Stacking interactions, also known as π-π or face-to-face interactions, occur between molecules whose π bonds are in parallel planes. They are used to design self-assembling structures in nanotechnology, influence organic reactions and are ubiquitous in nature. The stacking interactions of substituted benzene heterodimers and substituted benzene-natural nucleobase heterodimers are examined. Both electron-donating and withdrawing groups are studied by varying their type, number and location around the benzene ring. The studies are done by carrying out systematic scans of the potential energy surface at the MP2/6-31G*(0.25) level of theory. Charge transfer interactions and extent of charge separation in the monomer are found to be dominant when the difference in ESP between the monomers is large and small, respectively. Dipole-dipole interactions are also found to affect stacking interactions. The results from MP2/6-31G*(0.25) are checked against those at the CCSD(T)/CBS limit for select cases and are found to be within 81- 110%. / xii, 166 leaves : ill. ; 29 cm

The following thesis focuses on two areas of chemistry, pi-pi interactions and radical cation dimers. Approximations to the exact solution to the Schrodinger equation are investigated for these types of chemical systems with a variety of theoretical methods. The first chapter provides an introduction to the various quatum mechanical methods used in this research. The second chapter focuses specifically on pi-pi interaction. In this chapter, high quality quantum mechanical methods are used to examine how substituents tune pi-pi interactions between monosubstituted benzene dimers in parallel-displaced geometries. In addition, the role of dispersion and coulombic interactions in these systems is investigated to determine the nature of the substituent effect. In the third chapter radical cation dimers are investigated. Benchmark results with full configuration interaction (FCI) and equation-of-motion coupled-cluster for ionized systems (EOM-IP-CCSD) are presented for prototypical charge transfer species. Conclusions regarding chapters 2 and 3 are presented in the final chapter. This work may form the basis for improved approaches to rational drug design, organic optical materials, and molecular electronics.

Thesis (M.Sc.)--University of Alberta, 2010. / A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Department of Physiology. Title from pdf file main screen (viewed on March 20, 2010). Includes bibliographical references.

Thesis (Ph. D.)--Miami University, Dept. of Chemistry and Biochemistry, 2004. / Title from second page of PDF document. Includes bibliographical references.

Το φυσικό προϊόν αρτεμισινίνη και τα παράγωγά της αποτελούν σήμερα φάρμακα επιλογής για την αντιμετώπιση της ελονοσίας ενώ πολλά απ’αυτά παρουσιάζουν και ιδιαίτερα σημαντική αντικαρκινική δράση. Στο πλαίσιο της παρούσας διπλωματικής εργασίας έγινε χημική τροποίηση του μορίου της αρτεμισίνης, προκειμένου να συντεθούν διμερή συζεύγματά της με πολυαμίνες (πουτρεσκίνη, σπερμιδίνη, σπερμίνη). Αρχικά, η αρτεμισινίνη τροποποιήθηκε κατάλληλα έτσι ώστε να φέρει συνδέτη με δεσμό C-O (10-oξo) ή C-C (10-καρβο) στη θέση-10 και N-C με αλλαγή του ετεροατόμου στην θέση-11, προκειμένου στη συνέχεια να προσδεθεί στις πολυαμίνες μέσω δεσμού ουρεθάνης. Για το λόγο αυτό, συντέθηκαν ενεργοποιημένα ανάλογα της αρτεμισινίνης, τα οποία μετά από αντίδραση με κατάλληλα προστατευμένες πολυαμίνες, οδηγούν στο σχηματισμό διμερών πολυαμινικών συζευγμάτων της αρτεμισινίνης. Επιπλέον, για προκαταρκτικές βιολογικές μελέτες, συντέθηκε ένα ασύμμετρο πολυαμινικό σύζευγμα της αρτεμισινίνης με το αντικαρκινικό φάρμακο χλωραμβουκίλη, χρησιμοποιώντας το 10-oξo ενεργοποιημένο ανάλογο και την πουτρεσκίνη. / The natural product Artemisinin and its derivatives are currently the drugs of choice for the treatment of malaria, which some of them showing important anticancer activity. In the context of the present dissertation, three chemical modifications of the molecule of artemisinin were accomplished towards the synthesis of several Artemisinin dimer conjugates with polyamines (putrescine, spermidine, spermine). Initially, artemisinin was modified at position 10 and 11, in order to synthesize analogues bearing suitable linkers, through C-O (10-oxo), C-C (10-carbo) and C-N (11-aza, by replacement of O with N in the ring A of Artemisinin) bonds, able to form carbamate bonds with amino groups of polyamines. For this purpose, the corresponding activated intermediates were synthesized, which upon reaction with suitably protected polyamines afforded the Artemisinin symmetric conjugates. In addition, for the sake of preliminary biological evaluation a new asymmetric conjugate consisted of an 10-oxo Artemisinin and a chlorambucil moiety, using putrescine as a polyamine-type linker, was synthesized.

A radiação ultravioleta (UV) pode ser absorvida por diferentes moléculas celulares, incluindo o DNA no qual provoca distorções estruturais. As lesões mais comuns induzidas pela radiação UV são o ciclobutano de pirimidina (CPD) e o fotoproduto (6-4)-pirimidina-pirimidona [(6-4)PPs]. Estas lesões podem ser reparadas pela fotorreativação, caracterizada por ter uma única proteína (fotoliase) que remove lesões empregando luz visível (320-500 nm) como fonte de energia. Foram identificados dois tipos de fotoliases que diferem por sua especificidade ao substrato: CPD-fotoliase e (6-4)-fotoliase. Um outro mecanismo de reparo é o reparo por excisão de nucleotídeos (NER), um mecanismo que envolve múltiplos passos e proteínas. Enquanto os efeitos genotóxicos da UVC e UVB já estão relativamente esclarecidos e bem aceitos, ainda existem controvérsias sobre a genotoxicidade da radiação UVA, devido ao fato de ser fracamente absorvida pelo DNA. Alguns autores acreditam que os seus principais efeitos são gerados de forma indireta pela produção de espécies reativas de oxigênio enquanto outros acreditam que a UVA pode gerar danos ao DNA de forma direta, provocando a formação de dímeros de pirimidina. O objetivo deste trabalho foi verificar os efeitos genotóxicos da radiação UVA em fibroblastos humanos deficientes e proficientes em NER utilizando adenovírus recombinantes contendo uma ou outra fotoliase para verificar se as lesões CPD e (6-4)PP são geradas pela UVA e se elas teriam alguma importância nas respostas verificadas após irradiação. Foi verificado que as células deficientes no gene XPA são mais sensíveis à radiação UVA quando comparadas às células selvagens. Por meio da detecção imunológica, confirmamos a geração das lesões CPD, (6-4)PP e Dewar, fotoisômero da lesão (6-4)PP, após irradiação com UVA no genoma de células humanas. Empregando vetores adenovirais para transdução de fotoliase específica para lesões tipo CPD ou (6-4)PP, confirmamos que de fato essas lesões são formadas em células humanas deficientes em reparo de DNA após irradiação com UVA. Além disso, esses vírus permitiram verificar a relevância biológica dessas lesões na indução de morte celular em células XP-A irradiadas. De fato, os dados indicam que para doses baixas de radiação UVA essas lesões desempenham um importante papel na indução de morte. Não podemos descartar, porém, que lesões indiretas (provavelmente geradas por estresse oxidativo) também tenham papel na indução de morte pela radiação UVA, o que parece ser mais importante a doses médias e altas dessa radiação. / Ultraviolet radiation (UV) is absorbed by different cellular molecules, including DNA in which induces structural distortions. The most common lesions induced by UV radiation are the cyclobutane pyrimidine (CPD) and the photoproduct (6-4)-pyrimidine-pyrimidone [(6-4)PP]. These lesions can be repaired by the photoreactivation, characterized by a single protein (photolyase) that removes lesions using visible light (320-500 nm) as energy source. Two types of photolyases had been identified that differ by their substrate specificity: CPD-photolyase and (6-4)-photolyase. Another repair mechanism is the nucleotide excision repair (NER), a mechanism that involves multiple steps and proteins. While the genotoxic effects of UVB and UVC are already relatively well-understood and accepted, there is still controversy about the genotoxicity of UVA radiation, due to its low absorption by DNA. Some authors believe that the major effects are generated indirectly by the production of reactive oxygen species, while others believe that UVA can cause damage to DNA directly, inducing the formation of pyrimidine dimers. The aim of this study was to assess the genotoxic effects of UVA radiation in human fibroblasts deficient and proficient in NER, using recombinant adenovirus expressing the photolyases to verify if CPDs and (6-4)PPs are generated by UVA and whether they had any importance in the responses observed after irradiation. It was found that cells deficient in the XPA gene are more sensitive to UV radiation compared to wild type cells. By immunological detection, we confirm the generation of CPD, (6-4)PP and Dewar, photoisomer of the (6-4)PP lesion, in the genome of human cells after irradiation with UVA. Using adenoviral vectors for the transduction of photolyases specific for CPD or (6-4)PP lesions, we confirm that in fact these lesions are generated in human cells deficient in DNA repair after irradiation with UVA. Moreover, these viruses allowed us to verify the biological relevance of these lesions in the induction of cell death in irradiated XP-A cells. In fact, our data indicates that for low doses of UVA radiation, these lesions play important roles in the induction of death. We cannot rule out, however, that indirect lesions (probably caused by oxidative stress) could also have a role in the induction of death by UVA radiation, which seems to be more important in intermediate and high doses of this radiation.

Neste trabalho, métodos ab initio multiconfiguracionais de alto nível com extenso conjunto base e inclusão de correções relativísticas foram empregados para estudar vários sistemas diatômicos contendo metais de transição. As abordagens de Teoria de Pertur- bação de Segunda Ordem Multiconfiguracional (CASPT2) ou sua versão Multi-State (MS-CASPT2), baseadas em funções de onda do tipo Complete-Active-Space Self- Consistent-Field (CASSCF) foram utilizadas, com o conjunto base do tipo Orbitais Naturais contraídas em ambiente relativístico (ANO - RCC) com qualidade quádrupla- , para se estudar esses sistemas. Em relação aos dímeros de metais de transição homonucleares (Re2, Tc2, Ta2, Mo2 e W2), caracterizamos seu estado fundamental e diversos estados excitados através das curvas de energia potencial, constantes espectroscópicas e ordens de ligação efetiva. Todos os dímeros estudados por nós apresentam multiplicidades de ligação acima de quatro. Para esses sistemas também estudamos os efeitos do desdobramento causado pelo acoplamento spin-órbita com o intuito de determinar inequivocadamente a simetria do estado fundamental e, também, de auxiliar na interpretação dos espectros experimentais, quando existentes. Sobre as diatômicas formadas pela junção de um átomo de metal de transição e um elemento do grupo principal, enfocamos principalmente os nitretos e os boretos de metais de transição (CoN, MnN, TcN e RhB). Da mesma maneira, os sistemas foram descritos em termos de suas curvas de energia potencial e constantes espectroscópicas e foram comparadas com outros resultados teóricos e experimentais. Todas as moléculas estudadas nessa parte são caracterizadas por ligações triplas, com um par de elétrons sobre o átomo não metálico e os elétrons restantes localizados sobre o metal, acoplados de diferentes formas / In this work, high level ab initio multiconfigurational methods with extensive basis set and inclusion of relativistic e¤ects were employed to study several diatomic systems containing transition metals. The Multiconfiguration Second Order Perturbation Theory (CASPT2) or its Multi-State version (MS-CASPT2) approaches, based on Complete- Active-Space Self-Consistent-Field (CASSCF), were employed, with the Atomic Natural Orbital contracted in a relativistic environment (ANO-RCC) with quadruple- quality, in order to study these systems. In relation to the homonuclear dimers of transition metals atoms (Re2, Tc2, Ta2, Mo2, and W2), we have characterized their ground state and several excited states through potential energy curves, spectroscopic constants and e¤ective bond orders. All dimers we studied have the multiplicity of the chemical bond above four. To these kind of systems, we have also studied the splitting caused by spin-orbit coupling with the the aim of determine the symmetry of the ground state and help in the interpretation of the experimental spectras. About the diatomic formed by joining of a transition metal atom and an atom of the main group, we have focused, mainly, the transition metal nitrites and borides (CoN, MnN, TcN, and RhB) In the same way, these systems were described in terms of their potential energy curves, spectroscopic constants and wavefunctions and we have com- pared to other theoretical and experimental results. All molecules studied in this part were characterized as triple bonded, with a pair of electrons on the non–metalic center and the remaining electrons localized on the metal, coupled on di¤erent forms

A novel route for the synthesis of the polycyclic aromatic hydrocarbon peropyrene (Pp) is reported along with the efforts to synthesize derivatives of Pp, 2,2′- and 5,5′-linked tetracene dimers as candidates for study as singlet fission materials in photovoltaic devices. Peropyrene was synthesized by the McMurry coupling conditions from phenalenone and low-valent titanium species. The crystal structure of Pp is formed by π-stacked molecular pairs in a herringbone arrangement. The direct functionalization of Pp was studied, and several indirect methods for the functionalization of Pp via phenalenone derivatives are reported. Nucleophilicly dependent, regioselective Michael addition pathways for phenalenone are described. Phenalenone forms a nucleophilic complex with bispinacolatodiboron and yields chiral 3,3′-linked phenalenone dimers and a bicyclo[3.2.1]octane derivative product of an unusual 3,4 addition. An active complex product of phenalenone and (dimethylphenylsilyl)boronic acid pinacolic ester forms Pp directly. The synthesis of 2,2′- and 5,5′-linked tetracene dimers led to the study of the reduction of 1-arylprop-2-yn-1-ol derivatives via TFA-catalyzed hydride transfer from triethylsilane. Substrates with terminal and TMS-protected alkynes showed silane exchange upon reduction. A TMS-protected, terminal alkyne became triethylsilyl-protected by about 50% whereas only triethylsilyl-protected, terminal alkyne was observed from the reduction of an unprotected, terminal alkyne. A new conformational polymorph of 1,4-bis(triisopropylsilyl)buta-1,3-diyne is reported. Five other rotamers are studied by density functional theory as possible candidates of conformational polymorphism by the analysis of torsional strain energies. The relative stabilities and interconversion equilibria of the seven conformational isomers are studied.

The time-dependent visible spectra and the crystal structure of [Fe2(C20H24N8O2)(CH3CN)4]·PF6 (diketo-dimer) were studied. The spectra showed that the most significant chemistry occurred during the initial 1.5 hours of the synthetic reaction. The starting materials 343 nm peak shifted to a lower energy, at 360 nm, and a new shoulder appeared at 490 nm. This change suggests the formation of a new intermediate whose spectrum has an exceptional resemblance to the starting materials mixed valent species, [Fe2(TIED)(Cl)4]+1 (TIED = tetraiminethylene dimacrocycles). Two isosbestic points were found at 538 and 371 nm. The diketo-dimer's crystals appear to have individual colors, a physical characteristic called pleochroism. Pleochroism is a topic in the study of optical crystallography which is discussed and applied to the diketo-dimer. The extinction angle was estimated to be 14°, a value consistent for triclinic crystals. X-ray crystallography found that the diketo-dimer is triclinic, and has a space group of P-1. A noteworthy feature is the bond length, 1.406 Å, between the two linking bridgehead carbons. This bond length matches the value for partial double bonds of aromatic compounds. This argues for a delocalized electron circulating within the macrocycle. The NMR spectra of a diiron macrocycle, [Fe2(TIED)(CH3CN)4]4+, were examined. Temperature dependent, pH dependent, D+ substitution, selectively decoupled, and COSY 1H NMR experiments were performed. Two sets of structural equilibria were found. One set is temperature dependent, and the other is pH dependent. Of particular interest are the peaks centered at 9.7 ppm and assigned to the imine carbon protons H2. Its resonance indicates an imine proton in an extensively conjugated aromatic environment with an electron deficient metal.

For years, frequency standards have been the cornerstone of precision measurement. Among these frequency standards, atomic clocks have set records in both precision and accuracy, and have redefined the second. There is growing interest in more complex molecular systems to complement precision measurements with atoms. The rich internal structure of even the simplest diatomic molecules could provide new avenues for fundamental physics research, including searches for extensions to the Standard Model, dark matter candidates, novel forces or corrections to gravity at short distances, and tests of the variation of fundamental constants. In this thesis, we discuss the fundamental architecture for a precise molecular system based on a strongly forbidden weakly-bound to deeply-bound vibrational transition in 88Sr dimers. We discuss early studies to characterise our system and gain technical and quantum control over the experiment in anticipation of a precise metrological measurement. We, then, demonstrate a record-breaking precision for our 88Sr2 molecular clock ushering in a new era for precision measurement with clocks. Borrowing techniques from previous atomic clock architecture, we measure a ∼32 THz clock transition between two vibrational levels in the electronic ground state, achieving a fractional uncertainty of 4.6 × 10−14 in a new frequency regime. In this current iteration, our molecular clock is fundamentally limited by two-body loss lifetimes of 200 ms and light scattering induced by our high-intensity lattice. Given these limitations, we suggest improvements to combat the effects from both the lattice and two-body collisions in our 1D trap. These include technical improvements to our experiment and strategic choices of particular clock states in our ground electronic potential. We describe in-depth studies of the chemistry and polarizability behaviour of our molecule, which elucidates preferential future directions for a second generation clock system. These empirical results are substantiated by an improved theoretical picture. Ultimately, our molecular system is built in order to probe new physics and as a tool for precision measurement. Leveraging our record-precision clock and our new-found understanding of our molecule, we predict the capacity for our system to place meaningful, competitive constraints on new physics, in particular on Yukawa-type extensions to gravity. These predictions motivate improvements to our current generation clock and set the stage for future measurements with this system.