Articles by: Kenneth Hanson

Sandwiches, Gluttons and Picky Eaters

This post is contributed by John Spevacek, an industrial polymer chemist and the author of the blog “It’s the Rheo Thing

Quintus guest-blogged recently on that iconic sandwich molecule, ferrocene, an iron atom sandwiched between two cyclopentadiene rings. Ferrocene is the first discovered and best known of a broader class of molecules called metallocenes, molecules in which a metal atom is sandwiched between two aromatic ligands (not necessarily cyclopentadienes). The applications of ferrocene at present are rather limited, but that is not the case with metallocenes. I thought I would expand on this subject by showing the particular usefulness of these molecules – the metallocenes – to polymer chemistry. Most people, including chemists, have little idea how important these molecules are to their everyday life. The molecules themselves are not polymerized, but instead are catalysts for the polymerization of olefins such as ethylene and propylene.

 Before we can get into the reaction details, I first need to explain for the stereochemistry of polymers and why it is import. In a isotactic polymer, all the monomers have been added to the chain in the same orientation:

while in an atactic polymer, the orientation is random:

This stereochemistry is critical to the mechanical properties of a polymer. Atactic propylene is easy to make, but is a pile of goo that you can use as a pretty bad adhesive and not much else. The isotactic version however, can crystallize and that then builds the strength of the material. Crystalline polypropylene is a good strong material that we use every day in food packaging, dishwasher safe food containers, carpeting, nonwoven fabrics, ropes and hundreds of other uses.

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Gaussian’s Banhammer

In my last post, I briefly covered the ‘share or not to share’ debate involving non-commercial software. In this post I’ll delve deeper into the issue by discussing how commercially available research software further complicates the situation. I’ll focus on perhaps one of the most controversial conflicts in the chemistry software: Gaussian Inc. vs Banned by Gaussian.

In the 1950s and 60s Prof. John Pople (1998 Nobel Prize winner) and his research group at Carnegie-Mellon University were focused on the development of ab initio quantum calculation methods.  The group incorporated Gaussian orbitals – rather than Slater-type orbitals, which were more computationally intensive – into a computational chemistry program for molecular electronic structure calculations. The program, Gaussian 70, was released as open source software through the Quantum Chemistry Program Exchange (QCPE) in 1970.

In 1987, Carnegie Mellon University was issued a software license for the program and, ever since, it’s been developed and sold by Gaussian, Inc. Prices (pdf) for the Gaussian software package range from $2,500 for a single computer to $35,000 for an institution-wide license.

Gaussian was initially used only by theoreticians. However, as I mentioned in my last post, the continuously increasing power of personal computers as well as the addition of a user-friendly interfaces have made the software so accessible that even a computationally inept synthetic chemist (like myself) can perform high level ab initio calculations with a half dozen mouse clicks.

Gaussian is an important tool for many chemists, but it’s has also been a center of controversy. Since its commercial release a number of individuals and institutions have been Banned by Gaussian (BBG), which means they are prohibited by Gaussian Inc. from purchasing or using any version of Gaussian software.

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By May 9, 2012 7 comments science policy

The Source Code Debate

Few researchers were using computers 30 years ago.  This quickly changed with the release of several commercially viable personal computers in the 1980s. Since then, processing power has increased and the cost of computers decreased at an exponential rate (see Moore’s Law).

It’s no surprise that computers are now pivotal in chemistry research. We use them in a wide range of calculations – from determining the 40th decimal place of the absolute energy of He to modeling the release and distribution of toxic chemicals in river basins. The software used to address these complex problems is becoming increasingly accessible and easy to use too. There are already a variety of cell phone apps for chemistry related problem solving.

Yet, while the prevalence of software and computer-based research continues to grow, the rules for publishing results and sharing software lags behind. The magical/miracle nature of black-box calculations is disconcerting to individuals that want to know how the answers were obtained (see Sidney Harris cartoon).  A palpable concern is growing in the scientific community around the sharing of software – and the foundational source code -necessary to reproduce published results. Two recent opinion pieces, one in Science titled, “Shining Light into Black Boxes” and the other in Nature titled, “The case for open computer programs” are trying to bring attention to this issue. The articles discuss the advantages and apprehensions of sharing, as well as suggest possible changes. Below is a summary of the points raised by the authors of the two articles – as well as the thoughts others (including myself).

Advantages to sharing software and source code:

  • Reproducibility: As stated by Ince et. al., “The vagaries of hardware, software and natural-language will always ensure that exact reproducibility remains uncertain…” without the release of source code in its entirety.
  • Catching errors: A simple mistake in converting units, assigning missing values as zero, rounding errors, or a misplaced decimal point, can wildly skew outcomes (see Office Space). We can only see and correct errors if we can see the source code.
  • Facilitating progress: All publications require that data, equations, materials, methods, and instrumentation are disclosed so that the results can be tested and furthered by others. We are all better served when source code is disseminated in a similar manner so that programs can be studied and repurposed in future research.
  • Teaching tools: Real, applied examples – that are relevant to research – are useful for new students and researchers learning to program and develop code.
  • Openness: Despite the competition to acquire funding and to publish first, we are all joined in the endeavor of understanding the rules that govern the universe. The open sharing of information has been and will continue to be the foundation of scientific progress.
  • Relying on faith: No matter how prolific or respected you are as a researcher, the implicit assertion, “Trust me, the program works the way I say it does” is not an acceptable means of justifying your results. On a fundamental philosophical level, black box justifications like that should be socially unacceptable in the sciences.

Apprehensions against sharing software and source code:

By May 4, 2012 7 comments science policy

You Can Take the Chemist Out of the Lab but…

Synthetic chemists make a living by mixing together materials in the right ratios at the right temperature for the right amount of time.

This description makes the correlation between chemistry and cooking obvious, at least for those of us who have done synthetic chemistry. For those in the greater public, there have been a few recent efforts to draw attention to this connection.

One is the recent ACS webinar “Kitchen Chemistry: Combining Chemistry and Culinary Delights for the Holiday” on December 9th.

A more mainstream example is the show “Good Eats” with Alton Brown on the Food Network.

In programs like this we see fundamental concepts like density taught through simple suggestions like measuring sugar by weight rather than volume. The video below is an example of Alton Brown loosely referencing chemistry to explain why onions make you cry, as well as techniques for preventing it.

I would have enjoyed seeing a few chemical structures in his explanation. For those who agree, here is the stepwise reaction:

While on the subject of cooking, I’d also like to explore an anecdote I’ve heard from more than one professor: when no longer doing wet work, their interest in cooking increased.

It has been six months since I made the transition from predominantly synthetic chemistry to pure spectroscopy and I can honestly say that, in spite of my wife’s greatest hopes, my disinterest in cooking remains.

Regardless, I have noticed that my knowledge of chemistry and my finely tuned stirring, pouring, measuring and other mechanical skills are helpful when I do. My experience in lab has also led to tendencies that may border on the obsessive compulsive – and I am not the only one. For example, over the years I have noticed that:

  • I check the meniscus while measuring out a volume of milk.
  • I wash my hands obsessively.
  • After drinking a glass of orange juice, I feel the need to rinse the bottom of the glass with water and then drink the diluted solution in order to quantitatively transfer the juice to my stomach.
  • After five years of washing glassware on a daily basis I absolutely loathe doing dishes.
  • I have witnessed a friend (an organic chemist) finish a glass of water, pour and swirl a small amount of soda in the bottom, dump it down the sink and then fill the freshly washed glass with soda to drink.

I have no doubt that other chemists have lab-based quirks in (and out) of the kitchen. What are yours?

By January 9, 2011 6 comments chemical education, fun