ChemDes

An integrated web-based platform for molecular descriptor and fingerprint computation

  What is ChemMOP?

   MOPAC is a general-purpose semiempirical molecular orbital package for the study of solid state and molecular structures and reactions. Molecule optimization driven by mopac is widely applied not only in QSAR/SAR but also in other processes of drug discovery, such as docking. Here, we develop this tool for online-optimizing, providing origin 'ARC' file and converting it to format selected avoiding inconveniences of installing and deploying MOPAC package on machines.






Output data area...

Force Field working with MOPAC2012
  • MNDO: Modified Neglect of Diatomic Overlap is a semi-empirical method for the quantum calculation of molecular electronic structure in computational chemistry. It is based on the Neglect of Differential Diatomic Overlap integral approximation.
  • MNDO-d: The W. Thiel's group make an extension of MNDO, called MNDO/d, which adds d functions, is widely used for organometallic compounds.
  • AM1: AM1 (by Dewar and co-workers) takes a similar approach to MNDO in approximating two-electron integrals but uses a modified expression for nuclear-nuclear core repulsion. The modified expression results in non-physical attractive forces that mimic van der Waals interactions. The modification also necessitated reparameterization of the model, which was carried out with a particular emphasis on dipole moments, ionization potentials, and geometries of molecules. While this allows for some description of the hydrogen bond, other deficiencies, such as systematic over-estimates of basicities, remained. Also, the lowest energy geometry for the water dimer is predicted incorrectly by the AM1 model. On the other hand, AM1 improves nicely some properties, such as heats of formation, over MNDO.
  • PM3: PM3 (by James Stewart) uses a Hamiltonian that is very similar to the AM1 Hamiltonian but the parameterization strategy is different. While AM1 was parameterized largely based on a small number of atomic data, PM3 is parameterized to reproduce a large number of molecular properties. In some sense, chemistry gave way to statistics with the PM3 model. Different parameterization, and slightly different treatment of nuclear repulsion allow PM3 to treat hydrogen bonds rather well but it amplifies non-physical hydrogen-hydrogen attractions in other cases. This results in serious problems when analyzing intermolecular interactions (methane is predicted to be a strongly-bound dimer) or conformations of flexible molecules (OH is strongly attracted to CH3 in 1-pentanol). The accuracy of thermochemical predictions with PM3 is slightly better than that of AM1. The PM3 model has been widely used for rapid estimation of molecular properties and has been recently extended to include many elements, including some transition metals.
  • PM6: PM6 is a re-parameterization of the NDDO method. Three modifications to the approximations were made, these mainly affect the way the core-core interaction was defined,and is useful for semi-empirical charge calculations of small ligands as well as proteins . Besides that, all main group elements and transition metals are parameterized in PM6.
  • PM7: PM7 is a modified form of PM6. A few errors in NDDO theory that affect large systems have been removed. All atomic and diatomic parameters were re-optimized. Average errors in organic compounds have been reduced by ~10%, and errors in large organics and solids have been significantly reduced
  • more information about MOPAC

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