Experimental and theoretical investigation of the IR spectra and thermochemistry of four isomers of 2-N,N-dimethylaminecyclohexyl 1-N',N'-dimethylcarbamate

A combined experimental and Density functional theory (DFT) B3LYP/6-311+G* study on the IR spectra of four stable isomers of 2-N,N-dimethylaminecyclohexyl 1-N',N'-dimethylcarbamate was performed. Our theoretical calculations reveal that two new isomers of this compound exist and may be more stable than the known isomers. In addition the entropy, heat capacity, and the enthalpy content of the stable isomers are computed by fitting the calculated data to a standard Shomate equation and IR spectra for the two new isomers are presented.

Analysis of the structural and electronic properties of 1-(5-Hydroxymethyl - 4 -[ 5 - (5-oxo-5-piperidin-1-yl-penta-1,3dienyl)-benzo[1,3]dioxol-2-yl] -tetrahydro-furan-2-yl)-5-methyl-1H-pyrimidine-2,4dione molecule

The structural and electronic properties of 1-(5-Hydroxymethyl - 4 -[ 5 - (5-oxo-5-piperidin- 1 -yl-penta- 1,3 -dienyl)-benzo [1,3] dioxol- 2 -yl]-tetrahydro -furan-2 -yl)-5-methy l-1Hpyrimidine-2,4dione (AHE) molecule have been investigated theoretically by performing density functional theory (DFT), and semi empirical molecular orbital calculations. The geometry of the molecule is optimized at the level of Austin Model 1 (AM1), and the electronic properties and relative energies of the molecules have been calculated by density functional theory in the ground state. The resultant dipole moment of the AHE molecule is about 2.6 and 2.3 Debyes by AM1 and DFT methods respectively, This property of AHE makes it an active molecule with its environment, that is AHE molecule may interacts with its environment strongly in solution.

Effect of triplet encapsulated atoms in [60] fullerenes: a theoretical analysis

The present investigation reports on the interaction of the C/O triplet atoms inside of the [60] fullerene (C60) species with small polar molecules (H²O, CH³OH, HF, NH³) using Density Functional Theory (DFT) calculations. The calculations show that in all the computed cases the encapuslated complexes with the molecules are more stable than without internal atoms.

Molecular modeling of asymmetric induction in heterogeneously catalyzed hydrogenation of the C=O bond

Modifiering av metallytor med starkt adsorberade kirala organiska molekyler är eventuellt den mest relevanta teknik man vet i dag för att skapa kirala ytor. Den kan utnyttjas i katalytisk produktion av enantiomeriskt rena kirala föreningar som behövs t.ex. som läkemedel och aromkemikalier. Trots många fördelar av asymmetrisk heterogen katalys jämfört med andra sätt för att få kirala föreningar, har den ändå inte blivit ett allmänt verktyg för storskaliga tillämpningar. Detta beror t.ex. på brist på djupare kunskaper i katalytiska reaktionsmekanismer och ursprunget för asymmetrisk induktion. I denna studie användes molekylmodelleringstekniker för att studera asymmetriska, heterogena katalytiska system, speciellt hydrering av prokirala karbonylföreningar till motsvarande kirala alkoholer på cinchona-alkaloidmodifierade Pt-katalysatorer. 1-Fenyl-1,2-propandion (PPD) och några andra föreningar, som innehåller en prokiral C=O-grupp, användes som reaktanter. Konformationer av reaktanter och cinchona-alkaloider (som kallas modifierare) samt vätebundna 1:1-komplex mellan dem studerades i gas- och lösningsfas med metoder som baserar sig på vågfunktionsteori och täthetsfunktionalteori (DFT). För beräkningen av protonaffiniteter användes också högst noggranna kombinationsmetoder såsom G2(MP2). Den relativa populationen av modifierarnas konformationer varierade som funktion av modifieraren, dess protonering och lösningsmedlet. Flera reaktant–modifierareinteraktionsgeometrier beaktades. Slutsatserna på riktning av stereoselektivitet baserade sig på den relativa termodynamiska stabiliteten av de diastereomeriska reaktant–modifierare-komplexen samt energierna hos π- och π*-orbitalerna i den reaktiva karbonylgruppen. Adsorption och reaktioner på Pt(111)-ytan betraktades med DFT. Regioselektivitet i hydreringen av PPD och 2,3-hexandion kunde förklaras med molekyl–yta-interaktioner. Storleken och formen av klustret använt för att beskriva Pt-ytan inverkade inte bara på adsorptionsenergierna utan också på de relativa stabiliteterna av olika adsorptionsstrukturer av en molekyl. Populationerna av modifierarnas konformationer i gas- och lösningsfas korrelerade inte med populationerna på Pt-ytan eller med enantioselektiviteten i hydreringen av PPD på Pt–cinchona-katalysatorer. Vissa modifierares konformationer och reaktant–modifierare-interaktionsgeometrier var stabila bara på metallytan. Teoretiskt beräknade potentialenergiprofiler för hydrering av kirala α-hydroxiketoner på Pt implicerade preferens för parvis additionsmekanism för väte och selektiviteter i harmoni med experimenten. De uppnådda resultaten ökar uppfattningen om kirala heterogena katalytiska system och kunde därför utnyttjas i utvecklingen av nya, mera aktiva och selektiva kirala katalysatorer.

Computational modeling of the properties of TiO2 nanoparticles

In this study we discuss the electronic, structural, and optical properties of titanium dioxide nanoparticles, and also the properties of Ni(II) diimine dithiolato complexes as dyes in dye-sensitized TiO2 based solar cells. The abovementioned properties have been modeled by using computational codes based on the density functional theory. The results achieved show slight evidence on the structure-dependent band gap broadening, and clear blue-shifts in absorption spectra and refractive index functions of ultra-small TiO2 particles. It is also shown that these properties are strongly dependent on the shape of the nanoparticles. Regarding the Ni(II) diimine dithiolato complexes as dyes in dye-sensitized TiO2 based solar cells, it is shown that based on the experimental electrochemical investigation and DFT studies all studied diimine derivatives could serve as potential candidates for the light harvesting, but the e ciencies of the dyes studied are not very promising.

Novel technology for preparation of optically active chemicals

Asymmetric synthesis using modified heterogeneous catalysts has gained lots of interest in the production of optically pure chemicals, such as pharmaceuticals, nutraceuticals, fragrances and agrochemicals. Heterogeneous modified catalysts capable of inducing high enantioselectivities are preferred in industrial scale due to their superior separation and handling properties. The topic has been intensively investigated both in industry and academia. The enantioselective hydrogenation of ethyl benzoylformate (EBF) to (R)-ethyl mandelate over (-)-cinchonidine (CD)-modified Pt/Al2O3 catalyst in a laboratory-scale semi-batch reactor was studied as a function of modifier concentration, reaction temperature, stirring rate and catalyst particle size. The main product was always (R)-ethyl mandelate while small amounts of (S)-ethyl mandelate were obtained as by product. The kinetic results showed higher enantioselectivity and lower initial rates approaching asymptotically to a constant value as the amount of modifier was increased. Additionally, catalyst deactivation due to presence of impurities in the feed was prominent in some cases; therefore activated carbon was used as a cleaning agent of the raw material to remove impurities prior to catalyst addition. Detailed characterizations methods (SEM, EDX, TPR, BET, chemisorption, particle size distribution) of the catalysts were carried out. Solvent effects were also studied in the semi-batch reactor. Solvents with dielectric constant (e) between 2 and 25 were applied. The enantiomeric excess (ee) increased with an increase of the dielectric coefficient up to a maximum followed by a nonlinear decrease. A kinetic model was proposed for the enantioselectivity dependence on the dielectric constant based on the Kirkwood treatment. The non-linear dependence of ee on (e) successfully described the variation of ee in different solvents. Systematic kinetic experiments were carried out in the semi-batch reactor. Toluene was used as a solvent. Based on these results, a kinetic model based on the assumption of different number of sites was developed. Density functional theory calculations were applied to study the energetics of the EBF adsorption on pure Pt(1 1 1). The hydrogenation rate constants were determined along with the adsorption parameters by non-linear regression analysis. A comparison between the model and the experimental data revealed a very good correspondence. Transient experiments in a fixed-bed reactor were also carried out in this work. The results demonstrated that continuous enantioselective hydrogenation of EBF in hexane/2-propanol 90/10 (v/v) is possible and that continuous feeding of (-)-cinchonidine is needed to maintain a high steady-state enantioselectivity. The catalyst showed a good stability and high enantioselectivity was achieved in the fixed-bed reactor. Chromatographic separation of (R)- and (S)-ethyl mandelate originating from the continuous reactor was investigated. A commercial column filled with a chiral resin was chosen as a perspective preparative-scale adsorbent. Since the adsorption equilibrium isotherms were linear within the entire investigated range of concentrations, they were determined by pulse experiments for the isomers present in a post-reaction mixture. Breakthrough curves were measured and described successfully by the dispersive plug flow model with a linear driving force approximation. The focus of this research project was the development of a new integrated production concept of optically active chemicals by combining heterogeneous catalysis and chromatographic separation technology. The proposed work is fundamental research in advanced process technology aiming to improve efficiency and enable clean and environmentally benign production of enantiomeric pure chemicals.

First-principles study on electronic and structural properties of Cu(In/Ga)Se alloys for solar cells

Thin-film photovoltaic solar cells based on the Cu(In1−xGax)Se2 (CIGS) alloys have attracted more and more attention due to their large optical absorption coefficient, long term stability, low cost, and high efficiency. Modern theoretical studies of this material with first-principles calculations can provide accurate description of the electronic structure and yield results in close agreement with experimental values, but takes a large amount of calculation time. In this work, we use first-principles calculations based on the computationally affordable meta- generalized gradient approximation of the density-functional theory to investigate electronic and structural properties of the CIGS alloys. We report on the simulation of the lattice parameters and band gaps, as a function of chemical composition. The obtained results were found to be in a good agreement with the available experimental data.

Experimental and Computational Studies on Copper and Hydrobenzoin Derivatives in Catalytic Asymmetric Reactions

The use of theory to understand and facilitate catalytic enantioselective organic transformations involving copper and hydrobenzoin derivatives is reported. Section A details the use of theory to predict, facilitate, and understand a copper promoted amino oxygenation reaction reported by Chemler et al. Using Density Functional Theory (DFT), employing the hybrid B3LYP functional and a LanL2DZ/6-31G(d) basis set, the mechanistic details were studied on a N-tosyl-o-allylaniline and a [alpha]-methyl-[gamma]-alkenyl sulfonamide substrate. The results suggest the N-C bond formation proceeds via a cisaminocupration, and not through a radical-type mechanism. Additionally, the origin of diastereoselection observed with [alpha]-methyl-[gamma]-alkenyl sulfonamide arises from avoidance of unfavourable steric interactions between the methyl substituent and the N -protecting group. Section B details the computationally guided, experimental investigation of two hydrobenzoin derivatives as ligands/ catalysts, as well as the attempted synthesis of a third hydrobenzoin derivative. The bis-boronic acid derived from hydrobenzoin was successful as a Lewis acid catalyst in the Bignielli reaction and the Conia ene reaction, but provided only racemic products. The chiral diol derived from hydrobenzoin successfully increased the rate of the addition of diethyl zinc to benzaldehyde in the presence of titanium tetraisopropoxide, however poor enantioinduction was obseverved. Notably, the observed reactivity was successfully predicted by theoretical calculations.

A DFT Guided/Experimental Approach to Asymmetric Allylation and Phase-Transfer Catalysis

The Dudding group is interested in the application of Density Functional Theory (DFT) in developing asymmetric methodologies, and thus the focus of this dissertation will be on the integration of these approaches. Several interrelated subsets of computer aided design and implementation in catalysis have been addressed during the course of these studies. The first of the aims rested upon the advancement of methodologies for the synthesis of biological active C(1)-chiral 3-methylene-indan-1-ols, which in practice lead to the use of a sequential asymmetric Yamamoto-Sakurai-Hosomi allylation/Mizoroki Heck reaction sequence. An important aspect of this work was the utilization of ortho-substituted arylaldehyde reagents which are known to be a problematic class of substrates for existing asymmetric allylation approaches. The second phase of my research program lead to the further development of asymmetric allylation methods using o-arylaldehyde substrates for synthesis of chiral C(3)-substituted phthalides. Apart from the de novo design of these chemistries in silico, which notably utilized water-tolerant, inexpensive, and relatively environmental benign indium metal, this work represented the first computational study of a stereoselective indium-mediated process. Following from these discoveries was the advent of a related, yet catalytic, Ag(I)-catalyzed approach for preparing C(3)-substituted phthalides that from a practical standpoint was complementary in many ways. Not only did this new methodology build upon my earlier work with the integrated (experimental/computational) use of the Ag(I)-catalyzed asymmetric methods in synthesis, it provided fundamental insight arrived at through DFT calculations, regarding the Yamamoto-Sakurai-Hosomi allylation. The development of ligands for unprecedented asymmetric Lewis base catalysis, especially asymmetric allylations using silver and indium metals, followed as a natural extension from these earlier discoveries. To this end, forthcoming as well was the advancement of a family of disubstituted (N-cyclopropenium guanidine/N-imidazoliumyl substituted cyclopropenylimine) nitrogen adducts that has provided fundamental insight into chemical bonding and offered an unprecedented class of phase transfer catalysts (PTC) having far-reaching potential. Salient features of these disubstituted nitrogen species is unprecedented finding of a cyclopropenium based C-H•••πaryl interaction, as well, the presence of a highly dissociated anion projected them to serve as a catalyst promoting fluorination reactions. Attracted by the timely development of these disubstituted nitrogen adducts my last studies as a PhD scholar has addressed the utility of one of the synthesized disubstituted nitrogen adducts as a valuable catalyst for benzylation of the Schiff base N-diphenyl methylene glycine ethyl ester. Additionally, the catalyst was applied for benzylic fluorination, emerging from this exploration was successful fluorination of benzyl bromide and its derivatives in high yields. A notable feature of this protocol is column-free purification of the product and recovery of the catalyst to use in a further reaction sequence.

DFT Studies of the Organocatalytic Aldol Reaction and a Frustrated Lewis Pair

The computational study, and in particular the density functional theory (DFT) study of the organocatalytic α-chlorination-aldol reaction and the chiral backbone Frustrated Lewis Pair (FLP) system served as a valuable tool for experimental purposes. This thesis describes methods to consider different transition states of the proline- catalyzed α-chlorination aldol reaction to determine the reasonable transition state in the reaction between the enamine and α-chloro aldehydes. Moreover, the novel intramolecular Frustrated Lewis pair based on a chiral backbone for the asymmetric hydrogenation of imines and enamines was designed and the ability of hydrogen splitting by this new FLP system was examined by computational modeling and calculating the hydrogen activation energy barrier.

Mirroring Enzymes: The Role of H-Bonding In HQuin-BAM Catalyzed Asymmetric Aza-Henry Reactions: A DFT Study into the Reactivity, Mechanism, and Origins of Selectivity

The exact mechanistic understanding of various organocatalytic systems in asymmetric reactions such as Henry and aza-Henry transformations is important for developing and designing new synthetic organocatalysts. The focus of this dissertation will be on the use of density functional theory (DFT) for studying the asymmetric aza-Henry reaction. The first part of the thesis is a detailed mechanistic investigation of a poorly understood chiral bis(amidine) (BAM) Brønsted acid catalyzed aza-Henry reaction between nitromethane and N-Boc phenylaldimine. The catalyst, in addition to acting as a Brønsted base, serves to simultaneously activate both the electrophile and the nucleophile through dual H-bonding during C-C bond formation and is thus essential for both reaction rate and selectivity. Analysis of the H-bonding interactions revealed that there was a strong preference for the formation of a homonuclear positive charge-assisted H-bond, which in turn governed the relative orientation of substrate binding. Attracted by this well-defined mechanistic investigation, the other important aspect of my PhD research addressed a detailed theoretical analysis accounting for the observed selectivity in diastereoselective versions of this reaction. A detailed inspection of the stereodetermining C-C bond forming transition states for monoalkylated nitronate addition to a range of electronically different aldimines, revealed that the origins of stereoselectivity were controlled by a delicate balance of different factors such as steric, orbital interactions, and the extent of distortion in the catalyst and substrates. The structural analysis of different substituted transition states established an interesting dependency on matching the shape and size of the catalyst (host molecule) and substrates (guest molecules) upon binding, both being key factors governing selectivity, in essence, offering an analogy to positive cooperative binding effect of catalytic enzymes and substrates in Nature. In addition, both intra-molecular (intra-host) and inter-molecular (host-guest, guest-guest) stabilizing interactions play a key role to the high π-facial selectivity. The application of dispersion-corrected functionals (i.e., ωB97X-D and B3LYP-D3) was essential for accurately modeling these stabilizing interactions, indicating the importance of dispersion effects in enantioselectivity. As a brief prelude to more extensive future studies, the influence of a triflate counterion on both reactivity and selectivity in this reaction was also addressed.

Etude théorique des propriétés électroniques et optiques des super-réseaux de Si/SiO2

FRANCAIS: L'observation d'une intense luminescence dans les super-réseaux de Si/SiO2 a ouvert de nouvelles avenues en recherche théorique des matériaux à base de silicium, pour des applications éventuelles en optoélectronique. Le silicium dans sa phase cristalline possède un gap indirect, le rendant ainsi moins intéressant vis-à-vis d'autres matériaux luminescents. Concevoir des matériaux luminescents à base de silicium ouvrira donc la voie sur de multiples applications. Ce travail fait état de trois contributions au domaine. Premièrement, différents modèles de super-réseaux de Si/SiO2 ont été conçus et étudiés à l'aide de calculs ab initio afin d'en évaluer les propriétés structurales, électroniques et optiques. Les deux premiers modèles dérivés des structures cristallines du silicium et du dioxyde de silicium ont permis de démontrer l'importance du rôle de l'interface Si/SiO2 sur les propriétés optiques. De nouveaux modèles structurellement relaxés ont alors été construits afin de mieux caractériser les interfaces et ainsi mieux évaluer la portée du confinement sur les propriétés optiques. Deuxièmement, un gap direct dans les modèles structurellement relaxés a été obtenu. Le calcul de l'absorption (par l'application de la règle d'or de Fermi) a permis de confirmer que les propriétés d'absorption (et d'émission) du silicium cristallin sont améliorées lorsque celui-ci est confiné par le SiO2. Un décalage vers le bleu avec accroissement du confinement a aussi été observé. Une étude détaillée du rôle des atomes sous-oxydés aux interfaces a de plus été menée. Ces atomes ont le double effet d'accroître légèrement le gap d'énergie et d'aplanir la structure électronique près du niveau de Fermi. Troisièmement, une application directe de la théorique des transitions de Slater, une approche issue de la théorie de la fonctionnelle de la densité pour des ensembles, a été déterminée pour le silicium cristallin puis comparée aux mesures d'absorption par rayons X. Une très bonne correspondance entre cette théorie et l'expérience est observée. Ces calculs ont été appliqués aux super-réseaux afin d'estimer et caractériser leurs propriétés électroniques dans la zone de confinement, dans les bandes de conduction.

Étude, par principes premiers, des effets de la corrélation entre électrons sur les propriétés électroniques et magnétiques de polymères pontés et de supraconducteurs à haute température critique

La présente thèse traite de la description de systèmes complexes, notamment des polymères et des cuprates, par la théorie de la fonctionnelle de la densité. En premier lieu, la théorie de la fonctionnelle de la densité ainsi que différentes fonctionnelles utilisées pour simuler les matériaux à l’étude sont présentées. Plus spécifiquement, les fonctionnelles LDA et GGA sont décrites et leurs limites sont exposées. De plus, le modèle de Hubbard ainsi que la fonctionnelle LDA+U qui en découle sont abordés dans ce chapitre afin de permettre la simulation des propriétés de matériaux à forte corrélation électronique. Par la suite, les résultats obtenus sur les polymères sont résumés par deux articles. Le premier traite de la variation de la bande interdite entre les polymères pontés et leurs homologues non pontés. Le second se penche sur l’étude de polymères à faible largeur de bande interdite. Dans ce dernier, il sera démontré qu’une fonctionnelle hybride, contenant de l’échange exact, est nécessaire afin de décrire les propriétés électroniques des systèmes à l’étude. Finalement, le dernier chapitre est consacré à l’étude des cuprates supraconducteurs. La LDA+U pouvant rendre compte de la forte localisation dans les orbitales 3d des atomes de cuivre, une étude de l’impact de cette fonctionnelle sur les propriétés électroniques est effectuée. Un dernier article investiguant différents ordres magnétiques dans le La2CuO4 dopé termine le dernier chapitre. On trouve aussi, en annexe, un complément d’information pour le second article et une description de la théorie de la supraconductivité de Bardeen, Cooper et Schrieffer.

Influence de la structure moléculaire sur la structure cristalline et électronique de molécules organiques conjuguées : une étude spectroscopique

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Caractérisation et modélisation de l’aimant organique NIT-2Py

L'aimant organique NIT-2Py a été caractérisé expérimentalement et ses propriétés ont été simulées numériquement à partir de la théorie de la fonctionnelle de la densité. Le magnétisme dans ce matériau provient de la présence d'un électron non apparié sur chaque molécule qui a ainsi un moment magnétique non nul. Ceci a été confirmé par des simulations sur une molécule isolée. Les molécules de NIT-2Py cristallisent dans le groupe d'espace P21/c avec huit molécules par maille élémentaire pour former la structure cristalline Alpha étudiée dans ce document. Le moment effectif de la susceptibilité et l'entropie magnétique totale montre que ce matériau est un système de spins 1/2 avec un spin par molécule. Les mesures de chaleur spécifique ont mis en évidence la présence de deux phases magnétiques ordonnées à basse température qui sont séparées par un plateau en aimantation. Une première phase est observée à des champs magnétiques inférieurs à 2.2 T et a une température de transition de 1.32 K en champ nul. Les mesures de susceptibilité magnétique et d'aimantation ont permis d'établir que cette phase ordonnée est antiferromagnétique. Ceci est confirmé par les simulations numériques. La deuxième phase est induite par le champ magnétique avec une température de transition de 0.53 K à 6 T. L'information disponible sur cette phase est limitée et l'étude du système à l'extérieur des phases ordonnées en donne une meilleure compréhension. Un modèle de spins S=1/2 isolés et de dimères S=0 isolés reproduit bien les mesures d'aimantation et de chaleur spécifique au-dessus de 3 K. L'application d'un champ magnétique réduit l'écart d'énergie entre le singulet et le triplet du dimère jusqu'au croisement qui se produit à 6 T. La phase induite émerge précisément à ce croisement et on spécule l'existence d'un condensat de Bose-Einstein des états triplets.