Theoretical Studies Of The Preferred Conformation Of Cyclopeptide

Cyclopeptides that are a kind of biological molecules with cyclic conformations widely exist in nature. Many of them are provided with distinct bioactivities that play a vital role in the course of life. Cyclic dipeptides are the simplest members in the most common cyclic peptide family found in nature. Cyclic dipeptides have high stability because their structures take on the dioxopiperazine framework. Because of special spatial configurations, cyclic peptides have shown broad potentials in many areas including chemistry, pharmaceutical chemistry, biochemistry, and life sciences.The goal of this dissertation was five-fold: (1) Chapter 1 is the overview of this dissertation including the introduction about concepts of cyclopeptide, biological meaning, synthetical methods, ionophores and cyclopeptide nanotube of research development at present. (2) To search the preferred conformation of cyclic dipeptides by quantum chemistry method. 100 cyclic dipeptides were studied using Gaussian 03 program. (3) To identify the reaction mechanism of cyclization of dipeptide, the transition states were researched and confirmed by IRC method. (4) To probe cyclopeptides that can coordinate to metal ion in a way that mimics the coordination sites in enzymes conformation, 34 cyclopeptide ionophores were calculated in detail. (5) To explore the conformation information of cyclic peptide nanotubes, two nanotubes were primarily studied through two methods.The preferred conformations of cyclic dipeptides were first systemically studied using the density functional theory B3LYP method at 6-31G(d) level. The structural characteristics of cyclic dipeptides were revealed, most of which have not been confirmed until now. Our studies showed that the six-member main circles of cyclic dipeptides which were composed of natural L- amino acid residues appeared as boat conformations. The important factors that influence conformations of cyclic dipeptides, such as molecular total energy, nuclear repulsion energy, molecular orbit, spatial effects, and reactive mechanism, were discussed in detail.The ring-closure reactions of nine dipeptides were investigated at HF/6-31 G(d) level using Gaussian 03 program. Vibration analysis had been carried out to confirm their identities as transition states. The intrinsic reaction coordinate (IRC) method had been...