The dependence of thymine and thymidine Raman spectra on solvent

2004 ◽  
Vol 82 (6) ◽  
pp. 1092-1101 ◽  
Author(s):  
L Beyere ◽  
P Arboleda ◽  
V Monga ◽  
G R Loppnow
Keyword(s):  
Raman Spectroscopy ◽  
Hydrogen Bonding ◽  
Raman Spectra ◽  
Vibrational Modes ◽  
Frequency Shifts ◽  
Hydrogen Bonding Interactions ◽  
Lone Pairs ◽  
Vibrational Bands ◽  
Donor Numbers ◽  
Solvent Molecules

Recent work has focused on developing Raman spectroscopy as a noninvasive probe of DNA interactions with solvents, intercalants, proteins, and other ligands. Here, we report the Raman spectra of thymine in eight solvents and thymidine in nine solvents obtained with visible excitation. Raman spectra under acidic, neutral, and basic conditions were also obtained of both thymine and thymidine. Changes in both the frequencies and intensities of several of the vibrational bands in the 800–1800 cm–1 region are observed. No evidence of deprotonation in the different solvents is observed for either thymine or thymidine. Correlations of the observed frequency shifts of specific vibrational modes with characteristic properties of the solvent for both thymine and thymidine show a significant correlation with acceptor and donor numbers, measures of the hydrogen-bonding ability of the solvent, in both thymine and thymidine. These results are interpreted in terms of hydrogen-bonding interactions between the N-H protons of the thymine base and lone pairs of electrons on the solvent molecules and between the solvent hydrogens and lone pairs on C=O sites. The solvent-dependent intensity in vibrational bands of thymine between 1500 and 1800 cm–1 indicates a strong interaction between thymine and solvent at the C=O and N-H sites that leads to separation of the C=O stretches from the C=C stretch. The intensity variations with solvent were much smaller for thymidine than for thymine, perhaps as a result of replacing the N1 proton by the sugar. These results suggest that Raman spectroscopy is uniquely sensitive to specific interactions of thymine and thymidine with their environment.Key words: Raman spectroscopy, thymine, thymidine, solvent effects, hydrogen bonding.

Identification of Vibrational Modes in BaSi2 Epitaxial Films by Infrared and Raman Spectroscopy

2018 ◽  
Vol 386 ◽  
pp. 43-47 ◽  
Author(s):  
Hirofumi Hoshida ◽  
Naoki Murakoso ◽  
Takashi Suemasu ◽  
Yoshikazu Terai
Keyword(s):  
Raman Spectroscopy ◽  
Raman Spectra ◽  
Epitaxial Films ◽  
Ir Absorption ◽  
Vibrational Modes ◽  
Depolarization Ratio ◽  
Phonon Line ◽  
Infrared And Raman Spectroscopy ◽  
Raman Intensities ◽  
Polarized Raman

Infrared (IR) absorption and polarized Raman spectra were measured in BaSi2 epitaxial films to investigate the vibrational modes and the symmetry of Si4 cluster in BaSi2. By an analysis based on Raman and/or IR activity in the spectra, the symmetry of Si4 cluster was determined as Th-symmetry and the observed Raman lines and IR peaks were assigned to Ag, Eg, Fg, and Fu, respectively. In the three Raman lines of Fg-mode, one LO phonon line and two TO phonon lines were classified by the depolarization ratio of polarized Raman intensities.

scholarly journals Infrared spectroscopic study of hydrogen bonding topologies in the smallest ice cube

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Gang Li ◽  
Yang-Yang Zhang ◽  
Qinming Li ◽  
Chong Wang ◽  
Yong Yu ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Vacuum Ultraviolet ◽  
Structural Information ◽  
Distinct Species ◽  
Structural Motif ◽  
Infrared Spectroscopic Study ◽  
Hydrogen Bonding Interactions ◽  
Ice Cube ◽  
Vibrational Bands ◽  
Metastable Forms

Abstract The water octamer with its cubic structure consisting of six four-membered rings presents an excellent cluster system for unraveling the cooperative interactions driven by subtle changes in the hydrogen-bonding topology. Despite prediction of many distinct structures, it has not been possible to extract the structural information encoded in their vibrational spectra because this requires size-selectivity of the neutral clusters with sufficient resolution to identify the contributions of the different isomeric forms. Here we report the size-specific infrared spectra of the isolated cold, neutral water octamer using a scheme based on threshold photoionization using a tunable vacuum ultraviolet free electron laser. A plethora of sharp vibrational bands features are observed. Theoretical analysis of these patterns reveals the coexistence of five cubic isomers, including two with chirality. The relative energies of these structures are found to reflect topology-dependent, delocalized multi-center hydrogen-bonding interactions. These results demonstrate that even with a common structural motif, the degree of cooperativity among the hydrogen-bonding network creates a hierarchy of distinct species. The implications of these results on possible metastable forms of ice are speculated.

Raman Spectra of Human Dental Calculus

1993 ◽  
Vol 72 (12) ◽  
pp. 1609-1613 ◽  
Author(s):  
H. Tsuda ◽  
J. Arends
Keyword(s):  
Raman Spectroscopy ◽  
Raman Spectra ◽  
Octacalcium Phosphate ◽  
Spot Size ◽  
Spectral Features ◽  
Dental Calculus ◽  
Micro Raman Spectroscopy ◽  
Vibrational Bands ◽  
First Time ◽  
Mineral Constituents

Raman spectra of human dental calculus have been observed for the first time by use of micro-Raman spectroscopy. The spectral features of calculus were influenced easily by heating caused by laser irradiation. Therefore, the measurements were carried out at relatively low power (5 mW, 1-μm spot size). The spectra could be characterized as phosphate vibrational bands due to the v1, v2, v 3, and v4 modes. The overall spectral features did not resemble those of pure minerals such as brushite, octacalcium phosphate, and hydroxyapatite. There were spectral differences among mixed calculus particles obtained from 18 adults, probably due to variations in local mineral composition and differences among patients. However, the averaged spectral features did not vary significantly with formation period from 1 to 6 months. Freshly removed and stored (5-11 months) calculus also gave comparable Raman spectra. Measurements on a fractured sample indicated that Raman spectra at saliva and dentin interfaces are nearly identical, and major mineral constituents may not vary significantly along the growth axis of calculus.

scholarly journals Xanthine oxidase–product complexes probe the importance of substrate/product orientation along the reaction coordinate

2017 ◽  
Vol 46 (39) ◽  
pp. 13242-13250 ◽  
Author(s):  
Jing Yang ◽  
Chao Dong ◽  
Martin L. Kirk
Keyword(s):  
Raman Spectroscopy ◽  
Hydrogen Bonding ◽  
Xanthine Oxidase ◽  
Resonance Raman Spectroscopy ◽  
Resonance Raman ◽  
Reaction Coordinate ◽  
Substrate Orientation ◽  
Hydrogen Bonding Interactions

Resonance Raman spectroscopy has been used to probe substrate orientation and hydrogen bonding interactions in a xanthine oxidase catalytic intermediate.

scholarly journals (η6-Benzene)(carbonato-κ2O,O′)[dicyclohexyl(naphthalen-1-ylmethyl)phosphane-κP]ruthenium(II) chloroform trisolvate

2014 ◽  
Vol 70 (7) ◽  
pp. m272-m273
Author(s):  
Saravanan Gowrisankar ◽  
Helfried Neumann ◽  
Anke Spannenberg ◽  
Matthias Beller
Keyword(s):  
Hydrogen Bonding ◽  
Metal Complex ◽  
Room Temperature ◽  
Crystal Packing ◽  
The Other ◽  
Asymmetric Unit ◽  
Carbonate Group ◽  
Acta Cryst ◽  
Hydrogen Bonding Interactions ◽  
Solvent Molecules

The title compound, [Ru(CO3)(η6-C6H6){(C6H11)2P(CH2C10H7)}]·3CHCl3, was synthesized by carbonation of [RuCl2(η6-C6H6){(C6H11)2P(CH2C10H7)}] with NaHCO3in methanol at room temperature. The RuIIatom is surrounded by a benzene ligand, a chelating carbonate group and a phosphane ligand in a piano-stool configuration. The crystal packing is consolidated by C—H...O and C—H...Cl hydrogen-bonding interactions between adjacent metal complexes and between the complexes and the solvent molecules. The asymmetric unit contains one metal complex and three chloroform solvent molecules of which only one was modelled. The estimated diffraction contributions of the other two strongly disordered chloroform solvent molecules were substracted from the observed diffraction data using the SQUEEZE procedure inPLATON[Spek (2009).Acta Cryst.D65, 148–155].

The double-stranded ladder-like structure of poly[[bis(μ2-acetato-κ2O:O′)bis(acetato-κO)bis(μ-4,4′-bipyridine-κ2N:N′)dicopper(II)] 4-nitrophenol disolvate tetrahydrate]

2013 ◽  
Vol 69 (10) ◽  
pp. 1100-1103
Author(s):  
Sizwe J. Zamisa ◽  
Patrick Ndungu ◽  
Bernard Omondi
Keyword(s):  
Hydrogen Bonding ◽  
Coordination Polymer ◽  
Title Compound ◽  
Basal Plane ◽  
Copper Acetate ◽  
Water Solvent ◽  
Hydrogen Bonding Interactions ◽  
Complex Forms ◽  
Solvent Molecules ◽  
Unit Cell Length

The reaction of 4,4′-bipyridine with copper acetate in the presence of 4-nitrophenol led to the formation of the title compound, {[Cu(CH3COO)2(C10H8N2)]·C6H5NO3·2H2O}n. The complex forms a double-stranded ladder-like coordination polymer extending along thebaxis. The double-stranded polymers are separated by 4-nitrophenol and water solvent molecules. The two CuIIcentres of the centrosymmetric Cu2O2ladder rungs have square-pyramidal coordination environments, which are formed by two acetate O atoms and two 4,4′-bipyridine N atoms in the basal plane and another acetate O atom at the apex. The ladder-like double strands are separated from each other by one unit-cell length along thecaxis, and are connected by the water and 4-nitrophenol molecules through a series of O—H...O and C—H...O hydrogen-bonding interactions and two unique intermolecular π–π interactions.

scholarly journals Di-μ-oxido-bis({2,2′-[ethane-1,2-diylbis(nitrilomethanylylidene)]diphenolato}titanium(IV)) chloroform disolvate

2013 ◽  
Vol 69 (11) ◽  
pp. m626-m627 ◽  
Author(s):  
Kirill V. Zaitsev ◽  
Sergey S. Karlov ◽  
Galina S. Zaitseva ◽  
Elmira Kh. Lermontova ◽  
Andrei V. Churakov
Keyword(s):  
Hydrogen Bonding ◽  
Dihedral Angle ◽  
Title Compound ◽  
Crystal Packing ◽  
Complex Molecules ◽  
Coordination Environment ◽  
Hydrogen Bonding Interactions ◽  
Distorted Octahedral ◽  
Solvent Molecules

In the title compound, [Ti2(C16H14N2O2)2O2]·2CHCl3, the TiIVatom in the centrosymmetric complex has a distorted octahedral N2O4coordination environment and is linkedviatwo μ2-oxido bridges into a dinuclear centrosymmetric complex, with a Ti...Ti separation of 2.7794 (8) Å. In the salen (N,N′-ethylenebis(salicylimine)) ligand, the two salicylimine units make a dihedral angle of 45.31 (5)°. The complex molecules are stacked parallel to [100], forming channels in which the solvent chloroform molecules are located. C—H...O hydrogen-bonding interactions between the complex molecules and the solvent molecules consolidate the crystal packing.

scholarly journals Crystal structure of bis(2-{[(pyridin-2-yl)methylidene]amino}benzoato-κ3N,N′,O)cobalt(II)N,N-dimethylformamide sesquisolvate

2014 ◽  
Vol 70 (10) ◽  
pp. 164-166 ◽  
Author(s):  
Elena A. Buvaylo ◽  
Vladimir N. Kokozay ◽  
Olga Yu. Vassilyeva ◽  
Brian W. Skelton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Schiff Base ◽  
Coordination Sphere ◽  
Anthranilic Acid ◽  
Crystal Packing ◽  
Schiff Base Ligands ◽  
Complex Molecules ◽  
Hydrogen Bonding Interactions ◽  
Solvent Molecules

The title compound, [Co(C13H9N2O2)2]·1.5C3H7NO, is formed as a neutral CoIIcomplex with dimethylformamide (DMF) solvent molecules. The CoIIatom has a distorted O2N4octahedral coordination sphere defined by two tridentate anionic Schiff base ligands with the O atoms beingcis. The coordination sphere around the CoIIatom is geometrically different from that reported for the co-crystal [Co(C13H9N2O2)2]·AA·H2O (AA is anthranilic acid). One of the DMF solvent molecules was modelled as being disordered about a crystallographic inversion centre with half-occupancy. The crystal structure is made up from alternating layers of complex molecules and DMF molecules parallel to (010). C—H...O hydrogen-bonding interactions between the complex molecules and the solvent molecules consolidate the crystal packing.

Begleitbanden der Null-Phononenlinien des Phosphoreszenzüberganges dotierter Cr3+: Alha6J3-Einkristalle. Teil II. Gitterschwingungen in Alha6J3 / The Sidebands of the zero Phenon band of the Phosphorescence Transition in Cr3+ : Alha6J3 Single Crystals. 11. Vibrational Lattices in Alha6J3

1974 ◽  
Vol 29 (2) ◽  
pp. 219-223
Author(s):  
W. Krasser ◽  
E. Koglin ◽  
G. Wolff ◽  
H. W. Nürnberg
Keyword(s):  
Scattered Light ◽  
Correlation Method ◽  
Irreducible Representations ◽  
Site Symmetry ◽  
Vibrational Modes ◽  
Optical Phonons ◽  
Small Frequency ◽  
Frequency Shifts ◽  
Light Waves ◽  
Vibrational Bands

The optical phonons of an Al(ha)6J3 single crystal are measured in dependence of the polarisation of the incident and scattered light waves at K ≈ 0. The phonons are assigned to the irreducible representations according to the correlation method. At low wavenumbers, two intensive bands are found, which are assigned to vibrational modes of the aluminium and iodine atoms. The iodine atoms are classified according to irreducible representations of the site symmetries Ci and C2. The Raman spectrum suggests definitely the site symmetry C2. The phonons of the urea molecules agree with the phonons of a pure urea crystal except for small frequency shifts. Besides there are measured some vibrational bands in the range of 200 -450 cm-1, which result from vibrational modes caused by the coordinative bonding of the urea molecules via their oxygen atoms to the aluminium ions.

scholarly journals Crystal structure of μ-fluorido-bis{(η4-cyclooctadiene)[hexafluoridoantimonato(V)]platinum(II)} hexafluoridoantimonate(V) hydrogen fluoride 0.75-solvate

2016 ◽  
Vol 72 (1) ◽  
pp. 14-16
Author(s):  
Konrad Seppelt ◽  
Roland Friedemann
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Fluoride ◽  
Bond Angle ◽  
Complex Cation ◽  
Three Dimensional ◽  
The Third ◽  
Hydrogen Bonding Interactions ◽  
Square Planar ◽  
Solvent Molecules

In the complex cation of the binuclear solvated title salt, [Pt2F(SbF6)2(C8H12)2]SbF6·0.75HF, an F atom bridges the two platinum(II) atoms with a bond angle of 123.3 (2)°. The corresponding Pt—F bond lengths are in the range of other fluorine-bridged binuclear platinum(II) complexes. Two of the three SbF6−anions each coordinate with one F atom to one platinum(II) atom. Including the η4-bound cyclooctadiene (COD) ligands, the overall coordination sphere of each platinum(II) atom is square-planar. The third SbF6−anion is not bound to the complex. Hydrogen fluoride is present in the crystal structure as a solvent disordered over three positions, each with an occupancy of 0.25. F...F distances of 2.5512 (7), 2.6076 (8) and 3.2215 (10) Å to surrounding SbF6−anions are indicative of F—H...F hydrogen-bonding interactions although no H atoms could be localized for the disordered solvent molecules. The resulting hydrogen-bonded network is three-dimensional.

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