Saturday, May 10, 2014

"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.


Friday, May 9, 2014

"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.


Thursday, May 8, 2014

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:




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.

Wednesday, May 7, 2014

#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.







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. 



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



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.





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. 






Tuesday, May 6, 2014

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!



Monday, May 5, 2014

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. 


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. 


Thursday, May 1, 2014

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:


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.


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 edx.org 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.