Band Shape Analysis Research Articles

Fluorescent Labeling of DNA with Ethidium Homodimer without Measurable Decrease in DNA Mobility: Application to Automated Gel Electrophoresis Apparatus

Mobilities of DNA, fluorescently labeled with ethidium homodimer (EtD), and normalized to the mobility of the 50-bp fragment [ R f(50) ], are constant with time of electrophoresis, permitting one to conduct studies on DNA mobility in an automated electrophoresis apparatus with fluorescence detection. DNA mobility decreases with an increasing binding density of ethidium homodimer, as previously reported by others and expected since the dye decreases both the net charge and the conformational flexibility of the DNA. However, it was found that this effect of ethidium binding on electrophoretic mobility becomes undetectable at binding densities less than 1 EtD/40 bp. This implies that for the purposes of electrophoretic analysis in an apparatus with fluorescence detector, DNA with ethidium homodimer intercalated at dye-DNA ratios less than 1/40 bp behaves like unlabeled DNA and may be assumed to be in a conformation similar to that of the unliganded DNA. Necessarily, the low labeling ratio lowers the sensitivity of detection and, in particular, increases the load requirement for a full-scale band height required for the analysis of bandwidth and band shape during electrophoresis.

Resonance Raman study of the chromophore-specific vibrational and electronic of bilirubin

UV–VIS absorption and resonance Raman (RR) studies have been used to elucidate the chromophore-specific electronic and vibrational spectroscopic bands of bilirubin in chloroform and in aqueous solution at pH 10 and 7.4. RR excitation profiles reveal two sets of chromophore-specific bands in each case, arising from the AB and CD pyrromethenone chromophores. A band-shape analysis of the UV–VIS absorption spectra in combination with these excitation profiles provides the absorption maxima of the individual chromophores. In the neutral species which is present in chloroform, the AB chromophore absorbs at a longer wavelength than the CD chromophore. However, in alkaline aqueous solution, where the dianion is formed, the AB chromophore absorbs at the shorter wavelength as a consequence of a large blue shift of this band. In pH 7.4 aqueous solution, the AB chromophore absorbs at the longer wavelength owing to the formation of a monoanion in which the strong internal hydrogen bonding of the lactam A group is retained, while the proton which is hydrogen bonded to the lactam D group is removed. The RR spectra support this interpretation.

Fourier transform infrared studies of reduction of nitric oxide by ethylene over V 2O 5 layered on ZrO 2

The reduction mechanism of nitric oxide by ethylene in the presence or absence of oxygen on mono- and multi-layer V 2O 5/ZrO 2 and the structures of the catalysts under reaction conditions have been studied by Fourier transform infrared spectroscopy as well as by analysis of the reaction products. For the reaction of a mixture of NO + C 2H 4, only carboxylate species were observed at higher temperatures, although at lower temperatures nitrate species were formed. No bands due to a complex of NO + C 2H 4 were observed. From the results, it is proposed that ethylene is oxidized by the catalyst to form carbon dioxide via carbonyl and carboxylate species and nitric oxide reoxidizes the catalyst to form nitrogen. The quantitative analysis of the VO band in the region of 1100–900 cm −1 by band shape analysis indicates that only the surface VO species in the top layer of the catalyst interacts with the adsorbed species.

The structure of trans-1,4-diisocyanocyclohexane in solution, in the solid state, and as a ligand bridging bulky tungsten(II) complexes

The conformational structures of the bridging ligand trans-1,4-diisocyanocyclohexane were determined in solution, as a solid, and as a ligand bridging bulky seven-coordinate tungsten(II) complexes. In solution CNC6H10NC exists as an equilibrium mixture of diaxial and diequatorial conformers, with the diequatorial conformer preferred in a 2 : 1 ratio. Infrared data indicate that the bulk solid does not consist of the diequatorial conformer, and a single-crystal study verifies that the diaxial conformer is preferred in the solid state. The crystal data found for CNC6H10NC are: space group P21/n, Z = 2, a = 5.996(1) Å, b = 7.203(2) Å, c = 8.972(3) Å, β = 96.89(2)°, and V = 384.7(2) Å3. 13C NMR bandshape analysis provides a low activation barrier (40.7(4) kJ mol−1) in CH2Cl2 solution for diaxial—diequatorial conversion. In spite of the accessibility of both conformers in solution, the ligand unexpectedly adopts the diaxial conformation in the bimetallic complex (Br2(PEt3)2(CO)2W)2CNC6H10NC. The crystal data found for (Br2(PEt3)2(CO)2W)2CNC6H10NC are: space group Pca21, Z = 4, a = 17.162(5) Å, b = 16.226(6) Å, c = 18.233(3) Å, and V = 5077.3(25) Å3.

Quantitative interpretation of the red edge excitation (REE) effect of 9,9′-bianthryl in polyisobutene by band shape analysis of the temperature-dependent optical fluorescence spectra

Optical fluorescence spectra of 9,9′-bianthryl (BA) in polyisobutene (PIB) were measured as a function of the excitation wavelength at various temperatures between 210 and 293 K. Irradiation at the red edge of the absorption spectra selectively excites distinct conformers with respect to the torsional angle. This leads to a strong dependence of the vibronic band shape of the fluorescence spectra on the excitation wavelength. The marked temperature dependence of the band shape may be attributed to the viscosity-dependent deceleration of the torsional relaxation of BA in the highly viscous polymer which prevents the excited state ensemble from reaching thermal equilibrium. The predominant broadening mechanism affecting the band shape is given by a combination of the S1 torsional distribution and the torsional angle-dependent transition frequency. These effects are interpreted quantitatively within a torsional relaxation model based on the description of the torsional dynamics according to a Smoluchowski equation which is adapted to the steady state case. The band shape analysis of the fluorescence spectra enables the determination of the effective S1 torsional potential as well as the friction coefficient related to the internal torsional motion of BA in the polymer matrix. A value of ΔV = 325 cm−1 is deduced for the local barrier of the S1 double minimum potential at ϕ = 90° while the minimum torsional angle is found to be ϕmin = 61°. Additionally, model calculations on time-resolved fluorescence spectra of BA in apolar solvents are carried out as a function of excitation wavelength and temperature showing the importance of conformational relaxation for the interpretation of transient spectra of flexible molecules.

Molecular relaxation in dimethyldichlorosilane from Raman band shape studies

Rotational and vibrational relaxation of pure liquid dimethyldichlorosilane (DMDCS) at temperatures of 279, 293, 308 and 323 K and in carbon tetrachloride, dioxane, chloroform and cyclohexane solutions at 293 K were studied by Raman band shape analysis. The activation energy for molecular reorientation of DMDCS molecules was determined. The experimental vibrational correlation functions were compared with the Kubo-Rothschild and Oxtoby relationships.

Nuclear magnetic resonance studies of sulfur inversion in bis(cyclopentadienyl)-molybdenum and -tungsten complexes with dithioethers

The metallocene thioether derivatives [Cp 2M(MeSCH 2CH 2SMe)][PF 6] 2 ( 1, M = MO; 2, M = W), [Cp 2Mo(SCH 2CH 2SMe)][PF 6] ( 3) and [Cp 2M(SCH 2CH 2S)] ( 4, M = Mo; 5, M = W) exhibit temperature-dependent fluxional behavior in solution, owing to the pyramidal sulfur inversion process. The activation energies for this process were determined from proton band-shape analysis in the cases of 1 (54.9 ± 2 kJ mol −1), 2 (51.2 ± 4.6 kJ mol −1) and 3 (30.0 ± 3.1 kJ mol −1). Extended Hückel calculations on related model complexes suggest that local inversion at the sulfur atoms, rather that an inversion of the complete SCCS chain, is responsible for the observed fluxional behaviour.

Band-shape analysis of the charge-transfer fluorescence in barrelene-based electron donor-acceptor compounds

In this paper we analyze the band shapes of the stationary fluorescence spectra for the radiative charge transfer recombination D + -A - →D-A+hv in a series of barrelene-based organic bridged donor (D)-acceptor (A) molecules D-A, exploring solvent polarity and temperature effects on the band shape. Free energy changes for charge recombination, medium reorganization energies, and intramolecular reorganization energies (for high- and medium-frequency vibrational modes) were evaluated from the band maximum energies and the full widths at half-maximum and from the fits of standard Franck-Condon factors to the entire fluorescence band shape

Cholesteric liquid crystals for solvent vapour detection ? Elimination of cross sensitivity by band shape analysis and pattern recognition

Cholesteric liquid crystals are suitable as sensitive materials for the detection of solvent vapours, such as aromatic and halogenated hydrocarbons. The optical properties of these materials are determined by their molecular short range order, given by the so-called pitch which is influenced by analyte incorporation. Thus, the wavelength of the absorbance band is shifted and the sensor effects are followed in the visible range at a defined wavelength on the flank of the band. Even a variety of aromatic or halogenated solvents, e.g. tetrachloroethylene, can be detected in the ppm-range. By using the whole spectral information combined with partial least squares analysis a separation of solvent effects from that of the disturbing temperature is achieved. Furthermore, these spectral data allow the optimization of the detection of halogenated hydrocarbons whereas the cross sensitivity to other analytes can be diminished.

1,2-Metallotropic shifts in trimethylplatinum(IV) and tricarbonylrhenium(I) halide complexes of pyridazine and 4-methylpyridazine

Pyridazine (pydz) and 4-methylpyridazine (4Me-pydz) form stable bis(monodentate) complexes of general formulae fac-[PtXMe3L2](X = Cl, Br or I) and fac-[ReX(CO)3L2](X = Cl, Br or I). These complexes in above-ambient temperature solutions exhibit 1,2-fluxional shifts between the nitrogen donor pairs of each ring. All linkage isomers of the pydz complexes are equivalent whereas three NMR-distinct linkage isomers, namely (1,1), (1,2)/(2,1) and (2,2) species, occur in solutions of the 4Me-pydz complexes. Fluxional exchange kinetics have been measured by variable-temperature 1H NMR bandshape analysis and two-dimensional exchange spectroscopy (EXSY). Platinum-195 NMR data have been obtained for the complexes [PtXMe3(4Me-pydz)2](X = Br or I) and their fluxional dynamics investigated by 195Pt two-dimensional EXSY and total bandshape analysis. Energy barriers, ΔG‡(298.15 K) for the 1,2-M–N fluxion are in the ranges 69–74 kJ mol–1 for the PtIV complexes and 84–90 kJ mol–1 for the ReI complexes. The crystal structure of [PtClMe3(pydz)2] shows the cis pydz rings oriented in a propeller arrangement with their unco-ordinated nitrogens oriented away from the cis positioned chlorine.

Reorientational Motion and Phase Transitions of Cyclohexane in Restricted Geometries

ABSTRACTRotational motion of cyclohexane in the liquid and the solid plastic phase is studied using Raman light scattering. The results are compared with molecular dynamics simulations run for model pores of diameters similar to those used in the experiment. The presence of the surface layer and its effect on the relaxation times is discussed. The temperature of the solid-solid phase transition is determined from the analysis of the ν21 band shape. It is shown that the depression of the cubic to monoclinic phase transition depends on the pore diameter and is different for modified and unmodified surfaces. It is suggested that molecules near the pore walls form the amorphous structure and only molecules near the center of the pore form crystallographic structure.

An NMR investigation of 1,2-metallotropic shifts in transition metal complexes of benzo[ c]cinnoline and pyridazines

Complexes of types [W(CO) 5L], [ cis-Rh(CO) 2C1L] (L  benzo[ c]cinnoline) and [W(CO) 5L′] (L′ pyridazine, 3-methylpyridazine, and 4-methylpyridazine) have been synthesized and shown to exhibit, in organic solvents, intramolecular metal-nitrogen 1, 2-fluxional shifts, which have been quantitatively studied by 1D bandshape analysis and 2D-EXSY NMR experiments. Energy barriers for the metallotropic shifts in the pyridazine complexes are ca. 20 kJ mol −1 higher than in the benzo[ c]cinnoline complexes. These differences are discussed in terms of the ground state and likely transition state species for this fluxional process.

Vibrational band shape analysis of the C–H vibration of CH2I2 molecules in liquid CCl4

The vibrational band shapes and their parameters of the C–H vibration of CH2I2 diluted with liquid CCl4 were measured as a function of composition. The linewidth increases from 8.7 cm−1 with decreasing mole fraction X of CH2I2 reaches a maximum value of 15.92 cm−1 near X=0.4 and decreases again in the limit of the diluted case. The frequency of the band center increases with decreasing X from 2965.37 to 2984.75 cm−1. These results are compared with the model of Knapp and Fischer for the concentration dependence of the vibrational linewidths and shifts. For the line shift, good agreement is found between theory and experiment by introducing a microscopic mole fraction. The model can be used to get an estimation on the difference between macroscopic and microscopic concentration. The predictions for the band shape are rather satisfactory in the whole concentration range. Deviations are due to the assumption that the band shapes in the model are Lorentzian for both neat liquids, whereas the experimental line shape in neat CH2I2 is not.

I.r. spectroscopy characterization of various types of structural irregularities in pyrolytic boron nitride

Samples of pyrolytic BN ceramics were produced by CVD from BCl3-NH3-N2 mixtures at temperatures of 1300–2100°C, pressures 1–20 torr and varying partial pressures of the components. A theoretical analysis of the dependences of i.r. spectral band frequencies on interlayer distance and crystal block size is given. Five BN structure modifications have been found in BN ceramics from i.r. band shape analysis: hexagonal graphite-like, partially ordered, turbostratic, dense amorphous and highly dispersed amorphous, whose relative content strongly depends on the synthesis conditions.

Electrochemical and spectroscopic manifestations of donor-acceptor coupling in cyanide bridged transition metal complexes: contrasts between RuCNRu, CoCNRu and RhCNRu systems

An issue of contrasting donor-acceptor electronic coupling in cyano-bridged transition metal complexes containing ruthenium, rhodium or cobalt acceptors has been addressed by means of spectroscopic and electrochemical comparisons of several series of M(CNRu(NH 3) 5) 2 complexes where M is Ru II(bpy) 2, Co III(MCL), Rh III(bpy) 2 or Rh III(MCL) and MCL is a tetraazamacrocyclic ligand. All the complexes exhibit metal-to-metal (M II→Ru III(NH 3) 5 or Ru II(NH 3) 5→M III) charge transfer (MMCT) absorptions. These are highest in energy for M=Rh(III) and lowest for M=Ru(II). The electrochemical half-wave potentials of the Ru(NH 3) 3+,2+ 5 couples are strongly correlated with the energies of the MMCT transitions and span a 300 mV range. The M=Co III(MCL), Rh III(bpy) 2 and Rh III(MCL) complexes, in which Ru II(NH 3) 5→M IIIMMCT transitions are observed, have E 1 2 values greater than 0.22 V versus SCE, while the M=Ru II(bpy) 2 complexes have values of E 1 2 which are less than 0.0 V. The results suggest that common perturbational treatments of the MMCT transitions in RuCNRu complexes are inadequate owing to the exceptionally strong electronic coupling, and that the perturbational MMCT band shape analysis underestimates the electronic coupling. This work indicates that the donor-acceptor electronic coupling is greater in RuCNRu complexes than in RuCNCo complexes, qualitatively in accord with reports of contrasting MMCT excited state back electron transfer behavior.

Variable‐temperature NMR studies of 2,6‐dihydroxy acylaromatic compounds. Deuterium isotope effects on chemical shifts, isotopic perturbation of equilibrium and barriers to rotation

AbstractA series of 2,6‐dihydroxy acylaromatic compounds were investigated to characterize the rotational and hydrogen bonding properties of the carbonyl group. Deuterium isotope effects on 1H and 13C chemical shifts due to deuteriation of OH groups were determined at both ambient and low temperature. In the latter case isotope effects on chemical shifts of the individual rotamers can be determined. Deuteriation of one of the OH groups may lead to isotopic perturbation of the tautomeric equilibrium of the carbonyl group and the two hydroxyl groups. The perturbation was found to be larger in ketones than in esters. Complete band shape analysis of the OH resonances of the esters and ketones in a temperature interval above and below the coalescence temperature led to ΔG≠, AH≠ and ΔS≠ values for various concentrations of added THF‐d8. ΔS≠ was found to be strongly negative. Temperature coefficients for the shift of the OH resonances showed large variations for esters and ketones owing to the different hydrogen bond patterns. The esters have two intramolecular hydrogen bonds, one strong and an additional weaker one between the OH and OR groups. The second OH group of the ketones was shown to point primarily towards C‐5. Increasing amounts of THF‐d8 increased the amount of this rotamer. The anisotropy of the XCO group at C‐2, C‐6 was shown to lead to a low‐field shift of C‐2, very different from that found for CO groups without hydrogen bonds. The anisotropy caused by OH groups can also be estimated. On the basis of the thermodynamic parameters, a model for the rotation of the ester group is suggested. The rate‐determining step involves both intramolcular hydrogen bonds, which are twisted out of the ring plane to form hydrogen bonds to the solvent or other hydrogen bond acceptors.

NMR EXCHANGE STUDIES ON THE COMPLEXES cis-[Rh(CO)2(pyridine N-oxide)(X)] (X = Cl, Br)

Abstract 13C nmr spectra of the complexes cis-[Rh(CO))2(pyO)(X)] (X = Cl, Br; pyO = pyridine N-oxide) are discussed. Variable temperature 13C nmr spectroscopy has been used to monitor the exchange process occurring in acetone-d 6 solution. Rate constants for the exchange reaction have been determined by complete band shape analysis. The enthalpy of activation for the chloro- and bromo-complexes was found to be 53.3 ± 1.0 kJ mol−1 and 48.3 ± 0.8 kJ mol−1 respectively. The entropy of activation was found to be 5.5 ± 0.6 J mol−1 K−1 and -11.0 ± 0.3 J mol−1 K−1, for the chloro- and bromo-complexes, respectively. It is suggested that the fluxionality of the molecules results from an intermolecular exchange of pyridine N-oxide rather than from loss of carbon monoxide. A mechanism for the exchange process is proposed.

Surface vanadia species in V 2O 5-TiO 2 systems prepared by mechanically mixing: A Fourier transform infrared spectroscopy study

Surface vanadium-containing species supported on titania (97% rutile) prepared by manually grinding both oxides and calcined between 773 and 973 K in the presence of water vapour have been studied by Fourier transform infrared spectroscopy. The application of band-shape analysis to the overlapping and weak bands using a computer programme has provided information about the surface vanadium species existing in these samples. Up to four different species have been identified in samples calcined above 923 K.

Rotational analysis of the He I photoelectron spectrum of HF

Combined theoretical and experimental studies of He I photoelectron spectra for photoionization of the X 1Σ + ( v″ = 0) ground state HF leading to the X 2Π ( v + = 0–2) and A 2Σ + ( v + = 0–3) ionic states, including detailed analyses of the rotational bandshapes, are reported. Agreement between the measured bandshapes and the calculated spectra, convoluted with the experimental resolution function (22 meV FWHM), is excellent. Ionization potentials of 16.046(1) eV and 19.116(2) eV are obtained for formation of the X and A ionic states, respectively. The vibrational spacings, deduced from the measured data by careful bandshape analysis, are in very good agreement with spectroscopic values.

Rotationally Resolved Magnetic Vibrational Circular Dichroism of Hydrogen Chloride and Deuterium Chloride

The magnetic vibrational circular dichroism (MVCD) spectra of HCI and DCI are presented. The average rotational g-value of H35Cl in the first excited vibrational states was determined to be 0.45 l and 0.449 for the P and R branches, respectively, using moment analysis of the MVCD bandshapes. In addition, the gJ-values of H37Cl, D35Cl, and D37Cl were measured for the first time. Within our experimental error, the gJ-values obtained were consistent with the accepted gJ-values for the ground state of H35Cl and with theoretically calculated gJ-values for the other isotopomers. The results show that MVCD can provide an alternative method to microwave spectroscopy or molecular beam magnetic resonance spectroscopy for determining rotational g-values.