Out‐of‐plane deformations of the heme group in different ferrocytochrome c proteins probed by resonance Raman spectroscopy

We measured the low‐wavenumber polarized resonance Raman spectra of horse heart (hhc), chicken (chc) and yeastC102T (yc) ferrocytochromes c with Soret excitation. We examined the out‐of‐plane (oop) deformations of the heme groups by virtue of relative intensities and depolarization ratios of a variety of oop and in‐plane (ip) Raman active bands. Analysis of relative Raman intensities shows differences in deviation from planarity of the heme groups of yeast, horse heart and chicken cytochromes c. The heme groups in cytochrome c proteins have been shown by normal coordinate static deformation (NSD) analysis from crystal structures to exhibit a dominant ruffling (B_1u) deformation. As a consequence the B_1u modes, γ₁₀ − γ₁₂, become resonance Raman active. We used normalized Raman intensity ratios and depolarization ratios of oop Raman active modes, whose intensities are attributable to specific nonplanar deformations, to estimate and compare their Franck‐Condon‐type and Jahn‐Teller‐type coupling magnitudes for horse heart, chicken and yeast ferrocytochrome c at neutral pH. These coupling magnitudes allow for a quantitative comparison of oop deformations between individual heme groups. Chicken ferrocytochrome was found to have the largest ruffling deformation of the three investigated proteins, followed by horse heart and yeast cytochrome c. The heme group of the former is slightly more ruffled than the corresponding active site of the latter, while saddling in both proteins is substantially larger than in chicken ferrocytochrome c. The Raman data are sensitive enough to allow a comparison of lesser deformations. Doming, which is a kinetic coordinate in many heme proteins, is largest in chicken and smallest in yeast cytochrome c. Waving is largest in yeast, followed by horse heart and chicken cytochrome c. Propellering deformations could be compared for chicken and horse heart cytochrome c and were found to be substantially larger in the latter. A comparison with heme deformations obtained from X‐ray structures (for horse heart and yeast cytochrome c) and from molecular dynamics simulations (MDS) (performed for all three proteins) yields some agreement with the main ruffling and saddling deformations derived from the crystal structures, whereas the heme conformations produced by MDS seem to account better for smaller deformations like doming and propellering. The present study demonstrates the usefulness of resonance Raman spectroscopy for the analysis of nonplanar deformations in heme proteins. Copyright © 2008 John Wiley & Sons, Ltd.     

Polarized Raman and photoluminescence studies of a sub‐micron sized hexagonal AlGaN crystallite for structural and optical properties

The polarized Raman spectroscopy is capable of giving confirmation regarding the crystalline phase as well as the crystallographic orientation of the sample. In this context, apart from crystallographic X‐ray and electron diffraction tools, polarized Raman spectroscopy and corresponding spectral imaging can be a promising crystallographic tool for determining both crystalline phase and orientation. Sub‐micron sized hexagonal AlGaN crystallites are grown by a simple atmospheric pressure chemical vapor deposition technique using the self catalytic vapor–solid process under N‐rich condition. The crystallites are used for the polarized Raman spectra in different crystalline orientations along with spectral imaging studies. The results obtained from the polarized Raman spectral studies show single crystalline nature of sub‐micron sized hexagonal AlGaN crystallites. Optical properties of the crystallites for different crystalline orientations are also studied using polarized photoluminescence measurements. The influence of internal crystal field to the photoluminescence spectra is proposed to explain the distinctive observation of splitting of emission intensity reported, for the first time, in case of c‐plane oriented single crystalline AlGaN crystallite as compared with that of m‐plane oriented crystallite. Copyright © 2016 John Wiley & Sons, Ltd.     

The structure and proton affinity of N‐benzyl‐N‐(allenyl)trifluoromethanesulfonamide: FT‐IR,DFT and ab initio study,NBO analysis

The first N‐allenyl derivative of trifluoromethanesulfonamide, N‐benzyl‐N‐(allenyl)trifluoromethanesulfonamide ( 1 ), was studied experimentally by the FT‐IR spectroscopy and theoretically at the DFT and MP2 levels of theory. The intramolecular interaction of the nitrogen atom with the triflyl and the allenyl group was studied in comparison with the analogously substituted vinyl derivatives. Compound 1 in heptane solution at 295–183 K exists as an equilibrium mixture of conformational isomers. Protonation at different basic sites in a series of reference molecules is studied theoretically. The central C² atom of the allenyl group in 1 has the highest proton affinity, which is 16 kcal/mol higher than in the N‐vinyl analogues. The relative ability of the allenyl and vinyl groups to conjugation with an electron‐rich and electron‐deficient nitrogen atom lone electron pair is discussed. From the NBO analysis, the conjugation of the nitrogen lone electron pair with the allenyl group is much stronger than with the vinyl group. Copyright © 2013 John Wiley & Sons, Ltd.     

Nanomechanics of single silkworm and spider fibres: a Raman and micro‐mechanical in situ study of the conformation change with stress

The combination of micro‐Raman spectroscopy and an advanced universal fibre tester (UFT) made it possible to probe at the nanoscale (through monitoring the modification of chemical bonds) the change in conformation (α‐helix, β‐sheet, etc.), macromolecular fibroin chain orientation and coupling during the application of stress, quantitatively. Different single fibres of silkworms (Bombyx mori, Gonometa rufobrunea, Gonometa postica) and a spider (Nephila madagascariensis) were tested in a dry environment and compared with the behaviour of keratin fibre. As observed previously for single keratin fibres, a direct relationship is observed between nano‐ and micro‐mechanical tensile behaviour. The phase transition plateau, well defined for some pristine B. mori fibres, disappears in degummed fibres, which indicates a structural modification and increasing disorder with chemical treatments. Stress‐controlled micro‐Raman analysis shows that a few modes involving CH₂ and/or amide groups of β‐conformation chains undergo a wavenumber softening during the elastic behaviour (∼0–3%), although most of the modes are not affected. A different behaviour is observed for modes associated with ‘ordered’ and ‘disordered’ β‐sheets and helical chains. Larger softening is observed for lattice modes with increasing stress/strain, as expected. Structural changes and relationships with mechanical behaviour are discussed. Copyright © 2008 John Wiley & Sons, Ltd.     

Resonance Raman spectroscopic investigation of structural changes of CO‐heme in soluble guanylate cyclase generated by effectors and substrate

The influence of the effectors YC‐1 and BAY on the CO‐heme structure of bovine lung soluble guanylate cyclase (sGC) was investigated with resonance Raman spectroscopy. The effectors produced a five‐coordinate (5c) CO‐heme in addition to the His‐bound six‐coordinate (6c) CO‐heme, and both their Soret maxima were determined by simulation. On the basis of the absorption intensity, the amount of the 5c species was not dominant, in contrast to the high activity. The heme structural features common to the 5c and 6c CO‐hemes generated by effectors are that the vinyl and propionate side chains are more coplanar to the pyrrole rings. The out‐of‐plane Raman bands were observed only for the 5c species, for which the saddling and propeller distortions of heme were deduced to be large. The Fe CO stretching bands of the 5c species at 522 cm⁻¹ and of the 6c species at 488 cm⁻¹ were most enhanced upon excitation at 407 and 422 nm, respectively, which is consistent with the simulated spectra. Unexpectedly, the ¹³C¹⁸O isotope sensitivity appeared in low wavenumber porphyrin modes. From these observations, we propose that the high catalytic activity of sGC‐CO in the presence of effectors is a result of the concerted effects of protein conformational changes triggered by certain local interactions between the heme side chains and effectors/substrate in the heme pocket, which partly induce the cleavage of the Fe Hisβ 105 bond. Copyright © 2010 John Wiley & Sons, Ltd.     

Raman imaging and stress quantification in self‐assembled graphene oxide fiber ‘Latin Letters’

To probe the intrinsic stress distribution in terms of spatial Raman shift (ω) and change in the phonon linewidth (Γ), here we analyze self‐assembled graphene oxide fibers (GOF) ‘Latin letters’ by confocal Raman spectroscopy. The self‐assembly of GOF ‘Latin letters’ has been explained through surface tension, π–π stacking, van der Waals interaction at the air–water interface and by systematic time‐dependent investigation using field emission scanning electron microscopy analysis. Intrinsic residual stress due to structural joints and bending is playing a distinct role affecting the E_2g mode (G band) at and away from the physical interface of GOF segments with broadening of phonon linewidth, indicating prominent phonon softening. Linescan across an interface of the GOF ‘letters’ reveals Raman shift to lower wavenumber in all cases but more so in ‘Z’ fiber exhibiting a broader region. Furthermore, intrinsic stress homogeneity is observed for ‘G’ fiber distributed throughout its curvature with negligible shift corresponding to E_2g mode vibration. This article demonstrates the significance of morphology in stress distribution across the self‐assembled and ‘smart‐integrable’ GOF ‘Latin letters’. Copyright © 2016 John Wiley & Sons, Ltd.     

NIR‐FT Raman,FT‐IR and surface‐enhanced Raman scattering spectra,with theoretical simulations on chloramphenicol

Chloramphenicol (CLM), originally derived from the bacterium Streptomyces venezuelae, is an inhibitor of bacterial ribosomal peptidyl transferase activity. The near infrared Fourier transform (NIR‐FT) Raman, surface‐enhanced Raman spectroscopy (SERS) and Fourier transform infrared (FT‐IR) spectral analyses of CLM, a potential antibacterial drug for the treatment of typhoid fever, were carried out along with density functional computations. The vibrational spectral analysis reveals that the CH₂ asymmetric and symmetric stretching modes are shifted to higher wavenumbers than the computed values, owing to the electronic effects resulting from induction of methylene group with the adjacent electronegative atom. The lowering of CO stretching wavenumber is due to the presence of the strong electronegative atom, nitrogen, attached to the carbonyl carbon, causing large degree of molecular π‐electron delocalization and redistribution of electrons, which weakens the CO bond. The absence of a C H stretching vibration and the observed C H out‐of‐plane bending modes suggest that the CLM molecule may be adsorbed in a flat orientation with respect to the silver surface. Copyright © 2008 John Wiley & Sons, Ltd.     

Spectroscopic characterization of cadion: UV–vis,resonance Raman and DFT calculations of a versatile metal complexing agent

The spectroscopic characterization of cadion or 1‐(4‐nitrophenyl)‐3‐(4‐phenylazophenyl)triazene, its anionic species and its complexes with Hg²⁺, Cd²⁺ and Ni²⁺ in DMSO solution is presented. Resonance Raman (RR) and UV–vis spectroscopy were the techniques of choice with results supported by density functional theory calculations. As previously reported, the UV–vis data indicate distinct absorption spectra for the five species mentioned, allowing for spectrophotometric metal differentiation. In order to understand the electronic spectra of such species, we performed a detailed RR investigation, where the spectral profiles revealed the vibrational modes mainly involved in the chromophoric moieties. The distinct enhancement profile observed for each species suggests that the charge transfer from the π‐system to the electron withdrawing NO₂ group is modulated by the electron donating triazene moiety, depending on the metal attached. The results reported herein show that RR spectroscopy can be potentially used in the metal detection of multicomponent samples by the proper choice of the excitation wavelength. Copyright © 2012 John Wiley & Sons, Ltd.     

Conformational analysis of 4,4‐dimethyl‐1‐(trifluoromethylsulfonyl)‐1,4‐azasilinane and 2,2,6,6‐tetramethyl‐4‐(trifluoromethylsulfonyl)‐1,4,2,6‐oxazadisilinane

4,4‐Dimethyl‐1‐(trifluoromethylsulfonyl)‐1,4‐azasilinane 1 and 2,2,6,6‐tetramethyl‐4‐(trifluoromethylsulfonyl)‐1,4,2,6‐oxazadisilinane 2 were studied by variable temperature dynamic ¹H, ¹³C, ¹⁹F NMR spectroscopy and theoretical calculations at the DFT (density functional theory) and MP2 (Møller‐Plesset 2) levels of theory. Both kinetic (barriers to ring inversion) and thermodynamic data (frozen conformational equilibria) could be obtained for the two compounds. The computations revealed two minima on the potential energy surface for molecules 1 and 2 corresponding to the rotamers with the CF₃SO₂ group directed ‘inward’ and ‘outward’ the ring, the latter being 0.2–0.4 kcal/mol (for 1 ) and 1.1 kcal/mol (for 2 ) more stable than the former. The vibrational calculations at the DFT and MP2 levels of theory give the values of the free energy difference ΔG^o for the ‘inward’ ‘outward’ equilibrium consistent with those determined from the experimentally measured ratio of the rotamers. The structure of crystalline compound 2 was ascertained by X‐ray diffraction analysis. Copyright © 2011 John Wiley & Sons, Ltd.     

In‐plane deformations of the heme group in native and nonnative oxidized cytochrome c probed by resonance Raman dispersion spectroscopy

We determined the dispersion of the depolarization ratio (DPR) of several Raman bands of ferricytochrome c at different pH values using low‐ionic‐strength conditions. The experimental data predominantly cover the pre‐resonance and resonance region of Q‐band excitation. The selected pH values 7.5, 9.0, 10.0 and 11.0 correspond to the conformational states III, III*, IV, and V of the protein. While the existence of the states III, IV, and V is known for nearly 70 years, the nativelike state III* has only recently been obtained from optical measurements at low ionic strength [D. Verbaro, A. Hagarman, J. B. Soffer and R. Schweitzer‐Stenner, Biochemistry, 48, 2990, 2009]. We used group‐theoretical arguments to obtain in‐plane symmetry‐lowering deformations from the obtained DPRs of various Raman bands in the high‐wavenumber region of the obtained spectra. Thus, we found that a comparatively strong rhombic deformation along the B_1g mode, ν₁₈, is maintained at all pH values investigated. It most likely arises from static Jahn‐Teller distortion of the E‐symmetry ground state. While this distortion depends on the existence of a strong sixth ligand, its occurrence is rather independent of the nature of this ligand as long as a low‐spin configuration is maintained. The III → III* transition was found to modify A_1g‐type perturbations of the heme macrocycle. This is likely to reflect a decrease in nonplanar distortions such as ruffling and saddling. This drop in nonplanarity is slightly reversed by the subsequent transitions into states IV and V. Circular dichroism (CD) spectra of the Q‐band region suggest that the III → III* transition reduces the electronic contribution to the Q‐band splitting, which could reflect either a weakening or a reorientation of the internal electric field in the heme pocket. Our results underscore the relevance of state III* as a thermodynamic intermediate of the alkaline transition between states III and IV. Copyright © 2010 John Wiley & Sons, Ltd.     

Potential‐induced Raman behavior of individual (R)‐di‐2‐naphthylprolinol molecules on a Ag‐modified Ag electrode

The applicability of surface‐enhanced Raman spectroscopy is demonstrated to probe the adsorption behavior of individual molecules on a Ag electrode. High‐quality SERS spectra of (R)‐di‐2‐naphthylprolinol (DNP) were obtained from ultradilute solutions (10⁻¹² M ) on the Ag‐nanoparticle‐modified Ag electrode, which is attributed to the high electromagnetic (EM) effect of the SERS‐active system as well as to the strong adsorption and interaction of DNP molecules with Ag. The stable SERS spectra present remarkable potential dependence, which gives evidence for the behavior of individual DNP molecules on the Ag surface. Based on statistical analysis for the probability of DNP molecules located in ‘hot spots’, we propose an SERS mechanism for individual molecules in the electrode system, in combination with the hot‐spot model and orientation of the probe molecules. Copyright © 2010 John Wiley & Sons, Ltd.     

Surface‐enhanced resonance Raman spectroscopic characterization of cytochrome c immobilized on 2‐mercaptoethanesulfonate monolayers on silver

Single‐component self‐assembled monolayers (SAMs) of mercaptoethanesulfonate (MES) on Ag surfaces were studied with surface‐enhanced resonance Raman scattering (SERRS) spectroscopy with a view to their application to immobilize (ferro)cytochrome c (cyt c). SERS studies revealed that MES molecules adopt primarily trans (T) conformation even at early stages of the SAM growth and over wide range of pH values. High accessibility of the negatively charged groups for (bio)molecules in solution makes single‐component MES SAMs suitable linkage monolayers for electrostatic attachment of cyt c, which was verified with SERRS. Cyt c was successfully anchored to MES‐coated Ag at natural (∼5), neutral, and isoelectric point (10.6) pH. At pH = 7.0 and 10.6, SERRS bands characteristic of native six‐coordinated low‐spin (6cLS) heme iron configuration were detected. Lack of buffering resulted in additional appearance of five‐coordinated high‐spin (5cHS) SERRS markers and the presence of bands indicating ferric ion. An electrostatic attraction between protein and SAM was confirmed to exclude the hydrophobic interactions involved in cyt c binding. Cyt c attached to MES SAM on Ag was found to be electroactive at neutral pH, and protein oxidation was assisted with reversible conversion of 6cLS to the non‐native 5cHS state. Alteration of heme orientation deduced from SERRS spectra upon change of redox state allowed us to propose the protein dynamics as the electron transfer rate‐limiting step. Copyright © 2010 John Wiley & Sons, Ltd.     

Room‐temperature photoluminescence in quasi‐2D TlGaSe2 and TlInS2semiconductors

We reveal the intrinsic band‐to‐band photoluminescence (PL) in Tl‐based anisotropic semiconductors by means of confocal spectroscopy. The PL achieves largest value for k ⊥ c , where c is the layers stacking axis, and is dependent on polarization. In TlGaSe₂, the band edge absorption spectra were determined at different excitation geometry by using techniques of depth‐resolved free‐carrier absorption (FCA) and photoacoustic response (PAR). A strong absorption enhancement is detected in a large spectral area in the near‐surface region lateral to ab plane. The band‐to‐band absorption enhancement is the most probable cause for high PL intensity. The near‐surface behavior, different from the bulk, might implement useful photonic functionality at room temperature (RT). (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Solvation of AgTFSI in 1‐ethyl‐3‐methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquid investigated by vibrational spectroscopy and DFT calculations

In this paper we investigate the solvation of silver bis(trifluoromethylsulfonyl)imide salt (AgTFSI) in 1‐ethyl‐3‐methylimidazolium TFSI [EMI][TFSI] ionic liquid by combining Raman and infrared (IR) spectroscopies with density functional theory (DFT) calculations. The IR and Raman spectra were measured in the 200–4000 cm⁻¹ spectral region for AgTFSI/[EMI][TFSI] solutions with different concentrations ([AgTFSI] <0.2 mole fraction). The analysis of the spectra shows that the spectral features observed by dissolution of AgTFSI in [EMI][TFSI] solution originate from interactions between the Ag⁺ cation and the first neighboring TFSI anions to form relatively stable Ag complexes. The ‘gas phase’ interaction energy of a type [Ag(TFSI)₃]²⁻ complex was evaluated by DFT calculations and compared with other interionic interaction energy contributions. The predicted spectral signatures because of the [Ag(TFSI)₃]²⁻ complex were assessed in order to interpret the main IR and Raman spectral features observed. The formation of such complexes leads to the appearance of new interaction‐induced bands situated at 753 cm⁻¹ in Raman and at 1015 and 1371 cm⁻¹ in IR, respectively. These specific spectral signatures are associated with the ‘breathing’ mode and the S–N–S and S–O stretching modes of the TFSI anions engaged in the complex. Finally, all these findings are discussed in terms of interaction mechanisms enabling the electrodeposition characteristics of silver from AgTFSI/[EMI][TFSI] IL‐based electrolytic solutions. Copyright © 2015 John Wiley & Sons, Ltd.     

The vibrational spectra of the cyanide ligand revisited: the ν(CN) infrared and Raman spectroscopy of Prussian blue and its analogues

A careful analysis of the Raman spectra of the M′_x[M(CN)₆]_y Prussian blue species has enabled a general model for the interpretation of the ν(CN) vibrational spectra. The spectral patterns are derived from those of the metal ions with local O_h symmetry. Two limiting models are discussed. A ‘localized mode’ model, involving matrix‐isolated species, is in much better accord with the observations than a ‘factor group’ model. The use of the infrared feature as fingerprint of specific M CN M′ units arises from the axis‐specific nature of individual T_1u modes. The interpretation of the A_1g and E_g Raman features is done in terms of localized vibrations, with involvement of additional energy terms from the lattice motions. Copyright © 2011 John Wiley & Sons, Ltd.     

IR,Raman and SERS spectra of 3,5‐dinitrosalicylic acid

IR, Raman and surface enhanced Raman scattering (SERS) spectra of 3,5‐dinitrosalicylic acid (DNSA) were recorded and analysed. The vibrational wavenumbers were computed by the ab initio method using RHF/6–21G* basis and they were found to be in good agreement with the experimental values. The effect of the concentration dependence on the SERS intensity of the molecule was studied. The molecular plane assumes a tilted orientation with respect to the silver surface. Copyright © 2006 John Wiley & Sons, Ltd.     

Density functional study on the structural conformations and intramolecular charge transfer from the vibrational spectra of the anticancer drug combretastatin‐A2

Combretastatin‐A2 (CA2), a potential anticancer drug in advanced preclinical development, is extracted from the medicinal plant C ombretum caffrum. The NIR‐FT Raman and FT‐IR spectral studies of the molecule were carried out and a b initio calculations performed at the B3LYP/6‐31G(d) level to derive the equilibrium geometry as well as the vibrational wavenumbers and intensities of the spectral bands. The vibrational analysis showed that the molecule has a similar geometry as that of c is‐stilbene, and has undergone steric repulsion resulting in twisting of the phenyl ring with respect to the ethylenic plane. Vibrational analysis was used to investigate the lowering of the stretching modes, and enhancement of infrared band intensities of the C–H stretching modes of Me2 may be attributed to the electronic effects caused by back‐donation and induction from the oxygen atom. Analysis of phenyl ring modes shows that the CA2 stretching mode 8 and the aromatic C–H in‐plane bending mode are equally active as strong bands in both IR and Raman spectra, which can be interpreted as the evidence of intramolecular charge transfer (ICT) between the OH and OCH₃groups via conjugated ring path and is responsible for bioactivity of the molecule. Copyright © 2008 John Wiley & Sons, Ltd.     

Sub‐picosecond Raman spectrometer for time‐resolved studies of structural dynamics in heme proteins

We describe a pump–probe Raman spectrometer based on a femtosecond Ti:sapphire laser, an optical parametric generator and two optical parametric amplifiers for time‐resolved studies, with emphasis on the structural dynamics in heme proteins. The system provides a 100‐fs pump pulse tunable in the range 500–600 nm and a transform‐limited sub‐picosecond probe pulse tunable in the range 390–450 nm. The spectrometer has spectral (25 cm⁻¹) and temporal (∼0.7 ps) resolutions which constitute an effective compromise for identifying transient heme protein species and for following their structural evolution by spontaneous Raman scattering in the time range 0.5 ps to 2 ns. This apparatus was applied to time‐resolved studies of a broad range of heme proteins, monitoring the primary dynamics of photoinduced heme coordination state and structural changes, its interaction with protein side‐chains and diatomic gaseous ligands, as well as heme vibrational cooling. The treatment of transient Raman spectra is described in detail, and the advantages and shortcomings of spontaneous resonance Raman spectroscopy for ultrafast heme proteins studies are discussed. We demonstrate the efficiency of the constructed spectrometer by measuring Raman spectra in the sub‐picosecond and picosecond time ranges for the oxygen‐storage heme protein myoglobin and for the oxygen‐sensor heme protein FixLH in interaction with the diatomic gaseous ligands CO, NO, and O₂. Copyright © 2010 John Wiley & Sons, Ltd.