Archive ouverte UNIGE | last documents for author 'Fabien Tran'https://archive-ouverte.unige.ch/Latest objects deposited in the Archive ouverte UNIGE for author 'Fabien Tran'engThe role of density functional theory in chemistry: Some historical landmarks and applications to zeoliteshttps://archive-ouverte.unige.ch/unige:3647https://archive-ouverte.unige.ch/unige:3647Density functional theory (DFT) has progressively emerged in the last 40 years as a leading methodology for the modelling and simulation of chemical systems. In this paper, some historical landmarks in the development of this method are outlined, emphasizing on its main characteristic being an electron density-based theory. This is in contrast with wavefunction-based methodologies which were exclusively employed previously. Interestingly, DFT has been first applied to solids, with a rather late recognition by chemists and molecular scientists. After this historical survey, several applications of DFT to the structure and properties of zeolites are reviewed as a tribute to Dr Annick Goursot.Fri, 02 Oct 2009 17:19:20 +0200Mixed PbFBr1-xIx crystals: structural and spectroscopic investigationshttps://archive-ouverte.unige.ch/unige:3603https://archive-ouverte.unige.ch/unige:3603Mixed single PbFBr1−xIx crystals have been prepared. X-ray powder diffraction structure determinations show that all samples crystallize with the matlockite structure. However, the single crystal structure of PbFBr0.5I0.5 involves not only fractional occupation of one site corresponding to the stoichiometry, but also split positions of the Pb2+ ion. Raman spectra reveal the presence of new additional bands with respect to PbFBr and PbFI. DFT calculations of lattice vibrations for PbFI show good agreement with experimental spectra. The calculated phonon dispersion curve suggests that for the mixed crystals the centre of inversion is conserved locally. These combined results suggest the presence of domains with ordered F–Pb–Br–Br–Pb–F and F–Pb–I–I–Pb–F layers in the mixed crystals. Calculations on PbFBr0.5I0.5 show that this suggested structure is more stable than the structure consisting of the F–Pb–Br–I–Pb–F arrangement.Fri, 02 Oct 2009 17:18:46 +0200Approximation to the classical Coulomb energy for atomshttps://archive-ouverte.unige.ch/unige:3329https://archive-ouverte.unige.ch/unige:3329abstract not availableMon, 21 Sep 2009 18:23:23 +0200Theoretical Study of Neutral and Cationic Complexes Involving Phenolhttps://archive-ouverte.unige.ch/unige:3281https://archive-ouverte.unige.ch/unige:3281Geometry and interaction energy in complexes of the Ph-L type (L = Ar, N2, CO, H2O, NH3, CH4, CH3OH, CH3F) involving neutral or cationic phenol were determined using the density functional theory formalism based on the minimization of the total energy bifunctional and gradient-dependent approximations for its exchange-correlation and nonadditive kinetic-energy parts. For the neutral complexes the calculated interaction energies range from 1 kcal/mol for the Ph-Ar complex to about 10 kcal/mol for Ph-NH3. The interactions are stronger if the cationic phenol is involved (up to 25 kcal/mol). It is found, except for neutral Ph-Ar, that the hydrogen-bonded structure is more stable than the -bound one. Calculated interaction energies (De) correlate well with the experimental dissociation energies (D0).Mon, 21 Sep 2009 18:22:42 +0200One-Electron Equations for Embedded Electron Density and Their Applications to Study Electronic Structure of Atoms and Molecules in Condensed Phasehttps://archive-ouverte.unige.ch/unige:3269https://archive-ouverte.unige.ch/unige:3269Recent applications of one-electron equations for embedded electron density introduced originally for multi-level modeling of solvated molecules (T.A. Wesolowski, A. Warshel, J. Phys. Chem. 1993, 97, 8050) are reviewed. The considered applications concern properties directly related to the electronic structure of molecules (or an atom) in condensed phase such as: i) localized electronic excitations in a chromophore involved in a hydrogen-bonded intermolecular complex; ii) UV/Vis spectra of acetone in water; and iii) energy levels of f-orbitals for lanthanide cations in a crystalline environment. For each case studied, the embedding potential is represented graphically and its qualitative features are discussed.Mon, 21 Sep 2009 18:22:28 +0200Pi-Stacking Behavior of Selected Nitrogen-Containing PAHshttps://archive-ouverte.unige.ch/unige:3253https://archive-ouverte.unige.ch/unige:3253The packing preferences of dimers formed by nitrogen-containing planar polycyclic aromatic hydrocarbons ((C30H15N)2 and (C36H15N)2) were studied by means of theoretical calculations. Potential energy curves corresponding to various relative motions of the monomers (vertical displacement, rotating, slipping, and combinations of them) were derived. It was found that the monomers in such π-stacked dimers are rather strongly held together (the interaction energy is about −9 kcal/mol) in an off-centered arrangement. It emerges as a general picture that the aligned structures are less stable than the ones where the nitrogen atoms, as the centers of the considered monomers, are not on top of each other but offset by 1.8−2.7 Å. Displacing the centers further results in a rapid reduction of the interaction energy. Within these relatively large relative motions (up to about 3 Å) of the monomers, however, no significant loss of stability of the dimers is noted. In the case of C30H15N, changing the orientation of the enantiotopic faces in the dimer formation leads to two nonequivalent minimum energy structures of similar energies but notably different geometries. The most stable structure of both dimers studied resembles that of two adjacent layers of graphite. We conclude, therefore, that the studied molecules could be considered as good building block candidates for the fabrication of columnar organic conductors.Mon, 21 Sep 2009 18:22:18 +0200Gradient-free and gradient-dependent approximations in the total energy bifunctional for weakly overlapping electron densitieshttps://archive-ouverte.unige.ch/unige:3246https://archive-ouverte.unige.ch/unige:3246We analyze the performance of gradient-free local density approximation (LDA) and gradient-dependent generalized gradient approximation (GGA) functionals in a density functional theory variational calculations based on the total energy bifunctional (E[1,2]). These approximations are applied to the exchange-correlation energy and to the nonadditive component of the kinetic energy of the complex. Benchmark ab initio interaction energies taken from the literature for 25 intermolecular complexes for which the interaction energies fall into the 0.1–3.0 kcal/mol range are used as reference. At the GGA level, the interaction energies derived from E[1,2] are more accurate than the Kohn–Sham ones. LDA leads to very good interaction energies for such complexes where the 1,2 overlap is very small (Ne-Ne, Ar-Ar, for instance) but it is not satisfactory for such cases where the overlap is larger. Introduction of gradient-dependent terms into the approximate part of E[1,2] improves significantly the overall accuracy of the interaction energies. Gradient-dependent functionals applied in E[1,2] lead to the average error and the average absolute error of the interaction energies amounting to 0.08 kcal/mol and 0.29 kcal/mol, respectively.Mon, 21 Sep 2009 18:22:11 +0200Link between the Kinetic- and Exchange-Energy Functionals in the Generalized Gradient Approximationhttps://archive-ouverte.unige.ch/unige:3232https://archive-ouverte.unige.ch/unige:3232An approximate kinetic-energy functional of the generalized gradient approximation form was derived following the conjointness conjecture of Lee, Lee, and Parr. The functional shares the analytical form of its gradient dependency with the exchange-energy functionals of Becke and Perdew, Burke, and Ernzerhof. The two free parameters of this functional were determined using the exact values of the kinetic energy of He and Xe atoms. A set of 12 closed-shell atoms was used to test the accuracy of the proposed functional and more than 30 others taken from the literature. It is shown that the conjointness conjecture leads to a very good class of kinetic-energy functionals. Moreover, the functional developed in this work is shown to be one of the most accurate despite its simple analytical form.Mon, 21 Sep 2009 18:22:02 +0200Introduction of the explicit long-range nonlocality as an alternative to the gradient expansion approximation for the kinetic-energy functionalhttps://archive-ouverte.unige.ch/unige:3233https://archive-ouverte.unige.ch/unige:3233The approximate nonempirical kinetic-energy functional proposed by Tal and Bader is analyzed for polyatomic systems. The performance of this functional and the functionals derived from the gradient expansion approximation truncated to zeroth, second, and fourth order is investigated for a testing set of 68 neutral and charged molecules. It is shown that the Tal–Bader functional, despite the simplicity of the idea behind its construction, leads to significantly better total kinetic energies than the gradient expansion approximation functionals. The local behavior of the kinetic-energy density derived from the Tal–Bader functional is also discussed.Mon, 21 Sep 2009 18:22:02 +0200Physisorption of Molecular Hydrogen on Polycyclic Aromatic Hydrocarbons: A Theoretical Studyhttps://archive-ouverte.unige.ch/unige:3231https://archive-ouverte.unige.ch/unige:3231The repartition of molecular hydrogen in space, and its depletion on solid particles in particular, is an important question of modern astrophysics. In this paper, we report a theoretical study of the physisorption of molecular hydrogen, H2, on a major component of the interstellar dust known as polycyclic aromatic hydrocarbons (PAHs). Two different density functional theory approaches were used: (i) the conventional Kohn−Sham theory and (ii) the subsystem-based approach (Kohn−Sham equations with constrained electron density, KSCED) developed in our group. The approximate exchange-correlation energy functional applied in all calculations and the nonadditive kinetic-energy functional needed in KSCED have a generalized gradient approximation form and were chosen on the basis of our previous studies. The results of both approaches show similar trends: weak dependence of the calculated interaction energies on the size of the PAH and negligible effect of the complexation of two PAH molecules on the adsorption of molecular hydrogen. The KSCED interaction energy calculated for the largest considered PAH (ovalene), amounting to 1.27 kcal/mol, is in excellent agreement with experimental estimates ranging from 1.1 to 1.2 kcal/mol, whereas the one derived from supermolecular Kohn−Sham calculations is underestimated by more than 50%. This result is in line with our previous studies, which showed that the generalized gradient approximation applied within the KSCED framework leads to interaction energies of weakly bound complexes that are superior to the corresponding results of supermolecular Kohn−Sham calculations.Mon, 21 Sep 2009 18:22:01 +0200Theoretical Study of the Benzene Dimer by the Density-Functional-Theory Formalism Based on Electron-Density Partitioninghttps://archive-ouverte.unige.ch/unige:3218https://archive-ouverte.unige.ch/unige:3218The density-functional approach based on the partition into subsystems was applied to study the benzene dimer. For several structures, the calculated interaction energy and intermolecular distance were compared with the previous theoretical results. A good agreement with high level ab initio correlated methods was found. For instance, the interaction energies obtained in this work and the CCSD(T) method agree within 0.1 - 0.6 kcal/mol depending on the structure of the dimer. The structure with the largest interaction energy is T-shaped, in agreement with CCSD(T) results. The T-shaped structure of benzene dimer was suggested by several experimental measurements. The calculated interaction energy of 2.09 kcal/mol agrees also well with experimental estimates based on the dissociation energy which ranges from 1.6±0.2 to 2.4±0.4 kcal/mol and the estimated zero-point vibration energy of 0.3 - 0.5 kcal/mol.Mon, 21 Sep 2009 18:21:51 +0200