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.

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:

http://chemdiary.blogspot.com/search/label/symmetry

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. 

http://pubs.acs.org/doi/abs/10.1021%2Fja00796a058

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

Hobbit, Misty Mountain and Chemistry ?

It's probably my imagination, but while I was watching the movie Hobbit, the Misty Mountain (or Lonely Mountain) reminded me of DMSO peak in proton-NMR.

Since I couldn't get a screenshot of the mountain, I have to post this image that I found on google.

and here is the dmso peak :

Barrier Penetration : Can you walk through a wall ?

According to quantum mechanics even though a particle has a smaller energy than the barrier, there is still a chance that it can penetrate through the wall and can be found on the other side.

There is a movie called "Special" and a scene in the movie reminds me of this property.

spoiler alert !

Les runs and tries to jump through the wall repeatedly. He believes he can do that. Here is the scene from the trailer (starts at 0:50):

Jupiter in the lab !

Homonuclear Diatomic Molecules Practice

I just did them for practice and fast. Please also note that they are qualitative.

Why do I LOVE inorganic chemistry?

This might be my first "personal" post. But, I think it is worth trying. Everyone in my life (including facebook and twitter) know that I enjoy studying inorganic chemistry and I like to learn more about the role of transition metals in life. I think I should explain why it is so.

Before taking any chemistry course, I had always thought that "chemistry" was all about organic molecules and I believe most people think so. I had no idea how far chemistry goes and honestly, I didn't imagine metals having anything to do with chemistry. To me they were the subject of materials science. During my general chemistry courses, this didn't really change at all. I learned that chemistry is more than "organic chemistry." But, there were still no metals involved. They were right in the middle of the periodic table, but was "forbidden" to talk about. We would draw Lewis Dot Structures of any organic molecule, but never metal compounds. They were so forgotten that nobody would even ask anything about them. When I took my first inorganic chemistry course, I discovered that metals (transition metals here) are at least as important as carbon, hydrogen, nitrogen etc. I kind of thought that they are neglected and decided to learn more about them. With my limited understanding and knowledge of chemistry, I started to read inorganic chemistry research papers and my inorganic chemistry textbook. The more I read, the more amazed I was and I still am. They not only play an important role in material science, space exploration, communication, catalysis but also are responsible for many crucial reactions in organisms. There are several metalloproteins and metalloenzymes that contain a specific metal such as hemoglobin, plastocyanin etc. In fact, although you might think that metals are "poisons" and harmful, the metal concentration in brain for example is more than "normal" levels. [1] Luckily, I was accepted to an inorganic research group and I was able to have a closer look at the world of metals. Then came the symmetry and group theory. I am not obsessed with symmetry in my daily life, but how beautiful it is, right? Ever looked at a waste basket and saw the point group of it? I did. I like to find the point groups of objects around me now. I think it is better than sudoku. So, I strongly suggest anyone to learn symmetry and point group theory. I started to think that nothing new could make me more excited than this little game of mine. But, I was wrong. The day I started to learn molecular orbital theory, I was once more enchanted with inorganic chemistry's beauty. Isn't it art?

Everyone believes that transition metals mean "color" and I think they are right. Isn't this beautiful?

When somebody says "drug," the vast majority of people think of organic molecules. But, there are tens of metallodrugs out there if not hundreds.[2]  Some of them are still on trial and some of them are widely used. Probably the most famous chemotherapy drug cisplatin, is a platinum based drug.

Chemistry supplies answers to many questions and problems. It helps us to understand of the world, body, universe and how they work. It's a collaboration of several branches (physical, organic, inorganic, analytical chemistry etc.). They are all of equal importance. But, people have emotions and beauty is relative. It is in the eye of the beholder and I find inorganic chemistry beautiful.

[1] Bush, A. "Metals and neuroscience." Current Opinion in Chemical Biology. 2000, 4:184–191

[2] Barry, N.; Sadler, P. "Exploration of the medical periodic table: towards new targets" 

http://pubs.rsc.org | doi:10.1039/C3CC41143E

Symmetry and Group Theory- Point Group Tips 1

Since I have really become obsessed about point groups of objects and molecules, I decided to post some practice and tips about them.

Tip : Octahedral complexes with 3 chelating ligands have D3 point groups. Well if you don't want to believe this, you can always draw the molecule and see it yourself. Trischelates are tricky. So, I suggest that you should always draw a Newman Projection to see the perpendicular C2 axis.

Symmetry and Group Theory- How to find the point group of a molecule?

"Fundamental phenomena and laws of nature are related to symmetry and, accordingly, symmetry is one of science’s basic concepts. Perhaps it is so important in human creations because it is omnipresent in the natural world." This quote is from the introduction of the book "Symmetry through the Eyes of a Chemist." It is a wonderful book with great illustrations from art, architecture, nature etc.

As mentioned above, symmetry is everywhere. You can find it in math, biology, biochemistry and of course chemistry. The good thing about it is once you learn it you will never forget it and you will see how useful it is.

There is an excellent website here: http://symmetry.otterbein.edu/

It's a great source for point group practice and learning. Technische Universitat Darmstadt also has some good information and tutorials about symmetry and point group theory (it is in English) : Here

Let me continue with the post now. In general, if a molecule;

1. has two or more C5 axes, the point group is : Ih

2. has two or more C4 axes, the point group is : Oh

3. has two or more C3 axes, the point group is : Td

Now, how do we determine the point group of a molecule (or an object)?

I will write down the way I learned it and it works perfect.

First, find the principal axis. This is the axis with the highest order of axis. Suppose that the molecule has C2, C3 and C4 axes. So, C4 is the principal axis.

Second step: Check if there is a perpendicular C2 axis to the principal axis. If there is one (only one is enough), the point group is Dn. If you can't find any, then the point group is Cn.

Third step: Now it is time to check for a plane of symmetry. We are looking for the σh (Sigma h) now. This is a mirror plane perpendicular to the principal axis. If you find it, then the point group is either Cnh or Dnh.

If a perpendicular plane of symmetry is missing, we look for a mirror plane that is not perpendicular to the principal axis. If there is one then it is either Cnv or Dnd (don't ask why it is so. That's how it is called.) If you can't find another mirror plane, then the point group is Cn or Dn.

It's actually very simple to determine the point group of a molecule. But, you have to be very careful. Some molecules are really tricky. Let's do an example I am just making up a molecule for practice. L and X are different ligands.

So here how I determine its point group:

Symmetry and Group Theory- Point Group Tips and Practice 2

Instead of me making up metal complexes or molecules, I decided to use real ones that were published in chemistry journals. So here we go with the first one. In the latest issue of Inorganic Chemistry journal (ACS Publications), there is a "tungsten-alkylidyne complex" (DOI: 10.1021/ic401450u).

Here is how I determine its point group:

If you don't believe me you can read the article. It's also mentioned in the article that the point group is C4v. In the upcoming posts, I will try to explain why we need to find point groups of molecules and how we use them.

Symmetry and Group Theory- Point Group Tips and Practice 3

For this post, I chose a dirhodium complex from Prof. Kim Dunbar's paper (DOI: 10.1021/ar0302078). My drawing and handwriting is horrible, so I will also put an image of the complex.

Here we go:

Symmetry and Group Theory- Point Group Tips and Practice 4

I wasn't planning to write anything today. But, I've just seen this on Inorganic Chemistry journal and
decided to do another practice.

The paper is here (DOI:  10.1021/ic401499j).

I will assume each NO3 group is a perfectly symmetric sphere for simplicity. Here we go:

Since this molecule has 3 different C2 axes perpendicular to each other, you can choose any of them. You will still find a perpendicular C2 and mirror plane (Sigma h).

Symmetry and Group Theory- Point Group Tips and Practice 5

I was studying for GRE (I am taking it tomorrow)  and I couldn't help finding out the point group when I saw this molecule. Too bad I'm obsessed with symmetry.

The article is here (DOI: 10.1039/C3MT00162H).

And here is how I find out the point group of this molecule:

Since my drawing is not really good, I will try to explain where the "other" mirror plane is. If you imagine a plane that goes through the double bonded oxygen-Vanadium center and the equatorial OH2 molecule; the "right" and "left" side of the plane are the same.