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

Honorary Organometallic Molecule #chempaperaday 244

So, lately I've been reading a lot of Hoffmann papers to practice and more about MO theory. I found an incredibly helpful article of his that he published in 1981 in Science. I think textbooks can get away with pasting this article and not giving any more explanation on the theory. It's so well written that you can start with zero knowledge in MO theory and end up understanding pretty much everything about it. The interesting thing is that although the article's title is "Theoretical Organometallic Chemistry", the famous dirhenium complex [Re2Cl8]2- complex is among some organometallic compounds. The reason?

"10 Start-Ups To Watch" but why C&EN?

I usually don't write posts on debatable topics, but this article and a following Reddit AMA caught my attention. Before I write anything, I should mention that I am in no way related to anyone involved in the article or any of the people in those companies. I have also never interacted with any person involved so I am at a pretty safe position to write what I think.

While I understand C&EN is a Chemical and Engineering News agency/organization; I don't understand why these 10 companies were selected and they were (obviously) promoted. C&EN is free to do anything they want, but if I ran an organization like that I wouldn't highlight these companies the way it was done (especially I wouldn't do a Reddit AMA to endorse them even further). I had seen similar articles in several other science magazines or blogs where someone (usually who knows the author), picks up a company/paper and writes a "post"; but this is the first time I noticed it in C&EN. Most of these yield to more public attention and the author/owner somehow benefits from it. I have my own values, while I understand science needs to be promoted especially to get funding, I will never let my own research to be covered by ANY news agency as long as I have the power to do so. I can write my own article, and if someone wants it, go ahead and paste the whole thing. Good luck with that. 

Inorganic Chemistry - Housecroft & Sharpe

First of all, it's been some time I haven't posted anything but believe me I am incredibly busy reading and writing. I am preparing for my Ph.D. qualifying exam and there are tons of requirements such as writing a research progress (hopefully will be my first paper), research proposal (I wrote 5 of them) and answering some general inorganic chemistry questions in addition to a specific topic that I am given. 

To brush up some of the fundamental knowledge in inorganic chemistry, I skimmed through the book that is mentioned in the title and I realized that I've never said anything about this book. I think this book is by far the best inorganic chemistry textbook. I was taught by Miessler and Tarr's book (actually several times) and while it's a good book too, I think it's not appealing to an undergraduate student. There are already few of us who are interested in inorganic chemistry and that book doesn't help much to the ones that needed to be converted:) 

Housecroft's book is an excellent source in terms of giving background and relevant information and explaining the topics in detail. You usually don't get lost and there are literally tons of recent articles cited in the book so that you can find really good journal references. Moreover, there are these extra articles in the end of each chapter and almost all of them urges you to do more research on the subject. They are really well written and almost always about really interesting topic. Colors and nicely produced crystal structures also help you to see some molecules on the paper rather than reading a long and boring name.

I don't really know what else I can say or how I can explain how much I like this book, but if I ever teach IC (hopefully never), I am definitely making this book the textbook. If I ever meet one of the authors, I am going to thank them personally.

Isostructural Molecular and Surface Mimics of the Active Sites of the Industrial WO3/SiO2 Metathesis Catalysts #chempaperaday 243

"Silica-supported tungsten oxide has become a key catalyst of the petrochemical industry as part of the Lummus OCT process, allowing the production of propylene through the ethenolysis of butenes.(1, 2) Despite the now well-accepted Chauvin mechanism, alkylidenes and metallacyclobutane intermediates have however never been observed in such systems"

So, it is always worth trying to synthesize well defined supported mimics of these.
A very short but a really good paper. Great examples of synthetic work and problem solving. I am loving it.

Evaluating Molecular Cobalt Complexes for the Conversion of N2 to NH3 #chempaperaday 242

Another example of nitrogen fixation by a cobalt complex. Very similar to what I just posted. There are a few tables where you can see the comparison of similar complexes. I found it very useful.

http://pubs.acs.org/doi/abs/10.1021/acs.inorgchem.5b00645

Diiron Bridged-Thiolate Complexes That Bind N2 at the FeIIFeII, FeIIFeI, and FeIFeI Redox States #chempaperaday 241

We all know that nitrogenase cofactors have iron AND sulfur. But, if you look at the literature it's not very often that you see an iron complex with sulfur donors that bind N2. Here is a great example that ALSO yields ammonia!

http://pubs.acs.org/doi/abs/10.1021/jacs.5b04738

Characterization of an Fe≡N–NH2 Intermediate Relevant to Catalytic N2 Reduction to NH3 #chempaperaday 240

The first of the series of papers I will post from Peters lab this week. I absolutely love their projects and synthetic work.

In this paper, they used several spectroscopic techniques to identify an important intermediate and it was determined that the complex is "a doubly protonated hydrazido(2−) complex featuring an Fe-to-N triple bond." The structure and bonding probably similar to an intermediate in O2 reduction by Fe.

http://pubs.acs.org/doi/abs/10.1021/jacs.5b03432

The utilization of ceria in industrial catalysis #chempaperaday 239

Another heterogeneous catalysis paper that I read. This time, it's about ceria (CeO2). Ceria is the most important rare earth oxide in industrial catalysis and due to its price and not much investigated properties, I think it is a good starting point to find some important catalytic applications. 

http://www.sciencedirect.com/science/article/pii/S092058619800515X

Design, Preparation, and Characterization of Zn and Cu Metallopeptides... #chempaperaday 238

If you are following my blog, you are well aware that I am very much interested in bioinorganic chemistry and metallopeptides are one of my favorite topics. Here is an example of a cationic framework helping the metal to be more active for DNA cleavage. 

http://pubs.acs.org/doi/10.1021/acs.inorgchem.5b01680

Cr–Cr Quintuple Bonds: Ligand Topology and Interplay Between Metal–Metal and Metal–Ligand Bonding #chempaperaday 237

"The difference between Cr−Cr quadruple and quintuple bonds is not just another weak δ bond."

This is very nice study to find some correlation between several bond metrics, ligand types etc. and the M-M bond distance and bond order. As you can imagine, for some systems, there IS nice correlations. For example, systems like Cr2L4, weaker Cr-L interactions yield to stronger Cr-Cr bonds. I found this paper very useful to design new ligands to maybe break the record short distance and discover some unique properties.

Why Is Uranyl Formohydroxamate Red? #chempaperaday 236

Colors tell a lot in inorganic chemistry. While most of the reported U(VI) complexes are red, the complex in question here was reported as red. So, the reason was investigated and two factors were found to explain the color. If you are interested, you can read it here:

http://pubs.acs.org/doi/abs/10.1021/acs.inorgchem.5b00262

Why Combustions Are Always Exothermic ? #chempaperaday 235

A very simple question, but incredibly hard to answer without thinking about it. In fact, I don't think I can give a correct answer without looking up. Even then, I would probably be wrong. Luckily, this great article will help me in the future. It gives enough evidence and answers simple questions like "why fire is hot regardless of the fuel" and "why in spite of its high bond enthalpy, O₂ is abundantly present in our atmosphere.?"

 

http://pubs.acs.org/doi/abs/10.1021/acs.jchemed.5b00333

I printed this article and I will keep it as a reference and educational source for my own purposes.

Oxidation State, A Long-Standing Issue! #chempaperaday 234

Oxidation state is both the simplest and the hardest concepts of chemistry. To be honest, sometimes (maybe more often than sometimes), I get confused too.  In fact, you can even find slightly different definitions of oxidation state depending on what you are trying to reach in the end. To be honest, I found this paper a little bit confusing in the beginning. It's not the author's fault of course. Once again, oxidation state is not really straightforward. Overall, I think it is a nice paper to read and a good summary of interesting examples.

BONUS : It's open access.

http://onlinelibrary.wiley.com/doi/10.1002/anie.201407561/abstract

Improvements in the synthesis and understanding of the iodo-bridged intermediate en route to the Pt(IV) prodrug satraplatin #chempaperaday 233

Satraplatin is a Pt(IV) prodrug and the route to satraplatin is still in debate. In this article the authors propose a iodo-bridged intermediate and an improved synthesis to this intermediate. Really nice work and characterization methods.

http://www.sciencedirect.com/science/article/pii/S0020169314005477

Cellular interactions of platinum drugs #chempaperaday 232

This is a 2012 review paper and a really good summary on the fate of platinum drugs in model systems and in cells. 

While we know that cisplatin completely cures testicular cancer and is very effective in a few other cancer types, the mechanism of action is still not really known. It is also not known why it is so selective against testicular cancer. The article made me really realize how little we know about cisplatin and other platinum anticancer drugs. There are tens of cellular targets and it is still not understood what happens to cisplatin when it enters the cell. In fact, only 1% of cisplatin ends up binding to DNA. There is still so much work to do to answer these questions and develop better drugs. I hope I can help one day.

The Phenomenon of the Styrian Arsenic Eaters... #chempaperaday 231

This is new to me. So, apparently, it was long known (or believed) to be that there were/are people who eat white arsenic to become immune to certain diseases or to get healthier! Stories of these people were told in several parts of the world including Europe and several novels, poems etc. are based on these people.

In this interesting article, you can read whether this phenomenon is real or not. The author mentions as many of these literature examples as possible and like a detective, he tries to find the truth. I think it is a really good read if you enjoy history of chemistry.

Heterometallic Effects in Trinuclear Complexes Supported by p-Terphenyl Diphosphine Ligands #chempaperaday 230

Not the most conclusive study, but a good work on the synthesis and characterization of three trinuclear complexes.

One of the most interesting parts for me is that compound 3[BF4]  (-1.31V) was reduced by cobaltocene (-1.32 V).

 

http://pubs.acs.org/doi/abs/10.1021/acs.organomet.5b00579

Heterogeneous catalysis with metal nitrides #chempaperaday 229

Although I am working on making catalysts for homogeneous catalysis, one of my biggest passions is heterogeneous catalysis.

Metal nitrides are one of the most interesting class of these catalysts. There are several examples of them used and being explored in ammonia synthesis, hydrotreating, hydrogenation and so on. There are examples of these in this paper. You can also read several different methods to make these catalysts and some distinctive features of each.

There is a nice paragraph summarizing the limitations of the experiments and analysis of these catalysts too such as surface structure-activity reaction.

For those who know nothing about metal nitrides in heterogeneous catalysis, I think the key is that they are believed to show "noble-metal like behaviour."

 

Diiron Azadithiolates as Models for the [FeFe]-Hydrogenase Active Site... #chempaperaday 228

More on diiron complexes in this post. This is a nice and beautifully written summary of Prof. Rauchfuss' work on the topic.

"To the eyes of an organometallic chemist, the active site of the [FeFe]-H₂ases combines the familiar and unfamiliar."

A few things to note :

- Diiron, nickel-iron and iron based hydrogenases have no evolutionary relationship.

- low spin iron centers in general stabilizes hydrides better than high spin ones

Synthetic Advances Inspired by the Bioactive Dinitrosyl Iron Unit #chempaperaday 227

Ok, first of all, I am not dead and I didn't stop reading. In fact, I've probably read more than ever. I mostly read papers related to my research and a specific research problem though. That's why I keep them to myself. Hopefully, I will get on track again starting with this post.

This is a really good article on dinitrosyl iron units which are believed to be very important in cell biology. As the authors say "DNICs have been documented to be the largest NO-derived adduct in cells".

You can find some really cool synthetic routes to make these complexes and their electrochemistry in this paper. Hope you enjoy.

Cobalt(III) Werner Complexes with 1,2-Diphenylethylenediamine Ligands #chempaper 226

I think this is a really nice study. They checked 80 crystal structures of [Co(en)3]3+ and then came up with this useful approach to catalyze the addition of malonate esters to nitroalkenes. Classical Werner complexes once again proved that they are very promising in catalysis.

http://pubs.acs.org/doi/full/10.1021/acscentsci.5b00035

Amide-Functionalized Naphthyridines on a Rh(II)–Rh(II) Platform #chempaper 225

This is an interesting paper on dirhodium complexes where the authors try to synthesize some catalytically active compounds, but instead they found out and reported the steric effects of the ligands. Some of the complexes do show some catalytic activity but the known and simple dirhodium acetate complex is still much more active.

Anyway, it's worth reading and seeing some interesting ligands and synthetic work.


http://onlinelibrary.wiley.com/doi/10.1002/chem.201402936/full

Multiple Metal-Metal Bonds #chempaper 224

This is another paper by F.A. Cotton on (of course) multiple metal-metal bonds. It was basically a lecture he gave in ACS Seattle (1983). Not surprisingly he summarizes multiple M-M bonding starting as early as mid 18th century. So, I got to learn a lot from this paper that I had not known. There is also a really interesting quote and talk by Linus Pauling on metal-metal bonding where he tries to describe a few Mo-Mo, W-W and Ta-Ta bonds. Cotton also confesses that he had heard about Pauling's paper by pure coincidence.

On the famous Re-Re multiple bonding, Cotton says :

As always, it was a pleasure to read the paper. I hope you enjoy it too.

Learning Python - My First Program

I have tried to learn some coding before but didn't have enough time/ambition to do so. This year, I started learning Python again and I am taking it more seriously. I am determined to learn it and do something "useful" with it. One of the courses I am taking is An Introduction to Interactive Programming in Python on Coursera and the code below is for our first Miniproject (Rock-paper-scissors-lizard-Spock). Any feedback is appreciated.

# My first program
# Rock-paper-scissors-lizard-Spock

import random
import math

def name_to_number(name): # converts name to number
    if name == "rock":
        return "0"  
    elif name == "Spock":
        return "1"
    elif name == "paper":
        return "2"
    elif name == "lizard":
        return "3"
    elif name == "scissors":
        return "4"
    else:
        print "Please choose one of these : rock, Spock, paper, lizard, scissors."

def number_to_name(number): # converts number to a name
    if number == 0:
        return "rock"
   
    elif number == 1:
        return "Spock"
       
    elif number == 2:
        return "paper"
       
    elif number == 3:
        return "lizard"
       
    elif number == 4:
        return "scissors"
   
def rpsls(player_choice):
   
    print "New game!"
   
    print ""
   
    print "Player chooses " + player_choice
   
    comp_number = int(random.randrange(0 , 5)) # computes random guess for comp_number
   
    comp_choice = number_to_name(comp_number)
   
    player_number = int(name_to_number(player_choice))
       
    print "Computer chooses", comp_choice

    num = int((comp_number - player_number) % 5) # computes difference of comp_number and player_number modulo five
   
    if (num == 1) or (num == 2) or (num == - 1) or (num == - 2):
       
        print "Computer wins!"
       
    elif (num == 3) or (num == 4)or (num == - 3) or (num == - 4):
       
        print "Player wins!"
       
    elif (num == 0):
       
        print "Player and computer tie!"

rpsls("rock")
rpsls("Spock")
rpsls("paper")
rpsls("lizard")
rpsls("scissors")

Inorganic Chemistry Notes 1 - On Oxides

I have recently decided to write down some notes on inorganic chemistry for a few purposes:

    - so that I don't forget a few basic things

    - to memorize some of the tricky details

    - to be able to use the blog as my notebook

      and several other reasons.

These mostly will be from the papers or references I read from time to time.

Here comes the first one on oxides from Cotton and Wilkinson's Basic Inorganic Chemistry textbook.

Ionic oxides react with water to make metal hydroxides. But, they dissolve in acids to produce the metal cation and water.

Covalent oxides, on the other side are acidic in water. The water insoluble ones dissolve in bases. 

Amphoteric oxides are bases towards strong acids and they act as acids in bases.

Evaluating Molecular Cobalt Complexes for the Conversion of N2 to NH3 #chempaper 223

Another great (IMO) example and very well studied complex for nitrogen fixation. As an inorganic chemist, I love this type of work with synthetic routes and nice tables that give good information.

A fast metal–metal bonded water oxidation catalyst #chempaper 222

If you are one of those people who are interested in metal-metal bonding, you might have already read this article. It's in one of those less known journals (Journal of Catalysis). But, I try to look for some articles every once in a while. I think it's a really useful journal. 

To me, the most important part of the article is the proof that compounds having metal-metal bonds can be useful in catalysis. There are tons of examples of them, but this is one of the most recent ones. You don't have to develop an industrial catalyst, but you can still prove people that you can achieve catalysis using these complexes.