Inclusions of black-green serpentine jade determined by Raman spectroscopy

This work aims to determine the formation mechanism as well as the major mineral and inclusions of black-green serpentine jade by Raman spectroscopy. Scanning electron microscopy with energy-dispersive spectrometry was used to analyze the chemical composition of the inclusions and major mineral. The major mineral of black-green serpentine jade was antigorite, and the inclusions were actinolite, chlorite, calcite, quartz, magnetite, and goethite. Jade quality was preliminarily evaluated based on the area ratio of antigorite to the inclusions by optical microscopy. Formation mechanism of black-green serpentine jade was inferred based on the analysis of the inclusions, which demonstrated a new application of Raman spectroscopy in mineralogy.     

Site distribution in resin beads as determined by confocal Raman spectroscopy

Scanning confocal Raman spectroscopy was used to study the distribution of reactive sites within a resin bead used for solid-phase synthesis. The distribution of NH2 groups in aminomethylated polystyrene resin (APS) was determined by doping with varying amounts of 4-cyanobenzoic acid. The extent of loading was determined by both elemental analysis and ninhydrin assays. The spatial distribution of the coupled 4-cyanobenzamide within the bead was determined to an in-plane resolution of 1 microm and depth resolution of about 4 microm, using the strong Raman CN stretching vibrational transition at 2230 cm(-1). Dry and swollen beads were studied and the distribution was found to be essentially uniform throughout the bead in all cases.     

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.     

Conformational and phase transformations of chlorocyclohexane at high pressures by Raman spectroscopy

Pressure induced conformational and phase transformations of chlorocyclohexane (CCH) were investigated in a diamond anvil cell by Raman spectroscopy at room temperature. Pure CCH was compressed up to 20 GPa and then decompressed to ambient pressure. The conformational equilibrium was shifted by pressure from equatorial to axial conformers in the fluid phase below 0.7 GPa, consistent with previous observations. Upon further compression, several solid-to-solid phase transitions were identified by the observation of markedly different Raman patterns as well as different pressure dependences of characteristic Raman modes. The possible structures of these phases were analyzed in correlation with previously observed solid phases at low temperatures. Finally, CCH exhibits pressure hysteresis and partial reversibility upon decompression which result in the formation of the phases with different Raman patterns from those obtained upon compression. The difference can be interpreted as conformational contribution as well as the intrinsic plasticity of CCH crystals.     

Conformational studies of n-propylamine by combined ab initio MO calculations and Raman spectroscopy

The results of ab initio SCF-MO calculations performed with a 3-21G(N*) basis set, for fully optimized geometries of five conformations of n-propylamine, are presented. The calculated relative order of total energies for these conformers is TT≈GG′>TG>GT>GG. At 300 K, the Boltzmann distribution of populations is 18, 37, 20, 19 and 7%, respectively.Raman spectra of n-propylamine and n-propylamine-N-d₂ in the liquid phase exhibit a number of bands whose temperature-dependent intensities clearly suggest the occurrence of different conformers in simultaneous equilibria. Deuteration of the amine group originates pairs of Raman bands at 428 and 440 cm⁻¹ and at 863 and 885 cm⁻¹. The bands at 428 and 885 cm⁻¹ are favoured by reduction of temperature. Normal coordinate calculations permit the assignment of the Raman and i.r. spectra in good agreement with experimental evidence. Among the five possible conformers of n-propylamine, it is possible to detect the presence of at least three conformations in the liquid phase, corresponding to the skeletal trans (TT and GT) and at least one of the skeletal gauche (TG, GG or GG′) forms. In the solid phase, only the bands ascribed to the TT form were observed.The ab initio results for the isolated molecule show that the all-trans conformation, TT, and the conformation GG′ have the smallest energies. On the other hand, the vibrational results for the liquid and solid phases indicate that the all-trans conformation, TT, is the more populated form. In addition, this conformer presents the highest calculated dipole moment, in good agreement with the liquid phase Raman spectroscopic results which point out that this conformation is favoured by polar solvents. Intermolecular interactions operating in the liquid n-propylamine, possibly of the hydrogen bonding type, are responsible for altering the relative order of conformational stability as predicted by the ab initio SCF-MO results for the isolated molecule.     

Conformational studies of mercaptoacetaldehyde and mercaptoacetone by 1H-NMR,Raman and infrared spectroscopy

Molecular structures of mercaptoacetaldehyde and mercaptoacetone in the crystalline state and in solutions have been studied by ¹H-NMR, Raman and infrared spectroscopy. Both compounds exist as centrosymmetric dimers having six-membered 1,4-dithian ring skeletons in the crystalline state and in freshly-prepared dimethylsulfoxide and pyridine solutions. In equilibrium solutions, non-centrosymmetric dimers having 1,4-dithian ring skeletons and the monomer also exist. No evidence that suggests the existence of five-membered ring dimer in solutions has been obtained for both compounds. The most stable species in solution is the non-centrosymmetric dimer in the case of mercaptoacetaldehyde and the monomer in the case of mercaptoacetone.     

Conformational equilibrium and hydrogen bonding in liquid 2-phenylethylamine explored by Raman spectroscopy and theoretical calculations

2-Phenylethylamine (PEA) is the simplest aromatic amine neurotransmitter, as well as one of the most important. In this work, the conformational equilibrium and hydrogen bonding in liquid PEA were studied by means of Raman spectroscopy and theoretical calculations (DFT/MP2). By changing the orientation of the ethyl and the NH(2) group, nine possible conformers of PEA were found, including four degenerate conformers. Comparison of the experimental Raman spectra of liquid PEA and the calculated Raman spectra of the five typical conformers in selected regions (550-800 and 1250-1500 cm(-1)) revealed that the five conformers can coexist in conformational equilibrium in the liquid. The NH(2) stretching mode of the liquid is red-shifted by ca. 30 cm(-1) relative to that of an isolated PEA molecule (measured previously), implying that intermolecular N-H···N hydrogen bonds play an important role in liquid PEA. The relative intensity of the Raman band at 762 cm(-1) was found to increase with increasing temperature, indicating that the anti conformer might be favorable in liquid PEA at room temperature. The blue shift of the band for the bonded N-H stretch with increasing temperature also provides evidence of the existence of intermolecular N-H···N hydrogen bonds.     

Conformational changes in a photosensory LOV domain monitored by time-resolved NMR spectroscopy

Phototropins are light-activated kinases from plants that utilize light-oxygen-voltage (LOV) domains as blue light photosensors. Illumination of these domains leads to the formation of a covalent linkage between the protein and an internally bound flavin chromophore, destabilizing the surrounding protein and displacing an alpha-helix from its surface. Here we use a combination of spectroscopic tools to monitor the kinetic processes that spontaneously occur in the dark as the protein returns to the noncovalent ground state. Using time-resolved two-dimensional (2D) NMR methods, we measured the rate of this process at over 100 independent sites throughout the protein, establishing that regeneration of the dark state occurs cooperatively within a 1.6-fold range of observed rates. These data agree with other spectroscopic measurements of the kinetics of protein/FMN bond cleavage and global conformational changes, consistent with these processes experiencing a common rate-limiting step. Arrhenius analyses of the temperature dependence of these rates suggest that the transition state visited during this regeneration has higher energy than the denatured form of this protein domain despite the fact that there is no global unfolding of the domain during this process.     

Conformational changes of protein adsorbed on polyurethane studied by ftir-atr spectroscopy

We have studied the adsorption of human serum albumin and human gamma globulins onto a polyurethane (Pellethane 2363-80A) using an attenuated total reflectance (ATR) flow cell. Spectra of the proteins adsorbed onto the polyurethane surface, and of the same proteins in solution were collected for comparison. Significant spectral differences between the solution and surface adsorbed spectra of both proteins were observed.     

Molecular dynamics of liquid acetone determined by depolarized Rayleigh and low-frequency Raman scattering spectroscopy

Slow to ultrafast dynamics of liquid acetone at variable temperature was investigated by depolarized Rayleigh and low-frequency Raman scattering spectroscopy, in the region 0-200 cm(-1). A detailed analysis was performed on the spectra and corresponding time responses, and a consistent view of the molecular dynamics of this dipolar solvent was obtained. The effects of temperature on the spectra were interpreted, and distinct dynamical processes identified. At very low frequencies, or long time scales, acetone dynamics is characterized by a slow diffusive reorientation obeying the Stokes-Einstein-Debye hydrodynamic theory only in the limit of subslip boundary conditions. An alternative model based on the microviscosity concept proved to be able to reproduce this correlation time and its temperature dependence. A comparative analysis of collective and single-molecule reorientational times, these latter estimated from intramolecular Raman spectra, led to an orientational correlation parameter g(2) of unity, which denotes a statistical disorder of molecular polarizability tensors. A fast local restructuring process is putatively responsible for an additional contribution at subpicosecond time scales often referred to as intermediate response in other molecular liquids. The high frequency portion of the dynamical susceptibility showed the signature of librational intermolecular motions, giving rise to an ultrafast decay of the time correlation function of polarizability anisotropy. The overall approach, which provided valuable information on dynamics, structure and molecular interactions of neat acetone, will be applied to acetone electrolytic solutions.     

The conformation of tetraalanine in water determined by polarized Raman, FT-IR, and VCD spectroscopy

The present article reports the conformation of cationic tetraalanine in aqueous solution. The determination of the dihedral angles of the two central amino acid residues was achieved by analyzing the amide I' band profile in the respective polarized visible Raman, Fourier transform-IR, and vibrational circular dichroism (VCD) spectra by means of a novel algorithm which utilizes the excitonic coupling between the amide I modes of nearest neighbor and second nearest peptide groups. It is an extension of a recently developed theory (Schweitzer-Stenner, R. Biophys. J., 2002, 83, 523-532). UV electronic circular dichroism (ECD) spectra of the peptides were used to validate the results of the structure analysis. The analyses yielded the dihedral angles (phi(12), psi(12)) = (-70 degrees, 155 degrees ) and (phi(23), psi(23)) = (-80 degrees, 145 degrees ). The obtained values are very close to the Ramachandran coordinates of the polyproline II helix (PPII). The data suggest that this is the conformation predominantly adopted by the peptide at room temperature. This notion was corroborated by the corresponding electronic circular dichroism spectrum. Tetraalanine exhibits a higher propensity for PPII than trialanine for which a 50:50 mixture of polyproline II and an extended beta-strand-like conformation was obtained from recent spectroscopic studies (Eker et al., J. Am. Chem. Soc. 2002, 124, 14330-14341). The temperature dependence of the CD spectra rule out that any cooperativity is involved in the strand if PPII transition. This led to the conclusion that solvent-peptide interactions give rise to the observed PPII stability. Our result can be utilized to understand why the denaturation of helix-forming peptides generally yields a PPII rather than a heterogeneous random conformation.     

Listening to PS II: enthalpy, entropy, and volume changes

Photosystem II, located in the thylakoid membranes of green plants, algae, and cyanobacteria, uses sunlight to split water into protons, electrons, and a dioxygen molecule. The mechanism of its electron transfers and oxygen evolution including the structure of the protein and rates of the S-state cycle has been extensively investigated. Substantial progress has been made; however, the thermodynamics of PS II electron transfer and of the oxygen cycle are poorly understood. Recent progress in thermodynamic measurements in photosynthesis provides novel insights on the enthalpic and entropic contribution to electron transfer in proteins. In this review the thermodynamic parameters including quantum yield, enthalpy, entropy, and volume changes of PS II photochemistry determined by photoacoustics and other laser techniques are summarized and evaluated. Light-driven volume changes via electrostriction are directly related to the photoreaction in PS II and thus can be a useful measurement of PS II activity and function. The enthalpy changes of the reactions observed can be directly measured by photoacoustics. The apparent reaction entropy can also be estimated when the free energy is known. Dissecting the free energy of a photoreaction into enthalpic and entropic components provides critical information about mechanisms of PS II function. Potential limitations and future direction of the study of the thermodynamics of PS II electron transfer and oxygen evolution are presented.     

Simultaneous volume and enthalpy relaxation

The ratio between the relaxed enthalpy and volume (so-called aging modulus, K_a) was expressed in frame of the Tool-Narayanaswamy-Moynihan theory. The common case where various experimental arrangements are used for measuring these quantities was analyzed. It was found that relatively small differences between the conditions of enthalpy and volume relaxation experiments may cause a significant shift of observed K_a value. The sensitivity of K_a modulus to the difference between the enthalpy and volume relaxation conditions is significantly higher in the case of organic polymeric glasses in comparison with silicate and chalcogenide glasses. The reason for such grouping resides in higher values of glass transition temperature and lower values of activation enthalpy of inorganic glasses.     

Dihedral angles of trialanine in D2O determined by combining FTIR and polarized visible Raman spectroscopy

We have measured the polarized visible Raman and FTIR spectra of trialanine and triglycine in D(2)O at acid, neutral, and alkaline pD. From the Raman spectra we obtained the isotropic and the anisotropic scattering. A self-consistent spectral analysis of the region between 1550 and 1800 cm(-1) was carried out to obtain the intensities, frequencies, and halfwidths of the respective amide I bands. A model was developed by means of which the intensity ratios of the amide I bands in all spectra and the respective frequency differences were utilized to determine the orientational angle theta between the peptide groups and the strength of excitonic coupling between the corresponding amide I modes. By exploiting results from a recent ab initio study on triglycine (Torii, H; Tasumi, M. J. Raman Spectrosc. 1998, 29, 81), we used these parameters to determine the dihedral angles phi and psi between the peptide groups. Our results show that trialanine adopts a 3(1)-helical structure in D(2)O for all of its three protonation states. The structure is insensitive to the carboxylate protonation and changes only slightly with N-terminal protonation. Triglycine is structurally more heterogeneous in the zwitterionic and the cationic state. Our spectral analysis suggests that 3(1)-helices coexist with right-handed alpha-helical and/or with beta-turn conformations. The N-terminal protonation stabilizes the 3(1)-structure. Our study provides compelling evidence that tripeptides adopt stable conformations in aqueous solution and that they are suitable model systems to investigate the initiation of secondary structure formation.     

Structural changes in poyl(3,3 dimethyl oxetane) studied by Raman spectroscopy

The influence of the applied stress and stretch on Poly(3,3 dimethyl oxetane), thermically crystallized, has been studied using Raman spectroscopy. The effect of these mechanical deformations produces a transformation from the orthorhombic to monoclinic structure which is the thermodynamically most stable form.     

Conformational analyses of 2,3-dihydroxypropanoic acid as a function of solvent and ionization state as determined by NMR spectroscopy

Vicinal (1)H--(1)H coupling constants were used to determine the conformational preferences of 2,3-dihydroxypropanoic acid (1) (DL-glyceric acid) in various solvents and its different carboxyl ionization states. The stereospecific assignments of J(12) and J(13) were confirmed through the point-group substitution of the C-3 hydrogen with deuterium, yielding rac-(2SR,3RS)-[3-(2)H]-1, and the observation of only J(13) in the (1)H NMR spectra. While hydrogen bonding and steric strain may be expected to drive the conformational equilibrium, their role is overshadowed by a profound gauche effect between the vicinal hydroxyl groups that mimics other substituted ethanes, such as 1,2-ethanediol and 1,2-difluoroethane. At low pH, the conformational equilibrium is heavily weighted toward the gauche-hydroxyl rotamers with a range of 81% in DMSO-d(6) to 92% in tert-butyl alcohol-d(10). At high pH, the equilibrium exhibits a larger dependence upon the polarity and solvating capability of the medium, although the gauche effect still dominates in D(2)O, 1,4-dioxane-d(8), methanol-d(4), and ethanol-d(6) (96, 89, 85, and 83% gauche-hydroxyls respectively). The observed preference for the gauche-hydroxyl rotamers is believed to stem primarily from hyperconjugative sigma(C--H) --> sigma*(C--OH) interactions.     

Conformational identification of cyclohexylphosphine by microwave spectroscopy

The microwave spectra of cyclohexylphosphine have been recorded in the 18.0–26.5 GHz region. A-type rotational transitions have been assigned. The ground state rotational constants were determined to be A = 4153.75 ± 0.23, B = 1362.31 ± 0.01 and C = 1104.14 ± 0.01 MHz for C₆H₁₁PH₂, and A = 4030.03 ± 0.25, B = 1312.72 ± 0.01 and C = 1072.33 ± 0.01 MHz for C₆H₁₁PD₂. From the experimental rotational constants, it is suggested that the assigned spectra have resulted from the chair conformation with the gauche phosphine group in an equatorial position (CESG). This form is believed to be the most populated conformational isomer in the gas phase.