Topology of Charge Density from Pseudopotential Density Functional Theory Calculations

The absence of core electrons in pseudopotential electronic structure calculations poses some important problems on determining the topology of density. The key feature of valence-only densities is the lack of critical points (CPs) at the nuclear positions affected by core removal, which are sometimes substituted by local minimum CPs, the substitution of a maximum by a minimum must be necessarily accompanied by the creation of other compensating CPs, including at least either one maximum or one ring CP. As density is relatively unaffected at distance points far enough the removed cores, these new CPs are expected to lie in the proximity of the latter, and the topology of density to closely resemble that of the AE density in the chemically relevant valence regions. This difficulty is well-known in literature, and several works have been devoted to elucidate how to bypass it (Cioslowski and Piskorz, 1996). The correct topologies may be obtained from core-reconstructed pseudo-AE densities. This paper will show how the correct topology can be obtained from pseudopotential calculations. In order to analyze the problems that arise from the core electrons, results obtained for Alanine (CH3CH (NH2) COOH), Aminophenol (C6H4 (OH) NH2), Ethene (C2H4), and Propanone ((CH3)2CO) using all-electron, pseudo-valence wavefunctions are reported. Keywords: Pseudopotential, core electrons, all-electron (AE) density, QTAIM, charge density topology

Understanding the Bond Formation in Hetero Diels-Alder Reactions. An ELF Analysis of the Reaction of Nitroethylene with Dimethylvinylamine

[EN] The bonding evolution in hetero-Diels-Alder (HDA) reactions has been studied by an ELF analysis of the electron reorganization along the HDA reaction between nitroethylene 6 and dimethylvinylamine (DMVA) 9 at the B3LYP/6-31G* level. This cycloaddition takes place along a two-stages one-step mechanism. In the first stage of the reaction, the C1-C6 bond is formed by coupling of two pseudoradical centers positioned at the most electrophilic carbon of nitroethylene 6 and the most nucleophilic center of DMVA 9. In the second stage, the formation of the second O4-C7 bond takes place between a pseudoradical center positioned at the C7 carbon of DMVA and some electron-density provided by the lone pairs of the O4 oxygen. This behavior is in complete agreement with the analyses of the local electrophilicity and nucleophilicity indices, and the spin density of the radical anion of nitroethylene 6 and of the radical cation of DMVA 9. Finally, a relationship between the polar character of the reaction and the egioselectivity is established.We are grateful to the Spanish Government (project CTQ2009-11027/BQU), and the Fondecyt project No. 1100278. Profesor Domingo also thanks Fondecyt by support through the Cooperación InternacionalDomingo Asensi, LR.; Pérez, P.; Aurell Piquer, MJ.; Sáez Cases, JA. (2012). Understanding the Bond Formation in Hetero Diels-Alder Reactions. An ELF Analysis of the Reaction of Nitroethylene with Dimethylvinylamine. Current Organic Chemistry. 16:2343-2351. doi:10.2174/138527212803520263S234323511

Analysis of Local and Global Aromaticity in Si3C5 and Si4C8 Clusters. Aromatic Species Containing Planar Tetracoordinate Carbon

The minimum energy structures of the Si3C5 and Si4C8 clusters are planar and contain planar tetracoordinate carbons (ptCs). These species have been classified, qualitatively, as global (π) and local (σ) aromatics according to the adaptive natural density partitioning (AdNDP) method, which is an orbital localization method. This work evaluates these species’ aromaticity, focusing on confirming and quantifying their global and local aromatic character. For this purpose, we use an orbital localization method based on the partitioning of the molecular space according to the topology of the electronic localization function (LOC-ELF). In addition, the magnetically induced current density is analyzed. The LOC-ELF-based analysis coincides with the AdNDP study (double aromaticity, global, and local). Moreover, the current density analysis detects global and local ring currents. The strength of the global and local current circuit is significant, involving 4n + 2 π- and σ-electrons, respectively. The latter implicates the Si-ptC-Si fragment, which would be related to the 3c-2e σ-bond detected by the orbital localization methods in this fragment.Fil: Torres Vega, Juan J.. Universidad Nacional Mayor de San Marcos; PerúFil: Alcoba, Diego Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; ArgentinaFil: Oña, Ofelia Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; ArgentinaFil: Vasquez Espinal, A.. Universidad Andrés Bello; ChileFil: Baez Grez, R.. Universidad Andrés Bello; ChileFil: Lain, Luis. Universidad del País Vasco; EspañaFil: Torre, Alicia. Universidad del País Vasco; EspañaFil: García, Victor Raúl. Universidad Nacional Mayor de San Marcos; Perú. Universidad Andrés Bello; ChileFil: Tiznado, William. Universidad Andrés Bello; Chil

The Participation of 3,3,3-Trichloro-1-nitroprop-1-ene in the [3+2] Cycloaddition Reaction with Selected Nitrile N-Oxides in the Light of the Experimental and MEDT Quantum Chemical Study

The regioselective zw-type [3 + 2] cycloaddition (32CA) reactions of a series of aryl-substituted nitrile N-oxides (NOs) with trichloronitropropene (TNP) have been both experimentally and theoretically studied within the Molecular Electron Density Theory (MEDT). Zwitterionic NOs behave as moderate nucleophiles while TNP acts as a very strong electrophile in these polar 32CA reactions of forward electron density flux, which present moderate activation Gibbs free energies of 22.8-25.6 kcal·mol−1 and an exergonic character of 28.4 kcal·mol−1 that makes them irreversible and kinetically controlled. The most favorable reaction is that involving the most nucleophilic MeO-substituted NO. Despite Parr functions correctly predicting the experimental regioselectivity with the most favorable O-CCCl3 interaction, these reactions follow a two-stage one-step mechanism in which formation of the O-C(CCl3) bond takes place once the C-C(NO2) bond is already formed. The present MEDT concludes that the reactivity differences in the series of NOs come from their different nucleophilic activation and polar character of the reactions, rather than any mechanistic feature

Etudes de la croissance anisotrope de ZnO synthétisés par une méthode organométallique et étude cinétique de la gélification concomitante

Aujourd'hui, les nanosciences sont définies comme l'étude des structures (moléculaires) et dispositifs dont au moins une des dimensions caractéristiques se situe 1 - 100 nm. Ces nanomatériaux agissant comme des ponts entre les matériaux massifs et les structures atomiques et démontrent de nombreuses modifications dans les propriétés physiques, chimiques ou biologiques en raison de la taille réduite. Les nanomatériaux composés d'oxydes métalliques sont un tel type de matériaux intéressants. Leurs caractéristiques sont très intéressantes pour le développement d'applications électroniques, optiques, de capteurs et autres. Pour certains des oxydes métalliques, un manque d'oxygène crée des vacances agissant comme donneur d'électrons et induisant des propriétés de semi-conducteurs de type n. ZnO est un exemple typique. Il est caractérisé par une large bande interdite d'environ 3.4 eV, une énergie grande exciton de 60 meV, une grande mobilité électronique et une luminescence dans le visible et le proche ultraviolet. Ces caractéristiques électroniques en font un bon candidat pour le développement de sources d'émission lumineuse et de détecteurs. Il a été ainsi montré que ZnO pouvait, selon les conditions de préparation, émettre dans l'ultraviolet, le violet, le vert, le jaune et même le rouge. Ces propriétés optiques de ZnO dépendent fortement de la morphologie des matériaux. Dans le travail précédent, une méthode mature de synthèse des nanomatériaux ZnO a été développée - la méthode organométallique. Les nano ZnO bien définis avec différentes tailles, formes et morphologies (isotrope, anisotrope) peuvent être obtenus en changeant différents paramètres (milieu de réaction, types de ligands ou de surfactants, température, temps d'incubation, etc.). Cependant, lorsque des amines primaires sont utilisées comme ligands, le mécanisme de la croissance anisotrope n'est toujours pas clair. Les influences des amines secondaires et tertiaires sur nano ZnO obtenus ne sont pas encore dévoilées. Ainsi, la thèse s'attache tout d'abord à étudier les deux points ci- dessus. Premièrement, nous utilisons la méthode d'analyse de tracé 2D et d'analyse statistique pour extraire les informations sur la taille des particules à partir des images TEM. Les données traitées suggèrent que le mécanisme de croissance anisotrope est le processus d'attachement orienté, et finalement entravé par un processus de gélification induit par l'interaction du Zn précurseur avec les aminés. Deuxièmement, nous adoptons une amine de même longueur de chaîne mais de structure différente comme tensioactif (amine primaire, secondaire et tertiaire) pour synthétiser les NCs de ZnO. Les analyses RMN et DFT ont démontré que la différence de morphologie entre les NCs de ZnO viens d'une forte différence dans leur dynamique à la surface des NCs en croissance. L'interaction des liaisons H multiples à la surface du ZnO pour les amines primaires, conduit à une mobilité réduite de ces amines par rapport aux amines secondaires, qui restent mobiles à la surface des NCs dans toutes les dimensions de l'espace. Cette thèse s'intèresse aussi à la gélification qui a été trouvée pendant la synthèse du ZnO. Il a été démontré qu'elle était associée à la formation d'oligomères. Cependant, pour comprendre sa force motrice et étudier la révolution des propriétés rhéologiques avec le temps, d'autres amines primaires avec une longueur de chaîne différente sont utilisées. Les résultats de RMN montrent que la force intermoléculaire (force de Van der Waals, réticulation) contribue à la vitesse de gélification et explique les différents temps de début de gélification. Plus la chaîne est longue, plus la gélification est rapide. La première est déterminée par la force de VdW, et la seconde est déterminée par la réticulation entre les oligomères formés. Les résultats de la mesure rhéologique ont montré que le gel était composé d'une phase organique tridimensionnelle.Nowadays, nanoscience is defined as the studies of structures (molecules) and devices, in which at least one characteristic size is between 1 nm and 100 nm. These nanomaterials act as a bridge between bulk materials and atomic structures, and show many changes in the properties of physical, chemical or biological properties due to the reduction of the size of these structures. Nano materials composed of metal oxides are such kind of interesting materials. Their characteristics are very interesting for the development of electronic, optical, sensor and other applications. For some metal oxides, oxygen deficit will produce vacancies, act as electron donors, and naturally induce the performance of n-type semiconductors. ZnO is a typical example. It has characters of wide band gap of about 3.4 ev, high electron hole interaction energy (60 meV), high electron mobility, visible and near ultraviolet luminescence. These electronic characteristics make it a good candidate for the development of light source and detector. Recent studies have shown ZnO can emit in ultraviolet, violet, green, yellow and even red according to the preparation conditions. These optical properties of ZnO are closely related to the morphology of the material. In the previous work, we first developed a mature synthesis method of ZnO nano materials with organometallic method. By changing different parameters (reaction medium, type of ligand or surfactant, temperature, incubation time, etc.), clear ZnO nano objects with different sizes, shapes and morphologies (isotropic and anisotropic) can be obtained. However, when primary amine is used as ligand, which is the factor controlling this anisotropic growth, the mechanism of anisotropic growth is not clear. The effects of secondary and tertiary amines on nano ZnO are not clear either. Therefore, this paper first studies the above two points. First, we use 2D-plot analysis and statistical analysis to extract particle size information from TEM images. The processed data showed the anisotropic growth mechanism is realized firstly through the orientated attachment process, then finally hindered by the gelation process induced by the interaction between Zn precursor and amino ligand. Second, ZnO NCs was synthesized by using amines with the same aliphatic chain length but different structures as surfactants (primary, secondary and tertiary amines). The interaction between these surfactants and ZnO NCs metal precursors in the whole synthesis process was revealed by the complementary analysis of NMR and DFT. The results show the morphology of ZnO NCs varies with the amine structure, which is due to the great difference of their kinetics on the surface of growing NCs. The interaction of multiple H bonds of primary amines on the surface of ZnO leads to the decrease of the mobility of these amines relative to secondary amines, and the secondary amines remain on the surface of NCs in all spatial dimensions. This thesis work also contains topic of gelation which is discovered during the synthesis of ZnO. It was found the gel formation was related to the formation of oligomers. However, in order to understand the driving force of gelation and study the evolution of gel rheological properties over time, we used primary amines with different fatty chain lengths to study their effects. The NMR results showed the intermolecular force (van der Waals force, crosslinking) had a certain effect on the gelation rate, and explained the different gel initiation time. The longer the chain, the faster the gelation. The results of the rheological measurement showed the gel was composed of three- dimensional organic phase

Classical And Quantum Mechanical Simulations Of Condensed Systems And Biomolecules

This work describes the fundamental study of two enzymes of Fe(II)/-KG super family enzymes (TET2 and AlkB) by applying MD and QM/MM approaches, as well as the development of multipolar-polarizable force field (AMOEBA/GEM-DM) for condensed systems (ionic liquids and water). TET2 catalytic activity has been studied extensively to identify the potential source of its substrate preference in three iterative oxidation steps. Our MD results along with some experimental data show that the wild type TET2 active site is shaped to enable higher order oxidation. We showed that the scaffold stablished by Y1902 and T1372 is required for iterative oxidation. The mutation of these residues perturbs the alignment of the substrate in the active site, resulting in “5hmC-stalling” phenotype in some of the mutants. We provided more details on 5hmC to 5fC oxidation mechanism for wild type and one of the “5hmC-stallling” mutants (E mutant). We showed that 5hmC oxidizes to 5fC in the wild type via three steps. The first step is the hydrogen atom abstraction from hydroxyl group of 5hmC, while the second hydrogen is transferred from methylene group of 5hmC through the third transition state as a proton. Our results suggest that the oxidation in E mutant is kinetically unfavorable due to its high barrier energy. Many analyses have been performed to qualitatively describe our results and we believed our results can be used as a guide for other researchers. In addition, two MD approaches (explicit ligand sampling and WHAM) are used to study the oxygen molecule diffusion into the active site of AlkB. Our results showed that there are two possible channels for oxygen diffusion, however, diffusion through one of them is thermodynamically favorable. We also applied multipolar-polarizable force field to describe the oxygen diffusion along the preferred tunnel. We showed that the polarizable force field can describe the behavior of the highly polarizable systems accurately. We also developed a new multipolar-polarizable force field (AMOEBA/GEM-DM) to calculate the properties of imidazolium- and pyrrolidinium- based ionic liquids and water in a range of temperature. Our results agree well with the experimental data. The good agreement between our results and experimental data is because our new parameters provide an accurate description of non-bonded interactions. We fit all the non-bonded parameters against QM. We use the multipoles extracted from fitted electron densities (GEM) and we consider both inter- and intra-molecular polarization. We believe this method can accurately calculate the properties of condensed systems and can be helpful for designing new systems such as electrolytes

Computational Catalysis of Homogenous and Heterogeneous Systems: New Insights into the Activation of Small Molecules

Esta Tesis Doctoral se ubica en el contexto del estudio teórico y computacional de catalizadores, tanto homogéneos como heterogéneos, para la fijación de moléculas pequeñas, en concreto N2, O2, CO, NH3, HCOOH e hidrosilanos, empleando DFT. Estos procesos presentan un gran interés en investigación química, ya que un conocimiento en profundidad de los mismos facilitaría el diseño racional de nuevos catalizadores más activos y respetuosos con el medio ambiente. A continuación se presenta un resumen de los procesos estudiados.En el campo de la catálisis homogénea, se estudiaron cuatro procesos químicos diferentes, catalizados por complejos organometálicos de Rh e Ir:i) Fijación de amoniaco mediante complejos de Ir con ligandos de tipo pincer. En particular, se estudiaron los factores cinéticos y termodinámicos que afectan a laactividad del catalizador. Para ello, se emplearon diferentes métodos para el estudio del enlace químico, como IQA y la ELF.ii) La sililación de enlaces C–H aromáticos mediante un complejo bien definido de Ir(III)– NHC. Se propuso un mecanismo de reacción completo mediante cálculoscomputacionales. Asimismo, se realizaron una serie de experimentos que apoyan dicho mecanismo. Los resultados obtenidos revelaron el papel clave de los grupos directorespresentes en el sustrato en el control de la selectividad del proceso.iii) El empleo de hidrógeno molecular como vector energético. En particular, se estudió el proceso de deshidrogenación de ácido fórmico para generar H2 catalizado por uncompuesto de Rh–NHO muy activo. Los estudios computacionales permitieron proponer un mecanismo de reacción plausible, que está de acuerdo con las barreras energéticas determinadas experimentalmente.iv) La alcoxicarbonilación de alcoholes y aminas con CO para preparar carbamatos. El proceso está catalizado por un complejo de Rh y requiere le acción de un oxidante(KHSO5). El estudio teórico realizado permitió proponer un mecanismo de reacción y determinar el papel clave del oxidante.Con respecto a la catálisis heterogénea, se abordó la propuesta de nuevos descriptores de la actividad catalítica basados en las propiedades magnéticas del catalizador y los reactivos. Los diferentes procesos estudiados se resumen a continuación:v) Las reacciones de reducción de oxígeno (ORR) y de evolución de oxígeno (OER) catalizadas por materiales basados en perovskitas. En concreto, es analizaron laspropiedades magnéticas de diferentes catalizadores derivados de LaMnO3. Los resultados mostraron la importancia de tener en cuenta la entropía electrónica y la fasemagnética del catalizador. Basándonos en estos resultados, se propusieron una serie dereglas para el diseño de nuevos catalizadores heterogéneos derivados de óxidosmetálicos magnéticos para ORR y OER. Finalmente, estas reglas se emplearon en eldiseño de un nuevo catalizador para OER basado en la perovskita LaFeO3.vi) Los principios previamente presentados se ampliaron al estudio de procesos de fijación de N2 catalizados por nitruros de Mo. Los resultados muestran la validez de la aplicación del momento magnético del molibdeno como descriptor de la actividad catalítica.<br /