12 Aug 2014

A Tale of Two Structures

In-Class Activity

Submitted by Chip Nataro, Lafayette College

In this activity, students will compare and contrast two closely related structures, [Pd(dcpf)PR3]2+ (dcpf = 1,1'-bis(dicyclohexylphosphino)ferrocene; R = Me or Ph). They will be required to obtain the cif files from the supporting information of a paper. They will then make a variety of measurments in the two stuctures. These measurements can be made using a variety of different freely available programs. Instructions are provided for Mercury 3.3 and Olex2. Finally, students will be required to provide a rationale for the differences in the two structures. Students are expected to have some knowledge of crystallography, sterics vs. electronics and the trans effect.


This material is based upon work supported by the National Science Foundation under Grant Number (1057795).

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Learning Goals: 

After performing this activity students should be able to

1) Obtain cif files from the supporting information of an ACS journal

2) Open the cif files in a program that allows them to make measurements on the structures including drawing planes and finding centroids in rings.

3) Explain disorder in crystal structures.

4) Rationalize how electronics and/or sterics impact these particular structures.

Equipment needs: 

A computer with an internet connection.

Implementation Notes: 

The provided instructions have students search for the desired information using the ACS pubs search tools. Certainly SciFinder Scholar could be employed if access is available. I have chosen to provide directions for making measurements using Mercury 3.3 and Olex2. Certainly there are other options. Of the two, Mercury is far more user friendly which is certainly an attractive option in a classroom setting. However, Olex2 provides esd values for non-standard measurements (e.g. those involving centroids) which Mercury does not do (at least as far as I know). It might be valuable to have groups perform the measurements with different programs and then have them discuss their results. There should be little to no difference in the values, but the differences in esd's could be a valuable teaching moment.

Evaluation Methods: 

I have not used this in class yet. I plan on introducing it for the first time in the fall. I think it will be an in class activity. It might make more sense in a lab or homework setting. I don't have a lab in my fall course, so that somewhat limits my options. Hopefully more details will be forthcoming. I certainly would appreciate any feedback from anyone that adopts some or all of this Learning Object.

Creative Commons License: 
Creative Commons Licence


I used this for the first time, but actually gave it as a homework problem as opposed to using it in class. If you do this, be sure to clearly indicate to the students that there are instructions available. I put them on our course Moodle page, but apparently they didn't notice the instructions. And of course I only gave them the option of using Olex2, which is a little bit tough to work with.

There are 9 students in my class this semester. On the day the problem was due, one was away on a med school interview and one opted not to turn it in.

Q1)         7/7 got this question correct.

Q2)         5/7 got this correct

1/7 identified the solvents as propene and butadiene

1/7 did not identify the solvents

Q3)         5/7 got this correct

1/7 said there was disorder somewhere in the [Pd(dcpf)PMe3]2+ structure

1/7 said the anion was disordered

Q4)         1/7 got this correct

4/7 fine with bond lengths and angles, problems with the centroids and planes

1/7 all correct except the bond angles due to selecting atoms in wrong order (~11˚) 

1/7 all correct except did not list bond angles

Q5)         3/7 approximately square planar but P atoms bent towards Fe atom/ferrocene

1/7 nearly square planar

2/7 slightly distorted square planar

1/7 they are about 30˚ off from being square planar so they have some square pyramidal character

Q6)         6/7 longer in PPh3 because PMeis a better donor

1/7 longer in PMe3 because PMe3 is a better donor

Q7)         1/7 space filling model gives perspective of closeness

                1/7 due to the bulky cyclohexyl groups, the PPh3 can't get close enough 

                1/7 groups are bulky so it would be tough to add anything to the metal

                1/7 the PMeis much smaller so it is not as affected by the other ligands

                2/7 sterics definitely play a role

                1/7 sterics don’t play a role because PMe3 is smaller than PPh3

Q8)         1/7 the Fe-Pd length gets shorter as the Pd-P gets shorter


1/7 the Pd-P bonding either adds or removes electron density to/from the Pd, so it would change how the Pd interacts with the Fe


1/7 the ligands on P impact the amount of electrons that can be donated to the metal


1/7 the more electron rich the Pd, the more the Fe donates


3/7 the more electron rich the Pd, the less the Fe donates


Q9)         1/7 more backbone bending with a more donating ligand


                1/7 changing the strength of the Fe-Pd interaction will change the bond angles


                1/7 if the bond between Fe and Pd is stronger, the coordination of Fe to the ferrocenes will be weaker


                2/7 as the Fe-Pd bond distance decreases, the angle of the rings increases


                1/7 stronger Fe-Pd bond causes smaller angle between the rings


                1/7 the backbone wouldn’t be as strong as the Fe interacts with the Pd

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