Theoretical Investigation Of [2]Rotaxanes By Using Quantum Chemistry Calculations And Molecular Dynamics Simulations

With the rapid development in nanotechno logy, the size of macroscopic machines will be reduced to the nanoscale. The last decade has witnessed rapid advances in fabrication of various nanomachines and molecular devices. Among them, the interlocked rotaxanes have received considerable attention due to their potential applications in the creation of artificial molecular machines and functional assemblies. In this thesis, we focus on [2]rotaxane composed of macrocyclic compound (macrocycle) and an axle-shaped molecule (thread). Conformation changes for pseudorotaxanes and [2]rotaxanes are investigated by using quantum chemical, molecular mechanic and molecular dynamic methods, respectively. The computer image processing technology and data mining algorithm have also been employed to study the recognition interaction between the two components (macrocycle and thread) of the interlocked system. Our results will provide the useful information for the molecular design, synthesis and construction of interesting molecular interlocked architectures in the future.Our results are summarized as follows:1. Theoretical design of [2] rotaxanes and evaluation of binding strengthIt is still a challenge in experiment to synthesize controllable rotaxane-based molecular devices. The binding energies of dozens of new [2]rotaxanes are calculated. The factors, such as geometry and electronic structures on the macrocyle-thread binding strength are systematically studied. The binding strength is associated with the size of macrocyle and thread, H-bonding interactions, π-π stacking, etc. The orthogonality of site-specific binding interactions provides a clue to design novel [2]rotaxanes with some different functions. Furthermore, with the aid of computer image processing technology, a graph threshold segment method is developed to estimate the ability of proton donation and accepatance involved in ring-rod recognition and subsequently evalute the binding strength for [2]rotaxanes. The predicted relative binding strengths of [2]rotaxanes are in good agreement with the experimental association constants and DFT-calculated binding energies. The size and electrostatic compatibility criteria are introduced to guide the rational design of [2]rotaxane. Based on the fragment library consisting of eight rings and fifteen rods, 59 thermodynamically stable [2]rotaxane candidates have been generated. Our ESP-base image segmentation model is generic in the field of constructing other supramolecular architectures formed with donor/acceptor molecular recognition. 2. Simulations of conformational changes of [2]rotaxane in different enviromentsA series of molecular dynamics (MD) simulations based on ab initio models and force fields are preformed to investigate the conformational changes in vacuum, solution, supercritical CO2. The influence of shuttling dynamics, and the influence of different ensembles, solvents, and crystal packing on the NMR signals of pseudorotaxane and [2]rotaxane have been studied. In contrast with the highly distorted thread conformation in vacuum and nonpolar CDC13 solution, the solvated thread of [2]rotaxane in mix CD3CN-CDCl3 solvents exhibits a relatively rigid structure. The conformation of [2]rotaxane has a remarkable flexibility in supercritical CO2. The H-bonding network between macrocycle and thread stabilizes the pseudorotaxne and [2]rotaxane. The polarization effect is not negligible to account for the H-bonding interaction for supramolecular systems. The magnitude of the shift of MD ensemble-averaged 1HN NMR signals is correlated with the number of H-bonds. The solvent effect is more obvious on the conformations and NMR signals of flexible [2]rotaxane than rigid pseudorotaxane. We also adopted the principle component analysis, which uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables, to analysis H-bonding interactions between macrocyle and thread. In addition, the significant bulk effect is revealed by remarkable difference in the calculated chemical shifts due to the crystal π-π stacking.3. Simulation of cis-trans isomerization processes of azobenzeneThe reversible light-driven cis-trans isomerization of azobenzene enables its application to the fabrication of various molecular switch and stimuli-responsive functional materials. Traditional force field-based molecular dynamics simulation cannot to be used to describe the dynamical switching process of azobenzene. The reactive MD simulations is applied to study the cis-trans isomerization process of azobenzene-based [2]rotaxane. The cis-based [2]rotaxane is more stable than the trans-based [2]rotaxane. The threading and dethreading has little impact on the geometry of azobenzene, but the macrocyle experiences a conformational change.To summarized, the systematic investigation of the conformation changes of [2]rotaxane in different chemical environments and external stimuli have been carried out. The knowledge of the nature of recognition and conformation dynamics may guide the rational design of novel [2]rotaxanes in experiment.