Sunday, December 28, 2014

"Coping with Fritz Haber's Somber Literary Shadow" #chempaperaday 179

This is a beautiful article on Fritz Haber and how he was represented in several forms of art.

"Fritz Haber is often this scapegoat...Most of us are also teachers. We have to do better than the usual, traditional technical presentation of the ammonia synthesis, invoking it as a fine illustration of Le Chatelier's Principle. We have to talk also about Haber, the historical figure and the person. His choices and agony are a part of us."


http://onlinelibrary.wiley.com/doi/10.1002/1521-3773%2820011217%2940:24%3C4599::AID-ANIE4599%3E3.0.CO;2-K/abstract

"Valence Bond Theory in Coordination Chemistry" #chempaperaday 178

This is a very short paper by Linus Pauling. Apparently, he read an article where the author said that valence bond theory was not as popular and useful as it was. Obviously, the response came from Pauling and his response in fact was very short:

"I do not agree with this opinion."

The rest of the article explains how valence bond theory is still can be used in coordination compounds.

The article was published in Journal of Chemical Education, but here you can read it as pdf for free.

http://depa.fquim.unam.mx/amyd/archivero/VBPAULING_26400.pdf

Book: A Troublesome Inheritance

A few months ago (or maybe it was summer), I saw many people arguing about this book whether the author Nicholas Wade expressed "racist" ideas and whether the book had any "value" etc. I hate debates on what people call "controversial" topics. In my world, there is nothing controversial. You can say what you want. I respect everyone's ideas and even "insults." Also I had enough reasons to think that the book was worth reading. First, I read this post and then I saw several people's and "scientists" ' anger towards the author and his post. 

So, I bought the book and read it. 



I found the book really well written and clear. There are several parts that I do not agree with the author. But, there is no need to try to insult the author or the book. Moreover, there is no need to try to suppress others' ideas. Censor has no place in this century and in this country. It absolutely has no place in science. So, if you don't agree with him, you can try to write a better one and disprove what he said. It must be very simple if you are an expert in your field. This is where the problem stems from. Being a "science blogger" does not give you any credibility or expertise in a specific field of science. I saw people saying the he is not an expert so he is not eligible to write  book like this. Well, hello everyone can write anything as they want just like you write blogposts on topics that you have no understanding of. 

I saw a group of scientists wrote a letter saying "We are in full agreement that there is no support from the field of population genetics for Wade’s conjectures." This is the best way at least to tell public that there are flaws in the book. A better one would be to write a better book defending your position. But, I guess not many people will do that since it requires writing more than a few hundred sentences. 

As far as I know, Wade gave an answer and said that he had asked for feedback but had never gotten any or something along these lines (I don't remember where I read it). So, it looks like the debate will go on. Maybe he will write another book. We will see.

Anyway, I think the book is worth reading. Believe it or not, the whole book is not about race and genetics. 

A few quotes worth noting (not associated with race debate) :

"researchers do not act independently but rather as communities of scholars who constantly check and approve one another's work."
 "[Paul Samuelson] Knowledge advances, funeral by funeral."
"Science is about what is, not what ought to be."

Book : Memoirs by Edward Teller

No matter what people say about him, Edward Teller is one of my science heroes. I don't care about his personal life or some of his "controversial" ideas. I care about his approach to science and research. He was a great mind and truly a genius.

His Memoirs is a really long (602 pages) but a fun to read autobiography. The story of his life is also the story of science (nuclear physics/chemistry) that covers almost a century. I think you should read the book even though you don't like anything about him. There are tens of stories, memories, people that you will find interesting to learn about.



I really enjoyed his Memoirs and took some notes. I will quote a few of them here (as always I do not agree with him or others on everything they said):

"Before I was ten, I understood that in the United States foreigners are not foreign."
"Nationalism has little to contribute today except further suffering."
"Ignore teasing."
"...before the 1880s, science played almost no role in the advances of technology...Chemistry was the first science to undergo a merger with technology, and the first technology affected was dyemaking."
"He [Heisenberg] complained that physics had ceased to develop; there was hardly anything interesting left to do."
"Bohr:Where we find a paradox, we find something of real interest."
"Bohr said that to be properly understood, one should not lecture in his native tongue."
"The lesson is that the correct theory applied to the wrong data is better than no theory applied to correct measurements."
"[Bohr] Opennes is the basic condition necessary for science."
" Johnny [von Neumann] was the Euclid of quantum mechanics."
 "The scientist is not responsible for the laws of nature. It is his job to find out how these laws operate...Hydrogen bombs will not produce themselves."
"Science historically had moved forward because of openness."
"I find the idea of civil disobedience in a democracy wrong."
"Fermi and I both lacked formal religious beliefs"
"I believe that if a mentally superhuman race ever develops, its members will resemble Johnny von Neumann."
"I had begun teaching Paul[his son] relativity theory when he was five or six...he understood the theory of relativity by the time he was twelve."
[about Plato's Republic]" I was shocked that a book advocating a centralized government administered from above, much on the lines of totalitarianism, was so highly recommended to young people." 


Epoxidation #chempaperaday 167-177

Sharpless, Jacobsen, Shi

Comp.Org.Syn. 1991, 389
JOC 1986, 1922
JACS 1991, 113
JACS 1991, 106
JACS 1990, 2801
JACS 1991, 7063
TL 1990, 7345
Science 1997, 936
JACS 2002, 1307
JACS 1996, 9806
JACS 1997, 11224

Dihydroxylation #chempaperaday 159-166

Sharpless, Upjohn

JACS 1976, 1986
TL 1976, 1973
JACS 1980, 4263
JACS 1988, 10986
JACS 1989, 1123
JOC 1976, 766
TL 1990, 2999
JOC 1992, 2768

Hydrogenation #chempaperaday 144-158

Selected examples and mechanisms below:

Wilkinson, Crabtree, Knowles

JCS CC 1973, 629
JCS CC 1968, 1445
JACS 1977, 5946
JACS 1977, 2576
Science 1982, 401
JACS 1987, 1746

Noyori:

JACS 1987, 1596
JACS 1995, 1017
JACS 1995, 2675
JACS 2001, 7473
JACS 1995, 7562
JACS 1997, 8338
ACIE 2001, 2818
JOC 2003, 1998
JACS 2013, 2604

Asymmetric and Catalytic Conjugate Addition Reactions #chempaperaday 134-143

JACS 1979, 4236
ACIE 1998, 2099
Tetrahedron 1989, 349
JACS 2000, 1826
Chem.Rev. 2012, 2339
Chem.Soc.Rev. 2009, 1039
JACS 2005, 6877
JACS 2008, 446
JACS 2010, 14315
ACS Catalysis 2012, 95

C-H Activation #chempaperaday 125-133

Selected examples:

JACS 2004, 2300
JACS 2010, 14530
JACS 2004, 9542
Tetrahedron 2006, 11483
ACIE 2005, 2112
JACS 2009, 11234
JACS 2010, 14092
JACS 2012, 12002
JACS 2013, 1978

Buchwald-Hartwig Coupling #chempaperaday 109-124


Chem.Lett. 1983, 927
JACS 1994, 7901
ACIE 1995, 1348
TL 1995, 3609
JACS 2006, 3584
ACIE 1998, 2046
JOC 1999, 5575
JOC 2000, 1158
ACIE 2008, 6338
JACS 2008, 6586
JACS 2009, 11049
JACS 2006, 2180
JACS 2007, 10354
TL 1997, 6367
JACS 2006, 2180
ACIE 2011, 9943


Heck, Tsuji-Trost, Sonogashira Reactions #chempaperaday 101-109

Time to update the blog. Here are some examples from selected papers:

JACS 1992, 10091
TL 1994, 3453
JOC 1994, 2685
JOC 1994, 5583
TL 1993, 2505
JACS 1991, 1417
TL 1992, 2589
JACS 1999, 3543
JACS 1999, 7410

Wednesday, November 5, 2014

"A millennial overview of transition metal chemistry" #chempaperaday 100

I wanted to dedicate the 100th reading to F. Albert Cotton who I believe deserved a Nobel Prize in chemistry. You can read a short biography of him here:

http://rsbm.royalsocietypublishing.org/content/54/95.full.pdf

and here his biography as a book:

http://www.amazon.com/My-Life-Golden-Age-Chemistry/dp/0128012161/ref=la_B001IR1HU6_1_4?s=books&ie=UTF8&qid=1415238927&sr=1-4

The paper is a very short summary of transition metal chemistry starting with Werner complexes. I want to point a couple of his notes from the paper:

 "I note that the year 2000 is not the first year of the third millennium, no matter what the arithmetically-challenged of this world may like to think."
"At the beginning of the first millennium (i.e., six days after the birthday arbitrarily assumed for Jesus"
http://pubs.rsc.org/en/Content/ArticleLanding/2000/DT/B001668N#!divAbstract


"Fitting the Pieces of the Puzzle: The δ Bond" #chempaperaday 99

Multiple bonds between metal atoms! My favorite! I am in love with them since I've seen the first structure and molecular orbital diagram of [Re2Cl8]2-. I think there is nothing more amazing than having multiple bonds between two metals.




This is a "Viewpoint" and it's written for the "50th anniversary of the first paper describing a species with a quadruple bond by a team led by F. A. Cotton..."

It's not only a good summary of great work by him and his students, but also a great text full of hints how and with which instrumentation you should approach problems in your research.



http://pubs.acs.org/doi/abs/10.1021%2Fic500119h


 

"Homoleptic Organocobalt(III) Compounds with Intermediate Spin" #chempaperaday 98

This could be my favorite paper that I've read this week. I wrote it before. I like trends. I like systematic studies that allow you to compare results. This complex complete the "homoleptic perhaloaryl compounds of first-row transition metals" with the general formula of [M(C6X5)x]q-. So, now you can look at the first row transition metals with this formula and compare why they behave similar/different. I really like the discussion and characterization of the complex.
http://pubs.acs.org/doi/abs/10.1021%2Fic501719y

"Can One σ*-Antibonding Orbital Interact with Six Electrons of Lewis Bases? Analysis of a Multiply Interacting σ* Orbital" #chempaperaday 97

This paper is really interesting. Synthesis of the tin complex is very straightforward. But, the structure and the interpretation is exciting. To be honest, when I first saw the paper, I said "there is nothing special about it. I am sure thousands of complexes have similar structures and same interactions can be seen." But, after reading the discussion, (obviously) I changed my opinion. Also, I like the honesty of the authors

"We wish to report here the first example which is beyond our aforementioned common knowledge of dative bonds."

 http://pubs.acs.org/doi/abs/10.1021%2Fom500951e

"Formation of an Oxidant-Sensible Pd(II) Coordination Compound and Its 1H NMR Specific Characterization" #chempaperaday 96

Journal of Chemical Education is one of my favorite journals. There are so many papers that really help you to learn more about chemistry even if you are not an undergraduate student (anymore). But, you are always a student.

This paper is obviously one of them and in fact it's not a "simple" undergraduate experiment.

http://pubs.acs.org/doi/abs/10.1021%2Fed500447f


Sunday, October 19, 2014

Suzuki Coupling #chempaperaday 85-95

These are the papers that we're required to read for the organometallic chemistry (not exactly, but anyway) course I am taking. The topic is Suzuki coupling and some examples of it. Since I've read them all, it's time to share and record.

Chem.Rev. 1995, 2457
ACIE 2001, 4544
JOC 1999, 23
JOC 1994, 639
JACS 2000, 4020
JACS 2002, 9346
JACS 2005, 4685
ACIE 2004, 1871
JACS 2001, 10099
JACS 2002, 13662
ACIE 2003, 5749



Wednesday, October 15, 2014

Elitism

"Throughout my life, I have had a strong conscious and unconscious addiction to knowledge. Suppressing knowledge seems to me wrong and impractical. Obviously, knowledge can be used and misused. But, prevention of misuse, I firmly believe, must be kept separate from limitations on knowledge. Those believe that we are not yet ready for some knowledge consider themselves members of a world aristocracy that is ahead of everyone else in its value judgements. Some of the horrible events of the twentieth century may appear to justify their opinion. Nonetheless, I cannot help opposing aristocracy and elitism, whether they be an elite of nobility, race, money, morals, or even knowledge itself."

The quote above is from Edward Teller's Memoirs

Like him, I oppose any kind of "elitism." Today, I was thinking of people who consider themselves as smarter than other people based upon their education. Some people think a degree (especially an advanced degree) is a sign of intellectual capability. In fact, an advanced degree is just a degree that is earned mostly by hard work and sometimes even patience. A few exceptional people aside, most people just become highly professionalized in a certain field with an advanced degree. It does not show that are any smarter than a person without a degree. 


Wednesday, October 8, 2014

Male breast cancer

Here is a very short and informative review about male breast cancer. There is for sure a lot to learn from this rare disease and it will definitely help to understand female  breast cancer.

www.nature.com/nrc/journal/v14/n10/full/nrc3806.html

Stille coupling #chempaperaday 72-84

In this post, I will give you the papers I have read about Stille coupling and some total synthesis papers where Stille coupling used. Some of them are among the mist important papers on the topic.

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ja9742388
jo00099a018
ja991500z
om020896b
ja00336a033
ja00050a024
ja9829259
ja005644l
ja990215c

Monday, September 29, 2014

"Is Science Dangerous?"

I read this paper by Lewis Wolpert today. I think it was a talk that he gave and this is the transcript. Anyway, you can agree with him or not, it is up to you. But,  I think there are really important points in his speech. I try to stay away from "controversial: issues. So, I won't comment on what parts I agree with him and what parts I don't. It is worth reading.

You can read it free here:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1569503/#!po=87.5000

My "first" exposure to organometallic chemistry - #chempaperaday

Although I have always been interested in inorganic chemistry, I avoided reading organometallic chemistry papers as much as possible. The reason was that I really loved inorganic chemistry. Especially synthetic methods and coordination chemistry. Well, this summer, I started to read and study basics of organometallic chemistry and this semester I am taking a course where we learn A LOT about it. I now find the field really interesting and open to progress.

We spent almost a month of olefin metathesis and were expected to read tens of papers by the pioneers of the field. I will list them all below and I suggest that you read them ALL. You will notice that they are much better than ANY textbook. Amazing papers, written in such a wonderful way that everything makes so much sense. I will not write the titles of them though. The first list includes papers by Hoveyda, Schrock, Katz, Grubbs about his "First generation" and "Second generation" catalysts, ligand effects, type of olefins, mechanisms of the reactions, some organic synthesis papers where the catalysts were used efficiently etc. The second list is solely on Z-selective olefin metathesis papers by Grubbs, Schrock and Hoveyda (2011-present). I will give the DOI for those ones since I only have PDF's on my computer. I don't really want to open them one by one and write the details. I am sure you can easily find them.

JACS 1976, 1903
JACS 2001, 6543
JACS 2003, 10103
JACS 1992, 5426
JACS 2003, 14901
JACS 2003, 11360
JACS 2000, 1828
JACS 2002, 10779
ACIE 2007, 3860
JACS 2002, 773


ja202818v
ja203488e
ja210225e
ja301108m
ja4010267
ja4046422
9001_ftp (Angewandte)
c3sc52806e
om200150c
nature09957
ja205002v
ja210946z
ja210349m
ja303220j
ja304827a
ja404208a
ja403188t
8395_ftp (Angewandte)
2726_ftp (Angewandte)
1939_ftp (Angewandte)
1968_ftp (Angewandte)



Update: #chempaperaday and other things...

It's been a very long time I haven't written any posts. Well, the Fall semester started and it's been incredibly busy. I teach two lab sections, grade papers, hold office hours, answer tons of emails from students (this was unexpected!), take my own courses and study for them AND do the assignments! I also try to keep my research alive and move on to further steps in my "projects." 

If anyone is wondering, #chempaperaday is still alive and I do read papers almost everyday. The problem is most of these papers are related with my research and I do not want to write about them. Obviously,  I am trying to make new compounds. So, just by following the papers I read, one might figure out what I am onto (more or less). That's why I will keep them to myself.

I have read other papers too. But, as I mentioned above I have been busy and trying to figure out my new life schedule. So, I couldn't really focus on the blog. Tens of different blog post topics and ideas have come to my mind while I was dealing with all those stuff. Now that I am more comfortable with my schedule and more organized, I will write posts more often. The next post is coming tonight!

Thanks if you are reading here.

Wednesday, August 13, 2014

Shopping for symmetry!

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



Monday, July 28, 2014

"Why Are There No Terminal Oxo Complexes of the Late Transition Metals? or The Importance of Metal–Ligand π Antibonding Interactions" #chempaperaday 40/365

I was looking for some old papers and found this paper. It's in fact very similar to a lecture in inorganic chemistry. The title is very clear. So, there is not much to add. You can also look for "the oxo wall" to learn more about these complexes.

http://www.tandfonline.com/doi/abs/10.1080/02603598808035790#preview

It's all about bonding theory and symmetry.



Sunday, July 27, 2014

"Who should write books about science? "

This is a question I saw in one of Philip Ball's posts. By the way, in case you don't know, I think Philip Ball is by far THE BEST SCIENCE WRITER. Anyway, I do have my own ideas on the question mentioned here. But, I need to put them together in order to write a post on my own. The reason I wanted to mention the question here is the answer Philip Ball received from a Nobel laureate:

"I have a healthy disregard for anybody and everybody who has not made advances in the field in which they are pontificating."

I do believe that science writers should be SCIENTISTS that know how to write. I see many "science writers" around. But, most of them I think are just bloggers that cover scientific topics. Since they lack in the basics of the science they are writing about, I do not pay much attention to their ideas and writings. Sad but true.


"A Brief History of Catalysis" #chempaperaday Day 39/365

Although everyone might believe that they can define what "catalysis" or a catalyst is, it is really hard to find the correct definition for these terms. Simply and in general, a catalyst is a molecule/ion/element/heat/light etc. that lowers the activation energy of a chemical reaction. So, the reaction will go faster and in the end you'll end up regenerating your catalyst. A simple diagram is shown below.

                                          Catalysis. Source: Wikipedia article

The term catalysis was first introduced to chemistry by Berzelius. The paper I am sharing here is a really nice review on catalysis. In case you are wondering, there is not much "chemistry" in the paper. This is more like a history of science article that divided catalysis into five different periods and lists the major events and scientists chronologically. The five periods according to the authors are : production of alcohol by fermentation, "systematic research and the discovery of new catalytic processes," "industrial applications," synthetic fuel production, synthetic polymers. Of course I do not agree with these general and broad periods. But, as I said this is a really nice paper that gives you enough information on the history of catalysis. 

Catalysis is one of the greatest areas of research in chemistry. We know that enzymes easily catalyze several reactions at physiological conditions. But, when it comes to test tubes, reactors etc., this is not the case. So, discovering (or synthesizing) the right catalyst is not an easy task. It should also be relatively inexpensive and unique so that it stands out among the other catalyst candidates. 

It is free to read and I hope you enjoy the article:



Tuesday, July 22, 2014

#chempaperaday Day 38/365 : "Bringing Electron Paramagnetic Resonance (EPR) to Biochemistry: the Work of Helmut Beinert"

EPR is a powerful tool to study paramagnetic centers. So, it is widely used in inorganic and bioinorganic chemistry. In fact, I am not even sure if I should call bioinorganic chemistry as biochemistry. Sometimes I read papers and I can't tell if it is a bioinorganic or biochemistry study. Anyway, the short paper I read today was about Helmut Beinert and how he introduced EPR to biochemistry. Obviously, this led to great discoveries.

It is free to read here:

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.


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.