Bis(dicarbonyl-pi-cyclopentadienyliron)-A Solid-State Vibrational Spectroscopic Lesson #chempaperaday 253

I have highlighted J. Labinger's paper on cyclopentadienyl iron dicarbonyl dimer before. Today's read is a Journal of Chemical Education article focusing on Raman and IR spectroscopy of this dimer. I guess its main purpose is to show how useful these techniques are, but how difficult it is to determine a structure based on spectroscopy (especially for this dimer). I was actually just reading another paper on this dimer like 5 minutes ago. I'll probably post it soon.

I always think about Raman spectroscopy as some sort of esoteric technique. You always hear about it, read about it; but never see it. Certainly I haven't. We don't even have the instrument in the department. 

I like this paper because there is enough spectra and discussion about both IR and Raman spectroscopy of the dimer. You can also see a nice symmetry treatment and finding the IR and Raman active bands of the two isomers.

Bonding capabilities of transition metal carbonyl fragments #chempaperaday 252

The quest for metal carbonyl bonding is going on here. As I mentioned before, I am working on it. This is another article by R.Hoffmann where you can read one of the best MO theory explanations and examples. He makes it so simple that, there is no way you can't learn MO theory from him. It's a quite long article, so I am not going to try to summarize it for you. But, I will mention one of the most interesting observations in bioinorganic chemistry and how he explains it.

As you know, hemoglobin binds to oxygen giving us oxyhemoglobin; and when unbound, deoxyhemoglobin. Oxyhemoglobin has a six-coordinate iron atom in the plane of the porphyrin ring, but iron is out of the plane in deoxyhemoglobin. Why? Simply, it's the spin state and ionic radius. Because, we know from the experiments that the spin state changes from low to high spin. You can read it in any biochemistry or bioinorganic textbook. Well, in this article, you can read it in more detail and how it is actually predicted. So, I guess, even if we hadn't observed this phenomenon, we would have guessed it.

image source

So, assuming that the point group is C4v in these porphyrin complexes, for a d6 transition metal ion;

   - low spin complexes will prefer a square pyramid and metal will be in the plane

   - high spin ones will prefer to be out of the plane! (a1 orbital is occupied)


http://pubs.acs.org/doi/abs/10.1021/ic50147a021

http://www.ncbi.nlm.nih.gov/books/NBK22596/ 

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.

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.

Cobalt(III) Werner Complexes with 1,2-Diphenylethylenediamine Ligands #chempaper 226

I think this is a really nice study. They checked 80 crystal structures of [Co(en)3]3+ and then came up with this useful approach to catalyze the addition of malonate esters to nitroalkenes. Classical Werner complexes once again proved that they are very promising in catalysis.

http://pubs.acs.org/doi/full/10.1021/acscentsci.5b00035

Elongated dihydrogen complexes: what remains of the H–H Bond? #chempaperaday 208

Most transition metal dihydrogen complexes have an H-H distance less than 1 Angstrom. The rest of the complexes have longer H-H bond distances making them what is called "elongated dihydrogen" complexes. Of course if the distance is larger than 1.5 they become dihydride compounds.

http://pubs.rsc.org/en/content/articlelanding/2004/cs/b304879a#!divAbstract

In this short review, there is a lot and much useful information for those who want to learn more about these interesting complexes. Because it is difficult to resolve the crystal structures containing these ligands, there are a few methods to characterize them. Probably the simplest method is to use HD and measure the coupling constant and then plug it in in this formula :

There are ten "representative" complexes in the article that really help you to get a better understanding. I like the idea of listing these complexes and giving details about them. I think more authors should try this type of writing. Most review articles only cite other papers and avoid giving detailed information which makes following the paper really hard in some cases.

Shopping for symmetry!

Symmetry is a part of life. In fact, it is really hard to find an object without any symmetry operations. I found some objects for you!

"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.

#chempaperaday Day 36/365 : "Ligand Field Theory"

This is a great introduction and mostly qualitative explanation of Ligand Field Theory(LFT) written by F.A.Cotton for undergraduate students. 

Even if you are sure that you know everything about LFT, I still suggest that you should read it. It's a very simple but effective explanation.

http://pubs.acs.org/doi/abs/10.1021%2Fed041p466

Gypsum

Like thousands of other people, I have been taking an online course called "The Fascination of Crystals and Symmetry" on Iversity.

One of the lecture videos this week shows a Gypsum crystal and tells us that its crystal class is "prismatic." Now, I know my own gypsum's crystal class thanks to the course.

a screenshot of the relevant video from the course website.

My own gypsum (I am not sure of the purity though).

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.

Book: "Group Theory and Chemistry"

So far I have three other books on Symmetry, Group Theory and its applications in chemistry. You can follow each link to see them. This book is quite different than the other ones. In addition to basics of symmetry and group theory, this shows the mathematics behind the theory. So, in this book you will find long proofs, equations and theorems. You can skip those parts though. But, I think it is a very good book for a graduate level course or for someone who is interested in the math behind the group theory. But, knowing this, the author actually put all the math after each chapter. So, you can still use this book and once you learn the application, you can read the math to realize how the theory is derived.

This book also has one of the best prefaces I have read:

"Finally, a word of encouragement to those who are frightened by mathematics. The mathematics involved in actually applying, as opposed to deriving, group theoretical formulae is quite trivial. It involves little more than adding and multiplying."

 http://www.amazon.com/Group-Theory-Chemistry-Dover-Books/dp/0486673553

Book: "Chemical Applications of Group Theory"

If you have ever read SOMETHING in Inorganic Chemistry, I am sure you have heard of F. Albert Cotton! So, apart from countless publications and other textbooks, he wrote this book to help chemists understand group theory and use it. 

The importance of this book can easily be understood by the preface:

"Despite the fact that there seems to be a growing desire among chemists at large to acquire this knowledge, it is still true that only a very few, other than professional theoreticians, have done so...no book available which is not likely to strike some terror into the hearts of all but those with an innate love of apparently esoteric theory."

 

I tried to buy the first edition of this book (1963) and I did. Because, I think it has historical importance too.

 http://www.barnesandnoble.com/w/chemical-applications-of-group-theory-f-albert-cotton/1100519240?ean=9780471510949

 

Book: "Molecular Symmetry and Group Theory"

This book was the required text in the Advanced Inorganic Chemistry course in my school. It is really a great source and practice to learn Group Theory. It takes you and actually makes you learn it step by step by following the instructions. So, if you have problems in understanding or "imagining" symmetry operations, I suggest you read it.

http://www.amazon.com/Molecular-Symmetry-Group-Theory-Introduction/dp/0471489395/ref=sr_1_1?ie=UTF8&qid=1399914440&sr=8-1&keywords=Molecular+Symmetry+and+Group+Theory

Book: "Symmetry and Spectroscopy: An Introduction to Vibrational and Electronic Spectroscopy"

I read and studied this book when I was taking Advanced Inorganic Chemistry. I found it incredibly useful and helpful. To be honest, I used it more than I used my textbook. Not that the textbook was not well written, but because this book is so well organized and practical. 

The book starts with symmetry, symmetry elements/operations and point groups. In the end of this chapter, you start to learn matrix representation of those operations and learn how to use character tables. 

The second chapter gives very brief information on quantum mechanics. The authors really did great job to keep it as simple and useful for students. So, don't panic. You can easily understand this chapter as long as you are comfortable with calculus. On a side note, I should mention that EVERYONE should learn calculus.

The third chapter is about Vibrational Spectroscopy and the application of Group Theory. You can see how symmetry is used in spectroscopy. I promised to do some practice problems here on the blog and I am sorry I failed to do so. But, I will keep my word as soon as possible.

The next chapter is MO Theory and the last chapter is about Electronic Spectroscopy. I loved these two chapters because you can really learn how symmetry is used to interpret spectra and data. Textbooks have similar problems too. But, what makes this book special is that everything is explained in more detail and the practice and chapter problems are from REAL publications. I think this book really pushes you to read publications. You can see how EACH vibration of para-difluorobenzene is assigned to  an orbital!

I think anyone who is interested in Inorganic Chemistry, Physical Chemistry and spectroscopy should read this book.

http://www.amazon.com/Symmetry-Spectroscopy-Introduction-Vibrational-Electronic/dp/048666144X/ref=sr_1_1?ie=UTF8&qid=1399914095&sr=8-1&keywords=symmetry+and+spectroscopy+an+introduction+to+vibrational+and+electronic+spectroscopy

A square antiprismatic Lanthanum complex: [La(C5H5NO)8](ClO4)3

I wrote some "symmetry" posts before. But, for this one unfortunately I can not draw axes or show symmetry operations. I am not an artist. I just hope that you appreciate the beauty of the geometry and the structure like I do.

The image is from an open access publication and the complex has a square antiprismatic geometry:

http://pac.iupac.org/publications/pac/pdf/1979/pdf/5104x0925.pdf