Computational chemistry uses computers to calculate chemical structure, properties, and reactivity. The process typically involves three distinct steps: structure input, calculation, and result interpretation. In this assignment, CAChe software is used to build input molecules, perform molecular mechanics and molecular orbital calculations, and interpret the bond length, energy, geometry, and reactivity of molecules.

• Chemist’s Guide to CAChe (Editor tutorial)
• CAChe Reference (Editor, Mechanics, Visualizer reference manual)
• CAChe MOPAC Guide (MOPAC guide)

CAChe (Computer Aided Chemistry) is an integrated software package for inputting molecular structures, setting up and running calculations, and visualizing and interpreting results. The programs that will be used in this assignment are

CAChe programs are started by choosing the PEALE##:CAChe folder on any Macintosh computer in the Peale Mac Lab. When using CAChe, it is most efficient to store all files in a personal folder within PEALE##:Documents. CAChe stores all important results in a molecule file and additional nonessential information in a molecule folder. When you are done, copy all your molecule files (and optionally molecule folders) to a diskette. Next time you start to work, perhaps on a different computer, copy your files from your diskette to a personal folder on the harddisk.

In addition to the mouse, CAChe uses a 3-D trackball to rotate (R), translate (T), and zoom (Z) the workspace. To use the 3-D trackball, first click on the appropriate button and then move the ball. Since the trackball can be rotated about 3-axes, molecules can be rotated in any direction in space. Translate and zoom work similarly. If your molecule ever gets "lost," Edit:Find will locate, autosize, and center it.

The following instructions are the minimum set of instructions needed to perform the calculations in this assignment. Many alternate and/or useful procedures have been omitted for the sake of brevity. Some of these procedures will be covered in other assignments. Other procedures are covered in the reference manuals and in other courses.

The purpose of Editor is to build and edit molecular structures that are used as input for calculational programs.

To draw an atom, choose Tool:Atom Tool, choose Atom:{atom type} (or Atom:Periodic Table to get any atom), and click mouse button to insert current atom type. To draw a bond, drag between two atoms. Dragging between atoms again cycles through single, double, triple, etc. bond types. A shortcut to draw a bond and an atom is to click on an existing atom, drag to a new location, and release.

Atoms and bonds must be selected before they can be edited. To select an atom or bond, choose Tool:Select and click on the object. Shift-clicking adds/removes and object to/from the selection set. A shortcut to select everything is to click in the background.

Once objects are selected, they can be deleted with the delete key; copied, cut, and pasted with Edit:Cut, Edit:Copy, and Edit:Paste; and moved with Adjust:Via Trackball using the 3-D trackball in translate mode. Atomic configuration and bond types can be edited with the Select Tool by z-clicking on the item. After the atoms and bonds (less hydrogens) are drawn, Editor can beautify the structure (add missing hydrogens and approximate the geometry) by choosing Tool:Select Tool, clicking in the background to select the entire molecule, and choosing Beautify:Comprehensive.

Molecular geometry can be specified using atom distances (two atoms), bond angles (3 atoms), and dihedral angles (4 atoms). To examine or specify molecular geometry, choose Tool:Select, select the appropriate number (2, 3, or 4) atoms, and choose the corresponding Adjust command (Atom Distance, Bond Angle, or Dihedral Angle). Geometry information is displayed in a dialog box. To change molecular geometry, enter the new information, click on Apply, and click on Done (or Cancel to ignore the change). It is very important to note that the atom which was selected first is the atom that is moved.

The appearance of atoms and bonds can be controlled to display different kinds of models. To change the atom shape and label, select the atoms to be changed and choose View:Atom Shape. To change the bond shape and color, select the bonds to be changed and choose View:Bond Shape. Useful molecular representations include stick figure (uncheck all options in View:Atom Shape and select single cylinders colored by atom color in View:Bond Shape) space filling (select spheres with van der Waals radii scaled by 1.00 in View:Atom Shape) and default (select display atom labels and spheres with van der Waals radii scaled by 0.20 in View:Atom Shape and display bonds as multiple cylinders colored by atom color in View:Bond Shape).

To save a structure, activate the window of the structure to be saved, choose File:Save, navigate to your personal folder, type in a descriptive name, and click on Save. To recall a structure, choose File:Open, navigate to your personal folder, and double-click on the molecule file. To print a structure, activate the window of the structure, orient the molecule with the 3-D trackball, choose File:Print, select the Color/Grayscale option, and click OK.

The purpose of Mechanics is to investigate conformational energy of a molecule. The theoretical basis of mechanics is to calculate molecular steric energy using classical potential energy expressions.

To prepare a molecule for study by Mechanics, create the molecule with Editor, beautify the molecule to get a reasonable starting geometry, and use the Adjust menu to achieve a particular conformation. (Search labels can optionally be added using the corresponding Adjust menu item.)

To start the Mechanics program, choose Applications:Mechanics from within Editor. To calculate the steric energy of the input structure without minimizing the energy, choose Calculation type:Show Current Energy. To minimize the steric energy of the input structure, choose Calculation type:Optimize Structure. (Other selections are available for searching conformations and generating potential energy surfaces.) Start the calculation by clicking on the Run button. It is important to wait until the top line in the status box reports Job Done and the Stop button is dimmed before closing the calculation status box or switching to another application. To view the output of the Mechanics program, view the contents of the status box. The molecule file is automatically updated with the new energy and structure.

The purpose of MOPAC is to investigate electronic structure and dependent properties of a molecule. The theoretical basis of MOPAC is to calculate the molecular orbitals (MO's) of the molecule, from which energy and electron density may be calculated.

To prepare a molecule for study by MOPAC, create the molecule with Editor, beautify the molecule to get a reasonable starting geometry, use the Adjust menu to achieve a particular conformation, and optionally use Mechanics to pre-optimize the structure. (Search labels can optionally be added using the corresponding Adjust menu item.)

To start the MOPAC program, choose Applications:MOPAC from within Editor. All calcuations in this and future assignments will be done using the PM3 parameter set. To calculate the electronic energy of the input structure without minimizing the energy, choose Calculation type:SCF energy. To minimize the electronic energy of the input structure, choose Calculation type:Optimize geometry. (Other selections are available for calculating vibrational spectra, generating potential energy surfaces, and finding transition states.) Start the calculation by clicking on the Run button. It is important to wait until the top line in the status box reports Job Done and the Stop button is dimmed before closing the status box or switching to another application. To view the output of the MOPAC program, view the contents of the status box. The molecule file is automatically updated with the new energy and structure.

The primary purpose of Visualizer+ is to represent the computational chemistry results as pictures, and the secondary purpose is to provide an interface for accessing numerical results. Many of the commands in Visualizer+ are similar to commands in Editor; however, it is possible only to look at molecules and not to change molecular geometry or energy in the molecule file. (Additional commands permit viewing and analyzing conformational searches, potential energy surfaces, molecular orbital isosurfaces, and vibrational and electronic spectra.)

To start the Visualizer+ program after performing a Mechanics or MOPAC calculation, wait for the calculation to fully complete and then choose Applications:Visualizer+. Geometry can be examined by selecting 2, 3, or 4 atoms and choosing the appropriate Adjust menu item as described in the Editor. The appearance of atoms and bonds may be changed using View:Atom Shape and View:Bond Shape as described in the Editor. Numeric results may be accessed by optionally selecting the molecular feature, e.g., an atom or bond, choosing Select:Via Internals, and choosing the desired Object Class and Property.

The assignment is contained in a Word document on ChemBoard. Download the assignment, save it to your disk, and open it in Microsoft Word. You will find it convenient to have three applications open: Netscape Navigator (to view these instructions for CAChe), CAChe (to perform the requested calculations), and Word (to edit the assignment). As you complete the requested calculations, edit the document and insert your responses where indicated. When pasting images, be sure to select Edit: Paste Special... and uncheck Float over text. When your assignment is complete, turn it in electronically either by attaching it to an email message or on a PC-formatted diskette.