Nucleic acid and protein structures and interactions in viruses investigated by laser Raman spectroscopy

Raman spectroscopy may be profitably exploited to determine details of protein and nucleic acid structures and their mutual interactions in viruses and gene regulatory complexes. Present applications use data obtained from model nucleic acid crystals, fibers and solutions to reveal preferred backbone and nucleoside conformations for different morphological states of DNA and RNA in plant (TMV, BDMV) and bacterial viruses (P22, Pfl, Xf, Pf3, fd, Ifl, IKe). Interpretation of the results is enhanced by deconvolution methods which, in favorable cases, permit quantitative conclusions regarding macromolecular structures. Both equilibrium and dynamic Raman applications are described.     

Noncovalent interactions in paired DNA nucleobases investigated by terahertz spectroscopy and solid-state density functional theory

Cocrystallized adenine and thymine derivatives, along with the pure monomeric crystals, were investigated by terahertz spectroscopy and solid-state density functional theory (DFT). The methylated nucleobase derivatives crystallize in planar hydrogen-bonded adenine-thymine pairs similar to the manner found in DNA. The spectra obtained for 1-methylthymine, 9-methyladenine, and the 1:1 cocrystal in the range of 10-100 cm(-1) clearly demonstrate that absorptions in this spectral range originate from the uniquely ordered assembly and the intermolecular interactions found in each individual crystal system. The quality of spectral reproduction for the DFT simulations of each system was clearly improved by the inclusion of an empirical correction term for London-type dispersion forces to the calculations. Notably, it was found that these weak dispersion forces in the adenine-thymine cocrystal were necessary to produce a properly converged crystal structure and meaningful simulation of the terahertz vibrational spectrum.     

Difference of solute-solvent interactions of cis- and trans-1,2-dichloroethylene in supercritical CO2 investigated by raman spectroscopy

Vibrational Raman spectra of CC stretching modes of both cis- and trans-1,2-dichloroethylene (C2H2Cl2) were measured as a function of density in supercritical carbon dioxide (CO2). Measurements were performed with solute mole fraction of 0.01 at an isotherm of T r = T/ T c = 1.02. As the density of CO2 increased, peak frequencies of the CC stretching modes shifted toward the low energy side. By analyzing these density dependences using perturbed hard-sphere theory, we decomposed the shifted amounts into attractive and repulsive components. The amounts of repulsive shifts were almost equivalent, whereas those of the attractive shifts of trans-C2H2Cl 2 were larger than those of cis-C2H2Cl2 at all densities. This means that the nonpolar solute, trans-C2H2Cl2, shows stronger solute-solvent interactions than those of the polar solute cis-C2H2Cl2. The difference of attractive interactions between these isomers is the greatest at a density where local density enhancement of supercritical CO2 reaches the maximum.     

The squaric acid aggregate in mordenite investigated by Raman spectroscopy

A more detailed investigation of the squaric acid aggregate within mordenite was undertaken with the use of Raman spectroscopy. The previous reported investigation was limited to the carbonyl stretching region in the IR. In the present work the entire region from 500 to 2000 cm(-1) was investigated, revealing rather substantial vibrational shifts of the oxocarbon ring modes in the aggregate. Comparison of such shifts with those observed for the squaric acid (H2Sq)/4,4'-bipyridine (Bipy) charge transfer (CT) complex reveals that the interaction is much stronger in the aggregate, a clear effect of the restrict geometry. On the other hand, the shifts observed for the CO stretching modes are rather modest. The comparison of the ring modes present in the Raman spectra of squaric acid, potassium hydrogen squarate, potassium squarate, H2Sq/Bipy and squaric acid aggregate in mordenite strongly suggests that in the latter hydrogen bonded species are present.     

Li ion diffusion in LiAlO2 investigated by Raman spectroscopy

The temperature dependence of Li ions behavior of γ-LiAlO₂ has been studied from 78 to 873 K. On heating, the Li ions underwent positional disordering along the structural channels, with the Li ions related modes at 220, 366 and 400 cm⁻¹ broadening and weakening dramatically. An anomalous maximum in the bandwidths of the Li ions related modes is observed. It should be apparent that there are at least two distinct thermally activated processes. A model suggested by Andrade and Porto is used to describe the linewidth of a phonon.     

Local density enhancement in supercritical carbon dioxide studied by Raman spectroscopy

The polarized IVV and depolarized IVH Raman profiles of the Fermi dyad (1285 cm(-1) and 1388 cm(-1)) of supercritical (SC) CO2 have been measured along the isotherms 307, 309, 313, and 323 K in the reduced density range 0.04相似文献   

Electronic interactions in a branched chromophore investigated by nonlinear optical and time-resolved spectroscopy

The third order nonlinear optical properties of a trimer branched chromophore system and its linear molecule analog are investigated. Two-photon absorption and degenerate four wave mixing measurements were carried out on both systems. An enhancement in the nonlinear optical effect is observed for the branched trimer molecule in comparison to the linear chromophore system. Ultrafast time-resolved measurements were carried out to probe the excited state dynamics in the branched structures. The time-resolved measurements suggest that the two important processes affecting the nonlinear optical properties in the trimer system, charge transfer stabilization and initial electronic delocalization, occur on two different time scales.     

Ultrafast dynamics in thiophene investigated by femtosecond pump probe photoelectron spectroscopy and theory

A hybrid of a time-of-flight mass spectrometer and a time-of-flight "magnetic-bottle type" photoelectron (PE) spectrometer is used for fs pump-probe investigations of the excited state dynamics of thiophene. A resonant two-photon ionization spectrum of the onset of the excited states has been recorded with a tunable UV laser of 190 fs pulse width. With the pump laser set to the first intense transition we find by UV probe ionization first a small time shift of the maxima in the PE spectrum and then a fast decay to a low constant intensity level. The fitted time constants are 80+/-10 fs, and 25+/-10 fs, respectively. Theoretical calculations show that upon geometry relaxation the electronic state order changes and conical intersections between excited states exist. We use the vertical state order S1, S2, S3 to define the terms S1, S2, and S3 for the characterization of the electron configuration of these states. On the basis of our theoretical result we discuss the electronic state order in the UV spectra and identify in the photoelectron spectrum the origin of the first cation excited state D1. The fast excited state dynamics agrees best with a vibrational dynamics in the photo-excited S1 (80+/-10 fs) and an ultrafast decay via a conical intersection, presumably a ring opening to the S3 state (25+/-10 fs). The subsequently observed weak constant signal is taken as an indication, that in the gas phase the ring-closure to S0 is slower than 50 ps. An ultrafast equilibrium between S1 and S2 before ring opening is not supported by our data.     

Noncovalent interactions between modified cytosine and guanine DNA base pair mimics investigated by terahertz spectroscopy and solid-state density functional theory

Modified cytosine and guanine nucleobases cocrystallize in a hydrogen bonding configuration similar to that observed in native DNA. The noncovalent interactions binding these base pairs in the crystalline solid were investigated using terahertz (THz) spectroscopy and solid-state density functional theory (DFT). While stronger hydrogen bonding interactions are responsible for the general molecular orientations in the crystalline state, it is the weaker dipole-dipole and dispersion forces that determine the overall packing arrangement. The inclusion of dispersion interactions in the DFT calculations was found to be necessary to accurately simulate the unit cell structure and THz vibrational spectrum. Using properly modeled intermolecular potentials, the lattice vibrational motions of the cytosine and guanine derivatives were calculated. The vibrational characters of the modes exhibited by the DNA base pair mimic in the THz region were primarily rotational motions and are indicative of the energies and the nature of vibrations that would likely be observed between similar base pairs in DNA molecules.     

Acetone adsorption on ice investigated by X-ray spectroscopy and density functional theory

Using a combination of X-ray photoemission and near-edge X-ray absorption spectroscopy (NEXAFS) as well as density-functional theory (DFT), we have investigated the adsorption of acetone on ice in the temperature range from 218 to 245 K. The adsorption enthalpy determined from experiment (45 kJ mol(-1)) agrees well with the adsorption energy predicted by theory (41 to 44 kJ mol(-1)). Oxygen K-edge NEXAFS spectra indicate that the presence of acetone at the ice surface does not induce the formation of a pre-melted layer at temperatures up to 243 K. DFT calculations show that the energetically most favored adsorption geometry for acetone on ice is with the molecular plane almost parallel to the surface.     

Study on transport of molecules in gel by surface-enhanced Raman spectroscopy

Cellulose - Surface-enhanced Raman spectroscopy (SERS)-based biosensors have recently been extensively developed because of their high sensitivity and nondestructive nature. Conventional SERS...     

Role of hydration in the phase transition of polypeptides investigated by NMR and Raman spectroscopy

NMR, Raman spectroscopy and ab initio quantum-chemical calculations have been employed to investigate the role of the hydration water in the inverse temperature transition of elastin-derived biopolymers represented by poly(Gly-Val-Gly-Val-Pro) and poly(Ala-Val-Gly-Val-Pro). Temperature and concentration dependences of the Raman spectra measured for water solutions of polymers and of a low-molecular-weight model have been correlated with the vibrational frequencies calculated at the DFT (B3LYP) and MP2 levels for the peptide segment surrounded by a growing number of water molecules. The results indicate strong hydration before the transition that, in addition to water hydrogen-bonded to amide groups, includes hydrophobic hydration of non-polar groups by a dynamic cluster of several water molecules. According to ¹H longitudinal and transverse relaxation of HOD signals in D₂O solutions, the number of water molecules motionally correlated with the polymer is about 4 per one amino acid residue.     

Effective diffusion coefficients for methanol in sulfuric acid solutions measured by Raman spectroscopy

The diffusion of methanol into 0-96.5 wt % sulfuric acid solutions was followed using Raman spectroscopy. Because methanol reacts to form protonated methanol (CH 3OH 2 (+)) and methyl hydrogen sulfate in H 2SO 4 solutions, the reported diffusion coefficients, D, are effective diffusion coefficients that include all of the methyl species diffusing into H 2SO 4. The method was first verified by measuring D for methanol into water. The value obtained here, D = (1.4 +/- 0.6) x 10 (-5) cm (2)/s, agrees well with values found in the literature. The values of D in 39.2-96.5 wt % H 2SO 4 range from (0.11-0.3) x 10 (-5) cm (2)/s, with the maximum value of D occurring for 61.6 wt % H 2SO 4. The effective diffusion coefficients do not vary systematically with the viscosity of the solutions, suggesting that the speciation of both methanol and sulfuric acid may be important in determining these transport coefficients.     

Uptake and surface reaction of methanol by sulfuric acid solutions investigated by vibrational sum frequency generation and Raman spectroscopies

The uptake of methanol at the air-liquid interface of 0-96.5 wt % sulfuric acid (H2SO4) solutions has been observed directly using vibrational sum frequency generation (VSFG) spectroscopy. As the concentration of H2SO4 increases, the VSFG spectra reveal a surface reaction between methanol and H2SO4 to form methyl hydrogen sulfate. The surface is saturated with the methyl species after 15 min. The uptake of methyl species into the solutions by Raman spectroscopy was also observed and occurred on a much longer time scale. This suggests that uptake of methanol by sulfuric acid solutions is diffusion-limited.     

Conformational studies by Raman spectroscopy and statistical analysis of gauche interactions in n-butylamine

Raman spectra of n-butylamine recorded at different temperatures show pairs of bands whose temperature-dependent intensities clearly suggest their assignment to different conformers in simultaneous equilibria. Normal coordinate analysis and i.r. spectra of n-butylamine are also used to assign the spectra. These vibrational data are interpreted and correlated with structural information obtained from a statistical analysis of gauche skeletal arrangements in n-butylamine at different temperatures.     

Direct observation of taut tie molecules in high-strength polyethylene fibers by Raman spectroscopy

The Raman spectra of four gel-spun high-strength polyethylene fibers were recorded as a function of stress, with detailed study of the 1063 cm^?1 band. The change in the peak position of this band was linear at low stresses, but there was little change at high stresses. The center of mass of the band moved linearly with stress until fracture, and the shift per unit stress was almost the same for all the fibers studied at 4.0 ± 0.5 cm^?1/GPa. The line shape is symmetric at low stresses, and the full width at half maximum increases with stress. When plastic deformation begins the band develops a broad low intensity tail extending to 1000 cm^?1. This corresponds to stresses of up to 15 GPa, and the tail contains up to 18% of the band intensity when the maximum stress is applied. Equivalent wide-angle x-ray studies showed no such tail, so the highly stressed material is not crystalline, although it must be in the all-trans form to contribute to the Raman peak. Such load-bearing extended-chain-disordered material is described as taut tie molecules. The amount is much larger than that usually derived from mechanical modelling, it is essentially all the amorphous material if the DSC crystallinity of 85% is correct. It is thought to be interfibrillar, stressed when fibrils slide past each other in creep. On unloading the fiber, the band became more symmetrical again but did not always return to its initial position at zero stress. The peak moved to a wave number greater than its initial value on unloading and then over time relaxed to its original value. Thus tensile stresses in the disordered material, balanced by compression in the crystals, are slow to relax. Lower molecular weight fibers (M_n = 8 × 10⁵) had small anelastic effects, probably because they relaxed within the time of the experiment.     

Tautomers and electronic states of jet-cooled 2-aminopurine investigated by double resonance spectroscopy and theory

We present resonant two-photon ionization (R2PI), IR-UV, and UV-UV double resonance spectra of jet-cooled 2-aminopurine (2AP) as well as Fourier transform infrared (FTIR) gas phase spectra. 2AP is a fluorescing isomer of the nucleobase adenine. The results show that there is only one tautomer of 2AP which absorbs in the wavelength range 32,300-34,500 cm(-1). The comparison with the calculated IR spectra of 9H- and 7H-2AP points to 9H-2AP as the dominating tautomer in the gas phase but the spectra are too similar to allow an unambiguous assignment to the respective tautomer. Hence, we determined vertical and adiabatic excitation energies of both tautomers employing combined density functional theory and multi-reference configuration interaction techniques. For the 0-0 band of the first 1pipi* transition of 9H-2AP we obtain a theoretical value of 32,328 cm(-1), in excellent agreement with the band origin of our R2PI spectrum at 32,371 cm(-1). The first singlet pipi* transition of the less stable 7H-2AP tautomer is predicted to be red-shifted by about 1700 cm(-1) with respect to the corresponding transition in 9H-2AP. From the absence of experimental bands in the energy region between 30,300 and 32,350 cm(-1) we conclude that 7H-2AP is not present to an appreciable extent in the molecular beam. Our calculations yield nearly equal energies for the 1npi* and 1pipi* minima of isolated 2AP, similar to the situation in adenine. The hitherto existing argument that the energetic order of states is responsible for the different spectroscopic properties of these isomers therefore does not hold. Rather, vibronic levels close to the origin of the 1pipi* transition cannot access the conical intersection between the 1pipi* and S(0) states along a puckering coordinate of the six-membered ring, in contrast to the situation in electronically excited 9H-adenine. As a consequence, a rich vibrational structure can be observed in the R2PI spectrum of 2AP whereas the spectrum of 9H-adenine breaks off at low energies.     

Reversible phase transformation of MnO2 nanosheets in an electrochemical capacitor investigated by in situ Raman spectroscopy

The reversible phase transformation is reported from hexagonal to monoclinic structure responding to the intercalation/deintercalation of Na(+) between MnO(2) nanosheets upon potential cycling in aqueous electrolyte via an in situ Raman technique. This structural evolution will influence the Na(+) diffusion process in MnO(2) nanosheets and cause phase retention during the self-discharge process.     

Solute-solvent interactions in formamide and zinc chloride solutions: An investigation by Raman spectroscopy

Raman experiments of formamide and zinc chloride solutions in a wide concentration range (0.1-5.0 mol kg⁻¹) have been carried out. The spectral changes were interpreted on three different ways: (i) the rupture of the H-bonds of FA was evidenced by the trend observed in the ν_CO, δ_HNH and restricted (translation or libration) modes; (ii) the appearance of a new band in the ν_CN region (∼1338 cm⁻¹) was assigned to FA coordinated to Zn (II) through nitrogen atom; (iii) the electronic delocalization in the FA structure upon complexation provided the appearance of new features in the δ_CH and ν_CH regions. The quantitative treatment performed at the ν_CN region of FA allowed the determination of an average number of 3 FA molecules per Zn (II) in the first solvation shell. This value is supported by the appearance of features assigned to ZnCl⁺ and ZnCl₂ entities that also occupy vertices of the tetrahedron at higher salt concentrations. The present study may be useful for a better understanding on electrochemical processes employed in the production of dendritic zinc films as well as FA hydrolysis catalyzed by this metal.     

Symmetry properties of vibrational modes in mesoporphyrin IX dimethyl ester investigated by polarization-sensitive resonance Raman and CARS spectroscopy

The symmetry properties of selected vibrational modes of mesoporphyrin IX dimethyl ester (MP-IX-DME) in solution are investigated under different electronic resonance conditions. The Raman band parameters of the macrocycle modes nu(2), nu(10), nu(11), and nu(19) are determined from a quantitative analysis of polarized spontaneous resonance Raman (RR) and polarization-sensitive (PS) multiplex coherent anti-Stokes Raman scattering (CARS) spectra obtained with pre-resonant B band and resonant Qx band excitation, respectively. Additionally, the molecular geometry and the vibrational modes of MP-IX-DME are calculated by employing density functional theory (DFT) on the B3LYP/6-31G(d) level. Both the DFT-derived structure and the Raman spectroscopic parameters of MP-IX-DME indicate minor deviations from an ideal D2h macrocycle symmetry. To assess the influence of the beta substitution pattern on the in-plane symmetry, calculated normal-mode vectors and several experimentally detected parameters, such as peak positions, depolarization ratios, and coherent phases, are analyzed. The effects of the macrocycle substitution pattern are different for the selected vibrational modes: nu(2) in particular is very sensitive to subtle perturbations of the in-plane symmetry. The considerable activity of totally symmetric vibrations observed in the PS CARS spectra of MP-IX-DME and the correlation of mode symmetries with coherent phases confirm earlier PS CARS results on octaethylporphine (OEP) acquired under the same electronic resonance conditions.