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...
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...
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,...
This post is contributed by John Spevacek, an industrial polymer chemist and the author of the blog “It’s the Rheo Thing”
Nature had a report last week of a nice new catalytic procedure for preparation of spiroacetals – bicyclic compounds bridged through a single acetal carbon.
When I read the report, I was surprised that no mention was made of how these compounds could be useful in my field of polymer chemistry. Then again, maybe that shouldn’t be so surprising. After all, these researchers had worked quite hard to develop this new method for making these rings, yet the polymer chemist in me wants to do nothing more than take and rip them apart just like I was spatchcocking a chicken.
Ripping molecular rings apart to form polymers has a long history and is properly called ring-opening polymerization (ROP). There are a number of reasons for considering such a polymerization mechanism. Sometimes it is a way to get around a patent. When Carothers discovered nylon (polyamide), he prepared his novel polymers by copolymerizing a diamine with a diacid. Nylons made with this technique are given two numbers in their name, such as nylon 6,6 or nylon 6,10. The first number indicates the number of carbons in the diamine and the second number indicates the number of carbons in the diacid. The patents filed by DuPont claimed just this copolymerization technique. Unfortunately for DuPont, that left the door open for BASF to prepare polyamides by the ring-opening polymerization...
As many of you may have noticed the posting traffic on chemistry-blog.com has slowed as of late. One of the risks associated with any blog is the correlation between the number of posts and visitors: as the number of post goes down, so does the traffic. Allowing this downward spiral to continue can ultimately result in the end of a blog. Since we at chemistry-blog.com are proud of our small corner of the internet and love sharing chemistry with others we would hate to see it follow this path.
We need your help, especially if you’re an enthusiastic chemist interested in writing. The posts cover a broad range of topics related to chemistry – from random thoughts, literature reviews, humor, interesting youtube videos, and more – and we are eager to see what you are interested in contributing to our community.
There are two options for contributing to chemistry-blog.com. The first is to become a regular contributor to the site with your own login and chemblog identity. The second option is to be a onetime or sparse contributor where the members of chemblog would format your writing and post it under our ID with a clear disclaimer that you are the contributor.
If you are interested in becoming a regular contributor please contact Mitch Garcia. If you would like to be a one time or sparse contributor feel free to contact Mitch, Adam or myself.
We look forward to hearing from and working with you – and thank you in advance to helping our community thrive!
Sometimes, during research, we come up with or stumble upon something that is not only unique, interesting and scientifically important, but also has possible commercial viability. The question you might then ask is, “Can I patent it?” In other words, “Can I legally protect the intellectual property that I have created so that I have exclusive rights to pursue it for financial gain?” and “If I patent something, what rights will that grant?”
Unless you have already gone through the patent process you likely don’t have answers to these questions. Recently, a patent attorney – Jeremy Stipkala Ph.D., J.D., who has his own legal practice called Stipkala Law – visited the Meyer research group to help answer these questions. Jeremy received his Ph.D. in chemistry from Johns Hopkins University and then went on to get his J.D. from George Washington University Law School. His expertise allows him to share insight into the patent process from both a scientific and a legal perspective. He gave us a straight forward handout to provide some insight into the patent process. With his permission, I am now sharing this handout with you.
Assistant professors aspiring for tenure at major research institutions generally understand that poor teaching or instruction skills rarely count against them. Individual professors may take it upon themselves to improve these skills, but it isn’t expected or demanded.
Research (i.e. funding and publishing) is prioritized to the point that student learning barely registers in tenure decisions. As an aspiring academic, this continues to prompt me to ask: Would I have greater impact on the chemistry community if I focused on research or instruction? (The question implies a forced dichotomy that could be addressed. For example, universities could hire ‘research faculty’ and ‘instruction faculty’, but I digress…) Exploring this further, I wonder: Will I have greater impact if I dedicate myself to full-time research, ignoring the education aspect, and – through a combination of hard work and luck – maybe solve a big problem or discover something ground breaking? Or would I have greater impact if I committed myself to instructing and preparing bright and motivated students to solve the world’s problems? Collectively, could these students contribute more than I could alone?
While I sometimes revisit these questions, I’ve made a decision. My ultimate goal is to be a research professor and my overarching priority will be research. Yet, while my (hoped-for) job and tenure offers will be based on my research prowess, I do not plan to completely ignore my role...
In June I wrote a blog post titled “Artificial Leaf or Solar Powered Electrosynthesis?” about a photoelectrochemical cell (PEC) described in the Proceedings of the National Academy of Sciences (PNAS). The goal of this research was to create a PEC that can use sunlight to split water (H2O) into oxygen (O2) and hydrogen (H2). The stored energy in hydrogen can then be used to generate electricity via a hydrogen fuel cell.
In that post I described the device and how it operates. It essentially has a water oxidation catalyst on top of a p-n junction silicon solar cell. It was a step toward a solar driven device, but unfortunately the solar cell alone did not provide the force (>1.23 V) necessary to drive water oxidation and proton reduction. The cell had to be supplemented with an external power supply. The device marked a great step forward but not quite a standalone earth-abundant PEC. I concluded the post with the sentence “With further optimization, possibly involving a tandem solar cell architecture, I have no doubt we will see a fully functioning device within the next few years.” While I was technically right in my timeline (< a few years) my estimate was clearly too pessimistic.
A follow up paper to the PNAS publication was published last week in Science. The article “Wireless Solar Water Splitting Using Silicon-based Semiconductors and Earth-Abundant Catalysts” by Daniel Nocera and the team at Sun Catalytix introduces a fully functional hydrogen and oxygen...
A fictitious/sarcastic email disguised as a job opening from The Interdisciplinary Centre for Advanced Materials Simulation (ICAMS) at the Ruhr University in Bochum, Germany for a post-doctoral researcher to study “Atomistic simulations of structural rearrangements at solid-solid interfaces” was recently posted. Shortly after the announcement was posted the email below was sent to the PSI-K community – a network created by researchers all over Europe to facilitate cooperation and collaboration in the field of electronic structure calculations. Members usually use the PSI-K listserv to distribute and receive information about workshops, conferences and job announcements.
Subject: [ PSI-K ] postdoc position at Department Atomistic Simulation ICAMS Ruhr-Univ. Bochum
From: juttar ogal
Date: 09-Sep-2011 17:57
I am desperately searching for eager victims – postdocs or PhD students – mine or other supervisors’ – to make my workhorses and to plunder ideas from. I am a dirty Hun who seethes from jealousy out of every pore. I cannot do research myself because I’m narrow-minded, rigid-brained, and petty. Therefore, I have to recruit desperate scientists from anywhere in the world and then manage (harangue) them into submission. The smarter you are relative to me, the more I will hate you. If you complain, you will be threatened by my gang of goons – faculty and administration are all allied with...
Chemistry courses, particularly introductory courses, often cover at least some history of the field. I remember learning straight facts like “Dr. x discovered y in…” or theory development like “Greek atomism was replaced by the plum pudding model, which in turn was replaced by the Bohr model.” Yet, minimal time is spent discussing how the discovery or creation of new chemicals impacted the world outside of the lab and shaped human history.
This is understandable. There was plenty to cover and to be honest history was never my favorite subject anyway.
Despite my lack of interest in history, I have gained some piecewise stories and factoids over the years about chemistry’s impact on human history. It was after reading Napoleon’s Buttons: 17 Molecules That Changed History, by Penny Le Couteur and Jay Burreson, that I feel I can say I have an overview about the true history-shaping nature of molecules/chemistry.
Rather than being a chronological account, as with most history books, the molecules are the main characters in Napoleon’s Buttons. Each chapter is divided into different classes of molecules and their impact tracked from as early as 5000 BC to present day. The pursuit of specific atomic arrangements caused colonialism, vicious battles, and the end to these aggressions – particularly when just the right synthetic pathway was discovered. Our chemical history is not entirely bleak – chemicals have also been used to save innumerable lives.
In 1991 Brian O’Regan and Michael Gratzel published a paper titled “A low-cost, high-efficiency solar cell based on dye-sensitized colloidal TiO2 films.” This paper is the foundation for an entire branch of solar energy conversion research known as dye-sensitized solar cells (DSSC).
The basic operation of a DSSC is summarized in the schematic below. In roughly a stepwise manner:
Light (hν) hits a light-absorbing molecule ( chromophore, C), causing it to enter an energetically excited state (C*).
The excited chromophore injects an electron (e-) into the anode.
The iodine (I-) in solution donates an e- to the previously oxidized C and combines with I2 to become I3- .
The high energy e- from step 2 enters the external circuit where it can be used to perform work on a load (e.g., charge a battery, run a fan).
The low energy e- then continues to the cathode where it catalytically reduces I3- to I- and completes the circuit.
The 1991 Gratzel paper was groundbreaking because it introduced the use of a high surface area TiO2 semiconductor electrode as the anode material. With a higher surface area, more chromophore can be loaded on the surface to increase light absorption and thus can generate more photocurrent. Using this basic architecture – with variations to its components – has allowed us to realizef efficiencies greater than 10% in the lab. Companies like Dysol and others are currently commercializing this technology.
As well as being groundbreaking the DSSC...
The tendency for sensationalism in science reporting is a problem. Phrases in a peer-reviewed article that say “this discovery could lead to applications such as x, y, and z” undergo a sensationalist spin when it’s reported that scientists have “discovered a cure for cancer,” “found THE cause of schizophrenia,” or “increased solar cell efficiency by 50%!” Sometimes the reporter facilitates the translation. Other times it is the researcher. The unfortunate result of this type of reporting is desensitization and, even worse, an increased skepticism of scientific claims. When a really important discovery comes along it is appropriately met with “AGAIN? Really?” and “well, then where is my flying car?” For the sake of maintaining the public’s trust and support, scientists should do what they can to avoid sensationalism. To avoid sensationalism in the area of solar fuels research we should be more thoughtful and critical about the use of the term “artificial leaf.”
A leaf in nature uses the energy in sunlight to split water and convert carbon dioxide into energy-rich sugars, adenosine triphosphate, and other organic molecules in a process we know as photosynthesis. This complex process contains a number of stepwise events involving geometrically organized proteins and small molecules located in the chloroplast. I am not going to discuss the individual steps but I encourage everyone to read up on this incredible machinery. The question I now pose...