Structural changes upon oxygenation of an iron(II)(porphyrinato)(imidazole) complex (Ibers 1978)

November 10, 2017

Porphyrins are very important structures found in haemes centres such as those seen in haemoglobin. Trying to model them can be quite difficult because the porphyrin is attached to a protein which has more function than you might necessarily expect. This dense but short paper attempts to explore and model a “T” state of hemoglobin consider the difficulties of performing this task.

Why does iron bind oxygen in haemoglobin? What changes occur around the all important metal centre? These questions and their answers were worked out over a long period of time in the 1960’s and 1970’s. This paper ties in many of the concepts we learned in class such as high spin/ low spin, coordination numbers, and molecular orbits. Be prepared to get picked on so brush up on that material.

Some things to keep in mind when considering today’s short paper:

1) What is the role of the imidazole ring? What changes in structure occur when it has a methyl substituent in either the 1- or 2- positions. Where would the substituent be in the normal haemoglobin amino acid?

2) Why have the authors gone to so much effort to construct their “picket fence” around the molecule? What purpose does it serve?

3) On the second page the authors talk about the R and T states of haemoglobin. What does this represent?

See you all in class!


Hard Soft Acid Base theory (Pearson 1963)

November 10, 2017

Hello all you CHM650 people,

As we prepare for a well deserved Thanksgiving break, we have just two more papers to get through. The first will help supplement our lecture on Monday. Ralph Pearson is one of the last remaining “old school” inorganic chemistry and is retired from UC-SB. He is not a bio-inorganic chemist, but this paper allows us to understand much of bio-inorganic chemistry using the Hard-Soft Acid-Base concept. Remember that much of this concept is all about “polarizability”.

Some items to keep in mind when you read the paper.

1) If Pearson says that this material is already established, what is new?

2) What references (and authors) does Pearson invoke to support his hypothesis?

3) Do not spend too much time “wrassling” with electron correlation effects (pg. 3537).

4) Consider reading section 6.3 of Miessler and Tarr (4th Ed.) for some background on HSAB theory as it relates to molecular orbital (MO) theory.

See you all Friday!

Dewar and Healey (1982) Why life exists.

November 6, 2017

We’re almost to the Thanksgiving break, just a few more presentations.

On Wednesday we will be discussing the provocatively titled paper from Michael Dewar “Why Life Exists”. In this paper Dewar asks the question of why silicon has such different reactivity to its neighbour carbon. Dewar attributes the stability of carbon to its inability to go through associative mechanisms (higher coordination number) in comparison to silicon. The traditional explanation of why second-row elements like silicon (Sodium to Argon) can have more than four bonds (e.g. ClO4-, PF5, SF6, etc) is due to “hyper-valency” where these elements can access the energetically available d orbitals. The orbitals of the first row elements (Lithium to Neon) are considered to be too different in energy to access these d orbitals.

Some things to consider:

1) Who was Dewar? Who was Healy? What is the AM1 they discuss?

2) What is Dewar getting at when he discusses SN2 reaction? Hint: Compare Figure 1 and Figure 2.

3) How does he collect the data that he presents in Tables 1 and 2? What does MNDO stand for?

4) What is Dewar’s final conclusion for the reduced reactivity of carbon compared to silicon?

See you all Wednesday, remember no lecture this Friday.

Olah and Schlosberg (1968)

November 1, 2017

In 1967, George Olah and Joachim Lukas published an article which showed that magic acid could form carbocations via hydrogen abstraction. On Friday, we will see that studies of various alkanes in magic acid solution reveals that more than hydride extraction happens in solution. Some things to consider as you read through the article are as follows…


  1. Why were deuterated studies important in this research?
  2. How do reactions with neopentane change when the temperature is lowered?
  3. Was the CH5+ cation known before this article?
  4. How did a Christmas party help progress research into magic acid?
  5. How do Olah and Schlosberg feel about calling alkanes “parrafins”?


Hopefully this article does not totally shatter your foundation of acid-base chemistry, but admittedly it is quite uncommon to think of methane as a base. Looking forward to some good questions on the blog and Friday’s discussion!


Sharpless and coworkers (1974)

October 30, 2017

“Arrrgghh!! I be bloody one-eyed Sharpless see!! Argh!! Me clever epoxidation will cost ya a hefty dubloon!!” –Sharpless, unknown date.

    Barry Sharpless is a Nobel laureate and accomplished organic chemist. We will briefly discuss him on Wednesday, followed by an in-depth look at his article published in 1974 (4 years after his lab accident). This work looks to examine epoxidations of acyclic allylic alcohols using transition metal catalysts and hydroperoxide reagents to synthesize a hormone from Farnesol (if the title of the paper didn’t hint at this enough). Farnesol is used in perfumes and other odorants, as well as having applications as a natural pesticide for mites and being an additive in cigarettes (thank you, Wikipedia). The focus of this paper, however, isn’t necessarily an emphasis on the conversion of the natural product Farnesol. Rather, this paper is about a new way to enable epoxidations of alkenes that allow for selective facial addition. His later work earned him a Nobel Prize, so these epoxidations must be very important.

Some questions to ponder:

1) What is selective facial addition? How does this relate to alkenes (olefins)? Why is this important?

2) Why use transition metals instead of typical oxidizing reagents such as NPBA or MCPBA?

3) What is an epoxide? How do we achieve epoxidation? Why is this important?

I will see you all Wednesday morning! Thanks for reading.


Jacobsen and coworkers (1990)

October 25, 2017

The Jacobsen paper goes over a very important reaction for organic chemistry that utilizes transition metals in the catalyst as we discussed in class. On Friday we will go over a brief history, go through the paper and what it means, then see how it has gone into the future. This paper does get very intimidating quickly, take your time and don’t be afraid to google some of the words you are not sure of. For example enantioselectivity relates to a reaction where one form of a mirror images molecule is preferentially produced while an olefin is just a different word for an alkene. Prochiral is also used which just means that in one step a molecule can be converted from achiral to chiral which is very important when the product must be very specific. Some food for thought as you read the paper…


1) Who is Eric N. Jacobsen? Is there anyone in his past that might have influenced his work?


2) Did this paper involve any experimental or was it all conceptual?


3) What is the benefit to using the catalyst depicted in Figure 1?


4) The %ee in Table 1 means the enantiomeric excess from the reaction, why is this number important?


5) Would this be a homogeneous catalysis or a heterogeneous catalysis?


Hopefully this paper does not give you to many nightmares and anything that is unclear will be clarified on Friday. Happy reading!


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!

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.