The DFT/vdW-WF method, recently developed to include the Van der Waals interactions in Density Functional Theory (DFT) using the Maximally Localized Wannier functions, is applied to the study of the adsorption of rare-gas atoms (Ne, Ar, Kr, and Xe) on the Cu(111) and Pb(111) surfaces, at three high-symmetry sites. We evaluate the equilibrium binding energies and distances, and the induced work-function changes and dipole moments. We find that, for Ne, Ar, and Kr on the Cu(111) surface the different adsorption configurations are characterized by very similar binding energies, while the favored adsorption site for Xe on Cu(111) is on top of a Cu atom, in agreement with previous theoretical calculations and experimental findings, and in common with other closepacked metal surfaces. Instead, the favored site is always the hollow one on the Pb(111) surface, which therefore represents an interesting system where the investigation of high-coordination sites is possible. Moreover, the Pb(111) substrate is subject, upon rare-gas adsorption, to a significantly smaller change in the work function (and to a correspondingly smaller induced dipole moment) than Cu(111). The role of the chosen reference DFT functional and of different Van der Waals corrections, and their dependence on different rare-gas adatoms, are also discussed.

The method, recently developed to include van der Waals interactions in the density functional theory by using the maximally localized Wannier functions, is extended to the case of atoms and fragments weakly bonded (physisorbed) to metal and semimetal surfaces, thus opening the way to realistic simulations of surface-physics processes, where van der Waals interactions play a key role. Successful applications to the case of Ar on graphite and of Ar, He, and H(2) on the Al(100) surface are presented.

The first Co(iii) complexes with (1,3-selenazol-2-yl)hydrazones as an unexplored class of ligands were prepared and characterized by NMR spectroscopy and X-ray diffraction analysis. The novel ligands act as NNN tridentate chelators forming octahedral Co(iii) complexes. The impact of structural changes on ligands' periphery as well as that of isosteric replacement of sulphur with selenium on the electrochemical and electronic absorption features of complexes are explored. To support the experimental data, density functional theory (DFT) calculations were also conducted. Theoretical NMR chemical shifts, the relative energies and natural bond orbital (NBO) analysis are calculated within the DFT approach, while the singlet excited state energies and HOMO-LUMO energy gap were calculated with time-dependent density functional theory (TD-DFT). The electrophilic f and nucleophilic f Fukui functions are well adapted to find the electrophile and nucleophile centres in the molecules. Both (1,3-selenazol-2-yl)- and (1,3-thiazol-2-yl)hydrazone Co(iii) complexes showed potent antimicrobial and antioxidant activity. A significant difference among them was a smaller cytotoxicity of selenium compounds.

The popular biomolecular AMBER (ff99SB) force field (FF) has been extended with new parameters for the simulations of peptides containing α,α dialkylated residues with cyclic side chains. Together with the recent set of nitroxide parameters [E. Stendardo, A. Pedone, P. Cimino, M. C. Menziani, O. Crescenzi and V. Barone, Phys. Chem. Chem. Phys., 2010, 12, 11697] this extension allows treating the TOAC residue (TOAC, 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) widely used as a spin label in protein studies. All the conformational minima of the Ac-Ac(6)C-NMe (Ac = acetyl, Ac(6)C = 1-aminocyclohexaneacetic acid, NMe = methylamino) and Ac-TOAC-NMe dipeptides have been examined in terms of geometry and relative energy stability by Quantum Mechanical (QM) computations employing an hybrid density functional (PBE0) for an extended training set of conformers with various folds. A very good agreement between QM and MM (molecular mechanics) data has been obtained in most of the investigated properties, including solvent effects. Finally, the new set of parameters has been validated by comparing the conformational and dynamical behavior of TOAC-labeled polypeptides investigated by means of classical molecular dynamics (MD) simulations with QM data and experimental evidence. The new FF accurately describes the tuning of conformational and dynamical behavior of the Ac-TOAC-NMe dipeptide and double spin-labeled heptapeptide Fmoc-(Aib-Aib-TOAC)(2)-Aib-OMe (Fmoc, fluorenyl-9-methoxycarbonyl; Aib, α-aminoisobutyric acid; OMe, methoxy) by solvents with different polarity. In particular, we found that the 3(10) helical structure of heptapeptide is the most stable one in vacuo, with a geometry very similar to the X-ray crystallographic structure, whereas a conformational equilibrium between the 3(10)- and α-helical structures is established in aqueous solution, in agreement with EPR data.

Two new Zn(II) complexes with tridentate hydrazone-based ligands (condensation products of 2-acetylthiazole) were synthesized and characterized by infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy and single crystal X-ray diffraction methods. The complexes 1, 2 and recently synthesized [ZnL3(NCS)2] (L3 = (E)-N,N,N-trimethyl-2-oxo-2-(2-(1-(pyridin-2-yl)ethylidene)hydrazinyl)ethan-1-aminium) complex 3 were tested as potential catalysts for the ketone-amine-alkyne (KA2) coupling reaction. The gas-phase geometry optimization of newly synthesized and characterized Zn(II) complexes has been computed at the density functional theory (DFT)/B3LYP/6–31G level of theory, while the highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO and LUMO) energies were calculated within the time-dependent density functional theory (TD-DFT) at B3LYP/6-31G and B3LYP/6-311G(d,p) levels of theory. From the energies of frontier molecular orbitals (HOMO–LUMO), the reactivity descriptors, such as chemical potential (μ), hardness (η), softness (S), electronegativity (χ) and electrophilicity index (ω) have been calculated. The energetic behavior of the investigated compounds (1 and 2) has been examined in gas phase and solvent media using the polarizable continuum model. For comparison reasons, the same calculations have been performed for recently synthesized [ZnL3(NCS)2] complex 3. DFT results show that compound 1 has the smaller frontier orbital gap so, it is more polarizable and is associated with a higher chemical reactivity, low kinetic stability and is termed as soft molecule.

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The effects of adsorption on the graphite(0001) surface on the nonplanar distortions of nickel(II)octaethylporphyrin were studied by molecular mechanics (MM) approach. Using the Consistent Force Field (CFF) program with previously developed parameters for metalloporphyrins and supplemented to treat intermolecular interactions geometry optimizations were carried out for 43 conformations of 28 distinct conformers of nickel(II)octaethylporphyrin. The stable energy-minimized conformers were stereochemically characterized, analyzed by the Normal-coordinate Structural Decomposition (NSD) method and compared with the available theoretical and experimental data for the isolated nickel(II)octaethylporphyrin structures.

In search for future good adsorbents for CO2 capture, a nitrogen-rich triazole-type Metal–Organic Framework (MOF) is proposed based on the rational design and theoretical molecular simulations. The structure of the proposed MOF, named Zinc Triazolate based Framework (ZTF), is obtained by replacing the amine-organic linker of MAF-66 by a triazole, and its structural parameters are deduced. We used grand-canonical Monte Carlo (GCMC) simulations based on generic classical force fields to correctly predict the adsorption isotherms of CO2 and H2O. For water adsorption in MAF-66 and ZTF, simulations revealed that the strong hydrogen bonding interactions of water with the N atoms of triazole rings of the frameworks are the main driving forces for the high adsorption uptake of water. We also show that the proposed ZTF porous material exhibits exceptional high CO2 uptake capacity at low pressure, better than MAF-66. Moreover, the nature of the interactions between CO2 and the MAF-66 and ZTF surface cavities was examined at the microscopic level. Computations show that the interactions occur at two different sites, consisting of Lewis acid–Lewis base interactions and hydrogen bonding, together with obvious electrostatic interactions. In addition, we investigated the influence of the presence of H2O molecules on the CO2 adsorption on the ZTF MOF. GCMC simulations reveal that the addition of H2O molecules leads to an enhancement of the CO2 adsorption at very low pressures but a reduction of this CO2 adsorption at higher pressures.