The first part of this work reports a comparative study on electrochromic properties of two Donor-Acceptor-Donor (DAD) type polymers, namely poly(2-heptyl-4,7-di(thiophen-2-yl)-1H-benzo[d]imidazole) (BImTh) and poly(4,7-bis(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)-2-heptyl-1H-benzo[d]imidazole) (BImEd). DAD type polymers are designed to bear the same acceptor unit, benzimidazole and two different donor units, thiophene and 3,4-ethylenedioxy thiophene (EDOT) to make a comparison based on the donor unit effect. The resulting polymers are both multichromic and have low band gap values (1.93 eV for PBImTh and 1.74 eV for PBImEd). In the second part, 4,7-bis(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)-2-phenyl-1H-benzo[d]imidazole (BImBEd) is synthesized. In order to figure out the presence of an intramolecular hydrogen bonding between the amine bond of the imidazole ring and the oxygen of the EDOT molecule, different amounts of trifluoroacetic acid (TFA) and concentrated sodium hydroxide (NaOH) solutions were added during electrochemical polymerization. These treatments caused protonation of the imine and deprotonation of the amine bonds respectively. In order to prove the changes in the optical properties of the polymers due to different number of protonated and deprotonated imine and amine bonds, 1,4-bis(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)benzene (BEDOT-B) was also synthesized and treated with the same procedures. Results showed that it is possible to control the main chain conformation of even an insoluble polymer via acid and base treatments during in situ polymerization.

ABSTRACT SYNTHESIS OF BENZIMIDAZOLE CONTAINING DONOR ACCEPTOR ELECTROCHROMIC POLYMERS Akpinar, Hava Zekiye M. Sc., Department of Chemistry Supervisor: Prof. Dr. Levent Toppare February 2011, 60 pages Donor-acceptor-donor (DAD) type benzimidazole (BIm) and 3,4-ethylenedioxythiophene (EDOT) bearing monomers (4-(2,3-Dihydrothieno[3,4-b][1,4]dioxin-5-yl)-7-(2,3 dihydrothieno[3,4b][1,4] dioxin-7-yl)-2-benzyl-1H-benzo[d]imidazole (M1), 2,4-bis(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)-7-(2,3-dihydrothieno[3,4-b][1,4]dioxin-7-yl)-1H-benzo[d]imidazole (M2) and 4-(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)-7-(2,3-dihydrothieno[3,4-b][1,4]dioxin-7-yl)-2-ferrocenyl-1H-benzo[d]imidazole (M3)) were synthesized and electrochemically polymerized. Pendant group at 2-C position of the imidazole ring was functionalized with phenyl (P1), EDOT (P2) and ferrocene (P3) in order to observe substituent effect on electrochemical and electrochromic properties of corresponding polymers. Spectroelectrochemical results showed that different pendant groups resulted in polymers with slightly different optical band gaps (1.75, 1.69 and 1.77 eV respectively) and different number of achievable colored states. Optoelectronic performance were reported in detail. Keywords: Benzimidazole, EDOT, Donor-Acceptor Type Polymers, Electrochromism, Conjugated Polymers.

ABSTRACT SYNTHESIS OF BENZIMIDAZOLE CONTAINING DONOR ACCEPTOR ELECTROCHROMIC POLYMERS Akpinar, Hava Zekiye M. Sc., Department of Chemistry Supervisor: Prof. Dr. Levent Toppare February 2011, 60 pages Donor-acceptor-donor (DAD) type benzimidazole (BIm) and 3,4-ethylenedioxythiophene (EDOT) bearing monomers (4-(2,3-Dihydrothieno[3,4-b][1,4]dioxin-5-yl)-7-(2,3 dihydrothieno[3,4b][1,4] dioxin-7-yl)-2-benzyl-1H-benzo[d]imidazole (M1), 2,4-bis(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)-7-(2,3-dihydrothieno[3,4-b][1,4]dioxin-7-yl)-1H-benzo[d]imidazole (M2) and 4-(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)-7-(2,3-dihydrothieno[3,4-b][1,4]dioxin-7-yl)-2-ferrocenyl-1H-benzo[d]imidazole (M3)) were synthesized and electrochemically polymerized. Pendant group at 2-C position of the imidazole ring was functionalized with phenyl (P1), EDOT (P2) and ferrocene (P3) in order to observe substituent effect on electrochemical and electrochromic properties of corresponding polymers. Spectroelectrochemical results showed that different pendant groups resulted in polymers with slightly different optical band gaps (1.75, 1.69 and 1.77 eV respectively) and different number of achievable colored states. Optoelectronic performance were reported in detail.

Benzimidazole and benzotriazole derivatives, 4-(2,3-Dihydrothieno[3,4-b][1,4] dioxin-5-yl)-7-(2,3-dihydrothieno[3,4b][1,4]dioxin-7-yl)-2-benzyl-1H-benzo[d] imidazole (BIm-Ed), 2-benzyl-4,7-di(thiophen-2-yl)-2H-benzo[d] [1,2,3] triazole (BBTS), and 2-benzyl-4,7-bis(2,3-dihydrothieno[3,4-b][1,4]dioxin-5-yl)-2Hbenzo[ d] [1,2,3] triazole (BBTES) were employed as photosensitizers for diaryliodonium salt photoinitiators in cationic photopolymerization of various epoxide and vinyl ether monomers. Diphenyliodonium hexafluorophosphate (Ph2I+PF6&macr / ) salt was used as the photoinitiator in this study. Extended conjugation and electron-rich moieties of the photosensitizers enabled the use of long wavelength UV and visible light emitting light sources in cationic photopolymerizations. Polymerizations were achieved at room temperature and monitored by optical pyrometry. Photopolymerization of a diepoxide monomer with ambient solar irradiation was examined.

Microbe resistence is a serious issue, especially as they have become resistant to most well known drugs. Therefore this is considered as a global problem and is now dealt with at a poitical level. Since no new classes of antimicrobial agents have been discovered in the past three deacdes, the development of new drugs is extremely urgent. Therefore the aim of this project was to synthesise derivatives of benzimidazole, and then assesses their antimicrobial activities in vitro by using disc (well) diffusion and MICs tests. A total of 69 benzimidazole derivatives, with substituents at positions 1, 2, and 5, were synthesised, characterised and tested against selected bacteria and fungi. In addition, six bezimidazole silver complexes were prepared and evaluated for their antimicrobial behavior. The SAR showed that the antimicrobial activity of the compounds depended on the substituents attached to the bicyclic heterocycle. Some promising results were obtained. In particular, 5 compounds displayed antibacterial activity against two MRSA strains with MIC values corresponding to ciprofloxacin, which can be considered significant. The compounds have some common features; four possess 5-chloro or 5-bromo substituents; two are derivatives of (S)-2- ethanaminebenzimidazole and the others are derivative of one 2-(chloromethyl)-1Hbenzo[d]imidazole, (1H-benzo[d]imidazol-2-yl)methanethiol and 2-(methoxymethyl)-1-methyl-1H-benzo[d]imidazole. The results from the antifungal screening were very interesting as there were 26 compounds, including two silver complexes, which were potent fungicides against the selected fungal species. They showed equivalent or greater potentency in their MIC values than amphotericin B. In particular, the 5-fluoro, 5-chloro and 5-bromo benzimidazole showed broad spectrum activity.

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No. of bitstreams: 2 Dissertação - Guaraciara de Andrade Picanço - 2016.pdf: 2488180 bytes, checksum: d4bf0f4c94bf841c42ea4763fd1fcf0e (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2016-08-25 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The high prevalence of intestinal and tissue parasites combined with the breakthrough of parasites resistat to albendazole, encouraged the search for new drugs. Studies on the biochemical response of Taenia crassiceps metacestode to drugs has been shown to be important for the detection of modes of action of drugs within the parasite metabolic pathways. In order to develop new anti-parasitic drugs, the benzimidazole derivative 6-Chloro-5- (2,3-dichlorophenoxy) -2- (trifluoromethyl) -1H-benzimidazole (RCB15) was synthesized. The objective of this study was to determine the in vitro effect of a benzimidazole derivative, RCB15, in the energetic and respiratory metabolism of T. crassiceps cysticerci. For this, 30 larval stage cysticerci were plated in culture plates containing supplemented RPMI and albendazole sulfoxide (ABZSO) (6,5 μM, 13 μM, 26 μM, 52 μM or 104 μM) or RCB15 (6,5 μM, 13 μM, 26 μM, 52 μM or 104 μM) diluted in dimethyl sulfoxide (DMSO). After 24 hours of cultivation, the cysticerci were separated from the culture medium and frozen in liquid nitrogen. Analysis on high-performance liquid chromatography to assess the energetic and respiratory metabolism were performed. There was a decrease in glucose concentrations detected in vesicular fluid in all groups treated with RCB15 and the groups treated with the highest dosages of ABZSO. The non detection of lactate in the culture medium of the groups treated with RCB15 indicates that this acid was used as a precursor of gluconeogenesis. The group treated with RCB15 52 uM performed the aerobic energetic pathways due to the non detection of lactate neither in the vesicular fluid nor in the culture medium. With respect to the tricarboxylic acid (TCA) cycle, low concentrations of α-ketoglutarate or non-detection of this organic acid, indicates that the parasite has preferably used the fumarate reductase pathway. Probably the detected α-ketoglutarate was from the protein catabolism. The alternative routes of energy production, were observed in the groups treated with RCB15 26 uM and 104 uM and ABZSO 13 uM. In those groups acetate was used to produce β-hydroxybutyrate which was completely excreted in other treatments and in the control group acetate was excreted due to excess of acetyl-CoA which was not used in the TCA cycle. It is possible to conclude that the TCB15 treatment influenced glycolysis, diminished the energetic sources as it induced the parasite to use other sources to produce energy such as gluconecogenesis and fatty acid oxidation. Cysticerci that were treated with RCB15 and ABZSO preferred the fumarate reductase pathway. The drugs used in this study did not influence the proteins catabolism. The RCB15 treatment presented greater influence in the glucose uptake and consequently in glycolytic pathway when compared to the ABZSO treatment. / A alta prevalência de parasitoses intestinais e teciduais aliada ao surgimento de casos de resistência parasitária ao albendazol, incentivou a busca por novos fármacos. Os estudos da resposta bioquímica de Taenia crassiceps exposto a fármacos tem se mostrado importante para a detecção dos mecanismos de ação dos fármacos sobre as vias metabólicas do parasito. A fim de desenvolver-se novos fármacos anti-parasitários, sintetizou-se o derivado benzimidazólico 6-Cloro-5-(2,3-diclorofenoxi)-2-(trifluorometil)-1H-benzimidazol (RCB15). O objetivo deste trabalho foi determinar o efeito in vitro do derivado benzimidazólico, RCB15, no metabolismo energético e respiratório de cisticercos de T. crassiceps. Para tanto, 30 cisticercos em estádio larval foram semeados em placas de cultura contendo meio RPMI suplementado e acrescido de sulfóxido de albendazol (ABZSO) (6,5 μM, 13 μM, 26 μM, 52 μM ou 104 μM) ou RCB15 (6,5 μM, 13 μM, 26 μM, 52 μM ou 104 μM) diluídos em Dimetilsulfóxido (DMSO). Após 24 horas de cultivo, os cisticercos foram separados do meio de cultura e ambos congelados em nitrogênio líquido. Foram realizadas análises em Cromatografia Líquida de Alta Eficiência para avaliação do metabolismo energético e respiratório dos cisticercos, e por espectrofotometria para dosar glicose, ureia, creatinina e proteínas totais. Observou-se uma diminuição nas concentrações de glicose detectada no fluído vesicular em todos os grupos tratados com RCB15 e nos grupos tratados com as dosagens mais altas de ABZSO. A não detecção de lactato no meio de cultura dos grupos tratados com RCB15 indica que este ácido foi utilizado como precursor da glicose na via da gliconeogênese, o grupo tratado com RCB15 52 μM fez aerobiose, isto é comprovado pelo fato de não haver lactato nem no fluido vesicular nem no meio de cultura. Com relação ao ciclo do ácido cítrico, as baixas concentrações de α-cetoglutarato ou a não detecção deste ácido, indicam que o parasito deu preferência pela via da fumarato-redutase, assim o α-cetoglutarato detectado foi oriundo do catabolismo de proteínas. Quanto as vias alternativas de produção de energia, observou-se que nos grupos tratados com RCB15 26 μM e 104 μM e com ABZSO 13 μM o acetato foi utilizado para produzir β-hidroxibutirato que foi totalmente excretado, nos demais tratamentos e no grupo controle o acetato foi excretado devido ao excesso de acetil-CoA que não foi utilizado no ciclo do ácido cítrico. Conclui-se que o tratamento com RCB15 influenciou a glicólise, diminuiu as fontes energéticas induzindo o parasito a utilizar outras vias para a produção de energia, tais como, a gliconeogênese e a oxidação de ácidos graxos. Os cisticercos que receberam o tratamento com RCB15 e ABZSO preferiram utilizar a via da fumarato redutase. Os compostos utilizados neste estudo não influenciaram no catabolismo de proteínas. O tratamento com RCB15 teve maior impacto na captação de glicose e consequente maior influência na via glicolítica em comparação ao ABZSO.

The use of porous sorbents for physisorptive capture of CO2 from gas mixtures has been deemed attractive due to the low energy penalty associated with recycling of such materials. Porous organic polymers (POPs) have emerged as promising candidates with potential in the treatment of pre- and post- fuel combustion processes to separate CO2 from gas mixtures. Concurrently, significant advances have been made in establishing calculation methods that evaluate the practicality of porous sorbents for targeted gas separation applications. However, these methods rely on single gas adsorption isotherms without accounting for the dynamic gas mixtures encountered in real-life applications. To this end, the design and application of a dynamic gas mixture breakthrough apparatus to assess the CO2 separation performance of a new class of heteroatom (N and O) doped porous carbons derived from a Pyrazole precursor from flue gas mixtures is presented. Here in, two new benzimidazole linked polymers (BILPs) have been designed and synthesized. These polymers display high surface while their imidazole functionality and microporous nature resulted in high CO2 uptakes and isosteric heat of adsorption (Qst). BILP-30 displayed very good selectivity for CO2 in flue gas while BILP-31 was superior in CO­2 separation from landfill gas mixtures at 298 K and 1 bar. Additionally, a new POP incorporating a highly conjugated pyrene core into a polymer framework linked by azo-bonds is presented. Azo-Py displays a nanofibrous morphology induced by the π-π stacking of the electron rich pyrene core. Due to its high surface area and microporous nature, Azo-Py displays impressive CO2 uptakes at 298 K and 1 bar. Evaluation of the S value for CO2 separation of Azo-Py revealed competitive values for flue gas and landfill gas at 298 K and 1 bar. Finally, a highly cross-linked benzimidazole linked polymer, BILP-4, was successfully incorporated into Matrimid® polymer to form a series of new mixed matrix membranes. The surface functionality of BILP-4 was exploited to enhance the interaction with Matrimid® polymer matrix to produce robust MMMs which displayed significantly improved CO2 gas permeabilities and ideal selectivities for CO2/N2.

The thesis entitled “Benzimidazole based Novel Ligands for Specific Recognition of Duplex and G-Quadruplex DNA” deals with the design, synthesis and modeling of several benzimidazole based molecules and their interaction with duplex and G-quadruplex DNA structures. It also elucidates the inhibition effect of the ligands on the activity of Topoisomerase I and Telomerase. The work has been divided into six chapters. Chapter 1. DNA Interacting Small Organic Molecules: Target for Cancer Therapy This first chapter presents an overview on the various types of small molecules that interact with duplex and G-quadruplex structures of DNA or interfere with the activity of DNA targeted enzymes like topoisomerase and telomerase. The importance of such molecules as chemotherapeutic agents is highlighted. Chapter 2. DNA Recognition: Conformational Switching of Duplex DNA by Mg2+ ion Binding to Ligand Bis-benzimidazoles like Hoechst 33258 are well known ligands that bind to duplex DNA (ds-DNA) minor grooves. Here a series of dimeric bisbenzimidazole based ligands in which two Hoechst units are connected via oxyethylene based hydrophilic [Ho-4ox-Ho (1), Ho-3ox-Ho (2)] or via hydrophobic oligomethylene [Ho-(CH2)8-Ho (3)](Figure 1) spacers have been synthesized. The aim of this investigation is to examine the binding property of these dimers on the ds-DNA to explore whether the variation in the length of the spacer has any effect on DNA binding properties particularly in presence of selected metal ions. The changes of individual dimers in DNA binding efficiency was studied in detail by fluorescence, circular dichroism spectral titrations and thermal denaturation experiment with selected duplex DNA formed from appropriate oligonucleotides. We have also examined the changes that occur in geometry of the molecules from linear to hairpin motif in presence of Mg2+ ion. A large difference was observed in [ligand]/ [DNA] ratio and binding efficiency with ds-DNA upon change in the ligand geometry from linear to hairpin motif. The experimental results were then substantiated using docking and molecular dynamics simulations using a model ds-DNA scaffold. Both experimental and theoretical studies indicate that the DNA binding is highly dependent on the spacer type and length between the two monomeric Hoechst units. The spacer length actually helps to achieve shape complimentarity with the double-helical DNA axis. Figure1: Chemical structures of the dimeric ligands Ho-4ox-Ho, Ho-3ox-Ho, Ho-(CH2)8-Ho and Hoechst 33258 (Ho) used in this study. Chapter 3. DNA Binding and Topoisomerase I Inhibiting Properties of New Benzimidazole Substituted Polypyridyl Ruthenium (II) Mixed-Ligand Complexes In this study, we have synthesized and fully characterized three new Ru(II) based polypyridyl and benzimidazole mixed complexes: (1) [Ru(bpy)2(PMI)], 2+ (2) [Ru(bpy)2(PBI)]2+ and (3) [Ru(bpy)2(PTI)]2+ (Figure 2) . The affinities of these complexes toward duplex DNA were investigated. In addition, the photocleavage reaction of DNA and topoisomerase I inhibition properties of these metal complexes were also studied. The DNA binding efficiency of individual complexes was studied in detail by absorbance, fluorescence spectral titrations and thermal denaturation experiment using natural calf-thymus DNA. Upon irradiation at 365 nm, all three Ru(II) complexes were found to promote the cleavage of plasmid DNA from negatively supercoiled to nicked circular and subsequently to linear DNA. The inhibition of topoisomerase I mediated by these Ru(II) complexes was also examined. These experiments demonstrate that each complex serves as an efficient inhibitor toward topoisomerase I and such inhibition activity is consistent with interference with the DNA religation step catalyzed by topoisomerase. Figure 2. Chemical structures of the metal complexes used in this present study. Chapter 4. Synthesis and Evaluation of a Novel Class of G-Quadruplex-Stabilizing small molecules based on the 1,3-Phenylene-bis (piperazinyl benzimidazole) syatem Achieving stabilization of telomeric DNA in the G-quadruplex conformation by various organic compounds is an important goal for the medicinal chemists seeking to develop new anticancer agents. Several compounds are known to stabilize the G-quadruplexes. However, relatively few are known to induce their formation and/or alter the topology of the pre-formed G-quadruplex DNA. Herein, four compounds having the 1,3-phenylene-bis(piperazinyl benzimidazole) (Figure 3) unit as a basic skeleton have been synthesized, and their interactions with the 24-mer telomeric DNA sequences from Tetrahymena thermophilia d(T2G4)4 have been investigated using high-resolution techniques such as circular dichroism (CD) spectropolarimetry, CD melting, emission spectroscopy, and polyacrylamide gel electrophoresis. The data obtained, in the presence of one of three ions (Li+, Na+ or K+), indicate that all the new compounds have a high affinity for G-quadruplexDNA, and the strength of the binding with G-quadruplex depends on (i) phenyl ring substitution, (ii) the piperazinyl side chain, and (iii) the type of monovalent cation present in the buffer. Results further suggest that these compounds are able to abet the conversion of the intramolecular G-quadruplex DNA into parallel stranded intermolecular G-quadruplex DNA. Notably, these compounds are also capable of inducing and stabilizing the parallel stranded G-quadruplex DNA from randomly structured DNA in the absence of any stabilizing cation. The kinetics of the structural changes induced by these compounds could be followed by recording the changes in the CD signal as a function of time. Figure 3. Chemical structures of the ligands used in this study. Chapter 5A. The Spacer Segment in the Dimeric 1,3-phenylene-bis (piperazinyl benzimidazole) has a Dramatic Influence on the Binding and Stabilization of Human Telomeric G-Quadruplex DNA Ligand-induced stabilization of G-quadruplex structures formed by human telomeric DNA is an active area of basic and clinical research. The compounds which stabilize the G-quadruplex structures lead to suppression of telomerase activity. Herein, we present the interaction of a series of monomeric and dimeric compounds having 1,3-phenylene-bis(piperazinyl benzimidazole) (Figure 4) as basic pharmacophore unit with G-quadruplex DNA formed by human telomeric repeat d[(G3T2A)3G3]. These new compounds provide an excellent stabilization property to the pre-formed G-quadruplex DNA in the presence of one of three ions (100 mM Li+, Na+ or K+ ions). Also the G-quadruplex DNA formed in the presence of low concentrations of ligands in 100 mM K+, adopts a parallel-stranded conformation which attains an unusual thermal stability. The dimeric ligands having oxyethylene based spacer provide much higher stability to the pre-formed G-quadruplex DNA and the G-quadruplexes formed in presence of the dimeric compounds than the corresponding monomeric counterparts. Consistent with the above observation, the dimeric compounds exert significantly higher telomerase inhibition activity than the monomeric compounds. The ligand induced G-quadruplex DNA complexes were further investigated by computational molecular modeling, which provide useful information on their structure-activity relationship. Figure 4. Chemical structures of the monomeric and dimeric ligands used in this study. Chapter 5B. Role of Spacer in Symmetrical Gemini bisbenzimidazole based Ligands on the Binding and Stabilization of Dimeric G-Quadruplex DNA derived from Human Telomeric Repeats The design and development of anticancer agents that act via stabilization of the telomeric G-quadruplex DNA is an active area of research because of its importance in the negative regulation of telomerase activity. Several classes of G-quadruplex DNA binding ligands have been developed so far, but they mainly act on the DNA sequences which are capable of forming a single Gquadruplex unit. In the present work, we have developed few new dimeric (Gemini) bisbenzimidazole ligands (Figure 5), in which the spacer joining the two bisbenzimidazole units have been varied using oligooxyethylene units of different length. Herein we show the interaction of each of these ligands, with the G-quadruplex DNA, derived from oligodeoxynucleotides d(T2AG3)4 and d(T2AG3)8, which fold into a monomeric and dimeric (having two folded G-tetrad units) G-quadruplex DNA, respectively. We also present evidence that the G-quadruplex DNA structure formed by these sequences in K+ solution in presence of the ligands is parallel, with unusual stability, and the spacer length between the two bisbenzimidazole units has critical role on the G-quadruplex stability, particularly on the G-quadruplex structures formed by the 48-mer sequence. The computational aspects of the ligand-G-quadruplex DNA association have also been analyzed. Interestingly, the gemini ligand having longer spacer was highly potent in the inhibition of telomerase activity than the corresponding gemini ligands having shorter spacer or the monomeric ligand. Also, the dimeric ligands are more cytotoxic toward the cancer cells than normal cells. Figure 5. Chemical structures of the monomeric and gemini ligands used in this study. Chapter 6. Stabilization and Structural Alteration of G-Quadruplex DNA made from Human Telomeric Repeat Mediated by Novel Benzimidazole Derivatives based on Tröger’s Base Ligand-induced stabilization of G-quadruplex formation by the telomeric DNA single stranded 3'-overhang is a nice strategy to inhibit telomerase from catalyzing telomeric DNA synthesis and form capping telomeric ends. Herein we present the first report of the interactions of two novel bisbenzimidazoles (TBBz1 and TBBz2)(Figure 6) based on the Tröger’s base skeleton with the G-quadruplex DNA. These molecules stabilize the G-quadruplex DNA derived from a human telomeric sequence. Significantly strong binding affinity of these molecules to G-quadruplex DNA relative to duplex DNA was observed by CD spectroscopy, thermal denaturation and UV-vis titration studies. The above results obtained are in excellent agreement with the biological activity, measured in vitro using a modified TRAP assay. Additionally exposure of cancer cells to these compounds showed a remarkable decrease in the population growth. Also, it has been observed that the ligands are selectively more cytotoxic toward the cancerous cells than the corresponding noncancerous cells. To understand further, the ligand-G-quadruplex DNA complexes were investigated by computational molecular modeling. This provided additional insights on the structure activity relationship. Computational studies suggest that the adaptive scaffold not only allows these ligands to occupy the G-quartet but also binds with the grooves of the G-quadruplex DNA. Figure 6. Chemical structures of the ligands, TBBz1 and TBBz2 used in this study, (For structural formula pl see the abstact.pdf file.)

Benzannulation to porphyrin 2,3 positions has previously been accomplished using various methodologies in the past century, yet there remain limited methodologies to both annulate to the porphyrin periphery and add functional moieties that can then be derivatized for diverse applications. This dissertation describes the development of synthetic routes and characterization of a variety of linearly-annulated, functionalized, β,β'-π-extended porphyrins. There are five chapters in this dissertation, the first of which introduces synthesis and properties of porphyrins and π-extended porphyrins. Chapter 2 describes synthesis of pentacenequinone-fused and pentacene-fused poprhyrins with distinct and new optical absorbance properties. In chapter 3, synthesis and characterization of benzimidazole-fused porphyrins displaying external metal binding capability is described. The synthetic method developed in chapter 3 is extended in chapter 4 to synthesis of bisbenzimidazole-fused porphyrin dimers that show split Soret character, likely due to excitonic coupling between porphyrins of the dimer. Chapter 5 summarizes this dissertation and describes future directions that this dissertation provides foundation for.

Indiana University-Purdue University Indianapolis (IUPUI) / The DNA minor groove continues to be an important biological target in the development of anticancer, antiviral, and antimicrobial compounds. Among agents that target the minor groove, studies of well-established benzimidazole-based DNA binders such as Hoechst 33258 have made it clear that the benzimidazole-amidine portion of these molecules promotes an efficient, site-selective DNA association. Building on the beneficial attributes of existing benzimidazole-based DNA binding agents, a series of benzimidazole-amino acid conjugates was synthesized to investigate their DNA recognition and binding properties. In this series of compounds, the benzimidazole-amidine moiety was utilized as a core DNA “anchoring” element accompanied by different amino acids to provide structural diversity that may influence DNA binding affinity and site-selectivity. Single amino acid conjugates of benzimidazole-amidines were synthesized, as well as a series of conjugates containing 20 dipeptides with the general structure Xaa-Gly. These conjugates were synthesized through a solid-phase synthetic route building from a resin-bound amino acid (or dipeptide). The synthetic steps involved: (1) the coupling of 4-formylbenzoic acid to the resin-bound amino acid (via diisopropylcarbodiimide and hydroxybenzotriazole); followed by (2) introduction of a 3,4-diaminobenzamidoxime in the presence of 1,4-benzoquinone to construct the benzimidazole ring; and, finally, (3) reduction of the resin-bound amidoxime functionality to an amidine via treatment with 1M SnCl2•2H2O in DMF before cleavage of final product from the resin. The synthetic route developed and employed was simple and straightforward except for the final reduction that proved to be very arduous. All target compounds were obtained in good yield (based upon weight), averaging 73% mono-amino acid and 78% di-amino acid final compound upon cleavage from resin. Ultimately, the DNA binding activities of the amino acid-benzimidazole-amidine conjugates were analyzed using a fluorescent intercalator displacement (FID) assay and calf thymus DNA as a substrate. The relative DNA binding affinities of both the mono- and di-amino acid-benzimidazole-amidine conjugates were generally weaker than that of netropsin and distamycin with the dipeptide conjugates showing stronger binding affinities than the mono-amino acid conjugates. The dipeptide conjugates containing amino acids with positively charged side chains, Lys-Gly-BI-(+) and Arg-Gly-BI-(+), showed the strongest DNA binding affinities amongst all our synthesized conjugates.