Chem3D Users Manual - CambridgeSoft

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Administrator 6. The pi molecular orbitals are computed from the Fock matrix. 7. The pi molecular orbitals are used to compute a new Fock matrix, then this new Fock matrix is used to compute better pi molecular orbitals. 8. step 6 and Step 7 are repeated until the computation of Fock matrix and the pi molecular orbitals converge. This method is called the self-consistent field technique or a pi-SCF calculation. 9. A pi bond order is computed from the pi molecular orbitals. 10.The pi bond order is used to modify the bond length (BL res ) and force constant (KS res ) for each sigma bond in the pi system. 11.The values of KS res and BL res are used in the molecular mechanics portion of the MM2 computation to further refine the molecule. To examine the computed bond orders after an MM2 computation: 1. In the Pop-up Information control panel, select Bond Order. 2. Position the pointer over a bond. The information box contains the newly computed bond orders for any bonds that are in a pi system. 292• MM2 CambridgeSoft Chem3D Changes to Allinger’s Force Field
Appendix J: MOPAC Overview The appendix contains miscellaneous information about MOPAC. You can find additional information about MOPAC by visiting the MOPAC home page at: http://www.cachesoftware.com/mopac/index.shtml MOPAC Background MOPAC was created by Dr. James Stewart at the University of Texas in the 1980s. It implements semi-empirical methodologies for analyzing molecular models. (MOPAC stands for Molecular Orbital PACkage.) Due to its complexity and command line user interface, its use was limited until the mid 1990s. Since version 3.5 (1996), Chem3D has provided an easy-to-use GUI interface for MOPAC that makes it accessible to the novice molecular modeller, as well as providing greater usability for the veteran modeller. We are currently supporting MOPAC 2000. MOPAC 2000 is copyrighted by Fujitsu, Ltd.CS MOPAC is the licensed version that runs under Chem3D. Potential Functions Parameters MOPAC provides five potential energy functions: MINDO/3, MNDO, PM3, AM1, and MNDO-d. All are SCF (Self Consistent Field) methods. Each function represents an approximation in the mathematics for solving the Electronic Schrödinger equation for a molecule. Historically, these approximations were made to allow ab initio calculations to be within the reach of available computer technology. Currently, ab initio methods for small molecules are within the reach of desktop computers. Larger molecules, however, are still more efficiently modeled on the desktop using semi-empirical or molecular mechanics methodologies. To understand the place that the potential energy functions in MOPAC take in the semi-empirical arena, here is a brief chronology of the approximations that comprise the semi-empirical methods. The first approximation was termed CNDO for Complete Neglect of Differential Overlap. The next approximation was termed INDO for Intermediate Neglect of Differential Overlap, Next followed MINDO/3, which stands for “Modified Intermediate Neglect of Differential Overlap”. Next was MNDO, which is short for “Modified Neglect of Differential Overlap” which corrected MINDO/3 for various organic molecules made up from elements in rows 1 and 2 of the periodic table. AM1 improved upon MNDO markedly. Finally the most recent, PM3 is a reparameterization of AM1. The approximations in PM3 are the same as AM1. This sequence of potential energy functions represents a series of improvements to support the initial assumption that complete neglect of diatomic orbitals would yield useful data when molecules proved too resource intensive for ab initio methods. Appendices ChemOffice 2005/Appendix MOPAC • 293 Potential Functions Parameters
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DISCOVERY • Accessed through your
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