A natureza das ligações de hidrogênio e a influência destas interações na estrutura eletrônica de complexos neutros, catiônicos, aniônicos e radicalares foi estudada utilizando-se análises geométricas, energéticas, eletrônicas e topológicas. Inicialmente, verificaram-se alterações na aromaticidade do cátion pirílio após a complexação com uma a três moléculas de água. Tais complexos foram ainda estudados em meio reacional com constante dielétrica igual a da água com o emprego do modelo PCM (Polarizable Continuum Model). Adicionalmente, os efeitos da hidroxilação na estrutura eletrônica dos cátions benzopirílio e flavílio foram considerados. Posteriormente, analisaram-se os efeitos das fortes ligações de hidrogênio na ressonância do grupo carboxila em complexos formados entre o radical hidroperoxil e os ácidos fórmico, acético e trifluoroacético. Como extensão desse trabalho, estudos envolvendo complexos obtidos com e sem restrições na otimização de geometria possibilitaram obter informações a respeito da ressonância dos grupos carboxila e carboxilato quando o fluoreto de hidrogênio interage linear ou perpendicularmente com todos os átomos do ácido fórmico e do ânion formiato. O desenvolvimento das atividades supracitadas compreendeu a análise da função de onda pelos métodos NBO (Natural Bond Orbital), NSA (Natural Steric Analysis), NRT (Natural Resonance Theory) e AIM (Atoms in Molecules). As alterações em parâmetros geométricos e nas cargas atômicas foram consideradas. Uma análise energética foi realizada com o emprego do método de decomposição de energia proposto por Xantheas. As freqüências vibracionais e a intensidade das bandas do estiramento do grupo X-H, doador da ligação de hidrogênio, foram analisadas. As densidades de spin para os complexos radicalares também foram obtidas. A influência das ligações de hidrogênio e o efeito do substituinte na aromaticidade dos cátions foram verificados com o emprego dos métodos e índices NICS (Nucleus Independent Chemical Shifts), HOMA (Harmonic Oscillator Model of Aromaticity), HOSE (Harmonic Oscillator Stabilization Energy) e PDI (para-Delocalization Index). Os cálculos foram efetuados com os modelos B3LYP/6-31+G(d,p), B3LYP/6-311++G(3df,3pd) e UB3LYP/6-311++G(3df,3pd). Ocasionalmente, outras funções de base (EPR-III e cc-pVDZ), assim como o método MP2, foram utilizados para testar a confiabilidade dos resultados obtidos. As interações intermoleculares pouco alteraram a estrutura eletrônica e a aromaticidade do cátion pirílio. Analogamente, a substituição de um átomo de hidrogênio por um grupo hidroxila em diversas posições dos cátions benzopirílio e flavílio também não provocou modificações muito significativas na estrutura eletrônica desses cátions, embora tenha se verificado uma dependência da aromaticidade com a posição da hidroxila. Por outro lado, a distorção geométrica associada às ligações de hidrogênio foram responsáveis pelo incremento ou diminuição da ressonância do grupo carboxila nos ácidos fórmico, acético, trifluoroacético e do grupo carboxilato no ânion formiato. Os efeitos dos grupos doador e sacador de elétrons na estabilização dos complexos radicalares foram evidenciados. Adicionalmente, pode-se atribuir um caráter covalente parcial em algumas ligações de hidrogênio. / The nature of hydrogen bonds and their influence on electronic structure of neutral, cationic, anionic, and radical complexes was studied by using geometric, energetic, electronic, and topological analysis. The changes in aromaticity of the pyrylium cation upon complexation with one up to three water molecules were investigated. The PCM (Polarizable Continuum Model) model was employed to study the pyrylium-water complexes in a water reaction medium. In addition, the effects of hydroxylation on electronic structure of the benzopyrylium and flavilium cations were also considered. In addition, the effects of strong hydrogen bonds on carboxyl group resonance in the complexes formed between the hydroperoxyl radical and formic, acetic, and trifluoroacetic acids were analyzed. In extension of this work, studies including complexes, obtained with and without geometric restrictions, provided information about the resonance of the carboxyl and carboxylate groups when the hydrogen fluoride interacts, linear or perpendicularly, with all atoms of formic acid and formate anion. The analysis of the wavefunction by using NBO (Natural Bond Orbital), NSA (Natural Steric Analysis), NRT (Natural Resonance Theory), and AIM (Atoms in Molecules) methods was necessary to the development of the above mentioned activities. The changes in geometric parameters and atomic charges were also considered. An energetic analysis of complexes was done with the energy decomposition method proposed by Xantheas. The vibrational frequencies and the intensity of the X-H (hydrogen bond donor group) stretching bands were studied. The spin densities for the radical complexes were also obtained. The Nucleus Independent Chemical Shifts (NICS), Harmonic Oscillator Model of Aromaticity (HOMA), HOSE (Harmonic Oscillator Stabilization Energy), and PDI (para-Delocalization Index) aromaticity criteria were employed to verify the hydrogen bond influence and the effect of hydroxylation in the aromaticity of the cations. The calculations were carried out by using B3LYP/6-31+G(d,p), B3LYP/6-311++G(3df,3pd), and UB3LYP/6-311++G(3df,3pd) models. Occasionally, other basis set (EPR-III and cc-pVDZ), as well as the MP2 method, were applied to test the accuracy of the results. The intermolecular interactions lead to small alterations in the electronic structure and aromaticity of pyrylium cation. Similarly, the substitution at different positions of the benzopyrylium and flavilium cations by a hydroxyl group does not cause significant changes in the electronic structure of these cations. However, a dependence of the hydroxyl group position on aromaticity was observed. On the other hand, for formic, acetic, trifluoroacetic acids, as well as for the formate anion, the resonance of the carboxyl and carboxylate groups is affected not only by the geometric distortions but also by the hydrogen bonds. The effects of the electron-donating and electron-withdrawing groups in the stabilization of radical complexes were characterized. Furthermore, a partial covalent character can be attributed to some hydrogen bonds.

En la literatura sobre mecànica quàntica és freqüent trobar descriptors basats en la densitat de parells o la densitat electrònica, amb un èxit divers segons les aplicacions que atenyin. Per tal de que tingui sentit químic un descriptor ha de donar la definició d'un àtom en una molècula, o ésser capaç d'identificar regions de l'espai molecular associades amb algun concepte químic (com pot ser un parell solitari o zona d'enllaç, entre d'altres). En aquesta línia, s'han proposat diversos esquemes de partició: la teoria d'àtoms en molècules (AIM), la funció de localització electrònica (ELF), les cel·les de Voroni, els àtoms de Hirshfeld, els àtoms difusos, etc.L'objectiu d'aquesta tesi és explorar descriptors de la densitat basats en particions de l'espai molecular del tipus AIM, ELF o àtoms difusos, analitzar els descriptors existents amb diferents nivells de teoria, proposar nous descriptors d'aromaticitat, així com estudiar l'habilitat de totes aquestes eines per discernir entre diferents mecanismes de reacció. / In the literature, several electronic descriptors based in the pair density or the density have been proposed with more or less success in their pratical applications. In order to be chemically meaningful the descriptor must give a definition of an "atom" in a molecule, or instead be able to identify some chemical interesting regions (such as lone pair, bonding region, among others). In this line, several molecular partition schemes have been put forward: atoms in molecules (AIM), electron localization function (ELF), Voronoi cells, Hirshfeld atoms, fuzzy atoms, etc. The goal of this thesis is to explore the density descriptors based on the molecular partitions of AIM, ELF and fuzzy atom, analyze the existing decriptors at several levels of theory, propose new aromaticity descriptors, and study its ability to discern between different mechanisms of reaction.

La present tesi doctoral s'emmarca dins el camp de la química teòrica icomputacional. El primer objectiu, que va ser el de partida, consistia a veure si els índexosbielectrònics derivats de la teoria AIM podien ser útils per estudiar la reorganitzacióelectrònica al llarg d'una reacció. De forma paral·lela es va plantejar un objectiumetodològic, el càlcul dels índexos mencionats a altres nivells de teoria, com podia serDFT o CI. CI. Aquests dos objectius varen portar a molts d'altres, tot i que els principals són:Objectiu 1. Estudi de la reorganització de parells d'electrons al llarg d'unareacció.Objectiu 2. Efecte de la solvatació sobre l'estructura de parells d'electrons d'unamolècula.Objectiu 3. Càlcul dels índexos de localització i deslocalització als nivells de teoriadel funcional de la densitat i post-Hartree-Fock.Objectiu 4. Caracterització de l'enllaç per pont d'hidrogen per mitjà del'estructura dels parells d'electrons.Objectiu 5. L'índex de deslocalització: nou criteri electrònic d'aromaticitat.

This thesis reports the theoretical investigations aimed at understanding the structure, stability and properties of a few inorganic compounds. The first chapter presents an introductory overview of the theories used to solve the questions addressed in the thesis. A brief discussion of the work is also presented here. The second chapter deals with electron reservoirs which have been one of the basic motifs of single-electron device. Mononuclear vinylidene complexes of type Mn(C5H4R’)(R” 2 PCH2CH2PR "2)= C = C(R1)(H) were synthesized and reported [Venkatesan et al, Organometallics 25, 5190 (2006)] as potential electron reservoirs capable of storing and releasing electrons in a reversible fashion. These compounds have been of great interest because their red-ox chemistry (reversible oxidative coupling and reductive decoupling) is governed by the C - C bond. However slow oxidation of the mononuclear vinylidene complexes leads to undesired product. In our model compound Mn(C5H5)(PH3)2 = C = C(R1)(H), we substituted the cyclopentadienyl moiety by isolobal dianionic dicarbollyl ligand Dcab2- (C2B9H2-11 ). This simple substitution could reduce the production of undesired product. Calculations of vertical detachment energy, thermodynamic feasibility and molecular orbital analysis showed that this substitution was thermodynamically feasible and led to easy oxidation and dimerization of the parent compound accompanied with better reversibility of the reaction. The effect of substituents (R = H,Me,Ph) on Cβ atom of our model system was also analyzed. The substituent on β carbon had a great effect on the stability and reactivity of these complexes. Our comparative study between Mn(C5H5)(PH3)2 = C = C(R)(H) and Mn(Dcab)(PH3)2 = C = C(R)(H)−1 (where R = H,Me,Ph) predicted the latter to be a more potential electronic reservoir. Gas-phase observations on MAl 4- (M = Li, Na, Cu) and Li3Al-4 coupled with computations led to the conclusion that Al42− [Boldyrev and Wang et al, Science 291, 859 (2001)] is “aromatic” while Al44- is “antiaromatic” [Boldyrev and Wang et al, Science 300, 522 (2003)]. It has been reported by Pati et al [J. Am. Chem. Soc. 125, 3496 (2005)] that co-ordination with a transition metal can stabilize the “antiaromatic” Al4Li4. In the first section of chapter three, it has been reported that Al4Li4 can also be stabilized by capping it with main group element like C and its isoelectronic species BH. Calculations of binding energy, nuclear independent chemical shift (NICS), energy decomposition analysis and molecular orbital analysis supported the capping induced stability, reduction of bond length alternation and increase of aromaticity of these BH/C capped Al4Li4 systems. The interaction between px and py orbitals of BH/C and the HOMO and LUMO of Al4Li4 was responsible for such stabilization. Calculations suggested that capping might introduce fluxionality in the molecule at room temperature. Al has valence electronic configuration of s2p1 and Al42− has been shown to have multiple aromaticity [Boldyrev and Wang et al, Science 291, 859 (2001)]. Analogy between electronic configuration s2pof Al and d1sof Sc/Y prompted us to explore the aromaticity of M42− clusters (M = Sc, Y ) which have been described in the second section of chapter three. Different geometries of M42− clusters (M = Sc, Y ) were explored, and the planar butterfly-like D2h geometry (two fused triangles) was found to be the most stable isomer. This is unlike the case of Al42− where D4h isomer was the most stable one as reported in the literature. In D2h geometry of M42− clusters (M = Sc, Y ), significant electron delocalization in each wing of the butterfly indicated fused d aromaticity. Atomization energy and chemical hardness supported the preference of D2h geometry over the D4h geometry. Molecular orbital analysis showed that the d-electrons were delocalized in each triangle of D2h geometry. Our interest in the search of new kinds of binuclear sandwich compounds led us to consider sandwiched metal dimers CB5H6M - MCB5H6 (M = Si, Ge, Sn) which are at the minima in the potential energy hypersurface with a characteristic M - M single bond. This work has been described in the first section of chapter four. The NBO analysis and the M - M distances ( ˚A) (2.3, 2.44 and 2.81 for M= Si, Ge, Sn respectively) indicated substantial M - M bonding. Consecutive substitution of two boron atoms in B7H7−2 by M (Si, Ge, Sn) and carbon respectively led to neutral MCB5H7, where M - H bond bent towards the carbon side of the five membered ring. Dehydrogenation of two MCB5H7 might lead to our desired CB5H6M - MCB5H6 where similar bending of M -M bond has been observed. The bending of M - M bond in CB5H6M -MCB5H6 was more than the M - H bending in MCB5H7. Molecular orbital analysis has been done to understand the bending. Larger M - M bending observed in CB5H6M - MCB5H6 in comparison to M - H bending observed in MCB5H7 was suspected to be favored by stabilization of one of the M - M π bonding MO’s. Preference of M to occupy the apex of pentagonal skeleton of MCB5H7 over its icosahedral analogue MCB10H11 has been observed. Structures of sandwiched binuclear L- M – M - L where M = Ti, Zr and L = Cp, C3B3H6 were also investigated as described in second section of chapter four. We found that these compounds having bent geometry with short M - M distance (1.87˚A for M=Ti and 2.29˚A for M=Zr) lie at the minima in the potential energy hypersurface. Bending from the linear geometry led to the stabilization of M - L antibonding interaction in L - M – M - L. Molecular orbital analysis, NBO calculations, Wiberg bond index and charge analysis suggested M2+ unit to be embedded in between two L’s in L - M – M - L. Molecules that have the ability to perform interesting mechanical motions have always been of great interest. Umbrella inversion of ammonia is one of the most interesting and well studied phenomena. This study has led to the development of the MASER. The possibility of inversion of the molecule C9H9−Li+ by the movement of Li+ through the C9H9−ring was studied earlier [Das et al, Chem. Phys. Lett. 365, 320 (2002)]. In the fifth chapter theoretical investigation on a B12 cluster has been reported, which could exhibit a through ring umbrella inversion. Calculations showed that a part of the molecule, consisting of a three membered boron ring could invert through the rest, viz., a nine membered boron ring. Using a simple model, the double well potential for the motion was calculated. The barrier for inversion was found to be 4.31 kcal/mol. The vibrational levels and tunneling splitting were calculated using this potential. It was found that the vibrational excitation to the v = 17 level caused large amplitude “inversion oscillation” of the molecule. After considering the tunneling effect, inversion rate at 298K was calculated by using transition state theory and was found to be 1.17 x 1010/s. Finally, in the last chapter the main results of the thesis have been summarized.

The synthesis of benzo[e]dimethyldihydropyrene (BDHP) photoswitches with ter-27, quarter-36, and quinque-28 thiophene oligomers attached on the same side of the switch was achieved using Stille coupling reactions. BDHP photoswitches with bi-75, ter-76 and quinque-77 thiophene oligomers attached directly to the switch on one side, and via a carbonyl spacer on the opposite side of the switch were also synthesized. Dimethyldihydropyrene (DHP) photoswitches with a naphthoyl functional group in the 2 position were synthesized using a Friedel Crafts reaction, and ter-96, quinque-97 and septi-98 thiophene oligomers were attached on opposite sides of the switch using Stille coupling reactions. All compounds were characterized by NMR, IR UV-vis spectroscopy and mass spectrometry. The relative rates of the photo-opening reactions under excess light conditions and the UV closing reactions versus BDHP were measured. Improvements in the photo-opening properties of the oligothiophene functionalized switches compared to BDHP were observed. The most dramatic photo-opening improvement was found for the quinquethienyl substituted DHP switch 97 which photo-opened when irradiated with visible light over 100 times faster than BDHP. UV closing rates were virtually the same as that of BDHP. However the addition of oligothiophenes led to an increase in the thermal closing reaction rates. Compounds with the naphthoyl functional group in the 2 position of DHP were found to have dramatically increased thermal closing rates. The electrochemical properties of oligothiophene functionalized BDHP and naphthoyl functionalized DHP switches in the closed form were studied by cyclic voltammetry and spectroelectrochemistry. During the oxidation cycle, a closing reaction from the cyclophanediene (CPD) form to the DHP form of the switches occurred which prevented the study of the electrochemical properties of the switches in the open form. Conductivity testing was performed on the quinquethienyl substituted DHP switch 97 using a gold interdigitated micro electrode array. The conductivity of undoped 97 was greater in the closed DHP isomer than in the open CPD isomer. Irradiation with red or blue light allowed for repetitive switching between the more highly conducting closed form and the less conducting open form. When electrochemically doped, 97 showed improved conductivity over the undoped form but only the conductivity of the closed doped form could be measured due to electrochemically induced closing.

The thesis entitled “Addressing subtle physicochemical features exhibited by molecular crystals via Experimental and Theoretical Charge Density Analysis” consists of five chapters. An introductory note provides a brief description of experimental and theoretical charge density methodology, followed by its utilization in obtaining certain physical and chemical properties in molecular crystals. Chapter 1 addresses not so easily accessed molecular property arising due to electron conjugation, highlighting antiaromaticity in tetracyclones. A systematic study of six tetracyclone derivatives with electron withdrawing and electron donating substituents has been carried out using experimental and theoretical charge density analysis. A three pronged approach based on quantum theory of atoms in molecules (QTAIM), nucleus independent chemical shifts (NICS), and source function (SF) has been employed to establish the degree of antiaromaticity of the central five-membered ring in all the derivatives. Electrostatic potentials mapped on the is density surface reveal the finer effects of different electron withdrawing and electron donating substituents on the carbonyl group. Chapter 2 presents a temperature induced reversible first order single crystal to single crystal phase transition (Room temperature Orthorhombic, P22121 to low temperature Monoclinic, P21) in a  hybrid peptide, Boc-γ4(R)Val-Val-OH. The thermal behavior accompanying the phase transition of the dipeptide crystal was characterized by differential scanning calorimetry, visual changes in birefringence of the sample during heating and cooling cycles on a hot-stage microscope with polarized light. Variable-temperature unit cell check measurements from 300 to 100 K showed discontinuity in the volume and cell parameters near the transition temperature, supporting the first-order behavior. The reversible nature of the phase transition is traced to be due to an interplay between enthalpy and entropy. Chapter 3 brings out an unusual stabilizing interaction involving a cooperative -hole and ¬hole character in a short NCS···NCS bond. This chapter describes structural features of four isothiocyanate derivatives, FmocXCH2NCS; X=Leu, Ile, Val and Ala. Among these it is observed that only FmocLeuCH2NCS which crystallizes in a tetragonal space group, P41, (a=b=12.4405(5) Å; c= 13.4141(8) Å) transforms isomorphously to a low temperature form, P41, (a=b=17.4665(1) Å; c= 13.1291(1) Å). The characteristics of the phase transition have been monitored by Differential Scanning Calorimetry, variable temperature IR and temperature dependent unit cell measurements. The short NCS···NCS intermolecular interaction (3.296(1) Å) is analyzed based on detailed experimental charge density analysis which reveals the nature of this stabilizing interaction. Chapter 4 explains a comparative study of syn and anti conformations of carboxylic acids in peptides from both structural aspect and charge density features. Single crystal structures of four peptides having syn conformations [BocLeuγ4(R)Valγ4(R)ValOH, BocLeuγ4(R)ValLeuγ4(R)ValOH, Boc3(S)Leu3(S)LeuOH] and one with anti conformation, BocLeuγ4(R)ValValOH have been analyzed. Experimental charge density analysis has been carried out exclusively on BocLeuγ4(R)ValValOH having anti form, because of its rare occurrence in literature. However, low temperature datasets on the four peptides with syn conformations were collected and theoretical charge density analysis has been carried out on two of these compounds. Electrostatic potentials mapped on is density surface bring out a significant difference at the oxygen atoms of the carboxyl group in the two conformations. However, lone pair orientation of different types of Oxygen atoms in the two forms (urethane, amide, acid) doesn’t exclusively indicate the differences in the corresponding charge density features. Chapter 5 addresses the issue of how sensitive are the charge density features associated with amino acid residues when the backbone conformational angles are varied. Three model systems, 1, L-alanyl–L-alanyl–L-alanine dehydrate; 2, anhydrous L-alanyl–L-alanyl–L¬alanine and 3, cyclo-(D,L-Pro)2(L-Ala)4 monohydrate have been chosen for this evaluation. Compound 1 has ant parallel alignment of tripe tide strands, and compound 2 has parallel alignment. All the alanine residues in compound 1 and 2 are in the -sheet region of the Ramachandran plot, whereas, the four Alanine residues in the cyclic hex peptide 3 span different regions of the Ramachandran plot. Theoretical multipole modelling has been carried out in order to explore the plausibility of transferring multipole parameters across different regions of Ramachandran Plot. Appendix I contains a brief description of charge shift bonding in Ph-CH2-Se-Se-CH2-Ph, as determined based on both experimental and theoretical charge density analysis. Appendix II contains a reprint of a published article on “Conformation-Changing Aggregation in Hydroxyacetone: A Combined Low-Temperature FTIR, Jet, and Crystallographic Study”.

Conselho Nacional de Desenvolvimento Científico e Tecnológico / This work describes the molecular and supramolecular structure of fourteen pyrazolo[1,5-a]pyrimidines from bond lengths, torsion angles, angles between planes and interatomic distances. The data discussed were originated from xray and theoretical calculations. Torsion angle N1-N8-C3a-N4, algles between planes of pyrazole and pyrimidine rings and the pyrazolo[1,5-a]pyrimidine RMS value showed that the fused rings are plane. The heterocyclic ring bond lengths demonstrated that the p-electrons are delocalized by resonance and the peripheral electronic distribution of this p-electrons is similar to the naphthalene. The bond length obtained from theoretical calculations (AM1, PM3, RM1 e ab initio) have a correlation with experimental for pyrazolo[1,5-a]pyrimidine ring bonds and for bonds of their substituents.The supramolecular assembly of pyrazolo[1,5-a]pyrimidine reveals that interactions type halogen···Lewis base (Cl···N, F···F, Cl···Cl, Cl···Br), halogen···p (F···p, Cl···p e Br···p) and p-p interactions (pyrazole, pyrimidine and aryl) were the main interactions observed by self-assembly of the pyrazolo[1,5-a]pyrimidines. The atoms in supramolecular synthons were invariable with modifications of substituent at C5. However, was sensitive to variations of substituents at C3. This composes a notable example of substituent effect in the synthon robustness. The halogenated functions at C7(CCl3, CF3), C3 (Br) and in remote positions at C5 (4-Br-Ph) present the competition between chlorine and bromine atoms in the formation of supramolecular synthons. These observations are in accordance with recent s-hole theory and are some of few experimental example of theory. Finally, the aromaticity of pyrazolo[1,5-a]pyrimidines was determined by geometric index HOMA (Harmonic Oscillator Model of Aromaticity) from theoretical (AM1, PM3, RM1 e ab initio) and x-ray bond length. In this work, was also proposing new parameters to heterocyclic HOMA calculations. The results show HOMA values higher than 0.900 that is in accordance with aromaticity properties of these systems. / Este trabalho apresenta o estudo da estrutura molecular e supramolecular de uma série de 14 pirazolo[1,5-a]pirimidinas a partir de dados de comprimentos e ângulos de ligação, ângulos diedros, ângulos entre planos, distâncias interatômica de interações intermoleculares. Os dados apresentados foram obtidos por difratometria de raios-X e cálculos teóricos de orbitais moleculares. Os dados do ângulo diedro N1-N8-C3a-N4, ângulo entre os planos do pirazol e da pirimidina, e a média da raiz quadrada dos átomos do anel pirazol[1,5- a]pirimidina demonstraram que os anéis pirazol e pirimidina formadores do anel fundido estão no mesmo plano. Os comprimentos de ligação entre os átomos do núcleo heterocíclico demonstraram que os elétrons-p estão deslocalizados caracterizando um sistema em ressonância e que a distribuição eletrônica se assemelha a do naftaleno, com os elétrons distribuídos pela periferia do sistema heterocíclico. Os comprimentos de ligação obtidos por cálculos teóricos (Austin Method 1, Parametrized Method 3, Recife Method 1 e ab initio) apresentaram boa correlação com dados experimentais tanto para o núcleo pirazolo[1,5-a]pirimidina quanto para os substituintes. Ainda foram realizados estudos da organização supramolecular das pirazolo[1,5-a]pirimidina. As principais interações intermoleculares observadas nas pirazolo[1,5- a]pirimidinas foram do tipo halogênio···base de Lewis (Cl···N, F···F, Cl···Cl, Cl···Br), halogênio···p (F···p, Cl···p e Br···p) e interações do tipo p-p (entre anéis pirazol, pirimidina e arila). Os átomos envolvidos na interação foram persistentes com a variação do susbtituinte no C5 do anel. Entretanto as interações foram modificadas pela mudança de substituintes no C3 do anel, constituindo um exemplo notável do efeito do substituinte no empacotamento cristalino. A presença de funções halogenadas nas posições C7(CCl3, CF3), C3 (Br) e em posições remotas de substituintes em C5 (4-Br-Ph) mostraram a competição entre átomos de cloro e de bromo na organização supramolecular destes compostos. Estas observações estão de acordo com a recente teoria sobre a existência de uma superfície com potencial positivo na ligação Chalogênio (s-hole) e constituem um dos poucos exemplos experimentais para esta teoria. Por fim, foi determinada a aromaticidade de pirazolo[1,5-a]pirimidinas usando o índice geométrico HOMA (Harmonic Oscilator Model of Aromaticity) a partir dos dados de comprimentos de ligações obtidos por difratometria de raios-X e obtidos por cálculos teóricos (AM1, PM3, RM1 e ab initio). Neste trabalho também foram propostos novos parâmetros para a adequação do cálculo de aromaticidade para heterociclos. Os resultados mostraram valores de HOMA maiores que 0,900, que são condizentes com as características de aromaticidade descritas para estes compostos.

A natureza das ligações de hidrogênio e a influência destas interações na estrutura eletrônica de complexos neutros, catiônicos, aniônicos e radicalares foi estudada utilizando-se análises geométricas, energéticas, eletrônicas e topológicas. Inicialmente, verificaram-se alterações na aromaticidade do cátion pirílio após a complexação com uma a três moléculas de água. Tais complexos foram ainda estudados em meio reacional com constante dielétrica igual a da água com o emprego do modelo PCM (Polarizable Continuum Model). Adicionalmente, os efeitos da hidroxilação na estrutura eletrônica dos cátions benzopirílio e flavílio foram considerados. Posteriormente, analisaram-se os efeitos das fortes ligações de hidrogênio na ressonância do grupo carboxila em complexos formados entre o radical hidroperoxil e os ácidos fórmico, acético e trifluoroacético. Como extensão desse trabalho, estudos envolvendo complexos obtidos com e sem restrições na otimização de geometria possibilitaram obter informações a respeito da ressonância dos grupos carboxila e carboxilato quando o fluoreto de hidrogênio interage linear ou perpendicularmente com todos os átomos do ácido fórmico e do ânion formiato. O desenvolvimento das atividades supracitadas compreendeu a análise da função de onda pelos métodos NBO (Natural Bond Orbital), NSA (Natural Steric Analysis), NRT (Natural Resonance Theory) e AIM (Atoms in Molecules). As alterações em parâmetros geométricos e nas cargas atômicas foram consideradas. Uma análise energética foi realizada com o emprego do método de decomposição de energia proposto por Xantheas. As freqüências vibracionais e a intensidade das bandas do estiramento do grupo X-H, doador da ligação de hidrogênio, foram analisadas. As densidades de spin para os complexos radicalares também foram obtidas. A influência das ligações de hidrogênio e o efeito do substituinte na aromaticidade dos cátions foram verificados com o emprego dos métodos e índices NICS (Nucleus Independent Chemical Shifts), HOMA (Harmonic Oscillator Model of Aromaticity), HOSE (Harmonic Oscillator Stabilization Energy) e PDI (para-Delocalization Index). Os cálculos foram efetuados com os modelos B3LYP/6-31+G(d,p), B3LYP/6-311++G(3df,3pd) e UB3LYP/6-311++G(3df,3pd). Ocasionalmente, outras funções de base (EPR-III e cc-pVDZ), assim como o método MP2, foram utilizados para testar a confiabilidade dos resultados obtidos. As interações intermoleculares pouco alteraram a estrutura eletrônica e a aromaticidade do cátion pirílio. Analogamente, a substituição de um átomo de hidrogênio por um grupo hidroxila em diversas posições dos cátions benzopirílio e flavílio também não provocou modificações muito significativas na estrutura eletrônica desses cátions, embora tenha se verificado uma dependência da aromaticidade com a posição da hidroxila. Por outro lado, a distorção geométrica associada às ligações de hidrogênio foram responsáveis pelo incremento ou diminuição da ressonância do grupo carboxila nos ácidos fórmico, acético, trifluoroacético e do grupo carboxilato no ânion formiato. Os efeitos dos grupos doador e sacador de elétrons na estabilização dos complexos radicalares foram evidenciados. Adicionalmente, pode-se atribuir um caráter covalente parcial em algumas ligações de hidrogênio. / The nature of hydrogen bonds and their influence on electronic structure of neutral, cationic, anionic, and radical complexes was studied by using geometric, energetic, electronic, and topological analysis. The changes in aromaticity of the pyrylium cation upon complexation with one up to three water molecules were investigated. The PCM (Polarizable Continuum Model) model was employed to study the pyrylium-water complexes in a water reaction medium. In addition, the effects of hydroxylation on electronic structure of the benzopyrylium and flavilium cations were also considered. In addition, the effects of strong hydrogen bonds on carboxyl group resonance in the complexes formed between the hydroperoxyl radical and formic, acetic, and trifluoroacetic acids were analyzed. In extension of this work, studies including complexes, obtained with and without geometric restrictions, provided information about the resonance of the carboxyl and carboxylate groups when the hydrogen fluoride interacts, linear or perpendicularly, with all atoms of formic acid and formate anion. The analysis of the wavefunction by using NBO (Natural Bond Orbital), NSA (Natural Steric Analysis), NRT (Natural Resonance Theory), and AIM (Atoms in Molecules) methods was necessary to the development of the above mentioned activities. The changes in geometric parameters and atomic charges were also considered. An energetic analysis of complexes was done with the energy decomposition method proposed by Xantheas. The vibrational frequencies and the intensity of the X-H (hydrogen bond donor group) stretching bands were studied. The spin densities for the radical complexes were also obtained. The Nucleus Independent Chemical Shifts (NICS), Harmonic Oscillator Model of Aromaticity (HOMA), HOSE (Harmonic Oscillator Stabilization Energy), and PDI (para-Delocalization Index) aromaticity criteria were employed to verify the hydrogen bond influence and the effect of hydroxylation in the aromaticity of the cations. The calculations were carried out by using B3LYP/6-31+G(d,p), B3LYP/6-311++G(3df,3pd), and UB3LYP/6-311++G(3df,3pd) models. Occasionally, other basis set (EPR-III and cc-pVDZ), as well as the MP2 method, were applied to test the accuracy of the results. The intermolecular interactions lead to small alterations in the electronic structure and aromaticity of pyrylium cation. Similarly, the substitution at different positions of the benzopyrylium and flavilium cations by a hydroxyl group does not cause significant changes in the electronic structure of these cations. However, a dependence of the hydroxyl group position on aromaticity was observed. On the other hand, for formic, acetic, trifluoroacetic acids, as well as for the formate anion, the resonance of the carboxyl and carboxylate groups is affected not only by the geometric distortions but also by the hydrogen bonds. The effects of the electron-donating and electron-withdrawing groups in the stabilization of radical complexes were characterized. Furthermore, a partial covalent character can be attributed to some hydrogen bonds.

Neste trabalho foram estudados computacionalmente os [2.2]ciclofanos ([2.2]paraciclofano (1), anti-[2.2]metaciclofano (2a), sin-[2.2]metaciclofano (2b) e [2.2]metaparaciclofano (3)), que são os [2n]ciclofanos mais simples, contendo dois anéis fenílicos conectados por duas pontes etilênicas. Os ciclofanos têm apresentado inúmeras aplicações importantes, podendo atuar como auxiliares em sínteses assimétricas e como catalisadores que simulam funções enzimáticas, apresentando seletividade em relação aos substratos. Eles são empregados tanto em químicab supramolecular quanto em áreas biomédicas. Estudos que empregam ressonância de spin eletrônico ou que investigam propriedades ópticas não-lineares dos [2.2]ciclofanos indicam que os mesmos apresentam interações transanulares, que ocorrem através de recobrimento direto entre orbitais pertencentes a anéis diferentes, through-space, ou através de recobrimento entre orbitais dos anéis e das pontes, through-bond. As interações transanulares possuem um papel fundamental na química dos ciclofanos, alterando o comportamento reacional destes compostos e as transições espectroscópicas. Apesar dos métodos de preparação de ciclofanos, desde os mais simples aos mais complexos, serem intensamente investigados, estudos computacionais, que busquem compreender as correlações entre tensão e aromaticidade, estrutura eletrônica e o mecanismo de ocorrência das interações transanulares, são raramente encontrados na literatura. Desse modo, o objetivo deste trabalho foi estudar as interações transanulares, bem como correlacionar as diferenças estruturais, a tensão sobre anéis e pontes, cargas atômicas, aromaticidade e os deslocamentos químicos, não apenas para os isômeros dos [2.2]ciclofanos, mas também seus derivados fluorados (perfluoração de um dos anéis dos [2.2]ciclofanos), bem como avaliar os efeitos de diversos substituintes (CN, Cl, C=O, NH2 e NO2) e da protonação na estrutura eletrônica do isômero [2.2]paraciclofano. As otimizações de geometria de 1, realizadas com diferentes métodos e conjuntos de funções de base, mostraram que os modelos MP2/6-31+G(d,p) e B3PW91/6-31+G(d,p) fornecem os melhores resultados em comparação com os dados de raios-x. Buscas conformacionais mostraram que 2a e 2b são confôrmeros com energias diferentes e que 3 possui dois confôrmeros degenerados. As energias relativas e de tensão das pontes, seguiram a mesma ordem, indicando que a tensão sobre as pontes e a repulsão entre as nuvens ? dos anéis aromáticos são determinantes para a estabilidade dos [2.2]ciclofanos. As reações isodésmicas indicaram que os anéis comportam-se como absorvedores de tensão. NICS e HOMA mostraram que apesar das perdas de planaridade dos anéis a aromaticidade é mantida. O método NBO confirmou que todos os [2.2]ciclofanos apresentam interações through-bond, mas apenas 2a e 2b apresentaram interações through-space significantes. A análise AIM mostrou que as interações transanulares observadas são do tipo camada fechada (iônica ou ligação de hidrogênio) e que estabilizam os [2.2]ciclofanos. Para os derivados fluorados as principais alterações geométricas observadas foram para os diedros das pontes. As reações isodésmicas revelaram que as tensões das pontes e as energias relativas são afetadas pela fluoração. Além disso, os anéis dos isômeros fluorados absorvem mais tensão que os anéis dos isômeros não fluorados. NICS e HOMA mostraram que a substituição por flúor aumenta a aromaticidade dos [2.2]ciclofanos. A análise NBO indicou que a perfluoração aumentou o número e a intensidade das interações through-space, mas as mesmas ficaram restritas principalmente aos derivados fluorados de 2a e 2b. A mesma análise evidenciou que há uma conjugação dos pares de elétrons dos átomos de flúor com o sistema ?. Por outro lado, a análise AIM sugeriu que a substituição não aumenta o número de interações through-space, mas confirmou a conjugação dos pares de elétrons dos átomos de flúor. Os demais substituintes empregados afetam os parâmetros geométricos do [2.2]paraciclofano (1) de maneira diferenciada. A análise particionada das reações isodésmicas mostrou que as tensões nos anéis e nas pontes dependem não apenas do substituinte empregado, mas também da posição da substituição. NICS e HOMA indicaram que a aromaticidade no anel não-substituído dos derivados substituídos é maior que em 1. A análise NBO revelou que a substituição e a protonação aumentam a ocorrência de interações transanulares through-space. O método AIM indicou a presença de interações transanulares apenas para o derivado substituído com NH2 e CN e para a espécie protonada. No entanto, tais interações apresentaram características de interações de camada fechada. com pequenas estabilizações. As cargas atômicas e os deslocamentos químicos confirmaram as mudanças na densidade eletrônica, observadas através do método AIM. / In this work, the [2.2]cyclophanes ([2.2]paracyclophane (1), anti-[2.2]metacyclophane (2a), syn-[2.2]metacyclophane (2b) e [2.2]metaparacyclophane (3)), which are the simplest [2n] cyclophanes that contain two phenyl rings connected by two ethanediyl linkages, were studied computationally. Cyclophanes have presented several important applications, such as auxiliary in asymmetric synthesis, catalysts that simulate enzymatic functions, presenting selectivity in relation to the substrates. They are employed either in supramolecular chemistry or in biomedical areas. Studies that apply electron spin resonance or that investigate the non-linear optical properties of [2.2]cyclophanes, indicate that these compounds present transannular interactions, which occur through direct overlap of orbitals lying in different rings, throughspace, or through overlap between orbitals from rings and bridges, through-bond. The transannular interactions have a fundamental role in cyclophane chemistry, changing the reactional behavior of these compounds, and the spectroscopic transitions. Despite the fact that the well known methods of preparation, from the simplest to the most complex cyclophanes, have been studied intensively, computational studies that intent to comprehend the correlations between tension and aromaticity, electronic structure, and the mechanism of the transannular interactions are rarely found in the literature. Therefore, the aim of this work was not only to study the transannular interactions, correlating the structural differences, tension in rings and bridges, atomic charges, aromaticity, and chemical shifts of the [2.2]cyclophanes isomers but also to extent a similar treatment to the fluorinated derivatives. In addition, the effects of substituents such as (CN, Cl, C=O, NH2, and NO2) and the protonation on the electronic structure of [2.2]paracyclophane were also evaluated. The geometry optimizations of 1, carried out by using different methods and basis set, showed that the models MP2/6-31+G(d,p) and B3PW91/6-31+G(d,p) provide the best results in comparison with the x-ray data. Conformational searches showed that 2a and 2b are the conformers that present the same energy and the isomer 3 has two degenerated conformers. The strain energies of the bridges followed the same tendency as the relative energies, indicating that the tension on the bridges and the repulsions between the ? clouds of the aromatic rings are the key factors that determine the [2.2]cyclophane stabilities. The isodesmic reactions indicated that the rings are absorbents of tension. NICS and HOMA showed that the aromaticity of the rings is preserved despite the changes on the planarity. The NBO method confirmed that all [2.2]cyclophanes present through-bond interactions, but only 2a and 2b exhibit noteworthy through-space interactions. The AIM analysis pointed out that the transannular interactions behave as closed shell interactions (ionic or hydrogen bond), stabilizing the [2.2]cyclophanes. The main geometric changes, observed to the fluorinated derivatives, were those related with the dihedral angle of bridges. The isodesmic reactions pointed out that the tensions of bridges and the relative energies are affected by the fluorination. In addition, the fluorinated rings absorb more tension than the non-fluorinated rings. NICS and HOMA showed that the substitution by fluorine increases the aromaticity of the [2.2]cyclophanes. The NBO analysis indicated that the number of through-space interactions increase with the fluorination, but it is restrict to the derivatives of 2a and 2b. In addition, the same analysis pointed out a conjugation of the fluorine lone pairs with the ? system. On the other hand, the AIM analysis suggested that the substitution do not increase the number of through-space interactions, but confirmed the conjugation of the fluorine lone pairs. The other substituents can affect the geometric parameter of 1 noticeably. The partitioned analysis of isodesmic reactions showed that the tensions in bridges and rings not only depend on the substituents employed but also on the position of substitution. NICS and HOMA pointed out that the aromaticity is bigger in the non-substituted rings of [2.2]paracyclophane derivatives than in 1. The NBO analysis showed that the substitution and protonation increase the number of through-space interactions. AIM method indicated the transannular interactions occur only to the derivate substituted by NH2 and CN, and to the protonated specie. However, these interactions presented features of closed shell interactions with small stabilizations. The atomic charges and the chemical shifts confirmed the changes of the electronic density, observed through the AIM method.

The aim of the diploma thesis was to optimize the sequential fractionation method of organic matter to be used for physico-chemical characterization of extracted fractions. Humic acid isolated from oxidized brown coal of Leonardite was used as a source matrix of organic matter. An eluotropic series was assembled and sequential fractionation was performed by extraction on a Soxhlet apparatus. The original humic acid and fractions were characterized by elemental analysis (EA) and thermogravimetric analysis (TGA), followed by Fourier transform infrared spectrometry (FTIR), molecular absorption spectrometry (UV/VIS), fluorescence spectrometry and potentiometric titration. Atomic ratios were determined from the results of the elemental analysis. From the measured UV/Vis and fluorescence excitation and emission spectra, the absorption coefficients, resp. fluorescence coefficients. Used fractionation method proved to be a suitable method for studying HA structure. A total of 62 wt. % of initial materiál was extracted, indiivdual fraction amounted from 0.36–30.92 wt. %. From the results of the structural analysis, it is clear that with increasing polarity of the organic solvent, fractions with long aliphatic chains were first isolated and their aromaticity graddualy increased. Non-polar organic solvents were suitable for the extraction of lipid-like coumpounds, while the most polar organic fractions were rich in polar groups and their structual parameters were close to the original humic acid. The fraction extracted with acetonitrile was the most unique fraction. This fraction was rich on nitrogen and amine groups and was similar to protein-like structures. In the last two fractions, extracted with alcohols, a significant bathochromic shift typical of fluorophore type V was observed. Among other things, they were also characterized by a higher content of plant carbohydrate residues.