One Hundred Years of the Fritz Haber Institute #chempaperaday 192

Fritz Haber Institute is one of the "sub" institutes of Max Planck Institute. Unless you are interested what they do, you probably have not heard of the institute. Since, I follow some of their research areas, I can say I know a some about the institute and in fact it would be an honor for me to work there one day in the future.

So I was really happy when I came across this paper about a month ago. It's a short history of the institute and the research within covering one hundred years. I am glad I read it because I was able to learn much more than I know about FHI. I did not know FHI had seven Nobel laureates for example.

http://onlinelibrary.wiley.com/doi/10.1002/anie.201104792/abstract

                                                                   Photo: Wikipedia

If you read the paper, you will learn how much the institute contributed to modern science especially in surface chemistry, heterogeneous catalysis and electron microscopy. I would like to highlight a few titles that were also related to FHI: gas masks, methane detector, allotropes of hydrogen, symmetry. 

The fields of research explained by the paper are:

Gas-Phase Kinetics and Dynamics

Methane Detector

Haber-Born Cycle

Chemiluminescence

Combustion

Sttatistical Mechanics

The Franck-Hertz and the Compton Effects

Dispersion

Theoretical Chemistry

Molecular Beams

Physisorption

Colloid Chemistry

Electron Microscopy

Surface Science

[The] science research project of today is the temporary culmination of a very long, hard- fought struggle by a largely invisible community of our ancestors. Each of us may be standing on the shoulders of giants; more often we stand on the graves of our predecessors.

"In the words of the historian Fritz Stern, Haber' s Institute during the First World War became “ kind of forerunner of the Manhattan Project."

Gallium-Iron multiple bond controversy #chempaperaday 189-191

I have three papers starting with a report claiming that there is evidence for a Ga-Fe triple bond and they named it "ferrogallyne."

http://pubs.acs.org/doi/abs/10.1021/om970530c

As you can see the evidence for this so-called multiple bond was not so convincing. So, being an expert in multiple bonds, F.A. Cotton wrote his comments and concerns about this assignment. He explained his reasoning and suggested that there is also a dative bond between Ga and Fe.

http://pubs.acs.org/doi/abs/10.1021/om970971w

There was no reply from the original authors. So, this is unfortunate. I was able to find a computational paper on the issue. But, it's not the best paper to read on the subject. The authors simply say that the triple bond is a "pseudo-conflict" in this case because our bonding model is not "appropriate." Personally, I agree with Cotton and I think there should only be a Ga->Fe bond.

Lewis Acidity of Organofluorophosphonium Salts #chempaperaday 187-188

The paper I read was "Lewis Acidity of Organofluorophosphonium Salts: Hydrodefluorination by a Saturated Acceptor that was published in Science. The second one is the "perspective" by F.Gabbai in the same issue. 

Caputo, C. B.; Hounjet, L. J.; Dobrovetsky, R.; Stephan, D. W., Lewis Acidity of Organofluorophosphonium Salts: Hydrodefluorination by a Saturated Acceptor. Science 2013, 341 (6152), 1374-1377.

Gabbaï, F. P., Lewis Acids with a Difference. Science 2013, 341 (6152), 1348-1349.

I pretty much knew nothing about hydrodefluorination until I read these papers. Now I know some. Really difficult research but it's not very popular yet. So, there is a lot of opportunities in this area of research.

Whittlesey, M. K.; Peris, E., Catalytic Hydrodefluorination with Late Transition Metal Complexes. ACS Catalysis 2014, 4 (9), 3152-3159

"Synthesis, Characterization, and Structures of a Persistent Aniline Radical Cation" and the controversy #chempaperaday 183-186

The recent controversy and discussion starts with the publication of the report of a stabilized aninile radical cation.

http://onlinelibrary.wiley.com/doi/10.1002/anie.201205478/suppinfo

Here the authors claim that they were able to stabilize the radical cation and report x-ray structures, electrochemical studies and some EPR data.

Shortly after this paper, two comments appear:

Comment on “Synthesis, Characterization, and Structures of Persistent Aniline Radical Cation”: It Is a Protonated Aniline and Not an Aniline Radical Cation

http://onlinelibrary.wiley.com/doi/10.1002/anie.201305293/suppinfo 

and 

Comment on “Synthesis, Characterization, and Structures of a Persistent Aniline Radical Cation”: A New Interpretation Is Necessary

http://onlinelibrary.wiley.com/doi/10.1002/anie.201303991/suppinfo 

The commenters try to replicate the experiments and they basically say that it is not an aniline radical. They have some detailed studies and explanations.

Finally, the original authors publish a reply to those two comments here:

Reply to Comments on “Synthesis, Characterization, and Structures of Persistent Aniline Radical Cation”

http://onlinelibrary.wiley.com/doi/10.1002/anie.201308539/abstract;jsessionid=5279D35F4E3D1A886730106324AE798C.f01t03

The problem with the "reply" is that they accept some of their "mistakes" and claim that they obtained the aniline radical cation. But, they can't really clarify some of the other concerns that the commenters pointed out.

Really interesting read.

Book: Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves

George Church is a great mind and scientist. I had the chance to listen to his talk in Museum of Science last year. So, when I saw the book by him, I didn't even hesitate one second. I knew it would be a great read. After reading it, I can say I was absolutely right. Whether you like biology or not, whether you know some biology or not, you should read the book. It is not only a book about synthetic biology and the future of it, it is also about humanity, the fate of humans and our society.

"Imagine a future in which human beings have become immune to all viruses, in which bacteria can custom-produce everyday items, like a drinking cup, or generate enough electricity to end oil dependency. Building a house would entail no more work than planting a seed in the ground. These scenarios may seem far-fetched, but pioneering geneticist George Church and science writer Ed Regis show that synthetic biology is bringing us ever closer to making such visions a reality. In Regenesis, Church and Regis explore the possibilities—and perils—of the emerging field of synthetic biology. Synthetic biology, in which living organisms are selectively altered by modifying substantial portions of their genomes, allows for the creation of entirely new species of organisms. Until now, nature has been the exclusive arbiter of life, death, and evolution; with synthetic biology, we now have the potential to write our own biological future. Indeed, as Church and Regis show, it even enables us to revisit crucial points in the evolution of life and, through synthetic biological techniques, choose different paths from those nature originally took. Such exploits will involve far more than just microbial tinkering. Full-blown genomic engineering will make possible incredible feats, from resurrecting woolly mammoths and other extinct organisms to creating mirror life forms with a molecular structure the opposite of our own. These technologies—far from the out-of-control nightmare depicted in science fiction—have the power to improve human and animal health, increase our intelligence, enhance our memory, and even extend our life span. A breathtaking look at the potential of this world-changing technology, Regenesis is nothing less than a guide to the future of life."

The above paragraph is straight from the Amazon webpage for the book. I had to quote it because I can't write anything better than that. It's an easy to read book so I am pretty sure anyone who has 3-4 hours on a weekend will easily finish reading it. You will not only learn how synthetic biology can change our future but also how important it has become in our lives without even realizing it. Moreover, if you want to be an entrepreneur in biotech there are tens of examples of them; how they were founded, how and why they succeeded (or didn't), the challenges and even future directions.

Before you look up for the definition of synthetic biology, let's see how George Church describes it:

"the science of selectively altering the genes of organisms to make them do things that they wouldn;t do in their original, natural, untouched state."

As usual, I have quotes :

"Creating a mirror world might give us a fresh lease on life, one free of disease and unwanted agricultural pest species."

"...species that are lowest in diversity are most vulnerable to extinction."

"Give me a selection, and I will change the world."

"Multicellularity tends to come with a hard consequence-you give up your immortality."

"...just as individuals respond differently to drugs and to pathogens, they also respond differently to information."

"What should we do? Doing nothing, or doing what is traditional or natural, is not even close to a recipe for survival. If we choose tomorrow to behave in a way that our primitive ancestors did, nearly all of our 7 billion humans will die."

Alfred Werner's seminal 1910 paper on polynuclear cobalt complexes: What have we learnt since then?

Alfred Werner is one of my heroes in chemistry. He's probably in top 3 with Linus Pauling and Fritz Haber. I wrote posts about him before. Also here are two links about the controversy between him and Jorgensen:

S. M. Jørgensen and His Controversy with A. Werner: A Reconsideration 

Sophus Mads Jørgensen and the Werner-Jørgensen Controversy

But, he has some role on almost anything I write about inorganic chemistry since he is the founder of coordination chemistry and probably the most important chemist who showed people the importance and power of inorganic chemistry. What he did in his limited time (he died at the age of 53) and with his limited equipment is simply incredible. He left us hundreds of pages of publications, books and his legend. 

Karl Wieghardt is among my scientific heroes and as I said before I hope I can work for him one day. Here is an interview with him that I posted before. So, I am extremely happy to hear him giving a talk about Alfred Werner. I will not spoil it for you, because I really want you to watch/listen to this presentation by him about Alfred Werner. Once again, I hope you will realize and share my thoughts about Alfred Werner. Because, as Werner's life, the presentation is also full of surprises. I am pretty sure you will learn many things about Werner that you haven't heard so far. I hope you enjoy it.

http://presentations.acs.org/common/media-player.aspx/Fall2013/INOR/INOR004/17075

The Principle of Membrane Fusion in the Cell (Nobel Lecture) #chempaperaday 182

I try to read as many Nobel lectures as possible. You can often find really important pieces in those successful scientists' life and career that might help you figure out a problem in your research or a way to approach the problem.

This Nobel lecture on membrane fusion by J.E. Rothman is among the best. Just like many other Nobel laureates, he also has an interesting and diverse background that helped him throughout his career.

According to him, "the key elements for breakthrough" are:

-an ideal working environment

-The choice of the right problem at the right time

-A unique way of approaching the problem

         -hard work and persistence to develop a method that works in the wake of many painful failures

-the right partner to attack the problem

-stable research funding

"there is no process in biology that, at its very core, is not physical-chemical

in nature. As the direct consequence, we can expect that, in due course, all of

life—even human thought and emotion—will be understood as emergent from

physics and we will understand ourselves in health and in disease as complex,

organically composed self-determining machines. This is a perspective that may

frighten some, but it should not because it offers our species the best hope for

the long term."

 "How Does a Physicist Approach the World (including the Biological World)?

-Seeks universal laws to explain all related processes on a common basis

-Formulates the simplest hypothesis to explain the facts

The simplest hypothesis:

-Intrinsic chemical specificity governs transport, not intracellular anatomy"

Here is the lecture slides :

http://www.nobelprize.org/nobel_prizes/medicine/laureates/2013/rothman-lecture-slides.pdf

Here is where I read the lecture:

onlinelibrary.wiley.com/doi/10.1002/anie.201402380/abstract

Also here:

http://www.nobelprize.org/nobel_prizes/medicine/laureates/2013/rothman-lecture.pdf

Fritz Haber: The Damned Scientist - #chempaperaday 181

I couldn't help reading another article on Fritz Haber today.

 

Like every persont, he had a personal life and he made choices. All I am interested in him is his science and I admire his science.

Fritz Haber: Flawed Greatness of Person and Country #chempaperaday 180

This is the second article I have read (at least after I started to blog) on Fritz Haber. The first one, in case you are interested is here. This one is a more biographical article written by Fritz Haber's godchild Fritz Stern for the 100th year of Fritz Haber Institute. If you are interested in history of science, I think you should definitely read it.

"In our world so fond of denigration, of alleged honesty honed by political correctness, Haber is often remembered as a vain chauvinist."

"To understand Haber is to understand Germany and to some extent the opposite applies as well. They illuminate each other."

"He was a German patriot committed to an international enterprise, science."

"Haber flourished in Wilhemine Germany; the Kaiser set the tone and Haber played to the tune."

"The defense of scientific research as fundamental to national defense was an argument that Haber was to use throughout his career."

"I regret that we live in an age of denigration, and I want to mention an American instance of blemished greatness now being distorted in a faintly analogous process."

Transition metals in plant photosynthesis - #chempaperaday 179

This is a minireview about the roles of Cu, Fe, Mn and Zn in plant photosynthesis and finally there is a very short part on artificial leaves with Ni. The role of the transition metals in biology amazes me. They are so important that deficiency or higher concentrations of these metal ions have detrimental effects on the plants' or other living organisms' lives. Sometimes I think that some metal ions have very similar ionic radii and in fact it should not be a huge problem to have one instead of another. But, when you look at the biology you see only one ion instead of the other. How is this regulated? What brings those metal ions and places them in those proteins or organelles? Yes, there are chaperones but what is the source of this incredibly high selectivity and how are they transported? I hope one day we will learn.

http://pubs.rsc.org/en/content/articlelanding/2013/mt/c3mt00086a#!divAbstract

Book: The World's Greatest Fix by G.J.Leigh

This was the last book I read in 2014 and in fact I finished reading it on the 30th.

I was surprised that the first half of the book was about the history of fertilizers and agriculture (I should have understood it from the title!). Then comes the second part about the discovery of nitrogen and the historical progress towards Haber-Bosch process. These chapters were full of inorganic an industrial chemistry with several journal articles that I would love to read as soon as possible. I had always thought of Haber's method for nitrogen fixation as a more serendipitous discovery instead of a scientific research. I could not be more wrong. Also, Bosch's coworker Alois Mittasch tested "2500 different catalysts in 6500 runs within about one year." So much of the process (or reactions) were already studied in detail and there were other methods in use for nitrogen fixation. But, Fritz Haber (and Bosch) was the only one who made it work more efficiently and turned it into an industrial process. Final chapter is about nitrate and nitrite for those who are concerned of their affects on health and environment. Again, here you find a lot of peer reviewed journal articles as references. I think this was one of the best science books (chemistry in particular) I have ever read. Here are some quotes from the book:

"Alchemists, no less than modern scientists, were keen to find sponsors."

"No scientist ever makes a fundamental discovery that owes absolutely nothing to his predecessors."

"Today one can no longer whisper the magic words "nitrogen fixation" to granting bodies and expect to be funded."

"...%40 of all people alive today are dependent upon Haber-Bosch nitrogen...."

"There is a need for people to be much more educated scientifically, so they can make their own informed judgements."

"scientists...like the alchemists, so many employed by modern equivalents of rich princes hoping to find the philosopher's stone."

"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

"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

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

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. 

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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"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.

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!

"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.

"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:

http://image.sciencenet.cn/olddata/kexue.com.cn/upload/blog/file/2008/10/200810102212944318.pdf

#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:

http://www.jbc.org/content/284/21/e4.full.pdf+html

#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:

http://www.jbc.org/content/284/32/e10.long

#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.

http://pubs.acs.org/doi/abs/10.1021%2Fed041p466

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:

 http://pubs.acs.org/doi/abs/10.1021%2Fed041p466

#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."

#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!

http://onlinelibrary.wiley.com/doi/10.1002/wdev.96/full

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. "

http://pubs.rsc.org/en/Content/ArticleLanding/2013/CS/c2cs35236b#!divAbstract

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"

 

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.

Calm Before the Storm

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

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

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

It's still calm before the storm.

Book: "Classics in Coordination Chemistry Part I"

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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