José A. Dobado

Insight into the informational-structure behavior of the Diels-Alder reaction of cyclopentadiene and maleic anhydride

The course of the Diels-Alder reactions of cyclopentadiene and maleic anhydride were studied. Two reaction paths were modelled: endo- and exo-selective paths. All structures within the transient region were characterized and analyzed by means of geometrical descriptors, physicochemical parameters and information-theoretical measures in order to observe the linkage between chemical behavior and the carriage of information. We have shown that the information-theoretical characterization of the chemical course of the reaction is in complete agreement with its phenomenological behavior in passing from reactants to products. In addition, we were able to detect the main differences between the two reaction mechanisms. This type of informational analysis serves to provide tools to help understand the chemical reactivity of the two simplest Diels-Alder reactions, which permits the establishment of a connection between the quantum changes that molecular systems exert along reaction coordinates and standard physicochemical phenomenology. In the present study, we have shown that every reaction stage has a family of subsequent structures that are characterized not solely by their phenomenological behavior but also by informational properties of their electronic density distribution (localizability, order, uniformity). Moreover, we were able to describe the main differences between endo-adduct and exo-adduct pathways. With the advent of new experimental techniques, it is in principle possible to observe the structural changes in the transient regions of chemical reactions. Indeed, through this work we have provided the theoretical concepts needed to unveil the concurrent processes associated with chemical reactions.

Lignin as Renewable Raw Material

Lignin is by far the most abundant substance based on aromatic moieties in nature, and the largest contributor to soil organic matter. Millions of tonnes of several lignin preparations are produced by the paper industry every year, and a minimal amount of lignin is isolated by direct extraction of lignin from plants. Lignin is used either directly or chemically modified, as a binder, dispersant agent for pesticides, emulsifier, heavy metal sequestrant, or component for composites and copolymers. For value-added applications of lignin to be improved, medium- and long-term conversion technologies must be developed, especially for the preparation of low-molecular-weight compounds as an alternative to the petrochemical industry.

CoNTub: an algorithm for connecting two arbitrary carbon nanotubes.

We have developed the first computer program for determining the coordinates of heterojunctions between two arbitrary carbon nanotubes. This software implements the topological algebra based on the concept of strip, a continuous subset of carbon rings containing all the topological defects (nonhexagonal carbon rings). The user easily generates any heterojunction by merely introducing the indices (i,j) and length of the two nanotubes to be connected. The resulting structure is immediately visualized and can be exported in the protein-data-bank (PDB) format. Two classes of heterojunctions are distinguished depending on whether a cone between the connected nanotubes is required. This method is applicable to all kinds of two nanotube heterojunctions, including Dunlaps knees and others related. In addition, this program also generates single- and multiwalled carbon nanotubes (SWNT and MWNT). This application has been implemented as a Java applet, and it is freely available at the following web address: http://www.ugr.es/local/gmdm/java/contub/contub.html

Weakening C−O Bonds: Ti(III), a New Reagent for Alcohol Deoxygenation and Carbonyl Coupling Olefination

Investigations detailed herein, including density functional theory (DFT) calculations, demonstrate that the formation of either alkoxy- or hydroxy-Ti(III) complexes considerably decreases the energy of activation for C-O bond homolysis. As a consequence of this observation, we described two new synthetic applications of Nugents reagent in organic chemistry. The first of these applications is an one-step methodology for deoxygenation-reduction of alcohols, including benzylic and allylic alcohols and 1,2-dihydroxy compounds. Additionally, we have also proved that Ti(III) is capable of mediating carbonyl coupling-olefination. In this sense, and despite the fact that for over 35 years it has been widely accepted that either Ti(II) or Ti(0) was the active species in the reductive process of the McMurry reaction, the mechanistic evidence presented proves the involvement of Ti(III) pinacolates in the deoxygenation step of the herein described Nugents reagent-mediated McMurry olefination. This observation sheds some light on probably one of the mechanistically more complex transformations in organic chemistry. Finally, we have also proved that both of these processes can be performed catalytically in Cp(2)TiCl(2) by using trimethylsilyl chloride (TMSCl) as the final oxygen trap.

Basis set superposition error-counterpoise corrected potential energy surfaces. Application to hydrogen peroxide⋯X (X=F−, Cl−,Br−, Li+, Na+) complexes

Mo/ller–Plesset (MP2) and Becke-3-Lee-Yang-Parr (B3LYP) calculations have been used to compare the geometrical parameters, hydrogen-bonding properties, vibrational frequencies and relative energies for several X− and X+ hydrogen peroxide complexes. The geometries and interaction energies were corrected for the basis set superposition error (BSSE) in all the complexes (1–5), using the full counterpoise method, yielding small BSSE values for the 6-311+G(3df,2p) basis set used. The interaction energies calculated ranged from medium to strong hydrogen-bonding systems (1–3) and strong electrostatic interactions (4 and 5). The molecular interactions have been characterized using the atoms in molecules theory (AIM), and by the analysis of the vibrational frequencies. The minima on the BSSE-counterpoise corrected potential-energy surface (PES) have been determined as described by S. Simon, M. Duran, and J. J. Dannenberg, and the results were compared with the uncorrected PES.

Carbon-carbon weak interactions

A theoretical study of the complexes formed by systems with electron-deficient and electron-excessive carbon atoms was carried out using DFT and ab initio methods up to the CCSD(T)/aug-cc-pVTZ computational level. Stable complexes with interaction energies between -6.0 and -22.8 kJ mol(-1) were obtained that correspond to weak C...C interactions. The atoms in molecules analysis of the complexes confirmed the presence of these interactions. Natural energy decomposition analysis and electron localization function analysis were performed to gain further insight into the nature of the interaction. Polarization is the most important stabilizing term in these complexes.

Lignin and lignans as renewable raw materials : chemistry, technology and applications

As naturally occurring and abundant sources of non-fossil carbon, lignin and lignans offer exciting possibilities as a source of commercially valuable products, moving away from petrochemical-based feedstocks in favour of renewable raw materials. Lignin can be used directly in fields such as agriculture, livestock, soil rehabilitation, bioremediation and the polymer industry, or it can be chemically modified for the fabrication of specialty and high-value chemicals such as resins, adhesives, fuels and greases.

Reversible attachment of platinum alloy nanoparticles to nonfunctionalized carbon nanotubes.

The formation of monodisperse, tunable sized, alloyed nanoparticles of Ni, Co, or Fe with Pt and pure Pt nanoparticles attached to carbon nanotubes has been investigated. Following homogeneous nucleation, nanoparticles attach directly to nonfunctionalized single-walled and multi-walled carbon nanotubes during nanoparticle synthesis as a function of ligand nature and the nanoparticle work function. These ligands not only provide a way to tune the chemical composition, size, and shape of the nanoparticles but also control a strong reversible interaction with carbon nanotubes and permit controlling the nanoparticle coverage. Raman spectroscopy reveals that the sp(2) hybridization of the carbon lattice is not modified by the attachment. In order to better understand the interaction between the directly attached nanoparticles and the nonfunctionalized carbon nanotubes, we employed first-principles calculations on model systems of small Pt clusters and both zigzag and armchair single-walled carbon nanotubes. The detailed comprehension of such systems is of major importance since they find applications in catalysis and energy storage.

Clar-Kekule structuring in armchair carbon nanotubes.

Geometrical patterns on armchair nanotubes and their dependence on length (up to 10 nm) have been studied using first-principles methods. The results indicate that finite nanotubes do not show a uniform bond structure. The previous structural classification of armchair nanotubes in Clar, Kekule, and incomplete-Clar types becomes unified with lengthening, not in a bond-uniform structure, as PBC models report, but into an alternated sequence of Clar and Kekule domains in all cases, with possible mechanical and electronic consequences.

CoNTub v2.0 - Algorithms for Constructing C3-Symmetric Models of Three-Nanotube Junctions

Here, a method is described for easily building three-carbon nanotube junctions. It allows the geometry to be found and bond connectivity of C(3) symmetric nanotube junctions to be established. Such junctions may present a variable degree of pyramidalization and are composed of three identical carbon nanotubes with arbitrary chirality. From the indices of the target nanotube, applying the formulas of strip algebra, the possible positions of the six defects (heptagonal rings) needed can be found. Given the multiple possibilities that arise for a specific pair of indices, the relation between the macroscopic geometry (interbranch angles, junction size, and pyramidalization) and each specific solution is found. To automate the construction of these structures, we implemented this algorithm with CoNTub software, version 2.0, which is available at ( http://www.ugr.es/local/gmdm/contub2 ). In addition, a classification of three-nanotube junctions, 3TJ, in seven types based on the location of defects has been proposed, i.e. 3TJ(0:0:6), 3TJ(0:1:5), 3TJ(0:2:4), 3TJ(0:3:3), 3TJ(1:1:4), 3TJ(1:2:3), and 3TJ(2:2:2) types.