Molecular Dynamics Simulation Of The Transport Properties Of Small Biological Molecules Through Transmembrane Cyclic Peptide Nanotubes

The thesis mainly includes two parts.1) The dynamic behaviors and transport properties of O2, CO2and NH3moleculesthrough a transmembrane CPNT of8×(WL)4/POPE have been investigated by EMD,SMD simulations and ABF samplings. The findings suggest that a NH3moleculeencounters the least resistance when going across the tube mouth, and form the mostH-bonds with the surroundings (channel water and the CPNT inner wall) whentransporting in the channel. O2and CO2molecules can hardly form H-bonds with theCPNT framework except at the tube mouth. In addition to direct H-bondedinteractions, all three gases can form water bridges with the tube. The PMF profilesexhibit the periodical alternations of energy maxima and minima in-plane regionsand midplane zones, respectively, coinciding well with the variation trends of pullingforces in SMD simulations. The energy barriers at two mouths of the CPNT elucidatethe phenomenon that CO2and O2molecules are thoroughly confined in the narrowlumen while NH3molecule can easily go outside the tube. The diatomic O2moleculekeeps strong rocking motions when traveling in the lumen. The linear triatomic CO2molecule mostly travels with the orientation parallel or reverse to the tube axis. Thedipole of NH3molecule changes gradually, with just one complete flip when travelingacross the whole channel.2) Classical EMD simulations and ABF samplings have been performed toinvestigate the dynamic behaviors and transport properties of ethanol moleculesthrough three transmembrane CPNTs with various radii, i.e.,8×(WL)3,4,5/POPE. Theresults show that ethanol molecules fill spontaneously the octa-and deca-CPNTs except for the hexa-CPNT. In the octa-CPNT, ethanol molecules are trapped atdividual gaps with their carbon skeletons perpendicular to the tube axis, forming abroken single-file chain. As the channel radius increases, ethanol molecules inside thedeca-CPNT tend to form a tubular layer and the hydroxyl groups mainly stretchtowards to the tube axis. Computations of diffusion coefficients indicate that ethanolmolecules in the octa-CPNT almost lost their diffusion abilities, while those in thedeca-CPNT diffuse as4.5times as in a (8,8) SWNT with a similar tube diameter. Theosmotic and diffusion permeability (pfand pd) of the octa-and deca-CPNTstransporting ethanol have been deduced for the first time. The distributions of thegauche and trans conformers of ethanol molecules in two CPNTs are quite similar.The non-bonded interactions of channel ethanol with a CPNT wall and neighbouringethanol are explored. The potential of mean force (PMF) elucidates the mechanismunderlying the transporting characteristics of ethanol molecules through atransmembrane CPNT.