February 2013

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Here are some links to models (all B3LYP/6-31G*) that we will use in class today (Monday, Feb 25). Download and save the files (as needed). Then use Spartan to open them (they are in the Downloads folder).

Fragment MO Analysis of (CO)4Fe(C2H4)
Orientation Effects in (CO)4Fe(C2H4)

*(CO)4Fe fragment obtained from equilibrium geometry model of Fe(CO)5

Alkene Substituent Effects in (CO)4Fe(alkene)
Other metal-pi complexes





According to the standard M-CO bonding model, sigma donation from CO to the metal transfers electron density from CO to M, while pi donation from the metal to CO reverses the electron flow. The ultimate result of these opposing bonding mechanisms is far from obvious, but one can appeal to the MO model to make a prediction: greater transfer of electron density occurs when the fragment orbitals are:

  1. closer in energy (better energy match) and
  2. achieve greater overlap

The situation is further complicated when several ligands, either all CO, or a mix of CO and others, bond to the metal simultaneously. You can investigate the flow of electron density using Spartan’10 electrostatic potential maps of the (CO)5CrL models listed below. Spartan’10 models of (CO)4CrL fragments in which the CO trans to L has been removed are also provided for comparison (how does adding CO to the fragment affect the distribution of electron density?). All pentacarbonyl geometries have been optimized using B3LYP/6-31G*, while the geometries of the tetracarbonyls have been obtained by removing the trans CO in the pentacarbonyl.

The pentacarbonyl models also contain calculated IR frequencies (unscaled). These frequencies have traditionally been used to assess the degree of pi donation from metal to ligand (and the bonding properties of the ligand trans to CO). In fact, there is a fair correlation between frequencies and electrostatic potentials.

A short summary of the results can be found here.

To download a model: click link, Download, and Save File. Open Spartan, navigate to the Downloads folder, and open the file.



The standard model of metal-CO bonding invokes two simultaneous orbital interactions:

  • sigma donation by ligand: CO HOMO + metal LUMO (a hybrid of d-s-p valence orbitals)
  • pi donation by metal: metal HOMO (d) + CO LUMO (π*)

You can investigate these interactions for several compounds of increasing structural complexity by downloading and examining the Spartan’10 models listed below. The models have all been optimized as neutral singlets using B3LYP/6-31G* except where stated otherwise. Tips for downloading and examining the orbital energies and surfaces appear at the bottom.

  • CO
  • Cr (high-spin multiplicity = 7; ground state of Cr is 3d^5 4s^1; donor orbitals are occupied alpha orbitals, acceptor orbitals are unoccupied beta orbitals)
  • CrCO
  • Cr(CO)6
  • Cr(CO)5 (geometry obtained by deleted one CO from opt Cr(CO)6)

To download: click link, Download, and Save File. Open Spartan, navigate to the Downloads folder, and open the file.

To see potential MO interactions between fragments (Cr + CO, (CO)5Cr + CO) use Display: Orbital Energies to examine HOMO (donor) and LUMO (acceptor). Orbital energies are displayed in lower right-hand corner. (Note: this is not useful for Cr high-spin; in this case, use Display: Output to find orbital energies and use Display: Surfaces to generate and display orbital surfaces.)

To see resulting bonding orbitals (CrCO, (CO)6Cr) use Display: Orbital Energies to examine HOMO and HOMO-x orbitals. Look for orbitals that appear to combine fragment orbitals in a bonding fashion.

NMR, we all know, is the workhorse for figuring out what we’ve made. The problem with the typical NMR spectrum, though, is that it shows us signals from everything in the sample: the desired product (hooray!), by-products, leftover starting materials, and a variety of impurities (you’ve all heard the speech about how Reed’s CDCl3 always contains HCl, right?). At one time or another every chemist has been fooled by an “impurity” peak masquerading as something important.

Fortunately, help is at hand. Practically everyone encounters the same impurities so some chemists have sat down and tabulated the chemical shifts of these frequently-encountered impurities in several commonly used NMR solvents:

  • NMR Chemical Shifts of Trace Impurities: Common Laboratory Solvents, Organics, and Gases in Deuterated Solvents Relevant to the Organometallic Chemist by G.R. Fulmer et al., Organometallics 2010, 29, 2176–2179, DOI: 10.1021/om100106e
  • NMR Chemical Shifts of Common Laboratory Solvents as Trace Impurities by H.E. Gottlieb et al., Journal of Organic Chemistry, 1997, 62, 7512-7515, DOI: 10.1021/jo971176v

We will discuss a computational paper in class on Friday. Links to the paper and instructions are provided below. Some of the instructions ask you to prepare written responses that will be turned in at the end of the class discussion

Paper: A 2008 paper on the mechanism of the metal-catalyzed olefin metathesis reaction. (DOI 10.1021/om8008519). This reaction led to a Nobel prize in 2005 for Prof. Grubbs of Caltech (he’s the bearded fellow in the upper left corner of our course web page) and you can read more about it online and in our textbook.

Instructions for how to read the Rowley paper, prepare for the class discussion, and prepare items to turn in afterwards.

HW #1 feedback

Some ideas for you:

  1. Everyone offered a reliable way to find articles by their DOI. Several of you described an especially efficient route: just type this URL: dx.doi.org/DOI. So if your DOI is 10.1021/ed063p222, you would simply type dx.doi.org/10.1021/ed063p222 in your web browser. It doesn’t get any easier than that.
  2. Thank you for being so willing to articulate your interests in Chem 348 and beyond. I’m fascinated by the spectrum of interests that appeared even in a smallish upper-division chemistry course like ours. We seem to have an amazing collection of future profs, PhDs, green chemists, doctors, medical researchers, environmental activists, artists, chemical engineers, computer scientists, science writers, and more. I hope I will get to know each of you even better as the semester rolls along (and that you will get to know each other as well). FYI, the most popular paper chosen for Interview the Scientist appears to have been Palladium-Catalyzed Trifluoromethylation of Aromatic C-H Bond Directed by an Acetamino Group (4 mentions).
  3. Excellent analyses of the Parshall/Prutscher article. Sadly, there was much left unsaid in this article (probably because the background information was well-known to readers of that time period). In the late 70’s/early 80’s, large fluctuations in petroleum prices led to the creation of a federal government program to convert coal (plentiful in the US) into gasoline (US production has been declining since the early 70’s). This program began funding a lot of academic research and universities rushed to add organometallic chemists to their research departments so that they could receive some of this funding. Unfortunately, the program proved to be a classic example of boom-and-bust economics as gas prices fell, political support for coal-to-gas vanished, and chemical companies stopped investing in new manufacturing plants (the article explains this last item quite well). By the late-1980’s many organometallic chemists were being told by funding agencies (and their universities) to find new areas of research or else. Interestingly, while many chemists left the field, organometallic chemistry eventually roared back to life in the mid-90’s as a source of tools for organic synthesis and it doesn’t seem that this area of research will fade anytime soon. What is more, gas prices are starting to rise again and new feedstocks (natural gas, bio-based feedstocks) may offer new challenges to industrial chemists who need to convert these feedstocks into high-volume chemicals.
  4. Some of you said the lines in the figures were bonds. Some of you said they weren’t. I recall a remark that Prof. James Ibers (Northwestern University) made on this very topic back in the early 80’s. He was giving a seminar at UC Berkeley on some new organometallic compounds that he had made and someone in the audience (not me) asked him about the meaning of the lines in his drawings. Ibers instantly replied, “I used to worry about that when I was younger, but I don’t anymore,” and then went on with his talk as if nothing had happened.

We will discuss two papers in class on Wednesday. Links to the papers and instructions are provided below.

Paper #1: A 1986 paper on commercial drug manufacture based on asymmetric hydrogenation by Nobel laureate W.S. Knowles (DOI 10.1021/ed063p222).

Paper #2: Parshall/Putscher (1986) paper that you read for HW #1 (DOI 10.1021/ed063p189). This provides useful background/big picture information on industrial catalysis.

Instructions for how to read the Knowles paper and prepare for the class discussion.

I will have afternoon conflicts on several Fridays during the semester (going out of town, meeting with job candidates, and so on). When that happens, I will have to shift or cancel my office hours.

Based on the ‘office hour’ poll that I conducted Monday, it seems like alternate hours won’t affect your ability to reach me so the important is to let you know as soon as I can when there is a schedule change.

Today’s office hours are 12-2 PM (and then I’ll be off campus for the rest of the day). You can track my schedule at this web page (there is also a link to this schedule from my home page).