Computational studies of five macromolecular systems

Abstract

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] C-alkylpyrogallol[4]arenes have been studied by DFT computations and the results compared to experimental observations. Local minima of different conformers were located by geometry optimization of the trial structures using the B3LYP method and the 6-31G(d,p) basis set. The electronic structure calculations were carried out to examine the role of the R-group and solvent on the preferred conformations and configurations of the macrocycles. To evaluate the effect of solvent on these properties, free energies of solvation were calculated using the SMD-PCM, IEF-PCM, and CPCM-PCM methods. Although the trends in the relative energies of the stereoisomers differ for the three methods, all three predict the same most stable structure for a given R-group. Modification of resorcin[4]arenes and pyrogallol[4]arenes with the use of mixed (3 pyrogallols:1 resorcinol) macrocycles has been investigated to understand possible new chemical properties of the designed system. The lack of one hydroxyl group affects the intramolecular interactions and could change the properties of the system. Electronic structure calculations were employed to examine the relative stabilities of the stereoisomers of the macrocycle. In addition, the effect of the R-group and solvent on the properties of the macrocycle was considered. To comprehend the reactivity of the zinc-seamed pyrogallol[3]resorcin[1]arene dimeric mixed nanocapsule (3 pyrogallols, 1 resorcinol), the proton affinity of different sites was evaluated by DFT calculations using the PBE1PBE/LANL2DZ method. The most favored atoms for protonation were examined. The effect of introducing defects into the zinc-seamed pyrogallol[4]arene dimeric nanocapsule on characteristic electronic and chemical properties of the mixed capsule has been studied. Pyrogallol[4]arenes and resorcinol[4]arenes were chosen to assess their effectiveness for ion recognition and selectivity. Different approaches toward ion extractions by the macrocycles were considered. Metal binding of the cone structure of pyrogallol[4]arenes with linker groups R=H, Me, Et, Ph was evaluated by DFT calculations to investigate the effect of substituents on the binding energy of the metal ions Li+, Na+, K+, Be2+, Mg2+, Ca2+ with the macrocycle. The same calculations were done with the chair structure of Cmethyl pyragallol[4]arene and the cone structure of C-methyl resorcinol[4]arene. A comparison of the extractability of compounds having different cavity sizes and carrying different functional groups at the arenes is discussed. Finally, possible activation methods for the leaving groups of S-benzimidazolyl glycosides and glycosyl alkoxythioimidates were examined. The effect of changing the substituent on the leaving group of the glycosyl donor on its electronic properties and structure was also investigated. The nucleophilicity difference between the heteroatoms towards promotors was calculated by DFT calculations. Possible mechanisms for activation were considered for different promoters to understand oligosaccharide assembly.