Looking back at 2015

Another year's passed. I am getting older and this makes me sad. Here's the summary of my 2015:

1. I have read 10 books. You can see some of them here. I will write more reviews for the ones I am missing and hopefully read at least 10 more books in 2016.

The Violinist's Thumb
The Devil's Doctor
Linus Pauling: And the Chemistry of Life
The Kaiser's Chemists
The Time Machine and the Invisible Man

Up from Generality: How Inorganic Chemistry Finally Became a Respectable Field

Energy from Heaven and Earth

Half-Life: The Divided Life of Bruno Pontecorvo, Physicist or Spy

Python Pocket Reference

2. I have posted 75 articles that I had read using #chempaperaday tag. As I said in my very first post, these are not the only articles I have read in 2015. These are the ones I post here. I am not posting any article related to my research, thesis or anything closely related with our lab. You can be sure I've read at least 150 papers in addition to the ones I posted here. I save and annotate them in my EndNote folders.

3. I took some MOOC's and obtained some CS and Python certificates. I wrote some useful code. I built the homepage of my own website.

4. I solved my first crystal structure (with the help of the crystallographer).

5. Poster presentation at ACS Boston.

2016 goals?

1. Publish 3 papers. 

2. Read at least 10 books.

3. Learn Flask. 

4. Get Data Science certificates. 

5. Build a web app.

6. Finish building the website.

Hopefully, everything will be much better in 2016! 

Happy new year!

Syngas in perspective #chempaperaday 255

Closely related with the previous post, I wanted to highlight this paper too. This one is a little bit more technical. It covers the conversion of natural gas into Fischer-Tropsch products and how the manufacturing costs affect the process.

 

http://www.sciencedirect.com/science/article/pii/S0920586101004540

The Fischer–Tropsch process: 1950–2000 #chempaperaday 254

A nice and short review of the process where you can find some detailed information about the catalyst type and selectivity. Pretty much all the papers mention Fischer-Tropsch process in their introductions, but very little is said on the process itself. What are the roles of cobalt and iron based catalysts? Are there other metals that can do the synthesis? If so, why do they choose cobalt and iron? All these are answered.

http://www.sciencedirect.com/science/article/pii/S0920586101004539

Energy from Heaven and Earth - Book

I am behind in book reviews here. I have finished this book a few months ago but never got the chance to write my thoughts about it. 

The book is actually a collection of Edward Teller's 1975 lectures. He gave a series of lectures as a part of his Harvey Prize requirement.

The dedication on the first page actually was a big surprise to me. Teller dedicated the book to N. A. Rockfeller saying that "..whose vision and initiative, had they only been followed, would have made this book unnecessary." 

There are 5 "parts" in the book each of which consists of several chapters. I really like the way the chapters are arranged. They follow a nice logic: from simple to difficult; from past to future. 

In these chapters, especially in the beginning, you can get a nice summary of how the universe started and the origin of energy. I don't think it's too technical. I believe anyone can easily understand the nuclear reactions and how they yield energy with Teller's excellent explanations. 

If you follow the news and read a little bit of science, people constantly talk about global warming, record CO2 levels etc. I believe this book will help you to ask more scientific questions and evaluate the data and plans in a more scientific way. Should we focus on environment first or on improving our living standards? Can we get enough energy from sun, wind, waves? Ethics vs. science? You can find some clues to these dilemmas. I have to say I am with Teller on many issues.

I strongly suggest people read this book. Even though it was written in 1980, it is still much more relevant to 2015 than many more "popular" scientists' thoughts. 

It is also interesting to read his thoughts on bacteria that converts biomass into fuel, solar cells and devices like photoelectric cells. 

Some quotes:

In a peculiar way I am indebted to the antinuclear forces that staged the great nuclear debate of 1976 in California. Confucius said that if you walk between a wise man and a foolish one, you should learn from both.

I do not advocate a nuclear option. I believe that nuclear energy is an important component of the solution.

The next ice age may well arrive in five thousand years, unless technology finds a way to prevent it.

In the beginning there was matter and heat but no usable energy.

Geothermal energy....this source is no more abundant than coal. We may exhaust it in a few centuries.

Gloomy stories we may hear about out dying planet are most likely wrong.

How do living plants turn into fossil fuels? I have gone to the best geologists and the best petroleum researchers, and I can give you the authoritative answer: no one knows.

Environmentalists may take notice that small is not necessarily beautiful or clean.

Arabs reputedly cannot agree with anybody, least of all with other Arabs.

If one wastes energy, one should pay for it.

California is the most ultra-American of all American states. California's waste is prodigious. 

Electricity ...the most expensive form of energy.

Minimizing energy input is not the main purpose of industry.

It has been remarked that Moses managed to find the only spot in the Middle East where there is no oil.

In today's climate opinion, to be big is to be unpopular.

King Coal has lost his throne to the Sheikhs of Araby.

..a coal-burning electric generating station is apt to emit more radioactivity than a corresponding nuclear plant.

[about CO2] there is possibly not enough oil in the world to make a real difference.

Szilard told me "I found the neutrons"

The alchemists proved that secret science is no science. In the long run we cannot keep secrets, and we should not try.

If scientists consider themselves an elite with responsibility for the world resting on their shoulders, they will no longer be scientists.

The scientist's prime responsibility is scientific knowledge. The scientist's second responsibility is to turn knowledge into practical applications. Finally, the scientist should explain his findings so that everyone can understand. The nonscientific world then can choose to use or misuse the new knowledge.

Best earthquake experts in the US. are found among the members of Jesuit order.

To prophets of the apocalypse, reactors are precursors of the end of the world.

It seems that even in California the nuts are in a minority.

We have not yet gotten to the point where we are willing to sacrifice a tourist attraction to our economic needs.

The very word "patent" means the opposite of secret. But our present patent law is archaic.

Bis(dicarbonyl-pi-cyclopentadienyliron)-A Solid-State Vibrational Spectroscopic Lesson #chempaperaday 253

I have highlighted J. Labinger's paper on cyclopentadienyl iron dicarbonyl dimer before. Today's read is a Journal of Chemical Education article focusing on Raman and IR spectroscopy of this dimer. I guess its main purpose is to show how useful these techniques are, but how difficult it is to determine a structure based on spectroscopy (especially for this dimer). I was actually just reading another paper on this dimer like 5 minutes ago. I'll probably post it soon.

I always think about Raman spectroscopy as some sort of esoteric technique. You always hear about it, read about it; but never see it. Certainly I haven't. We don't even have the instrument in the department. 

I like this paper because there is enough spectra and discussion about both IR and Raman spectroscopy of the dimer. You can also see a nice symmetry treatment and finding the IR and Raman active bands of the two isomers.

Bonding capabilities of transition metal carbonyl fragments #chempaperaday 252

The quest for metal carbonyl bonding is going on here. As I mentioned before, I am working on it. This is another article by R.Hoffmann where you can read one of the best MO theory explanations and examples. He makes it so simple that, there is no way you can't learn MO theory from him. It's a quite long article, so I am not going to try to summarize it for you. But, I will mention one of the most interesting observations in bioinorganic chemistry and how he explains it.

As you know, hemoglobin binds to oxygen giving us oxyhemoglobin; and when unbound, deoxyhemoglobin. Oxyhemoglobin has a six-coordinate iron atom in the plane of the porphyrin ring, but iron is out of the plane in deoxyhemoglobin. Why? Simply, it's the spin state and ionic radius. Because, we know from the experiments that the spin state changes from low to high spin. You can read it in any biochemistry or bioinorganic textbook. Well, in this article, you can read it in more detail and how it is actually predicted. So, I guess, even if we hadn't observed this phenomenon, we would have guessed it.

image source

So, assuming that the point group is C4v in these porphyrin complexes, for a d6 transition metal ion;

   - low spin complexes will prefer a square pyramid and metal will be in the plane

   - high spin ones will prefer to be out of the plane! (a1 orbital is occupied)


http://pubs.acs.org/doi/abs/10.1021/ic50147a021

http://www.ncbi.nlm.nih.gov/books/NBK22596/ 

The Anion of Zeise's Salt #chempaperaday 251

Zeise's Salt is accepted as the first organometallic compound and it was prepared by William Christopher Zeise. Before talking about his life, let's see what this salt is. Apparently, Zeise first prepared this compound in 1825, but it did not draw much attention. In 1830, he publishes a detailed paper on the synthesis and properties of this interesting "brown residue". He does some analytical work in addition to adding KCl to the compound and names the salt as "inflammatory potassium platinum salt". He was one of those early chemists who tastes his compounds and now we know that it tastes as "metallic, astringent, long lasting".

A few years later, he was challenged by the famous Justus Liebig. Liebig doesn't believe the composition of the compound and suggests that it contain oxygen. He believes that the compound has an alkoxy group. Zeise does more analytical work and shows that there is no oxygen but of course Liebig was not convinced and writes a paper in reply to Zeise.

15 years later, Karl Birnbaum repeats Zeise's experiments and determines that his formulation is correct. The crystal structure of Zeise's salt was first solved in 1954 and you can see a representation below. For the untrained person, coordination mode of olefin is really weird. For an inorganic chemist, it is perfectly fine. I will write another post on the bonding and molecular orbital diagram of this compound soon, so I am moving on to Zeise's life now.

To be honest, I only knew Zeise by his famous compound. To my surprise, he turned out to be one of the greatest chemists ever! His research was focused on chemistry of sulfur and he discovered xanthates and thiols! He also tried to study components of tobacco smoke!

It turns out he did most of his experiments at home and his cats were killed by his landlord due to a terrible smell. In fact, he was even removed from a play because he smelled so bad.

What a character, what a chemist. This short but fantastic article really urged me to read more about Zeise. I've just started to collect some papers now.

* all images are from wikipedia pages for Zeise's salt and Zeise himself.

First examples of neutral and cationic indenyl nickel(II) complexes... #chempaperaday 250

I read this paper yesterday and found it interesting. Cationic nickel complexes are not new. They often used as polymerization catalysts and you'll often see them coordinatively unstaturated which makes the olefin coordination easier.

In this work, the authors synthesized four complexes in total (2 neutral, 2 cationic) and they showed some catalytic activity. They are not impressive but this is just a communication so, I am guessing there will be a follow up with improved yields and reaction conditions.

http://pubs.rsc.org/en/content/articlelanding/2015/dt/c5dt02794b#!divAbstract

Metal-phosphine Bonding Revisited #chempaperaday 249

Any inorganic chemist knows that phosphines (in general) are good sigma donors. When phosphines are involved, however, there is a lot of suspicion about pi accepting abilities of phosphines or whether the empty d orbitals are involved in bonding or not. I have to admit, it's confusing. So, here is a great article on phosphines where the authors try to answer these questions. It was published in 1992 and I did not check how many times it was cited or if there have been any corrections made.

- The most surprising result for me was that ALL phosphines ( PMe3, PH3, P(OMe)3, PF3) are GOOD sigma donors. Yes, even PF3? Who would have thought?

- When it comes to pi acidity though the trend is as follows :

                                         PMe3 < P(OMe)3 <  PF and they conclude that PF3's pi acidity is "of comparable strength to CO" 

-So, you want a pi-acceptor, but not the beast? Use PF3, if you can find it in the lab.

-How about d-orbitals? Well, according to the study, d-orbitals do not directly act as pi-acceptors, instead, they are "polarization functions" that help to increase pi acidity.

Also, this article looks like a good follow-up. Maybe I'll read at too.

http://pubs.acs.org/doi/abs/10.1021/cr00029a008

Complexes of Carbon Monoxide and Its Relatives #chempaperaday 248

This is a review article written for the 100th year anniversary of the synthesis of nickel tetracarbonyl. The author is one of the greatest chemists ever (IMO) Helmut Werner. I will probably write another post focused on his research and contributions to let people know what he did.

Since the article is about CO complexes, here you can read more about CO analogues and isoelectronic ligands and their coordination properties. It looks like it's open access, so I hope everyone will be able to read it. A fantastic review of coordination chemistry of CO and its analogues with a lot of historically important names and papers.

Is CO a Special Ligand in Organometallic Chemistry? #chempaperaday 247

As I mentioned in a recent post, I have been reading a lot of Hoffmann papers to study and learn more about MO theory. So, be ready if I post several of them in the next couple weeks. 

Transition metal carbonyl complexes are very important in organometallic chemistry.  Sometimes they are used as catalysts or precursor to catalysts, and sometimes they are used to explain our understanding of important industrial processes like Fischer-Tropsch synthesis. 

It looks like CO is very special in terms of sigma donating and pi accepting capabilities. But why? Is it unique? Can we find better ligands? This paper is probably the first of the series I'll post where I am trying to find an answer (not experimentally, just by reading literature). So, if you follow the series, you will probably learn a lot with me.

Fischer and Schrock Carbene Complexes: A Molecular Modeling Exercise #chempaperaday 246

Transition metal carbene complexes are really important complexes in organometallic chemistry and they are used to produce important organic molecules like the ones in olefin metathesis for example. Two of these complexes are much more important and in fact they both have names: Fischer and Schrock type carbenes. You can read about these in any inorganic chemistry textbook. But, I think you can never find a better summary of these complexes. This paper, although a molecular modeling exercise, does a great job explaining the general properties of these two type carbenes.  I wish textbooks were as clear and as simple as this article.

Tutorial on Oxidative Addition #chempaperaday 245

Organometallics has just started a new series called "Tutorial" where hopefully we will read about fundamental topics in organometallic chemistry. I think this is a really good attempt to educate not only students but all chemists. You will notice that there are several groups which I will call "organic" doing some catalysis using Pd, Ni, Co and Fe with some ligands. So, it is really hard to distinguish an organometallic chemist from an organic chemist just by looking at his publications nowadays. What these organic heavy people lack (I think) is some fundamental knowledge of transition metals. Some people think they can just pick a metal salt (or a M(0) source) and throw it in with hundreds of ligands and expect to see some reactivity. Well, to be honest, this approach does work if you screen hundreds of ligands with hundreds of different reaction conditions using tens of students spending 80 hours/week in the lab. This is one of the biggest reasons that organometallic chemistry is not my favorite. I am on the other side. I like people who design a ligand using the fundamental knowledge about the reaction and the metal they are working with. Let's face it, a lot of reactions only need a Lewis Acid, of course they will be catalyzed by one of the combinations you are using if you try hard enough. My call to them is that instead of using brute force, if they just use some intelligence, I will read their papers.

This first of the series is on oxidative addition by Jay Labinger. I will consider myself among the lucky people who have read his papers (in fact a lot of them!). I have always liked they way they're written and most of the time, I learned from their chemistry. I've finished his book "Review of Up from Generality: How Inorganic Chemistry Finally Became a Respectable Field" and I will write a post about it too.

As I had expected, this tutorial is not only a good starting point for a learner, but it is also a great source for organometallic chemistry enthusiasts. It is full of incredibly useful hints and trends about d-block if you know how to read it. I hope and I wish everyone read it. I am not sure if it's open access, but if I were to decide, I'd keep it open access so that people can learn.

http://pubs.acs.org/doi/abs/10.1021/acs.organomet.5b00565?journalCode=orgnd7