Utilizing Lifetimes to Suppress Random Coil Features in 2D IR Spectra of Peptides

We report that the waiting time delay in 2D IR pulse sequences can be used to suppress signals from structurally disordered regions of amyloid fibrils. At a waiting time delay of 1.0 ps, the random coil vibrational modes of amylin fibrils are no longer detectable, leaving only the sharp excitonic vibrational features of the fibril β-sheets. Isotope labeling with (13)C(18)O reveals that structurally disordered residues decay faster than residues protected from solvent. Since structural disorder is usually accompanied by hydration, we conclude that the shorter lifetimes of random-coil residues is due to solvent exposure. These results indicate that 2D IR pulse sequences can utilize the waiting time to better resolve solvent-protected regions of peptides and that local mode lifetimes should be included in simulations of 2D IR spectra.     

Study of Photochemical Reactions of Coniferyl Alcohol. II. Comparative Structural Study of a Photochemical and Enzymatic Polymer of Coniferyl Alcohol

The structure of the polymer synthesized by UV irradiation of coniferyl alcohol was studied, using UV-visible, Raman, IR, H-NMR and ¹³C-NMR spectroscopy. The photochemical polymer was compared with the structure of the polymer obtained by peroxidase-catalyzed polymerization of coniferyl alcohol. General similarity of the spectra of the two polymers was shown. However, differences in the fine structure of particular regions of the NMR spectra, as well as in certain bands in the Raman and IR spectra, could be explained through the various bond types and organization within the polymers. These results are consistent with molecular mass distribution of the polymers. Two fractions of enzymatic polymer correspond to the main two fractions of photochemical polymer. The later polymer has additional fractions that are probably the main reason for the observed spectral differences.     

Vibrational spectra and noncovalent interactions of carbohydrates molecules

The differences between the vibrational spectra of carbohydrates of the same chemical structure caused by the noncovalent intra- and intermolecular interactions have been systematized. In the general case, these differences show up as the following specific features of changes in the bond intensities: change in the intensity ratio of closely spaced bands (IR and Raman spectra); selective change (increase, decrease) in intensities of individual bands (IR and Raman spectra); change (increase, decrease) in intensities of practically all bands (IR and Raman spectra); appearance of strong bands in the region of low frequencies from 50 to 200 cm⁻¹ (Raman spectra); appearance of strong diffuse bands in the low-frequency range with a simultaneous great reduction in the other bands (practical disappearance of the majority of bands) (Raman Spectra). The causes of such a kind of changes in the band intensities in the vibrational spectra of carbohydrates are discussed.     

A comparative vibrational and NMR study of cis-cinnamic acid polymorphs and trans-cinnamic acid

The IR and Raman spectra of the two polymorphic forms (58 degree- and 68 degree-forms) of cis-cinnamic acid were measured, and the spectral differences discussed on the basis of the crystal structures of the two forms. The IR bands related to the COOH group differ in the frequencies and band shape, reflecting differences in the hydrogen bonding between the two modifications. These spectra were compared with those of trans-cinnamic acid. The IR, Raman, and NMR spectra of the isotopic compounds, including the deuterated and 13C analogs of the cis and trans acids, were also recorded in the solid state and in solution to confirm the spectral assignments.     

Revised vibrational band assignments for the experimental IR and Raman spectra of 2,3,4-trifluorobenzonitrile based on ab initio, DFT and normal coordinate calculations

In the present study, a systematic vibrational spectroscopic investigation for the experimental IR and Raman spectra of 2,3,4-trifluorobenzonitrile (TFB), aided by electronic structure calculations has been carried out. The electronic structure calculations – ab initio (RHF) and hybrid density functional methods (B3LYP) – have been performed with 6-31G* basis set. Molecular equilibrium geometries, electronic energies, IR intensities, harmonic vibrational frequencies, depolarization ratios and Raman activities have been computed. The results of the calculations have been used to simulate IR and Raman spectra for TFB that showed excellent agreement with the observed spectra. Potential energy distribution (PED) and normal mode analysis have also been performed. The assignments proposed based on the experimental IR and Raman spectra have been reviewed. A complete assignment of the observed spectra has been proposed.     

Vibrational spectra and chemical quantum calculations for 2-adamantylamino-5-nitropyridine crystals--a novel material for laser Raman converters

Polycrystalline infrared and polarized FT-Raman spectra have been measured for 2-adamantylamino-5-nitropyridine, a novel organic material for laser Raman converters. The assignment of IR and Raman bands is given on the basis of DFT calculations. The spectroscopic studies have not indicated the presence of any significant intermolecular interactions in the crystal structure of this compound. The lines observed in the stimulated Raman spectrum of this crystal are assigned to the respective molecular vibrations.     

Deep-UV Raman spectrometer tunable between 193 and 205 nm for structural characterization of proteins

A new deep-UV Raman spectrometer utilizing a laser source tunable between 193 and 205 nm has been designed, built, and characterized. Only selected wavelengths from this range have previously been accessible, by Raman shifting of the second, third, and fourth harmonics of the Nd:YAG fundamental in hydrogen. The apparatus was demonstrated to be a useful tool for characterizing hen egg white lysozyme structural rearrangements at various stages of fibril formation. High-quality deep-UV resonance Raman spectra were obtained for both a protein solution and a highly-scattering gelatinous phase formed by fibrillogenic species. In addition to amide bands, strong contribution of ₁₂ and ring-C phenylalanine vibrational modes was observed at excitation wavelengths below 200 nm. Remarkably, the Raman cross-section of these modes revealed dramatic change of lysozyme in response to heat denaturation and fibril formation. These results indicate that phenylalanine could serve as a new deep-UV Raman probe of protein structure.     

C-H stretching vibrations of methyl, methylene and methine groups at the vapor/alcohol (N = 1-8) interfaces

In IR and Raman spectral studies, the congestion of the vibrational modes in the C-H stretching region between 2800 and 3000 cm(-1) has complicated spectral assignment, conformational analysis, and structural and dynamics studies, even with quite a few of the simplest molecules. To resolve these issues, polarized spectra measurement on a well aligned sample is generally required. Because the liquid interface is generally ordered and molecularly thin, and sum frequency generation vibrational spectroscopy (SFG-VS) is an intrinsically coherent polarization spectroscopy, SFG-VS can be used for discerning details in vibrational spectra of the interfacial molecules. Here we show that, from systematic molecular symmetry and SFG-VS polarization analysis, a set of polarization selection rules could be developed for explicit assignment of the SFG vibrational spectra of the C-H stretching modes. These polarization selection rules helped assignment of the SFG-VS spectra of vapor/alcohol (n = 1-8) interfaces with unprecedented details. Previous approach on assignment of these spectra relied on IR and Raman spectral assignment, and they were not able to give such detailed assignment of the SFG vibrational spectra. Sometimes inappropriate assignment was made, and consequently misleading conclusions on interfacial structure, conformation and even dynamics were reached. With these polarization rules in addition to knowledge from IR and Raman studies, new structural information and understanding of the molecular interactions at these interfaces were obtained, and some new spectral features for the C-H stretching modes were also identified. Generally speaking, these new features can be applied to IR and Raman spectroscopic studies in the condensed phase. Therefore, the advancement on vibrational spectra assignment may find broad applications in the related fields using IR and Raman as vibrational spectroscopic tools.     

A density functional theory study of van der Waals interaction in carbon nanotubes

In this article, we investigate the effect of van der Waals force in zigzag carbon nanotubes (CNTs) including single-wall CNT (SWCNT) and double-walled CNT (DWCNT) structures with several interaction configurations. The solid-state density functional theory is employed to calculate the geometric optimization, normal mode frequencies, and IR and Raman spectra with the periodic boundary condition. For SWCNTs, we find that the Raman intensity is not affected by the tube diameter or the electronic structure. The IR absorption, however, increases with the tube diameter. We find that the close metallicity of the electronic structure has a significant impact on the IR simulations. When the van der Waals force is applied outside the CNTs at a distance longer than 3.0, the effect on Raman spectra is minimal but some effects can still be confirmed by IR absorption. When the van der Waals force acts inside the CNTs, the effect on the spectrum can be observed, especially at a distance of 2.8 Å, both IR and Raman can be significantly enhanced in many modes.     

Initial Steps of Amyloidogenic Peptide Assembly Revealed by Cold‐Ion Spectroscopy

The early stages of fibril formation are difficult to capture in solution. We use cold‐ion spectroscopy to examine an 11‐residue peptide derived from the protein transthyretin and clusters of this fibre‐forming peptide containing up to five units in the gas phase. For each oligomer, the UV spectra exhibit distinct changes in the electronic environment of aromatic residues in this peptide compared to that of the monomer and in the bulk solution. The UV spectra of the tetra‐ and pentamer are superimposable but differ significantly from the spectra of the monomer and trimer. Such a spectral evolution suggests that a common structural motif is formed as early as the tetramer. The presence of this stable motif is further supported by the low conformational heterogeneity of the tetra‐ and pentamer, revealed from their IR spectra. From comparison of the IR‐spectra in the gas and condensed phases, we propose putative assignments for the dominant motif in the oligomers.     

用密度泛函方法研究α-[XMo12O40]n－杂多阴离子的振动光谱

采用第一性原理密度泛函方法,在考虑极化函数的双数字(DND)基组水平上,对α-[XMo12O40]n－(X=P, Si, Ge)杂多阴离子进行了几何构型优化,得到了与X-ray晶体衍射实验结果相一致的结构参数;并在优化几何构型基础上进行了振动频率分析,首次得到了非经验计算的杂多阴离子的振动光谱,计算的频率及强度与实验结果总体上吻合得较好.对全部22个有红外活性(IR)和44个有拉曼(R)活性的频率进行了指认,并与经验方法得到的结果进行了比较,同时,对部分频率的归属加以进一步的澄清与确认.     

Theoretical prediction of the Infrared and Raman spectra of O-ethyl S-2-diisopropylaminoethylmethylphosphonothiolate

We have extended our computations of the structure and of the infrared and Raman spectra of methylphosphonates and related compounds to the O-ethyl S-2-diisopropylaminoethylmethylphosphonothiolate molecule (we abbreviate the name to ESD). We have computed the optimized geometry and the vibrational infrared and Raman frequencies of ESD by means of the Guassian 92 Program Package using 6–31G * basis sets. We assign the vibrational frequencies and we correct each frequency by multiplying it with a previously derived 6–31G * correction factor. The result is a computer-generated prediction of the IR and Raman spectra of ESD . The agreement between our theoretical predictions and the experimental IR spectrum of ESD is surprisingly good. © 1994 John Wiley & Sons, Inc.     

Structural and dynamical characterization of fibrils from a disease-associated alanine expansion domain using proteolysis and solid-state NMR spectroscopy

The nuclear poly(A) binding protein PABPN1 possesses a natural 10 alanine stretch that can be extended to 17 Ala by codon expansion. The expansions are associated with the disease oculopharyngeal muscular dystrophy (OPMD), which is characterized histopathologically by intranuclear fibrillar deposits. Here, we have studied the Ala extended fibrillar N-terminal fragment of PABPN1, (N-(+7)Ala), comprising 152 amino acids. At natural abundance, cross-polarized 13C MAS NMR spectra are dominated by the three Ala signals with characteristic beta-sheet chemical shifts. In contrast, directly polarized 13C MAS spectra show a multitude of narrow lines, suggesting a large portion of highly mobile sites. Proteolytic cleavage of the protein combined with MALDI-TOF mass spectrometry revealed a protease-resistant peptide encompassing residues 13/14 to 50-52 with the poly-Ala stretch in the center. Measurements of the 1H-13Calpha dipolar couplings of 13C/15N-labeled N-(+7)Ala revealed high order parameters of 0.77 for the poly-Ala stretch of the fibril, while the majority of the residues of N-(+7)Ala exhibited very low order parameters between 0.06 and 0.15. Only some Gly residues that are flanking the Ala-rich region had significant order parameters of 0.47. Thus, site-specific dynamic mapping represents a useful tool to identify the topology of fibrillar proteins.     

Raman spectroscopy reveals direct chromophore interactions in the Leu/Gln105 spectral tuning switch of proteorhodopsins

Proteorhodopsins are an extensive family of photoactive membrane proteins found in proteobacteria distributed throughout the world's oceans which are often classified as green- or blue-absorbing (GPR and BPR, respectively) on the basis of their visible absorption maxima. GPR and BPR have significantly different properties including photocycle lifetimes and wavelength dependence on pH. Previous studies revealed that these different properties are correlated with a single residue, Leu105 in GPR and Gln105 in BPR, although the molecular basis for the different properties of GPR and BPR has not yet been elucidated. We have studied the unexcited states of GPR and BPR using resonance Raman spectroscopy which enhances almost exclusively chromophore vibrations. We find that both spectra are remarkably similar, indicating that the retinylidene structure of GPR and BPR are almost identical. However, the frequency of a band assigned to the retinal C13-methyl-rock vibration is shifted from 1006 cm (-1) in GPR to 1012 cm (-1) in BPR. A similar shift is observed in the GPR mutant L105Q indicating Leu and Gln residues interact differently with the retinal C13-methyl group. The environment of the Schiff base of GPR and BPR differ as indicated by differences in the H/D induced down-shift of the Schiff base vibration. Residues located in transmembrane helices (D-G) do not contribute to the observed differences in the protein-chromophore interaction between BPR and GPR based on the Raman spectra of chimeras. These results support a model whereby the substitution of the hydrophilic Gln105 in BPR with the smaller hydrophobic Leu105 in GPR directly alters the environment of both the retinal C13 group and the Schiff base.     

FT-IR, FT-Raman, NMR and UV-vis spectra, vibrational assignments and DFT calculations of 4-butyl benzoic acid

The solid phase FTIR and FT-Raman spectra of 4-butyl benzoic acid (4-BBA) have been recorded in the regions 400-4000 and 50-4000cm(-1), respectively. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by density functional theory (DFT) using B3LYP method with 6-311++G(d,p) as basis set. The vibrational frequencies were calculated for monomer and dimer by DFT method and were compared with the experimental frequencies, which yield good agreement between observed and calculated frequencies. The infrared and Raman spectra were also predicted from the calculated intensities. (13)C and (1)H NMR spectra were recorded and (13)C and (1)H nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compound was recorded in the region 200-400nm and the electronic properties HOMO and LUMO energies were measured by time-dependent TD-DFT approach. The geometric parameters, energies, harmonic vibrational frequencies, IR intensities, Raman intensities, chemical shifts and absorption wavelengths were compared with the available experimental data of the molecule.     

Solid-state vibrational spectra and theoretical study of alaninamide acetate

Solid-state IR and Raman spectroscopic elucidation of alaninamide acetate is preformed by means of the possibilities of linear-polarized IR and Raman methods. The experimental assignment is compared with theoretical vibrational analysis with the intention to explain the influence of intermolecular interactions in solid phase on the spectroscopic properties of the compound studied. The 1H and ¹³C NMR spectra in solution are compared with the corresponding ones of alanine, studying the amidation effect on the chemical shift signals in the alanine moieties.     

DFT calculations of vibrational spectra and nonlinear optical properties for MgO nanotube clusters

The IR and Raman spectra, nonlinear optical properties of MgO nanotube clusters are studied by density-functional theory at B3LYP/6-31G(d) level. The IR spectra are match closely to those in the corresponding MgO cluster and bulk materials. The strongest peaks of the IR spectra are located in the range from 650 to 750 cm⁻¹. The Raman spectra are very sensitive to structural variations in MgO clusters, and redshift of vibrational frequency is observed in Raman spectra as increasing cluster length. The motion of the strongest peaks in spectra is discussed. The total dipole moment and the first hyperpolarizabilities oscillate between zero and a constant when the layer is grown for the layer dependence of symmetry in MgO nanotube clusters.     

Vibrational assignment of aluminum(III) tris-acetylacetone

The geometry, frequency and intensity of the vibrational bands of aluminum(III) Tris-acetylacetone Al(AA)3 and its 1,3,5-(13)C derivative were obtained by the Hartree-Fock (HF) and Density Functional Theory (DFT) with the B3LYP, B1LYP, and G96LYP functionals and using the 6-31G* basis set. The calculated frequencies are compared with the solid IR and Raman spectra. All of the measured IR and Raman bands were interpreted in terms of the calculated vibrational modes. Most computed bands are predicted to be at higher wavenumbers than the experimental bands. The calculated bond lengths and bond angles are in good agreement with the experimental results. Analysis of the vibrational spectra indicates a strong coupling between the chelated ring modes. Four bands in the 500-390 cm(-1) frequency range are assigned to the vibrations of metal-ligand bonds.     

DFT and Raman spectroscopy of porphyrin derivatives: Tetraphenylporphine (TPP)

Raman spectrum of the meso tetraphenylporphine (TPP) deposited onto smooth copper surface as thin film were recorded in the region 200–1700 cm⁻¹. To investigate the effect of meso-phenyl substitution rings on the vibrational spectrum of free base porphyrin, we calculated Raman and infrared (IR) spectra of the meso-tetraphenylporphine (TPP), meso tetramethylporphine (TMP), copper (II)porphine (CuPr) and free base porphine (FBP) at the B3LYP/6-311+G(d,p) level of the density functional theory (DFT). The observed Raman spectrum of the TPP is assigned based on the calculated its Raman spectrum in connection with the calculated spectra of the TMP, CuPr and FBP by taking into account of their corresponding vibrational motions of the Raman modes of frequencies. Results of the calculations clearly indicated that the meso tetraphenyl substitution rings are totally responsible for the observed Raman bands at ∼1593, 1234 and 1002 cm⁻¹. The calculated and observed Raman spectra also suggested that the observed Raman band with a medium intense at 962 cm⁻¹ might result from the surface plasmon effect. Furthermore, the observed Raman bands with medium intense at ∼334 and ∼201 cm⁻¹ are as results of the dimerization or aggregation of the TPP or would be that related to intramolecular interaction. We also calculated IR spectra of these molecules at same level of the theory. To investigate the solvent effect on the vibrational spectrum of porphine, the Raman and IR spectra of the TPP and FBP are calculated in solution phase where water used as solvent. The results of these calculation indicated that there is no any significant effect on the vibrational spectrum of the TPP.     

Electronic and vibrational properties of fluorenone in the channels of zeolite L

Fluorenone (C13H8O) was inserted into the channels of zeolite L by using gas-phase adsorption. The size, structure, and stability of fluorenone are well suited for studying host-guest interactions. The Fourier transform IR, Raman, luminescence, and excitation spectra, in addition to thermal analysis data, of fluorenone in solution and fluorenone/zeolite L are reported. Normal coordinate analysis of fluorenone was performed, based on which IR and Raman bands were assigned, and an experimental force field was determined. The vibrational spectra can be used for nondestructive quantitative analysis by comparing a characteristic dye band with a zeolite band that has been chosen as the internal standard. Molecular orbital calculations were performed to gain a better understanding of the electronic structure of the system and to support the interpretation of the electronic absorption and luminescence spectra. Fluorenone shows unusual luminescence behavior in that it emits from two states. The relative intensity of these two bands depends strongly on the environment and changes unexpectedly in response to temperature. In fluorenone/zeolite L, the intensity of the 300 nm band (lifetime 9 micros) increases with decreasing temperature, while the opposite is true for the 400 nm band (lifetime 115 micros). A model of the host-guest interaction is derived from the experimental results and calculations: the dye molecule sits close to the channel walls with the carbonyl group pointing to an Al3+ site of the zeolite framework. A secondary interaction was observed between the fluorenone's aromatic ring and the zeolite's charge-compensating cations.