Alder and Wainwright (1959)

October 19, 2017

Hello everyone!

I hope this week of P-Chem hasn’t been too painful for you all, we’ve almost made it.
This Friday we’ll be delving further into the world of statistical mechanics, more specifically molecular dynamics.
A few points to consider as you read Alder and comment:
1) What is the importance of molecular dynamics? Why is it a powerful tool for chemists?
2) Does it make sense to choose periodic boundary conditions instead of reflecting ones?
3) Do the series of options for what a molecule can do make sense?
And just a bit of background for everyone to make this paper a little easier to digest, Monte Carlo was the only computational method prior to Alder’s introduction of MD. Monte carlo method is based around randomness, and that randomness is how these simulations are able to explore different possibilities. It essentially explores all possibilities for a system and evaluates the results of these different conditions.
One way to think of it is exploring a potential energy boundary, or exploring a topographical map, by taking a random step in any direction and considering whether or not this step improved upon the last.
The history of the name is a fun one, and if you’re curious you should delve into it!
Cheers and hope the math doesn’t frighten you off!
Shy
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The Structure and Entropy of Ice – Pauling (1935)

October 17, 2017

Dear all,

On Wednesday we will be covering the Ice Paper by Linus Pauling from 1935. This paper was not originally in the packet, but was given as a stapled handout.

This paper is a chance for us to refresh some physical chemistry. Each week we try and cover a facet of chemistry that represents out own disciplines (e.g. analytical, organic, etc) from the perspective of inorganic chemistry. On Friday, Shy will be presenting the Alder and Wainwright paper (also a handout), and so this is her week to shine.

For the Pauling paper, we can prepare by asking a few questions. These were also posed at the end of Monday’s lecture.

1) What are the three laws of Thermodynamics?

2) Is there a zeroth law?

3) What is entropy? Is there more than one answer to this question?

4) What is high-tridymite? This is an easy internet search, and so not a good question for the blog.

5) The key portion of the paper is on page 2. Read this carefully and if necessary draw diagrams to show what Pauling is talking about.

 

See you all on Wednesday!

Nature (1953). (Watson and Crick), (Wilkins, Stokes and Wilson) and (Franklin and Gosling).

October 12, 2017

Greetings students and all,

On Friday we will be having a discussion on the famous 1953 paper by Watson and Crick. Although this paper is barely a page long, of possibly greater importance are the two other papers which followed the Watson and Crick paper in that edition of Nature. These papers are all reproduced in your packet in sequential order. In addition the follow up paper by Watson and Crick is also included so please look at all of these.

Some points to consider while you read include:

1) What were the backgrounds of, and relationship between the three principal players (Watson, Crick and Franklin)?

2) Broadly what information does Figure 2 on page 178 convey?

3) How did the presence of water influence Franklin and Gosling’s interpretation for the possible structure for DNA (see page 740)?

Pauling and Corey (1953)

October 10, 2017

Hello Chm650 humans composed of nucleic acids, RNA, and DNA. On Wednesday, we will be discussing Linus Pauling and Robert Corey’s proposed structure of nucleic acids and the triple helix.  … My proteins fall apart just thinking about that “masterpiece”.

 

A lot of hard work for X-ray diffraction of cytoside (sp?) and X-ray photography on sodium thymonucleate from other scientists help aid these Pauling and Corey towards their triple structure.

 

  1. Why have a single helix when you can have a triple?
  2. Which famous people published recently after this proceeding that contradicts the triple helix?

 

If you figured out what seems wrong, you’re in luck. If not, hopefully the science behind our discussion can sway you to agree or disagree with the triple helix.

Haiges et al. 2004, “High Energy Density Materials”

October 4, 2017

Hello chm650 WordPress readers! On Friday, we will be racing explosively into the 21st century with polynitrogen chemistry. Pun intended. Haiges et al. demonstrate a method for using displacement reactions to isolate pentazenium containing salts. Using our recently acquired knowledge of molecular vibrations and symmetry, we can start making some deductions about the highly unstable N5+ (pentazenium) cation. Some things to consider are…

  1. How many vibrations are we expecting for the N5+ cation?
  2. What point group does the pentazenium cation belong to?

 

Other than the highly unstable pentazenium cation, there is a considerably more stable polynitrogen molecule which sees worldwide application. Can you figure out what this molecule is? Hint: airbags. Further considerations for this discussion that you should ponder are as follows…

  1. Where does the poly-bifluoride peak appear in the Raman spectra?
  2. Would 1H NMR have been useful for these experiments?
  3. Why was it desirable to use a synthetic precursor other than N5+[SbF6]?

 

Find out the answers to all this, and more, during the 2017 season premiere of Graduate-Led Discussions: A CHM650 Interactive Extravaganza!

Chemical Applications of Group Theory (1990)

October 3, 2017

Understanding the concept of symmetry is easy. Using symmetry can be hard. F. Albert Cotton published his famous book “Chemical Applications of Group Theory” in 1963. It is now in its Third Edition.

We will be reading over select portions of Chapter 10, the chapter deals specifically with applications of Group Theory to molecular vibrations. The specific example used is common molecular species the carbonate dianion (CO3)2-.

 

Some questions.

Who is F. Albert Cotton? What does the F. Stand for?

How does Matrix Multiplication work?

What is Raman spectroscopy? How does it differ from Infra-Red spectroscopy?

What are the equations for the number of molecular vibrations?

How many vibrations does CO2 display? Why?

Griffith and Orgel (1957)

September 27, 2017

Dear all,

Thank you for sticking with the course through this important part of inorganic chemistry. When it comes to chemistry I think we can say that inorganic chemists have the prettiest colours of all. Why? Good old d orbital splitting. We can even predict what the material might look like. The power of prediction will lead us into symmetry and group theory next week.

I am hoping that you will all have some good questions about the Orgel paper, it is longer than the papers we have looked at in the past, but please read it all the way through.

Some things to get you primed and pumped for Friday!
Who?_______________________
What? ______________________
Where? _____________________
When? _____________________
How? ______________________
Why? ______________________

Impact Factor? Shape of orbitals? Ligand Field Theory thinks its too good for CFT?

See you all Friday.
Prof. Hurst

Van Vleck (1935)

September 26, 2017

Not all the papers we will be looking at are easy to read. Some represent the first stirrings and conceptions about ideas that will later go on to change the field.

The Van Vleck paper perhaps at first does not seem relevant to the discussions we are having. Magnetic susceptibilities, what on earth is that? Why look at one method when you can discuss three! Which one does Van Vleck prefer?

Remember the who, the what, the where, the when and the how. How many times has this paper been cited? Do we know anything more about the author?

On Wednesday we will be diving deeper into the discussion of the chemistry surrounding this section of inorganic chemistry, before another discussion of a related paper on Friday.

Post your questions below before Tuesday 5 pm (not Thursday).

Gillespie (1967) and Spingler (2001)

September 18, 2017

Hello all you avid CHM650 readers!

We have two papers to consider for Wednesday which will assist in our introduction to (or remembrance of) inorganic chemistry. We covered oxidation states and d electron configurations previously. We now understand coordination geometry and coordination number, plus how ligands and metals interact. The paper of Gillespie is longer (6 pages) than previous papers, but not too long.

The other paper discusses what is referred to as a “Werner complex”. Werner is a co-author on the Spingler et al. paper despite the fact he was dead for over 80 years by that point. You should assign oxidation states, electron configuration, coordination number, coordination geometry, etc on your own (don’t post your answer in the comments) for discussion on Wednesday.

Have a read over these papers (they are all short) and post your questions.

Don’t forget to find and uncover (perhaps even scan in and discuss with your advisor) the papers that you will be leading the discussion for later in the semester.

Energy Production in Stars (1938)

September 13, 2017

Dear all CHM650 students,

On Friday we will be discussing two papers. “Energy Production in Stars” by Hans Bethe (1939, Physical Review, pg 103). This paper is a single page, although I also suggest you briefly read the first two pages of the longer paper (same author, year and journal) that follows it.

There is a interesting story about this paper, can you discover it?

The second paper that we will be considering is the paper “Nuclear reactions in Stars without Hydrogen” by E.E. Salpeter from 1951 (Astrophysical Journal).

Please have your questions posted here by Thursday lunchtime for the in-class discussion!