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Parameter Table Use Parameter Table Use Administrator Conjugated Pisystem Bonds.xml Electronegativity Adjustments.xml Elements.xml Pi system portion of the force field for pi bonds. Adjusts optimal bond length between two atoms when one atom is attached to an atom that is electronegative. Contains elements available for building models. Torsional Parameters.xml VDW Interactions.xml Computes the portion of the force field for the torsional angles in your model. Adjusts specific VDW interactions, such as hydrogen bonding. Parameter Table Fields MM2 Atom Type Parameters.xml MM2 Constants.xml van der Waals parameters for computing force field for each atom. Constants used for computing MM2 force field. Most of the tables contain the following types of fields: • Atom Type Numbers • Quality • Reference Atom Type Numbers Out-of-Plane Bending Parameters.xml References.xml Substructures.xml Parameters to assure atoms in trigonal planar geometry remain planar. In force field analysis, parameters to assure atoms in trigonal planar geometry remain planar. Contains information about where parameter information is derived. Contains predrawn substructures available for speeding up model building. The first column in a parameter table references an atom type using an Atom Type number. An Atom Type number is assigned to an atom type in the Atom Types table. For example, in Chem3D, a dihedral type field, 1–1–1–4, in the Torsional Parameters table indicates a torsional angle between carbon atoms of type alkane (Atom Type number 1) and carbon atoms of type alkyne (Atom Type number 4). In the 3-membered ring table, the angle type field, 22-22-22, indicates an angle between three cyclopropyl carbons (Atom Type number 22) in a cyclopropane ring. 650• Parameter Tables CambridgeSoft Parameter Table Fields
Quality The quality of a parameter indicates the relative accuracy of the data. Quality Accuracy Level 1 Parameter guessed by Chem3D. 2 Parameter theorized but not confirmed. 3 Parameter derived from experimental data. 4 Parameter well confirmed. Reference The reference for a measurement corresponds to a reference number in the References table. References indicate where the parameter data was derived. Estimating Parameters In certain circumstances Chem3D may estimate parameters. For example, during an MM2 analysis, a non-MM2 atom type is encountered in your model. Although the atom type is defined in the Atom Types table, the necessary MM2 parameter will not be defined for that atom type. For example, torsional parameters are missing. This commonly occurs for inorganic complexes, which MM2 does not cover adequately. More parameters exist for organic compounds. In this case, Chem3D makes an educated “guess” wherever possible. A message indicating an error in your model may appear before you start the analysis. If you choose to ignore this, you can determine the parameters guessed after the analysis is complete. To view the parameters used in an MM2 analysis: • From the Calculations menu, point to MM2, and choose Show Used Parameters. Estimated parameters have a Quality value of 1. Creating Parameters The MM2 force field parameters are based on a limited number of MM2 atom types. These atom types cover the common atom types found in organic compounds. As discussed in the previous section, parameters may be missing from structures containing other than an MM2 atom type. NOTE: Adding or changing parameter tables is not recommended unless you are sure of the information your are adding. For example, new parameter information that is documented in journals. NOTE: A method for guessing at missing MM2 Parameters can be found in “Development of an Internal Searching Algorithm for Parameterization of the MM2/MM3 Force Fields”, Journal of Computational Chemistry, Vol 12, No. 7, 844–849 (1991). To add a new parameter to a parameter table: 1. From the View menu, point to Parameter Tables and choose the parameter table to open. The parameter table appears. 2. Right click on a row header and choose Append Row from the context menu. A blank row is inserted. Appendices ChemOffice 2005/Appendix Parameter Tables • 651 Estimating Parameters
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