Sunday, July 20, 2014

#chempaperaday Day 37/365 : "The Discovery and Characterization of Molybdopterin: the Work of K. V. Rajagopalan"

I am not sure if I mentioned before, but one of my favorite journals is Journal of Biological Chemistry. The journal has these "Classics" series where you can read really nice reviews, biographies about scientists and important scientific discoveries. 

So, this one is a short introduction for Prof. Rajagopalan and his discovery of molybdopterin. You can go for the references for the details of his discoveries and research.

It is a free article that you can read here:



Wednesday, July 16, 2014

#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.

Monday, July 14, 2014

A Chemical Conundrum and Ligand Field Theory

I was planning to write some more about Ligand Field Theory (LFT). Then I found this paper and decided to write the planned post in the near future. First, I wanted to share this interesting riddle or puzzle that was asked in the Journal of Chemical Education. The paper is titled "Ligand Field Theory" and was written by F. Albert Cotton. It could be the first and the best source to read about the theory. I hope you enjoy it. Here is the question I mentioned above:



Sunday, July 13, 2014

#chempaperaday Day 35/365 : "Bioinorganic modeling chemistry of carbon monoxide dehydrogenases"

A really nice review on CODHs and relevant bioinorganic chemistry.

http://pubs.rsc.org/en/content/articlelanding/2014/dt/c4dt00729h#!divAbstract

"Carbon monoxide dehydrogenases (CODHs) use CO as their sole source of carbon and energy and are found in both aerobic and anaerobic carboxidotrophic bacteria. Reversible transformation of CO to CO2 is catalyzed by a bimetallic [Mo–(μ2-S)–Cu] system in aerobic and by a highly asymmetric [Ni–Fe–S] cluster in anaerobic CODH active sites. The CODH activity in the microorganisms effects the removal of almost 108 tons of CO annually from the lower atmosphere and earth and thus help to maintain a sub-toxic concentration of CO. Despite an appreciable amount of work, the mechanism of CODH activity is not clearly understood yet. Moreover, biomimetic chemistry directed towards the active sites of CODHs faces several synthetic challenges. The synthetic problems associated with the modeling chemistry and strategies adopted to overcome those problems are discussed along with their limitations. A critical analysis of the exciting results delineating the present status of CODH modeling chemistry and its future prospects are presented."

Monday, July 7, 2014

#chempaperaday Day 34/365 : "The evolution of vision"

I love biology. This is a 40 page review on the evolution of vision. There is incredible amount of information here in this article. It is also very easy to understand with very little biology background. So, if you are worried that you don't know much biology, don't be afraid. It is very easy to understand and very well written.



Due to my new busy lab life, it took me ~1 month to read it, but it's worth. I highlighted tens of parts so that I can use them as reference even when I am talking to my "non-science" friends. I think this is an article that every person should read as a course material in some kind of elective course. The article tells you everything you would ever want to know about the evolution of vision. It is also open access!



Wednesday, June 18, 2014

Coordination chemistry and neurodegenerative diseases

I think I've shared at least one paper by Chris Orvig before. This paper is a short review on the role of coordination chemistry in neurodegenerative diseases. As you know, many of these diseases are closely related with certain metal ions and I think inorganic (and bioinorganic) chemists are key people to help us understand more about these diseases. I hope one day an inorganic (or medicinal inorganic/bioinorganic) chemist makes a groundbreaking discovery and will never be forgotten for his contribution to medicine.

"Neurodegenerative diseases are capturing the world's attention as being the next set of diseases we must tackle collectively. Not only are the patients experiencing gradual cognitive and physical decline in most cases, but these diseases are fatal with no prevention currently available. As these diseases are progressive, providing care and symptom treatment for the ageing population is becoming both a medical and a financial challenge. This review discusses how Werner coordination chemistry plays a role in three diseases – those of Alzheimer's, Parkinson's, and prions. Metal ions are considered to be involved in these diseases in part via their propensity to cause toxic aggregation of proteins. First, the coordination of metal ions, with emphasis on copper(II), to metalloproteins that are hallmarks of these diseases – amyloid β, α-synuclein, and prion, respectively – will be discussed. We will present the current understanding of the metal coordination environments created by the amino acids of these proteins, as well as metal binding affinity. Second, a diverse set of examples of rationally designed metal chelators to outcompete this deleterious binding will be examined based on coordination mode and affinity toward bio-relevant metal ions. Overall, this review will give a general overview of protein and metal chelator coordination environments in neurodegenerative diseases. "

Friday, June 13, 2014

I miss my bike!

Due to the horrible weather around here and some technical problems, I still haven't started to ride my bike. I hope I can ride very soon.

"I  ride, I ride the winds that bring the rain
A creature of love and I can't be tamed"
 

Wednesday, June 4, 2014

Grad school update

It's been 2.5 weeks since I started. The first week, I was exhausted when I got home. There were a few days that I fell asleep! I think I started to get better (especially physically) during the second week. This week, I am sure I am fit enough to think and plan the next day and conduct the experiments. I am now in a better position in terms of my personal schedule. I have just started to go back to reading my books and textbooks again. I am really happy that I started grad school early in the summer without even giving any break after my graduation from the college.

About research? I have been reading some literature and running experiments. Although I am having hard time to characterize my paramagnetic metal complexes, I am learning a lot. Overall, I like what I am doing and it totally makes sense.

Sunday, May 18, 2014

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.

Friday, May 16, 2014

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.


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!


Wednesday, May 14, 2014

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.

Tuesday, May 13, 2014

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.


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

Monday, May 12, 2014

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

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:



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.

 

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.