Giacomo Saielli

Addressing the Stereochemistry of Complex Organic Molecules by Density Functional Theory-NMR: Vannusal B in Retrospective

We have employed density functional theory (DFT) protocols to calculate the NMR properties of the vannusals, a class of natural products whose structures have been the subject of recent investigations. The originally assigned structure of vannusal B was revised after a long synthetic journey which generated a series of closely related diastereomers. In this work we show how DFT calculations based on density functionals and basis sets designed for the prediction of NMR spectra (M06/pcS-2 level of theory) can be used to reproduce the observed parameters, thereby offering to the synthetic chemist a useful tool to discard or accept putative structures of unknown organic molecules.

Effect of the Chain Length on the Structure of Ionic Liquids: from Spatial Heterogeneity to Ionic Liquid Crystals

Ionic liquids with intermediate nonpolar cationic side-chain lengths are known to have nanoscale spatial heterogeneities with nonpolar tail domains separated by a continuous polar network. In this work, we use coarse-grained molecular dynamics simulations to show that, when the nonpolar cationic side chain is sufficiently long, due to the stronger van der Waals interactions between the side chains, the structure of ionic liquids goes through a transition from spatially heterogeneous to liquid crystalline-like. For XMIm(+)/NO(3)(-) ionic liquids, change occurs when the number of carbon groups on the cationic side chain varies from 14 to 16. In the liquid crystal-like phase, the cationic side chains tend to be parallel to each other, while the cationic head groups and anions, although being mostly layered perpendicularly to the direction along the side chains, still form a continuous polar network.

Can two molecules have the same NMR spectrum? Hexacyclinol revisited.

An in-depth DFT computational investigation (B97-2/cc-pVTZ level) of the 1H and 13C NMR spectra of the recently disputed natural substance hexacyclinol, including J(1H,1H) couplings, is presented. Structures 1 and 2 have been compared with regard to the suggested possibility that two molecules have very similar NMR spectra as to be indistinguishable. Despite a remarkable similarity of functional groups present, the two calculated spectra differ in many features related both to chemical shifts and connectivities.

Through‐Space Spin–Spin Coupling in van der Waals Dimers and CH/π Interacting Systems. An Ab Initio and DFT Study

The through-space J(HH) and J(CH) spin-spin coupling constants of model van der Waals dimers (involving methane, ethylene, and benzene), and of selected compounds showing the CH/pi interaction, have been investigated by means of DFT and ab initio calculations. In the range of intermolecular separations for which the interaction is stabilizing, weak couplings (0.1-0.3 Hz) are predicted for J(CH), while the corresponding J(HH) couplings are much smaller. The relative contributions (Fermi-contact, spin-orbit, and spin-dipole) are strongly dependent on the geometry of the dimers and on the distance; the non-negligible values of J(CH) for pi systems stem largely from an incomplete cancellation of spin-orbit terms. The results obtained for the larger molecules, that is, acetonitrile@calix[4]arene 5, the imine 6, and the aryl ester 7 are consistent with those on the model dimers. For 7, the occurrence of a through-space mechanism for the transmission of coupling is established by examining trends in the magnitude of couplings as a function of the number of intervening covalent bonds.

DFT Calculation of 1J(119Sn,13C) and 2J(119Sn,1H) Coupling Constants in Di- and Trimethyltin(IV) Compounds

We have tested several computational protocols, at the nonrelativistic DFT level of theory, for the calculation of 1J(119Sn, 13C) and 2J(119Sn, 1H) spin-spin coupling constants in di- and trimethyltin(IV) derivatives with various ligands. Quite a good agreement with experimental data has been found with several hybrid functionals and a double-zeta basis set for a set of molecules comprising tetra-, penta-, and hexa-coordinated tin(IV). Then, some of the protocols have been applied to the calculation of the 2J(119Sn, 1H) of the aquodimethyltin(IV) ion and dimethyltin(IV) complex with D-ribonic acid and to the calculation of 1J(119Sn, 13C) and 2J(119Sn, 1H) of the dimethyltin(IV)-glycylglycine and glycylhistidine complexes in water solutions. Solvent effects have been considered in these cases by including explicit water molecules and/or the solvent reaction field, resulting in a good agreement with experimental data. The proposed protocols constitute a helpful tool for the structural determination of di- and triorganotin(IV) derivatives.

Effect of asymmetric substitution on the mesomorphic behaviour of low-melting viologen salts of bis(trifluoromethanesulfonyl)amide

We report on the synthesis and characterisation of novel ionic liquid crystals and ionic liquids based on asymmetric viologen salts of bis(trifluoromethanesulfonyl)amide (Tf2N−). The thermotropic behaviour of the salts has been thoroughly characterized by DSC, X-ray diffraction and polarized light optical microscopy. The occurrence of smectic mesophases and the temperature range over which they are stable has been discussed as a result of the asymmetry of the viologen dications. Strongly asymmetric systems, not showing mesomorphism, have a rather low melting point (just beyond 40 °C) while slightly asymmetric samples exhibit a smectic phase with a wide range of stability, from about 0 °C up to above 140 °C, thus increasing the range of stability of the mesophase observed for the symmetric compounds. Finally, we report on the lyotropic behaviour in non-polar solvents, such as benzene, where liquid clathrates have been found.

DFT study of the interaction free energy of π–π complexes of fullerenes with buckybowls and viologen dimers

We present a theoretical investigation, by means of DFT protocols, of the complexation thermodynamics of (i) complexes of C70 and C60 fullerenes with bowl-shaped hexabenzocoronene derivatives and (ii) complexes of C60 with viologen dimers. The recent functionals of the M06 family, accounting for π–π interactions to a good level of approximation, have been used to calculate the interaction free energies. For the former complexes, the good agreement between the calculated results and the experimental data confirms the reliability of the protocol used. On these grounds, we then checked the stability of a series of complexes of C60 with some viologen dimers, 1BPnBP1 (n = 6–9), where two N-methylated bipyridinium units are linked by an alkyl chain of variable length, acting as molecular tweezers. Both forms of the viologen cores, that is the cation (each core doubly charged) and the reduced neutral form, were considered. For a suitable chain length a free energy gain upon complexation is predicted for the neutral form while the complexation of C60 by the cationic form is disfavoured mainly for entropic reasons.

DFT Calculation of Intermolecular Nuclear Spin–Spin Coupling in van der Waals Dimers

A small but detectable intermolecular spin-spin coupling (JC,H ) is predicted by density functional calculations on van der Waals bonded dimers like methane-benzene and benzene-benzene, as shown in the picture.

Insights on Nuclease Mechanism: The Role of Proximal Ammonium Group on Phosphate Esters Cleavage

The role of remotely located ammonium groups in the active site of many phosphate-cleaving enzymes is investigated by using model systems thus providing mechanistic hints to a still unsolved problem.

Differential solvation free energies of oxonium and ammonium ions: insights from quantum chemical calculations.

We have employed computational protocols to determine the differential solvation free energy in water of oxonium and ammonium ions. We have focused our analysis on pairs of onium ions having the same hydrocarbon content and substitutional pattern (HCSP pairs). In agreement with previous suggestions (Taft, R. W.; Wolf. J. F.; Beauchamp, J. L.; Scorrano, G.; Arnett, E. M. J. Am. Chem. Soc. 1978, 100, 1240), we found that cavitation and van der Waals terms do not contribute to the differential solvation free energy. Moreover, we observe that oxonium ions are more strongly solvated than the analogous ammonium ions even though the former ones have fewer H-bond donor sites. The performance of two different continuum solvation models, PCM and SMD, is discussed.