Friday, January 31, 2014

#chempaperaday Day 15/365: "Minor-Groove Binding Drugs: Where Is the Second Hoechst 33258 Molecule?"

It was such a busy day. So, I couldn't read anything new. Here's something I read some time ago.

Hoechst 33258

Basically, they studied the binding modes of more than one Hoechst molecules at AT rich regions.

More reading:

Wednesday, January 29, 2014

#chempaperaday Day 13/365: "A Twelve-Coordinated Iodide in a Cuboctahedral Silver(I) Skeleton"

I was attracted by the nice colors and the geometry of the complex. I read most of it and I had to skip the DFT parts again. I am really dying to know what it is. 

Anyway, it's really good to see a high coordination number like this one has. Also there is some discussion about molecular orbitals, symmetry and the point group of the complex which is my favorite part!

Tuesday, January 28, 2014

#chempaperaday Day 12/365: " Molecular and Electronic Structures of the Members of the Electron Transfer Series [Mn(bpy)3]n (n = 2+, 1+, 0, 1−) and [Mn(tpy)2]m (m = 4+, 3+, 2+, 1+, 0). An Experimental and Density Functional Theory Study"

One of the greatest inorganic chemists is Karl Wieghardt. I wish one day I work for him. I try to read and understand his publications as much as possible and this one has just come out

I am also providing a link to an interview with him here.

As I told before, I do not know anything about DFT, but I read (or sometimes skip) that part anyway. Sooner or later, I will (I hope) learn what DFT is and how to do those calculations. 

It's the first time I have ever read the term "broken symmetry" approach (BS) and I didn't really understand what it is. But, it is OK. I am not worried about it yet. 

As far as I understand, one of the most important results of the research is that the electron density caused by the reduction is localized on the ligands. You can see this on the spin density plots. I really liked the paper. Seeing the useful tables that show the formula of each complex, relevant reference, ground states, reduction potentials etc. really makes it easier to follow the paper.

Interview with Karl Wieghardt

Monday, January 27, 2014

#chempaperaday Day 11/365: "Cyclometalated Iridium(III) Complexes of Azadipyrromethene Chromophores"

I try to synthesize Ir(III) complexes. So, whenever I see papers about Ir(III) complexes, I try to read them. I read the reaction conditions and reagents. Just like this synthesis reported here, I start with silver triflate and Iridium(III) chloride hydrate.

The metal complex could be a good practice for my symmetry and point group practice posts too. I will try to write a post there too.

Saturday, January 25, 2014

#chempaperaday Day 9/365: "Rhodium, Iridium, and Ruthenium Half-Sandwich Picolinamide Complexes as Anticancer Agents"

Although many people think that I have no life and I just study and read, I do go out and have fun a lot. I just don't like to share every detail of my life and I plan my time and try to stick to my plan/schedule. As most of the other Saturday nights, I will be going out again. So, I will share what I will be reading when I come back. I did read the abstract though.

If you are interested in anticancer metal complexes, I am sure you know that there are a lot of Ru, Rh, Ir and Pt complexes around. I might try to write why this is the case in the future for the undergrad students who don't know the reasons yet. But, usually you can read a few reasons in the introductions of the papers. Very shortly, Ru(II), Os(II), Rh(III) and Ir(III) are inert complexes with d6 electron configurations and there are reasons why the second and third row transition metals are more common than the first row ones. By the way, there are fewer Osmium complexes. Pt(II) anticancer complexes are very common too. The most popular and effective (testicular cancer as far as I can remember) one is cisplatin and there are several others being investigated.

Anyway, I hope you enjoy your night and the paper.

Happy birthday Robert Boyle !

Robert Boyle was born on 25 January 1627 in Ireland. He is considered as " founder of modern chemistry" by many people. We all know him for the Boyle's Law. What he did was to take a J-shaped glass tube and to trap some air in it over mercury. He found that when he doubled the weight of the mercury, the volume of the trapped air was half. Then he did many other experiments by changing the ratios. He also realized that it wasn't possible to compress gas, so he deduced that air must consist of particles.
His masterpiece is The Sceptical Chymist.
He was also very religious and published a lot of religious books.

Friday, January 24, 2014

#chempaperaday Day 8/365: "Two Hundred Years of Cancer Research"

Today's read is about cancer here on the New England Journal of Medicine's website. I know it's not a chemistry paper but that's what I read today. Besides, it's always good to know more about cancer. There are a lot of chemistry and biology articles that give facts and statistics about cancer in their introduction sections.

 It's a short piece on the history, discovery and treatment of cancer. There are nice figures about cancer that show some important events in chronological order like this one below:

Thursday, January 23, 2014

#chempaperaday Day 7/365: "Superheavy Element Flerovium (Element 114) Is a Volatile Metal"

Element 114 was discovered several years ago and was added to the periodic table a few years ago. So, today I read a paper about the properties of Flerovium. Obviously, there is no way I can understand the full article. But the title, introduction and conclusion parts are clear enough to understand that Fl behaves more like a metal than a noble gas. Moreover, it is the least reactive and most volatile in Group 14. And the experiments and calculations have answered the questions that were asked here.

Wednesday, January 22, 2014

#chempaperaday Day 6/365: "Selective DNA Purine Base Photooxidation by Bis-terdentate Iridium(III) Polypyridyl and Cyclometalated Complexes"

My research project is to design and synthesize new Ir(III) metal complexes and to study their DNA binding abilities. The latest issue of Inorganic Chemistry has this article about Ir(III) complexes and the authors report "selective DNA purine bases oxidation." So, I found it really interesting and read it today.

Tuesday, January 21, 2014

#chempaperaday Day 5/365: "Ocean–Atmosphere Interactions in the Emergence of Complexity in Simple Chemical Systems"

I was just organizing my pdf files folder and noticed this article. Just like everyone (I guess) I am also wondering how "life" arose on earth from elements and simple molecules to highly complex proteins, enzymes, molecules and systems. So, in this paper the authors investigate "water-air" interactions to find out the evolution of biomolecules.

Interview with Edward Keller

Many people think that certain scientists are/were "evil." Or you might have heard that some brilliant people led the world to catastrophes etc. Anyway, I don't like to discuss these issues since they tend to end up in hot and undesired discussions. But, please watch this interview with Edward Teller and listen to his really interesting ideas about science/technology, scientists and ethics in general. 

On Irving-Williams Series

If you take Inorganic Chemistry, you are very likely to learn Irving-Williams Series. Even if you don't learn it in the class, you will have to learn the series by yourself. Because, it shows up almost everywhere! Simply, the series is about the stability of complex ions and it is extremely important (at least that's what I think now). Anyway, my purpose in writing this post is not to give a lecture on the series. 

Although I define myself as a "curious" person, I have never wondered why the series was named so. I bought Advances in Inorganic Chemistry (Volume 36) long time ago and I have just started to read it.  This volume was dedicated to R.J.P. Williams and it has an introduction by A.G.Sykes. 

So, I started to read the introduction and learned that Prof.Williams is recognized as the "founder" of bioinorganic chemistry. He was very interested in the inorganic elements in biology and as an undergrad he worked with Prof.Irving on a project that would lead to the Irving-Williams Series. This must have been one of the best moments in his career. What a start! Now I know why the series was named after those two names. I hope you too.


Monday, January 20, 2014

#chempaperaday Day 4/365: "Interaction of Antidiabetic Vanadium Compounds with Hemoglobin and Red Blood Cells and Their Distribution between Plasma and Erythrocytes"

Today I read this very new paper about Antidiabetic Vanadium complexes and their binding to hemoglobin and interaction with red blood cells. Obviously, there are many parts that I couldn't really understand such as DFT calculations. So, I skipped that part and a few other paragraphs. But, overall I enjoyed it.

Sunday, January 19, 2014

#chempaperaday Day 3/365: "Bioinorganic Chemistry: A New Field or Discipline? Words, Meanings, and Reality"

Today I read this paper that was published long ago in The Journal of Biological Chemistry. The title reveals what the paper is all about. I really enjoyed reading it and there are a few parts that I think the author states the facts about Bioinorganic Chemistry very clear. Like this one : 

"... there was a gap of about 30 years between the 1940s and the 1970s when there must have been a great step forward in appreciating the significance of transition metals in biology."

But, as he further mentions, an important reason for this was that the spectroscopic techniques were not developed enough to study the metals in proteins.

Anyway, I suggest that you should read this paper if you are interested in metals in biology. It also has really cool details and stories about important names in chemistry/physics. So, it was like reading an introduction to a science history book and I really liked it. 

I think the figure below summarizes the importance of the field.

Saturday, January 18, 2014

#chempaperaday Day 2/365: "Exploration of the medical periodic table: towards new targets"

One of the scientists that does everything I want to do is Prof. Peter Sadler. I try to read the papers published by his group. So, this one is a really nice ChemComm feature article on metallodrugs.

When people think of drugs, they (except chemists) usually think that they are small organic molecules. Well, maybe there are thousands of these drugs, but there are also tens of metal based drugs for several different purposes and in fact they are extremely important as anticancer therapeutics in particular. There are of course metallodrugs that are used in medical imaging, treatment of manic depression, arthritis, ulcer etc. I think, medicinal inorganic chemistry is a great field to study and metals have so many useful properties in designing and synthesizing drugs.

Anyway, in this paper you will find a great introduction and history of metal based anticancer, antiviral and antidiabetic, antineurodegenerative etc. therapeutics and related recent studies. There is a table that lists these drugs and what phases they are at.

Friday, January 17, 2014

#chempaperaday Day 1/365: "Synthesis and Spectroelectrochemistry of Ir(bpy)(phen)(phi)3+, a Tris(heteroleptic) Metallointercalator"

I have been working on my honors thesis for some time and reading a lot lately to write the "introduction." So, I decided to blog/tweet the papers I read even though some of them are not related with my research. Then, I thought I should turn this into a challenge for myself and keep track of the papers I read for at least a year. I am hoping to turn this into a lifelong challenge. I know it is really hard, but challenge is always good for progress and success. Note that most of the papers will be about Inorganic and Bioinorganic Chemistry. 

The first paper (although I read it a long time ago) is here. This paper is one of my favorites. Firstly, as far as I know it is one of the earliest papers on metallointercalators. It is full of characterization techniques such as NMR, UV-Vis, EPR, CV etc. Moreover, you can read about really useful discussions about the complex such as; the similarity/difference between its Rhodium analogs, one electron reduction in solution and a two electron reduction upon intercalation, becoming less stable when intercalated, charge transfer, electronic environment within the helix vs. the solution etc.

Anyway I hope you like it.

Tuesday, January 14, 2014


Myoglobin is a very common protein in red blood cells. Its "duty" is to store oxygen and only under extreme conditions it releases the oxygen. So, it has a higher affinity for oxygen than hemoglobin has. It is almost identical to a single unit of hemoglobin. Anyway, I will not go into details and if you want to learn more about it, you can just read a Biochemistry textbook or even google it.

Another reason why it is a special protein is that it was the first protein that was "solved." After years of work, John Kendrew and his team finally solved the structure of the protein and built a model. Below is the model and I have learned that you can visit it at Science Museum in London. Unfortunately, it looks disgusting. I wish they had chosen a better color and material to build the model.

And here is a model generated by PyMOL on my laptop. It looks cute now:

Book: Why Evolution Is True?

Even before reading this book, I knew evolution was true (because I trust science) and it has been in action since life appeared on Earth. So, the reason for me to read this book was not to look for further evidence or examples of evolution.

The book is a really well written and it follows a logic starting with the scientific definition and components of evolution. I think it is this chapter that really helps to show the relationship between natural selection and evolution. As the author says "(Natural selection) It produces the fitter, not the fittest." It is just one of the components of evolution. Other components cause "evolutionary change" too.

Throughout the book, there are tens of evidences of evolution that support each other such as DNA sequences, fossil records, the distribution of species over the continents, islands etc.

I have never read any other book about evolution before. So, I am not able to compare this book with others. But, I think this is an excellent book that everyone (even if you are a creationist) should read.

Image Source:

Sunday, January 12, 2014

Chemistry at unexpected places

Although chemistry is literally everywhere around us, it is really hard to see posters of chemists, periodic table themed home accessories or element names that you can hang on your wall. Well, yesterday I was at Jordan's furniture and it was one of the most surprising days of my life.

Friday, January 10, 2014

(Text)Book : Metals in Biological Systems

I should warn the popular science book readers that this is not a popular science book. I am trying to take advantage of my winter break and reading as many books as possible. As you know (I guess), I am very interested in Inorganic and Bioinorganic Chemistry. So, this book is one of the books that helped me to refresh my knowledge about the roles of metal ions in biology.

As many other books I read, this is an old edition (1992) too. So, instead of trying to focus on the details like crystal structures, bond angles, bond lengths or characterization techniques; I tried to get the general information about the metals and their roles in different proteins, enzymes and/or reactions.

Like other "short" books on Bioinorganic Chemistry, this one also has a chapter assigned for each metal ("essential" metals) and its role. The last chapter is called "Inorganic Drugs" where you can see some structures, names and uses of several metal based drugs (as of 1992).

It's very easy to read and follow and especially I like the discussions about the evolution of metalloproteins.

Tuesday, January 7, 2014

Book: Hitler's Scientists

This is absolutely one of the best "popular" science books I have ever read. It is not a list of scientists with their discoveries and inventions. The books is written like a novel. So, once you start to read, you can't really stop. The flow of events and the language the author use make you finish the book as soon as possible.

First of all, I think the primary objective of the author is to ask (and show) us how important ethics in science is. Are the scientists independent from their governments, sponsors or funders? How responsible is a scientist for the outcome of his/her invention or discovery? Should a scientist continue his/her research under cruel (even crazy) people?

What John Cornwell does in the book is that without being subjective, he just presents us the evidences and events as they occurred and usually in a chronological order. So, I think it is our duty to answer the questions above. I want to quote from the book here:

"...(of Wernher von Braun) that he did not care whether he worked for Uncle Joe or Uncle Sam: 'all I really wanted was an uncle who was rich.'"

Secondly, we see how developed science was in Germany in the first third of 20th century. It is clear how important the Jewish scientists and others that were expelled and ran away from Germany were to modern science. They basically changed the leadership of science and changed the balance of the WWII as well.

Even under the power of Nazis and the Third Reich, Germany did huge progress in science.

We can also see the greed of people. Nazi scientists tried to influence the government to get promotion, better positions or sometimes to have the government assign a certain person to a position. This is not special to that certain era. These people are still around us in every aspect of life, science and business.

The book is full of details about Hitler himself too. For example he wasn't fond of jets, atomic bomb and rockets at first. I can not imagine what would have happened if he was interested in these areas when he came to power. We learn the way he look at science and technology sometimes surprisingly stupid and sometimes surprisingly smart.

There were moments that scientists such as Max Planck, Heisenberg and several others opposed Hitler for his decision of dismissal of the Jews from civil service and science. Actually, this book helped me to learn about the role of Heisenberg (although still debated) in the building of an atomic bomb in Germany.

On the other hand, horrible things were done in concentration camps as "experimental science"and we all know that. I don't think anybody can support or defend this kind of science.

I can really write 10 pages about this book, but instead I strongly suggest that you should own the book and read it. The book literally tells us about hundreds of scientists from different disciplines (physics, chemistry, math, biology etc.). Fritz Haber, Otto Frisch, Niels Bohr, Ida and Walter Noddack, Lise Meitner just to name a few of the most famous ones. There are several other scientists that I haven't even heard their names.

The final thoughts and suggestions of the author is striking. He asks very important questions. Today, there is no Hitler. But, will the scientists oppose their "bosses" for the unpleasant use and outcomes of their research or will they obey their governments and funders? He suggests that scientists should come together and assemble small communities to determine what kind of actions they should take in these situations. He asks scientist to behave like Joesph Rotblat who resigned from Manhattan Project.

So i participated in a science event today...

I have done some demos and experiments for kids before  as part of STEM and related programs. But, today instead of younger children, there were high school students. As far as I know, they were all science majors with higher grades than other students (I don't really know the US school system. So, I don't know the details).

Anyway, so I got to interact with ~80 students and I asked questions about their plans and interests in science in general etc. To my surprise, most of them said that they did not like physical sciences (especially chemistry). There were ~10 students that said they really liked science. As far as I can remember, only 2 of them were boys and the rest were girls. These 10 students (although they were mostly interested in biomedical engineering/biochemistry/biology) really knew what they were talking about. For example, some of them knew a lot about PCR, DNA, proteins, DNA sequencing etc. I was really impressed with their education and enthusiasm. But,  I couldn't really find and talk to anybody (except one) who was interested in chemistry.

It looks like chemistry is still not popular and I really don't know why.

Sunday, January 5, 2014

Symmetry and Group Theory- Point Group Tips and Practice 6

I couldn't help but write about this interesting metal complex tonight.Two of the authors are Richard Schrock (a Nobel Prize winner) and another great chemist Stephen Lippard. Here is the paper and the structure :

This is a very interesting geometry (at least for me), because the O=W-O-W=O is linear! Honestly, I didn't know that you could get an oxygen in between two metals in a linear way. I know bridging oxygens, but I have never seen/known and imagined something like this.

Anyway, to make it easier I will draw a simpler structure assuming the R groups are spherical and determine the point group of the metal complex. As you can see from the figure above, the R groups are staggered. 

There is a nice and comprehensive discussion about IR and Raman active vibrations in the paper and it is written that the symmetry is D3. But, I don't know why they don't say anything about its being D3d. I don't think I am wrong. If anyone knows more about it, please let us know.  May be I am missing something.

Related posts:

Saturday, January 4, 2014

Burgi-Dunitz Angle

We all learn nucleophilic attack on aldehydes and ketones in organic chemistry courses. To be honest, I have never wondered the angle of the attack. I always thought that the nucleophile should attack perpendicular to the C=O bond axis. The reason I was thinking like this was that the R groups should cause steric hindrance and make the attack less likely at any other angle. I thought the electron rich bond and the lone pairs on oxygen couldn't have much effect on the attack. Looks like I was quite wrong. I should have considered hybridization and molecular orbitals too. To be clear, you can see the way I thought the attack happens below:

Last night,  I learned that nucleophiles attack the carbon at ~107 degrees to the C=O bond axis. So, my curiosity took me to the original paper by Burgi and Dunitz. 

I read the paper a few times and here is what I learned:

1. As the nucleophile attacks, the R groups bend and C-O bond becomes longer.
2. As the nucleophile approaches even more, RRCO becomes even more nonplanar. Looks like sp2 hybridized carbon becomes sp3 hybridized. 

One of the R's in aldehydes is hyrdogen. This also explains why aldehydes are more reactive than ketones. They have less steric hindrance in the system. (This is one of the reasons.)

I think this is the way it happens:

From molecular orbital theory approach; the electrons in the HOMO of the nucleophile interact with the antibonding orbital (LUMO) of the C=O bond. Both the bonding and antibonding orbitals are occupied now. This breaks the Pi bond and the electrons move to the most electronegative atom (oxygen) in the bond. 

Particle in the Box

Museum of Fine Arts in Boston.

Acidity vs. basicity

Slater's Rule practice

I did a few practice problems using Slater's Rule.

Crystal Field Theory practice