Chapter 12 Mark Menu
This menu contains commands that
H Bonds Hydrogen Bonds
Pi Atoms Pi atoms.
Metal Coord Set electron count, charge and coordination of metal atoms.
TS_BondOrders Set the bond orders for transition state bonds.
Fix Distance Fix a distance between any two atoms-up to 10 pairs
Fix Angle Fix an angle. Up to 10;
Fix Torsions Fix a dihedral angle
Reset Reset any of the above and also substructure membership.
The MMX force field contains an extra term to correct deficiencies (in the original MM2 force field) in describing hydrogen bonds. This term is turned on or off depending upon whether the hydrogen bonds are marked. The default is to automatically mark hydrogen bonds and to turn on the extra term in the force field. If the hydrogen bond marking is turned off using the Reset option (see below), then the H_Bond option is used to turn on the hydrogen bond term again. Hydrogen bonds are shown in red between a donor hydrogen and acceptor atom when the distance between the two is less than 2.10 angstroms.
The MM2 and MM3 force field only contains one atom type to describe alkenes (atom type 2), which is used to describe all types of unsaturation. The default parameters for atom type 2 are set to reproduce the geometry of an isolated double bond, such as ethylene, and will not accurately represent the geometry or energy of a conjugated system such as butadiene or benzene. The solution to this problem is to do a simple pi vescf calculation on conjugated systems. This calculation gives the bond orders of all the bonds in the conjugated system, and these bond orders are used to adjust the stretching and torsional parameters for those atoms in the conjugated system. The pi atom marking is used to tell PCMODEL which atoms belong to the conjugated system and that a pi calculation should be done. Selecting the Pi atom marking will automatically mark all conjugated atoms. Reset is used to unmark the atoms. When Pi atoms are marked and minimize is selected PCMODEL will first do a pi calculation on the conjugated system, the parameters will be adjusted and then 15 iterations of geometry optimization will be done. A pi calculation is then done on the updated geometry, the parameters are again adjusted, and a complete minimization is done. When the minimization is complete another pi calculation is done, followed by another minimization. The minimization ends when no change in the geometry is observed after a pi calculation.
Metal Coordination
|
|
The Metal Coord option is used for coordinating lone pairs and pi systems to a metal atom, setting the electron count and geometry of a metal, and setting the charge on the metal. The metal atom of interest and any coordinated atoms must first be selected using the SELECT button on the TOOLS menu. After selecting Metal Coord a dialog box will be presented showing the metal atom symbol, the current charge if any, and a set of radiobuttons describing the electron count and geometry.
The force field model was designed with no charges on the metal atoms (default charge is 0). Setting a charge will turn on electrostatic interactions with other atoms and should be treated with caution. The electrostatic model within molecular mechanics is not well defined or well tested, but it is known that formal charges do not work well. You should check your calculations against known compounds as you make modifications.
If the Metal Coord option is not used, all metals are assumed to be coordinately
saturated, and there will be no attractive potential between the metal and the lone pair or
p-orbitals of ligands which were not explicitly bonded during the DRAW phase of the input. Atoms coordinated to the metal will be shown with a dotted line between the atom and the metal.
If transition state atom types are used, their bond orders must be set before a minimization can be done. When the TS_BondOrders option is selected a dialog box appears listing the transition state bonds found and the current bond orders (if any are known). The bond orders should be entered in the appropriate edit boxes. This data will be written to the structure file when the file is saved.
The Fix_Distances option is used to fix the distance between two atoms, and up to ten pairs can be fixed at one time. The two atoms whose distance is to be fixed should be selected using the SELECT button on the TOOLS menu, then Fix_Distances can be selected from the MARK menu. A dialog box will appear listing the two atoms, the current distance and two edit boxes, one for the distance to fix at, and the other for a force constant (default 5.0 mdyne/angstrom ). The distance is fixed by creating a bond between the two atoms with the default distance set at the fixed distance, and with a force constant input. The default force constant works for most cases. Fixed distances can be combined with energy minimization or dynamics to build large structures with specific interactions, for example, folded peptides (where the fixed distances come from NMR experiments).
The Fix Angle option is used to fix the angle made by three atoms and up to ten angles can be fixed at one time. The three atoms of the angle should be selected first using the Select button, and then Fix Angle from the Mark menu. A dialog box will appear giving the atom numbers of the atoms of the angle, the current angle and edit boxes for the angle to fix at and the force constant to use.
The Fix_Torsions options is used to fix up to two dihedral angles. The four atoms defining the dihedral angle must first be selected using the SELECT button in the TOOLS menu. The Fix_Torsion option will then present a dialog box listing the four atoms, the current angle, and an edit box for entering the angle to fix at. The routines used for fixing a torsion are the same as those used for the dihedral driver and are limited to two dihedral angles at one time.
The Reset option brings up a dialog box which allows resetting all the options given above, and also substructure membership.