|Interview by David Bradley
A Chemist's Thoughts on Computational Power and the Future of 'The Chemical Web'
Computational chemist Steven Bachrach was torn between physics and chemistry. Luckily for the chemical community he found a happy medium in which to explore. Born, August 14, 1959, and graduated from the University of Illinois at Urbana in 1981, he obtained his PhD on Organolithium and Organosilicon Chemistry under Andrew Streitwieser, Jr., from University of California at Berkeley in 1985.
He is currently the Dr. D. R. Semmes Distinguished Professor of Chemistry at Trinity University, San Antonio, Texas. Professor Bachrach has more than 100 research papers to his name on everything from potential energy curves of CO and Ne-He, to computational studies of pericyclic reactions between phosphinoboranes and alkenes.
Can you tell me briefly about your route into chemistry?
My father was a professor of chemistry, first at the University of Illinois at Chicago, and then at Northeastern Illinois University. I do not recall any time he pushed me towards science or chemistry, but undoubtedly he was an influence on my career choice. When I started my collegiate career at the University of Illinois, I was torn between physics and chemistry. I opted for the latter based mostly on career opportunities?I figured there were more job opportunities in chemistry than physics.
What drove you towards the theoretical/quantum end of the chemical equation?
Given my interests in physics, the decision to pursue computational chemistry seemed pretty natural. I took many physics course at Illinois, and in fact my favorite course was quantum mechanics taught by a fantastic professor in the physics department. I was also fortunate that Prof. Cliff Dykstra had recently joined the chemistry department. Cliff, a graduate of Fritz Schaefer's group, was doing computational/theoretical chemistry and I joined his research group in the second semester of my junior year, and continued this for my senior year as well. We examined a new theoretical method called ACCD (an approximated coupled-cluster doubles treatment) and its application to carbon monoxide and the He-Ne cluster.
This led to my first publication, a full paper in the Journal of Chemical Physics that appeared shortly before I started graduate school at Berkeley. I chose to go to Berkeley for my doctorate mainly because there were two professors I was interested in studying with, Fritz Schaefer and Andy Streitwieser. I ended up choosing to work with Streitwieser because I wanted to apply quantum mechanics and computational methods to organic reactions.
Software for accurate predictions of pKa, solubility logP, logD, boiling point and more based on chemical structure.
Generate Systematic nomenclature from chemical Structure. CAS and IUPAC compatible. InChI and SMILES
View spectroscopic, chromatographic, other forms of analytical data, text and chemical structures together in a web browser interface.
As computational power rises, do you think we will begin to solve more and more complex molecules to the point where Schrodinger can be solved even for proteins?
Undoubtedly computers are getting faster and algorithms are becoming more powerful. We are all studying much larger molecules than I did as a graduate student some 20 years ago, let alone even 5 years ago. Nonetheless, tackling proteins is a huge challenge primarily because of the enormous number of possible configurations. I think a different approach will be necessary to deal with the protein folding problem. However, if all we wish to do is compute the energies and properties of a given structure, certainly that will be amenable at the ab initio level within the near future for proteins of reasonable size.
You played a significant role in pioneering the chemical net, as it were, how have things changed since those heady days of the early to mid-90s?
Technology has changed the playing field dramatically. Back in the beginning, we had to worry about access to the internet, let alone broadband access. And the development of XML and Java and related web languages has meant that the kinds of ideas we were developing back then have a real framework now.
Culturally, things have also changed, but very slowly within the discipline of chemistry. Electronic journals are now the norm, and my guess is that print journals will begin to disappear within the next 10 years. But the current state-of-the-art in electronic publishing is Adobe's PDF, essentially just electronic print. Very little of a revolutionary nature that we were trying to do with the Internet Journal of Chemistry exists even today. The new Prospect initiative from the RSC [see the interview in issue 62 with RSC's Robert Parker] is a real step forward, but this is 10 years after we launched IJC.
How have things progressed? Do you feel we are "there" yet?
While chemistry publishing is better off today in terms of what is being done with the Internet, we still have a ways to go. Journal articles could be so much richer, with reusable data, and commentary, and live objects, etc. The community also has to come to grips with the cost of information, whether that is subscription-based, Open Access, or some other model.
Can you tell me briefly about your input into the InChI movement? What drivers do we need to push that into mainstream chemistry?
I have mainly been a cheerleader, serving on some committees and championing the adoption of InChI, but I have not participated in its development. The one area that I think can rapidly change the marketplace regarding InChI is if a federal agency or some international body would require the InChI as the identifier. I know that some US agencies face significant costs because they require the use of the CAS number to identify compounds. A move to InChI would save real money and allow all suppliers, agencies, and consumers equal access to the compound identifier without having to pay for what is simply a name from a third-party.
How should chemists embrace Wikis, blogs, and so-called Web 2.0 to further our cause?
Well, this is really an issue of culture. My personal hesitancy to adopt Web 2.0 technologies is that I don't have the time to read random thoughts by random individuals. I barely have time to keep up with the old-school (i.e., traditional journals) literature in my field. The blogosphere just seemed to me to be filled with the rantings of people who have nothing better to do with their time. Peter Murray-Rust's blog was the first to demonstrate to me that real chemistry content could be had, that interesting and novel ideas could be found and shared and discussed.
So I am actually starting up my own blog in the next few weeks. I am having a book called Computational Organic Chemistry published with Wiley, to appear in July 2007. Now, this is a survey of how computational methods have been used in solving organic chemical problems. I sent in the manuscript in October, but science never stops, and so in some sense the book is already out of date. The blog will allow me to write about new articles that have appeared relevant to the topics of the book; it's a way to keep the book up to date, sort of continuous new editions coming out as needed.
I will also have an ancillary web site for the book which will have links to all the cited materials that are available in some electronic form on the web and also include the 3-D coordinates of all the molecules discussed in the text so that readers can manipulate these structures in 3-D and even pipe them into their own applications. The books web site will be http://www.trinity.edu/sbachrac/coc and the blog will be available at http://hackberry.chem.trinity.edu/blog. Simple prototypes are there right now, but the finished versions will appear over the next few weeks. I hope that these web resources will serve as models for how the Internet can really enhance scientific communication.
The main hurdle for wider adoption of Web 2.0 communications in chemistry rests largely on changing attitudes in academe. Until blogs and wikis are recognized as meaningful contributions towards tenure and promotion consideration, these tools will be largely ignored.