The compounds are listed with their systematic names (IUPAC), an alternative name, their Chemical Abstracts Service registry number (CAS), ChemSpider ID (CSID) and formula. A full description of how the topologies were generated and how the physical properties are calculated can be found in ref. 2 (available for download here).
The force fields used for the benchmark underlying part of this website [2,3], were the Generalized Amber force field (GAFF) and the Optimized Potential for Liquid Simulations for all atoms (OPLS/AA). More information on these force fields can be found the references and on their respective websites (click on Links).
- Berk Hess and Carsten Kutzner and David van der Spoel and Erik Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation, J. Chem. Theor. Comp. 4, 435-447 (2008). DOI
- Carl Caleman and Paul J. van Maaren and Minyan Hong and Jochen S. Hub and Luciano T. Costa and David van der Spoel Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant, J. Chem. Theor. Comput. 8, 61-74 (2012). DOI
- David van der Spoel and Paul J. van Maaren and Carl Caleman GROMACS Molecule & Liquid Database, Bioinformatics 28, 752-753 (2012). DOI
- J. Wang and R. M. Wolf and J. W. Caldwell and P. A. Kollman and D. A. Case Development and testing of a general AMBER force field, J. Comp. Chem. 25, 1157-1174 (2004).
- William L. Jorgensen and Julian Tirado-Rives Potential energy functions for atomic-level simulations of water and organic and biomolecular systems, Proc. Natl. Acad. Sci. U.S.A. 102, 6665-6670 (2005).