Directions for HyperChem Modeling Program-Experimental Chemisty II, CH 463-OSU Chemsitry

Directions for HyperChem Modeling Program
Experimental Chemistry II, CH 463

The PC's in GBAD 311 and one in the SAACS room have the HyperChem ver 5.01, program setup. The following directions are intended to get you started - for advanced applications consult the Help menus and the manuals in GBAD 311 (or consult with Dr. Pastorek.) The topics covered in this handout are: construction of a molecular structure, geometric optimization for the structure, generation of the infrared and electronic spectra, orbital rendering and animation of the vibrational modes, and generating colored isosurface maps. HyperChem is a Windows program, so it is easy to learn how to do things by just trying something: when all else fails...there is on-line help!

Table of Contents

Sketch a Molecular Skeleton	Structure and Energy Calculations
Select Tool	Find the Geometrically Optimized Structure
Printing	Calculate and Animate the Vibrational Spectrum
Different Molecular Model Forms - termed "Rendering "	Calculate and View the Electronic Spectrum
Rendering IsoSurfaces -charge/distance	View the Molecular Orbitals

Sketch a Molecular Skeleton

bond, etc. L-click three times on a ring bond to make the ring aromatic (dotted line).

	Double left-click on the Drawing tool ( first choice, left side on the tool-bar). This selects the drawing tool and opens a copy of the periodic table. Select atoms from the periodic table to add to your structure. You can move the periodic table box off to one corner while you build the molecule by clicking and dragging the top border of the box. To see an example, click here.
	Point and L(eft)-click on desired element (e.g., Carbon).
	Go to the drawing screen (work screen area) and build the carbon molecular skeleton by pointing to a spot and L-clicking. To erase an atom, point to it and R(ight)-click.
	Change the default element if needed, finish rough molecular skeleton. Close Element Table.
	Make bonds by L-clicking and dragging between desired atoms. Click twice for double bond, click again for triple, click again to make aromatic, click again to start over.

Select the X-Y rotation tool from the tool bar. (This gets you out of the drawing mode).
On the Top Menu Bar, select Build - Add Hydrogens (if hydrogens are needed). Next go to Build - Model Build to generate the standard 3-D structure of the molecule based on standard bond lengths and angles. The structure you have sketched out on the screen will be automatically updated. If you are happy with this structure, Save it to a File. The structure file is saved with the .HIN extension that only HyperChem reads. Other formats are available, e.g., pdb (protein data base.)

Select Tool

The Select tool is the second tool from the left. The Select tool is used to perform some operation on one of several molecules on the screen or one part of a molecule. Use the select tool, for example, to set desired angle and bond length constrains before building, for selecting angles and bonds to be listed out in the dialog box at the bottom of the screen. Some examples follow.

Click and drag over an angle in the molecular framework to readout the bond angle value on the bottom dialog box.

Set Select - Molecules from the top menu, then click on the molecule that you want to rotate relative to another molecule, pick the X-Y rotation tool with the left mouse button as usual but use the RIGHT mouse button to move only the selected molecule.
The Click-Draw technique is another useful shortcut. This is an easy way to change the stereochemistry of a group about an atom. Pick the Draw tool, and press and hold the Shift key while using the left mouse button to click on the atom about which the flip should occur. Try changing the position of the methyl group in methylcyclohexane from exo to endo using this shortcut.

Printing
Print is a choice under File. Pressing the Print Screen key copies whatever is on the screen to the Windows Clipboard (also done by pressing F9 key). This screen copy can be pasted into other Windows programs (note: use this method if you are printing to the color deskjet in GBAD 311). The image can also be sent to a file (see Setup Image in File-Preferences.)
HyperChem will open and save as other structure file formats including: PDB, ENT, MOL, SKC, CHM, ML2 and ZMT. Note: to open protein data base (pdb) files, you have to rename the file as a .ENT file. There are mucho examples of pdb files around the web.

Different Model Forms-Rendering

Look under Display-Rendering to pick a structure display format that you like (i.e., Ball and Stick, Spheres (space filling), etc. The default rendering is usually Stick. Use this when performing calculations (the program runs faster.)
To change or set labels for the atoms in the molecular structure, go to Display-Label. Display - Element Color to change these if desired.

Calculations

Find the Geometrically Optimized Structure

Note: The program runs faster if the Display-Rendering is set to Stick.

Select Setup, SemiEmpirical, PM3 with no CI (configuration interaction). This method is suggested to give the best model for vibrational analysis.
Select Compute, Geometric Optimization. After the optimization is done, save the updated structure file (File, Save). The energy gradient for the molecule has been minimized by slight changes in the geometry. If you want to refine the optimization, or change the criteria, consult the manuals. To achieve a global minimum in the molecular geometry, the calculated heat of formation should be the lowest value possible (most negative value). You might try starting the optimization procedure from different molecular geometries and checking the value for the heat of formation: the structure that gives the lowest heat of formation is the best optimized structure. The heat of formation is printed to the log file (see point below) after a single point calculation and it is accessible from the main menu in HyperChem by selecting Compute, Properties, Details next to Total Energy.
Select File, Start a Log File (extension .LOG) to output parameters of interest, e.g., Heat of formation, dipole moment, etc. Consult the help or the manual for what value of PrintQuantumLevel to use to get the parameters you want. After starting the Log File, run a single point calculation using the geometrically optimized molecule. This will write the parameters of interest to the log file. File- Close the log file and view the file with a text editor.

Calculate and Animate the Vibrational Spectrum

Select Compute-Vibrations. (Note: The actual vibrational analysis can be slow for large molecules.)
When the vibrational analysis is 100% done (look at the dialog window at the bottom of the screen), save the .HIN file. Now Compute-Vibrational Spectrum should now be active. Select it to show the stick model of the vibrational modes.

Use the Translational Tool to drag the molecule off to one side of the screen. Select Compute- Vibrational Spectrum. Drag the Vibrational Spectrum box to the other side of the screen. Highlight a vibrational mode by pointing to it and L-clicking. The IR active modes are on the bottom of the spectrum, and modes active in both the Raman and IR are on the top. Select Animate vibrations, Apply. To see an example, click here.
Saving the generated calculated vibrational spectrum takes two steps. First, the IR.SCR macro needs to be copied and stored on a local drive (edit the macro in any text editor). Second, the IR.SCR macro is run after you have generated the vibrational spectrum above. Run the macro-or here called SCRIPT- from HyperChem. Select Script from the top menu to run it. This will cause all important IR parameters to be written to a default outfile called "CHEM_IR.SCR." To re-load the IR spectrum at a later session, first open the .HIN structure file, then go to Script and select the script that now contains the generated IR spectrum (above this default file is CHEM_IR.SCR) . If the IR parameters are re-loaded correctly, Compute-Vibrational Spectrum should be active.

Electronic Spectrum

If not already done, optimize the geometric structure for the molecule.

Go to Setup-Semi-Empirical-ZINDO/S-Options. Set the Total Charge to 0, Spin Multiplicity to 1, Spin pairing to RHF, and select Lowest State. ZINDO/S is optimized for spectroscopic calculations, but other computational methods will work as well.
Select: CI (i.e., Configuration Interaction), Singly Excited, Orbital Criterion should be set to 3 Occupied and Unoccupied. OK to go back to the top menu.
Select Compute-Single Point.
Finally, Compute-Electronic Spectrum. The top set of lines show both singlets and triplets, whereas the bottom set shows spectroscopically active states and relative intensities. Highlight modes to readout information. To see an example, click here.

Orbitals

Reset the Setup method to PM3 and set CI to None. Select Compute-Orbitals. Select the Labels box to fill the electrons in the orbitals in ascending order of energy. Pick an orbital and Plot. (See Example.) Different orbital rendering schemes are available under Options.
The LUMO and HOMO are the orbitals where the valance electrons of molecules are found. They are refereed to as the "Frontier Orbitals". LUMO stands for Lowest Unoccupied Molecular Orbital (the lowest energy antibonding orbital) and HOMO stands for Highest Occupied Molecular Orbital. Select a different orbital by pointing and clicking and Plot. Can you tell the difference between bonding and antibonding orbitals?

Rendering Isosurfaces

Set File- Preferences-Isosurface Colors. For example, you might choose Red-Postive and Green - Negative.
After a single point calculation, go to Compute-Plot Molecular Properties-Molecular properties-3D mapped
Rendering - Gouraud Shaded Surface.
If you want to change the maximum and minimum charge/distance ranges, first find the maximum positive charge values: Display-Labels-Charges. Next, go to Plot Molecular Properties menu, set the maximum positive and minimum values in Mapped Function Options.
To copy the output to the Windows clipboard, press F9 key. If you want to copy directly to a file, set this option under File-Preferences-Setup Image. Select RGB bitmap for the best resolution-but beware-the files can be large!
Examples.