QUANTUM MECHANICS-BASED COMPUTATIONAL CHEMISTRY HAS BECOME A POWERFUL PARTNER IN THE SCIENTIFIC RESEARCH OF NITROGEN-RICH COMPOUNDS, PAVING THE WAY FOR IMPORTANT ADVANCES IN BIOCHEMICAL, PHARMACOLOGICAL AND OTHER RELATED FIELDS

The Computational Chemistry of Nitrogen-Rich Compounds; Insight into Pioneering Research Nitrogen-rich functional groups have long been studied for their diversity; nitrogen can form single, double and triple bonds with itself, and will therefore exist in a very broad range of molecular arrangements. Poly-nitrogen compounds are highly energetic and electron rich, and many compounds display unique properties that allow participation in very specialized chemical reactions. Of import is their ubiquity in biological systems, and throughout the past century and currently, their biological relevance is deeply and widely explored in biochemistry and biomedicine, from their involvement in natural biological processes and complex biomolecules, to the harnessing of their intrinsic properties for drug development and bioimaging. Computational Chemistry constitutes a major area of scientific research, constantly developing since the mid 2Oth century, where the smallest components of atoms and molecules are studied through quantum mechanics, approximations and empirical data, providing energetic and geometric data to predict and elucidate their macro properties and behaviors. Computational analysis introduces extensive applications in investigating compounds and reactions, including but not limited to; biomedical applications, including drug design and development; gaining an understanding of chemical properties where experiments fail; and predicting the interactions and reaction pathways between compounds – the feasibility and energetics of reactants, potential products and intermediates. Computational chemistry is an extremely versatile field, in that it can provide singular insight into the intricacies of an individual molecule yet extends to the behavior and arrangements of a crystal lattice, for example. This thesis is an exploration of recent research devoted to the chemistry of azides, heterocycles, and other small nitrogen-containing molecules through quantum mechanics. Computational chemistry has emerged over the past decades as a fundamental partner in research and vital to its advancement. With selective studies, a window is provided into the computational chemistry approach to researching these compounds; covering important heterocyclic reactions including click chemistry; the broader application of those reactions in biological systems – bioorthogonal chemistry – ; the exploration and characterization of various intrinsic and fascinating properties of heterocycles; and finally, a comprehensive look at studies of complex biomolecules that feature heterocycles in their chemical makeup. The immense range of theoretical methods available to address countless aspects and characteristics of these compounds demonstrates the tremendous value in this evolving field

Chemical applications of electron localization-delocalization matrices (LDMs) with an emphasis on predicting molecular properties

ix, 123 leaves : col. ill. ; 29 cmIncludes abstract and appendices.Includes bibliographical references.A matrix is constructed where the vertices (atoms) are connected by edges (bonds) resulting in a square matrix that is symmetrical. The localization index (unshared electrons) occupies the long diagonal where the delocalization index (shared electrons between two di erent atoms divided by 2) represent the o -diagonal elements. Such a matrix is called a localization-delocalization matrix or LDM. These matrices have shown promise as a novel Quantitative Structure Activity Relationship (QSAR) method via the Frobenius Distance, a method to compare matrices of similar sizes that returns a Euclidean distance. Some notable results that will be expanded upon are that for a series of 14 para-substituted benzoic acids for pKa prediction (r2 = 0.986), and a series of 13 polycyclic benzenoid hydrocarbons (PBH) separated by inner and outer rings (r2= 0.97). A program (AIMLDM) was developed in Python 3.4.1 to construct these matrices and perform the required calculations

Searching for Neutralisers of Energetic Organic Compounds: A Theoretical Approach from the Perspective of Quantum Chemistry

Neutralising energetic molecules is a valuable approach to minimize the risks of unpredictable explosions and associated tragic events. Quantum chemical methods offer highly efficient and effective tools for studying these compounds. The main objective of this dissertation is to quantify the impact of intermolecular interactions on the sensitivity of energetic compounds. Concerning the cyclic compounds RDX (1,3,5- trinitro-1,3,5-triazinane) and HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazocane), a quantitative analysis with MEP evidenced anomalies arising from the marked depletion of negative charge distribution. The EDA-NOCV results reveal that the electrostatic and orbital contributions are the dominant factors driving the assembly of the M = {Ti, Zr, Hf}-based complexes. The chemical nature of the O· · ·M = {Ti, Zr, Hf} bonding has been investigated by using the QTAIM theory. Additionally, the topological properties of the N–NO2 trigger bonds were quantified before and after the O· · ·M interaction. These intermolecular interactions strengthens the trigger bonds, revealing an increased stability to decomposition. The IRI-based analysis was carried out to further investigate the electronic properties of group 4 transition metals in coordination environments. With regard to the aliphatic compound FOX-7 (1,1-diamino-2,2-nitroethylene), we examined three types of interactions: oxygen and nitrogen from a nitro group interacting with the metal atom, as well as nitrogen from an amino group interacting with the same metal atom. The local chemical reactivity of FOX-7 was elucidated through a quantitative study of MEP. Results derived from QTAIM showed that the C–NO2 bonds are influenced by the O· · ·M = {Ti, Zr, Hf} bonding. Furthermore, this interaction rules the complex formation when a nitro group interacts with MMCs. The interaction energies calculated by EDA-NOCV revealed that the (H2N)2C=C(NO2)- (O)NO· · · Cp2MCH+3 complexes are significantly more structurally stable (by about 21.8 kcal/mol) than the (O2N)2C=C(NH2)-H2N· · · Cp2MCH+3 complexes. This work is crucial to validate the proposal of using MMCs (metallocene methyl cations) as a neutraliser of energetic molecules

Exploration of Free Energy Surface and Thermal Effects on Relative Population and Infrared Spectrum of the Be6B11− Fluxional Cluster

The starting point to understanding cluster properties is the putative global minimum and all the nearby local energy minima; however, locating them is computationally expensive and difficult. The relative populations and spectroscopic properties that are a function of temperature can be approximately computed by employing statistical thermodynamics. Here, we investigate entropy-driven isomers distribution on Be6B11− clusters and the effect of temperature on their infrared spectroscopy and relative populations. We identify the vibration modes possessed by the cluster that significantly contribute to the zero-point energy. A couple of steps are considered for computing the temperature-dependent relative population: First, using a genetic algorithm coupled to density functional theory, we performed an extensive and systematic exploration of the potential/free energy surface of Be6B11− clusters to locate the putative global minimum and elucidate the low-energy structures. Second, the relative populations’ temperature effects are determined by considering the thermodynamic properties and Boltzmann factors. The temperature-dependent relative populations show that the entropies and temperature are essential for determining the global minimum. We compute the temperature-dependent total infrared spectra employing the Boltzmann factor weighted sums of each isomer’s infrared spectrum and find that at finite temperature, the total infrared spectrum is composed of an admixture of infrared spectra that corresponds to the lowest energy structure and its isomers located at high energies. The methodology and results describe the thermal effects in the relative population and the infrared spectra

Density Functional Theory

Density Functional Theory (DFT) is a powerful technique for calculating and comprehending the molecular and electrical structure of atoms, molecules, clusters, and solids. Its use is based not only on the capacity to calculate the molecular characteristics of the species of interest but also on the provision of interesting concepts that aid in a better understanding of the chemical reactivity of the systems under study. This book presents examples of recent advances, new perspectives, and applications of DFT for the understanding of chemical reactivity through descriptors forming the basis of Conceptual DFT as well as the application of the theory and its related computational procedures in the determination of the molecular properties of different systems of academic, social, and industrial interest

Organophosphorus Chemistry 2018

Organophosphorus chemistry is an important discipline within organic chemistry. Phosphorus compounds, such as phosphines, trialkyl phosphites, phosphine oxides (chalcogenides), phosphonates, phosphinates and >P(O)H species, etc., may be important starting materials or intermediates in syntheses. Let us mention the Wittig reaction and the related transformations, the Arbuzov- and the Pudovik reactions, the Kabachnik–Fields condensation, the Hirao reaction, the Mitsunobu reaction, etc. Other reactions, e.g., homogeneous catalytic transformations or C-C coupling reactions involve P-ligands in transition metal (Pt, Pd, etc.) complex catalysts. The synthesis of chiral organophosphorus compounds means a continuous challenge. Methods have been elaborated for the resolution of tertiary phosphine oxides and for stereoselective organophosphorus transformations. P-heterocyclic compounds, including aromatic and bridged derivatives, P-functionalized macrocycles, dendrimers and low coordinated P-fragments, are also of interest. An important segment of organophosphorus chemistry is the pool of biologically-active compounds that are searched and used as drugs, or as plant-protecting agents. The natural analogue of P-compounds may also be mentioned. Many new phosphine oxides, phosphinates, phosphonates and phosphoric esters have been described, which may find application on a broad scale. Phase transfer catalysis, ionic liquids and detergents also have connections to phosphorus chemistry. Green chemical aspects of organophosphorus chemistry (e.g., microwave-assisted syntheses, solvent-free accomplishments, optimizations, and atom-efficient syntheses) represent a dynamically developing field. Last, but not least, theoretical approaches and computational chemistry are also a strong sub-discipline within organophosphorus chemistry

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 /

Cornerstones in Contemporary Inorganic Chemistry

A collection of essential research articles and scientific reviews covering some of the most pertinent and topical areas of study that currently constitute Inorganic Chemistry in the early 21st century