• All molecule or crystal structure building begins in Editor, which may be launched by double-clicking on its icon from the desktop or the Cache directory.
• Save your files in the Chem445 subdirectory and record the filenames you choose in your lab notebook.
• The trackball has several functions: rotate (default), magnify/reduce and translate, which may be chosen by the three mouse buttons on the trackball/mouse.
  

Contents:

I. Crystal Structures and YBa₂Cu₃O_7-x  
II. Ferrocene
III. DMSO/AlCl₃ Model
IV. CAChe Optimization and Spectra Generation: A Step-by-Step Guide, Using Be(acac)₂ as a Model Compound
V. Li_xWO₃, an Intercalation Material
VI. ZSM-5, an Open Framework Aluminosilicate

I. Crystal Structures and YBa₂Cu₃O_7-x  

     The crystal shape feature of the CAChe modeling program may be used to build asymmetric atoms, molecular crystals and infinite lattices.  This will be particularly useful and informative when used in conjunction with the zeolite and Li_xWO₃ laboratories.  In order to use this feature, three items are necessary: a space group, cell parameters and the fractional coordinates of the asymmetric atoms.

     For example, the space group of the superconducting compound YBa₂Cu₃O_7-x is Pmmm.  The cell parameters are a = 3.82030Å, b = 3.88548Å and c = 11.68349Å.¹

Table 1. The fractional coordinates of the asymmetric atoms of YBa₂Cu₃O_7-x contains eight atoms.¹

     With this information, you may build the infinite lattice of YBa₂Cu₃O_7-x.  Open a new file and save it in the Chem 445 folder.  Select the appropriate space group and enter the cell parameters using the crystal shape command in the view menu.  Click on the fractional coordinates dialog box and enter the fractional coordinates (the tab, return or enter keys allow you to move the cursor within the dialog box).  The multiplier should be set at one, since the coordinates that you enter are divided by the multiplier to give the fractional coordinates.  Select OK when data entry is complete and you will be returned to the first screen of the crystal shape dialog box.  Select the "Build" option and the "Asymmetric atoms" option to view the asymmetric atoms entered in the fractional coordinates dialog box.  You may return to this option and start fresh at any point.  Next, select "Build" and "Molecular Structure" to construct the lattice.  You may then adjust your lattice boundaries and "Build" the "Infinite Lattice" by specifying the number of unit cells that will appear on the screen.  Also in the crystal shape dialog box, you may select the "Draw" function and draw an outline of the asymmetric cell, unit cell, or boundaries of the portion of the crystal that you are seeing.

References

1. Williams, A.; Kwei, G. H.; Von Dreele, R. B.; Larson, A. C.; Raistrick, I. D.; Bish, D. L. Phys. Rev. B 1988, 37, 7960.

II. Ferrocene

1. Find the eclipsed ferrocene model in the fragment library using the fragment tool (ligand-p-complex).  Using atom tools, examine the hybridization and charge of each atom until you are satisfied that you understand their method of construction.  You will use this knowledge to construct a staggered ferrocene molecule.
     In the library molecule, you should find that the charge of iron is +2 and the overall charge on each ligand is -1.  You may verify (using the atom tool and the alt/option key) that in each cyclopentadienyl ligand there are four carbons with a zero charge and sp² hybridization and one carbon with a -1 charge and sp² hybridization.  What other things can you deduce by examining the eclipsed ferrocene model?  What type of bonds are the h-5 bonds between the cyclopentadienyl ligand and the Fe²⁺ atom?

2. Now you are ready to build the staggered ferrocene model from the cyclopentadienyl ligand fragment (Cp), which is also in the fragment library.  Use the beautify option to remove the lone pairs on the cyclopentadienyl ligand fragment that will be your basic building block.  Adjust the cyclopentadienyl fragment until it meets the criterion that you obtained from part 1.
     Next, use the atom tool (atom/periodic table) to select an Fe²⁺ atom.  Bond it to the cyclopentadienyl ligand (tool/atom: drag from the center of each carbon atom to the center of each iron atom; rotate if necessary as you go along).  Designate the type of bond (remember part 1).  Now you are ready to import a second cyclopentadienyl ligand (remember to stagger the cyclopentadienyl ligands).  Draw in your five carbon-iron bonds and you are ready to optimize the geometry of the molecule using Mechanics and ZINDO (you will leave the editor file at this point; the optimized geometry will be available following ZINDO in the EDITOR file).
     To obtain a UV-vis spectrum, choose the configuration interaction spectra option (CI) in ZINDO.  Select a level for CI (7 or 8 is adequate for benzene; the highest level that the instrument will optimize is 14 for a singlet or 9 for a doublet).
     Open the molecule in VISUALIZER+ to view the UV-VIS spectrum.  Use the Electronic Spectra command in the analyze menu to overlay the spectrum and the molecule.  You may put the cursor on the spectrum and select a point that will highlight the molecular orbitals involved.

3. An alternative to building the staggered ferrocene molecule from two cyclopentadienyl ligands and one Fe²⁺ atom is to use the Fragment Tool to obtain a [(Cp)₂Ni] staggered molecule from the Ligand-p-Complex option of the Fragment Library.  The Ni²⁺ atom is changed to an Fe²⁺ atom by using the alt/option key in the Atom Tool.  Verify the charge (2) and configuration (d²sp³, octahedron) of the iron atom.  The geometry is then optimized using Mechanics and ZINDO, followed by Configuration Interaction, as in step 2, above.

III. DMSO/AlCl₃ Model

See the DMSO experiment for a step-by-step guide using the monodentate DMSO (dimethyl sulfoxide) ligand and coordinate covalent bonds with Al as the model metal.

     By examining the CAChe Periodic table, it is easy to see why Be(acac)₂, [Bis(acetylacetonate)beryllium, [CH₃COCH=C(O-)CH₃]₂Be, is selected as a model compound: CAChe can optimize compounds containing the beryllium atom using both MOPAC and ZINDO (Figure 1).  

     The steps for this optimization are order very specific.  A step-by-step guide, along with depictions of the computer screen, will now be shown.  The acetylacetonate ligand is known as a bidentate ligand because it contains two oxygen donor atoms.  Beryllium compounds are highly toxic and cancer suspect agents. Computer modeling might save time in the lab.

Step 1: In Editor, draw the molecule or obtain the molecule from the "Fragment" library.

Step 2: Optimize the geometry in Mechanics, in the default mode (or increase updates to 1300, to insure that the molecule runs to completion).  Remember that in Mechanics, structures are solved using classical mechanics.  Optimization, whether classical (steric energy minima) or quantum mechanical, attempts to find the nearest stable geometry, taking into account all the interactions within the molecule.

Step 3: Optimize the geometry in MOPAC (Molecular Orbital PACkage).  MOPAC is a quantum mechanical optimization program and calculates the heat of formation, bond strengths, atom hybridization, partial charges and orbitals.  Examine the CAChe periodic table to insure that all elements in the molecule to be optimized have a black square in the upper right hand corner.  Verify the molecular charge displayed on the screen.  The system will suggest changing the multiplicity and parameters when necessary.  You may have to change the parameter set (MINDO/3, MNDO, PM3 or AM1).  Solvents may be simulated.  Refer to the CAChe Manuals for further explanation.

Step 4: To calculate the vibrational spectrum, use the vibrational frequency (force) option in MOPAC with the same parameters as above.

Step 5: Open the molecule in "Visualizer" and choose "Vibrational Spectra" in the "Analyze" menu.  The spectrum will be displayed.

     The axis parameters may be adjusted by double- clicking on either the x or the y axis and entering new values.  The stretching modes responsible for each peak may be obtained by double clicking on a peak contained in the theoretical vibrational spectrum.  The molecule will be displayed on the screen behind the spectra and may be brought to the foreground by clicking on the screen near the molecule.  To obtain the spectrum a second time, go to the beginning of step 5.

Step 6: Select ZINDO (Zernerís Intermediate Neglect of Differential Overlap) within the Applications menu. Select the Configurational Interaction (Spectra) option.

Step 7: Open the molecule in "Visualizer" and choose " Electronic Spectra" in the " Analyze" menu.  The molecular orbitals responsible for each absorption may be highlighted by double clicking on the peak(s) contained in the electronic spectra.  The molecule will be displayed on the screen behind the spectra and may be brought to the foreground by clicking on the screen near the molecule.  To obtain the spectrum a second time, go to the beginning of step 7.

Step 8: A "Project Leader" table may be generated to tabulate the theoretical results of the above calculations. "Project Leader" is opened by double-clicking on its icon on the CAChe main screen.  A new blank table will automatically appear, or an old table may be reopened.  Title and save the new table.  Double click on "1A", or any "A" field, under "chemical sample".  Open the advanced inorganic folder and select chemical samples by "Adding" the compound of interest.  The appropriate folder will be displayed in the roster with NO ICON to the left of the name.  Do not add the samples with folder icons to the left of their name.

Step 9: Column headers are entered by double-clicking on the lettered (B, C, D etc.) fields.  Notes are displayed at the bottom of each screen, defining each term.

Step 10: To receive data, highlight fields such as 1B, 1C, 1D, 1E.  In the pull-down menu, select "Evaluate" and "Cells".  Calculations will take place and parameters will be displayed.  Save the table.  At the completion of steps 1 through 10, each refined molecule will have an editor file, a folder, a potential energy surface map and a project leader table.

Figure 21. A view of the unit cell with cell parameters displayed.  By definition, a = (b, c); b = (a, c); g = (a, b).

Crystal Systems

1. Triclinic
        no restrictions for a, b, c, a, b, g 

2. Monoclinic
        no restrictions for a, b, c, b; a = g = 90°

3. Orthorhombic
        no restrictions for a, b, c; a = b = g = 90°

4. Tetragonal
        no restrictions for a or c, but a = b and a = b = g = 90°

5. Hexagonal
        no restrictions for a or c but a = b, a = b = 90°, g = 120°

6. Trigonal
        no restriction for a, but a = b = c; no restriction for a, but a = b = g 

7. Cubic
        no restriction for a, but a = b = c; a = b = g = 90° 

Figure 23. A view of the unit cell of Li_xWO₃, a cubic perovskite.

     Following section I, above, the crystal shape feature may be used to generate the unit cell or crystal lattice of Li_xWO₃.  You must first decide which atoms belong to the asymmetric unit and assign their fractional coordinates.  The space group for the cubic perovskite is Pm3m.¹  The value for a is 3.72 Å.²  A cubic structure by definition has a = b = c.

References

1. Galasso, Francis. S., Structure, Properties and Preparation of Perovskite-Type Compounds; Pergamon Press: Hungary, 1969; p. 7.

2. Ibid., p. 23.

     To obtain the necessary fractional coordinates, space group and unit cell parameters, see: Olson, D. H.; Kokotailo, G. T.; Lawton, S. L.; Meier, W. M., "Crystal Structure and Structure-Related Properties of ZSM-5", J. Phys. Chem. 1981, 85, 2238-2243.  They are also available at: http://www.iza-sc.ethz.ch/cgi-IZA-SC/collection.  Follow the instructions in section I, above, to generate the framework.  Ortho-, meta-, and para-xylenes may then be built and driven into the three dimensional channels, to obtain a visual estimate of the size of the channels, cavities and windows of the size/shape selective material.