Ab initio calculations of the ultraviolet resonance Raman spectra of uracil

An equation been derived to calculate, ab initio, the frequencies and intensities of a resonant Raman spectrum from the transform theory of resonance Raman scattering. This equation has been used to calculate the intensities of the ultraviolet resonance Raman spectra from the first π-π* excited state of uracil and 1,3-dideuterouracil. The protocol for this calculation is as follows: (1) The force constant matrix elements in Cartesian coordinate space, the vibrational frequencies, and the minimum energy ground and excited state geometries of the molecule are calculated ab initio using the molecular orbital program Gaussian 92, (2) the force constants in Cartesian coordinates are transformed into force constants in the space of a set of 3N – 6 nonredundant symmetrized internal coordinates, (3) the G matrix is constructed from the energy minimized ground state Cartesian coordinates and the GFL = LΛ eigenvalue equation is solved in internal coordinate space, (4) the elements of the L and L^?1 matrices are calculated, (5) the changes in all of the internal coordinates in going from the ground to the excited state are calculated, and (6) these results are used in combination with the transform theory of resonance Raman scattering to calculate the relative intensities of each of the 3N – 6 vibrations as a function of the exciting laser frequency. There are no adjustable parameters in this calculation, which reproduces the experimental frequencies and intensities with remarkable fidelity. This indicates that the Dushinsky rotation of the modes in the excited state of these molecules is not important and that the simplest form of the transform theory is adequate. © 1995 John Wiley & Sons, Inc.     

Analytical applications of ultraviolet resonance Raman spectroscopy

UV resonance Raman spectroscopy (UVRR) is a new analytical technique with a unique selectivity which is capable of speciating individual analytes in complex samples. The new instrumentation is discussed as are applications of this technique to studies of polycyclic aromatic hydrocarbons (PAHs) in coal liquids and in tissue. UVRR can also be used to speciate PAHs eluting from high-performance liquid chromatography columns. Other applications to studies of protein structure are also described.     

The Raman and near ultraviolet spectra of thioanisole

The liquid Raman and vapour phase u.v. absorption spectra of thioanisole have been recorded and vibrational analyses performed. The vibrational structure accompanying the π* ← π electronic transition is similar to that in related monosubstituted benzenes and shows activity in the in-plane ring vibrations 1, 7a, 6a, 6b, 12 and 18b.     

“Parallel factor analysis of multi-excitation ultraviolet resonance Raman spectra for protein secondary structure determination”

Protein secondary structural analysis is important for understanding the relationship between protein structure and function, or more importantly how changes in structure relate to loss of function. The structurally sensitive protein vibrational modes (amide I, II, III and S) in deep-ultraviolet resonance Raman (DUVRR) spectra resulting from the backbone C–O and N–H vibrations make DUVRR a potentially powerful tool for studying secondary structure changes. Experimental studies reveal that the position and intensity of the four amide modes in DUVRR spectra of proteins are largely correlated with the varying fractions of α-helix, β-sheet and disordered structural content of proteins. Employing multivariate calibration methods and DUVRR spectra of globular proteins with varying structural compositions, the secondary structure of a protein with unknown structure can be predicted. A disadvantage of multivariate calibration methods is the requirement of known concentration or spectral profiles. Second-order curve resolution methods, such as parallel factor analysis (PARAFAC), do not have such a requirement due to the “second-order advantage.” An exceptional feature of DUVRR spectroscopy is that DUVRR spectra are linearly dependent on both excitation wavelength and secondary structure composition. Thus, higher order data can be created by combining protein DUVRR spectra of several proteins collected at multiple excitation wavelengths to give multi-excitation ultraviolet resonance Raman data (ME-UVRR). PARAFAC has been used to analyze ME-UVRR data of nine proteins to resolve the pure spectral, excitation and compositional profiles. A three factor model with non-negativity constraints produced three unique factors that were correlated with the relative abundance of helical, β-sheet and poly-proline II dihedral angles. This is the first empirical evidence that the typically resolved “disordered” spectrum represents the better defined poly-proline II type structure.     

Temperature dependence of resonance Raman spectra of carotenoids

To understand the mechanism of the photoprotective and antioxidative functions of carotenoids, it is essential to have a profound knowledge of their excited electronic and vibronic states. In the present study we investigate the most powerful antioxidants: β-carotene and lutein by means of resonance Raman spectroscopy. The aim was to study in detail their Raman spectra in solution at room temperature and their changes as a function of temperature. To measure the spectra in their natural environment pyridine has been used as a solvent. It has been chosen because of its polarizability (n=1.5092) which is close to that of membrane lipids and proteins. The temperature dependence of the most intensive ν(1) band in the range from 77 K to 295 K at 514.5 nm excitation has been obtained. It was found that in pyridine the CC stretching frequency, its intensity, line shape, and line width are very sensitive to the temperature (the sensitivity being different for the two studied carotenoids). The observed linear temperature dependence of the CC stretching frequency is explained by a mechanism involving changes of the vibronic coupling and the extent of π-electron delocalization. The different behavior of the temperature-induced broadening of the ν(1) band and its intensity for the two studied carotenoids can be associated with the different nature of their solid matrices: glassy for β-carotene and crystalline-like for lutein, owing to their different chemical structures.     

Raman,resonance Raman and infrared spectra of potassium uranyl croconate

The Raman, resonance Raman and IR spectra of potassium uranyl croconate, UO₂(H₂O)K₂(C₅O₅)₂ were obtained and interpreted. Several croconate modes are split indicating a substantial decrease in the oxocarbon symmetry, as is to be expected from a recent crystallographic investigation, revealing the coordination of the oxocarbon to be two non-equivalent UO²⁺₂ moieties in a monodentate fashion. In terms of vibrational frequency shifts it can be concluded that the UO²⁺₂ moiety behaves as an isolated oscillator.The resonance Raman results suggest that the strong band centered around 450 nm in the UV—vis spectrum should be assigned to a charge transfer transition from the oxocarbon to the uranyl ion. In fact, as resonance is approached, both uranyl and croconate modes are enhanced. It can also be inferred that the chromophore is rather delocalized into the oxocarbon ring, rather than localized in the carbonyl groups as previously observed for other croconate complexes.     

The resonance Raman spectra of intermediate-spin ferrous porphyrin

The resonance Raman and absorption spectra of unligated ferrous octaethylporphyrin [Fe²⁺ (OEP)] and its adduct with 2-MeIm or THF were observed. The resonance Raman spectrum of Fe²⁺ (OEP) in CH₂Cl₂ displayed characteristic features of iron porphyrin with three d_π electrons, suggesting ³E_g as the intermediate-spin (S = 1) ground state. Fe²⁺(OEP) in THF exhibited the ferrous high spin feature like Fe²⁺ (OEP) (2-MeIm) in CH₂Cl₂.     

Electronic and vibrational resonance Raman spectra of octamethyluranocene

The Raman spectrum of bis(tetramethylcyclo-octatetraene)uranium (U(TMCOT)₂), excited in resonance with its visible charge-transfer transitions shows an anomalously polarized electronic band at 473 cm^?1, twice as broad as the analogous band of uranocene, at 466 cm^?1. The broadening is attributed to crystal-field splitting associated with the lowered symmetry introduced by the methyl group, and/or a distribution of rotamer populations. Totally symmetric vibrational modes are observed at 879, 750, 580, 513 and 95 cm^?1; possible assignments are discussed.     

The resonance Raman spectra of spheroidene revisited with a first-principles approach

The resonance Raman (RR) spectra of different configurations of spheroidene are calculated by means of quantum chemical methods to investigate the nature of the cis configuration of this carotenoid molecule in the photosynthetic reaction center (RC) of the purple bacterium Rhodobacter sphaeroides. For validation of our methodology, we also calculate the spectrum of the all-trans structure present in the light-harvesting complexes of this bacterium. While former theoretical resonance Raman studies only considered truncated models of spheroidene, we report on calculations employing the full pigment here. The calculated frequencies for the all-trans configuration are in good agreement with former experimental and simulated data. Among the possible cis structures, the 15,15'-cis configuration shows a RR spectrum that is in best agreement with the experimental spectrum of spheroidene in the RC. In order to assess model truncation effects, we compare calculations for the full spheroidene molecule to those for the truncated model. While the main features can already be found in the latter, the full model leads to considerably different intensities in the region around 1150 cm(-1), which improve the agreement with experiment. A slight mismatch for the vibrational frequencies in the C=C stretch region is investigated by considering a model for spheroidene in the binding pocket comprising more than 500 atoms in total. The results do not lead to improved agreement with experiment, in contrast to the simpler strategy of introducing constraints in the structural optimization of a truncated spheroidene model. The calculated RR spectrum of the 13,14-cis configuration shows additional features which can also be identified in the experimental RR spectrum. This shows that the most likely cis structure is the 15,15'-cis configuration. Besides this, the 13,14-cis configuration remains a candidate for an additional spheroidene structure in the RC of Rhodobacter sphaeroides mutant R26.     

Molecular structure and vibrational spectra of spin-crossover complexes in solution and colloidal media: resonance Raman and time-resolved resonance Raman studies

The spin-crossover system [Fe(btpa)](PF(6))(2) (btpa = N,N,N',N'-tetrakis(2-pyridylmethyl)-6,6'-bis(aminomethyl)-2,2'-bipyridine) and the predominantly low-spin species [Fe(b(bdpa))](PF(6))(2) ((b(bdpa) = N,N'-bis(benzyl)-N,N'-bis(2-pyridylmethyl)-6,6'-bis(aminomethyl)-2,2'-bipyridine) have been characterized by means of X-ray diffraction. The unit cell of [Fe(btpa)](PF(6))(2) contains two crystallographically independent molecules revealing octahedral low-spin and quasi-seven-coordinated high-spin structures. The unit cell of [Fe(b(bdpa))](PF(6))(2) contains two crystallographically independent molecules one of which corresponds to a low-spin structure, while the other reveals a disordering. On the basis of magnetic susceptibility and M?ssbauer measurements, it has been proposed that this disorder involves low-spin and high-spin six-coordinated molecules. The structures of [Zn(btpa)](PF(6))(2) and [Ru(btpa)](PF(6))(2) have been determined also. Pulsed laser photoperturbation, coupled here with time-resolved resonance Raman spectroscopy (TR(3)), has been used to investigate, for the first time by this technique, the relaxation dynamics in solution on nanosecond and picosecond time scales of low-spin, LS ((1)A) --> high-spin, HS ((5)T) electronic spin-state crossover in these Fe(II) complexes. For the nanosecond experiments, use of a probe wavelength at 321 nm, falling within the pi-pi transition of the polypyridyl backbone of the ligands, enabled the investigation of vibrational modes of both LS and HS isomers, through coupling to spin-state-dependent angle changes of the backbone. Supplementary investigations of the spin-crossover (SCO) equilibrium in homogeneous solution and in colloidal media assisted the assignment of prominent features in the Raman spectra of the LS and HS isomers. The relaxation data from the nanosecond studies confirm and extend earlier spectrophotometric findings, (Schenker, S.; Stein, P. C.; Wolny, J. A.; Brady, C.; McGarvey, J. J.; Toftlund, H.; Hauser, A. Inorg. Chem. 2001, 40, 134), pointing to biphasic spin-state relaxation in the case of [Fe(btpa)](PF(6))(2) but monophasic in the case of [Fe(b(bdpa))](PF(6))(2). The picosecond results suggest an early process complete in 20 ps or less, which is common to both complexes and possibly includes vibrational relaxation in the initially formed (5)T(2) state.     

Automated parameter optimization in modeling absorption spectra and resonance Raman excitation profiles

An automated method is described for optimizing the molecular parameters in simultaneous modeling of optical absorption spectra and resonance Raman excitation profiles. The method utilizes a previously developed Fortran routine that calculates absorption spectra and Raman excitation profiles for polyatomic molecules in solution from a model for the potential energy surfaces and spectral broadening mechanisms. It is combined here with an optimization routine from the commercial MATLAB package that iteratively adjusts the parameters of the molecular model to minimize the least-squared error between calculated and experimental spectra. Optimizations that typically require days to weeks of human time when performed interactively can be accomplished automatically in less than an hour of computer time. The method can handle large molecules (we show results for as many as 23 Raman-active modes) and mixtures of spectral broadening mechanisms (lifetime, Brownian oscillator, and inhomogeneous), and is robust toward noise or missing data points.     

On mode mixing effects in absorption-emission spectra and resonance Raman excitation profiles

The Dushinsky effect is studied in absorption and fluorescence spectra and in resonance Raman excitation profiles of totally-symmetric fundamentals, overtones and combination bands. It is demonstrated that even for strong mode mixing the absorption or emission spectrum of a strongly allowed electronic transition can be analyzed in terms of displaced harmonic oscillators, but in that case the displacement parameters for the two spectra will be quite different. If no emission spectrum can be obtained, Raman excitation profiles of combination bands provide a sensitive probe of mode mixing.     

Raman spectra phthalocyanines

Raman spectra of amorphous phthalocyanine thin films have been studied. Theoretical and experimental correlations in polarization ratios are applied to vibrational assignments of symmetry species and to the problem of molecular orientation in thin solid films.     

Substituent effects on the resonance Raman spectra of bis(dithiobenzil)nickel

The influence of substituents on the resonance Raman spectra of bis(p-substituted dithiobenzil)nickels has been examined. The assigned sulfur—nickel stretching vibrations in the complexes appeared in the range 390–410 cm⁻¹ with a shift to higher frequency being observed for the electron-donating substituent. It was found that Raman intensities at vibrations of the benzene ring for ligands excited with a 457.9 nm laser line are about 1.5–3.0 times larger than with a 514.5 nm laser line. The assignments of electronic transitions in the visible region of the nickel complexes were made on the basis of observed resonance Raman intensity patterns.     

The ultraviolet spectra of silocyclobutanes

The UV spectra of Si-substituted silocyclobutanes in vacuum were studied. The bathochromic shift of the absorption band, disclosed by comparison with bands of the corresponding acyclic compounds, can be explained by the highly strained state of the four-membered ring. This same principle in disilocyclobutanes leads to the reduction of the barrier effect of the methylene group, disrupting the interaction of the silicon atoms in the unstrained molecule.     

Raman and surface Raman spectroscopy with ultraviolet excitation

We record the accurate and reliable Raman spectra of benzoic acid (BA), p-nitrobenzoic acid (PNBA) and o-nitrobenzoic (ONBA) in aqueous solution with ultraviolet excitation. And we find that the ultraviolet (UV) Raman spectrum of aqueous BA solution has one-to-one correspondence to that of BA solid whereas the others are less resemble to the solid counterparts. We also report surface Raman spectroscopy of them in silver colloid without any enhancement in UV region and call it surface-unenhanced Raman spectroscopy (SUERS) while the surface-enhanced Raman scattering (SERS) effects are perfect in near infrared or visible regions. It demonstrates the SERS effects are strongly dependent on the excitation wavelength. On the basis of the experiments, we discuss the mechanism of SERS excited in different regions.     

Calculation of intensity in the resonance Raman and two-photon absorption spectra of polyatomic molecules

A direct method for calculating the resonance Raman and two-photon absorption spectra of polyatomic molecules is described in detail The method is based on the adiabatic model and uses Herzberg-Teller’s approximation. Relations ruling out direct summation over vibrational quantum numbers of excited electronic states and representing the matrix elements of the Green function of a multidimensional oscillator as functions of vibration frequencies and Dushinsky transformation parameters are derived. The relations are convenient for constructing algorithms. Translated from Zhumal Struktumoi Khimii, Vol. 38, No. 2, pp. 248–255, March–April, 1997.     

Deep ultraviolet tip-enhanced Raman scattering

Electromagnetic mechanism of deep ultraviolet tip-enhanced Raman scattering (DUV-TERS) is investigated theoretically with the finite-difference time-domain (FDTD) method, stimulated by recent DUV-TERS experimental reports. FDTD results reveal that the strongest electromagnetic enhancement factor for DUV-TERS is as high as 7 orders in the optimal geometry.     

T ≠ 0 K Multimode modeling of optical absorption spectra and resonance Raman profiles

We discuss the superiority of the time-correlator approach over conventional sum-over-states methods for exact multimode modeling of T ≠ 0 K optical absorption and resonance Raman profiles. Numerical illustrations of thermal broadening are given, and a short-time approximation is shown to be very convenient for modeling this effect.     

Infrared and resonance enhanced Raman spectra of some metal vic-dioximes with short hydrogen bonds

Infrared and enhanced Raman spectra were recorded of bis(2,3-butanonedioximato-N,N′) nickel (II) and palladium (NiDMG, PdDMG) as well as the i.r. spectra of bis(ethanedialdioximato-N,N′) nickel (II) (NiHG), bis(2,3-pentanonedioximato-N,N′) nickel (II) (NiEMG), and of bis(2,3-butanonedioximato-N,N′) copper (II) (CuDMG). The mutual exclusion of i.r. and Raman active modes of NiDMG and PdDMG prove the existence of an inversion centre whereas the coupling of the in-plane OH deformation with two skeletal modes of CN stretching character indicates that the molecular symmetry is likely to be C_2h only. The B _u OHO stretching mode has been identified in the nickel complexes with a strong, broad band near 900 cm⁻¹. The resonance Raman enhancement is observed mainly with skeletal vibrations of CN character and, less, with those having NO character. The effects of high pressure upon i.r. spectra were observed. The possible symmetry of the hydrogen bond is discussed.