In this study, the templating role of bimolecular triple hydrogen bonded honeycomb network consisting perylene-3,4,9,10-tetracarboxydi-imide and melamine is investigated, using scanning tunneling microscopy. Although the stability of the network upon modification is a major obstacle toward higher complexity, three different approaches in this work highlight formation of successful architectures in a sequential way. 1. Insertion of pore modifier star shaped molecules based on tri(phenylene ethynylene)benzene core in the pores to construct a new template. 2. Insertion of iodinated molecules in the pores to study the network as a nanoreactor. 3. Electrochemical deposition of metals in the pores. Self-assembly monolayer of four different molecules based on tri(phenylene ethynylene)benzene core on uniform gold surface revealed different structures. The degree of the order within the structures depends highly on the symmetry of the molecules, and hence asymmetric molecule formed disordered structure. Upon insertion into the pores of the network, one of molecules did not match the pores size, while others fitted and illustrated rotation depending on the strength of their interaction with the network components and the substrate. The rotation is significantly reduced by modifying the molecules. These new architectures are used as templets hosting C₆₀ molecules which resulted in isolated single C₆₀ molecules. Self-assembly of iodinated molecule under different conditions on uniform gold surface leads to formation of different structures including monomers and dimers. Upon thermal treatment on the uniform surface oligomers are formed, whereas for the molecules confined in the pores of the network, the covalent bond formation was limited to dimerisation. Electrochemical copper deposition into the pores of the network under acidic condition (pH = 1 - 2) is not possible because of the stability of the network. However, by increasing pH of the electrolyte (pH = 5 – 7), a bilayer of Cu and anion is formed in the pores of the network, confirmed by scanning tunneling microscopy and X-ray photoelectron spectroscopy.

MSc (Chemistry) / Department of Chemistry / The computational study of biologically active molecules is particularly important for drug development because it provides crucial information about the properties of a molecule, which determine its biological activities. The current work considers the results of a computational study of myristinin A and a structurally-related molecule (2-(4-hydroxyphenyl)-4-[2,4,6-trihydroxy-3-(9tetradecenoyl)phenyl]-3,4-dihydro-2H-benzopyran-7-ol, here denoted as DBPO). The two compounds pertain to the class of acylphloroglucinols. They were firstly isolated from Horsfieldia amygdaline, and they exhibit a variety of biological activities, including potent anti-inflammatory activity, potent DNA-damaging activity and DNA-polymerase ß inhibition. Their molecular structures differ only by the acyl chain. Both molecules have a bulky substituent meta to the acyl group consisting of a ring system (2-(4-hydroxyphenyl)-3,4-dihydro-2H-chromen-7-ol). The DBPO molecule can exist as cis and trans isomers in relation to the double bond present in the R chain, and both isomers are here investigated individually. The OHs ortho to the acyl group can form an intramolecular hydrogen bond (referred to as the first IHB) with the sp2 O atom of the acyl group. The phenol OHs neighbouring the substituent ring system can form O–Hπ interaction with the aromatic rings of the substituent, if suitable oriented. This study focuses on the identification of the stable conformers of these molecules (considering all the possible geometries obtainable by rotations about relevant single bonds), and of the factors stabilising the conformers. Full-optimisation calculations were performed in vacuo and also in three conveniently selected solvents. The results show that the dominant stabilising factors are the first IHB and the O–Hπ interactions. Other factors which have significant influence on conformational preferences are the orientation of the ring systems of the substituent, the orientation of the OHs on substituent, the mutual orientation of the OHs of the phloroglucinol moiety and also the orientation of the acyl chain. The results in solution are consistent with the findings of other acylphloroglucinols, for instance, the narrowing of the energy gaps and the increase of the dipole moment with the increase of solvent polarity. / NRF

We report here the development of very efficient sulfonate based leaving groups, termed Nucleophile Assisting Leaving Groups (NALGs), to accelerate the rate of nucleophilic substitution reactions involving poor nucleophiles and/or substrates traditionally considered too hindered to undergo nucleophilic attack. Indeed NALGs have shown exceptional ability in improving rate of nucleophilic substitution reactions. New very mild stereoretentive halogenations and azidation reactions have also been developed for secondary cyclic alcohols using NALGs involving titanium(IV) reagents. This reaction is particularly significant since the carbon-halogen bond is found widely in natural products and is used extensively as a synthesis intermediate. Azide is also a synthetically important functional group from which a variety of biologically important functional groups are conveniently obtained. Though stereoretentive chlorination and bromination reactions are known, we have developed, for the first time, a stereoretentive azidation reaction using titanium(IV) azide, a reagent not previously used in organic synthesis. During our development of stereoretentive reactions, we eventually developed very efficient, mild, two-step one-pot stereoretentive halogenations (chlorination and bromination) using titanium(IV) halides as catalysts or stoichiometric reagents. These reactions were found to be particularly efficient for cyclic alcohols. An efficient one pot stereoretentive amidation reaction for secondary cyclic alcohols is also reported. The important features of this reaction are that, for the first time, chlorosulfite (prepared in situ from alcohol using thionylchloride) has been used as a leaving group and titanium(IV) fluoride as an activator. / Utilization of those two reagents is unique as thionylchloride has never been used for nucleophilic substitution reactions except in chlorination procedures. In addition, this work has found new and creative applications for titanium (IV) fluoride, a reactant rarely used in organic synthesis. Further exploiting the unique reactivity of titanium(IV), reactions of alkenes with various nucleophiles have been developed with this reagent in both catalytic and stoichiometric quantities. It was observed that a-substituted aromatic conjugated alkenes dimerize to generate important indan class of compounds which are very important in the polymer industry. In addition, non conjugated unactivated alkenes react with various nucleophiles to yield the adduct. / by Deboprosad Mondal. / Thesis (Ph.D.)--Florida Atlantic University, 2010. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2010. Mode of access: World Wide Web.

Advantages such as chemical, mechanical and thermal stability together with high selectivity for the templated analyte render molecularly imprinted polymers MIPs interesting alternatives to routinely applied separation materials or antibodies. Nevertheless, many factors such as the choice of functional monomer, cross-linker, and porogenic solvent, as well as the ratio between template, functional monomer, and cross-linker will affect the resulting imprinting efficiency and polymer particle size and morphology. The research described in this thesis contributes to the development of new synthetic strategies for the generation of imprinted micro- and nanospheres for 17beta-estradiol (E2) focusing on accurate control and optimization of the governing parameters for precipitation polymerization, including the polymerization temperature and the cross-linker, yielding a one-step synthetic approach with superior control on the bead diameter, shape, monodispersity and imprinting efficiency. Thus synthesized imprinting materials for E2 were successfully applied in HPLC separation, solid phase extraction and radioligand binding assays. As the optimization of imprinted materials is based on fundamental understanding of the binding site properties, the investigations is aimed at establishing a more rational basis for further tailoring imprinted materials to the desired analytical application. The relationships between the particle porosity and rebinding properties were detailed, providing useful guidelines for controlling the particle properties for the desired application including, SPE pre-concentration, HPLC separations, and biomimetic binding assays. Furthermore, analytical techniques (1H-NMR and IR, etc.) and molecular modeling were combined in this thesis to facilitate advanced understanding of the fundamental principles governing selective recognition of molecularly imprinted polymers at a molecular level. The molecular interactions involved in the templating process of molecularly imprinted polymers based on the self-assembly approach were simulated in molecular dynamic simulation model by building a modeling system include all the imprinting components with correct ratio, which has never been reported before. Molecular level interactions such as hydrogen bonding, π-π stacking interactions as well as the free energy governing complex formation of E2 with the functional monomers 4-vinylpyridine (4VP) and methacrylic acid (MAA), and the cross-linker divinylbenzene (DVB) were discussed.