title: Force-field parametrization and molecular dynamics simulations of Congo red.
abstract: Congo red, a diazo dye widely used in medical diagnosis, is known to form supramolecular systems in solution. Such a supramolecular system may interact with various proteins. In order to examine the nature of such complexes empirical force field parameters for the Congo red molecule were developed. The parametrization of bonding terms closely followed the methodology used in the development of the charmm22 force field, except for the calculation of charges. Point charges were calculated from a fit to a quantum mechanically derived electrostatic potential using the CHELP-BOW method. Obtained parameters were tested in a series of molecular dynamics simulations of both a single molecule and a micelle composed of Congo red molecules. It is shown that newly developed parameters define a stable minimum on the hypersurface of the potential energy and crystal and ab initio geometries and rotational barriers are well reproduced. Furthermore, rotations around C-N bonds are similar to torsional vibrations observed in crystals of diphenyl-diazene, which confirms that the flexibility of the molecule is correct. Comparison of results obtained from micelles molecular dynamics simulations with experimental data shows that the thermal dependence of micelle creation is well reproduced.
authors.affiliation: Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Kopernika 17, 31-501 Kraków, Poland. mykrol@cyf-kr.edu.pl
authors.forename: Marcin
authors.initials: M
authors.lastname: Król
authors.forename: Tomasz
authors.initials: T
authors.lastname: Borowski
authors.forename: Irena
authors.initials: I
authors.lastname: Roterman
authors.forename: Barbara
authors.initials: B
authors.lastname: Piekarska
authors.forename: Barbara
authors.initials: B
authors.lastname: Stopa
authors.forename: Joanna
authors.initials: J
authors.lastname: Rybarska
authors.forename: Leszek
authors.initials: L
authors.lastname: Konieczny
mesh_terms: D001713:Biphenyl Compounds / Q000737:chemistry; D003198:Computer Simulation; D003224:Congo Red / Q000737:chemistry*; D003627:Data Interpretation, Statistical; D008823:Micelles; D008958:Models, Molecular; D009281:Naphthalenes / Q000737:chemistry
chemical_list: D001713:Biphenyl Compounds; D003224:Congo Red; D008823:Micelles; D009281:Naphthalenes; C031721:naphthalene; C010574:biphenyl