Laser-raman spectra of d-fructose in aqueous solution

Laser-Raman spectra of d-fructose in water at different concentrations were recorded, and assignments of the frequencies were proposed, based on earlier work on the Raman spectra of other sugars, and determination by other techniques of the composition of aqueous solutions of d-fructose as regards different isomers. It was found that the frequencies of vibration of the furanoid are higher than those of the pyranoid ring. The proportions of the furanoses and pyranoses, found from the ratio of the Raman intensities for the same modes of vibration, were similar to those found by other techniques. Shifts of intensities and frequencies were observed in the region of OH and CH bands, and were assigned to probable association between molecules of d-fructose and water.     

F.T.-I.R. and laser-raman spectra of d-ribose and 2-deoxy-d-erythro-pentose (“2-deoxy-d-ribose”)

Laser-Raman spectra of d-ribose and 2-deoxy-d-erythro-pentose in aqueous solution are reported. F.t.-i.r. and Raman spectra have been obtained for crystals of these sugars. Assignments of the Raman bands observed in solution are proposed. The spectral differences between the two sugars are discussed in terms of the structural difference. The analysis of the frequencies observed permits identification of each of the sugars and their isomeric analogs, and can be used as a basis for study of nucleosides and nucleotides by vibrational spectroscopy.     

Adenine residue: A normal-coordinate analysis of the vibrational spectra

The frequencies observed for adenine in the Raman spectra of adenosine monophosphate (AMP) and biopolymers such as poly(A), DNA, and RNA are compared with those calculated for a model compound, 9-methyladenine, in which the methyl group is taken as a unit mass concentrated on the carbon. The force field used is a Urey-Bradley field already tested on polycrystalline adenine and its analogs D -substituted on the nitrogens, on the carbon at position 8, and on both. Assignments for adenine residue Raman bands are proposed and discussed on the basis of observed and calculated D-shifts. These assignments are examined, in particular, for bands common to both adenine and guanine residues by analysis of their behavior for Raman hypochromism.     

Low-frequency Raman spectra of lysozyme.

New techniques in laser Raman spectroscopy are used to obtain spectra of aqueous solutions of lysozylme for frequency shifts as small as 5 cm^?1. In addition, Raman measurements are made on two crystalline forms of hen egg white lysozyme. The spectra obtained from the solution and from the crystal are found to be similar for frequencies above 100 cm^?1. However, a low-frequency band at 25 cm^?1 observed in crystalline lysozyme is not found in the solution, indicating that this band cannot be attributed to an internal molecular vibration.     

Vibrational analysis and spectra of orotic acid

The IR and Raman spectra of polycrystalline anhydrous orotic acid and its N1, N3, and O12 trideuterated isotopomer are recorded in the 4000-40 cm(-1) spectral interval as part of a series of vibrational analyses of nucleosides, nucleotides, and related compounds carried out in our laboratory. The frequencies of the fundamental transitions and the potential energy distributions of the 39 normal modes of orotic acid and its isotopomer are calculated by an ab initio density functional theory Becke3P86/6-311G** treatment. Assignments of the vibrational modes are proposed that consider the results of these calculations and the observed spectra. The results of the ab initio treatment are related to crystallographic and spectral data, and they are compared with previous assignments for similar molecules.     

Characterization of DNA structures by laser Raman spectroscopy

Oriented fibers drawn from aqueous gels of calf-thymus DNA were maintained at constant relative humidites of 75 and 92% to yield canonical A-DNA and B-DNA structures, respectively. Raman spectra of the two forms of DNA were recorded over the spectral range 300–4000 cm^?1. The authenticated DNA fibers were deuterated in hygrostatic cells containing D₂O at appropriate relative humidities, and the corresponding spectra of deuterated DNAs were also obtained. The spectra reveal all of the Raman scattering frequencies and intensities characteristic of A- and B-DNA structures in both nondeuterated and deuterated froms, as well as the frequencies and intensities of adsorbed solvent molecules from which the hydration content of DNA fibers can be calculated. Numerous conformation-sensitive vibrational modes of DNA bases and phosphate groups have been identified throughout the 300–1700-cm^?1 interval. Evidence has also been obtained for conformation sensitivity of deoxyribosyl CH stretching modes in the 2800–3000-cm^?1 region. Raman lines of both the backbone and the bases are proposed as convenient indicators of A- and B-DNA structures. The results are extended to Z-DNA models investigated previously. Some implications of these findings for the determination of DNA or RNA structure from Raman spectra of nucleoproteins and viruses are considered.     

Laser Raman spectroscopy of lyophilized bacterial spores

Laser-excited Raman spectra were examined in lyophilized spores of Bacillus cereus. In a comparison of the spectrum of the dormant spore with that of the germinated spore, we found several Raman bands which occurred in the former but not in the latter. Among these Raman bands, the 1,573, 1,395, 1,017, 822, and 662 cm-1 bands were assigned to the vibrational frequencies of calcium dipicolinate (CaDPA). No Raman bands and peaks due to dipicolinic acid (H2DPA) were observed. This Raman evidence indicates that CaDPA is the predominant DPA species in this spore. We also proposed a tentative assignment for other vibrational frequencies due to several components of the spore.     

Inelastic neutron-scattering study of the proton transfer dynamics in polyglycine I at 20 K

Inelastic neutron-scattering (INS) spectra of three isotopic derivatives of polyglycine I (-COCH2NH-)n, (-COCD2NH-)n, and (-COCH2ND-)n at 20 K are presented from 30 to 4000 cm(-1). The band frequencies are compared to those observed in the infrared and Raman. Assignments in terms of group vibrations are proposed. These mostly resemble previous assignment schemes, except for the amide bands. The INS intensities reveal that the proton dynamics for the (N)H proton are totally different from those proposed previously. They are independent of the molecular frame and the valence bond approach is not consistent with observation. A phenomenological approach is proposed in terms of localized modes. The calculated intensities reveal that the (N)H stretching mode has two components at approximately 1377 and 1553 cm(-1). This is a dramatic change compared to all former assignments at approximately 3280 cm(-1) based on infrared and Raman data. These proton-dynamics are associated with a weakening of the NH bond due to the ionic character of the hydrogen bond (N(delta-)...H+...O(delta'-)) and proton transfer. The infrared and Raman spectra are re-examined and a new assignment scheme is proposed for the amide bands; the amide A and B bands are re-assigned to the overtones of the stretching modes. A symmetric double-minimum potential for the proton is consistent with all the observations.     

Raman studies of nucleic acids. VII. Poly A-poly U and poly G-poly C

Laser-excited Raman spectra of the double-helical complexes poly A·poly U and poly G·poly C are reported for ²H₂O and H₂O solutions. The spectra are discussed in relation to their use as quantitative reference spectra for determining the dependence of the Raman scattering of RNA on secondary structure. The Raman line at 815 cm^?1, due to the phosphodiester group, exhibits the same intrinsic intensity in spectra of poly A·poly U and poly G·poly C and is thus dependent only upon the amount of ordering of the helix and not on the kinds of nucleotides involved. The hypochromic Raman lines in spectra of poly A·poly U are identified and their intensity changes are determined quantitatively over the temperature range 32–85°C. Comparison of the spectra in the 1500–1750 cm^?1 region reveals that the Raman lines from carbonyl group vibrations of uracil are about sevenfold more intense than those of guanine and cytosine for both paired and unpaired states and will thus dominate the spectra of RNA. The Raman frequencies in this region are also compared with previously reported infrared frequencies and give evidence of being strongly perturbed by base-stacking interactions in the helices.     

Chromophore interactions in flavocytochrome c552: a resonance Raman investigation

Resonance Raman spectra with both Soret and visible excitation have been obtained for Chromatium flavocytochrome c552 and its isolated diheme subunit under varying conditions of pH and inhibitor binding. The spectra are generally consistent with previously established classification schemes for porphyrin ring vibrations. The presence of covalently bound flavin in the protein was apparent in the fluorescent background it produced and in flavin-mediated photoeffects observed in heme Raman spectra obtained at high laser power. No flavin modes were present in the Raman spectra, nor was any evidence of direct heme-flavin interaction found by using this technique; however, a systematic perturbation of heme B1g vibrational frequencies was found in the oxidized holoprotein. The heme vibrational frequencies of c552 are compared to those of the diheme peptide and of other c-type cytochromes. They are consistent with an interpretation that involves pH-dependent changes in axial ligation and treats the hemes and flavin as isolated chromphores communicating via protein-mediated interactions.     

Raman studies of nucleic acids. XII. Conformations of oligonucleotides and deuterated polynucleotides

Laser Raman spectra of the trinucleoside diphoshate ApApA and dinucleoside phosphates ApU, UpA, GpC, CpG, and GpU are reported and discussed. Assignments of conformationally sensitive frequencies are-facilitated by comparison with spectra reported here of poly(rA), poly(rC), and poly(rU) in deuterium oxide solutions. The significant spectral differences between ApU and UpA, and between GpC and CpG, reveal that the sequence isomers have nonidentical conformations in aqueous solution. In UpA at low temperature the bases are stacked and the backbone conformation is similar to that found in ordered polynucleotide structures and RNA. In ApU no base stacking can be detected and the backbone conformation differs from that found in UpA, both in the orientation of phosphodiester linkages and in the internal conformation of ribose. At the conditions employed neither ApU nor UpA exhibits base pairing in aqueous solutions. In both GpC and CpG the bases are stacked and the phosphodiester conformations are similar to those encountered for UpA and RNA. However, major differences between spectra of GpC and CpG indicate that the geometries of stacking and ribosyl conformations are different. In GpC the Raman data favor the formation of hydrogen bonded dimers containing GC pairs. Protonation of C in GpC is sufficient to eliminate the ordered conformation detected by Raman spectroscopy. Despite the ordered backbone conformation evident in GpU, this dinucleoside apparently contains neither stacked nor hydrogen bonded bases at the conditions employed here. The Raman data also confirm the stacking interactions in ApApA, poly(rA), and poly(rC) but suggest that the backbone conformation in poly(rC) differs qualitatively from that found in most ordered polynucleotide structures and is thermally more stable. The present results demonstrate the sensitivity of the Raman technique to sequence-related structural differences in oligonucleotides and provide additional spectra–structure correlations for future conformational studies of RNA by laser Raman spectroscopy.     

Transport of d-glucose by brush border membranes isolated from the renal cortex

The transport of d-glucose by brush border membranes isolated from the rabbit renal cortex was studied. At concentrations less than 2 mM, the rate of d-glucose uptake increased linearly with the concentration of the sugar. No evidence was found for a “high-affinity” (μM) saturable site. Saturation was indicated at concentrations of d-glucose greater than 5 mM. The uptake of d-glucose was stereospecific and selectively inhibited by d-galactose and other sugars. Phlorizin inhibited the uptake of d-glucose in the presence and absence of Na⁺. The glycoside was a potent inhibitor of the efflux of d-glucose. Preloading the brush border membrane vesicles with d-glucose, but not with l-glucose, accelerated exchange diffusion of d-glucose. These results demonstrate that the uptake of d-glucose by renal brush borders represents transport into an intravesicular space rather than solely binding. The rate of d-glucose uptake was increased when the Na⁺ in the extravesicular medium was high and the membranes were preloaded with a Na⁺-free medium. The rate of d-glucose uptake was inhibited by preloading the brush border membranes with Na⁺. These results are consistent with the Na⁺ gradient hypothesis for d-glucose transport in the kidney. Thus, the presence of a Na⁺-dependent facilitated transport of d-glucose in isolated renal brush border membranes is indicated. This finding is consistent with what is known of the transport of the sugar in more physiologically intact preparations and suggests that the membranes serve as an effective model system in examining the mechanism of d-glucose transport in the kidney.     

F.t.-i.r. and laser-Raman spectra of thymine and thymidine

F.t.-i.r. and laser-Raman spectra of thymine and thymidine in the solid state were recorded. Assignments were proposed for the frequencies observed. The influence of the deoxy sugar on the vibrations of the nucleoside are discussed as a function of its particular puckering. The aim of this work is to elucidate the differences between the molecules constituting the nucleic acids, in order the better to comprehend their biological functions.     

Resonance raman spectroscopy of iron (3)--ovotransferrin and iron (3)--human serum transferrin

We report the resonance Raman spectra in the frequency range 300–1800 cm^?1 of Fe (III)-ovotransferrin and Fe (III)-human serum transferrin in aqueous solution at about 10^?4M protein concentration. This is the first observation of resonance Raman scattering ascribable to amino acid ligand vibrational modes of a nonheme iron protein. The resonance Raman spectra of the transferrins are similar except that the resonance band near 1270 cm^?1 is shifted to a higher frequency for Fe(III)-human serum transferrin than that for Fe(III)-ovotransferrin. The resonance Raman bands observed near 1170, 1270, 1500 and 1600 cm^?1 may reflect resonance enhancement of p-hydroxy-phenyl frequencies of tyrosine residues and/or imidazolium frequencies of histidine residues.     

Spectroscopic studies of metal complexes containing π-delocalized sulfur ligands. The pre-resonance Raman spectra of the antitumor agent 2-formylpyridine thiosemicarbazone and its Cu(II) and Zn(II) complexes

The pre-resonance Raman spectra of 2-formylpyridine thiosemicarbazone have been measured at three pH values corresponding to the fully protonated (H₂FPT⁺), half protonated (HFPT) and deprotonated (FPT⁻) forms of the ligand. Assignments of the vibrations coupled with the π→π^* transition have been made by comparison with the spectrum of the deuterated form (DFPT). The pre-resonance Raman spectra of the Zn(II) and Cu(II) complexes, [ZnFPT]⁺, [CuFPT]⁺ and [CuHFPT]²⁺, have also been measured. The spectral pattern of the Cu(II) complexes shows resonance enhancement of vibrations coupled with the π→π^*, as well as with the ligand to metal charge transfer transitions. In addition, it is consistent with coordination through thiolate sulfur in [CuFPT]⁺ and thione sulfur in [CuHFPT]²⁺.     

Guanine residue: A normal-coordinate analysis of the vibrational spectra

The force field established for guanine is applied here to guanine-containing biopolymers by considering the model compound 9-methylguanine, in which the methyl group is taken as a dynamic unit whose mass is concentrated on the carbon. In-plane normal-mode frequencies for this model compound and its N-deuterated analog are calculated. Band frequencies observed for guanine residue in Raman biopolymer spectra, such as those for DNA, RNA, or poly(G), are associated with calculated modes having similar wavelengths. They are discussed by taking into account observed and calculated D, ¹⁵N, and ¹⁸O isotopic shifts. The atomic displacements for the normal modes corresponding to the principal bands are illustrated and a number of assignments proposed.     

Two-dimensional 1H-N.M.R. studies of cello-oligosaccharides: The utility of multiple-relay chemical-shift-correlated spectroscopy

500-MHz, ¹H-n.m.r. spectra of cello-oligosaccharides were studied. The resonance assignments for cellotriose were made by combined use of multiple-relayed, coherence-transfer chemical-shift-correlated spectroscopy (multiple-RELAY-COSY). Spectra of a mixture of the α and β anomers of d-glucose were completely separated into the respective spectra by four-fold-RELAY-COSY. Resonance assignments for cellulose were made on the basis of the results for cello-oligosaccharides.     

Subpicosecond resonance Raman spectra of the early intermediates in the photocycle of bacteriorhodopsin

The resonance Raman spectra are presented for the species formed during the photocycle of bacteriorhodopsin (bR) on a timescale of 800-900 fs. In the ethylenic stretch region two intermediates were found with frequencies of 1,510 and 1,518 cm^-1, corresponding to species with optical absorption maxima at 660 and 625 nm, respectively. This leads to the assignment of the 1,518 cm^-1 band to the J₆₂₅ intermediate. In the fingerprint region, the appearance of a vibration at 1,195 cm^-1 strongly suggests that the isomerization indeed has taken place in a time less than the pulsewidth of our laser. This supports the previous proposals made on the basis of the optical spectra. The spectra are compared with those observed in tens of picoseconds up to nanoseconds.     

The conformation of polycytidylic acid, polyguanylic acid, polyinosinic acid, and their helical complexes in aqueous solution from laser Raman scattering

The Raman spectra of the double helical complexes of poly C–poly G and poly I–poly C at neutral p^H are presented and compared with the spectra of the constituent homopolymers. When a completely double-helical structure is formed in solution a strong sharp band at 810–814 cm^?1 appears which has previously been shown to be due to the A-type conformation of the sugar–phosphate backbone chain. By taking the ratio of the intensity of the 810–814 cm^?1 band to the intensity of the 1090–1100 cm^?1 phosphate vibration, one can obtain an estimate of the fraction of the backbone chain in the A-type conformation for both double-stranded helices and self-stacked single chains. This type of information can apparently only be obtained by Raman spectroscopy. In addition, other significant changes in Raman intensities and frequencies have been observed and tabulated: (1) the Raman intensity of certain of the ring vibrations of guanine and hypoxanthine bases decrease as these bases become increasingly stacked (Raman hypochromism), (2) the Raman band at 1464 cm^?1 in poly I is asigned to the amide II band of the cis-amide group of the hypoxanthine base. It shifts in frequency upon base pairing to 1484 cm^?1, thus permitting the determination of the fraction of I–C pairs formed.