The first water-soluble 3(10)-helical peptides

Two water-soluble 3(10)-helical peptides are synthesized and fully characterized for the first time. The sequence of these terminally blocked heptamers comprises two residues of the Calpha-trisubstituted alpha-amino acid 2-amino-3-[1-(1,4,7-triazacyclononyl)]propanoic acid and five residues of a Calpha-tetrasubstituted alpha-amino acid (either alpha-aminoisobutyric acid or isovaline). Using CD and NMR techniques we were able to show that both heptapeptides are well structured in water, and that the type of conformation adopted is indeed the ternary 3(10)-helix.     

Coupled-cluster calculations of vibrational Raman optical activity spectra

We present the first calculations of Raman optical activity spectra at the coupled-cluster level of theory. Calculations are presented for (S)-methyloxirane and compared to recent experimental gas-phase measurements as well as the results obtained at the Hartree-Fock and density functional level of theory using the popular B3LYP functional. For the experimentally relevant frequency region of 400-1600 cm(-1), the Hartree-Fock, B3LYP and coupled-cluster spectra are very similar when the same force field is used, and the results also agree well with experiment. For high-frequency vibrational modes, differences in the ROA difference parameters are observed and are analyzed. The new coupled-cluster ROA code will allow for critical benchmarking of the accuracy of modern exchange-correlation functionals in the calculation of ROA spectra.     

Relevance of the electric-dipole--electric-quadrupole contribution to Raman optical activity spectra

We examine the importance of the electric-dipole--electric-quadrupole polarizability tensor in the intensity theory of Raman optical activity (ROA) spectra. Using density functional theory, ROA spectra of organic cyclic compounds, alanine, oligoalanines, and examples from the literature are analyzed in detail, and a statistical investigation is performed. It is found that the contribution of the electric-dipole--electric-quadrupole tensor is often small, except for some special cases that involve C-H stretching vibrations.     

Surface enhanced Raman optical activity (SEROA)

Raman optical activity (ROA) directly monitors the stereochemistry of chiral molecules and is now an incisive probe of biomolecular structure. ROA spectra contain a wealth of information on tertiary folding, secondary structure and even the orientation of individual residues in proteins and nucleic acids. Extension of ROA to an even wider range of samples could be facilitated by coupling its structural sensitivity to the low-concentration sensitivity provided by plasmon resonance enhancement. This leads to the new technique of surface enhanced ROA, or SEROA, which is complementary to both SERS and ROA. In this tutorial review, we present a survey of theoretical and experimental work undertaken to develop SEROA and discuss these efforts in the context of the ROA technique, and, based on the authors' work, outline possible future directions of research for this novel chiroptical spectroscopy.     

Chain-terminus triggered chiral memory in an optically inactive 3(10)-helical peptide

A new optically inactive 3(10)-helical peptide with a side-chain cross-linking was found to exhibit chiral memory stored in the peptide backbone, whose chirality was induced by a noncovalent interaction of a chiral molecule at the N-terminal end of the peptide.     

An analytical derivative procedure for the calculation of vibrational Raman optical activity spectra

We present an analytical time-dependent Hartree-Fock algorithm for the calculation of the derivatives of the electric dipole-magnetic dipole polarizability with respect to atomic Cartesian coordinates. Combined with analogous procedures to determine the derivatives of the electric dipole-electric dipole and electric dipole-electric quadrupole polarizabilities, it enables a fully analytical evaluation of the three frequency-dependent vibrational Raman optical activity (VROA) invariants within the harmonic approximation. The procedure employs traditional non-London atomic orbitals, and the gauge-origin dependence of the VROA intensities has, therefore, been assessed for the commonly used aug-cc-pVDZ and rDPS:3-21G basis sets.     

Solvent effects on Raman optical activity spectra calculated using the polarizable continuum model

The integral equation formulation of the polarizable continuum model (IEFPCM) has been extended to the calculation of solvent effects on vibrational Raman optical activity spectra. Gauge-origin independence of the differential scattering intensities of right and left circularly polarized light is ensured through the use of London atomic orbitals. Density functional theory (DFT) calculations have been carried out for bromochlorofluoromethane, methyloxirane, and epichlorhydrin. The results indicate that solvent effects on the ROA differential scattering intensities can be substantial, and vary in sign and magnitude for different vibrational modes. It is demonstrated that both direct and indirect effects are important in determining the total solvent effects on the ROA differential scattering intensities. Local field effects are shown to be in general small, whereas electronic nonequilibrium solvation has a profound effect on the calculated solvent effects compared to an equilibrium solvation model. For molecules with several conformations, the changes in the relative stability of the different conformers also lead to noticeable changes in the ROA spectra.     

Theoretical study of vibrational and optical spectra of methylene-bridged oligofluorenes

We report a systematic characterization of methylene-bridged fluorene oligomers constructed of two, four, six, and eight aromatic rings using time-dependent density functional theory (TDDFT), the ab initio approximate coupled-cluster singles and doubles (CC2) method, and semiempirical spectroscopic Zerner's intermediate neglect of differential overlap method (ZINDO/S). Geometry optimizations have been performed for the ground state and for the first electronically excited state. Vertical excitations and the fluorescence transition from the lowest excited state have been calculated. Computed ground-state geometries and infrared spectra for fluorene are in good agreement with experimental results. The RI-CC2 and ZINDO/S absorption and fluorescence spectra agree very well with the available experimental data for studied fluorene oligomers and for para oligophenylenes films. On the other hand, TDDFT calculations underestimate excitation and fluorescence energies systematically for larger systems (N > 4) in comparison with the above-mentioned results. The effective conjugation length was estimated to 13-14 repeat units. The computed radiative lifetimes for the fluorene molecule show good agreement with experiment within realistic expectations. The decrease of the radiatiave fluorescence lifetime with the increase in the conjugation length has been discussed also.     

Charge mapping in 3(10)-helical peptide chains by oxidation of the terminal ferrocenyl group

Two series of 3(10)-helical peptides of different lengths and rigidity, based on the strongly foldameric α-aminoisobutyric acid and containing a terminal ferrocenyl unit, have been synthesized. Oxidation-state sensitive spectroscopic tags of helical peptides, the N-H groups, allowed mapping of the charge delocalization triggered by oxidation of the terminal ferrocenyl moiety and were monitored by IR spectroelectrochemistry.     

Theoretical study of the structure of tetraborane(10)

Fully optimized geometries are reported for two possible isomers of B₄H₁₀. At the restricted Hartree-Fock level, the unobserved bisdiborane isomer is lower in energy than the observed isomer. Generalized-molecular-orbital, configuration-interaction calculations show that electron correlation is responsible for this reversal. Electron correlation may be important in stabilizing other cluster molecules.     

CCSD(T) study of dimethyl-ether infrared and Raman spectra

CCSD(T) state-of-the-art ab initio calculations are used to determine a vibrationally corrected three-dimensional potential energy surface of dimethyl-ether depending on the two methyl torsions and the COC bending angle. The surface is employed to obtain variationally the lowest vibrational energies that can be populated at very low temperatures. The interactions between the bending and the torsional coordinates are responsible for the displacements of the torsional overtone bands and several combination bands. The effect of these interactions on the potential parameters is analyzed. Second order perturbation theory is used as a help for the understanding of many spectroscopic parameters and to obtain anharmonic fundamentals for the 3N - 9 neglected modes as well as the rotational parameters. To evaluate the surface accuracy and to verify previous assignments, the calculated vibrational levels are compared with experimental data corresponding to the most abundant isotopologue. The surface has been empirically adjusted for understanding the origin of small divergences between ab initio calculations and experimental data. Our calculations confirm previous assignments and show the importance of including the COC bending degree of freedom for computing with a higher accuracy the excited torsional term values through the Fermi interaction. Besides, this work shows a possible lack of accuracy of some available experimental transition frequencies and proposes a new assignment for a transition line. As an example, the transition 100 → 120 has been computed at 445.93 cm(-1), which is consistent with the observed transition frequency in the Raman spectrum at 450.5 cm(-1).     

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.     

Decelerated chirality interconversion of an optically inactive 3(10)-helical peptide by metal chelation

A dynamically optically inactive 3(10)-helical peptide possessing metal chelating ability between the side-chains at the i and i + 3th residues was synthesized, and its metal complexes were shown to stabilize the peptide structure and the helical sense.     

Theoretical determination of the vibrational Raman optical activity signatures of helical polypropylene chains.

Raman and vibrational Raman optical activity (VROA) spectra of helical conformers of polypropylene chains are simulated using ab initio methods to unravel the relationships between the vibrational signatures and the primary and secondary structures of the chains. For a polypropylene chain containing three units, conformational effects are shown to lead to more acute signatures for VROA than for Raman spectra. In addition to regular polypropylene chains, which can display right and left helicities with the same probability, chirality and therefore helicity are enforced by substituting one chain end with a phenyl group. The simulations predict that the threefold helical structures, which correspond to (TG)(N) conformations of the backbone, have a specific VROA backward signature in the form of an intense couplet around 1100 cm(-1). This couplet is associated with collective wagging and twisting motions, while most of its intensity comes from the anisotropic invariants combining normal coordinate derivatives of the electric dipole-electric dipole polarizability and of the electric dipole-magnetic dipole polarizability. A similar signature has already been found in model helical polyethylene chains, whereas it is very weak in forward VROA.     

Raman spectra of tetrathiofulvalene (TTF)

The Raman spectra of TTF and d₄-TTF has been obtained on the powder and benzene solution. Preliminary assignments to several bands can be made from depolarization studies, isotope shifts and analogy to related systems.     

Tunnel splitting in the Raman spectra for μ-HW2(CO) 10 −

Conclusions The structure of the Raman spectra of -HW₂(CO) ₁₀ ^– complexes in the vicinity of 800 cm^–1 and of -DW₂(CO) ₁₀ ^– in the vicinity of 600 cm^–1 is a result of tunnel splitting.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 9, pp. 2145–2146, September, 1984.     

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 study of the local structure and Raman spectra of CaO-SiO2 binary melts

A procedure for the Raman spectra calculation of vitreous and molten silicates was presented in this paper. It includes molecular dynamics MD simulation for the generation of equilibrium configurations, Wilson's GF matrix method for the calculations of eigenfrequencies and corresponding vectors, electro-optical parameters method (EOPM) for the Raman intensity calculations, and the bond polarizability model (BPM) for the determination of polarizability and polarizability derivative. One of the most important characteristics of this procedure is the achievement of the partial Raman spectra of five tetrahedral units, as well as the total spectral envelope. In this paper, the calculation was carried out for the vitreous and molten calcium silicates with different compositions and at various temperatures. It is worthwhile to note that the calculation is based on statistical configurations distribution in the space and so it is not needed to artificially adjust the full width at half maximum (FWHM) of spectra. It was also tested through the good agreement of the calculated spectra with the experimental, including some regularity of spectral properties. According to the calculation, the symmetrical stretching of whole tetrahedral units, to which the stretching of Si-O(nb) bond gives the main contribution to intensity, is proven to be the dominance in the high-frequency range (800-1200 cm(-1)) and the symmetrical bending of Si-O(b)-Si, to which the stretching of Si-O(b) bond exhibits the main contribution, is the dominance in the medium-frequency range (400-700 cm(-1)). As the first theoretical results, the Raman scattering coefficient of each Q(i) was found little change along with the variation of composition and temperature.     

Two-dimensional Raman and Raman optical activity correlation analysis of the alpha-helix-to-disordered transition in poly(L-glutamic acid)

Rich and complex Raman scattering and Raman optical activity (ROA) spectra have been measured monitoring the pH induced alpha-helix-to-disordered conformational transition in poly(L-glutamic acid). Two-dimensional (2D) correlation techniques have been applied to facilitate a comprehensive analysis of these two complementary spectral sets. Synchronous contour plots have identified band assignments of alpha-helical and disordered conformations, and have revealed bands characteristic of changes in the protonation state of the polypeptide. Asynchronous plots, on the other hand, have probed the relative sequential orders of intensity changes indicating a decrease in intensity of alpha-helical bands in the backbone skeletal stretch region, followed by a subsequent decrease in intensity in the extended amide III and amide I regions, underlying the appearance of disordered structure, including poly(L-proline) II (PPII) helix. The application of a 2D correlation 'moving' window has also disclosed two distinct phases during helix unfolding in the alpha-helix-to-disordered transition, occurring at approximately pH 4.9 and approximately pH 5.2, possibly a result of the difference in helical stability between the end and central regions of the alpha-helix. This paper demonstrates the potential value of combining 2D Raman, 2D ROA and moving window correlation techniques for the detailed investigation of complex and subtle changes of secondary structure during the unfolding mechanisms of polypeptides and proteins.