including multiphoton and Raman spectra in addition to the common electric dipole absorptions. Many different interactions can be included in the calculation, including those arising from electron and nuclear spin, and external electric and magnetic fields. Multiple states and interactions between them can also be accounted for, limited only by available memory. Fitting of experimental data can be to line positions (in many common formats), intensities or band contours and the parameters determined can be level populations as well as rotational constants. PGOPHER is provided with a powerful and flexible graphical user interface to simplify many of the tasks required in simulating, understanding and fitting molecular spectra, including Fortrat diagrams and energy level plots in addition to overlaying experimental and simulated spectra. The program is open source, and can be compiled with open source tools. This paper provides a formal description of the operation of version 9.1. - Highlights: • Easy-to-use graphical interface for assigning and understanding molecular spectra. • Simulates rotational and vibrational structure of many types of molecular spectra. • Fits molecular properties to line positions or spectral contours. • Handles linear molecules and symmetric and asymmetric tops. • Handles perturbations, nuclear and electron spin, and electric and magnetic fields.

  20. Scattering of 14.6 MeV neutrons from Fe and evidence for structure in the emitted neutron spectra

    International Nuclear Information System (INIS)

    Gul, K.; Anwar, M.; Ahmad, M.; Saleem, S.M.; Khan, N.A.

    1984-06-01

    Structure in the spectra of neutrons emitted from iron on bombardment with 14.6 MeV neutrons has been investigated and explained in terms of excitation of levels in iron 56. The energies of scattered neutrons have been measured by the time-of-flight technique based on the associated particle method. The observed excitations have been correlated with the reported levels in a satisfactory manner. Evidence for new excitations at 8.8 +- 0.02, 9.8 +- 0.1, 10.2 +- 0.1, 12.44 +- 0.03 and 12.52 +- 0.03 MeV has been obtained. The excitation of possible components of Ml giant resonance in iron 56 is discussed. (author)

  1. UV-POSIT: Web-Based Tools for Rapid and Facile Structural Interpretation of Ultraviolet Photodissociation (UVPD) Mass Spectra

    Science.gov (United States)

    Rosenberg, Jake; Parker, W. Ryan; Cammarata, Michael B.; Brodbelt, Jennifer S.

    2018-04-01

    UV-POSIT (Ultraviolet Photodissociation Online Structure Interrogation Tools) is a suite of web-based tools designed to facilitate the rapid interpretation of data from native mass spectrometry experiments making use of 193 nm ultraviolet photodissociation (UVPD). The suite includes four separate utilities which assist in the calculation of fragment ion abundances as a function of backbone cleavage sites and sequence position; the localization of charge sites in intact proteins; the calculation of hydrogen elimination propensity for a-type fragment ions; and mass-offset searching of UVPD spectra to identify unknown modifications and assess false positive fragment identifications. UV-POSIT is implemented as a Python/Flask web application hosted at http://uv-posit.cm.utexas.edu. UV-POSIT is available under the MIT license, and the source code is available at https://github.com/jarosenb/UV_POSIT. [Figure not available: see fulltext.

  2. A case study of microphysical structures and hydrometeor phase in convection using radar Doppler spectra at Darwin, Australia

    Energy Technology Data Exchange (ETDEWEB)

    Riihimaki, Laura D.; Comstock, Jennifer M.; Luke, Edward; Thorsen, Tyler J.; Fu, Qiang

    2017-07-28

    To understand the microphysical processes that impact diabatic heating and cloud lifetimes in convection, we need to characterize the spatial distribution of supercooled liquid water. To address this observational challenge, vertically pointing active sensors at the Darwin Atmospheric Radiation Measurement (ARM) site are used to classify cloud phase within a deep convective cloud in a shallow to deep convection transitional case. The cloud cannot be fully observed by a lidar due to signal attenuation. Thus we develop an objective method for identifying hydrometeor classes, including mixed-phase conditions, using k-means clustering on parameters that describe the shape of the Doppler spectra from vertically pointing Ka band cloud radar. This approach shows that multiple, overlapping mixed-phase layers exist within the cloud, rather than a single region of supercooled liquid, indicating complexity to how ice growth and diabatic heating occurs in the vertical structure of the cloud.

  3. UV-POSIT: Web-Based Tools for Rapid and Facile Structural Interpretation of Ultraviolet Photodissociation (UVPD) Mass Spectra.

    Science.gov (United States)

    Rosenberg, Jake; Parker, W Ryan; Cammarata, Michael B; Brodbelt, Jennifer S

    2018-04-06

    UV-POSIT (Ultraviolet Photodissociation Online Structure Interrogation Tools) is a suite of web-based tools designed to facilitate the rapid interpretation of data from native mass spectrometry experiments making use of 193 nm ultraviolet photodissociation (UVPD). The suite includes four separate utilities which assist in the calculation of fragment ion abundances as a function of backbone cleavage sites and sequence position; the localization of charge sites in intact proteins; the calculation of hydrogen elimination propensity for a-type fragment ions; and mass-offset searching of UVPD spectra to identify unknown modifications and assess false positive fragment identifications. UV-POSIT is implemented as a Python/Flask web application hosted at http://uv-posit.cm.utexas.edu . UV-POSIT is available under the MIT license, and the source code is available at https://github.com/jarosenb/UV_POSIT . Graphical Abstract.

  4. [The effect of electromagnetic waves of very high frequency of molecular spectra of radiation and absorption of nitric oxide on the functional activity of platelets].

    Science.gov (United States)

    Kirichuk, V F; Maĭborodin, A V; Volin, M V; Krenitskiĭ, A P; Tupikin, V D

    2001-01-01

    A study was made of the effect of electromagnetic EMI MMD-fluctuation on the frequencies of molecular spectra of radiation, and nitric oxide absorption under in vitro conditions on the functional activity of platelets in patients with unstable angina pectoris, with the help of a specially created generator. At amplitude-modulated and continuous modes of EMI MMD-irradiation of platelet-rich plasma for 5, 15 and 30 min the platelet functional activity decreases, which was shown up in reduction of their activation and fall of aggregative ability. The degree, to which platelet functional activity was inhibited, depended on the mode of irradiation and on duration of EMI MMD effect. The most obvious changes in platelet activation and in their readiness to aggregative response were observed at a continuous mode of irradiation within a 15 min interval.

  5. Satellite structure in Auger and (e,2e) spectra of germanium

    International Nuclear Information System (INIS)

    Went, M.R.; Vos, M.; Kheifets, A.S.

    2006-01-01

    The interpretation of electron spectroscopy data is often complicated by the presence of satellites. These satellites are either due to different final states reached after the excitation (intrinsic satellites) or due to energy loss experienced by the escaping electron on its way out the target (extrinsic satellites). Unravelling these two contributions in an unambiguous way is difficult. In this paper we compare the intrinsic satellite structures obtained for germanium by two different high-energy spectroscopies: Auger spectroscopy of deep core levels and valence band electron momentum spectroscopy. Despite the different nature of the two probes we find a similar shape of the intrinsic satellites and comparable intensity

  6. EXANA, a program for analysing EXtended energy loss fine structures, EXELFS spectra

    International Nuclear Information System (INIS)

    Tafreshi, M.A.; Bohm, C.; Csillag, S.

    1992-09-01

    This paper is a users guide and reference manual for the EXANA, an IBM or IBM compatible PC-based program used for analysing extended fine structures occurring on the high energy side of the ionisation edges. The RDF (Radial Distance Function) obtained from this analysis contains information about the number, distance, and type of the nearby atoms, as well as the inelastic mean free path and disorder in distances from the centre atom to the atoms in a atomic shell around it. The program can be made available on request. (au)

  7. Teaching Structure-Property Relationships: Investigating Molecular Structure and Boiling Point

    Science.gov (United States)

    Murphy, Peter M.

    2007-01-01

    A concise, well-organized table of the boiling points of 392 organic compounds has facilitated inquiry-based instruction in multiple scientific principles. Many individual or group learning activities can be derived from the tabulated data of molecular structure and boiling point based on the instructor's education objectives and the students'…

  8. Effects of structural and chemical disorders on the vis/UV spectra of carbonaceous interstellar grains

    Science.gov (United States)

    Papoular, Robert J.; Yuan, Shengjun; Roldán, Rafael; Katsnelson, Mikhail I.; Papoular, Renaud

    2013-07-01

    The recent spectacular progress in the experimental and theoretical understanding of graphene, the basic constituent of graphite, is applied here to compute, from first principles, the ultraviolet extinction of nanoparticles made of stacks of graphene layers. The theory also covers cases where graphene is affected by structural, chemical or orientation disorder, each disorder type being quantitatively defined by a single parameter. The extinction bumps carried by such model materials are found to have positions and widths falling in the same range as the known astronomical 2175 Å features: as the disorder parameter increases, the bump width increases from 0.85 to 2.5 μm-1, while its peak position shifts from 4.65 to 4.75 μm-1. Moderate degrees of disorder are enough to cover the range of widths of the vast majority of observed bumps (0.75 to 1.3 μm-1). Higher degrees account for outliers, also observed in the sky. The introduction of structural or chemical disorder amounts to changing the initial sp2 bondings into sp3 or sp1, so the optical properties of the model material become similar to those of the more or less amorphous carbon-rich materials studied in the laboratory: a-C, a-C:H, HAC, ACH, coals, etc. The present treatment thus bridges gaps between physically different model materials.

  9. Structure and intensities of microwave lines in the spectra of diatomic molecules

    International Nuclear Information System (INIS)

    Tatum, J.B.

    1986-01-01

    The structure of the rotational levels in a diatomic molecule, and the intensities of microwave transitions between them, are reviewed. Attention is given to the statistical weights of levels that may have hyperfine structure on account of one or two nuclear spins, in the case of heteronuclear molecules and of homonuclear molecules. A new treatment is given, involving the concept of energy surfaces in a ternary diagram in the form of a triangular prism, in which the three vertices represent three limiting cases, while the interior of the prism displays energy levels where all three intermediate coupling parameters are of comparable magnitude. An example is given of a simple J = 2 to J = 1 transition in a molecule with nuclear spins 3/2 and 1, showing the 56 hyperhyperfine components into which the rotational line is split, and a movie film is described which shows how the resulting ''fingerprint'' varies with the relative strengths of the interactions between the nuclear and electronic angular momenta

  10. Molecular Weight and Structural Properties of Biodegradable PLA Synthesized with Different Catalysts by Direct Melt Polycondensation

    Directory of Open Access Journals (Sweden)

    Hyung Woo Lee

    2015-09-01

    Full Text Available Production of biodegradable polylactic acid (PLA from biomassbased lactic acid is widely studied for substituting petro-based plastics or polymers. This study investigated PLA production from commercial lactic acid in a batch reactor by applying a direct melt polycondensation method with two kinds of catalyst, γ-aluminium(III oxide (γ-Al2O3 or zinc oxide (ZnO, in reduced pressure. The molecular weight of the synthesized PLA was determined by capillary viscometry and its structural properties were analyzed by functional group analysis using FT-IR. The yields of polymer production with respect to the theoretical conversion were 47% for γ-Al2O3 and 35% for ZnO. However, the PLA from ZnO had a higher molecular weight (150,600 g/mol than that from γ-Al2O3 (81,400 g/mol. The IR spectra of the synthesized PLA from both catalysts using polycondensation show the same behavior of absorption peaks at wave numbers from 4,500 cm-1 to 500 cm-1, whereas the PLA produced by two other polymerization methods – polycondensation and ring opening polymerization –showed a significant difference in % transmittance intensity pattern as well as peak area absorption at a wave number of 3,500 cm-1 as –OH vibration peak and at 1,750 cm-1 as –C=O carbonyl vibrational peak.

  11. Experimental and Computational Approaches to the Molecular Structure of 3-(2-Mercaptopyridine)phthalonitrile

    International Nuclear Information System (INIS)

    Tanak, Hasan; Koysal, Yavuz; Isik, Samil; Yaman, Hanifi; Ahsen, Vefa

    2011-01-01

    The compound 3-(2-Mercaptopyridine)phthalonitrile has been synthesized and characterized by IR, UV-vis, and X-ray single-crystal determination. The molecular geometry from X-ray determination of the title compound in the ground state has been compared using the Hartree-Fock (HF) and density functional theory (DFT) with the 6-31G(d) basis set. The calculated results show that the DFT and HF can well reproduce the structure of the title compound. The energetic behavior of the title compound in solvent media was examined using the B3LYP method with the 6-31G(d) basis set by applying the Onsager and polarizable continuum model. Using the TD-DFT and TD-HF methods, electronic absorption spectra of the title compound have been predicted and good agreement with the TD-DFT method and the experimental determination was found. The predicted nonlinear optical properties of the title compound are much greater than those of urea. Besides, molecular electrostatic potential of the title compound were investigated by theoretical calculations. The thermodynamic properties of the compound at different temperatures have been calculated and corresponding relations between the properties and temperature have also been obtained

  12. Experimental and Computational Approaches to the Molecular Structure of 3-(2-Mercaptopyridine)phthalonitrile

    Energy Technology Data Exchange (ETDEWEB)

    Tanak, Hasan [Amasya University, Amasys (Turkmenistan); Koysal, Yavuz; Isik, Samil [Ondokuz Mayis University, Samsun (Turkmenistan); Yaman, Hanifi; Ahsen, Vefa [Gebze Institute of Technology Department of Chemistry, Gebze-Kocaeli (Turkmenistan)

    2011-02-15

    The compound 3-(2-Mercaptopyridine)phthalonitrile has been synthesized and characterized by IR, UV-vis, and X-ray single-crystal determination. The molecular geometry from X-ray determination of the title compound in the ground state has been compared using the Hartree-Fock (HF) and density functional theory (DFT) with the 6-31G(d) basis set. The calculated results show that the DFT and HF can well reproduce the structure of the title compound. The energetic behavior of the title compound in solvent media was examined using the B3LYP method with the 6-31G(d) basis set by applying the Onsager and polarizable continuum model. Using the TD-DFT and TD-HF methods, electronic absorption spectra of the title compound have been predicted and good agreement with the TD-DFT method and the experimental determination was found. The predicted nonlinear optical properties of the title compound are much greater than those of urea. Besides, molecular electrostatic potential of the title compound were investigated by theoretical calculations. The thermodynamic properties of the compound at different temperatures have been calculated and corresponding relations between the properties and temperature have also been obtained.

  13. Drug Repositioning by Kernel-Based Integration of Molecular Structure, Molecular Activity, and Phenotype Data

    Science.gov (United States)

    Wang, Yongcui; Chen, Shilong; Deng, Naiyang; Wang, Yong

    2013-01-01

    Computational inference of novel therapeutic values for existing drugs, i.e., drug repositioning, offers the great prospect for faster and low-risk drug development. Previous researches have indicated that chemical structures, target proteins, and side-effects could provide rich information in drug similarity assessment and further disease similarity. However, each single data source is important in its own way and data integration holds the great promise to reposition drug more accurately. Here, we propose a new method for drug repositioning, PreDR (Predict Drug Repositioning), to integrate molecular structure, molecular activity, and phenotype data. Specifically, we characterize drug by profiling in chemical structure, target protein, and side-effects space, and define a kernel function to correlate drugs with diseases. Then we train a support vector machine (SVM) to computationally predict novel drug-disease interactions. PreDR is validated on a well-established drug-disease network with 1,933 interactions among 593 drugs and 313 diseases. By cross-validation, we find that chemical structure, drug target, and side-effects information are all predictive for drug-disease relationships. More experimentally observed drug-disease interactions can be revealed by integrating these three data sources. Comparison with existing methods demonstrates that PreDR is competitive both in accuracy and coverage. Follow-up database search and pathway analysis indicate that our new predictions are worthy of further experimental validation. Particularly several novel predictions are supported by clinical trials databases and this shows the significant prospects of PreDR in future drug treatment. In conclusion, our new method, PreDR, can serve as a useful tool in drug discovery to efficiently identify novel drug-disease interactions. In addition, our heterogeneous data integration framework can be applied to other problems. PMID:24244318

  14. Chemistry and structure of giant molecular clouds in energetic environments

    Science.gov (United States)

    Anderson, Crystal Nicole

    2016-09-01

    Throughout the years many studies on Galactic star formation have been conducted. This resulted in the idea that giant molecular clouds (GMCs) are hierarchical in nature with substructures spanning a large range of sizes. The physical processes that determine how molecular clouds fragment, form clumps/cores and then stars depends strongly on both recent radiative and mechanical feed- back from massive stars and, on longer term, from enhanced cooling due to the buildup of metals. Radiative and mechanical energy input from stellar populations can alter subsequent star formation over a large part of a galaxy and hence is relevant to the evolution of galaxies. Much of our knowledge of star formation on galaxy wide scales is based on scaling laws and other parametric descriptions. But to understand the overall evolution of star formation in galaxies we need to watch the feedback processes at work on giant molecular cloud (GMC) scales. By doing this we can begin to answer how strong feedback environments change the properties of the substructure in GMCs. Tests of Galactic star formation theory to other galaxies has been a challenging process due to the lack of resolution with current instruments. Thus, only the nearest galaxies allow us to resolve GMCs and their substructures. The Large Magellanic Cloud (LMC), is one of the closest low metallicity dwarf galaxies (D˜ 50 kpc) and is close enough that current instruments can resolve the sub- structure of its GMCs to molecular gas tracers (e.g. HCO+, HCN, HNC, CS, C2H, N2H+) detected in the LMC at 1.5-40 pc scales and in NGC 5253 at 40 pc scales. I then compare the molecular gas detections to the Central Molecular Zone in our Galaxy. Dense molecular gas was detected in all of the sources. For the regions in the LMC, molecular lines of CS, N2H+, C 2H, HNC, HCO+ and HCN were all detected in N159W and N113 while only HCN, HCO+, HNC, and C2H were detected in 30Dor-10. Toward NGC 5253 only HCO+, HCN, C2H and CS were detected. I

  15. Functional Annotation of Ion Channel Structures by Molecular Simulation.

    Science.gov (United States)

    Trick, Jemma L; Chelvaniththilan, Sivapalan; Klesse, Gianni; Aryal, Prafulla; Wallace, E Jayne; Tucker, Stephen J; Sansom, Mark S P

    2016-12-06

    Ion channels play key roles in cell membranes, and recent advances are yielding an increasing number of structures. However, their functional relevance is often unclear and better tools are required for their functional annotation. In sub-nanometer pores such as ion channels, hydrophobic gating has been shown to promote dewetting to produce a functionally closed (i.e., non-conductive) state. Using the serotonin receptor (5-HT 3 R) structure as an example, we demonstrate the use of molecular dynamics to aid the functional annotation of channel structures via simulation of the behavior of water within the pore. Three increasingly complex simulation analyses are described: water equilibrium densities; single-ion free-energy profiles; and computational electrophysiology. All three approaches correctly predict the 5-HT 3 R crystal structure to represent a functionally closed (i.e., non-conductive) state. We also illustrate the application of water equilibrium density simulations to annotate different conformational states of a glycine receptor. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  16. Transmission spectra changes produced by decreasing compactness of opal-like structures

    Science.gov (United States)

    Andueza, A.; Echeverría, R.; Morales, P.; Sevilla, J.

    2009-01-01

    Artificial opal-like structures based on spheres and colloidal particles have been fabricated in a controlled way, presenting optical band-gap properties in the optical frequency range. Nonclose packed artificial opals have also been fabricated and studied recently. In order to gain a better understanding of these phenomena, we have studied macroscopic models of nonclose packed fcc lattices using glass spheres (ɛ =7) of 8 mm diameter, and measuring in the microwave region (from 10 to 30 GHz). The results have shown a Bragg resonance tunable with filling factor of the opal, and a strong rejected band similar, also present in close packed samples, much less affected by compactness. The relation of this high order band with spheres single layer behavior is also discussed.

  17. Electronic structure and optical absorption spectra of Y2 and Zr2 dimers

    International Nuclear Information System (INIS)

    Gutsev, G.L.

    1989-01-01

    The electron structure, ionization potentials from valent levels and energies of optic transitions of Y 2 and Zr 2 dimers are calculated within the framework of discrete-variatin X α -method. It is shown that the symmetry state 1 Σ g + is the main state of Y 2 and Zr 2 dimers, and the atoms in dimers have high-spin 4d n+1 5s 1 configuration. The chemical binding in Y 2 has the dominating 5s-5s nature which is revealed in a considerable interatomic distance; binding of 4d-electrons brings about a significant decrease in the bond length in Zr 2 dimer. The theoretical spectrum of optical absorption of Zr 2 agrees well with the obtained experimental spectrum of this molecule isolated in the organ matrix

  18. Exact free oscillation spectra, splitting functions and the resolvability of Earth's density structure

    Science.gov (United States)

    Akbarashrafi, F.; Al-Attar, D.; Deuss, A.; Trampert, J.; Valentine, A. P.

    2018-04-01

    Seismic free oscillations, or normal modes, provide a convenient tool to calculate low-frequency seismograms in heterogeneous Earth models. A procedure called `full mode coupling' allows the seismic response of the Earth to be computed. However, in order to be theoretically exact, such calculations must involve an infinite set of modes. In practice, only a finite subset of modes can be used, introducing an error into the seismograms. By systematically increasing the number of modes beyond the highest frequency of interest in the seismograms, we investigate the convergence of full-coupling calculations. As a rule-of-thumb, it is necessary to couple modes 1-2 mHz above the highest frequency of interest, although results depend upon the details of the Earth model. This is significantly higher than has previously been assumed. Observations of free oscillations also provide important constraints on the heterogeneous structure of the Earth. Historically, this inference problem has been addressed by the measurement and interpretation of splitting functions. These can be seen as secondary data extracted from low frequency seismograms. The measurement step necessitates the calculation of synthetic seismograms, but current implementations rely on approximations referred to as self- or group-coupling and do not use fully accurate seismograms. We therefore also investigate whether a systematic error might be present in currently published splitting functions. We find no evidence for any systematic bias, but published uncertainties must be doubled to properly account for the errors due to theoretical omissions and regularization in the measurement process. Correspondingly, uncertainties in results derived from splitting functions must also be increased. As is well known, density has only a weak signal in low-frequency seismograms. Our results suggest this signal is of similar scale to the true uncertainties associated with currently published splitting functions. Thus, it seems

  19. Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

    Directory of Open Access Journals (Sweden)

    Aparecido R. Silva

    2008-05-01

    Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

  20. Molecular structures from density functional calculations with simulated annealing

    International Nuclear Information System (INIS)

    Jones, R.O.

    1991-01-01

    The geometrical structure of any aggregate of atoms is one of its basic properties and, in principle, straightforward to predict. One chooses a structure, determines the total energy E of the system of electrons and ions, and repeats the calculation for all possible geometries. The ground state structure is that with the lowest energy. A quantum mechanical calculation of the exact wave function Ψ would lead to the total energy, but this is practicable only in very small molecules. Furthermore, the number of local minima in the energy surface increases dramatically with increasing molecular size. While traditional ab initio methods have had many impressive successes, the difficulties have meant that they have focused on systems with relatively few local minima, or have used experiments or experience to limit the range of geometries studied. On the other hand, calculations for much larger molecules and extended systems are often forced to use simplifying assumptions about the interatomic forces that limit their predictive capability. The approach described here avoids both of these extremes: Total energies of predictive value are calculated without using semi-empirical force laws, and the problem of multiple minima in the energy surface is addressed. The density functional formalism, with a local density approximation for the exchange-correlation energy, allows one to calculate the total energy for a given geometry in an efficient, if approximate, manner. Calculations for heavier elements are not significantly more difficult than for those in the first row and provide an ideal way to study bonding trends. When coupled with finite-temperature molecular dynamics, this formalism can avoid many of the energetically unfavorable minima in the energy surface. We show here that the method leads to surprising and exciting results. (orig.)

  1. Mathematical analysis of compressive/tensile molecular and nuclear structures

    Science.gov (United States)

    Wang, Dayu

    Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

  2. Using polarized Raman spectroscopy and the pseudospectral method to characterize molecular structure and function

    Science.gov (United States)

    Weisman, Andrew L.

    Electronic structure calculation is an essential approach for determining the structure and function of molecules and is therefore of critical interest to physics, chemistry, and materials science. Of the various algorithms for calculating electronic structure, the pseudospectral method is among the fastest. However, the trade-off for its speed is more up-front programming and testing, and as a result, applications using the pseudospectral method currently lag behind those using other methods. In Part I of this dissertation, we first advance the pseudospectral method by optimizing it for an important application, polarized Raman spectroscopy, which is a well-established tool used to characterize molecular properties. This is an application of particular importance because often the easiest and most economical way to obtain the polarized Raman spectrum of a material is to simulate it; thus, utilization of the pseudospectral method for this purpose will accelerate progress in the determination of molecular properties. We demonstrate that our implementation of Raman spectroscopy using the pseudospectral method results in spectra that are just as accurate as those calculated using the traditional analytic method, and in the process, we derive the most comprehensive formulation to date of polarized Raman intensity formulas, applicable to both crystalline and isotropic systems. Next, we apply our implementation to determine the orientations of crystalline oligothiophenes -- a class of materials important in the field of organic electronics -- achieving excellent agreement with experiment and demonstrating the general utility of polarized Raman spectroscopy for the determination of crystal orientation. In addition, we derive from first-principles a method for using polarized Raman spectra to establish unambiguously whether a uniform region of a material is crystalline or isotropic. Finally, we introduce free, open-source software that allows a user to determine any of a

  3. Structures, Energetics, and IR Spectra of Monohydrated Inorganic Acids: Ab initio and DFT Study.

    Science.gov (United States)

    Kołaski, Maciej; Zakharenko, Aleksey A; Karthikeyan, S; Kim, Kwang S

    2011-10-11

    We carried out extensive calculations of diverse inorganic acids interacting with a single water molecule, through a detailed analysis of many possible conformations. The optimized structures were obtained by using density functional theory (DFT) and the second order Møller-Plesset perturbation theory (MP2). For the most stable conformers, we calculated the interaction energies at the complete basis set (CBS) limit using coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The -OH stretching harmonic and anharmonic frequencies are provided as fingerprints of characteristic conformers. The zero-point energy (ZPE) uncorrected/corrected (ΔEe/ΔE0) interaction energies and the enthalpies/free energies (ΔHr/ΔGr at room temperature and 1 bar) are reported. Various comparisons are made between many diverse inorganic acids (HmXOn where X = B/N/P/Cl/Br/I, m = 1-3, and n = 0-4) as well as other simple inorganic acids. In many cases, we find that the dispersion-driven van der Waals interactions between X in inorganic acid molecules and O in water molecules as well as the X(+)···O(-) electrostatic interactions are important.

  4. Catecholaminergic systems in stress: structural and molecular genetic approaches.

    Science.gov (United States)

    Kvetnansky, Richard; Sabban, Esther L; Palkovits, Miklos

    2009-04-01

    Stressful stimuli evoke complex endocrine, autonomic, and behavioral responses that are extremely variable and specific depending on the type and nature of the stressors. We first provide a short overview of physiology, biochemistry, and molecular genetics of sympatho-adrenomedullary, sympatho-neural, and brain catecholaminergic systems. Important processes of catecholamine biosynthesis, storage, release, secretion, uptake, reuptake, degradation, and transporters in acutely or chronically stressed organisms are described. We emphasize the structural variability of catecholamine systems and the molecular genetics of enzymes involved in biosynthesis and degradation of catecholamines and transporters. Characterization of enzyme gene promoters, transcriptional and posttranscriptional mechanisms, transcription factors, gene expression and protein translation, as well as different phases of stress-activated transcription and quantitative determination of mRNA levels in stressed organisms are discussed. Data from catecholamine enzyme gene knockout mice are shown. Interaction of catecholaminergic systems with other neurotransmitter and hormonal systems are discussed. We describe the effects of homotypic and heterotypic stressors, adaptation and maladaptation of the organism, and the specificity of stressors (physical, emotional, metabolic, etc.) on activation of catecholaminergic systems at all levels from plasma catecholamines to gene expression of catecholamine enzymes. We also discuss cross-adaptation and the effect of novel heterotypic stressors on organisms adapted to long-term monotypic stressors. The extra-adrenal nonneuronal adrenergic system is described. Stress-related central neuronal regulatory circuits and central organization of responses to various stressors are presented with selected examples of regulatory molecular mechanisms. Data summarized here indicate that catecholaminergic systems are activated in different ways following exposure to distinct

  5. Solving structures of protein complexes by molecular replacement with Phaser

    International Nuclear Information System (INIS)

    McCoy, Airlie J.

    2006-01-01

    Four case studies in using maximum-likelihood molecular replacement, as implemented in the program Phaser, to solve structures of protein complexes are described. Molecular replacement (MR) generally becomes more difficult as the number of components in the asymmetric unit requiring separate MR models (i.e. the dimensionality of the search) increases. When the proportion of the total scattering contributed by each search component is small, the signal in the search for each component in isolation is weak or non-existent. Maximum-likelihood MR functions enable complex asymmetric units to be built up from individual components with a ‘tree search with pruning’ approach. This method, as implemented in the automated search procedure of the program Phaser, has been very successful in solving many previously intractable MR problems. However, there are a number of cases in which the automated search procedure of Phaser is suboptimal or encounters difficulties. These include cases where there are a large number of copies of the same component in the asymmetric unit or where the components of the asymmetric unit have greatly varying B factors. Two case studies are presented to illustrate how Phaser can be used to best advantage in the standard ‘automated MR’ mode and two case studies are used to show how to modify the automated search strategy for problematic cases

  6. Effect of processing on carbon molecular sieve structure and performance

    KAUST Repository

    Das, Mita; Perry, John D.; Koros, William J.

    2010-01-01

    Sub-micron sized carbon molecular sieve (CMS) materials were produced via ball milling for subsequent use in hybrid material formation. A detailed analysis of the effects of the milling process in the presence of different milling environments is reported. The milling process apparently alters the molecular scale structure and properties of the carbon material. Three cases: unmilled, air milled and nitrogen milled, were analyzed in this work. The property changes were probed using equilibrium sorption experiments with different gases. Furthermore, WAXD and BET results also showed differences between milling processes. Finally in order to improve the interfacial polymer-sieve region of hybrid membranes, the CMS surface was chemically modified with a linkage unit capable of covalently bonding the polymer to the sieve. A published single-wall carbon nanotube (SWCNTs) modification method was adopted to attach a primary aromatic amine to the surface. Several aspects including rigidity, chemical composition, bulky groups and length were considered in selecting the preferred linkage unit. Fortunately kinetic and equilibrium sorption properties of the modified sieves showed very little difference from unmodified samples, suggesting that the linkage unit is not excessively filling or obstructing access to the pores of the CMSs during the modification process. © 2010 Elsevier Ltd. All rights reserved.

  7. Effect of processing on carbon molecular sieve structure and performance

    KAUST Repository

    Das, Mita

    2010-11-01

    Sub-micron sized carbon molecular sieve (CMS) materials were produced via ball milling for subsequent use in hybrid material formation. A detailed analysis of the effects of the milling process in the presence of different milling environments is reported. The milling process apparently alters the molecular scale structure and properties of the carbon material. Three cases: unmilled, air milled and nitrogen milled, were analyzed in this work. The property changes were probed using equilibrium sorption experiments with different gases. Furthermore, WAXD and BET results also showed differences between milling processes. Finally in order to improve the interfacial polymer-sieve region of hybrid membranes, the CMS surface was chemically modified with a linkage unit capable of covalently bonding the polymer to the sieve. A published single-wall carbon nanotube (SWCNTs) modification method was adopted to attach a primary aromatic amine to the surface. Several aspects including rigidity, chemical composition, bulky groups and length were considered in selecting the preferred linkage unit. Fortunately kinetic and equilibrium sorption properties of the modified sieves showed very little difference from unmodified samples, suggesting that the linkage unit is not excessively filling or obstructing access to the pores of the CMSs during the modification process. © 2010 Elsevier Ltd. All rights reserved.

  8. Electronic structure and molecular dynamics of Na2Li

    Science.gov (United States)

    Malcolm, Nathaniel O. J.; McDouall, Joseph J. W.

    Following the first report (Mile, B., Sillman, P. D., Yacob, A. R. and Howard, J. A., 1996, J. chem. Soc. Dalton Trans , 653) of the EPR spectrum of the mixed alkali-metal trimer Na2Li a detailed study has been made of the electronic structure and structural dynamics of this species. Two isomeric forms have been found: one of the type, Na-Li-Na, of C , symmetry and another, Li-Na-Na, of C symmetry. Also, there are two linear saddle points which correspond to 'inversion' transition structures, and a saddle point of C symmetry which connects the two minima. A molecular dynamics investigation of these species shows that, at the temperature of the reported experiments (170 K), the C minimum is not 'static', but undergoes quite rapid inversion. At higher temperatures the C minimum converts to the C form, but by a mechanism very different from that suggested by minimum energy path considerations. 2 2v s s 2v 2v s

  9. Transmission electron microscopy in molecular structural biology: A historical survey.

    Science.gov (United States)

    Harris, J Robin

    2015-09-01

    In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. Explicit Hilbert-space representations of atomic and molecular photoabsorption spectra: Computational studies of Stieltjes-Tchebycheff functions

    International Nuclear Information System (INIS)

    Hermann, M.R.; Langhoff, P.W.

    1983-01-01

    Explicit Hilbert-space techniques are reported for construction of the discrete and continuum Schroedinger states required in atomic and molecular photoexcitation and/or photoionization studies. These developments extend and clarify previously described moment-theory methods for determinations of photoabsorption cross sections from discrete basis-set calculations to include explicit construction of underlying wave functions. The appropriate Stieltjes-Tchebycheff excitation and ionization functions of nth order are defined as Radau-type eigenstates of an appropriate operator in an n-term Cauchy-Lanczos basis. The energies of these states are the Radau quadrature points of the photoabsorption cross section, and their (reciprocal) norms provide the corresponding quadrature weights. Although finite-order Stieltjes-Tchebycheff functions are L 2 integrable, and do not have asymptotic spatial tails in the continuous spectrum, the Radau quadrature weights nevertheless provide information for normalization in the conventional Dirac delta-function sense. Since one Radau point can be placed anywhere in the spectrum, appropriately normalized convergent approximations to any of the discrete or continuum Schroedinger states are obtained from the development. Connections with matrix partitioning methods are established, demonstrating that nth-order Stieltjes-Tchebycheff functions are optical-potential solutions of the matrix Schroedinger equation in the full Cauchy-Lanczos basis

  11. Coding considerations for standalone molecular dynamics simulations of atomistic structures

    Science.gov (United States)

    Ocaya, R. O.; Terblans, J. J.

    2017-10-01

    The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

  12. On the nodal structure of atomic and molecular Wigner functions

    International Nuclear Information System (INIS)

    Dahl, J.P.; Schmider, H.

    1996-01-01

    In previous work on the phase-space representation of quantum mechanics, we have presented detailed pictures of the electronic one-particle reduced Wigner function for atoms and small molecules. In this communication, we focus upon the nodal structure of the function. On the basis of the simplest systems, we present an expression which relates the oscillatory decay of the Wigner function solely to the dot product of the position and momentum vector, if both arguments are large. We then demonstrate the regular behavior of nodal patterns for the larger systems. For the molecular systems, an argument analogous to the open-quotes bond-oscillatory principleclose quotes for momentum densities links the nuclear framework to an additional oscillatory term in momenta parallel to bonds. It is shown that these are visible in the Wigner function in terms of characteristic nodes

  13. Influence of the molecular structure on hydrolyzability of epoxy resins

    International Nuclear Information System (INIS)

    Pays, M.F.

    1996-01-01

    EDF has decided to use glass reinforced composites for certain pipework in Pressurized Water Reactors (service water, emergency-supplied service water, fine pipe works, etc...) as a replacement for traditional materials. In practice, steel is prone to rapid corrosion in these circuits; introducing composites could prove economically viable if their long term behaviour can be demonstrated. However, composite materials can undergo deterioration in service through hydrolysis of the resin or the fibre-matrix interface. Different resins can be chosen depending on the programmed use. A first study has covered the hydrolyzability of polyester and vinyl ester resins. The present document undertakes the resistance to hydrolysis of epoxy resins, concentrating on those reputed to withstand high temperatures. This research uses model monomer, linking the molecular structure of the materials to their resistance to hydrolysis. (author)

  14. Calculations of optical rotation: Influence of molecular structure

    Directory of Open Access Journals (Sweden)

    Yu Jia

    2012-01-01

    Full Text Available Ab initio Hartree-Fock (HF method and Density Functional Theory (DFT were used to calculate the optical rotation of 26 chiral compounds. The effects of theory and basis sets used for calculation, solvents influence on the geometry and values of calculated optical rotation were all discussed. The polarizable continuum model, included in the calculation, did not improve the accuracy effectively, but it was superior to γs. Optical rotation of five or sixmembered of cyclic compound has been calculated and 17 pyrrolidine or piperidine derivatives which were calculated by HF and DFT methods gave acceptable predictions. The nitrogen atom affects the calculation results dramatically, and it is necessary in the molecular structure in order to get an accurate computation result. Namely, when the nitrogen atom was substituted by oxygen atom in the ring, the calculation result deteriorated.

  15. Hamiltonian flow over saddles for exploring molecular phase space structures

    Science.gov (United States)

    Farantos, Stavros C.

    2018-03-01

    Despite using potential energy surfaces, multivariable functions on molecular configuration space, to comprehend chemical dynamics for decades, the real happenings in molecules occur in phase space, in which the states of a classical dynamical system are completely determined by the coordinates and their conjugate momenta. Theoretical and numerical results are presented, employing alanine dipeptide as a model system, to support the view that geometrical structures in phase space dictate the dynamics of molecules, the fingerprints of which are traced by following the Hamiltonian flow above saddles. By properly selecting initial conditions in alanine dipeptide, we have found internally free rotor trajectories the existence of which can only be justified in a phase space perspective. This article is part of the theme issue `Modern theoretical chemistry'.

  16. Artificial intelligence applied to the automatic analysis of absorption spectra. Objective measurement of the fine structure constant

    Science.gov (United States)

    Bainbridge, Matthew B.; Webb, John K.

    2017-06-01

    A new and automated method is presented for the analysis of high-resolution absorption spectra. Three established numerical methods are unified into one `artificial intelligence' process: a genetic algorithm (Genetic Voigt Profile FIT, gvpfit); non-linear least-squares with parameter constraints (vpfit); and Bayesian model averaging (BMA). The method has broad application but here we apply it specifically to the problem of measuring the fine structure constant at high redshift. For this we need objectivity and reproducibility. gvpfit is also motivated by the importance of obtaining a large statistical sample of measurements of Δα/α. Interactive analyses are both time consuming and complex and automation makes obtaining a large sample feasible. In contrast to previous methodologies, we use BMA to derive results using a large set of models and show that this procedure is more robust than a human picking a single preferred model since BMA avoids the systematic uncertainties associated with model choice. Numerical simulations provide stringent tests of the whole process and we show using both real and simulated spectra that the unified automated fitting procedure out-performs a human interactive analysis. The method should be invaluable in the context of future instrumentation like ESPRESSO on the VLT and indeed future ELTs. We apply the method to the zabs = 1.8389 absorber towards the zem = 2.145 quasar J110325-264515. The derived constraint of Δα/α = 3.3 ± 2.9 × 10-6 is consistent with no variation and also consistent with the tentative spatial variation reported in Webb et al. and King et al.

  17. Computer-assisted structure elucidation from 13C-NMR-Spectra. I. The development of a three-dimensional structure code. II. The development of an isomer generating program

    International Nuclear Information System (INIS)

    Schuetz, V.

    1999-05-01

    The presented thesis consists of two separate programs which both aid the automated structure elucidation in the CSEARCH database system. A successful utilization of a large collection of NMR reference spectra for the prediction of chemical shift values is dependent on a strong correlation between the spectral data and the structural information via unique coding. By now, this was done using the two-dimensional HOSE code, which turned out to be insufficient whenever stereochemical effects other than cis/trans-isomerism contribute to the chemical shift values. Therefore, this new algorithm has been developed to derive the demanded three-dimensional descriptors. The calculation is performed by matching the query structures against pattern molecules taken from a carefully selected library of ring skeletons. No three-dimensional coordinates are necessary, since the algorithm elucidates the descriptors on base of two-dimensional structures having their stereocenters specified using 'up/down' bonds. The descriptors are defined as number of interactions over 3 to 5 bonds, number of cis-substituents over 1 to 2 ringbonds and markers for axial substituents. This approach of deriving descriptors for steric interactions has successfully extended the HOSE coding scheme and has been implemented into a neural network; both methods allow for high-quality prediction of 13 C-NMR chemical shift values. The second algorithm is an isomer generating program named GENERAL, which efficiently supports the structure elucidation process by calculating all mathematically possible structures to a given molecular formula. The resulting list of structures is exhaustive and free of redundancy. Besides the basic input information - like the molecular formula and the specification of structural fragments, constraints can be defined to restrict the number of resulting structures. The most valuable information is provided by state-of-the-art 2D-NMR experiments and can be easily incorporated into

  18. Determining the stereochemical structures of molecular ions by ''Coulomb-explosion'' techniques with fast (MeV) molecular ion beams

    International Nuclear Information System (INIS)

    Gemmell, D.S.

    1980-01-01

    Recent studies on the dissociation of fast (MeV) molecular ion beams in thin foils suggest a novel alternative approach to the determination of molecular ion structures. In this article we review some recent high-resolution studies on the interactions of fast molecular ion beams with solid and gaseous targets and indicate how such studies may be applied to the problem of determining molecular ion structures. The main features of the Coulomb explosion of fast-moving molecular ion projectiles and the manner in which Coulomb-explosion techniques may be applied to the problem (difficult to attack by more conventional means) of determining the stereochemical structures of molecular ions has been described in this paper. Examples have been given of early experiments designed to elicit structure information. The techniques are still in their infancy, and it is to be expected that as both the technology and the analysis are refined, the method will make valuable contributions to the determination of molecular ion structures

  19. Synthesis, crystal structure, and vibrational spectra of the anhydrous lithium dicyanamide Li[N(CN){sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Reckeweg, Olaf [Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301 (United States); Institut fuer Anorganische Chemie, Universitaet Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart (Germany); DiSalvo, Francis J. [Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301 (United States); Schulz, Armin [Max-Planck-Institut fuer Festkoerperforschung, Heisenbergstrasse 1, 70569 Stuttgart (Germany); Blaschkowski, Bjoern; Schleid, Thomas [Institut fuer Anorganische Chemie, Universitaet Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart (Germany); Jagiella, Stefan [Institut fuer Physikalische und Theoretische Chemie, Universitaet Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart (Germany)

    2014-04-15

    Crystals of Li[N(CN){sub 2}] were synthesized from a metathesis reaction of stoichiometric amounts of aqueous solutions of Na[N(CN){sub 2}] and Li{sub 2}[SO{sub 4}] followed by subsequent treatment with ethanol and evaporation of the filtered-off solution at 80 C under normal atmospheric conditions. The single crystals of the title compound are transparent, colorless, and extremly hygroscopic. X-ray structure analysis showed that Li[N(CN){sub 2}] crystallizes in the monoclinic space group P2/c with the cell parameters a = 530.79(8) pm, b = 524.89(9) pm, c = 1149.77(17) pm, β = 101.551(7) , and Z = 4. The crystal structure contains Li{sup +} cations in both tetrahedral and octahedral nitrogen coordination of the boomerang-shaped [N≡C-N-C≡N]{sup -} anions. The vibrational spectra of Li[N(CN){sub 2}] are reported as well, together with ab initio calculations for geometry and harmonic frequencies of the free dicyanamide anion. (Copyright copyright 2014 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  20. A theoretical study of molecular structure, optical properties and bond activation of energetic compound FOX-7 under intense electric fields

    Science.gov (United States)

    Tao, Zhiqiang; Wang, Xin; Wei, Yuan; Lv, Li; Wu, Deyin; Yang, Mingli

    2017-02-01

    Molecular structure, vibrational and electronic absorption spectra, chemical reactivity of energetic compound FOX-7, one of the most widely used explosives, were studied computationally in presence of an electrostatic field of 0.01-0.05 a.u. The Csbnd N bond, which usually triggers the decomposition of FOX-7, is shortened/elongated under a parallel/antiparallel field. The Csbnd N bond activation energy varies with the external electric field, decreasing remarkably with the field strength in regardless of the field direction. This is attributed to two aspects: the bond weakening by the field parallel to the Csbnd N bond and the stabilization effect on the transition-state structure by the field antiparallel to the bond. The variations in the structure and property of FOX-7 under the electric fields were further analyzed with its distributional polarizability, which is dependent on the charge transfer characteristics through the Csbnd N bond.

  1. A generalized modal shock spectra method for spacecraft loads analysis. [internal loads in a spacecraft structure subjected to a dynamic launch environment

    Science.gov (United States)

    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.

  2. Structural and molecular basis of starch viscosity in hexaploid wheat.

    Science.gov (United States)

    Ral, J-P; Cavanagh, C R; Larroque, O; Regina, A; Morell, M K

    2008-06-11

    Wheat starch is considered to have a low paste viscosity relative to other starches. Consequently, wheat starch is not preferred for many applications as compared to other high paste viscosity starches. Increasing the viscosity of wheat starch is expected to increase the functionality of a range of wheat flour-based products in which the texture is an important aspect of consumer acceptance (e.g., pasta, and instant and yellow alkaline noodles). To understand the molecular basis of starch viscosity, we have undertaken a comprehensive structural and rheological analysis of starches from a genetically diverse set of wheat genotypes, which revealed significant variation in starch traits including starch granule protein content, starch-associated lipid content and composition, phosphate content, and the structures of the amylose and amylopectin fractions. Statistical analysis highlighted the association between amylopectin chains of 18-25 glucose residues and starch pasting properties. Principal component analysis also identified an association between monoesterified phosphate and starch pasting properties in wheat despite the low starch-phosphate level in wheat as compared to tuber starches. We also found a strong negative correlation between the phosphate ester content and the starch content in flour. Previously observed associations between internal starch granule fatty acids and the swelling peak time and pasting temperature have been confirmed. This study has highlighted a range of parameters associated with increased starch viscosity that could be used in prebreeding/breeding programs to modify wheat starch pasting properties.

  3. Fast electronic structure methods for strongly correlated molecular systems

    International Nuclear Information System (INIS)

    Head-Gordon, Martin; Beran, Gregory J O; Sodt, Alex; Jung, Yousung

    2005-01-01

    A short review is given of newly developed fast electronic structure methods that are designed to treat molecular systems with strong electron correlations, such as diradicaloid molecules, for which standard electronic structure methods such as density functional theory are inadequate. These new local correlation methods are based on coupled cluster theory within a perfect pairing active space, containing either a linear or quadratic number of pair correlation amplitudes, to yield the perfect pairing (PP) and imperfect pairing (IP) models. This reduces the scaling of the coupled cluster iterations to no worse than cubic, relative to the sixth power dependence of the usual (untruncated) coupled cluster doubles model. A second order perturbation correction, PP(2), to treat the neglected (weaker) correlations is formulated for the PP model. To ensure minimal prefactors, in addition to favorable size-scaling, highly efficient implementations of PP, IP and PP(2) have been completed, using auxiliary basis expansions. This yields speedups of almost an order of magnitude over the best alternatives using 4-center 2-electron integrals. A short discussion of the scope of accessible chemical applications is given

  4. Molecular structure-adsorption study on current textile dyes.

    Science.gov (United States)

    Örücü, E; Tugcu, G; Saçan, M T

    2014-01-01

    This study was performed to investigate the adsorption of a diverse set of textile dyes onto granulated activated carbon (GAC). The adsorption experiments were carried out in a batch system. The Langmuir and Freundlich isotherm models were applied to experimental data and the isotherm constants were calculated for 33 anthraquinone and azo dyes. The adsorption equilibrium data fitted more adequately to the Langmuir isotherm model than the Freundlich isotherm model. Added to a qualitative analysis of experimental results, multiple linear regression (MLR), support vector regression (SVR) and back propagation neural network (BPNN) methods were used to develop quantitative structure-property relationship (QSPR) models with the novel adsorption data. The data were divided randomly into training and test sets. The predictive ability of all models was evaluated using the test set. Descriptors were selected with a genetic algorithm (GA) using QSARINS software. Results related to QSPR models on the adsorption capacity of GAC showed that molecular structure of dyes was represented by ionization potential based on two-dimensional topological distances, chromophoric features and a property filter index. Comparison of the performance of the models demonstrated the superiority of the BPNN over GA-MLR and SVR models.

  5. Molecular structure of tetramethylgermane from gas electron diffraction

    Science.gov (United States)

    Csákvári, Éva; Rozsondai, Béla; Hargittai, István

    1991-05-01

    The molecular structure of Ge(CH 3) 4 has been determined from gas-phase electron diffraction augmented by a normal coordinate analysis. Assuming tetrahedral symmetry for the germanium bond configuration, the following structural parameters are found: rg(GeC) = 1.958 ± 0.004 Å, rg(CH) = 1.111 ± 0.003 Å and ∠(GeCH) = 110.7 ± 0.2° ( R=4.0%). The methyl torsional barrier V 0 is estimated to be 1.3 kJ mol -1 on the basis of an effective angle of torsion 23.0 ± 1.5°, from the staggered form, yielded directly by the analysis. The GeC bond length of Ge(CH 3) 4 is the same, within experimental error, as that of Ge(C 6H 5) 4 and is in agreement with the prediction of a modified Schomaker-Stevenson relationship.

  6. Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

    Science.gov (United States)

    Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

    2012-06-01

    The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

  7. Bonding and structure in dense multi-component molecular mixtures.

    Science.gov (United States)

    Meyer, Edmund R; Ticknor, Christopher; Bethkenhagen, Mandy; Hamel, Sebastien; Redmer, Ronald; Kress, Joel D; Collins, Lee A

    2015-10-28

    We have performed finite-temperature density functional theory molecular dynamics simulations on dense methane, ammonia, and water mixtures (CH4:NH3:H2O) for various compositions and temperatures (2000 K ≤ T ≤ 10,000 K) that span a set of possible conditions in the interiors of ice-giant exoplanets. The equation-of-state, pair distribution functions, and bond autocorrelation functions (BACF) were used to probe the structure and dynamics of these complex fluids. In particular, an improvement to the choice of the cutoff in the BACF was developed that allowed analysis refinements for density and temperature effects. We note the relative changes in the nature of these systems engendered by variations in the concentration ratios. A basic tenet emerges from all these comparisons that varying the relative amounts of the three heavy components (C,N,O) can effect considerable changes in the nature of the fluid and may in turn have ramifications for the structure and composition of various planetary layers.

  8. Molecular clouds in the North American and Pelican Nebulae: structures

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shaobo; Xu, Ye; Yang, Ji, E-mail: shbzhang@pmo.ac.cn [Purple Mountain Observatory, and Key Laboratory for Radio Astronomy, Chinese Academy of Sciences, Nanjing 210008 (China)

    2014-03-01

    We present observations of a 4.25 deg{sup 2} area toward the North American and Pelican Nebulae in the J = 1-0 transitions of {sup 12}CO, {sup 13}CO, and C{sup 18}O. Three molecules show different emission areas with their own distinct structures. These different density tracers reveal several dense clouds with a surface density of over 500 M {sub ☉} pc{sup –2} and a mean H{sub 2} column density of 5.8, 3.4, and 11.9 × 10{sup 21} cm{sup –2} for {sup 12}CO, {sup 13}CO, and C{sup 18}O, respectively. We obtain a total mass of 5.4 × 10{sup 4} M {sub ☉} ({sup 12}CO), 2.0 × 10{sup 4} M {sub ☉} ({sup 13}CO), and 6.1 × 10{sup 3} M {sub ☉} (C{sup 18}O) in the complex. The distribution of excitation temperature shows two phases of gas: cold gas (∼10 K) spreads across the whole cloud; warm gas (>20 K) outlines the edge of the cloud heated by the W80 H II region. The kinetic structure of the cloud indicates an expanding shell surrounding the ionized gas produced by the H II region. There are six discernible regions in the cloud: the Gulf of Mexico, Caribbean Islands and Sea, and Pelican's Beak, Hat, and Neck. The areas of {sup 13}CO emission range within 2-10 pc{sup 2} with mass of (1-5) × 10{sup 3} M {sub ☉} and line width of a few km s{sup –1}. The different line properties and signs of star-forming activity indicate they are in different evolutionary stages. Four filamentary structures with complicated velocity features are detected along the dark lane in LDN 935. Furthermore, a total of 611 molecular clumps within the {sup 13}CO tracing cloud are identified using the ClumpFind algorithm. The properties of the clumps suggest that most of the clumps are gravitationally bound and at an early stage of evolution with cold and dense molecular gas.

  9. The au-scale structure in diffuse molecular gas towards ζ Persei

    Science.gov (United States)

    Boissé, P.; Federman, S. R.; Pineau des Forêts, G.; Ritchey, A. M.

    2013-11-01

    Context. Spatial structure in molecular material has a strong impact on its physical and chemical evolution and is still poorly known, especially on very small scales. Aims: To better characterize the small-scale structure in diffuse molecular gas and in particular to investigate the CH+ production mechanism, we study the spatial distribution of CH+, CH, and CN towards the bright star ζ Per on scales in the range 1-20 AU. Methods: We use ζ Per's proper motion and the implied drift of the line of sight through the foreground gas at a rate of about 2 AU yr-1 to probe absorption line variations between adjacent lines of sight. The good S/N, high or intermediate resolution spectra of ζ Per, obtained in the interval 2003-2011, allow us to search for low column-density and line width variations for CH+, CH, and CN. Results: CH and CN lines appear remarkably stable in time, implying an upper limit δN/N ≤ 6% for CH and CN (3σ limit). The weak CH+λ4232 line shows a possible increase of 11% during the interval 2004-2007, which appears to be correlated with a comparable increase in the CH+ velocity dispersion over the same period. Conclusions: The excellent stability of CH and CN lines implies that these species are distributed uniformly to good accuracy within the cloud. The small size implied for the regions associated with the CH+ excess is consistent with scenarios in which this species is produced in very small (a few AU) localized active regions, possibly weakly magnetized shocks or turbulent vortices. Based on observations made at McDonald Observatory (USA) and Observatoire de Haute-Provence (France).

  10. SFG analysis of the molecular structures at the surfaces and buried interfaces of PECVD ultralow-dielectric constant pSiCOH

    Science.gov (United States)

    Zhang, Xiaoxian; Myers, John N.; Huang, Huai; Shobha, Hosadurga; Chen, Zhan; Grill, Alfred

    2016-02-01

    PECVD deposited porous SiCOH with ultralow dielectric constant has been successfully integrated as the insulator in advanced interconnects to decrease the RC delay. The effects of NH3 plasma treatment and the effectiveness of the dielectric repair on molecular structures at the surface and buried interface of a pSiCOH film deposited on top of a SiCNH film on a Si wafer were fully characterized using sum frequency generation vibrational spectroscopy (SFG), supplemented by X-ray photoelectron spectroscopy. After exposure to NH3 plasma for 18 s, about 40% of the methyl groups were removed from the pSiCOH surface, and the average orientation of surface methyl groups tilted more towards the surface. The repair method used here effectively repaired the molecular structures at the pSiCOH surface but did not totally recover the entire plasma-damaged layer. Additionally, simulated SFG spectra with various average orientations of methyl groups at the SiCNH/pSiCOH buried interface were compared with the experimental SFG spectra collected using three different laser input angles to determine the molecular structural information at the SiCNH/pSiCOH buried interface after NH3 plasma treatment and repair. The molecular structures including the coverage and the average orientation of methyl groups at the buried interface were found to be unchanged by NH3 plasma treatment and repair.

  11. Ab initio study of structural and mechanical property of solid molecular hydrogens

    Science.gov (United States)

    Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

    2015-06-01

    Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

  12. Q-mode curve resolution of UV-vis spectra for structural transformation studies of anthocyanins in acidic solutions

    International Nuclear Information System (INIS)

    Marco, Paulo Henrique; Scarminio, Ieda Spacino

    2007-01-01

    Chemometric analysis of ultraviolet-visible (UV-vis) spectra for pH values 1.0, 3.3, 5.3, and 6.9 was used to investigate the kinetics and the structural transformations of anthocyanins in extracts of calyces of hibiscus flowers of the Hibiscus acetosella Welw. ex Finicius for the first time. Six different species were detected: the quinoidal base (A), the flavylium cation (AH + ), the pseudobase or carbinol pseudobase (B), cis-chalcone (C C ), trans-chalcone (C t ), and ionized cis-chalcone (C C - ). Four equilibrium constant values were calculated using relative concentrations, hydration, pK h =2.60+/-0.01, tautomeric, K T =0.14+/-0.01, acid-base, pK a =4.24+/-0.04, and ionization of the cis-chalcone, pK C C =8.74+/-1.5x10 -2 . The calculated protonation rate of the tautomers is K H + =0.08+/-7.6x10 -3 . These constants are in excellent agreement with those measured previously in salt form. From a kinetic viewpoint, the situation encountered is interesting since the reported investigation is limited to visible light absorption in acid medium. These models have not been reported in the literature

  13. Q-mode curve resolution of UV-vis spectra for structural transformation studies of anthocyanins in acidic solutions

    Energy Technology Data Exchange (ETDEWEB)

    Marco, Paulo Henrique [Laboratorio de Quimiometria em Ciencias Naturais, Departamento de Quimica, Universidade Estadual de Londrina, Caixa Postal 6001, CEP 86051-970 Londrina, Parana (Brazil); Scarminio, Ieda Spacino [Laboratorio de Quimiometria em Ciencias Naturais, Departamento de Quimica, Universidade Estadual de Londrina, Caixa Postal 6001, CEP 86051-970 Londrina, Parana (Brazil)]. E-mail: ieda@qui.uel.br

    2007-01-30

    Chemometric analysis of ultraviolet-visible (UV-vis) spectra for pH values 1.0, 3.3, 5.3, and 6.9 was used to investigate the kinetics and the structural transformations of anthocyanins in extracts of calyces of hibiscus flowers of the Hibiscus acetosella Welw. ex Finicius for the first time. Six different species were detected: the quinoidal base (A), the flavylium cation (AH{sup +}), the pseudobase or carbinol pseudobase (B), cis-chalcone (C{sub C}), trans-chalcone (C{sub t}), and ionized cis-chalcone (C{sub C}{sup -}). Four equilibrium constant values were calculated using relative concentrations, hydration, pK{sub h}=2.60+/-0.01, tautomeric, K{sub T}=0.14+/-0.01, acid-base, pK{sub a}=4.24+/-0.04, and ionization of the cis-chalcone, pK{sub C{sub C}}=8.74+/-1.5x10{sup -2}. The calculated protonation rate of the tautomers is K{sub H{sup +}}=0.08+/-7.6x10{sup -3}. These constants are in excellent agreement with those measured previously in salt form. From a kinetic viewpoint, the situation encountered is interesting since the reported investigation is limited to visible light absorption in acid medium. These models have not been reported in the literature.

  14. Light-operated machines based on threaded molecular structures.

    Science.gov (United States)

    Credi, Alberto; Silvi, Serena; Venturi, Margherita

    2014-01-01

    Rotaxanes and related species represent the most common implementation of the concept of artificial molecular machines, because the supramolecular nature of the interactions between the components and their interlocked architecture allow a precise control on the position and movement of the molecular units. The use of light to power artificial molecular machines is particularly valuable because it can play the dual role of "writing" and "reading" the system. Moreover, light-driven machines can operate without accumulation of waste products, and photons are the ideal inputs to enable autonomous operation mechanisms. In appropriately designed molecular machines, light can be used to control not only the stability of the system, which affects the relative position of the molecular components but also the kinetics of the mechanical processes, thereby enabling control on the direction of the movements. This step forward is necessary in order to make a leap from molecular machines to molecular motors.

  15. BETA SPECTRA. I. Negatrons spectra

    International Nuclear Information System (INIS)

    Grau Malonda, A.; Garcia-Torano, E.

    1978-01-01

    Using the Fermi theory of beta decay, the beta spectra for 62 negatrons emitters have been computed introducing a correction factor for unique forbidden transitions. These spectra are plotted vs. energy, once normal i sed, and tabulated with the related Fermi functions. The average and median energies are calculated. (Author)

  16. Rosetta Structure Prediction as a Tool for Solving Difficult Molecular Replacement Problems.

    Science.gov (United States)

    DiMaio, Frank

    2017-01-01

    Molecular replacement (MR), a method for solving the crystallographic phase problem using phases derived from a model of the target structure, has proven extremely valuable, accounting for the vast majority of structures solved by X-ray crystallography. However, when the resolution of data is low, or the starting model is very dissimilar to the target protein, solving structures via molecular replacement may be very challenging. In recent years, protein structure prediction methodology has emerged as a powerful tool in model building and model refinement for difficult molecular replacement problems. This chapter describes some of the tools available in Rosetta for model building and model refinement specifically geared toward difficult molecular replacement cases.

  17. A novel tridentate Schiff base dioxo-molybdenum(VI) complex: synthesis, experimental and theoretical studies on its crystal structure, FTIR, UV-visible, ¹H NMR and ¹³C NMR spectra.

    Science.gov (United States)

    Saheb, Vahid; Sheikhshoaie, Iran; Stoeckli-Evans, Helen

    2012-09-01

    A new dioxo-molybdenum(VI) complex [MoO(2)(L)(H(2)O)] has been synthesized, using 5-methoxy 2-[(2-hydroxypropylimino)methyl]phenol as tridentate ONO donor Schiff base ligand (H(2)L) and MoO(2)(acac)(2). The yellow crystals of the compound are used for single-crystal X-ray analysis and measuring Fourier Transform Infrared (FTIR), UV-visible, (1)H NMR and (13)C NMR spectra. Electronic structure calculations at the B3LYP and PW91PW91 levels of theory are performed to optimize the molecular geometry and to calculate the UV-visible, FTIR, (1)H NMR and (13)C NMR spectra of the compound. Vibrational assignments and analysis of the fundamental modes of the compound are performed. Time-dependent density functional theory (TDDFT) method is used to calculate the electronic transitions of the complex. All theoretical methods can well reproduce the structure of the compound. The (1)H NMR shielding tensors computed at the B3LYP/DGDZVP level of theory is in agreement with experimental (1)H NMR spectra. However, the (13)C NMR shielding tensors computed at the B3LYP level, employing a combined basis set of DGDZVP for Mo and 6-31+G(2df,p) for other atoms, are in better agreement with experimental (13)C NMR spectra. The electronic transitions calculated at the B3LYP/DGDZVP level by using TD-DFT method is in accordance with the observed UV-visible spectrum of the compound. Copyright © 2012 Elsevier B.V. All rights reserved.

  18. Molecular structure of human aortic valve by μSR- FTIR microscopy

    Science.gov (United States)

    Borkowska, Anna M.; Nowakowski, Michał; Lis, Grzegorz J.; Wehbe, Katia; Cinque, Gianfelice; Kwiatek, Wojciech M.

    2017-11-01

    Aortic valve is a part of the heart most frequently affected by pathological processes in humans what constitute a very serious health problem. Therefore, studies of morphology and molecular microstructure of the AV are needed. μSR- FTIR spectroscopy and microscopy represent unique tools to study chemical composition of the tissue and to identify spectroscopic markers characteristic for structural and functional features. Normal AV reveals a multi-layered structure and the compositional and structural changes within particular layers may trigger degenerative processes within the valve. Thus, deep insight into the structure of the valve to understand pathological processes occurring in AV is needed. In order to identify differences between three layers of human AV, tissue sections of macroscopically normal AV were studied using μSR- FTIR spectroscopy in combination with histological and histochemical stainings. Tissue sections deposited onto CaF2 substrates were mapped and representative set of IR spectra collected from fibrosa, spongiosa and ventricularis were analysed by Principal Component Analysis (PCA) in the spectral range between 1850-1000 cm-1 and 3050-2750 cm-1. PCA revealed a layered molecular structure of the valve and it was possible to identify IR bands associated to different tissue parts. Spongiosa layer was well differentiated from other two layers mainly based on IR bands characteristic for the distribution of glycosaminoglycans (GAGs) in the tissue - like 1170 cm-1 (υas(C-O-S)) and 1380 cm-1 (acetyl amino group). Additionally, it was distinguished from fibrosa and ventricularis based on 1085 cm-1 and 1240 cm-1 bands characteristic for GAGs and for carbohydrates- ν(C-O) and ν(C-O-C) respectively and nucleic acids -νsym(PO2-) and νasym(PO2-) respectively, which were less specific for this layer. The use of μSR- FTIR spectroscopy demonstrated co-localization of GAGs and lipids in spongiosa layer what may indicate their contribution in the very

  19. Local hydrated structure of an Fe2+/Fe3+ aqueous solution: an investigation using a combination of molecular dynamics and X-ray absorption fine structure methods

    International Nuclear Information System (INIS)

    Ye Qing; Zhou Jing; Zhao Haifeng; Chen Xing; Chu Wangsheng; Zheng Xusheng; Marcelli, Augusto; Wu Ziyu

    2013-01-01

    The hydrated shell of both Fe 2+ and Fe 3+ aqueous solutions are investigated by using the molecular dynamics (MD) and X-ray absorption structure (XAS) methods. The MD simulations show that the first hydrated shells of both Fe 2+ and Fe 3+ are characterized by a regular octahedron with an Fe-O distance of 2.08Å for Fe 2+ and 1.96Å for Fe 3+ , and rule out the occurrence of a Jahn-Teller distortion in the hydrated shell of an Fe 2+ aqueous solution. The corresponding X-ray absorption near edge fine structure (XANES) calculation successfully reproduces all features in the XANES spectra in Fe 2+ and Fe 3+ aqueous solution. A feature that is located at energy 1 eV higher than the white line (WL) in an Fe 3+ aqueous solution may be assigned to the contribution of the charge transfer. (authors)

  20. Molecular structures of fructans from Agave tequilana Weber var. azul.

    Science.gov (United States)

    Lopez, Mercedes G; Mancilla-Margalli, Norma A; Mendoza-Diaz, Guillermo

    2003-12-31

    Agave plants utilize crassulacean acid metabolism (CAM) for CO(2) fixation. Fructans are the principal photosynthetic products generated by agave plants. These carbohydrates are fructose-bound polymers frequently with a single glucose moiety. Agave tequilana Weber var. azul is an economically important CAM species not only because it is the sole plant allowed for tequila production but because it is a potential source of prebiotics. Because of the large amounts of carbohydrates in A. tequilana, in this study the molecular structures of its fructans were determined by fructan derivatization for linkage analysis coupled with gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS). Fructans were extracted from 8-year-old A. tequilana plants. The linkage types present in fructans from A. tequilana were determined by permethylation followed by reductive cleavage, acetylation, and finally GC-MS analysis. Analysis of the degree of polymerization (DP) estimated by (1)H NMR integration and (13)C NMR and confirmed by MALDI-TOF-MS showed a wide DP ranging from 3 to 29 units. All of the analyses performed demonstrated that fructans from A. tequilana consist of a complex mixture of fructooligosaccharides containing principally beta(2 --> 1) linkages, but also beta(2 --> 6) and branch moieties were observed. Finally, it can be stated that fructans from A. tequilana Weber var. azul are not an inulin type as previously thought.