title: Molecular Dynamics Simulations of Dynamic Combinatorial Catenanes
author: Piotr Nowak
description: Raw results of the molecular dynamics simulations performed for the paper: Catenanes from Catenanes: Quantitative Assessment of Cooperativity in Dynamic Combinatorial Catenation, J. Li, P. Nowak, H. Fanlo-Virgos and S. Otto, Chemical Science, 2014, DOI: 10.1039/C4SC01998A This fileset contains results of MD simulations on the self-assembled tetrameric azobenzene macrocycle (4AB), beta-cyclodextrin (BCD), gamma-cyclodextrin (GCD) and [2]- and [3]catenanes formed by them. In case of [3]catenanes there are two possible orientations of the cyclodextrins - parallel and antiparallel. They are denoted by "p" and "ap" suffixes. Example: filenames containing "4AB-2BCDap" correspond to the [3]catenane composed of a single tetrameric azobenzene macrocycle and two beta-cyclodextrins oriented in an antiparallel fashion. Files with the "-structure_" prefix are snaphots from MD simulations at the time indicated in the filename. Files with the ".traj" extension are 40 ns trajectory files (without water box) which can be loaded into a trajectory visualisation program (e.g. VMD, http://www.ks.uiuc.edu/Research/vmd/). The corresponding topology/parameter files have the ".prmtop" extension. Files with the "distCD_" prefix contain the distance between the center of a cyclodextrin (CD1 and CD2 for the first and the second, respectively) and the 4AB macrocycle in the function of time. Files with the "distSS_" prefix contain the distance between the centers of the opposite disulfide bonds in the 4AB macrocycle in the function of time. Files with the "sasa_" prefix contain the solvent accessible surface areas in the function of time. The surface was partitioned between different molecules (4AB, CD1, and CD2 suffixes) and with respect to the hydrophobicity/hydrophilicity (denoted by the suffix). Files with the "hbond_" prefix contain the number of hydrogen bonds between the 4AB macrocycle and cyclodextrins in the function of time. File "AB2.mol2" is the azobenzene fragment used to construct the 4AB macrocycle with the leap program. It was generated using restrained electrostatic fit (RESP) with RED.III.5 program. 