Raman Band Profiles Research Articles

The combined use of amide I bands in polarized Raman, IR, and vibrational dichroism spectra for the structure analysis of peptide fibrils and disordered peptides and proteins

AbstractRaman spectroscopy is generally a versatile tool to explore the structure of proteins and peptides in solution. However, in spite of the development of ultraviolet (UV) resonance Raman spectroscopy as a tool that allows for the investigation of samples with lower concentrations, Raman has not played the same role as infrared (IR) spectroscopy with regard to secondary structure analysis. Reported UV Raman studies have recently focused on the ψ‐dependence of amide III as a useful tool for the structural analysis even of disordered peptides. Amide I based structural analysis generally uses visible excitation. Rather than describing the traditional secondary structure analysis of proteins, this review focusses on work that used Raman in conjunction with other vibrational spectroscopies such as IR and vibrational circular dichroism to probe the conformational distribution of amino acid residues in unfolded peptides and the self‐assembling of peptides into fibrils. We argue against the use of spectral decomposition into Gaussian bands particularly if this type of analysis is exclusively applied to either IR or Raman band profiles. The article emphasizes the delocalized excitonic character of amide I wavefunctions which has to be accounted for in any attempt to use the respective bands for structure analysis.

Biogenic silver nanoparticles: understanding the antimicrobial mechanism using Confocal Raman Microscopy

The antimicrobial properties of silver nanoparticles (AgNPs) have made them ubiquitous in a number of real-world industrial applications; however, the antimicrobial mode of action of biogenic AgNPs is not entirely understood. The use of Raman spectroscopy can provide molecular fingerprint information on various chemical and biochemical components in complex systems like microbial cultures, without the need for any complex sample pre-treatment. Consequently, the antimicrobial mechanism of AgNPs can be inferred through morphological and compositional changes of microbial cells that are monitored via changes in Raman band profiles. Here we show the synthesis of biogenic AgNPs using the extracellular cell-free filtrates of Penicillium expansum. The antimicrobial activity of the Penicillium expansum synthesized silver nanoparticles (hereafter PeNPs) was evaluated and the interactions between the nanoparticles and Escherichia coli were studied using Transmission Electron Microscopy (TEM) and Environmental Scanning Electron Microscopy (ESEM), showing the attachment of PeNPs to the surface of the bacteria and rupture of the bacterial cell membrane. Importantly, we show how Confocal Raman Microscopy can be used as an innovative approach to study the antimicrobial mechanisms, the results of which confirm that the PeNPs induce damage to bacterial and fungal cells, resulting in critical changes to polysaccharides, lipids, proteins and nucleic acids.

Femtosecond Time-Resolved Raman Spectroscopy Reveals Structural Evidence for meta Effect in Stilbenols.

The meta effect in substituted aromatics plays a crucial role in their excited-state photophysical properties. Meta-substituted hydroxyarenes such as naphthols, stilbenols, and chromophoric constituents of green fluorescent proteins show unusual photoacidity and enhanced fluorescence lifetime and quantum yield when compared to their para-derivatives. Variation in the excited state features of the meta-derivatives when compared to the para-derivatives in stilbenols has been attributed to the enhanced torsional barrier for interconversion between the planar and the twisted perpendicular forms. Herein, we employed femtosecond time-resolved Raman spectroscopy to provide the direct structural evidence for the enhanced torsional barrier in meta-stilbenol. The Raman band profiles of the olefinic C═C stretch related to the torsional motion are found to decay with time constants of ∼750 and ∼13 ps in meta-stilbenol and para-stilbenol respectively, unraveling the structural evidence for the observed enhanced photoacidity originating from enhanced rates of excited-state proton transfer. Further, time-resolved fluorescence measurements are performed to elucidate the relaxation pathways of the excited states of the stilbenols.

Raman Spectroscopic Investigation of Speciation in MnSO4(aq)

Raman spectroscopic measurements have been made on aqueous solutions of Mn(ClO4)2, MnSO4, and (NH4)2SO4 in the terahertz frequency region (45–600 cm−1), in a few cases to higher wavenumbers of 4,200 cm−1 and also down to low concentrations (0.0027 mol·L−1). In solutions of Mn(ClO4)2 with water and heavy water, the hexahydrate species and its corresponding deuterate, [Mn(OH2)6]2+ and [Mn(OD2)6]2+, were characterized and weak, strongly polarized bands are observed at 354 and 338 cm−1. These modes were assigned to ν 1(MnO6) of the species [(Mn(OH2)6]2+ and [(Mn(OD2)6]2+, respectively. In MnSO4(aq) the ν 1( $$ {\text{SO}}_{4}^{2 - } $$ ) mode at 980 cm−1 broadens with increasing concentration and shifts to higher wavenumbers. At the same time, a band at 995 cm−1 was detected and assigned to the bound sulfate of [MnOSO3], an inner-sphere complex (ISC). Confirmation of this assignment is provided by the simultaneous appearance of stretching bands of the Mn2+− $$ {\text{OSO}}_{3}^{2 - } $$ bond of the complex at 216 cm−1 and for the MnO5O* skeleton mode of [(H2O)5MnOSO3] at 321 cm−1 that is visible as a weak component next to the symmetric stretching mode, ν 1(MnO6), of the [Mn(OH2)6]2+(aq) species at 354 cm−1. The similarity of the ν 1( $$ {\text{SO}}_{4}^{2 - } $$ ) Raman band profiles for MnSO4 in H2O and D2O is further strong evidence for formation of an ISC. After subtraction of the ISC component at 995 cm−1, the ν 1( $$ {\text{SO}}_{4}^{2 - } $$ ) band in MnSO4(aq) showed systematic differences from that in (NH4)2SO4(aq). This is consistent with a ν 1( $$ {\text{SO}}_{4}^{2 - } $$ ) mode at 982.7 cm−1 that can be assigned to the occurrence of outer-sphere complex ions (OSCs). These observations are shown to be in qualitative agreement with results derived from previous relaxation measurements. The band profile of the much weaker asymmetric S–O stretching modes, ν 3( $$ {\text{SO}}_{4}^{2 - } $$ ), shows asymmetry and was fitted with four band components {including ν 3( $$ {\text{SO}}_{4}^{2 - } $$ (aq))}. Quantitative Raman measurements showed that the formation of ISCs in MnSO4(aq) is comparable to that found in the similar MgSO4(aq) system.

Simulated IR, Isotropic and Anisotropic Raman, and Vibrational Circular Dichroism Amide I Band Profiles of Stacked β-Sheets

The amide I mode is a highly structure sensitive vibration of polypeptides that gives rise to a very strong band in IR absorption and a moderate band in Raman spectra. Many theoretical simulations of IR-band profiles have been undertaken thus far in order to expand the usability of amide I for the structure analysis of peptides and proteins. These simulations have thus far focused on the IR band profiles and to a limited extent on calculating the corresponding vibrational circular dichroism (VCD) signal. In this paper, we use excitonic coupling theory to simulate the IR, isotropic Raman, anisotropic Raman, and VCD band profiles of amide I of parallel and antiparallel β-sheets as well as of two layers of stacked β-sheets with antiparallel and parallel orientations of the respective sheets. Our calculations reveal anisotropic Raman and to a lesser extent VCD amide I profiles rather than the corresponding IR profile as suitable tools to discriminate between parallel and antiparallel β-sheets. Stacking has a very limited influence on the Raman and IR band profiles, but enhance the VCD signal, the sign of which allows one to discriminate between parallel and antiparallel orientations of stacked sheets. Helical twisting and bending of parallel β-sheets give rise to a very enhanced positive couplet, in agreement with the recent work of Schweitzer-Stenner and Measey (J. Am. Chem. Soc., 2011, 133, 1066). Stochastic uncorrelated inhomogeneity of individual peptide groups causes significant asymmetric broadening of Raman bands and, to a lesser extent, of IR bands and reduces the VCD-couplet of stacked β-sheets.

Pressure-induced phase transitions in stearic acid C form

Pressure-dependent Raman scattering studies have been performed on stearic acid single crystal, C form. The vibrational spectra have been recorded in the 20–1200 cm −1 and in the 2800–3100 cm −1 spectral regions. The behavior of the Raman modes indicates that the crystal undergoes a series of structural modifications. The change observed between 0.8 and 1.27 GPa was associated with a conformational modification or tilting of the dimer. A second modification was observed at ∼2.5 GPa accompanied by jump of lattice mode frequencies, and the appearance and disappearance of bands. Finally, a third set of changes in the Raman band profile was observed between 3.3 and 3.8 GPa and was associated with another structural phase transition.

Time-Domain Theoretical Analysis of the Noncoincidence Effect, Diagonal Frequency Shift, and the Extent of Delocalization of the CO Stretching Mode of Acetone/Dimethyl Sulfoxide Binary Liquid Mixtures

A time-domain method for simulating vibrational band profiles that simultaneously takes into account both the diagonal and off-diagonal effects is developed and applied to the C=O stretching bands of neat liquid acetone and the acetone/dimethyl sulfoxide (DMSO) binary liquid mixtures. By using this method, it is possible to examine the influence of liquid dynamics on the noncoincidence effect (NCE), which arises from the off-diagonal vibrational interactions, as well as the frequency shifts and band broadening, which are related to both the diagonal and off-diagonal effects. It is shown that the simulations for the C=O stretching bands of acetone in acetone/DMSO binary liquid mixtures on the basis of this method can reproduce the experimentally observed concave curvature of the concentration dependence of the NCE and the unusually large frequency shift of the anisotropic Raman band. The widths of the infrared, isotropic Raman, and anisotropic Raman bands calculated for neat liquid acetone are also in good agreement with those observed. Based on these calculations, the extent of delocalization of the C=O stretching vibrational motions is examined by referring to two quantitative measures of this property, one calculated in the frequency domain and the other in the time domain. It is shown that the extent of delocalization gets larger as the mole fraction of acetone increases, the C=O stretching vibrations being delocalized over a few tens of molecules in neat liquid acetone. It is also shown that the extent of delocalization is related to the quantity called NCE detectability, which is the ratio between the magnitude of NCE and the bandwidth. It is therefore suggested that the extent of delocalization of vibrational motions may be estimated from observable features of Raman band profiles.

Influence of Liquid Dynamics on the Band Broadening and Time Evolution of Vibrational Excitations for Delocalized Vibrational Modes in Liquids

A theoretical method for treating the effects of liquid dynamics on vibrational band profiles is developed for the situation where resonant intermolecular vibrational interactions are operating. The liquid dynamics is simulated by the molecular dynamics (MD) technique, and the coupled vibrational Hamiltonian is constructed at each time step of the MD runs. Time evolution of delocalized IR and Raman excitations caused by this time-dependent coupled vibrational Hamiltonian is calculated to obtain IR and Raman band profiles as the Fourier transform of the corresponding time correlation functions. This method is applied to the case of the CO stretching band of neat liquid acetone, a typical case where the effect of resonant intermolecular vibrational interactions is known to be significant. The noncoincidence effect observed in this band is well reproduced. In addition, a better agreement between the observed and calculated bandwidths is obtained by using the present method as compared to the result of the calculation using only static liquid structures. As such, the present method is suggested to be a useful one for treating the effects of liquid dynamics on vibrational band profiles when the vibrations are resonantly coupled. The time scale of the modulation of vibrational eigenstates caused by the liquid dynamics is also discussed.

Electronic Raman transitions from the vanadium(III) hexa-aqua cation, in guanidinium vanadium sulphate

Electronic Raman transitions ( 3 A→ 3 E( C 3) ) have been observed between the trigonally split components of the 3 T 1 g ( O h ) ground term of the vanadium(III) hexa-aqua cation in guanidinium vanadium sulphate hexa-hydrate. The magnitude of the trigonal field splitting is considerable, ∼2720 cm −1, which is consistent with expectations based on the stereochemistry of the [V(OH 2) 6] 3+ complex. It is shown that a satisfactory reproduction of the electronic Raman band profile can be obtained only by assuming a ( 3 A⊕ 3 E)⊗e vibronic coupling model.

An Investigation of the Digitized Raman Band Profiles of Aqueous Mg(ClO4)2 - NaSCN Solutions

Raman spectra, together with factor analysis and band deconvolution procedure, have been used to study formation of magnesium thiocyanate complexes in aqueous solutions at ambient and elevated temperatures. The total salt concentration in solutions, containing different mole ratio of Mg2+ to SCN, varied between 3.4 and 7.5 mol dm−3. Factor analyses indicated that two linearly independent scattering components in the band envelopes, recorded in the V1 and v3 stretching regions of SCN, for all solutions with total salt concentration of 3.4 mol dm−3. The appearance of a pseudo-isosbestic point in the area normalized spectra supported this result, as well as the baud resolution procedure. The latter revealed the third scattering component in the spectra of solutions with total salt concentration above 3.5 mol dm−3 Resolved components have been assigned to the free thiocyanate, the 1:1 and 1:2 magnesium thiocyanate complexes. The equilibrium constant Kc of the 1:1 complex is of an order of 10−1 mol dm−3.

Far-infrared reflectivity and Raman spectra of Ba5Nb4O15.

We report low-temperature, far-infrared reflectivity, and Raman-scattering measurements for layered Ba5Nb4O15 . We find that this material is characterized by a strong anharmonic lattice where the symmetric stretching vibration of the empty octahedra, a singular feature of this layer compound, splits into two narrow Raman-active bands. We assign them to the same phonon in a slightly different environment, and suggest a small local departure of the reported centrosymmetric D3d 3 -P3m1 space group. We think that the infrared and mainly the Raman band profiles indicate that the lattice of Ba5Nb4O15 is close to collapsing into a lower symmetry structure.

Spectroscopic studies of vibrational relaxation and chemical exchange broadening in hydrogen bonded systems. IV. Analysis of the isotropic Raman bands of pyridine/water system

Raman (isotropic) band profiles for the v 1 band of pyridine in binary mixtures with water have been interpreted in terms of a dynamic exchange model which includes multiple ‘sites’, according to a reasonable equilibrium distribution of ‘complex’ species. At the simplest level, application of the Bratos-Strauss two-site model results in a k 21 value near 3 × 1010 s-1. This exchange rate leads to a rather small additional broadening and, indeed, has proved difficult to detect in the overall band profile. Extension to a three-site model, while useful to achieve a better ‘fit’ to the observed spectra, does not, for this system at least, cast additional light on the relaxation processes involved. In fact, the site-site exchange models may not be adequate for binary mixtures of water with organic bases. This is due to the existence of a very wide distribution, on the time scale of the experiment, of hydrogen bonded environments.

Studies on the Instrumental Factors Determining Errors in the Measurements of Raman Band Profiles. Part II: Effect of the Signal Noise on Vibrational Relaxation Functions and Relaxation Times

A method for the determination of the effect of the signal noise on vibrational correlation functions and relaxation times obtained in stationary spectroscopic measurements is proposed. It rests upon the assumption that electronic noise is mainly due to the photon counting which, for fast electronics, is described by Poisson statistics. The application of this method leads to results expressed as standard deviations which, for correlation functions, appear in very close agreement with the conclusions of statistical analysis, while for the relaxation times the results are lower than those delivered by statistical analysis.

Studies on the Instrumental Factors Determining Errors in the Measurements of Raman Band Profiles. Part I: Optical Factors—A Comparison of Three Different Methods

A treatment is proposed which takes into account the following error sources in Raman band shape measurements: incident beam polarization, polarization analyzer misorientation, monochromator response, and observation over a finite solid angle. Three methods generally adopted for this type of measurements are compared in terms of the amount of spurious anisotropic component which enters the isotropic profile. The pertinence zones of each method are shown. The percentage of error is expressed by well-defined quantities entering analytical equations; this allows the experimentalist to choose the more suitable method on the basis of the experimental setup.

Reply to comment on “The evolution between slow and rapid chemical exchange processes in a liquid binary mixture”

We emphasise that a collapsing infrared or Raman band profile with increasing temperature does not necessarily imply a movement between the “slow” and “rapid” exchange regimes. We point to systems where band collapse occurs in the slow regime and suggest that for a CH 3CN/CH 3OH binary mixture the spectra are so complex that unambiguous analysis is difficult.

Theoretical analysis of the resonance Raman spectra of diacetylene single crystals

Resonance Raman spectra of polymer chains in the single crystals of the diacetylenes FBS (2,4-hexadiynylene-di-p-fluorobenzene sulfonate), TS/FBS [6-(p-toluenesulfonyloxy)-2,4-p-fluorobenzene sulfonate] and TS6 (2,4-hexadiynylene-di-p-toluene sulfonate) are described theoretically by means of a Franck–Condon model, which considers a chain length dependence. The electronic transition energies and matrix elements are calculated by means of a linear-combination-of-atomic-orbitals–molecular-orbital method calculation in the Hückel approach. We are able to describe the Raman excitation profiles as well as the Raman band profiles for two Raman active modes, i.e., the C+C-, and the C 3/4 C-stretching vibrations of the polymer chains. The model also contains a description of a side group vibrational mode which is enhanced by Fermi resonance with the C=C-stretching vibration. Observed Raman excitation profiles can be well simulated by these calculations. An evaluation of the parameters shows a strong influence of defects, which is described by including inhomogeneous broadening in the theoretical model. An interaction between ensemble and intramolecular properties due to defects can be shown. Simulation of the Raman band profiles yields information on the influence of chain length distribution. Changes of position and Raman band profile as well as of the strength of the Fermi resonance can be explained by the enhancement of modes belonging to polymer chains having different chain lengths. A considerable influence of the substitutents results in remarkable changes of several parameters on which the model calculation is based.

Rotational relaxation times from Raman band profiles for benzonitrile in different solvents

The Raman band profiles of two vibrational bands of benzonitrile belonging to the a1 species (2243 and 1000 cm-1) were analysed by separating the isotropic and anisotropic components. Spectra of benzonitrile were recorded, using argon laser excitation, in solutions of CC14, CS2, cyclohexane, cyclohexanol and tertiary butyl alcohol-all having different viscosities. The rotational correlation times were evaluated from the band profiles. The results indicate that (a) the isotropic (and not the anisotropic) linewidth increases with increasing viscosity, which is attributed to the greater effect of intermolecular interactions on vibrational relaxation; and (b) the two modes of the same species give different relaxation times.

Molecular motion of n-alkane chains in urea inclusion adducts studied by analysis of Raman band profiles

A quantitative analysis of the temperature dependence of the motional broadening of the Raman bands associated with the guest alkane molecules accommodated in the hexagonal phase of urea inclusion adducts of even-numbered n-alkanes of n–C14H30 through n–C22H46 was performed according to the site-hopping theory. The profiles of a certain polarization component of the following five bands; the CH2 antisymmetric stretch νa(CH2) (XY), the CH2 scissoring δ(CH2)(ZZ) and the CH2 twist t(CH2)(XZ), and the symmetric and antisymmetric CC stretches νs(CC)(ZZ) and νa(CC)(XZ)[Z∥c,X,Y⊥c], were found to be reproducible by a single Lorentzian function in the whole temperature range covering both the orthorhombic and hexagonal phases. Difference in the broadening behavior among the five Raman bands was interpreted quantitatively in terms of the equation derived previously by the authors. For each adduct, the value of the potential barrier height E* to the rotational motion of the alkane molecules was obtained in a good constancy from the temperature dependence of the half-width of the bands which belonged to different symmetry species and exhibited different broadening behavior. The value of E* for the C-16 adduct agreed well with the barrier height calculated on the basis of van der Waals intermolecular potential functions and the crystal structure. The E* value was found to increase monotonically with an increase in the chain length of the guest n-alkane molecule, except for an anomalous increase at C-20, as has been observed in the chain-length dependence of the transition temperature between the orthorhomic and hexagonal phases. The end-gauche content of the guest molecules in the hexagonal phase was evaluated as about 5 mol% irrespective of the chain length. For the alkane vibrations, bandshifts with variation in temperature were measured and analyzed according to the libration–torsion theory presented by Wood et al.

Effect of temperature on the hydrogen bond distribution in water as studied by infrared spectra

The effect of temperature on the distribution of oxygen-oxygen distances between hydrogen-bonded nearest neighbors in water has been studied by measuring infrared band profiles of the OD stretching vibration of dilute HDO in H 2O at various temperatures in the −6 to 80°C range. The distribution functions obtained from the infrared band profiles closely resemble those obtained from Raman band profiles. Both the O…O bond length at maximum distribution and the breadth of the distribution increase linearly with increasing temperature.

Vibrational spectroscopic studies of tervalent hexa-aqua cations: oriented single-crystal Raman spectra between 275 and 1 200 cm–1of the caesium rhodium alums, CsRh(SO4)2·12H2O, CsRh(SeO4)2·12H2O, and CsRh(SO4)2·12D2O

Oriented single-crystal Raman spectra of the caesium α-alums CsRh(SO4)2·12H2O, CsRh(SeO4)2·12H2O, and CsRh(SO4)2·12D2O have been recorded at or below 80 K. The external modes of water co-ordinated to the mono- and ter-valent cations as well as the internal modes of S(Se)O42– and [Rh{OH(D)2}6]3+ are found in the spectral region 275–1 200 cm–1. A full assignment of the spectra in this region has been completed and the results are in close agreement with the predictions of factor group analysis. This work provides the first full vibrational characterisation of the Raman-active modes of the sulphate α-alum lattice. The site and factor group splitting of the XO42– vibrational modes is independent of the identity of X but highly dependent on the alum type, with the internal modes of SO42– in the caesium rhodium sulphate α-alums giving similar Raman band profiles to those of SeO42– in the caesium selenate α-alums. The internal modes of [Rh(OH2)6]3+ are found at 548[ν1(RhO6)], 533 [ν2(RhO6)], and 315 cm–1[ν5(RhO6)] in the low-temperature single-crystal spectra, while the ν1(Rho6) mode occurs at 529 cm–1 in solution (300 K, 1 mol dm–3 H2SO4). The relationship between the wavenumber of the ν1(RhO6) mode and the Rh–O bond length is significantly different compared with that obtained for the first-row transition-metal tervalent hexa-aqua ions.