Cache molecular modeling in advance inorganic chemistry

APPLICATIONS OF CACHE MOLECULAR MODELING IN ADVANCED INORGANIC CHEMISTRY

Charles E. Ophardt
Chemistry Department
Elmhurst College
email: charleso@elmhurst.edu

Abstract on the Internet: http://www.elmhurst.edu/`chm/onlcourse/inorganic/cacheinorg.html

TABLE OF CONTENTS

MOLECULES LAB # 1 MOLECULAR GEOMETRY**

Molecules Lab # 2 - DIATOMIC MO'S**

Molecules Lab # 3 HOMO - LUMO Predictions of a Possible Reaction Pathway**

**CD-ROM: Inorganic Molecules: AVisual Database by C. Ophardt

Laboratory # 1 PREPARATION OF SODIUM TETRATHIONATE

Laboratory # 2 CHEMICAL PROPERTIES OF A CHROMIUM - EDTA COMPLEX

Laboratory # 3 METAL COMPLEXES OF DIMETHYL SULFOXIDE

Lab # 5 TRIS AMINO ACID COBALT COMPLEXES

Lab # 7 VANADIUM COMPLEX/SPECTRA

Lab # 8 SYNTHESIS OF METAL CARBONYLS

Laboratory # 9 SYNTHESIS AND USE OF WILKINSON'S CATALYST

Laboratory # 10 NMR Investigation of Molecular Fluxionality:
Synthesis of Allylpalladium Complexes

MOLECULES LAB # 1 MOLECULAR GEOMETRY

This homework exercise requires the use of a a CD-ROM: Inorganic Molecules: AVisual Database by C. Ophardt and the Personal Cache Molecular Modeling Program on the Macintosh Computers found in the Science Center.

QUES 1-3: Use the CD ROM to find info on a variety of molecules such as Lewis Diagrams, geometries, hybridization.

QUES. 4: Use the CAChe molecular modeling program to construct the following molecules. Also write the Lewis Diagram to serve as an independent check on the results of the CAChe program. List the hybridization, electron pair geometry, and the molecular geometry.

a. BBr3, PBr3, ClBr3

b. ClF2- (for one of the F atoms, go to the periodic table and give it a -1 charge), ClF2+, (for the Cl atom, go to the periodic table and give it a +1 charge)

QUES. 5: Use the CAChe molecular modeling program to construct the following molecules. Also write the Lewis Diagram to serve as an independent check on the results of the CAChe program. Use Mechanics, MOPAC, and Zindo to do the minimization of energy on the molecules.
- Report the bond angles obtained by each method and compare to the experimental bond angles.
- Comments on similarities or differences.
- Explain why the molecules with fluorine have a smaller bond angle than with hydrogen.

a. NH3 107; NF3 102

b. H2O 104.5; F2O 101.5

Molecules Lab # 2 - DIATOMIC MO'S

Use the CD-ROM: Inorganic Molecules: AVisual Database

1. Draw a picture of the following types of molecular orbitals:

sigma s-s sigma * s-s antibonding

sigma p-p sigma * p-p antibonding

pi py-py pi * py-py antibonding

2. Sketch and fill in a M.O. diagram for:

O2, N2

3. Make one of the following molecules, run Mechanics, ExtHuckel, and Tabulator to make all of the Molecular Orbitals ( M.O.s). Then use the Visualizer to open the M.Os. Label the MOs by number and sketch a simple picture. Compare and explain the similarities and differences of them to the M.O.s for nitrogen.

CO; NO+; CN-; ClF

Molecules Lab # 3 NAME __________________________

HOMO - LUMO Predictions of a Possible Reaction Pathway

Use the Inorganic Molecule Database to find which molecular orbitals are used for the following reactions: Start By:

1. Selecting one of the two molecules
2. From the "Optional Views" menu on the top bar, select "M.O. Reactions Predict".
3. Use the "Compare button", then select "All molecules", then select your second molecule.
4. Now use the "Compare Property" menu to select molecule properties. A good first one to check is the "Lewis Diagrams".
The Lewis diagrams may give information about whether the molecules under consideration may be Lewis acids or bases. HINT: Look for the presence or absence of lone pair electrons.
5. Next from the Property Menu, select the HOMO: LUMO combination. Look at the M.O.'s to see whether they may overlap the correct atoms to form a bond. Check the M.O. energies, the correct combination is a HOMO/LUMO pair that has the smallest energy difference. If you do not understand what to look for try the "Visual Help" button and select: Summary: MO Reactions Predict, HOMO/LUMO and LUMO/HOMO for further examples.
6. From the Property Menu, select the opposite combination LUMO:HOMO to again look for possible overlaps of the orbitals.
7. Based upon your analysis, make a drawing of the molecular orbitals showing proper orientation for a possible reaction.

Reactions for HOMO-LUMO Predications

The instructor may assign which ones you are to do.

BF3 + NH3
CO2 + H2O
SO2 + H2O
SO3 + H2O
NO + O3 ------> NO2 + O2
H2 + I2 - Show that this reaction cannot take place
in a one step bimolecular reaction.
Use Cl2 as a substitute for I2 in the data base.
C2H4 + H2 ------> Show that this RX is not direct bimolecular reaction.
HCl + H2O ------>
NH3 + H2O ------>
H2O + SO3-2 ------> OH- + HSO3-

Laboratory # 1 PREPARATION OF SODIUM TETRATHIONATE

Adapted from Pike et. al, "Microscale Inorganic Chemistry", Exp. 16, p. 204-207.

INTRODUCTION:

Sulfur forms a large variety of oxo-anions, the best known of which are the sulfate, SO42-, and sulfite ions, SO32-. The polythionates are a second class of sulfur-oxygen anions having a general formula, SnO62-, where n ranges to greater than 20. These anions, containing more than one sulfur, are normally named according to the number of sulfur atoms present. Thus the anion, S4O62-, is named tetrathionate. The polythionates are stable only as salts--the free acids cannot be isolated.
The sodium tetrathionate and sodium iodide is synthesized by the reaction of elemental iodine with sodium thiosulfate, (S2O32-). The reaction is quantitative and is the basis of the iodometric titration used in analytical chemistry. The product can be recovered if the reaction is carried out in alcohol.

CHARACTERIZATION OF THE PRODUCT AND RELATED COMPOUNDS:

Make a KBr pellet of the product and obtain an FTIR spectrum. Also obtain IR spectra for the following related compounds: sodium sulfate, sodium sulfite, sodium thiosulfate, sodium bisulfite, potassium peroxodisulfate, sodium dithionite.

QUES. 5: Additional items for the lab report:
Determine the structure and Lewis diagram for each of sulfur oxo anions above.
Then determine the point group classification (p. 29-30) for each anion (sulfite, sulfate, thiosulfate). Use this information to determine the number of IR active modes which are expected and compare this to the actual IR's obtained. Discuss the results.

Point Groups and IR active modes:

Example Expected IR peaks in cm-1
C3v 1010 and 961 (maybe one broad); 633, and 496

Td (Tetrahedral) 1105 and 611

C3v * 995, 446, 1123 and 669, 541 and 335

* If one of the Y atoms of an XY4 molecule is replaced by a X atom, the symmetry of the molecule is lowered to C3v. This lowering of the symmetry splits the degenerate vibrations in the Td point group and activates two more vibrations in a X2Y3 molecule.
Other ranges of vibrations for other molecules that are more complex are: Vas SO2 1440-1310;
Vs SO2 1230-1120; Vs S=O 1200-1040; Vs S-O 900-700; S-S 580 - 450; O-S-O 725 - 400

MOLECULAR MODELING

1. Use the CAChe Editor to make the following sulfur oxy anions: sulfate, sulfite, bisulfite, thiosulfate, peroxodisulfate, dithionite, dithionate, and tetrathionate. Use the textbook (Shriver, p. 533) as a reference for the structures. It would probably be best if you write the Lewis structures of the ions to assist in the placement of double bonds and to check for reasonableness of geometry. Make at least four of the structures, and consult with other groups to be sure that all of the structures are built. Carefully check on things like some double bonds, lone pairs, and hybridization to be sure that the structures are reasonable. If any questions, consult instructor before proceeding.
After one molecule is complete, you may just modify portions of the molecule to make the second or third molecule. But be sure to use File and SAVE AS and change the name to the new molecule.

2. Use Mechanics . After all of the structures have been made and saved, use Mechanics to minimize the energy in the structures. Use all of the default settings.
Run all of your molecules at this time using the File and Open .

3. Use MOPAC. Check with the instructor about whether the computer you are using is capable of doing the MOPAC calculations which are the next step. Set up the MOPAC screen as follows:
Calculation type: Vibrational spectrum (FORCE)
Parameters: PM3
Run all of your molecules at this time using the File and Open .

4. Use the Visualizer . Open the various files in the Visualizer. Then when a molecule is active select Analyze and then select Vibrational Spectra .
Click on a graph symbol of the spectra. This will select the portion of the molecule that causes that absorption in the spectrum. Continue to select other portions of the spectrum.
If you wish to change any aspect of either axis, double click on the axis and make changes in the dialog box.
If more than one molecule is open in the Visualizer, and Vibrational Spectra has been selected, multiple spectra are displayed for comparison.

EXPERIMENTAL AND MOLECULAR MODELING COMPARISON:
QUES. 6: For several of the molecules, make a table to list the atoms causing a vibration and the location. Compare the same vibration location in several molecules.

QUES. 7: Compare the computer generated spectra to the answers to Q. 5, especially regarding the number of peaks that should be present. Comments.

QUES. 8: Compare the computer generated spectra with FT-IR spectra. Comments.

Laboratory # 2
CHEMICAL PROPERTIES OF A CHROMIUM - EDTA COMPLEX

Purposes are to study:
1. Reactions and mechanisms associated with a chromium - EDTA complex.
2. Kinetics of the formation reaction.

INTRODUCTION:

When a chromium(III) solution is mixed with an excess of EDTA, various color changes are observed at various pH values. Some of the changes are slow enough so that the kinetics may be determined using a spectrophotometer. Although the main purpose of this experiment is to study the kinetics of the Cr-EDTA complex, a variety of other reactions will be studied to determine the nature and formula of the complex.

MOLECULAR MODELING

1. Use the CAChe Editor to make the following molecules:
a. EDTA (ethylenediaminetetraacetic acid; Shriver, p. 322)
b. Hexaaquochromium(III) ion. The easiest way to make a coordination complex is to select Tool , then select Atom tool; then from the Atom menu, select the Periodic Table , select chromium and type: +3 in the Charge box. Then OK.
- Place the cursor in the middle of the screen and click to place the chromium atom.
- Now from the Atom menu, select oxygen. Use the cursor to place, click six oxygen atoms in place in a hexagon shape. Now place the cursor on first (order is important) oxygen, click-hold-drag to the chromium atom and release to draw a bond. Continue for the other five oxygens.
- Create Coordinate Covalent Bonds . Use the Tool menu to select the Select mode. Position the cursor on a bond, press and hold the command key and click-hold-drag the mouse to select Coordinate . This should give an arrow pointing toward the chromium - if not repeat and select reverse. Continue on the other bonds. Finally do all the things in Beautify .

c. EDTAchromium(III) (see Shriver, p. 322) - Make the structure 6 coordinate using only the EDTA and no water molecule. Start from the hexaaquochromium(III) ion. First change all of the coordinate bonds back to single bonds (the reason for this is to make the program create the rings in a latter step).
- Use the Tool menu to select the Atom tool. Place the cursor on one oxygen atom, click-hold and press the Option key. This brings up the Periodic Table and allows the selection of a nitrogen atom. Click OK. Repeat on a second adjacent oxygen atom.
- Repeat the process with the other four oxygen atoms -- only this time, make each of the remaining oxygen atoms to have a -1 charge.
- Use the View menu to turn off the hydrogen atoms. Use the Atom menu to select either carbon or oxygen (no charge) to construct the rest of the EDTA molecule. Put in the double bonds to the extra oxygens.
- Use Beautify menu.
- Now go back to part b) - Create Coordinate Covalent Bonds, then Beautify again.
d. Use Mechanics to get a minimum energy structure for the EDTAchromium complex. Use all of the default settings.
e. Use the Editor to make EDTA aquochromium(III). Start with the previous structure. Click on one of the acetate oxygen-chromium bonds, then press delete. Use the Atom tool to place another oxygen very near the previous oxygen. Use the procedures to create a coordinate bond. Use the Beautify menu.
f. Make EDTA hydroxochromium(III). Start with the last structure completed and use the Tool menu to select the Atom mode. Put the cursor on the water molecule oxygen, click-hold and press the Option key. Change the oxygen charge to -1 to make the hydroxide ion. Use the Beautify menu. Use Save As and give another name.

Laboratory # 3 METAL COMPLEXES OF DIMETHYL SULFOXIDE

Adapted from Pike et. al, "Microscale Inorganic Chemistry", Exp. 20, p. 218-222.

INTRODUCTION:

In this experiment, IR spectroscopy is used to investigate a series of DMSO (dimethyl sulfoxide, CH3SOCH3) complexes. Dimethylsulfoxide is structurally similar to acetone, with sulfur replacing the carbonyl carbon. The normal absorption of the S=O bond occurs at 1050 cm-1. This is lower than the C=O frequency, since the SO bond has a larger reduced mass than the CO, resulting in a frequency shift.
Metals can bond to DMSO either through its oxygen or its sulfur. If the bonding is to the sulfur , the metal donates electrons from its pi orbitals into the empty pi* antibonding orbital (LUMO ) on the DMSO ligand, thereby increasing the S=O bond order, increasing the frequency of the S=O absorption .
If the bonding of the metal is to the oxygen of the DMSO, the metal forms a bond with one of the lone pairs on the oxygen , (HOMO ), and thereby withdraws electron density from the oxygen. Since the oxygen will "seek" to regain electrons to compensate for the electrons donated to the metal, the net effect is that the S=O bond order declines and the S=O absorption appears at a lower frequency .
In this experiment, we will use two different metals, copper and palladium, to react with the DMSO. Then we will analyze the compounds using the FTIR to characterize the complexes to find the mode of metal bonding. If you have had the principles of SHAB theory, perhaps you can make a prediction about the most likely mode of bonding for each metal.

MOLECULAR MODELING

1. Use the Editor to make the following molecules:

a. DMSO - Dimethylsulfoxide
b. DichlorodiDMSOcopper(II) - make this first complex with the oxygen bonded to the copper. Make sure that the chlorides are -1. The copper should have a sp3 configuration and the sulfur should have sp2. Save as Cu-O-DMSO.

c. DichlorodiDMSOcopper(II) - make the second complex with the sulfur bonded to the copper. Make sure that the chlorides are -1. The copper should have a sp3 configuration and the sulfur should have sp3. Save as Cu-S-DMSO.

2. Use Mechanics to find the minimum energy structure for the three complexes.

3. Use ZINDO or as per instructors advice - ExtHuckel to calculate the molecular orbitals for the above three molecules. In ZINDO - Calc. type: Energy ; Multiplicity: Doublet ; SCF type: ROHF

4. Use the Tabulator to calculate the molecular orbitals: HOMO -7 to LUMO 1 . Also change the isosurface value to 0.025

5. Use the Visualizer to open a series of molecular orbitals. The object of your search is to try to find supporting evidence for the statements made in the second and third paragraphs of the introduction. First look at DMSO. The appropriate MOs may not be exactly the HOMO or the LUMO but will be close in energy. Sketch what you think are the appropriate orbitals and cite the MO numbers.
- Now look at the MOs of the complexes and see if any of the bonding orbitals in the complexes were derived from the metal d orbitals and the MOs of the pure DMSO. You may or may not find some that will match. Sketch and cite the MO numbers that do match.

6. Use the cursor to select one or both of the S=O double bonds. Then use the Analyze menu to select Via Internals . Then from the Analyze menu, select Via Internals. Then select bond in the left menu, then select bond order in the middle menu, then look for the check mark in the right menu - it should be close in value to a double bond. What value do you obtain? Compare repeat this for all three molecules and report the values obtained. Again compare to the second and third paragraphs of the introduction.

7. Find the proper folders on the hard drive, CAChe, Inorganic, Your name, and the folder name that you made. First highlight Cu-S-DMSO, then from the File menu select Duplicate to get a copy of that file. Repeat with Cu-O-DMSO. Change the names of these new copy files to Zn-S-DMSO and Zn-O-DMSO.
- Use the Editor to open the file Zn-S-DMSO and change the copper ion to the Zinc +3 atom. (This is the only way to do a calculation later on since zinc will have to serve as a model for the copper ion. Repeat this procedure with the file Zn-O-DMSO. Check names or do Save AS to save them.

8. Use the MOPAC program to set Calc. type: Vibrational spectrum force ; Multiplicity: Doublet ; Parameters: PM3 . Do this for the two complexes with Zn as the central metal. Also do this for the DMSO molecule.

9. Use the Visualizer to open each of the molecules. Use the Analyze menu to select Vibrational Spectra. Compare the frequency of vibration for the three molecules. Again compare with statements in the introduction and the the experimental FTIR results. Note: They may not agree.

Report Summary:
a. Try to assign all of the major peaks, especially those in the vicinity of 1000 cm-1.
b. Determine the mode of bonding (S or O) of the DMSO to the metal in each case.
Combine the experimental FTIR results with bond order and IR calculations from the molecular modeling.
c. Make detailed drawings of the metal complexes with DMSO. Then make a detailed drawing showing the bonding orbitals of the metal involved with DMSO sulfur or oxygen (read intro and use the molecular modeling results). Be sure to contrast the differences between copper and palladium.
d. Explain the mode of bonding based upon the SHAB theory.

Lab # 5 TRIS AMINO ACID COBALT COMPLEXES

INTRODUCTION:
It is known that the coordination compounds of trivalent cobalt with three amino acids can exist in two geometric forms. A trans forms and an all cis form. Amino acids bond through the amine nitrogen and the carboxylate oxygen. The relative relation of the amine nitrogens and the oxygen determines the form. If all three amine nitorgens are cis, then the three oxygen atoms are also cis. The other geometric isomer has two of the nitrogen and two of the oxygen atoms trans to each other. In addition each of these geometric isomers may also have optical isomers.
Various procedures have been developed to obtain a pure form of the various isomers including the optical isomers. The procedure given in this lab is designed to produce one of the isomers. The analysis of this compound using NMR should give information about which isomer is obtained. The all cis isomer should produce a doublet for the methyl proton resonances, while the trans isomer produces a set of overlapping triplets.

EXPERIMENTAL PROCEDURE:
Adapted from: Inorg. 6,2063(1967)

MOLECULAR MODELING:

1. Use the Editor to make the two geometric isomers cited in the introduction. This is somewhat complicated because of the the number of rings involved.
- First make the two cobalt isomer complexes using three ammonia and three hydroxide (this will need oxygen as -1 which is needed later.) molecules. Use cobalt as +3 . Use Beautify to get them into the octahedral form. Do not bother to make the bonds coordinate at this time. Save this as a separate file in case you need to start over to make the rings a second time.
- Now delete the hydrogens from the oxygen and nitrogen. Next connect a nitrogen - oxygen pair with two carbons. To make the amino acid alanine, the carbon closest to a nitrogen gets a methyl branch. The carbon closest to the oxygen gets a double bonded oxygen to make the carboxyl group. Try to rotate the molecule as you try to form the rings so that they are in good approximate positions in the plane of the monitor.
- Finally use the Beautify. Hopefully you have reasonable structures if not try again, maybe one ring at a time.
- Convert the ligand metal bonds to coordinate and then use Beautify and use Valence and geometry to clean up the structures. Save AS.

2. Run Mechanics on both complexes.

3. Reopen the complexes in the Editor and determine which of the optical isomers that you have made. Refer to the section in the Lab Manual called Inorganic Stereochemistry and follow the procedure involving specific rotation/orientations for viewing.

4. Use the Adjust menu and select Mirror to make a mirror image of the molecule. Now look at this new molecule and try to determine the type of optical isomer to see if it is really different. Use Save As to give this new molecule a different name.

Report Summary:
1. Make drawings of the two geometric isomers and the optical isomer. Clearly label each including the type of optical isomer.
2. Outline the reactions that are probably occurring during the synthesis including the change in oxidation state.
3. Discuss the results of the visible spectrum and the NMR to identify the isomer synthesized.

Lab # 7 MOLECULAR MODELING - VANADIUM COMPLEX/SPECTRA

1. Use the CAChe Editor to make the following molecules.
a. Hexaaquovanadium(II)
b. Hexaaquovanadium(III)
c. Oxopentaaquovanadium(IV) - the oxo is an oxygen with a -2 charge.
d. Bis(acetylacetonate)oxovanadium(IV) - abbrev. - VO(acac)2
- Use the Tool menu to select Fragment , then use the fragment library to select All ligands , finally select acac . Click OK.
- Click near the bottom of the screen. Click near the top of the screen. Use the Tool menu to get the Select tool.
- The last acac fragment should now be selected, press command T so that you can rotate, flip, position that acac over so that the oxygen atoms form a square.
- Complete the molecule by adding the +4 vanadium in the middle of the oxygens. Then connect the oxygen to vanadium (leave as a single bond for now). Use the Select tool to change the vanadium to dsp2 configuration, use Beautify , Rings and Geometry only at this time.
- Next rotate the molecule so that the square plane is almost flat (in/out of plane of the monitor. Now add the -2 oxygen atom. Make all coordinate bonds to the metal, put the vanadium configuration to square pyramid, and finally use Beautify , omit the configuration.

e. Tartratooxovanadium(IV) - see tartrate structure earlier in the lab book. This structure will challenge your skills because Beautify does not do a good job on this one. Picture the last molecule that you made - the oxygens are in a square pyramid structure. This one will be the same except that the carbon connecting atoms form a "bowl" beneath the four oxygen atom square plane.
- To start Open the Oxopentaaquovanadium(IV) and delete all of the hydrogens.
- Use the Atom tool, positions the cursor over an oxygen atom, click-hold,press the option button to change the oxygen to -1 charge. Repeat with the other three oxygen atoms.
- Rotate the molecule so that two oxygens are in the plane of the monitor and the other two are in/out of the monitor plane. Place two carbon atoms below the two oxygens in the plane.
- Rotate the molecule so that the other two oxygens are now in the plane of the monitor and put two more carbons below them. Rotate the molecule so that you can see the 3-D effect of the four carbon atoms under the oxygens of the square plane.
- Connect the carbons to each other and to the appropriate oxygens.
- Place a zero charge oxygen double bond on the two terminal carbons of the tartrate group
- Use the select tool and check the configuration of the atoms. Vanadium should be set for square pyramid and two the carbons with two oxygens should be sp2.
- Beautify ONLY valence , (you might have to delete an extraneous hydrogen on vanadium, then Save it.
f. If you have time and want a challenge make the VOtart complex in the acidified solution. (see description in the the lab book.)

2. Use Mechanics to minimize all of the above structures using the default settings.

3. Go back to the Editor to check the structures for Oxopentaaquovanadium(IV) and VO(acac)2. Are the planes for the acac similar? Textbooks usually show them as being coplanar with the vanadium slightly above the plane. An interesting exercise is to run a Dynamics simulations to see whether you have found the global energy minimum or a local minimum.
- First go to the hard drive folders and find the file for VO(acac)2. Highlight this file and then use the File menu and select Duplicate . This gives a copy of the file.
- Start the Dynamics program and open the VO(acac)2. copy. Use the default settings and click Run. This program creates a series of random structures with more or less energy by stretching bonds and bending bond angles. Think of it as creating a kinetic energy profile for the molecule.
- When the program is complete, start the Visualizer and open the file VO(acac)2 copy.Trj. This opens two side by side windows. Click any where on the left energy profile and view the structure for that energy in the right window. Another option is to use Geometry menu and select Animate to view an animated series of molecules structures which correspond to the energy profile. Look carefully at the structures at the bottom two or three minimum and you should find one with both rings coplanar.
- What does this show about the ability of the Mechanics or any geometry optimization program to find the global energy minimum for a molecule?

4. Use the Editor and check the oxygen bond distances in Oxopentaaquovanadium(IV) and VO(acac)2 and compare them to the literature values as follows:
- For Oxopentaaquovanadium(IV): Four water molecules in plane should be 2.3 A, while the perpendicular oxo oxygen should be 1.67 A. That same oxygen in the acac complex should be 1.56 A. What values do you get?

5. For Oxopentaaquovanadium(IV), first use the copy command to copy the molecule, open a New file, and then paste the molecule into it. Then do the procedure to lock the bond distances of all of the oxygens at the appropriate values. Save the file with a similar name to the first appended with "lock".
- Now run Mechanics on this file.

6. Run ExtHuckel or ZINDO (Energy only) as per instructors direction on both the original and the ".lock" Oxopentaaquovanadium(IV) molecules.
- Run the Tabulator - Molecular Orbitals ; from HOMO -7 to LUMO +3 ; Isosurface value: 0.05

7. Use the Visualizer to look at the two molecules. First what is the evidence that the oxo bond is a double bond as usually indicated in the textbooks? First select the vanadium oxo bond. Then from the Analyze menu, select Via Internals. Then select bond in the left menu, then select bond order in the middle menu, then look for the check mark in the right menu - it should be about 1.7 which is close to a double bond. What value do you obtain? Compare for the unlocked and the locked molecule.

8. Now Open some of the molecular orbital files. Which MO indicates a sigma bond between the vanadium and oxo oxygen? How about any indication of a pi type bond? Again compare the locked versus the unlocked molecule.

9. Find the Inorganic folder and open the molecules which have made been precalculated for electronic vibrations using ZINDO. Some of these required 15 to 20 minutes to calculate. From the Analyze menu, select Electronic Spectra. Compare the calculated spectra to the experimental spectra and note similarities and differences.

Report Summary: Draw structures and summarize your findings by reviewing the questions asked in the various procedures.

Lab # 8 SYNTHESIS OF METAL CARBONYLS

Adapted from: Szafran, Z., Pike, R., Singh, M., Microscale Inorganic Chemistry , John Wiley. 1991, p. 313-317

INTRODUCTION

Compounds in which a metal atom is directly bonded to carbon are known as organometallic compounds. Organometallic compounds are heavily used in the area of organic synthesis and in industrial chemistry. Metals in organometallic compounds are generally found in low oxidation states, with the most common carbon ligands being CO (called a carbonyl ligand), alkenes, C5H5- (cyclopentadienyl anion, abbreviated Cp), and C6H6 (benzene). The bonding to olefins in these compounds was first described by M.J.S. Dewar as consisting of two aspects.

1. Electrons are donated from the filled olefin orbital to an empty metal sigma orbital.
2. Electrons are "back-donated" from filled metal d orbitals to empty olefin * orbitals.

This "give and take" arrangement is termed synergistic bonding. Bonding to the CO group is similarly synergistic. The carbonyl ligand donates the lone pair of electrons on the carbon to an empty metal sigma orbital, and the metal "back-donates" electrons from the filled metal d orbital to the empty pi* orbital of the carbonyl.

The donation of electrons from the metal to the pi* orbitals of the carbonyl has a drastic effect on the IR frequency of the CO stretch. As the metal donates electron density to the pi* orbital, the bond order of the carbonyl will decrease (an antibonding orbital is being filled). Infrared spectroscopy is therefore a very sensitive indicator of the nature of bonding in metal carbonyls.

Metal carbonyls are most often prepared by the direct reaction of a metal with carbon monoxide gas. This reaction is quite dangerous, as CO will bind nonreversibly with hemoglobin, and is therefore extremely toxic. In this reaction, CO in generated in situ (within the reaction system) employing the much safer reagent DMF as the source of the CO group. A square planar triphenylphosphine complex is prepared via the reaction of the starting material, rhodium (III) chloride hydrate, with triphenylphosphine and DMF (unbalanced).

RhCl3.3H2O + 2(C6H5)3P + HCON(CH3)2 ----> RhCl(CO)(P(C6H5)3)2
Questions

1. What is the hybridization of the rhodium atom in the product, Rh(CO)Cl(PPh3)2?
2. The infrared CO stretching frequency is higher for mer-Rh (CO)Cl3(PPh3)2 (Note Rh is (III) ) than for Rh(CO)Cl(PPh3)2. Explain. (HINT : Consider the oxidation states of the the Rh and the ability of the metal to back-donate electrons to the carbonyl group.) Where would you expect the CO band for Rh (CO)Cl2(PPh3)2 to appear?

MOLECULAR MODELING:

1. Use the Editor to make the following molecules:

a. trans-Chlorocarbonylbis(triphenylphosphine)rhodium(I)
b. Substitute into the above compound and put phosphine in place of the triphenyl phosphine.
c. mer - carbonyltrichlorodiphosphinerodium(III)

2. Run Mechanics on all of the above compounds.

3. Use ZINDO or ExtHuckel as per instructors direction on compound b and c only. In ZINDO use the default and calculate the Energy only.

4. Use the Tabulator and calculate the Molecular Orbitals: HOMO -15 to LUMO 3 at the Isosurface value of 0.05 .

5. Use the Visualizer to look at the molecular orbitals. Cite and draw any that resemble those listed in the Introduction.

6. While still using the visualizer, compare the bond order for the CO ligand on the b and c, compounds. First select the CO bond. Then from the Analyze menu, select Via Internals . Then select bond in the left menu, then select bond order in the middle menu, then look for the check mark in the right menu. What value do you obtain? Compare all of the molecules.

Report Summary:
Write the structures of the complexes and summarize findings relating to molecular orbitals, bond order, and IR frequencies.

Laboratory # 9

SYNTHESIS AND USE OF WILKINSON'S CATALYST

Adapted from Pike et. al, "Microscale Inorganic Chemistry", Exp. 34, p. 271-282.

INTRODUCTION:
Homogeneous catalysis is a process where a catalyst and reactants remain in the same phase. If the reaction is carried out in the liquid phase, then the homogeneous catalyst must be soluble in the reaction medium. Organometallic compounds are used extensively as catalysts (heterogeneous and homogeneous) in industrial chemistry.
The first successful homogeneous system developed for the reduction of olefins involved the use of RhCl(PPh3)3, called Wilkinson's catalyst. Most catalytic reactions for hydrogenation of double bonds in organic compounds require high hydrogen pressures and high temperatures. It was found that some organometallic compounds can catalyze such hydrogenation reactions under mild reaction conditions.
In this experiment, Wilkinson's catalyst will be synthesized form rhodium chloride. The catalyst will then be used to make a dihydrido complex which can be isolated and is an intermediate for the hydrogenation of cyclohexene.
See Shriver, "Inorganic Chemistry", p. 719-23 for details of this reaction.

WRITE DETAILED STRUCTURES AND MECHANISMS FOR ALL PROCEDURES as part of your report.

MOLECULAR BONDING

1. Use the Editor to make all of the molecules in the Wilkinson's catalyst cycle. See Shriver p. 719-722. --the compounds below have the same "letter" designations.
a'. Chloro tri(triphenylphosphine) rhodium(I) - Note after making this one time, you may substitute PH3 for the triphenylphosphine.
b'. Chlorodihydridotriphosphinerhodium(III)
c. Chlorodihydridocylohexenediphosphinerhodium(III)
d. See text

e. A fragment: RhH2 (+1 ox. state) Make a coordinate bond from the bond of the hydrogen molecule to the rhodium. See Shriver p. 649-650, the purpose is to look at an intermediate step in the bonding before the hydrogen molecule is split into two hydride ions. See instructor if any questions.

f. Use the fragment library to find Zeise's salt - probably in coordination compounds. Transfer to the editor and Save it. Note the orientation of the ethylene group in relation to the square plane.

2. Use Mechanics on molecules a-d using the default settings.

3. Use ZINDO or ExtHuckel as per instructor's direction to optimize geometry for the two molecules listed in e. and f.

4. Use the Tabulator to calculate the Molecular Orbitals. Do all MOs for molecule e.
Do HOMO -7 to LUMO + 3 for molecule f. Set the Isosurface value for 0.05 for both.

5. Use the Visualizer to look at the MO's for both compounds. Which atomic orbitals on the hydrogen in one case and the ethylene in the second case are use for bonding with the metal orbitals. Draw and cite the MOs used in the bonding. Can you find anything that resembles p. 685?

Report Summary: Summarize the synthetic steps and findngs, as well as discuss the findings from the MO studies.

Laboratory # 10
NMR Investigation of Molecular Fluxionality:
Synthesis of Allylpalladium Complexes

Adapted from: Szafran, Z., Pike, R., Singh, M., Microscale Inorganic Chemistry , John Wiley. 1991, p. 298-301

INTRODUCTION

Palladium (II) forms a large variety of square planar organometallic complexes with various olefinic organic groups. In the case of the reaction of PdCl2 with allyl bromide, the allypalladium bromide complexes shown in Figure 9.3 may be synthesized.

Complexes between a metal salt and an olefin have been known since 1827. In the palladium complexes, the olefin donates electron density from its filled orbital to an empty palladium symmetry orbital. The palladium, in turn, donates electron density from a filled pi orbital to the empty olefin pi* orbital. This results in a lowering of the C=C bond order and a consequent lowering of the olefin IR absorption frequency.

When the allyl group is bound, the complex is stereochemically rigid. There are three types of nonequivalent hydrogen atoms, shown in Figure 9.4. Hydrogen c is clearly unique, being part of the only CH group. The b hydrogen atoms are syn to hydrogen c, and the a hydrogen atoms are anti to hydrogen c. The 1H NMR spectrum would therefore show three signals. When the allyl group is sigma bound, there is free rotation about the C-C single bond, thus rendering the a and b hydrogen atoms equivalent. The 1H NMR spectrum would therefore show only two signals. Molecules showing this kind of motion are said to be fluxional.

MOLECULAR BONDING

1. Use the Editor to make all of the allyl palladium complexes shown in Figure 2 of Lindley. J., J. Chem. Educ. 57 , 671 (1980).
I. For this molecule, use two weak bonds from each of the resonance carbon carbon bonds rather than a single bond to the center carbon as shown. Also try to get the ally groups in a perpendicular and staggered position as shown. This will be difficult to build this molecule.
II.
III.

e. Redo III. and replace the DMSO with chloride groups.

f. Use the fragment library to find Zeise's salt - Look for ligand pi complexes, then [(C2H4)PtCl3]-. Transfer to the editor and Save it. Note the orientation of the ethylene group in relation to the square plane.

2. Use Mechanics on molecules I, II, III, e using the default settings.

3. Use ZINDO or ExtHuckel as per instructor's direction to optimize geometry for the two molecules listed in e. and f.

4. Use the Tabulator to calculate the Molecular Orbitals.
Do HOMO -7 to LUMO + 3 for molecule e, f. Set the Isosurface value for 0.05 for both.

5. Use the Visualizer to look at the MO's for both compounds. Which atomic orbitals on the hydrogen in one case and the ethylene in the second case are use for bonding with the metal orbitals. Draw and cite the MOs used in the bonding. Can you find anything that resembles p. 685?
- What is the bond distance for the Pd-Pd in compound I?

6. Use the Editor to open the file for complex e made previously. Make a copy of it and paste it into a New file.

- The following exercise allows the examination of the change of energy as the olefin rotates on the C-C single bond. This free rotation on the bond renders the a and b protons equivalent. The NMR spectrum will show only a single doublet. This rotation will illustrate a kind of motion called fluxional.
- Follow carefully to set up a search of the Dihedral angle. The cursor should be in the Select mode. Select the atoms in order listed. Click on the terminal carbon of the olefin to select it. Now hold and continue to hold down the shift key as you select the other atoms. Next select carbon # 2 then carbon # 3, and finally Pd. This defines a dehedral angle angle.
- Use the Adjust menu to select Dihedral Angle . This will bring up a dialog box. Click in the box Define Geometry Label and then click the Search circle. This will bring up a further dialog box. Use the defaults except change the number of steps to 12. Then click Apply , then Done .
- To check how the search will look, use the Analyze menu, to select Preview Conformations. Use the slider to look at the various conformations.
- Use Mechanics to generate an energy map of the rotations. For Calc. type: select Exhaustive Search .(Map) , then select Optimized , then Done , then Run .
- Use the Visualizer to open the file name now appended with .map.

Report Summary:

Make drawings of the complexes, discuss the results of the MO studies, and the rotation about the dihedral angle. Summarize the results from the synthesis and characterization.