Wednesday, April 30, 2014

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:

Tuesday, April 29, 2014

Symmetry and Automobile Tires

It has been months since I have written a post on symmetry. The previous posts are here in case you are interested. 

Since I have taken Symmetry and Group Theory, I am obsessed with daily objects' point group symmetries. At first, it was like a game. But now, it is like a duty. So, I read a few papers about tires and their point group symmetries. 

They were both published in Journal of Chemical Education and I think they do a great job to visualize the topic. I really like the author's enthusiasm about tires and their symmetries:

"A stroll through a parking lot becomes an adventure in group theory."

Unfortunately, both articles are still not open access. So, I am not sure if I can copy and paste the photos they used in their papers here. If you have access, I suggest you should read them. It will take 15 minutes the most. There are all sorts of point groups including point groups like D80, C22 etc.

Monday, April 28, 2014

About "open access"

As much as I hate paying money to visit museums, I hate seeing this:

All I wanted to do was to see the first Mossbauer spectra! It was published in 1958! What is the point of charging people to read a publication that not only has a scientific value but also a historical one?

When I google "the first Mossbauer spectrum," I can see what it looks like. But, I wanted to see it in the original context. 

Anyway, you can see the first spectrum here at this link if it means anything to you:

#chempaperaday Day 32/365: "New insights into the chemical and isotopic composition of human-body biominerals. I: Cholesterol gallstones from England and Greece"

I had to give up my #chempaperaday challenge for a few months. As some of you might know, I applied to graduate schools and got some answers. So, I spent some serious amount of time THINKING about my future. I just couldn't concentrate on anything else. I couldn't concentrate on my classes, my personal life, friends etc. After I made my final decision, I started to prepare myself towards what I am going to do in grad school (Yes, I know where I am going to and what I am going to do there.). So, I read TOO MANY inorganic chemistry papers and books. Once again, I started to feel relaxed. That's why, it's time to go back to reading and writing.

I can safely say that I am starting my Ph.D. in a few weeks. But, I will still wait to announce it here until I get the paperwork in my hands. 

I decided to start my posts with a paper I read a few weeks ago. The researchers (mostly from Greece) studied 20 gallstones from four patients and finally chose four gallstones to use for their research purposes. Using several different analytical and spectroscopic techniques, they conclude that calcium is the most abundant metal in gallstones. I was surprised to see there is also some Sr in the samples. But, it can be explained by the similar ionic radius of Sr to Ca. 

Interestingly, Zn and Mn was only found in the samples from England and they were rich in Pb, As and Ni. The authors note this fact as follows:

"Thus, gallstones from England are mostly rich in toxic elements."

Friday, April 25, 2014

"A Case History: The Determination of the Solid-state Structure of Triiron Dodecacarbonyl"

I tried so hard to come up with a title for this post. But, I really think there is nothing more interesting than the title above. I will write a very brief summary for the history of the compound and give some great links to read more about this fascinating story.

I built this one using Avogadro. 

image: wikipedia

Triiron Dodecacarbonyl was first synthesized by Sir James Dewar (Yes! the inventor of the Dewar flask) in 1907 and it was the third iron carbonyl complex that was discovered[1]. But, it took about 20 years for chemists to determine the molecular formula. In the next ~ 10 years, several structures were suggested by different chemists. The speculations and discussions continued and by 1963, there was enough evidence suggesting that three iron atoms were located in a triangular geometry, and two of them were equivalent (can be seen in Mossbauer spectrum below). 

In 1965,  a series of interesting events led Nils Erickson to determine the correct structure. 

He was a graduate student who was studying Mossbauer spectra of some iron complexes. But, it looks like it was not easy for him to publish his findings:

Finally in 1974, Cotton published a "further refinement" for the structure. I think this story clearly shows how important Mossbauer Spectroscopy is. I don't know when, but the first time I will look at a Mossbauer spectrum, I will definitely remember this great story.

Below you can find all the papers I have read about this complex and the events and research that led to the determination of the structure. 

3. Mossbauer Effect in Iron Pentacarbonyl and Related Carbonyls

4. Mossbauer Spectra of Iron in Na,[Fe(CO),] and Na [Fes(CO)llH1 and Comments Regarding the Structure of Fe3(CO)

Wednesday, April 16, 2014

Book: NMR, NQR, EPR and Mössbauer Spectroscopy in Inorganic Chemistry

When I read a book and if like it, I try to buy it. I really love this book, but even the used ones start from $88 on Amazon. So, it looks like I will not be able to own this book for some time. But, I tried to write down as much as possible for my notes until I buy one.

So, the book is about four different methods as you can understand from the title. As the author says in the preface, the book "is not a spectroscopic textbook, nor is it written for those with a need for detailed theory."  There is really very little about the theory of the techniques and they were kept as simple as possible. I was able to understand almost everything without any further reading or help. 

To be honest, I don't remember seeing any NQR spectra in publications and that's the only chapter I didn't pay much attention. 

What I like the most about the book is the chapter problems which are mostly from  journal articles. So, you are given a spectrum and asked to interpret it. Or you are given the complex and asked to make an educated guess on how the spectrum should look like. Or calculate isomer shifts, g values etc.

I wrote a post about one of these simple problems here. After studying the chapter on NMR, I dived into some papers and tried to apply what I learned. I am happy that I was able understand them better. 

I have also just finished two Mossbauer spectra posts and right now I am trying to read some literature so that I can write a longer and more detailed discussion for my posts. I also discovered a fascinating story on the determination of a molecular geometry for a transition metal complex. It is really amazing and I loved it. I will write a summary of the story and link all the published data and discussions in a post hopefully this weekend. 

In summary, I think this book is a must read/study book for a student like me. If I were teaching inorganic chemistry and spectroscopy, I would also ask similar problems in my exams.

Wednesday, April 9, 2014

NMR problems about transition metal hydrides

I have just done some NMR practice and I thought I should write about them.

So, the problem asks to assign four different Pt and Pd complexes to each spectrum given. (only high field is given)

Here are the spectra and the complexes ( I will explain the reasons below the figure):

1st complex and its spectrum: There is a bidentate ligand so the complex has to have cis geometry. This makes two phosphines non-equivalent and the complex should give two sets of doublets (doublet of doublets). 

2nd complex and its spectrum: So, there are two doublets of triplets. Triplets are due to the cis phosphines and the doublet is the result of the trans phosphine. The weaker resonances on each side of the spectrum are called satellites and maybe I should write a paragraph about them in a future post. (Only Pt-195 isotope has a spin and its abundance is 33%.) 

3rd complex and its spectrum: There are two equivalent phosphines (trans). So, this complex should just give a triplet. No satellites, because the metal is Pd.

4th complex and its spectrum:  There are two equivalent phosphines and we expect to see a triplet. We can see the satellites again due to Pt metal center.

Wednesday, April 2, 2014

A simple enthalpy and heat problem

I was reviewing physical chemistry and I saw a problem where you are supposed to calculate the heat required to produce Mg2+(g) starting with 1.00 g Mg(s) at 25 C.

This is a simple problem and here is the solution.

The interesting part (for me) is that to learn this heat is almost same as the heat needed to vaporize 43 g of water. It's ~ 97.24 kJ.

Metals and the Brain I

I have read several papers and books on metal ions in neurodegenerative diseases. So, I decided to start another series of posts as long as I find something to write on the topic.

I just read this article in one of my favorite magazines; The Scientist. I think it is a great review on copper in Alzheimer's disease. I read some of the references long time ago and I think I will read them all as soon as possible. Because, I do not know anything about pharmacology, kinetics of drugs etc., I usually try to understand the structures and read the papers very fast. I do know how to interpret IC50, Ki or other very basic data, graphs or values though. While at it, I should mention that there is a free online medicinal chemistry course on and it is in the 3rd week I guess.

Although we still know little about the true roles and concentrations of the metal ions, new and more powerful techniques (like X-ray fluorescence as the article mentions)  help the scientists to have better information each day. 

Several transition metals are essential for biological processes. One of the most important ones for brain is copper. Actually, the highest concentration of copper in body, is found in brain [1]. So, it is not surprising to see it as a key in neurodegenerative diseases such as Prion diseases, Wilson's disease and Alzheimer's disease. Recently, a group of scientists suggested that zinc is not a biomarker for Alzheimer's Disease. But, as Nigel Hooper says "these data do not rule out a role for altered zinc in the brain being involved in the disease process." Some of the authors of the research article are also working in the same university with the The Scientist article writer. The writer also mentions something similar :
Although overall zinc and iron levels did not vary significantly between AD and healthy brains in Kirsch’s 2011 meta-analysis, this doesn’t rule out complex subcellular changes to the location of these metals.

Even though one can determine the malfunction of the regulation of the metal, the biggest challenge is to fix the problem. One of the methods is using metal complexes (chelates). Here is a library of them by the same author's publication:

In summary, there is a lot of way to find out the cause and the cure for these diseases and I think this is a great article with beautiful infographics and I strongly suggest reading it.

1. Hughes, M.N.; The Inorganic Chemistry of Biological Processes ; Wiley and Sons, 1981;  p 298.

Tuesday, April 1, 2014

42nd Annual James R. Killian Jr. Faculty Achievement Award Lecture:Understanding and Improving Platinum Anticancer Drugs

If you have been following the blog for some time (or if you actually know me), you must know that I am also interested in metal based anticancer drugs. Today I attended Stephen Lippard's award lecture at MIT where he gave a talk about platinum anticancer drugs for 1.5 hours.

Here is the recognition for his work and award:

Stephen J. Lippard, who is widely acknowledged as one of the founders of the field of bioinorganic chemistry, is this year's recipient of MIT's James R. Killian Jr. Faculty Achievement Award.
Established in 1971 to honor MIT's 10th president, the Killian Award recognizes extraordinary professional achievements by an MIT faculty member.

In announcing this year's award at the May 15 faculty meeting, the award committee noted that Lippard's groundbreaking work has pushed back the frontiers of inorganic chemistry, while simultaneously paving the way for improvements in human health and the conquering of disease.

Lippard, the Arthur Amos Noyes Professor of Chemistry, has spent his career studying the role of inorganic molecules, especially metal ions and their complexes, in critical processes of biological systems. He has made pioneering contributions in understanding the mechanism of the cancer drug cisplatin and in designing new variants to combat drug resistance and side effects.

His research achievements include the preparation of synthetic models for metalloproteins; structural and mechanistic studies of iron-containing bacterial monooxygenases including soluble methane monooxygenase; and the invention of probes to elucidate the roles of mobile zinc and nitric oxide in biological signaling and disease. 
 Especially, he focused on one of his recent projects : Osmium complexes. I also think that he is equally interested in Pt(IV) complexes. It was great to see and listen to him again after ACS Dallas national meeting.