Hélio A. Duarte

An Efficient a Posteriori Treatment for Dispersion Interaction in Density-Functional-Based Tight Binding.

The performance of density functional theory (DFT) (VWN-LDA, PBE-GGA, and B3LYP hybrid functionals), density-functional-based tight binding (DFTB), and ab initio methods [HF, MP2, CCSD, and CCSD(T)] for the treatment of London dispersion is investigated. Although highly correlated ab initio methods are capable of describing this phenomenon, if they are used with rather large basis sets, DFT methods are found to be inadequate for the description of H2/PAH (polycyclic aromatic hydrocarbon) interactions. As an alternative approach, an a posteriori addition of a van der Waals term to DFTB is proposed. This method provides results for H2/PAH interactions in close agreement with MP2 and higher-level ab initio methods. Bulk properties of graphite also compare well with the experimental data.

Mechanism of anion retention from EXAFS and density functional calculations: Arsenic (V) adsorbed on gibbsite

Abstract X-ray absorption fine structure spectroscopy and density functional calculations were used to determine the structural model of arsenic surface complex on gibbsite mineral. The structural environment of arsenic at the solid surface may determine its potential for remobilization and stability. Data were collected for arsenate adsorbed on gibbsite surface at pH 5.5. The X-ray absorption fine structure spectroscopy results showed that As(V) forms an inner sphere bidentate binuclear complex on the surface of Al oxyhydroxyl octaedra. Quantitative results showed an average interatomic As(V)-Al distance of 3.19 ± 0.05 A and a coordination number of 1.3 ± 1.0 atoms. Four different adsorption sites in which arsenate can interact with gibbsite have been studied using density functional calculations, i.e., bidentate binuclear complex, bidentate mononuclear complex, monodentate mononuclear complex, and monodentate binuclear complex. The density functional calculations confirm that the most stable structure predicted for As(V)-gibbsite system is the bidentate-binuclear complex.

Imogolite Nanotubes: Stability, Electronic, and Mechanical Properties

The aluminosilicate mineral imogolite is composed of single-walled nanotubes with stoichiometry of (HO)(3)Al(2)O(3)SiOH and occurs naturally in soils of volcanic origin. In the present work we study the stability and the electronic and mechanical properties of zigzag and armchair imogolite nanotubes using the density-functional tight-binding method. The (12,0) imogolite tube has the highest stability of all tubes studied here. Uniquely for nanotubes, imogolite has a minimum in the strain energy for the optimum structure. This is in agreement with experimental data, as shown by comparison with the simulated X-ray diffraction spectrum. An analysis of the electronic densities of states shows that all imogolite tubes, independent on their chirality and size, are insulators.

Density-functional based tight-binding: an approximate DFT method

The DFTB method, as well as its self-consistent charge corrected variant SCC-DFTB, has widened the range of applications of fundamentally well established theoretical tools. As an approximate density-functional method, DFTB holds nearly the same accuracy, but at much lower computational costs, allowing investigation of the electronic structure of large systems which can not be exploited with conventional ab initio methods. In the present paper the fundaments of DFTB and SCC-DFTB and inclusion of London dispersion forces are reviewed. In order to show an example of the DFTB applicability, the zwitterionic equilibrium of glycine in aqueous solution is investigated by molecular-dynamics simulation using a dispersion-corrected SCC-DFTB Hamiltonian and a periodic box containing 129 water molecules, in a purely quantum-mechanical approach.

Study of angiotensin-(1-7) vasoactive peptide and its β-cyclodextrin inclusion complexes : Complete sequence-specific NMR assignments and structural studies

We report the complete sequence-specific hydrogen NMR assignments of vasoactive peptide angiotensin-(1-7) (Ang-(1-7)). Assignments of the majority of the resonances were accomplished by COSY, TOCSY, and ROESY peak coordinates at 400MHz and 600MHz. Long-side-chain amino acid spin system identification was facilitated by long-range coherence transfer experiments (TOCSY). Problems with overlapped resonance signals were solved by analysis of heteronuclear 2D experiments (HSQC and HMBC). Nuclear Overhauser effects (NOE) results were used to probe peptide conformation. We show that the inclusion of the angiotensin-(1-7) tyrosine residue is favored in inclusion complexes with beta-cyclodextrin. QM/MM simulations at the DFTB/UFF level confirm the experimental NMR findings and provide detailed structural information on these compounds in aqueous solution.

H2 Adsorption in Metal‐Organic Frameworks: Dispersion or Electrostatic Interactions?

Materials to store molecular hydrogen for mobile applications have been intensively studied over the past years. In summary, two storage mechanisms have been proposed: chemisorption (e.g. metal hydrides, aminoboranes), and physisorption in nanoporous materials. In contrast to most hydride storage media, materials physisorbing H2 offer reversible (un)loading processes without intensive external heating or cooling. As H2 is a nonpolar molecule, the two principal contributions to the adsorption energy are weak London (dispersion) interactions (LDI) and interactions due to the electrostatic potential of the host material. LDI depend on the polarisability of the host material and on the distance between H2 and the host surface. Therefore, systems designed for H2 storage should be highly polarisable and have a large specific surface area with favourable pore sizes of ~0.6 nm. Graphitic (sp) carbon structures (graphene slit pores, carbon nanotubes, fullerenes and more advanced materials (C60 intercalated graphite, [11] honeycomb graphite etc.)) belong to this group. However, with none of them the 2010 goal of the US Department of Energy (6 wt.% of stored H2 and 45 gL 1 volumetric density) could be reached for moderate pressure and ambient temperature. Higher H2 adsorption capacities might be possible if attractive electrostatic interactions are introduced by a non-negligible charge separation in the host. One of the most promising materials with these properties are metal-organic frameworks (MOFs, see Figure 1a), a family of nanoporous materials that are built of well-defined building blocks, polar metal oxide centers (connectors) and nonpolar organic linkers containing aromatic carbons. As it is possible to tailor their chemical composition and pore size distribution, many potential applications have been proposed for MOFs, among them H2 storage. It has been shown experimentally that some MOFs show indeed excellent storage capacities for H2. [21,22] It is, however, unclear, which underlying mechanism is responsible for this property. To tune the capability of MOFs to store H2 the fundamental interactions leading to the adsorption have to be well understood. So far, it is not clear which interaction (LDI or electrostatics, for certain connectors possibly even chemisorption) is responsible for the H2 adsorption in MOFs. Experimental evidence emphasizes that the strongest H2 adsorption sites are close to the metal oxide connectors, which is interpreted such that M O (M=Zn, Cu, Mg, etc.) dipoles are most effective in polarizing the gas molecules and lead to strong interactions. There is no consensus in the interpretation of the adsorption mechanism; the quantification of the adsorption energy depends on various variables and is matter of discussion, but lowenergy adsorption sites have been identified in agreement between experiment and theory. It is important to obtain the host–guest potential theoretically, as it cannot be accessed experimentally due to the complex nature of the interaction. Also, the theoretical determination is not straightforward: So far, severe approximations had to be made in all theoretical approaches, and no final conclusion on the interaction mechanism could be drawn from their results: Either, an extended model for the MOF/H2 system was made, but the interaction energy has been calculated using density-functional theory (DFT) which is well-known to fail to describe LDI. The second approach is to reduce the MOF structure to model clusters (MOF connectors and linkers); however, the host–guest interaction is treated at higher computational level, most commonly using MP2 theory, as it is the compu[a] A. Kuc, Prof. G. Seifert Physikalische Chemie, Technische UniversitAt Dresden 01062 Dresden (Germany) [b] A. Kuc, Prof. T. Heine School of Engineering and Science, Jacobs University Bremen 28759 Bremen (Germany) Fax: (+49)421200493223 E-mail : t.heine@jacobs-university.de [c] Prof. H. A. Duarte Departamento de QuGmica–ICEx Universidade Federal de Minas Gerais 31.270-901 Belo Horizonte, MG (Brazil) Supporting information for this article is available on the WWW under http://dx.doi.org/10.1002/chem.200800878.

Improved quantum mechanical study of the potential energy surface for the bithiophene molecule

The potential energy surface (PES) for the 2,2′-bithiophene molecule was investigated using Hartree–Fock, correlated MP2, MP4(SDQ), CCSD, and density functional theory levels. Distinct basis sets ranging from double-zeta to triple-zeta quality, with polarization functions added on all atoms, were employed as well as the Dunning correlated consistent polarized valence double-zeta (cc-pVDZ) basis set. Single point configuration interaction CISD calculations were also performed using the cc-pVDZ basis set. Harmonic frequency calculations were performed for the unambiguous characterization of the stationary points located on the PES and also to calculate thermal Gibbs free energy corrections. Regarding the structural predictions we found that the B3LYP/6-311G** and MP2/cc-pVDZ fully optimized geometries exhibit the best agreement with the gas phase electron diffraction data. The calculated B3LYP/6-311G**, MP2/cc-pVDZ and experimental torsional angle for the syn-gauche structure are, respectively, 37.4° (B3LYP...

Quantum-mechanical study of the interaction of α-cyclodextrin with methyl mercury chloride

Abstract The inclusion process involving α-cyclodextrin (α-CD) and methyl mercury chloride (CH 3 HgCl) was investigated using the PM3 quantum-mechanical semi-empirical method. Fully unconstrained geometry optimizations were carried out for the free α-CD and the complexed forms with CH 3 HgCl. The inclusion orientation with the methyl mercury chloride passing perpendicular to the center of the cyclodextrin ring was found to be favored over the experimentally hinted parallel structure. It was also observed that the inclusion takes place in a more favored way when solvation water molecules are explicitly included, therefore stabilizing the complex in relation to the free species. The experimentally observed Raman shift for the Hg–Cl stretching mode after the complexation was used in conjunction with the respective PM3 calculated vibrational frequencies for the determination of the preferred structure for the inclusion complex.

Density functional study of the NO dimer using GGA and LAP functionals

The nature of the ON-NO bonding in the NO dimer still remains a challenge for currently available theoretical and experimental methods. Most of the theoretical studies reported so far predict a singlet cis ground state. However, the fully optimized geometry of the NO dimer may favor a triplet ground state, depending on the approximate method used. In this work we explore in detail the electronic structure of the fully optimized trans- and cis-NO dimer including a vibrational analysis in different electronic states, using several exchange-correlation functionals within the Kohn-Sham DFT method. The recently developed LAP exchange-correlation schemes that use the Laplacian of the density and the self-consistent kinetic energy density, improves significantly the results. The N-N bond distance is in better agreement with the experimental results, and the triplet/singlet gap is smaller, however, still predicting a triplet ground state. The nature of the electronic ground state is discussed in detail. We explor...

First-Principles Calculations and Electron Density Topological Analysis of Covellite (CuS)

Covellite (CuS) is an important mineral sulfide that can be used in many technological applications. It has a simple formula but a complex structure consisting of alternating layers of planar CuS3 triangles and CuS4 tetrahedrons with S-S bonds. Accurate first-principles calculations are performed for covellite structure (CuS), aiming to provide insights about its structural, mechanical and electronic properties and to unveil the nature of its chemical bonding. DFT and DFT+U methods have been used and showed to be sensitive to the correlation treatment (U value). Although it is not possible to extract a universal value of the U, this study indicates that U = 5 eV is an adequate value. The electronic structure analysis shows a significant metallic character due to p(S)-d(Cu) orbital interactions up to Fermi level. The projected density of states indicates that most of the contribution comes from the atomic orbitals in the [001] plane of the covellite, explaining the conductivity anisotropy observed experimentally. Topological analysis of the electron density was performed by means of quantum theory of atoms in molecules (QTAIM). Two different topological charges in Cu and S were calculated, confirming an ionic model with mix-charges. This mineral presents ionic degree of ∼ 32%. On the basis of the QTAIM analysis, the covalent character of S-S bond is confirmed, and the favored cleavage of CuS at the [001] surface might be at the Cu-S bond. The S atoms occupy most of the cell volume, and their contributions dominate the crystal compressibility: κ(S) ≈ κ(CuS).