Biomedical subjects

Paolo Lazzeretti

Publications and source records attributed to Paolo Lazzeretti.

8 recordsLinked to original sources

PubMed2006

From pentalene to dicyclopenta[b,g]naphthalene, or the change towards delocalized structures.

Using triples-corrected coupled-cluster methods as well as other high-level theoretical approximations, the optimized parameters and isomerization barriers of the family of compounds cyclopentadiene-(benzene)x-cyclopentadiene (x = 0, 1, 2) are computed. In contrast to previous studies, s-indacene presents a localized C(2h) geometry. Also, the localized structure of pentalene is found to be the most stable, but when two benzene rings are intercalated between the five-member rings of pentalene, the resulting molecule preferably adopts a delocalized D(2h) conformation.

Journal Article↗

PubMed2006

Structure, magnetizability, and nuclear magnetic shielding tensors of bis-heteropentalenes. IV. Dihydrophospholophosphole isomers.

The geometry of the heteropentalenes formed by two phosphole units has been determined at the DFT level. The magnetic susceptibility and the nuclear magnetic shielding at the nuclei of these systems have also been calculated using gauge-including atomic orbitals and a large Gaussian basis set to achieve near Hartree-Fock estimates. A comparative study of the various isomers, of their flattened analogs, and of the parent phosphole molecule, shows that the [3,4-c] isomer is the most aromatic system in the set considered, assuming diatropicity and degree of planarity as indicators, even if it is the less stable in terms of total molecular energy. Plots of magnetic field-induced current densities confirm diatropicity of P-containing bis-heteropentalenenes, showing, however, significant differences from the analogous systems with distinct heteroatoms. The maps give evidence of spiral flow nearby C-C bonds, compatible with prevalent distortive behavior of pi electrons exalted by pyramidalization at P, and competing against the sigma electron compression, which would favor planar structure.

Journal Article↗

PubMed2005

Parity violation energy of biomolecules--I: polypeptides.

A computational algorithm is developed to compute the energy of parity-violation (E(pv)) due to weak-nuclear forces acting within chain polymers. The method is applied to estimate the magnitude of E(pv) associated with the folding of alpha-helices in polypeptide chains and, in turn, of typical proteins. Implications to the development of biological homochirality in nature are discussed in terms of a simple evolutionary model to assess the likelihood for energies of the order of the computed E(pv) to have determined the direction of natural homochirality.

Algorithms↗

PubMed2004

Are ring currents still useful to rationalize the benzene proton magnetic shielding?

[structure: see text] The conventional interpretation of proton NMR chemical shifts is supported by large basis set ab initio quantum mechanical calculations. The benzene protons are predicted to lie within the deshielding zone defined in terms of the out-of-plane magnetic shielding domain. However, ring currents by themselves are not sufficient to account quantitatively for the observed benzene proton downfield chemical shift. sigma-Electron contributions must also be taken into account. The conventional explanation for the ethyne proton chemical shift is valid.

Journal Article↗

PubMed2004

Calculation of electric dipole hypershieldings at the nuclei in the Hellmann-Feynman approximation.

The third-rank electric hypershieldings at the nuclei of four small molecules have been evaluated at the Hartree-Fock level of theory in the Hellmann-Feynman approximation. The nuclear electric hypershieldings are closely related to molecular vibrational absorption intensities and a generalization of the atomic polar tensors (expanded in powers of the electric field strength) is proposed to rationalize these intensities. It is shown that the sum rules for rototranslational invariance and the constraints imposed by the virial theorem provide useful criteria for basis-set completeness and for near Hartree-Fock quality of nuclear shieldings and hypershieldings evaluated in the Hellmann-Feynman approximation. Twelve basis sets of different size and quality have been employed for the water molecule in an extended numerical test on the practicality of the proposed scheme. The best results are obtained with the R12 and R12+ basis sets, designed for the calculation of electronic energies by the explicitly correlated R12 method. The R12 basis set is subsequently used to investigate three other molecules, CO, N2, and NH3, verifying that the R12 basis consistently performs very well.

Journal Article↗

PubMed2003

Calculation of dipole-shielding polarizabilities (sigma(alphabetagamma)I): the influence of uniform electric field effects on the shielding of backbone nuclei in proteins.

A significant contribution to the chemical shielding of a nucleus can arise from uniform electric fields that act to distort the electronic charge distribution surrounding a nucleus and, hence, affect the nuclear shielding. It has been shown by Buckingham (Buckingham, A. D. Can. J. Chem. 1960, 38, 300) that the nuclear magnetic shielding tensor sigmaalphabetaI of a nucleus in the presence of an external weak static uniform electric field E may be expanded using sigmaalphabetaI(E) = sigmaalphabetaI + sigmaalphabetagammaIEgamma + 1/2sigmaalphabetagammadeltaIEgammaEdelta + sigmaalphabeta,gammadeltaIEgammadelta ... The third rank tensor sigmaalphabetagammaI is referred to as the dipole-shielding polarizability and describes the nonlinear response of the electron cloud to first order in E, muI, and B0. We report calculations of sigmaalphabetagammaI for the N, HN, and C' nuclei in N-methyl acetamide (NMA) and show that these tensors can be used to provide considerable insight into the behavior of uniform electric fields upon the shielding of backbone nuclei in proteins. The sigmaalphabetagammaI values for the N, HN, and C' of NMA were calculated using the continuous transformation of the origin of the current density (CTOCD) scheme with the diamagnetic contribution set to zero (CTOCD-DZ). Values are given for the individual tensor components of sigmaalphabetagammaI for each nucleus. To test that the calculations have provided a reasonable estimate for the sigmaalphabetagammaI of N, HN, and C' nuclei in proteins, a pH titration was performed using Hen Lysozyme (HEWL). The pH-induced isotropic shielding changes for the C', N, and HN nuclei in some peptide bonds close to E35 ( approximately <8 A) were extracted from sets of fitted titration curves. Assuming the experimental shielding changes arise solely from uniform electric field effects caused by the deprotonation of E35, without any other pH-induced structural alterations which might lead to a shielding change, the experimental shielding differences were compared to those calculated via the product Agamma(I).Egamma where Agamma(I) = (1/3)sigmaalphaalphagammaIota. The agreement with the experimental data is in many cases reasonable and suggests that, within the Buckingham formalism, the complete sigmaalphabetagammaI tensors reported here will be helpful to resolve the importance of uniform electric fields upon isotropic and anisotropic shielding in proteins and their complexes.

Acetamides↗

PubMed2002

The leap-frog effect of ring currents in benzene.

Symmetry arguments show that the ring-current model proposed by Pauling, Lonsdale, and London to explain the enhanced diamagnetism of benzene is flawed by an intrinsic drawback. The minimal basis set of six atomic 2p orbitals taken into account to develop such a model is inherently insufficient to predict a paramagnetic contribution to the perpendicular component of magnetic susceptibility in planar ring systems such as benzene. Analogous considerations can be made for the hypothetical H(6) cyclic molecule. A model allowing for extended basis sets is necessary to rationalize the magnetism of aromatics. According to high-quality coupled Hartree-Fock calculations, the trajectories of the current density vector field induced by a magnetic field perpendicular to the skeletal plane of benzene in the pi electrons are noticeably different from those typical of a Larmor diamagnetic circulation, in that (i) significant deformation of the orbits from circular to hexagonal symmetry occurs, which is responsible for a paramagnetic contribution of pi electrons to the out-of-plane component of susceptibility, and (ii) a sizable component of the pi current density vector parallel to the inducing field is predicted. This causes a waving motion of pi electrons; streamlines are characterized by a "leap-frog effect".

Journal Article↗

PubMed2001

Understanding parity violation in molecular systems.

Parity-violation energy (E(PV)) due to weak nuclear interactions between nucleons and electrons in chiral molecular systems provides a fundamental tool to verify our understanding of electronic behavior in complex systems. We used both a relativistic and a nonrelativistic approach to study a number of simple molecules and analyze the corresponding E(PV) in terms of intuitive electrodynamic concepts. We developed a qualitative model to predict the sign of E(PV) and its behavior against selected geometric distortions. Our model provides a valuable tool to screen large sets of molecules and select interesting candidates for more expensive investigations.

Biophysical Phenomena↗