We have designed and synthesized a fluorescent, self-assembled molecular square containing a highly fluorescent well known flurophore boradiazaindacene (BODIPY) dye. Pt(II) complexes were used to hold together BODIPY derivatives and give the right angle to form the square structure. Usage of BODIPY fluorophore is very important on such structures because its variety of superior properties. BODIPY is a well studied fluorophore in our group and it is known that this self assembled square can be easily modified to any area of use it is needed.

ABSTRACT TOWARDS PRACTICAL APPLICATIONS FOR MOLECULAR LOGIC GATES: &ldquo / AND&rdquo / LOGIC AS AN ADDITIONAL LAYER OF SELECTIVITY IN SINGLET OXYGEN RELEASE FOR PHOTODYNAMIC THERAPY &Ouml / zlem, Suriye M.S., Department of Chemistry Supervisor: Prof. Dr. Engin Umut Akkaya June 2008, 54 pages There have been many examples of individual molecular logic gates and molecular equivalents of more complex digital designs in recent years such as half adder, half subtractor, multiplexer. Neverethless, the unresolved issues of addressability and lack of communication between logic gates remain to be the Achille&rsquo / s heel for molecular logic gates. A few years ago we have demonstrated that appropriately decorated bodipy dyes can be very efficient generators for singlet oxygen, thus act as a satisfactory photodynamic agents. As a bonus, these dyes absorb very strongly at 660 nm which is considered to be within the therapeutic window of mammalian tissue. So, combining our earlier experience in molecular logic gates and rational design of photodynamic agents, we proposed a photodynamic therapy agent that would release singlet oxygen at a much larger rate when the cancer related cellular parameters are above a threshold value at the same location. Following the survey of the relevant literature for cancer related parameters, we decided that sodium ion concentration and pH (H+ concentration) could be very promising targets. In the tumor regions the pH can drop below 6 and the Na+ concentration is also significantly higher then normal tissues. As a result, in the proposed logic system the chemical inputs could be Na+ and H+. The system in fact is an automaton which is to seek higher concentration of both hydrogen and sodium ions, and release the toxic agent (singlet oxygen) only when both concentrations are high. Thus, the proposed logic gate is an AND logic gate, the output of which is singlet oxygen. Keywords: Photodynamic therapy, singlet oxygen, molecular logic gates, AND logic operation

Supramolecular chemistry is an emerging field of chemistry which has attracted much attention in recent years as a result of its broad applicability in many areas. Thus, the design of functional supramolecular systems is strongly in demand in this field. For this purpose, we have developed near-IR emitting ratiometric fluorescent chemosensors for transition metal ions. Judicious placement of dithiodioxaazamacrocycles on the BODIPY chromophore generates this chemosensor which is selective for Hg(II) ions and both absorption and emission spectra display large changes that would allow ratiometric sensing.

2-Aminopyrrole-3-carboxylate derivatives are important starting materials for biologically active compounds like pyrrolotriazole, pyrrolotriazine so their synthese has great importance in the synthetic organic chemistry. There are only two methods for the synthesis of 2-aminopyrrole-3-carboxylates in the literature. Therefore, there is a great need for the design and development of a new method for the synthesis of 2-aminopyrrole-3-carboxylates. In this work, 2-aminopyrrole-3-carboxylate derivatives were synthesized starting from cyano acetic acid ethyl ester with a new method. In the first step, cyanoacetic acid ethyl ester was alkylated with bromo acetone in the presence of NaH. Then, obtained gamma-ketoester was reacted with primary amines in the presence of catalytic amount of zincpechlorate (Zn(ClO4)2). As a result, 2-aminopyrrole-3-carboxylate derivatives were obtained. Cyanoacetic acid ethyl ester was also alkylated with various bromo acetophenone derivatives in the presence of DBU (1,8-Diazabicycloundec-7-ene). As a result of these reactions, different gamma-ketoesters were obtained. The reaction of these gamma-ketoesters with primary amines in the presence of catalytic amount of Zn(ClO4)2 concluded with 2-aminopyrrole-3-carboxylate derivatives.

Pyrazoles have been studied for over a century as an important class of heterocyclic compounds and continue to attract considerable interest due to the broad range of biological activities they possess. The electrophilic cyclization of the acetylenic hydrazones initiated by molecular iodine could provide new ways of synthesizing biologically active 4-iodopyrazole derivatives, which are important precursors for the synthesis of highly substituted pyrazole derivatives. For this reason, we investigated the synthesis of 4-iodopyrazole derivatives, such as 1-aryl- 5-alkyl/aryl-4-iodopyrazoles, starting from phenylhydrazine and ,-acetylenic aldehyde derivatives. Initially, ,-acetylenic aldehydes were synthesized by formylation reaction of corresponding alkynes with DMF. Then, hydrazone derivatives of these aldehydes were prepared by heating them with phenylhydrazine in a neat manner at 55 &deg / C for 5 h. Finally, acetylenic phenyl hydrazone derivatives were subjected to electrophilic cyclization by treating with excess molecular iodine at 80 &deg / C for 3 h. Although electrophilic cyclization is commonly used in organic chemistry, it has not been employed for the cyclization of acetylenic phenyl hydrazones to pyrazole derivatives. Under optimized conditions, these reactions afforded 1-aryl-5-alkyl/aryl-4-iodopyrazole derivatives in moderate to good yields as the single or the major product of the reactions. In some cases, 1-aryl-5-alkyl/arylpyrazole derivatives resulted from these reactions as minor products. In conclusion, 4-iodopyrazole derivatives were synthesized for the first time directly from acyclic starting materials, ,-acetylenic phenylhydrazones and iodine, via electrophilic cyclization.

Rational design of fluorescent chemosensors is an active area of supramolecular chemistry, photochemistry and photophysics. Ratiometric chemosensors are even more important, as they have an internal system for selfcalibration. In order to develop a new methodology for a ratiometric chemosensor design, we proposed coupling of energy transfer phenomenon to ion sensing. In this study, we targeted energy transfer cassette type chemosensors, where the efficiency of transfer is modulated on the donor side, by metal ion binding which changes the spectral overlap. This work involves the synthesis of a number of EET systems with varying degrees of EET efficiency. The results suggest that this strategy for ratiometric ion sensing is a promising one, enabling a modular approach in chemosensor design.

Supramolecular chemistry is an emerging field of chemistry which has attracted much attention in recent years as a result of its broad applicability in many areas. Thus, the design of functional supramolecular systems is strongly in demand in this field. For this purpose, we have developed novel phenylethynyl-BODIPY oligomer series which have absorption and emission maxima at the red part of the visible region of electromagnetic spectrum. Careful design to assemble the decyl groups to the system allowed us to dissolve the molecules in organic solvents easily. That`s why, not only we could characterize the molecules, but also spectroscopic and photopysical properties of them were investigated. As expected, as the number of repeating units &ldquo / n&rdquo / increase, peak absorption and emission wavelengths are shifted to the red end of the visible spectrum, with smaller increments as &ldquo / n&rdquo / increases. Consequently, these rigid rod like overall arrangement of oligomers could lead to applications as functional building blocks.

We have designed and synthesized boradiazaindacene (BODIPY) derivatives, appropriately functionalized for metal ion mediated supramolecular polymerization. Thus, ligands for 2- and 2,6-terpyridyl and bipyridyl functionalized BODIPY dyes were synthesized through Sonogashira couplings. These new fluorescent building blocks are responsive to metal ions in a stoichiometry dependent manner. Octahedral coordinating metal ions such as Zn(II), result in polymerization at a stoichiometry which corresponds to two terpyridyl ligands to one Zn(II) ion. However, at increased metal ion concentrations, the dynamic equilibria are re-established in such a way that, monomeric metal complex dominates. The position of equilibria can easily be monitored by 1H NMR and fluorescence spectroscopy. As expected, open shell Fe(II) ions while forming similar complex structures, quench the fluorescence emission of all four functionalized BODIPY ligands.

ABSTRACT ADDITION OF CARBONYL COMPOUNDS TO THE CYCLIC OLEFINS: SYNTHESIS OF CYCLITOLS Altun, Yasemin M.S., Department of Chemistry Supervisor: Prof. Dr. Metin Balci October 2008, 160 pages Cyclitols have attracted a great deal of attention in recent years owing to biological activities exhibited by them and also their usefulness in the synthesis of other natural products and pharmaceuticals. Carbasugars are also a derivative of cyclitols and they are cyclic monosaccharide analogues which posses &amp / #8211 / CH2OH group in their structure. In this study, novel synthetic strategies leading to cyclitol derivatives were investigated and the synthesis of tetraol (72) and pentaol (73) derivatives containing &amp / #8211 / CH2OH group were achieved successfully. Moreover, by the use of manganese(III) acetate oxidation reactions having considerable synthetic utilities in organic chemistry we developed new synthetic methodologies for the cyclitol derivatives. 1,3- and 1,4-Cyclohexadiene (71 and 10) were synthesized from easily available starting materials in order to be used as key compounds. The use of manganese(III) acetate oxidation reaction provides the creation of &amp / #8211 / CH2OH group and one of the hydroxyl groups and the remaining hydroxyl groups were introduced into the key compounds by the use of singlet oxygen reaction. As a result of this, we had considerable advance in the synthesis of cyclitol derivatives.

Imatinib mesylate is indicated for the treatment of chronic myeloid leukemia (CML) and unresectable and/or metastatic malignant gastrointestinal stromal tumors (GIST). By the application of this anticancer drug, problems occurs in terms of stability and activity. Computer assisted design (CAD) works showed that the modification of the B and C part molecule can increase the effectivity of the drug. The new derivatives of the drug will be obtained to change some part of the B and C segments. The total synthesis of a new imatinib mesylate will be done and the activity tests are going to be determined in collaboration with other groups.