Minimum cross-sectional diameter: calculating when molecules may not fit through a biological membrane.
Some compounds that are predicted to be toxic to aquatic organisms instead show no toxicity. In some cases, this phenomenon occurs because the molecules are too large physically to pass through biological membranes, at least by passive transport. The size of the smallest circle through which a molecule can pass is called its minimum effective cross-sectional diameter. Until now, no method has been generally available for determining this parameter. Here, we present such a method, based on vector analysis, that produces results in seconds or minutes, even for relatively large molecules, on a desktop computer. The only input required is the Cartesian coordinates and van der Waals radii of the constituent atoms. The gas-phase, energy-minimized structure is used as an approximation, because to our knowledge, no practical means of experimentally measuring an effective diameter in solution is currently available.
Cash
Gordon G
GG
Risk Assessment Division, Office of Pollution Prevention and Toxics, U.S. Environmental Protection Agency,Washington, DC 20460, USA. cash.gordon@epa.gov
Nabholz
J Vincent
JV
D001692:Biological Transport; D002462:Cell Membrane / Q000502:physiology*; D008432:Mathematical Computing; D008954:Models, Biological; D008958:Models, Molecular