Metal-phosphine Bonding Revisited #chempaperaday 249

Any inorganic chemist knows that phosphines (in general) are good sigma donors. When phosphines are involved, however, there is a lot of suspicion about pi accepting abilities of phosphines or whether the empty d orbitals are involved in bonding or not. I have to admit, it's confusing. So, here is a great article on phosphines where the authors try to answer these questions. It was published in 1992 and I did not check how many times it was cited or if there have been any corrections made.

- The most surprising result for me was that ALL phosphines ( PMe3, PH3, P(OMe)3, PF3) are GOOD sigma donors. Yes, even PF3? Who would have thought?

- When it comes to pi acidity though the trend is as follows :

                                         PMe3 < P(OMe)3 <  PF and they conclude that PF3's pi acidity is "of comparable strength to CO" 

-So, you want a pi-acceptor, but not the beast? Use PF3, if you can find it in the lab.

-How about d-orbitals? Well, according to the study, d-orbitals do not directly act as pi-acceptors, instead, they are "polarization functions" that help to increase pi acidity.

Also, this article looks like a good follow-up. Maybe I'll read at too.

http://pubs.acs.org/doi/abs/10.1021/cr00029a008

Is CO a Special Ligand in Organometallic Chemistry? #chempaperaday 247

As I mentioned in a recent post, I have been reading a lot of Hoffmann papers to study and learn more about MO theory. So, be ready if I post several of them in the next couple weeks. 

Transition metal carbonyl complexes are very important in organometallic chemistry.  Sometimes they are used as catalysts or precursor to catalysts, and sometimes they are used to explain our understanding of important industrial processes like Fischer-Tropsch synthesis. 

It looks like CO is very special in terms of sigma donating and pi accepting capabilities. But why? Is it unique? Can we find better ligands? This paper is probably the first of the series I'll post where I am trying to find an answer (not experimentally, just by reading literature). So, if you follow the series, you will probably learn a lot with me.

Fischer and Schrock Carbene Complexes: A Molecular Modeling Exercise #chempaperaday 246

Transition metal carbene complexes are really important complexes in organometallic chemistry and they are used to produce important organic molecules like the ones in olefin metathesis for example. Two of these complexes are much more important and in fact they both have names: Fischer and Schrock type carbenes. You can read about these in any inorganic chemistry textbook. But, I think you can never find a better summary of these complexes. This paper, although a molecular modeling exercise, does a great job explaining the general properties of these two type carbenes.  I wish textbooks were as clear and as simple as this article.

Honorary Organometallic Molecule #chempaperaday 244

So, lately I've been reading a lot of Hoffmann papers to practice and more about MO theory. I found an incredibly helpful article of his that he published in 1981 in Science. I think textbooks can get away with pasting this article and not giving any more explanation on the theory. It's so well written that you can start with zero knowledge in MO theory and end up understanding pretty much everything about it. The interesting thing is that although the article's title is "Theoretical Organometallic Chemistry", the famous dirhenium complex [Re2Cl8]2- complex is among some organometallic compounds. The reason?

Cr–Cr Quintuple Bonds: Ligand Topology and Interplay Between Metal–Metal and Metal–Ligand Bonding #chempaperaday 237

"The difference between Cr−Cr quadruple and quintuple bonds is not just another weak δ bond."

This is very nice study to find some correlation between several bond metrics, ligand types etc. and the M-M bond distance and bond order. As you can imagine, for some systems, there IS nice correlations. For example, systems like Cr2L4, weaker Cr-L interactions yield to stronger Cr-Cr bonds. I found this paper very useful to design new ligands to maybe break the record short distance and discover some unique properties.

Why Is Uranyl Formohydroxamate Red? #chempaperaday 236

Colors tell a lot in inorganic chemistry. While most of the reported U(VI) complexes are red, the complex in question here was reported as red. So, the reason was investigated and two factors were found to explain the color. If you are interested, you can read it here:

http://pubs.acs.org/doi/abs/10.1021/acs.inorgchem.5b00262

Oxidation State, A Long-Standing Issue! #chempaperaday 234

Oxidation state is both the simplest and the hardest concepts of chemistry. To be honest, sometimes (maybe more often than sometimes), I get confused too.  In fact, you can even find slightly different definitions of oxidation state depending on what you are trying to reach in the end. To be honest, I found this paper a little bit confusing in the beginning. It's not the author's fault of course. Once again, oxidation state is not really straightforward. Overall, I think it is a nice paper to read and a good summary of interesting examples.

BONUS : It's open access.

http://onlinelibrary.wiley.com/doi/10.1002/anie.201407561/abstract

"Valence Bond Theory in Coordination Chemistry" #chempaperaday 178

This is a very short paper by Linus Pauling. Apparently, he read an article where the author said that valence bond theory was not as popular and useful as it was. Obviously, the response came from Pauling and his response in fact was very short:

"I do not agree with this opinion."

The rest of the article explains how valence bond theory is still can be used in coordination compounds.

The article was published in Journal of Chemical Education, but here you can read it as pdf for free.

http://depa.fquim.unam.mx/amyd/archivero/VBPAULING_26400.pdf

"Why Are There No Terminal Oxo Complexes of the Late Transition Metals? or The Importance of Metal–Ligand π Antibonding Interactions" #chempaperaday 40/365

I was looking for some old papers and found this paper. It's in fact very similar to a lecture in inorganic chemistry. The title is very clear. So, there is not much to add. You can also look for "the oxo wall" to learn more about these complexes.

http://www.tandfonline.com/doi/abs/10.1080/02603598808035790#preview

It's all about bonding theory and symmetry.

Symmetry and Group Theory- Point Group Tips and Practice 7 (K2ReH9)

Time to add another example to point group practice problems. I got this complex from the publication below:

http://pubs.acs.org/doi/abs/10.1021%2Fic50014a026
S. C. Abrahams, A. P. Ginsberg, K. Knox

Inorg. Chem., 1964, 3 (4), pp 558–567

Publication Date: April 1, 196

------------Update-----------

Dr. Frank Hoffmann was very kind enough to contact me and "make the threecapped trigonal prism  visible through the polyhedral representation in VESTA.." So, he sent me the Vesta file and I just changed the color of the atoms so that it looks clear on my blog's template. You can see the screenshots below.  As I mentioned in my other posts, there is a free online course named "The Fascination of Crystals and Symmetry" on iversity.org . The course has started three weeks ago. So, you are not late to register and start enjoying the symmetry. Just check it out:

https://iversity.org/courses/the-fascination-of-crystals-and-symmetry

 Hydrogens are black, potassium ions are blue and rhenium ions are shown as pink.

 ------------Update-----------


I tried to draw and show the geometry, but I really couldn't figure out how I am supposed to show it using a software. I think you can see one of my unsuccessful attempts on Avogadro below.

  an unsuccessful drawing attempt!

Anyway, you can see the metal complex here:

 

 http://pubs.acs.org/doi/abs/10.1021%2Fic50014a026

So, the principal axis goes through the center of the "triangles." Then it is very easy to see that there is a C3 rotation axis. Now it is time to look for a perpendicular C2. You can see it (actually three of them) going along one of those equatorial atoms (7, 8, 9). Obviously, we are assuming that this is a perfect geometry with equal angles and bond lengths. This says that our point group will be D3. 

There is a mirror plane going through atoms #7, #8 and #9. This means there is a perpendicular mirror plane divides complex into two equal "parts." Finally, this mirror plane tells us that the point group is D3h.

If you had difficulty to follow how I found out the point group, you can look at the very simple "flowchart" I made here. 

Actually, this is a  really nice paper with a molecular orbital diagram too. I feel like it is an inorganic chemistry lecture. Also, this complex was one of the first ones that helped chemists think as "M-H bond as a normal covalency." [1].

Reference :

1. Crabtree, H.R. The Organometallic Chemistry of the Transition Metals , John Wiley and Sons, 2001. Print.

Molecular Orbital Theory Notes III

The first two posts in the series gave brief information about the d-orbitals and the metal-ligand orbital interactions. Now it is time to construct a molecular orbital diagram for a metal complex in the form of ML6. 

A few things you should never forget:

- Ligands are mostly more electronegative than the transition metal. Therefore, ligand orbitals should be drawn lower than metal orbitals. This also tells us that the bonding orbitals are mainly on ligand orbitals! 

- Nonbonding orbitals will be drawn at the same level as the atomic orbitals. So, they are mainly on the metals!

- Antibonding orbitals are closer to the metal. Actually, if you learn more about the MO theory and transition metal reactions, you can see the importance of this fact.

There is a really nice method to draw the diagram. 

1. Find the point group (I have many posts and a simple flowchart to determine point groups here.) 

2. Go to the character table for the point group and assign the symmetry properties (those t2g, eg, B1u etc. things) to each orbital. Sounds hard, but the character table gives you all. Very easy!

3. Because, there has to be symmetry and there is to have interactions, do the same thing for the ligand orbitals.

4. Following the rule that Sigma interactions > Pi > Delta, match the ligand and metal atomic orbitals. The ones that are the same (bonding) will go down, the ones that has no corresponding orbitals will be the nonbonding d-orbitals and the rest will be the antibonding ones.

Here is the first and the most important example:

For a perfect octahedral metal complex like ML6, the point group is Oh and the character table for Oh looks like this:

Now we are in the second step. The shortcut is that the first column with x, y, z is for the P orbitals.  So, our p-orbitals for this character group have the T1u "label." The first row (A1g) is always the s orbital. The second column with xy, xz etc. is for d-orbitals. So, in an octahedral field; dxz, dxy, dyz orbitals will be degenerate! And dz^2 and dx^2-y^2 are degenerate. If you are careful enough, you will notice that this looks like the "famous" d-orbital splitting in an octahedral field. I hope now you can see the relation.

http://chemwiki.ucdavis.edu/@api/deki/files/959/Octahedral_Splitting.png?size=bestfit&width=450&height=350&revision=1

Finally, let's draw the diagram. Once the orbitals are written for the metals on left, and the ligand orbitals on right (lower than the metal atomic orbitals), look for the symmetry and just connect them. A very important thing not to be forgotten is that for a transition metal, the d-orbital is always a (n-1) orbital. For example, Cr is in the first row and the electron configuration for the free atom is "3d5, 4s1" That's why we draw the d-orbitals lower than the s and p orbitals. I guess it is clear. The diagram below is from wikipedia. The antibonding t1u and a1g orbitals can change places. It is not a big deal. In the end, you should always count the number of MO's. The number should be equal to the some of the ALL atomic orbitals.  In this case; 

9 (from the metal) + 6 (ligands) = 15 MO's

Then you can place the electrons obeying the Aufbau Principle, Hund's Rule and obviously Pauli Exclusion Principle.  I hope this was helpful. 

Molecular Orbital Theory Notes II

After making an introduction to d-orbitals in the previous post, I guess it is time for some information about the types of interactions. As I said before, the symmetry (therefore the overlap) is essential for an interaction between ligand and metal orbitals. 

There are three types of interactions between a ligand and metal orbital. These are Sigma, Pi and Delta interactions.

Sigma Interactions: These are the strongest interactions resulting from the best overlap between the orbitals. So the bonding molecular orbitals will be low in energy and the antibonding MO's will be high in energy. To give some examples, I can say two s-orbitals, two Pz orbitals, two dz^2 orbitals or an s and Pz orbital will give Sigma interactions. So, when we draw the bonding orbitals, they will be the lowest.

This image and the other one below are from Miessler and Tarr's Inorganic Chemistry textbook.

Pi Interactions: These are the second strongest interactions and we can usually see them between two Px, dxz, dyz orbitals. Since Sigma interactions are stronger than these, Pi interactions will strengthen Sigma bonds. 

Delta Interactions: They are the weakest interactions and they usually occur between orbitals like dxy or dx^2-y^2. Don't let the image trick you. They are the weakest!

http://www.chemexplore.net/delta-MO.gif

Molecular Orbital Theory Notes I

I took intermediate and advanced Inorganic Chemistry courses last year. Since then, I have been asked several questions by my friends who are just taking these courses and I tried to answer them as much as I could. So, I decided to write some posts about the MO Theory and how to construct simple molecular orbital diagrams for students like me. Another reason for me to write these is that writing (or teaching someone else) helps me too (win-win). I will try not to go into anything deep, so obviously you will need to read your textbook to get more information or a quantitative approach. Please correct me if there is anything wrong with my explanations.

First of all, to understand ANY discussion about orbitals, one HAS TO know the "shapes" of the d orbitals. You can see them below. The role of symmetry is also very important in understanding the electronic structure of a complex and in drawing a molecular orbital diagram. Because, the overlap integral (you can read more about it in a book) should be non zero in order to have an interaction. This means that orbitals must have some kind of symmetry to interact. 

image: http://upload.wikimedia.org/wikipedia/commons/5/58/D_orbitals.png

Let me give some very general information about d-orbitals here. 

Both dxz, dxy, dyz orbitals have two nodal planes (xy, yz; xz, yz; xz, xy respectively). Some people are confused with the signs of the lobes of these and other orbitals. If you imagine a coordinate system and give + and - signs for each coordinates, then you will notice that the sign of each lobe changes as you move along the quadrants. For example, for dxz orbital, when both x and z coordinates are +, the sign will be + too. But, when you assign - to x and + to z, the sign will be negative. You can try this on your own.

Now it's time to think about dx2-y2 orbital. This orbital as you can see above, lies along the x and y axes. Just like the other ones, this one also has two nodal planes. You can imagine them bisecting between x and y axes. The sign of each lobe will again change as you move from one lobe to another. Just by basic math skills, you can assign + to x and 0 to y and you can see how they will change. 

dz2 has an interesting shape. In fact this orbital is represented as "2z^2-x^2-y^2"for some mathematical reasons which I do not fully understand. But, for an undergraduate student, it is OK not to know it. At least, this has been my experience. Anyway, 2z^2 tells us that no matter the sign of z is, the sign of the lobe will be + along the z axis. But, when z is zero, the sign has to be -. It is that simple. 

Homonuclear Diatomic Molecules Practice

I just did them for practice and fast. Please also note that they are qualitative.