This is the end, my only friend the end…

December 8, 2017

Of our elaborate plans, the end…

 

The end of the semester is here. We’ve been through so much, encountered so many personal demons, accumulated so many experience points, leveled up and moved onto greater things.

There won’t be a lecture tomorrow (Friday 8th December 2017), please just fill in your evaluations and keep the memory of our inorganic journey in your mind.

 

Best wishes,

Prof. Hurst

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Farman (1985)

December 4, 2017

Ozone. It’s something we’re all aware of, and a term that many non-scientists even know, as demonstrated by the great prophets Smash Mouth in their song ‘All Star.’

 

It’s a cold world and they say it gets colder, but the meteor men beg to differ- judging by the hole in the satellite picture.

 

Who are these meteor men and what is this hole they speak of? Well, it’d be easy to guess that the meteor men are NASA, but as we see in this last paper, this isn’t the case. It’s Farman! A British scientist who found a USA sized hole in the ozone layer centered over the Antarctic that was completely overlooked by NASA scientists.

 

Ozone is a vital component in our Earth’s stratosphere (the second lowest layer in the atmosphere) as it shields the planet from the majority of damaging solar radiation. The dramatic loss that is seen in the Antarctic does not bode well for the entire planet. Ozone is an unstable atom that is very easy to break down, and is most commonly broken down by man-made pollutants including aerosols and refrigerants. The discovery of the ozone hole by Farman and team was a major one, and eventually led to the Montreal Protocol in 1987, which we will discuss more tomorrow.

 

Some things to consider while reading this paper:

 

1) Why is Farman so adamant on errors of his instruments and their performance in extreme weather conditions?

2) What is ClX and where does it come from?

3) Why is the ozone hole over Antarctica and nowhere else?

 

Nothing like cancer-causing doom and gloom to finish out the semester! – Shy

Koplin (2002)

December 3, 2017

Dana Koplin was a pioneer for water contamination research with 100 published papers and counting (surprisingly successful for someone with conflicting credentials from two in-state rival universities in Iowa).  He focused on this paper on hormones, pharmaceuticals, and other OWCs where the movement and eventual fate of the compounds was undiscovered.

 

The unknown pathways to OCWS being broken down, metabolizing, and persisting mixed with fears of physical abnormalities, cancer cases rising, and antibiotic resistant bacteria lead to the strong desire to further study these compounds. Koplin’s work on creating a national baseline prompted more focused studies for detailed chronic toxicological effects on various species (aquatic and terrestrial) and humans. It is obvious, his methods were a success because thousands of papers have cited the article due to its vast implications to many different fields of study.

 

  1. Why were these particular 95 OWCs chosen and other OCWs were not?
  2. Looking at Table 1, brainstorm some things you use on your skin or ingest that contain an OCW.
  3. What is an RL and how is it determined for the analytical instrumentation used such as LC-MS?
  4. How does frequency of detection of compounds play an important role in validating the primary objective of identifying the most prevailing compounds in streams across the United States?
  5. What is an additive or synergistic toxic effect?

 

P.S. Want to learn more about the Rio de Flag and bullfrogs? Then respond to the blog ASAP before class Monday. See you then. –Josh Froyum

 

 

Patterson (1956)

November 29, 2017

The question that has always left people in wonder, “How old is the Earth?” This is a question that has boggled minds much longer that has been recorded and still can be modified to this day. Taran gave a great overview of meteorites and how they can be used to explain things on Earth that leads very well into this paper, so keep that in mind. Patterson discovered that he could use meteorites to tell the age of Earth then goes over a few different methods that verify his results. We will go over these methods in class then relate them back to Earth and hopefully end with an age of the Earth and clear understanding of how we got there.

Questions:

1) We have discussed many different types of leads like uranium leads, actinium leads, and lead meteorites. Patterson discussed earth leads, what are they and do they relate to other leads?

2) Certain assumptions are made in the third paragraph (bottom of the first page, going into the second). Are all the assumptions reasonable and justified?

3) Equation 1 might look familiar to you, what is being found and what does that mean?

4) Is there any trend between the three types of ratios used that explains why they are so reliable?

5) What is an isochron and why is it so important to this paper?

– Zabrina

Harkins (1917)

November 27, 2017

Hey y’all! Time to tune in to some Harkins! No, not the movie theater but something even better… a journal article from days long past. A journal article from 1917 by a man, a scientist-man (man-scientist?), who studied nuclear chemistry and whose research findings helped inform and subsequently produce the atomic bomb! An article that, in all of its glory, outlines and describes the history of the elements and their radioactive nature that in turn give rise to these said elements! What! Fantastic! Outstanding! Splendid! Can’t find this sort of entertainment from a simpleton movie picture show!

Now, that being said…

  1. What is it about the elements that may be responsible for their atomic structures? Conjectures please?
  2. What field of work was Harkins referencing when he described tables that detailed the composition of certain elements?
  3. Did Harkins use more than one discipline to help bolster his narrative of the elements? If so, what disciplines? How did they (if they exist) inform the readers of the argument Harkins is proposing?
  4. What do we know now, relative to 1917, that could inform us of how correct and close Harkins was to the truth?
  5. What evidence was proposed that really elucidated the relationships that exist in nature? Think lithosphere, meteorites, and Earth skin!
  6. Finally, the proposed system of the production of the elements that Harkins provides is very interesting and is said to not follow the Mendeleef system. How then does the Mendeleef system differ from Harkins’ system?

Thanks for tuning in, folks! This wasn’t a movie (it should be), but it sure was science! Journally, articley science.

-Taran

Aston (1929) and Rutherford (1929)

November 27, 2017

Dear all,

 

Just a quick reminder that we’ll be completing our last few presentations soon. If your’re presenting, please have your presentations ready to go and your in-depth blog post.

 

On Monday we’ll be covering the Aston and Rutherford papers. These are two very short “notes” or letters to the editors and present a nice book end to the semester.  This will lead us into Analytical chemistry, so we’ll be asking a lot of questions of Zabrina and Josh.

 

Some things to consider:

1) Who was Aston? Where was he from, where did he end up?

2) Rutherford won his Noble prize in what year, and specifically for what?

3) Half-life. More than a game, and for more than just radioactivity. What was that equation again?

4) What is methide, give the formula? What happened to the first sample?

5) The year is 1929, and they mention mass spectra lines. What do they mean? What was the state of instruments at this time.

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?

http://pubs.acs.org/doi/abs/10.1021/ja00489a046

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!