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.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.