Computation And Simulation Of Controlled Supramolecular Self-assembly

Understanding of the controlled assembly and disassembly at the molecular levelhas become a very important and challenging subject in the filed of physical chemistry,materials science, nanoscience, biological science, and so on. In this dissertation, weinvestigate the microscopic mechanism of controlled assembly and disassembly basedon the physical and chemical properties of targeting systems, utilizing multiscaleapproach combining quantum chemistry, all-atom molecular dynamics, coarse-grainedmolecular dynamics and non-equilibrium molecular dynamics, to better understand thekey role of non-covalent interactions in controlled assembly and disassembly process,and to explain and predict the experimental phenomenon.First, the halide-binding properties of heteroatom-bridged heteroaromaticcalixarene are investigated based on new developed DFT by quantum chemistrymethods. The calculated Gibbs free energies display similar trends as the experimentalobservations. It has been shown that different types of non-covalent interactionsincluding H-bond, anion-π, and lone-pair-π interactions are concurrent, leading to acooperative effect. The respective contributions of the interactions to overall stabilityare evaluated by using appropriate reference systems. In addition, in the presence of awater molecule, the complexes stability enhanced greatly. Investigations of the solventeffect by continuum solvent model show that the weak halide binding energies insolution offer potential applications for anion transport in the membrane environment.Then, we study a model system that undergoes photocontrolled assembly anddisassembly utilizing the supramolecular assembly between a photoswitchableazobenzene-containing surfactant, AzoC10, and α-cyclodextrin (α-CD). To clarify therole of azobenzene photoisomerization in the reversible assembly and disassembly, weperform atomistic molecular dynamics simulaitons of the host-guest complexationbetween AzoC10and α-CD in aqueous solution, and reveals the key role of noncovalentinteractions and photoisomerization in supramoleclar assembly and disassembly. On topof that, we carry out coarse-grained molecular dynamics simulations of extendedassembly and disassembly of monomers on larger time and length scales. Thespontaneous assembly of cis-AzoC10, trans-AzoC10, and cis-AzoC10/α-CD into micelle-like aggregates, and the disassembly of a pre-assembled micelle based ontrans-AzoC10/α-CD were directly simulated. Our results of simulation revealed asignificant size and shape dependence of aggregates on molecular structure andconcentrations of monomers. As demonstrated, with careful design, coarse-grainedmolecular dynamics simulations are useful in study of controlled assembly anddisassembly to bridge the gap between atomistic simulations and experiments.In the last part of the dissertation, by employing a multi-scale theoreticalapproach combining nonequilibrium molecular dynamics, first-principles calculations,and kinetic Monte Carlo simulations using charge transfer rates based on the tunnelingenabled hopping model, we investigate charge transport properties of TIPS-P undervarious lattice strains. To achieve efficient and targeted modulation of charge transportin organic semiconductors, we seek to elucidate the relationship between lattice strain,molecular packing, and charge carrier mobility of TIPS-P crystals. We first show thatshear-strained TIPS-P indeed exhibits one-dimensional charge transport, which agreeswith the experiment. Further, we predict the charge carrier mobilities of TIPS-P crystalsunder other types of lattice strains. It is found that, by combining the shear and tensilestrains, we could realize almost isotropic charge transport in TIPS-P crystal with holemobility improved by at least one order of magnitude. Our approach enables a deepunderstanding of the influence of lattice strains on charge carrier transport properties inorganic semiconductors.