Caterina Benzi

Quantum mechanical study of the conformational behavior of proline and 4R-hydroxyproline dipeptide analogues in vacuum and in aqueous solution.

The conformational behavior of the title compounds has been investigated by Hartree–Fock, MP2, and DFT computations on the most significant structures related to variations of the backbone dihedral angles, cis/trans isomerism around the peptide bond, and diastereoisomeric puckering of the pyrrolidine ring. In vacuum the reversed γ turn (γl), characterized by an intramolecular hydrogen bridge, corresponds to the absolute energy minimum for both puckerings (up and down) of the pyrrolidine ring. An additional energy minimum is found in the helix region, but only for an up puckering of the pyrrolidine ring. When solvent effects are included by means of the polarizable continuum model the conformer observed experimentally in condensed phases becomes the absolute minimum. The down puckering is always favored over its up counterpart, albeit by different amounts (0.4–0.5 kcal/mol for helical structures and about 2 kcal/mol for γl structures). In helical structures cis arrangements of the peptide bond are only slightly less stable than their trans counterparts. This is no longer true for γl structures, because the formation of an intramolecular hydrogen bond is possible only for trans peptide bonds. In most cases, proline and hydroxyproline show the same general trends; however, the electronegative 4(R) substituent of hydroxyproline leads to a strong preference for up puckerings irrespective of the backbone conformation.

Building cavities in a fluid of spherical or rod‐like particles: A contribution to the solvation free energy in isotropic and anisotropic polarizable continuum model

A general formalism for the calculation of cavitation energies in the framework of the scaled particle theory has been implemented in the Polarizable Continuum Model (PCM), contributing to the nonelectrostatic part of the molecular free energy in solution. The solute cavity and the solvent molecules are described as hard spherocylinders, whose radius and length are related to the actual molecular shape, while the solvent density is estimated from experimental data, or from the solvent molecular volume, suitably scaled. The present model can describe isotropic solutions of spherical and rod‐like molecules in spherical or rod‐like solvents, and also anisotropic solutions in which the solvent molecules are oriented in space: in this case, the cavitation energy also depends on the relative orientation of solute and solvent molecules. Test calculations have been performed on simple systems to evaluate the accuracy of the present approach, in comparison with other methods and with the available experimental estimates of the cavitation energy, giving encouraging results.

Integrated Approach for Modeling the Emission Fluorescence of 4-(N,N-Dimethylamino)benzonitrile in Polar Environments

A stochastic model for the interpretation of the emission fluorescence of 4-( N, N-dimethylamino)benzonitrile (DMABN) is discussed. We proceed by reviewing the stochastic modeling approach ( Polimeno, A. ; Barbon, A. ; Nordio, P. L. ; Rettig, W. J. Phys. Chem. 1994, 98, 12158 ), in which internal degrees of freedom are coupled with an effective solvent relaxation variable. Potential energy surfaces are obtained using a reliable but computationally cost-effective quantum mechanical (QM) approach, and estimates of dissipative parameters are calculated on the basis of direct hydrodynamic arguments. Emission fluorescence is estimated by solving numerically a diffusion/sink/source equation for the stationary population of excited state and compared to emission fluorescence of DMABN measured experimentally.

Accurate prediction of electron-paramagnetic-resonance tensors for spin probes dissolved in liquid crystals

High-level ab initio g and A tensor components have been calculated for PD-tempone and tempo-palmitate (TP) radical spin probes dissolved in n-pentyl and n-hexyl cyanobiphenyl liquid crystals. Solvent effects have been included in the proposed approach by means of the polarizable continuum model, allowing for solvent anisotropy. An in-depth analysis of the electronic structure of probes was performed to choose a suitable model for TP and make the calculations more accessible. Computed magnetic tensor components have been compared with corresponding values measured in the rigid limit. The quality of the results suggests the use of quantum-mechanical data to determine the order parameter of the nematic from experimental electron-spin resonance measurements.

Accurate and effective calculation of amide proton magnetic shieldings in a calcium binding peptide

NMR amide proton chemical shifts of the calcium complex with the bicyclic nonapeptide BCP2, cyclo-(Glu1–Ala2–Pro3–Gly4–Lys5–Ala6–Pro7–Gly8)-cyclo-(1γ→5e)Gly9 were calculated by means of Hartree–Fock and DFT methods within the GIAO framework. Calculated results yielded a good agreement with experimental data: computed chemical shifts well reproduced the strong changes induced by the presence of the metal. The nature of the metal–peptide interaction, as well as other non-local effects on magnetic shielding, were discussed. Further, different hybrid methods have been tested to set up an affordable approach to study magnetic properties in metal–protein complexes.

Order parameters of α,ω-diphenylpolyenes in a nematic liquid crystal from an integrated computational and C13 NMR spectroscopic approach

The orientational order parameters and conformational behavior of five relatively large rodlike molecules, biphenyl, trans-stilbene, 1,3-diphenyl-butadiene, 1,3,5-diphenyl-hexatriene, and 1,3,5,7-diphenyl-octatetraene, dissolved in the thermotropic liquid crystal ZLI-1167, have been studied using an integrated approach combining C13 NMR measurements and quantum mechanical computations of carbon chemical shift tensors. Besides biphenyl, the phenyl moiety of all structures has been found to have a high rotational mobility in the temperature range of the present experiments. The rank-two order parameter ⟨P2⟩ in the nematic phase is found to increase steadily from the shortest to the longest term of the series at any temperature within the nematic range. The molecular biaxiality order parameter ⟨D022⟩ is found to be small and essentially constant with temperature, giving further support to the common assumption of effective uniaxiality for these probes.