Annick Goursot

Interaction between n-Alkane Chains: Applicability of the Empirically Corrected Density Functional Theory for Van der Waals Complexes.

The geometries, interaction energies, and vibrational frequencies of a series of n-alkane dimers up to dodecane have been calculated using density functional theory (DFT) augmented with an empirical dispersion energy term (DFT-D). The results obtained from this method for ethane to hexane dimers are compared with those provided by the MP2 level of theory and the combined Gaussian-3 approach with CCSD(T) being the highest correlation method [G3(CCSD(T))]. Two types of dimer isomers have been studied. The most stable isomers have the two carbon chains in parallel planes, whereas the second ones have the two carbon chains in the same plane. Butane is found to be the shortest carbon chain to form dimers with similar properties, that is, a constant average distance between the monomer carbon skeletons, a similar increment per CH2 unit for the dimer interaction energy, and comparable dimer symmetric stretching frequencies. The values and trends obtained from the DFT-D approach agree very well with those obtained from MP2 for the geometries and vibrational frequencies and from the G3(CCSD(T)) method for the energies, validating the use of DFT-D for the study of large hydrocarbon complexes.

Toward a molecular description of heterogeneous catalysis: transition metal ions in zeolites

Abstract Quantum mechanical modeling of the properties of transition metal ions (TMI) in zeolites gives a picture of the material which corresponds to that of a large organometallic system in which the zeolite framework behaves as a multidentate ligand. The electron density is distributed among the whole system with highly delocalized frontier orbitals. Analyses of the electron density changes in Cu ZSM-5 and Cu FAU models upon adsorption and desorption of donor or acceptor ligands point to a supermolecular behavior of the whole system where the zeolite framework acts as a reservoir of electronic charge. This molecular description of TMI-zeolites provides a rational explanation of various aspects of their catalytic behavior in the decomposition and selective catalytic reduction (SCR) of nitrogen oxides, such as the nature of the rate determining step and the positive influence of protons in the SCR of NO by NH 3 .

Investigation of the interface in silica-encapsulated liposomes by combining solid state NMR and first principles calculations.

In the context of nanomedicine, liposils (liposomes and silica) have a strong potential for drug storage and release schemes: such materials combine the intrinsic properties of liposome (encapsulation) and silica (increased rigidity, protective coating, pH degradability). In this work, an original approach combining solid state NMR, molecular dynamics, first principles geometry optimization, and NMR parameters calculation allows the building of a precise representation of the organic/inorganic interface in liposils. {(1)H-(29)Si}(1)H and {(1)H-(31)P}(1)H Double Cross-Polarization (CP) MAS NMR experiments were implemented in order to explore the proton chemical environments around the silica and the phospholipids, respectively. Using VASP (Vienna Ab Initio Simulation Package), DFT calculations including molecular dynamics, and geometry optimization lead to the determination of energetically favorable configurations of a DPPC (dipalmitoylphosphatidylcholine) headgroup adsorbed onto a hydroxylated silica surface that corresponds to a realistic model of an amorphous silica slab. These data combined with first principles NMR parameters calculations by GIPAW (Gauge Included Projected Augmented Wave) show that the phosphate moieties are not directly interacting with silanols. The stabilization of the interface is achieved through the presence of water molecules located in-between the head groups of the phospholipids and the silica surface forming an interfacial H-bonded water layer. A detailed study of the (31)P chemical shift anisotropy (CSA) parameters allows us to interpret the local dynamics of DPPC in liposils. Finally, the VASP/solid state NMR/GIPAW combined approach can be extended to a large variety of organic-inorganic hybrid interfaces.

Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: Application to polycyclic aromatic hydrocarbon clusters

The density functional based tight binding (DFTB) is a semiempirical method derived from the density functional theory (DFT). It inherits therefore its problems in treating van der Waals clusters. A major error comes from dispersion forces, which are poorly described by commonly used DFT functionals, but which can be accounted for by an a posteriori treatment DFT-D. This correction is used for DFTB. The self-consistent charge (SCC) DFTB is built on Mulliken charges which are known to give a poor representation of Coulombic intermolecular potential. We propose to calculate this potential using the class IV/charge model 3 definition of atomic charges. The self-consistent calculation of these charges is introduced in the SCC procedure and corresponding nuclear forces are derived. Benzene dimer is then studied as a benchmark system with this corrected DFTB (c-DFTB-D) method, but also, for comparison, with the DFT-D. Both methods give similar results and are in agreement with references calculations (CCSD(T) and symmetry adapted perturbation theory) calculations. As a first application, pyrene dimer is studied with the c-DFTB-D and DFT-D methods. For coronene clusters, only the c-DFTB-D approach is used, which finds the sandwich configurations to be more stable than the T-shaped ones.

Properties of CO adsorbed in ZSM5 zeolite: Density functional theory study using the embedding scheme based on electron density partitioning

The CO molecule is frequently used as a probe in studies of zeolites where it adsorbs on metal cations. Compared with the free CO molecule, the stretching frequency of CO adsorbed in a zeolite is blue-shifted. The magnitude of the shift depends on the cation. The theoretical studies by Ferrari et al. [J. Chem. Phys., 105, 4129 (1996)] show that the isolated cation does not provide a good model of the zeolite because the calculated shifts are significantly overestimated. In this work, the effects of the interactions between the Me+CO (Me=Li, Na, or K) complex and the zeolite framework on the properties of CO adsorbed on the cation site are investigated. The properties of the investigated complexes are studied using the embedded molecule approach applying the orbital-free effective embedding potential derived within the subsystem formulation of density functional theory. In order to identify the major microsopic effects affecting the properties of the bound probe molecule, a hierarchy of cluster models is u...

First principles molecular dynamics calculation of the structure and acidity of a bulk zeolite

Local density functional theory within the framework of the Car-Parrinello method has been used to study the structural parameters and the energetics of offretite, when a Si4+ ion is substituted by (Al3+, H+). The calculations have been performed on a periodically repeated unit cell with 54 atoms and a proton. in agreement with previous cluster calculations, we conclude that the sites with the lowest (Al, H)/Si substitution energies are also those with the largest proton affinity. In addition a correlation previously reported between acidity and Al-O-Si bond angles is confirmed.

Electronic and magnetic properties of a carbon atom chemisorbed on model clusters simulating the (100) surface of nickel

Both spin‐polarized and unpolarized linear combinations of Gaussian‐type orbitals‐model core potential‐local spin density (LCGTO‐MCP‐LSD) calculations have been performed for clusters representing the three possible high symmetry chemisorption sites for carbon on the (100) surface of nickel. We found that the most stable chemisorption site is the fourfold hollow, in agreement with the experimental evidence. For this site, the computed equilibrium NiC distances are 1.79 and 1.77 A at the spin‐polarized and unpolarized levels, very close to the most recent experimental measurements. The calculated spin‐polarized vibrational frequency perpendicular to the surface is found to be 407 cm−1 (410 cm−1 expt). The values of the binding energy are 11.5 and 11.8 eV at polarized and unpolarized levels, respectively (∼7 eV, expt); the carbon atom is strongly bound, essentially by a triple bond formed by interaction of the px, py, and pz orbitals of carbon with, primarily, the d orbitals of the four nearby surface nicke...

Density Functional Theory-Based Conformational Analysis of a Phospholipid Molecule (Dimyristoyl Phosphatidylcholine)

The conformational space of the dimyristoyl phosphatidylcholine (DMPC) molecule has been studied using density functional theory (DFT), augmented with a damped empirical dispersion energy term (DFT-D). Fourteen ground-state isomers have been found with total energies within less than 1 kcal/mol. Despite differences in combinations of their torsion angles, all these conformers share a common geometric profile, which includes a balance of attractive, repulsive, and constraint forces between and within specific groups of atoms. The definition of this profile fits with most of the structural characteristics deduced from measured NMR properties of DMPC solutions. The calculated vibrational spectrum of the molecule is in good agreement with experimental data obtained for DMPC bilayers. These results support the idea that DMPC molecules preserve their individual molecular structures in the various assemblies.

Atomic multiplet energies from density functional calculations

Abstract Atomic multiplet term energies for d n configurations have been estimated within density functional theory (DFT) exploiting symmetry to the largest possible extent. The electrostatic two-electron integrals, as well as term energies, are expressed in function of only three non-redundant single determinants (NRSDs), each of them being obtained from density functional calculations. The influence of correlation effects described with a gradient-corrected functional (GGA) is examined and discussed. Comparison with experimental data shows the reliability of this symmetry-based density functional approach.

Theoretical study of the structure and properties of Na-MOR and H-MOR zeolite models.

This work presents calculated structural parameters and energetic properties of Na- and H-mordenites (MORs) using cluster models with more than 400 atoms. These state of the art calculations were performed within the framework of density functional theory, using both the local density approximation and the generalized gradient approximation, employing all-electron basis sets. The most populated T3, T4, and T1 Al sites have been investigated using two different MOR models, each containing two isolated Al sites. A detailed analysis of the structures, three-dimensional contours of molecular electrostatic potential, binding energies of Na cations and protons, and BrOnsted O–H harmonic frequencies are presented. These properties are compared with available experimental results. The structural changes among Si∕Al substitution as well as Na∕H exchange are discussed.