Calm Before the Storm

It's an exciting night for me. Although I don't get excited often, this night is special. Tomorrow is officially the first day in grad school. So, my heart beats a little faster than it regularly does. I am not sure how many hours I will sleep (if I can sleep any).

I have always thought the best music was produced in 80's and 90's. OK, this one was released in 2000. But, it belongs to 90's for me!

The sky is so clear tonight;
It's so calm before the storm.
All the stars shine so bright
Like the world has been reborn.
I'm think I'm in a dream tonight.
It's still calm before the storm.
But I dream of rising light
A sign it's time to be reborn.

It's still calm before the storm.

Book: "Classics in Coordination Chemistry Part I"

I mentioned Alfred Werner's name several times on this blog. I also wrote a separate blog post about him here. That will definitely be the first one not the last one!

One of the book I have just finished reading is Classics in Coordination Chemistry Part I and I want to start with the Preface here.

Occasionally, one man will play such a central and monopolistic role in a particular field of science that his name virtually becomes synonymous with that field. Alfred Werner, the undisputed founder of coordination chemistry, is just a man.

Not surprisingly, the book was dedicated to Alfred Werner whose name can still be seen in many recent inorganic chemistry publications. I learned that he was called "inorganic Kekule" and he published 174 publications and 45 of them were actually on organic chemistry. The book consists of 6 publications of him.

The first "paper" (chapter) starts with a legendary tale; how he woke up one night at 2 AM and started writing the "coordination theory" until 5 PM!

It is like a journey in history of science to read his papers. You can often see how strongly he advocates his theory. 

"...the metal atoms must posses the property of binding six such residues."

"The Blomstrand-Jorgensen view of metal-ammonia salts can in no way explain this peculiar transition of basic metal-ammonia radicals to similar complexes acting as acids, and therefore this theory seems to me to be untenable."

 "...all water molecules, and all acid residues are bound directly to the metal atom, since otherwise the relationships of these compounds to one another cannot be explained."

Paper Five in the book is especially important as the author explains in detail. The year that this paper came out was also the year that he published 27 other papers. He wrote to his Ph.D. adviser:

 " I must search around for a new, larger subject...for the investigation of the metal-ammines has succeeded to such an extent that I can no longer hope for really new results."

The optical activity of carbon was known and accepted. This was one of the reasons that his opponents challenged him despite his data and evidence. They suggested that the optical activity was due to carbon atoms in the molecules. But in 1914 he published a paper on a  metal complex that did not have a single carbon atom. Finally, there were no objections. 

"The proof that molecules of optically active compounds do not absolutely have to contain carbon is of importance because with such a proof the difference still existing between carbon compounds and purely inorganic compounds disappears.

Therefore I have occupied myself for quite some time with proving this and have now reached the goal

       ... proof is that carbon-free inorganic compounds can also exist as mirror image    isomers. "

In this paper he prepared "dodecammine-hexol-tetracobalti salts." 

I think the importance of the book is that it makes you realize how much time, effort and thinking he put into his studies. It's not just he went and did some experiments and figured out the coordination. It is actually THE WAY he did it.  Only then can you understand what a genius he was. Despite the lack of analytical equipment and technique and the pressure from the biggest names and their followers ( Kekule, Jorgensen, Gay-Lussac, Liebig, Berzelius etc.), he defended his ideas with MORE EXPERIMENTS and more EVIDENCE. Jorgensen, in particular, tried to discredit Werner's work several times. I think this is what makes Werner really special that he did his studies by careful planning and in a systematic method y and he finally proved everyone that he was right!

Book: "The Chemistry of Phosphorus"

I have been reading this book slowly for about two months now. It is such a rare book that I was not able to find it online. So, I took notes carefully during the time I have kept it. Unfortunately, I have to give it back tomorrow to the library I borrowed it from.

http://johnemsley.com/books/chemistry_of_phosphorus.html

Although the book is really old (published in 1976), it is fascinating how much you can learn about phosphorus. Phosphorus has always impressed me (the other element impresses me is technetium)! After all, the whole life depends on it! Why did life evolve around phosphorus? It really bothers me.

One of the most interesting things I learned from this book is the "increase in enthalpy of 3.3 kJ/mol per pm decrease in bond length (0.8 kcal/mol per 0.01 A)."

"bond angles are always narrower in phosphine derivatives than in their nitrogen counterpart" This one is not counterintuitiv but I wanted to write here.

- PH3 has a small s-character than PI3 !

To tie it up I will paraphrase: In PH3, the lone pair is less available than in NH3. Because, 3s orbital is somehow buried between 3p orbitals.You can compare the basicity and of amines and phosphines to see this effect.

This book is a great source and looks like the most serious attempt to explain the chemistry of phosphorus with in-depth discussions, useful data and tables showing several trends in phosphorus chemistry and reactions. I wish I owned a copy. So, if you ever want to buy me a present, you can try to find one for me!

H2PtCl6 - Chloroplatinic acid

"What do you think is the proper formulation for H2PtCl6? Why do you think the compound is commonly called chloroplatinic acid?" 

I was doing some practice problems and I have just read the problem above. Well, if you are careful enough, this is a very easy question and the "common" name gives it away. As a result, this complex is not a  metal hydride. It has to be an acid and therefore it can be written as H2[PtCl6]. 

Bonus:

Here is a video on how to make this metal complex from my favorite chemistry guy&channel:

I wonder how much money he spent to do these videos! By the way, he hasn't uploaded anything since last year. I hope he is fine and away from trouble.

On Funding and Research Interests

I have read some papers by Paul Lindahl lab and I strongly suggest that you should read his publications too. Today, I was checking something on his lab website and ended up reading "History of the Lindahl Lab." I noticed that he quit a few projects due to lack of funding and interest. 

"Despite publishing a couple of good papers on hydrogenase, I never obtained funding for these studies, so I eventually dropped the project."

It's not clear from the text how many years he spent doing research the project he mentioned above, but even if it took just one year, it must have been really hard to quit a project. After all, it is something that bothers your mind and with all your curiosity, you want to explore it. Unfortunately, if nobody gives you money for that, you end up switching to a different project. I don't know the details of that project but I am wondering how he felt when other people moved on that or a similar project and kept discovering new things.

"Meanwhile it became increasingly difficult to entice new graduate students to work on ACS/CODH, as attitudes had shifted. Why study an enzyme that does not cause or cure any disease, they asked? Responding that the chemistry was interesting simply wasn't enough."

In this case, he says that he couldn't find students with interests in his research projects. I understand that people are looking for more "interesting" projects. But, it is hard to accept that someone finds a project uninteresting just because it has no role in a disease. Well, isn't it one of the reasons for scientific research? Maybe there are no known pathways or roles yet, but you will discover that the enzyme indeed has a role in Disease X or something else. Especially when it comes to diseases and biology, I don't think you can rule out anything in an organism. Every component of a cell has a role in something. There are countless pathways. I might be totally wrong, but that's what I think.

image: http://www.greenbookblog.org/wp-content/uploads/2011/01/challenges.jpg

By the way, here is a recent review article on carbon monoxide dehydrogenase and Acetyl-CoA Synthase.

http://pubs.acs.org/doi/abs/10.1021/cr400461p

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).

Are you happy with your work?

I don't remember posting anything except chemistry here (I hope). But, this one deserves to be shared on this blog too. I have just seen this blog post on Brainpickings. I try not to read anything other than chemistry or science (and sci-fi and a little bit literature and a little bit of philosophy), but I couldn't help but reading this post and I saw several quotes that I can relate to my past and present life. I believe that you should quit your job if you are not happy with it. I can not see any excuses to keep working in the same job but not liking it. Maybe a few very extreme examples, but that's all. It's very simple. If you don't like what you are doing, just stop doing it. It's never too late.

You can easily translate some of these quotes into your research and science I think. So, I decided to write some of them here. By the way, I should mention that I have never read any of those "personal development" or "self-help" books. There is absolutely no chance that I will ever read one. I think you can only learn from experience (yours or somebody else's) in the life and quotes or autobiographies might be helpful too since they are usually directly related with experience. But, those books not! I will not discuss this with anyone. So, I am not planning to read the book in the article linked. But, I am glad I saw these quotes in the blogpost on Brainpickings:

“Life really begins when you have discovered that you can do anything you want.”

 "Much the same thing happens when you take a person and put him in a job which he does not like. He gets irritable in his groove. His duties soon become a monotonous routine that slowly dulls his senses."

"Whether you are flying the Atlantic or selling sausages or building a skyscraper or driving a truck, your greatest power comes from the fact that you want tremendously to do that very thing, and do it well."

 "The greatest satisfaction you can obtain from life is your pleasure in producing, in your own individual way, something of value to your fellowmen. That is creative living!"

"The next time you feel that you ‘haven’t the time’ to do what you really want to do, it may be worth-while for you to remember that you have as much time as anyone else — twenty-four hours a day. How you spend that twenty-four hours is really up to you."

How to Avoid Work: A 1949 Guide to Doing What You Love | 

Brain Pickings

 http://www.brainpickings.org/index.php/2012/12/14/how-to-avoid-work/

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

"Do difficult research"

This month's issue of The Scientist has a great quote. It is now one of my favorite quotes. I might even print and hang it on my wall. 

Do difficult research—it’s where the true answers lie. When doing research, don’t look where everyone else is. You’ll just confirm their findings. Look along the untrodden path going the wrong way—that’s where the unimaginable, disruptive, game-changing discoveries are.

—Neurosurgeon and former NASA researcher Mark Wilson, speaking about the future of emergency medicine on the Imagine the Future of Medicine blog (March 28)

http://www.the-scientist.com/?articles.view/articleNo/39758/title/Speaking-of-Science/

I think it is really important to take the risk and go for challenging projects instead of repeating other people's work over and over again or doing derivatives of other people's projects. Of course it is important to contribute other people's findings.  Your results might support them or maybe you will prove them to be wrong. But, I still believe that the greatest joy in science is to be the one doing something unique, to be a leader in your field/project. Of course it is very risky to be one of the first in that specific research area, but I think the rewards are worth taking the risk.

http://bgcpoco.files.wordpress.com/2013/07/mad_science_flask_girl_yq8e.jpg

"Why is pyridine several places to the left from bipyridine on the spectrochemical series? "

It all started with a question that one of my friends asked a few weeks ago. He came to me and asked what kind of ligand pyridine was. Without hesitating I said that it is a "strong field" ligand. Suddenly I was bothered by my answer. Not that it was wrong, but I realized that bipyridine was a stronger field ligand. Why was that? I looked at spectrochemical series maybe hundred times and I have never wondered why this was the case. Moreover, (although I know the reason for the general trend in the series) I was never curious why the series followed the order of pyridine<ammonia<ethylenediamine<bipyridine<phenathroline . 

image: spectrochemical series (as you move right, you go to the stronger field ligands)

 

In order to find an answer (as expected), I googled things! Looks like someone else also asked a similar question and a discussion took place on Researchgate website here.Well, you can read the answers to the question but I am not satisfied. Those answers are not THE ONE I am looking for. I feel like this trend should be explained in a better way. Since I was busy with my final lab reports, assignments, finals, personal life and the surprises of life etc., I did not have enough time to read and find out an answer. Today, I tried to look for literature on spectrochemical series. Thanks to chemistry gods, I found this one:

"The Position of 2,2'-Bipyridine and 1,10-Phenanthroline in the Spectrochemical Series"

It is not what I was looking for. But, it is very very very helpful. Better news (for some of you) is that the pdf file is free to read here. It is a really interesting article even with the "dedication" part. The authors from Denmark dedicated the paper to Prof. K. A. Jensen for his 70th birthday. I know there is a term for these papers, but I forgot. 

Anyway, although the paper was published in 1977, I think it is awesome. This is exactly one of the main reasons I LOVE inorganic chemistry. There are theories, there are not fully investigated complexes and trends. There is a lot of thinking, experimenting and discussing. People come up with ideas, theories and you can challenge them if you work hard and carefully. And some luck ? Sure.

I quickly read the paper and I will really spend time on it tomorrow. So, I might write another post after reading it or I can wait until I find more answers. We'll see. In summary, the authors prepared several cobalt and chromium bipy and phen complexes and studied/compared their spectra.

For cobalt(III) complexes the series; 

ammonia<en<phen<bipy

and for chromium(III) complexes the series is as follows:

phen<bipy=<ammonia<en

Please don't hesitate to suggest papers or answers for the trend in the series. I believe I will find a satisfying answer since these ligands are among the most used and studied ligands in inorganic chemistry.

The "Cytochrome Cascade"

I have a final tomorrow and I didn't even study more than 2 hours. Maybe it is because it will be my last final as an undergrad or maybe I had a horrible day. I just can't concentrate. Everything I did sucked, every news I heard was bad etc.

I have been reading/studying a Physical Chemistry textbook for some time. It is called The Elements of Physical Chemistry with Applications in Biology. Check it out here on amazon:

http://www.amazon.com/dp/0716735385/ref=cm_sw_r_tw_dp_7mdBtb0XQ70DR

I don't want to offend anyone but this is a very "soft" physical chemistry book obviously for biological science and biochemistry majors. But at the same time, it is my favorite P.Chem textbook now. I will write a long post in my "books" series. So, for now I will skip the details and will share this very useful (IMO) scheme with you.

Maybe similar diagrams exist, but I have never seen before. This is a great MAP that shows how electrons are transferred to oxygen molecules in the end.

#chempaperaday Day 33/365 : "In-cell NMR: an emerging approach for monitoring metal-related events in living cells"

I have to confess, I did not know that you could do this !

So, this paper is obviously about in-cell NMR and the main focus is not to determine the structure of a protein. But, they tend to focus on how NMR can be used to study the binding of metallodrugs and the metalloprotein binding interactions. 

Also, this is the first time I have read/heard this :

"...metal selectivity of metalloproteins in vivo is different from that in vitro and this may hold true for metalloprotein folding." 

Actually, you can read a few examples on the difference of in-vitro and in-vivo selectivity of proteins for certain metal ions.

I will also try to find and read some of the references in this paper. My interest in these studies is aboslutely greater now.

The paper was open access when I read it. But, I am not sure now. Just try it.

http://pubs.rsc.org/en/content/articlelanding/2014/mt/c3mt00224a#!divAbstract

Synthesis of Zykadia (ceritinib)

I think I saw it on the net this morning that a drug named Zykadia (ceritinib) was approved by FDA. It is a lung cancer drug for patients who were already treated by another drug (crizotinib). Anyway, according to the press release it is an "anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitor that blocks proteins that promote the development of cancerous cells." 

I just wondered what the molecule looked like and searched for the structure and not surprisingly I found it. 

http://www.medchemexpress.com/product_pic/LDK378.gif

Then I wondered how it was synthesized and tried to google the synthesis. Surprisingly, this came up:

http://www.yaopha.com/2013/06/08/chemical-structure-and-synthesis-of-zykadia-ceritinib-novartis-breakthrough-therapy-for-lung-cancer/

Assuming that the website and the synthesis is legit, I want to say that I find the synthesis really easy compared to some syntheses I have seen on one of my favorite apps Chemistry by Design.

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. 

Ship-in-Bottle Synthesis

I just learned this term yesterday. The name reveals itself. It looks like you can build molecules, complexes or even metal clusters in zeolites or nanostructures(?) and then trap them there. Really interesting. I have always liked "ship-in-a-bottle" things. By the way, I made a quick search on ACS using both "ship-in-a-bottle" and "ship-in-bottle," a total number of 9 publications were found. So, it might not be used so frequently. Or may be it is a really difficult technique just like building a ship in a bottle. 

image is from : “Ship-in-Bottle“ Catalyst Technology by  Masaru lchikawa. If you google it, you can download the pdf for free.

A Mossbauer Spectroscopy problem

I believe this is the second post about Mossbauer Spectroscopy. The first one is here. So here is the problem that I saw in the book:

Some iron complexes in the form of FeX2(py)2 can be monomeric or polymeric as shown below (X=Cl, I).

Using the Mossbauer data given in the table below, determine which complex is polymeric.

Complex	IS	QS
FeCl2(py)2	1.21	1.25
FeI2(py)2	0.86	1.33

Solution:

First of all, for Iron we should know that the increased electron density at the nucleus will cause the isomer shift (IS) to decrease. Lower coordination number will also have a decreasing effect on IS. All these tell us that iodide complex will have the pseudo tetrahedral geometry like the one on left. 

I also know that complexes with lower symmetries have higher QS. This might explain the QS value for the iodide complex.

This problem was adapted from a publication:

http://pubs.acs.org/doi/pdf/10.1021/ic50190a021

If you read the paper, you will see that the authors did not have a crystal structure for the iodide complex. So, this problem is another example how useful Mossbauer Spectroscopy is. You can also read their discussion. To be correct, I read the paper first and then wrote my post.