Articles you may be interested inSingle-conformation infrared spectra of model peptides in the amide I and amide II regions: Experiment-based determination of local mode frequencies and inter-mode coupling An empirical correction to amide group vacuum force fields is proposed in order to account for the influence of the aqueous environment on the CvO stretching vibration ͑amide I͒. The dependence of the vibrational absorption spectral intensities on the geometry is studied with density functional theory methods at the BPW91/6-31G** level for N-methyl acetamide interacting with a variety of of water molecule clusters hydrogen bonded to it. These cluster results are then generalized to form an empirical correction for the force field and dipole intensity of the amide I (CvO stretch͒ mode. As an example of its extension, the method is applied to a larger ͑␤-turn model͒ peptide molecule and its IR spectrum is simulated. The method provides realistic bandwidths for the amide I bands if the spectra are generated from the ab initio force field corrected by perturbation from an ensemble of solvent geometries obtained using molecular dynamic simulations.

Raman and Raman optical activity (ROA) spectra of molecules reflect not only molecular structure and conformation but also the dynamics and interactions with the solvent. For polar, biologically relevant molecules in aqueous environment, this often complicates the band assignment and interpretation of the spectra. In the present study, implicit dielectric and explicit solvent models are compared with respect to the influence of the choice of solvent model on the spectral shape. Lactamide and 2-aminopropanol were selected as model compounds, and the Raman and ROA spectra were measured for both enantiomers. Geometries of explicitly solvated clusters were derived from quantum-mechanical calculations, classical (MD), and Car-Parrinello (CPMD) molecular dynamics. The results indicate that although the dielectric model reasonably well reproduces the main spectral features, more faithful intensity profiles, including the inhomogeneous band broadening, are obtained from the explicit MD and CPMD clusters. Additionally, the CPMD clusters are capable of reproducing most spectral features better than the classical dynamics, provided the simulation time is long enough to allow for a complete sampling of the conformational space. The hydrogen-bonded water molecules of the first hydration shell significantly influence the spectral intensities, whereas the effect of loosely attached or distant solvent molecules is minor. In order to average the signal, however, a relatively large number of MD geometries need to be considered, as was also exemplified by simulations of the ROA spectrum of the achiral molecule glycine. An explicit solvent modeling of sizable systems thus requires extensive computations, which became possible only recently due to the development of efficient analytical computational techniques.

Raman and Raman optical activity spectra of L- and D-proline zwitterionic (PROZW) forms were recorded for H(2)O and D(2)O solutions in a wide frequency range and analyzed with respect to the motion of the proline ring and rotation of the carbonyl group. The solution spectra were additionally compared to Raman scattering of glass and crystalline powder proline. Solution and glass spectral band broadenings are similar and reveal information about the extent of internal molecular motion. Two distinct but equally populated flexible forms were found in the glass and the solution. The equal population is consistent with NMR data, temperature, and concentration dependencies. The molecular flexibility is reduced significantly in the crystal, however, where only one conformer is present. Consequently, the crystal bands are narrow and exhibit minor frequency shifts. The spectra were interpreted with the aid of density functional theory computations involving both continuum and explicit solvent. A two-dimensional potential energy surface pertaining to the five-member ring puckering coordinates was constructed and used for dynamical averaging of spectral properties. Comparison of the computed and experimental bandwidths suggests that the puckering is strongly correlated with the carbonyl rotation. An averaging over these two motions produces similar results. The interpretation of the Raman experiments with the aid of the simulation techniques also indicates that the environment modulates properties of the hydrophobic part of the molecule indirectly by interacting with the ionic group. Such behavior may be important for the reactivity and biological activity of proline-containing peptides and proteins.

A normal mode coordinate-based molecular optimization algorithm was implemented and its performance tested against other optimization techniques. In certain cases the method was found to be computationally simpler and numerically more stable than the optimization algorithms based on Cartesian or internal valence coordinates. The usual redundant/internal coordinate scheme provided fastest convergence for compact covalently bonded molecules, while the normal mode method was found to be more suitable for more weakly bonded molecular complexes. For constrained optimizations use of the normal coordinates allows one to naturally separate the lower-energy modes from those more typically studied with vibrational spectroscopy. Thus, it provides an appropriate tool for simulations of IR and Raman spectra of larger molecules and complex systems when specific conformations are desired.

Previously proposed solvent correction to the amide I peptide vibration was extended so that it can be applied to a general solvated chromophore. The combined molecular and quantum mechanics (MMQM) method is based on a linear dependence of harmonic force field and intensity tensor components of the solute on solvent electrostatic field. For N-methylacetamide, realistic solvent frequency and intensity changes as well as inhomogeneous band widths were obtained for amide A, I, II , and III modes. A rather anomalous basis set size dependence was observed for the amide A and I vibrations, when bigger basis lead to narrowing of spectral bands and lesser molecular sensibility to the environment. For a model alpha-helical peptide, a W-shape of the vibrational circular dichroism signal observed in deuterated solvent for the amide I band was reproduced correctly, unlike with previous vacuum models.

The formation and structure of the potassium complex with valinomycin in solution were studied by means of Raman and Raman optical activity (ROA) spectroscopy. The complexation caused significant spectral changes, particularly in the region 1200-1400 cm(-1). The experimental spectra were interpreted using first principles computations. A complete computational conformational search combined with the spectral analysis revealed the arrangement of the isopropyl side chains in the complex. From a total of 6579 unique conformers two predominant ones were confirmed in the solution by ROA. A third one was predicted theoretically, but its population in the experiment could be estimated only roughly. The most populated conformer does not exhibit C(3) symmetry, and is different from that present in the crystal and the NMR-derived structure. Molecular dynamics techniques were used to estimate the molecular flexibility and its effect on the spectra. Density functional computations and Cartesian coordinate transfer (CCT) techniques provided the ROA and Raman spectral shapes and intensities well comparable with the experiment. The polar solvent (methanol) environment modeled with a polarizable continuum model (PCM) leads to rather minor changes in the conformer populations and vibrational properties as compared to vacuum computations, due to the hydrophobic character of the complex. Additional computational experiments suggest that the vibrational interactions determining the ROA spectra are quite local, which contributes to the good spatial resolution of the method. A reduction of the noise in the experimental spectra as well as increased precision of the simulations is desirable for the further exploration of the potential of the ROA spectroscopy for biomolecular studies in the future.

The B-Z conformational transition was induced by Mn 2+ ions in a synthetic oligonucleotide (dG-dC) 20 and monitored by the vibrational circular dichroism (VCD). For the first time, the spectra were analyzed on the basis of quantum-mechanical computations. Force field and intensity tensors computed ab initio for smaller DNA fragments were transferred to a d(GCGCGCGC) 2 octamer model including explicit water molecules. The method allowed us to assign and explain most of the frequency and intensity features observed in the absorption and VCD spectra of the B-and Z-forms. Particularly, the computations reproduced the VCD sign flip caused by the transition due to the CdO stretching and allowed us to assign most spectral bands in the nitrogen bases vibrational region. Also, known isotopic effects (deuteration and a 18 O substitution) were reproduced correctly. For the sugar-phosphate modes, the assignment of the VCD bands was hindered by a weak experimental signal. The approach based on quantum-mechanical computations was found superior to previous models based on coupled oscillator theory. Water molecules hydrogen-bonded to the DNA skeleton had to be included for reliable interpretation of the VCD and IR spectral patterns, namely, for the sugarphosphate vibrations.

Absorption and vibrational circular dichroism (VCD) spectra of six 1,1′-binaphthyl derivatives were measured and analyzed on the basis of ab initio modeling. The spectra of both enantiomers were recorded with a high signal-to-noise ratio. The BPW91/6-31G** density functional theory level and the gauge invariant atomic orbitals were used for the simulations of VCD intensities. The binaphthyl moiety behaves as a chiral chromophore with a strong VCD signal because the 1,1′-substitution hinders its rotation. Most of the VCD bands were assigned, and the contributions of the binaphthyl skeleton and the functional groups could be clearly distinguished. Distinct VCD characteristics were found for the compounds exhibiting C 2 and C 1 symmetry. A very good agreement between the calculated and experimental spectra was observed. Apart from indication of enantiomeric purity, the spectra contain readable information about molecular conformation. The dihedral angle between the naphthyls planes, equal to about 55°when naphthyl residues were connected with PO 4 covalent bridge, was found close to 90°for all the other derivatives.