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| Tips: |
◊ If default molecule not showing, you may drag mouse over drawing area to display it.
| INSTRUCTIONS |
SIMULATION MODES
You can perform 3 modes of molecular modeling and simulation (and then use any of the Mouse Operations for 3-dimensional visualization):
1. View Known Structure: select a structure from the "Known Structures" drop-down list
2. Modify Known Structure: select a structure from the "Known Structures" drop-down list, select elements from the "Elements" drop-down list, add atoms and bonds as necessary
3. Create New Structure: select "-Clear-" from the "Known Structure" drop-down list, select elements from the "Elements" drop-down list, add and manipulate atoms and bonds as necessary.
MOUSE OPERATIONS
(S=shift, C=control, air=any empty space in program's window)
◊ pan: S-drag air
◊ rotate: drag air
◊ zoom: C-drag air horizontally
◊ move atom: drag atom
◊ atom info: click atom
◊ add atom: S-click air
◊ delete atom: select "-Delete-" from the "Elements" drop-down list, then S-click atom
◊ recenter: C-click air
◊ perspective: C-drag air vertically
◊ add bond: S-drag atom to atom
◊ delete bond: C-drag atom to atom
◊ Double and triple bonds: do repeated add-bonds between the same pair of
atoms. Valences: carbon 4, hydrogen 1, nitrogen 3, oxygen 2
'Energy Minimize' Button: Click this to make the molecule approximately geometrically correct, i.e. takes a natural configuration that gives it the lowest potential energy. Click any time you change the structure (add or delete atoms or bonds), and whenever you load a new structure. Repeat clicks until structure appears to move an insignificant amount.
'Forces' Check-box: For the display/non-display of the net force vector acting on each atom in the molecule in question. Long-range forces (electrostatic and van-der-Waals) are only partially implemented.
| THEORY |
This 'calculator' is a slightly modified version of the program NanoCAD written by Will Ware of MIT, Boston in the late 1990's. It uses the principle of molecular modeling to provide behavioral modeling of a design that can be optimized by energy minimization.
The mathematical model of molecular mechanics used is called MM2. It was developed by Norman Allinger of the University of Georgia, and it essentially treats a group of atoms as a collection of masses, non-linear springs, torsion bars, etc.