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Molecular Dynamics Simulations Of The Transport Behaviors Of NH4+ And NH3 In Transmembrane Cyclic Peptide Nanotubes

Posted on:2017-01-10Degree:MasterType:Thesis
Country:ChinaCandidate:M M ZhangFull Text:PDF
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In this work, the transport behaviors of NH4+ and NH3 in water-filled transmembrane cyclic peptide nanotubes(CPNTs) of 8×cyclo-(WL)n=4,5, and the influences of NH4+ on the structure, dipole orientation and diffusion behavior of channel water have been investigated through molecular dynamics simulations.The size, electronic charge, ability to form H-bonds of a specie and channel radius all significantly influence the behaviors of the species in a nanochannel. Positively charged NH4+ forms stronger electrostatic interactions with the surroundings, thus meets higher energy barriers in the two CPNTs. NH4+ can freely enter or exit the octa-CPNT. While, it encounters energy wells at the mouths of the deca-CPNT, and may be trapped in the tube. Nevertheless, NH3 can enter, exit and permeate the two CPNTs effortlessly. The increase of channel radius may reduce the energy barriers of NH4+ moving through a CPNT, while has little influence on those of NH3. When forming H-bonds with water molecules, NH3 can not only act as a proton acceptor but also has a chance to act as a donor, thus may reside among the water layer when permeating a CPNT. Nevertheless, NH4+ can only act as a proton donor, resulting in it only resides between the water layer and channel axis in a CPNT. NH4+ and NH3 both mainly form water bridges(water-mediated indirect H-bonds) with the wall of a CPNT.NH4+ at the center of a CPNT makes the channel water molecules suffer a dipole orientation effect which is opposite to that coming from the bare carbonyl groups at the tube mouths. The dipole orietations of water molecules near the mouths of a CPNT weakened. In the region near NH4+, the dipole orientations of water molecules in the octa-CPNT enhanced, and those in the deca-CPNT reversed. Besides, NH4+ gives rise to an increase of the number of water molecules in its neighboring two α-plane zones, while have no distinct affect on the axial ditribution of channel water in other regions. Compared with the influence of NH4+ on the dipole orientations of channel water molecules, the affect of NH4+ on the axial distribution of channel water is only in a short range. Due to the strong electrostatic interactions between NH4+ and water molecules, the diffusion coefficient of channel water in a CPNT distinctly reduces, only a half of that with no ion in the CPNT.
Keywords/Search Tags:NH4+, NH3, Molecular dynamics simulations, Cyclic peptide nanotubes, water molecules
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