Maurizio Sironi

Halogen Bonds with Benzene : an Assessment of DFT Functionals

The performance of an extensive set of density functional theory functionals has been tested against CCSD(T) and MP2 results, extrapolated to the complete basis set (CBS) limit, for the interaction of either DCl or DBr (D = H, HCC, F, and NC) with the aromatic system of benzene. It was found that double hybrid functionals explicitly including dispersion, that is, B2PLYPD and mPW2PLYPD, provide the better agreement with the CCSD(T)/CBS results on both energies and equilibrium geometry, indicating the importance of dispersive contributions in determining this interaction. Among the less expensive functionals, the better performance is provided by the ωB97X and M062X functionals, while the ωB97XD and B97D functionals are shown to work very well for bromine complexes but not so well for chlorine complexes.

New basis set superposition error free ab initio MO-VB interaction potential: Molecular-dynamics simulation of water at critical and supercritical conditions

Recently, a controversy has come to light in literature regarding the structure of water in nonambient conditions. Disagreement is evident between the site–site pair correlation functions of water derived from neutron diffraction and those obtained by computer simulations which employ effective pairwise potentials to express the intermolecular interactions. In this paper the SCFMI method (self-consistent field for molecular interaction) followed by nonorthogonal CI (configuration interaction) calculations was used to determine a new water–water interaction potential, which is BSSE (basis set superposition error) free in an a priori fashion. Extensive calculations were performed on water dimer and trimer and a new parametrization of a NCC-like (Niesar–Corongiu–Clementi) potential was accomplished. This was employed in the molecular-dynamics simulation of water. The effect of temperature and density variations was examined. Acceptable agreement between site–site correlation functions derived from neutron di...

Determination of extremely localized molecular orbitals and their application to quantum mechanics/molecular mechanics methods and to the study of intramolecular hydrogen bonding

The extremely localized molecular orbitals (ELMOs) are a set of molecular orbitals strictly localized only on a few atoms of a molecule. They are obtained in an a priori fashion through the direct application of the variation principle. Even if the theoretical aspects of their determination have been discussed already in the literature, stable and fast algorithms to obtain ELMOs are still not trivial and a comparison between different methods is reported. We furthermore investigate the applicability of ELMOs to quantum mechanics/molecular mechanics (QM/MM) methods which employ frozen localized orbitals to represent covalent bonds across the QM and the MM region. In addition it is shown that ELMOs can be used to describe species with intramolecular hydrogen bonds, where a correct elimination of the intramolecular basis set superposition error can be essential to perform accurate conformational studies.

Expansion of the spin-coupled wavefunction in Slater determinants

SummaryThe expansion of the spin-coupled wavefunction in Slater determinants constructed from nonorthogonal spin-orbitals is discussed. It proves possible to generate from cofactors of the appropriate overlap matrix all the density matrices, up to fourth order, required for the variational optimization of the wavefunction. The computational effort inherent in this ‘super-cofactor’ strategy scales in a very acceptable manner with the number of electrons.

Molecular dynamics simulation of aqueous solutions of trimethylamine-N-oxide and tert-butyl alcohol

In this work we have investigated hydration properties of aqueous solutions up to a solute molar fraction X2 = 0.125 of two isosteric molecules – the bioprotectant trimethylamine-N-oxide (TMAO) and the denaturant tert-butyl alcohol (TBA) – using molecular dynamics simulation at 298 K. Statistical analyses of the trajectories show in particular that as the solute concentration increases the number of the water molecules in the first hydration shell decreases uniformly for TMAO, while for TBA it decreases more rapidly in a concentration range where experiments indicate that TBA starts to self-aggregate. No appreciable solute segregation occurs for TMAO even in the most concentrated solution, where on the average each water molecule is shared by two solutes. This result parallels what has been recently found for glycine betaine, an organic osmolyte closely related to TMAO.

Classical and quantum dynamics on the collinear potential energy surface for the reaction of Li with H2

Abstract Extensive Valence Bond (VB) calculations using non-orthogonal, spin-coupled wavefunctions with optimized orbitals have been employed to analyse the reactive region for the title process. Both the exothermic channel and the reverse, endothermic process are of strong astrophysical interest although no previous calculations have been available on both the reactive dynamics and the interaction energy surface. The specific features of the potential are analysed for some indicative configurations and classical trajectory calculations are carried out for the special collinear arrangement. In the latter instance, quantum time-dependent wavepacket calculations have also been performed and the two sets of results are found to be in rather good accord with each other. Some consequences of these exploratory calculations are discussed in detail.

Interaction forces and energy transfer dynamics of LiH (1gE+) and helium atoms. I. The ab initio evaluation of the lowest potential energy surface

Abstract The weak van der Waals (vdW) forces which preside over the interaction of helium with the LiH molecule in its ground electronic state are evaluated very accurately using a recently developed spin-coupled Valence Bond (VB) approach. The target molecule is initially treated as a rigid rotor (RR) at its equilibrium geometry and the behaviour of the interaction is examined over a wide range of orientations and relative distances for the impinging projectile. The general features of the potential anisotropy are analysed in relation to earlier calculations on the same system and foun found to be rather different, especially in the short-range repulsive region for both directions of He approach along the diatomic bond. The full, vibrational PES is also presented by repeating the calculations for five different values of the molecular bond length.

cis-[Pt(NH3)2]2+ coordination to the N7 and O6 sites of a guanine–cytosine pair: disruption of the Watson–Crick H-bonding pattern

The coordination of cis-[Pt(NH3)2]2+ to the N7 and O6 sites of guanine of the guanine–cytosine (GC) nucleic base pair is studied at the SCF, DFT and MP2 levels of theory, and by an ab initio BSSE-free optimization algorithm, concerning the possible mechanisms of the antitumor activity of cis-[Pt(NH3)2Cl2]. The calculations show that the cis-[Pt(NH3)2]2+ coordination results in the breakage of the (cytosine)N4–H–O6(guanine) H-bond and a substantial non-planarity of the GC moiety. From an analysis of the electrostatic potential at the O6, N1–H and N2–H sites of cis-[Pt(NH3)2G]2+ we can explain the predicted changes in geometry and binding energy of the GC complex.

Halogen‐Bonding Interactions with π Systems: CCSD(T), MP2, and DFT Calculations

Halogen bonding is a noncovalent interaction between a halogen atom and a nucleophilic site. Interactions involving the π electrons of aromatic rings have received, up to now, little attention, despite the large number of systems in which they are present. We report binding energies of the interaction between either NCX or PhX (X = F, Cl, Br, I) and the aromatic benzene system as determined with the coupled cluster with perturbative triple excitations method [CCSD(T)] extrapolated at the complete basis set limit. Results are compared with those obtained by Møller-Plesset perturbation theory to second order (MP2) and density functional theory (DFT) calculations by using some of the most common functionals. Results show the important role of DFT in studying this interaction.

In silico design of tubulin-targeted antimitotic peptides

Microtubules are polymeric structures formed by the self-assembly of tubulin dimers. The growth and shrinkage of these dynamic arrays have a key role during the cell-proliferation process. This makes tubulin the molecular target of many anticancer drugs currently in use or under clinical trial. Their impressive success is limited by the onset of resistant tumour cells during the treatment, so new resistance-proof molecules need to be developed. Here we use molecular dynamics and free-energy calculations to study the network of interactions that allow microtubule formation. Modelling the protein-protein interface allows us to identify the amino acids responsible for tubulin-tubulin binding and thus to design peptides, which correspond to tubulin subsequences, that interfere with microtubule formation. We show that the application of molecular modelling techniques leads to the identification of peptides that exhibit antitubulin activity both in vitro and in cultured cells.