Conformational analysis of XA and AX dipeptides in water by electronic circular dichroism and 1H NMR spectroscopy

We measured the temperature-dependent electronic circular dichroism (ECD) spectra of AX, XA, and XG dipeptides in D2O. The spectra of all XA and AX peptides indicate a substantial population of the polyproline II (PPII) conformation, while the ECD spectra of LG, KG, PG, and AG were found to be quantitatively different from the alanine-based dipeptides. Additional UV absorption data indicate that the ECD spectra of the XG peptides stem from electronic coupling between the peptide and the C-terminal group, and that spectral differences reflect different orientations of the latter. We also measured the 1H NMR spectra of the investigated dipeptides to determine the 3JHalphaNH coupling constants for the C-terminal residue. The observed temperature dependence of the ECD spectra and the respective room-temperature 3JHalphaNH coupling constants were analyzed by a two-state model encompassing PPII and a beta-like conformation. The PPII propensity of alanine in the XA series is only slightly modulated by the N-terminal side chain, and is larger than 50%. As compared to AA, XA peptides containing L, P, S, K V, E, T, and I all cause a relative stabilization of the extended beta-strand conformation. The PPII fractions of XA peptides varied between 0.64 for AA and 0.58 for DA, whereas the PPII fractions of AX peptides were much lower. From the investigated AX peptides, only AL and AQ showed the expected PPII propensity. We found that AT, AI, and AV clearly prefer an extended beta-strand conformation. A quantitative comparison of AA, AAA, and AAAA revealed a hierarchy AAAA > AAA approximately AA for the PPII population, in agreement with predictions from MD calculations and results from Raman optical activity studies (McColl et al. J. Am. Chem. Soc. 2004, 126, 5076).     

Far IR and Raman vibrational spectra of nitramines

Vibrational spectra of several nitramines in the long-wave region (50–450 cm⁻¹) were studied. The frequencies of intra- and intermolecular vibrations were separated and a tentative assignment of the frequencies of self-associative complexes was performed. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2241–2244, November, 1998.     

IR and polarized Raman spectra of strontium tartrate trihydrate

The IR and polarized Raman spectra of SrC₄H₄O₆ · 3H₂O have been recorded and analysed. The factor group analysis of the divalent tartrate ion has been carried out on the basis of C₂ symmetry. As the ion possesses lower symmetry in the crystal, splittings have been observed for the different vibrational modes. Separate bands in the bending region of water suggest the existence of three crystallographically different water molecules in the crystal, which is confirmed by deuterium substitution.     

IR, Raman and SERS spectra of disodium terephthalate

The IR and Raman spectra of disodium terephthalate were recorded and analysed. Surface enhanced Raman scattering (SERS) spectrum was recorded in silver colloid. The vibrational wavenumber of the compound have been computed using the Hartree-Fock/6-31G* basis and compared with the experimental values. SERS studies suggest a flat orientation of the molecule at the metal surface.     

IR, Raman and SERS spectra of 2-phenoxymethylbenzothiazole

The FT-IR and FT-Raman spectra of 2-phenoxymethylbenzothiazole were recorded and analyzed. The surface enhanced Raman scattering (SERS) spectrum was recorded in a silver colloid. The vibrational wavenumbers of the compound have been computed using the Hartree–Fock/6-31G* basis and compared with the experimental values. The appearance of the Ag–O stretching mode at 237 cm⁻¹ in the SERS spectrum along with theoretically calculated atomic charge density, leads us to suggest that the molecule is adsorbed through the oxygen atom with the molecular plane tilted on the colloidal silver surface. The direction of charge transfer contribution to SERS has been discussed from the frontier orbital theory.     

Fourier transform Raman and IR spectra of snake skin

The Fourier transform (FT) Raman and IR spectra of the shed dorsal skin of the snake Elaphe obsoleta (American black rat snake) are reported. Vibrational spectroscopic assignments are proposed for the first time. Although good quality Raman spectra were obtained from the hinge regions using an FT Raman microscope, the dorsal scale regions fluoresced even with 1064 nm IR excitation. This was ascribed to pigmentation markings on the scales.     

Simulation studies of amide I IR absorption and two-dimensional IR spectra of beta hairpins in liquid water

Amide I IR absorption and two-dimensional (2D) IR photon echo spectra of a model beta hairpin in aqueous solution are theoretically studied and simulated by combining semiempirical quantum chemistry calculations and molecular dynamics simulation methods. The instantaneous normal-mode analysis of the beta hairpin in solution is performed to obtain the density of states and the inverse participation ratios of the one-exciton states. The motional and exchange narrowing processes are taken into account by employing the time-correlation function theory for the linear and nonlinear response functions. Numerically simulated IR absorption and 2D spectra are then found to be determined largely by the amide I normal modes delocalized on the peptides in the two strands. The site-specific isotope-labeling effects on the IR and 2D IR spectra are discussed. The simulation results for the ideal (A17) beta hairpin are directly compared with those of the realistic 16-residue (GB1) beta hairpin from an immunoglobulin G-binding protein. It was found that the characteristic features in IR and 2D spectra of both the ideal (A17) beta hairpin and the GB1 beta hairpin are the same. The simulated IR spectrum of the GB1 beta hairpin is found to be in good agreement with experiment, which demonstrates that the present computational method is quantitatively reliable.     

Polarised IR and Raman spectra of monoglycine dihydrogenphosphate single crystal

Polarised Raman, IR and FIR spectra of the monoglycine dihydrogenphosphate (glycinium dihydrogenphosphate) single crystal samples are presented and discussed with respect to the crystal structure on the basis of oriented gas model approximation. The IR and FIR spectra were measured by specular reflection method and spectra of an imaginary part of the refractive indices were computed by the Kramers-Kronig transformation. The polarisation properties of the internal vibrations of the glycinium cation, H₂PO₄¹⁻ anion and hydrogen bonds are predicted and compared to the experimentally determined.     

The low-frequency Raman and IR spectra of nitric acid hydrates

The low-frequency region of the infrared and Raman spectra of nitric acid hydrates is analyzed. Theoretical calculations of the vibrational normal modes of the crystals of nitric acid monohydrate and the β-phases of the dihydrate and trihydrate are carried out, focusing the results in the regions below 175 cm⁻¹ and near the symmetric stretch of the nitrate ion NO₃⁻, around 1000–1100 cm⁻¹. A prediction of the corresponding infrared spectra is presented. A joint study is performed of the calculated normal modes, the predicted IR spectra, and the recently published Raman spectra of these compounds, based on symmetry considerations and using the atomic displacements associated to each normal mode as a further source of information. Although most of the modes present a strong mixture of atomic motions, assignments can be proposed for some of the vibrations.     

Polarised IR and Raman spectra of the gamma-glycine single crystal

Complete (full) set of the polarised IR and Raman spectra for the gamma-glycine single crystal at room temperature are presented. The polarised IR spectra were measured by the specular reflection method and the spectra of the imaginary parts of the refractive indices were computed by Kramers-Kronig transformation. The polarised properties of the bands are discussed with respect to the normal coordinate analysis (literature data) and diffraction crystal data (oriented gas model approximation). A very good agreement between the polarised properties of the bands and simple models of vibrations are observed for the stretching vibrations of the CH2 and COO- group. It is not the case for most of the deformation vibrations of the carboxylic group and of the skeleton. The polarization properties of the stretching vibrations of the NH3+ group are determined by their hydrogen bondings.     

Anharmonic effects in IR, Raman, and Raman optical activity spectra of alanine and proline zwitterions

The difference spectroscopy of the Raman optical activity (ROA) provides extended information about molecular structure. However, interpretation of the spectra is based on complex and often inaccurate simulations. Previously, the authors attempted to make the calculations more robust by including the solvent and exploring the role of molecular flexibility for alanine and proline zwitterions. In the current study, they analyze the IR, Raman, and ROA spectra of these molecules with the emphasis on the force field modeling. Vibrational harmonic frequencies obtained with 25 ab initio methods are compared to experimental band positions. The role of anharmonic terms in the potential and intensity tensors is also systematically explored using the vibrational self-consistent field, vibrational configuration interaction (VCI), and degeneracy-corrected perturbation calculations. The harmonic approach appeared satisfactory for most of the lower-wavelength (200-1800 cm(-1)) vibrations. Modern generalized gradient approximation and hybrid density functionals, such as the common B3LYP method, provided a very good statistical agreement with the experiment. Although the inclusion of the anharmonic corrections still did not lead to complete agreement between the simulations and the experiment, occasional enhancements were achieved across the entire region of wave numbers. Not only the transitional frequencies of the C-H stretching modes were significantly improved but also Raman and ROA spectral profiles including N-H and C-H lower-frequency bending modes were more realistic after application of the VCI correction. A limited Boltzmann averaging for the lowest-frequency modes that could not be included directly in the anharmonic calculus provided a realistic inhomogeneous band broadening. The anharmonic parts of the intensity tensors (second dipole and polarizability derivatives) were found less important for the entire spectral profiles than the force field anharmonicities (third and fourth energy derivatives), except for a few weak combination bands which were dominated by the anharmonic tensor contributions.     

Theoretical IR and Raman spectra of diketene and its 3-methylene isomer

The IR and Raman spectra of diketene, 4-methylene-2-oxetanone, and its less stable isomer, 3-methylene-2-oxetanone, were calculated at the MP2, DFT B3PW91 and RHF levels using 6-311++G** basis set. The internal coordinates were defined for both isomers and used in potential energy distribution (PED) analysis. The PED analysis of the theoretical spectra forms the basis for a detection of the 3-methylene isomer traces in a reaction mixture as well as for elucidation of the future matrix isolation IR and/or Raman spectra.     

IR and Raman spectra of a water-methane disperse system. Computer experiment

Methane adsorption by water clusters is studied using a flexible molecule model. An increase in the number of methane molecules surrounding a water cluster leads to their structurization in its vicinity. The pattern of the frequency spectrum of complex permittivity strongly changes after methane molecules are captured by the disperse water system. The integral intensity of IR absorption grows with methane adsorption, whereas the Raman spectrum of the system is considerably depleted. Methane absorption markedly enhances the reflectivity and IR emission ability of the disperse system.     

Theoretical IR,Raman and NMR spectra of 1,2- and 1,3-dimethylenecyclobutane

Equilibrium geometries, rotational constants, harmonic vibrational frequencies, infrared intensities, Raman activities, and ¹H and ¹³C NMR spectra were calculated for 1,2-dimethylenecyclobutane and its less stable isomer 1,3-dimethylenecyclobutane by using MP2, DFT (B3PW91), and RHF theoretical methods involving the 6-311++G⁷ basis set.The properties calculated theoretically have been compared with the experimental values. The internal coordinates defined for both isomers were used in the potential energy distribution (PED) analysis. The theoretical vibrational and NMR spectra form the basis to differentiate particular compounds in reaction mixture.     

Calculations of intermode coupling constants and simulations of amide I,II, and III vibrational spectra of dipeptides

Amide I, II, and III vibrations of polypeptides are important marker modes whose vibrational spectra can provide critical information on structure and dynamics of proteins in solution. The extent of delocalization and vibrational properties of amide normal mode can be described by the amide local mode frequencies and intermode coupling constants between a pair of amide local modes. To determine these fundamental quantities, the previous Hessian matrix reconstruction method has been generalized here and applied to the density functional theory results for various dipeptide conformers. The calculation results are then used to simulate IR absorption, vibrational circular dichroism, and 2D IR spectra of dipeptides. The relationships between dipeptide backbone conformations and these vibrational spectra are discussed. It is believed that the present computational method and results will be of use to quantitatively simulate vibrational spectra of complicated polypeptides beyond simple dipeptides     

Density functional theory studies on the Raman and IR spectra of meso-tetraphenylporphyrin diacid

The vibrational spectra of meso-tetraphenylporphyrin diacid (H4TPP2+) have been studied with the density functional theory. Raman and IR spectra of H4TPP2+ and its N-deuterated analogue (D4TPP2+) are measured and compared with the computational results. Complete assignments of observed IR and Raman bands were proposed on the bases of calculation results. The DFT calculations reproduce 140 observed fundamentals with the RMS 8.6 cm-1. The computational as well as the experimental results reveal that the saddle-distortion of porphyrin macrocycle for the diacid leads to a significant effect on its vibrational spectra. Especially, several out-of-plane skeletal modes, which were either unobserved or very weak in the Raman spectra of CuTPP and H2TPP, are activated in the Raman spectra of the diacids. In addition, enhancement for the Raman bands of phenyl CC stretching modes were observed and attributed to the conjugation effect of pi-systems of the phenyl and the porphyrinato macrocycles.     

Experimental and theoretical IR and Raman spectra of picolinic, nicotinic and isonicotinic acids

The experimental and theoretical (B3PW91/6-311++G**) vibrational (IR and Raman) spectra of picolinic, nicotinic and isonicotinic acids (pyridine-2-, -3-, and -4-carboxylic acid, respectively) were studied. Three stable calculated structures were found for picolinic acid: the structure with intramolecular hydrogen COOH?N bond, and the two without hydrogen bond. For the nicotinic acid two stable theoretical structures differ in orientation of the COOH group with respect to the nitrogen atom, whereas for the isonicotinic acid only one form was stable. The theoretical vibrational spectra of the three acids were interpreted by means of potential energy distributions (PEDs) using VEDA 3 program. Next, selected experimental bands were assigned based on the scaled theoretical wavenumbers. Finally, the wavenumbers and intensities for the three isomeric acids were compared and discussed in terms of location of the carboxylic group.     

Calculation of intensity in the resonance Raman and two-photon absorption spectra of polyatomic molecules

A direct method for calculating the resonance Raman and two-photon absorption spectra of polyatomic molecules is described in detail The method is based on the adiabatic model and uses Herzberg-Teller’s approximation. Relations ruling out direct summation over vibrational quantum numbers of excited electronic states and representing the matrix elements of the Green function of a multidimensional oscillator as functions of vibration frequencies and Dushinsky transformation parameters are derived. The relations are convenient for constructing algorithms. Translated from Zhumal Struktumoi Khimii, Vol. 38, No. 2, pp. 248–255, March–April, 1997.     

Comparison of quantitative conformer analyses by nuclear magnetic resonance and Raman optical activity spectra for model dipeptides

Interpretation of the Raman optical activity (ROA) of peptides is difficult because of molecular flexibility and interaction with the solvent. Typically, simulations and experiments are compared in terms of a qualitative agreement between the spectra. However, on a series of the Pro-Gly, Gly-Pro, Pro-Ala, and Ala-Pro dipeptides more precise conformer ratios could be obtained with the aid of the density functional computations and numerical decomposition of the spectral shapes. All observed transitions were assigned, and the computed transition frequencies were scaled accordingly. Then the populations predicted by the optical spectroscopy agreed within a few percent with an analysis of the spin-spin coupling constants based on the Karplus equations, which was confirmed also by a comparison of calculated and experimental NMR couplings. The results are supported by molecular dynamics simulations and related to the previous conformational studies of similar molecules.     

IR and Raman spectra with Gaussian-09 molecular analysis of some other parameters and vibrational spectra of 5-fluoro-uracil

Research on Chemical Intermediates - Recorded IR and Raman spectra of 5-fluoro-uracil have been analyzed with the carried out theoretical computation by Gaussian-09 [DFT/B3LYP/6-311?++G**]...