Chem3D 8.0 Manual - CambridgeSoft

van der Waals RadiusThe van der Waals radius is used when displayingthe Ball & Stick, Cylindrical Bonds or Space Fillingmodels.The Close Contacts command in the Analyze menualso determines close contacts by comparing thedistance between pairs of non-bonded atoms to thesum of their van der Waals radii.NOTE: The van der Waals radii specified in theAtom Types table do not affect the results of an MM2computation. The radii used in an MM2computation are specified in the MM2 Atom Typestable.Atom Type NumberAtom Type numbers are used to determine whichmeasurements apply to a given group of atoms.For example, to determine the standard bond lengthof a bond between a C Alkane atom (atom typenumber 1) and an O Alcohol atom (atom typenumber 6), you should look at the 1-6 record in theBond Stretching table.ChargeThe charge of an atom type is used when assigningatom types to atoms in a model.When the information about an atom is displayed,the atom symbol is always followed by the charge.Charges can be fractional. For example, the chargeof a carbon atom in a cyclopentadienyl ring shouldbe 0.200.Maximum Ring SizeThe maximum ring size field indicates whether thecorresponding atom type should be restricted toatoms found in rings of a certain size. If this cell iszero or empty, then this atom type is not restricted.For example, the maximum ring size of CCyclopropane is 3.Rectification TypeThe rectification type is an atom type assigned to theatoms which automatically fills open valences onthe selected atom. The rectification atoms are addedor deleted when you have selected theAutomatically Rectify checkbox from the Buildingcontrol panel. Typically, rectification atom types arehydrogen atom types.To change the rectification type for a specific atomtype:1. Double-click the rectification type cell in theappropriate atom type record.A dialog box appears that contains a list of allatom types.2. To choose a new rectification type, select thenew type from the list.3. Click OK.When you specify a rectification type, thebound-to type of the rectification type shouldnot conflict with the atom type. If there is norectification type for an atom, it is neverrectified.For example, if the rectification type of O Carboxylis H Carboxyl, the bound-to type of H Carboxylshould be either O Carboxyl or empty. Otherwise,when assigning atom types, hydrogen atoms boundto O Carboxyl atoms are not assigned H Carboxyl.GeometryThe geometry for an atom type describes both thenumber of bonds that extend from this type of atomand the angles formed by those bonds.AppendixChem3D 8Atom Types• A19