Abstract This study was part of a project targeted at developing chemical sensors for organic cations and metal ions by exploiting the interactions between cations and anionic borate derivatives. As well, the chemical synthesis of thiophene monomers with charged or neutral ion-recognition sites was investigated. The primary task in the first part of the work was to prepare anionic receptor molecules based on synthesized borate derivatives and study their complexation with N-heteroaromatic and tropylium cations. The complexation was studied in solution by 1H NMR and ESIMS techniques and in solid state by X-ray crystallography. Crystal structures showed evidence of weak noncovalent interactions–hydrogen bonding, cation···π interactions, and π-stacking. In addition, the crystal structure of the alkali metal complex of tris[3-(2-pyridyl)pyrazolyl]hydroborate was determined. Stability constants of borate complexes were measured by 1H NMR titration in methanol/acetonitrile (1:1) solution at 30 °C. Various derivatives of aromatic borate anions synthesized within this project, some commercially available derivatives, and two neutral carriers containing aromatic anthryl groups were also studied as recognition sites for aromatic cations where N-methylpyridinium was used as primary ion in PVC membrane-based all-solid-state ion sensors. The results showed that borate derivatives offer new possibilities for molecular recognition by ion-selective electrodes (ISEs). The aim of the second part of the study was to develop chemical ion sensor materials where the ion-recognition unit and the charge-compensating ion are covalently coupled to the backbone of a conductive polymer. Sulfonated thiophenes were used as doping ions for the fabrication of Ag+-ISEs. More than 15 differently substituted monomers were synthesized. The materials differed with respect to the receptor unit, extent of oxidation, counteranion, and length of the chain.

No description available.

Chirality is a key principle in organic chemistry. All chiral compounds are non-superimposable mirror images of each other and therefore lack an improper axis of rotation (Sn). These mirror images often have identical properties in an achiral environment, however when two chiral molecules interact, they produce different shapes and properties. Nature, to this extent takes advantage of this aspect through unique formation of shape defined biological macromolecules that are tailored to carry out various life processes. This level of shape control is only made possible because of natural chiral monomers such as amino acids or glycosides that make up such macromolecules. Under new methods such as Chirality Assisted Synthesis (CAS), shape and size-controlled polymers and macromolecules can be realized through the use of chiral monomers to make well defined macromolecules. Because chirality dictates shape, and shape defines function in reference to macromolecules, controlling the chirality of monomers, while concurrently dictating shape and size can lead to the potential of biomimetic methodologies and cage like structures. Accessing shape defined monomers can be difficult especially when in reference to chiral compounds. The unique structure of enantiopure tribenzotriquinacenes show promise in the formation of well-defined cage like structures through utilization of CAS methodology. Synthesis of functionalized tribenzotriquinacenes along with development of an enantioselective electrophilic aromatic nitration method was attempted. Further exploration into the effectiveness of through-space enantioselective nitrations found a dependence on solvent temperature, and the auxiliary that is used. Synthetic difficulties, results, modifications and processes toward a generalized method are presented herein. In addition, controlling the size of polymers has always been a difficult synthetic challenge. Overall selectivity toward one product over another is determined via a variety of chemical properties. However, the formation of sequence and size defined polymers are a prominent aspect of natural polymers. The size selective synthesis, of unique ABAB sequenced polymers was attempted using an iterative exponential growth method. The ability to scale up these processes and create monodisperse oligoethers is also presented and described herein.

Noncovalent interactions play a vital role throughout much of chemistry. The understanding and characterization of these interactions is an area where theoretical chemistry can provide unique insight. While many methods have been developed to study noncovalent interactions, symmetry-adapted perturbation theory (SAPT) stands out as one of the most robust. In addition to providing energetic information about an interaction, it provides insight into the underlying physics of the interaction by decomposing the energy into electrostatics, exchange, induction and dispersion. Therefore, SAPT is capable of not only answering questions about how strongly a complex is bound, but also why it is bound. This proves to be an invaluable tool for the understanding of noncovalent interactions in complex systems. The wavefunction-based formulation of SAPT can provide qualitative results for large systems as well as quantitative results for smaller systems. In order to extend the applicability of this method, approximations to the two-electron integrals must be introduced. At low-order, the introduction of density fitting approximations allows SAPT computations to be performed on systems with up to 220 atoms and 2850 basis functions. Higher-orders of SAPT, which boasts accuracy rivaling the best theoretical methods, can be applied to systems with over 40 atoms. Higher-order SAPT also benefits from approximations that attempt to truncate unneccesary unoccupied orbitals.

Density-functional theory has become an indispensible tool for studying matter on the atomic level, being routinely applied across diverse disciplines from solid-state physics to chemistry and molecular biology. Its failure to account for dispersion interactions has spurred intensive research over the past decade. In this thesis, a semilocal density-functional approximation including dispersion is developed by combining standard functionals for exchange and correlation with the nonempirical “exchange-hole dipole moment“ (XDM) dispersion model of Becke and Johnson. With a minimum of empiricism, the method accurately describes all types of noncovalent interactions, from the extremely weak dispersion forces in rare-gas systems to the hydrogen bonding and stacking interactions responsible for the structure and function of biological macromolecules such as DNA and proteins. The method is compatible with a wide variety of standard Gaussian basis sets, and is easily applied to any system that can be modeled with density-functional theory.

PEGylation has been used for decades to enhance the pharmacokinetic properties of protein therapeutics. This method has been effective at increasing the serum half-life of these drugs, but the mechanism of how it does this is unclear. Chapter 1 is an introduction to the methods of PEGylation. In chapter 2 we show that the effect of PEGylation on the conformational stability of the WW domain differs based on amino acid linker and conjugation site. We show that all positions in the WW domain that were tested can be stabilized by at least one amino acid linker. The rate of proteolysis is proportional to the degree of conformational stability. Chapter 3 shows that PEG-based desolvation can increase the strength of the interaction between two salt bridge residues, though the effect of structural context is unclear. A crystal structure shows that PEG occupies the space between the PEGylation site and the salt bridge, displacing water. In Chapter 4 we discuss the effect that PEGylation has on the interaction strength of a solvent exposed hydrophobic patch. When the c Log P of the hydrophobic patch increases, PEG increases the conformational stability of the WW domain more dramatically. Chapter 5 is about the effect of PEG based desolvation on the strength of an NH-π hydrogen bond in the WW domain between Trp11 and Asn26. When Trp11 is mutated to Phe, Tyr and naphthylalanine (Nal), the melting temperatures correlate with the calculated interaction energies between the sidechain arene of the hydrogen bond acceptor and formamide. When Asn26 is PEGylated in the presence of each of these amino acids, the effect that PEG has on the conformational stability of the WW domain correlates with the melting temperature of the nonPEGylated variants, the calculated interaction energies, the arene molecular polarizability, and the arene molar volume.

Thesis (MSc (Chemistry and Polymer Science))--University of Stellenbosch, 2009. / Please refer to full text for abstract. Abstract contains special characters.

Computational chemists are concerned about two aspects when choosing between the myriad of theoretical methodologies: the accuracy (the "truth") and the computational cost (the tractability). Among the least expensive methods are the Hartree-Fock (HF), density functional theory (DFT), and second-order Moller-Plesset perturbation theory (MP2) methods. While each of these methods yield excellent results in many cases, the inadequate inclusion of certain types of electron correlation (either high-orders or nondynamical) can produce erroneous results. The compromise for the computation of noncovalent interactions often comes from empirically scaling DFT and/or MP2 methods to fit benchmark data sets. The DFT method with an empirically fit dispersion term (DFT-D) often yields semi-quantitative results. The spin-component scaled MP2 (SCS-MP2) method parameterizes the same- and opposite-spin correlation energies and often yields less than 20% error for prototype noncovalent systems compared to chemically accurate CCSD(T) results. There is no simple fix for cases with a large degree of nondynamical correlation (such as transition metal-salen complexes). While testing standard and new DFT functionals on the spin-state energy gaps of transition metal-salen complexes, no DFT method produced reliable results compared to very robust CASPT3 results. Therefore each metal-salen complex must be evaluated on a case-by-case basis to determine which methods are the most reliable. Utilizing a combination of DFT-D and SCS-MP2 methods, the reaction mechanism for the addition of cyanide to unsaturated imides catalyzed by the Al(Cl)-salen complex was performed. Various experimental observations are rationalized through this mechanism.

Noncovalent interactions in complex chemical systems are examined by considering model systems which capture the essential physics of the interactions and applying correlated electronic structure techniques to these systems. Noncovalent interactions are critical to understanding a host of energetic and structural properties in complex chemical systems, from base pair stacking in DNA to protein folding in organic solids. Complex chemical and biophysical systems, such as enzymes and proteins, are too large to be studied using computational techniques rigorous enough to capture the subtleties of noncovalent interactions. Thus, the larger chemical system must be truncated to a smaller model system to which rigorous methods can be applied in order to capture the essential physics of the interaction. Computational methodologies which can account for high levels of electron correlation, such as second-order perturbation theory and coupled-cluster theory, must be used. These computational techniques will be used to study several types (pi stacking, S/pi, and C-H/pi) of noncovalent interactions in two chemical contexts: biophysical systems and organic solids.

The theoretical part of the Master´s thesis describes ab initio methods in quantum chemistry and semiempirical methods, which represents a way in overcoming of main disadvantages in ab initio methods (costs, speed). The experimental part was focused on comparison highly accurate CCSD(T) method with used semiempirical methods (AM1, PM3, PM6, and PM7). The data were mostly compared on small model systems with ions, which are an essential part of many biological systems. Furthermore, the applicability of semiempirical methods was examined for the description of intra- and intermolecular hydrogen bonds and van der Waals interactions.