Category Archives: conference report

253rd ACS National Meeting & Expo

The ACS National Meeting in April was one of the most significant trips I have been on, and by far the largest conference I have attended. I presented my poster, attended fascinating research talks, and networked with chemistry professionals.

Presenting my poster yielded some interesting discussions with the people who stopped by — mostly other computational chemistry professionals, in fact. One evaluated me for the poster award, and he even one-upped me by knowing the directions of the transition dipole moments of indole, which I did not. Presenting to him was a good experience, because it was fun to walk through my entire project. Another professional said that if we could find a successful functional with TD-DFT, perhaps we could eventually publish our results. Talking to other students gave me an idea of how vastly different research topics could be within the domain of computational chemistry.

I went to some great talks. I heard Harry Gray present on Solar Fuels, using catalysts inspired by plant photosystems, giving me a paper topic for my bioinorganic chemistry class. Later I got to hear the big talk on CRISPR, the gene-editing process and its potential implications in our lives. There were a lot of other good talks, but some less than inspiring ones — I heard someone present his graduate research on organic dyes for solar cells, a topic I was familiar with, but I was bored by his lack of passion. However, most of the talks were given with enthusiasm and depth.

Networking was an interesting experience. The career fair got me out of my comfort zone and helped me practice speaking with people in a professional environment. At a speed networking workshop, I talked to a lot of retired chemistry professionals, which was not as useful, because they had only generalized advice to give me and no real leads. Nonetheless, I became more confident in myself after the networking experiences I had at the Meeting.

A cool thing that happened was that I got to speak with the tech support at Gaussian about our research group’s problem with the Gaussian software — the confusion issue with excited state optimizations — and he gave me a few ideas to try. They haven’t worked so far, but they at least gave us something to move us forward on the issue and identify what does not work. I remain hopeful that we will resolve this issue with the software.

Other than that, Kristine and I got to explore the city a bit and walk on the Golden Gate Bridge. Can’t beat the view from there! I hope I get to go on a similar trip in the future.

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Interesting talks and workshops at the ACS National Meeting

In addition to presenting my work at the poster session as Dr. Kennerly already mentioned, I attended a wide variety of talks and events at the ACS National Meeting. Some of the talks were related to my field of research, such as one by Dr. Joseph Subotnik. That said, one of my favorite things to do at ACS is always learning about new areas of chemistry, so I went to quite a few talks out of sheer curiosity. One I particularly enjoyed discussed modifying the surface coatings of solar cells to allow dust to be washed off more easily, making them more useful in desert areas. I had never realized how significant of a problem dust was for solar technology, so it was fascinating listening to someone who had devoted significant amounts of time to fixing this problem.

Since I am graduating this year and searching for a job, I also participated in some of career building workshops offered at the conference. In particular, I attended one which was designed to allow undergraduates to network with professionals from all areas of chemistry. There were quite a few people representing academia at this event, and I think it would have been a bit more helpful if there were more from industry and perhaps also the government. That said, I met with a representative from ACS who directed me to some helpful resources for recent graduates, so it was a worthwhile event.

Overall the conference was fun and instructive and definitely worth the trip.

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MERCURY conference 2016 — a great time for students to experience computational chemistry!

Alexandra Cassell presenting her poster at MERCURY 2016

Alexandra Cassell presenting her poster at MERCURY 2016

Last week  Alex, Justin and I traveled (along with the Navea group) to the MERCURY conference at Bucknell University,
a conference devoted to computational chemistry done by undergraduates.  Its a a great opportunity to see the wide diversity of work that qualifies as ‘computational chemistry’, everything from really detailed studies of small molecules using high-level theory, to simulations of huge biomolecules with an aim towards discovering better drugs.   Not to mention mechanistic organic chemistry, applied materials research, and lots more.     Six speakers from research institutions and companies also come in to talk about their careers and research programs.   Its a not-to-miss conference every year!

Justin Gerard presenting his poster at MERCURY 2016

Justin Gerard presenting his poster at MERCURY 2016

Justin and Alex both presented results from their summer research on excited-state time-dependensity density functional theory calculations of indole and tryptophan (respectively).  Both spoke for a quick 1-minute abstract talk in front of the entire audience of 100+ attendees and then presented their poster for an hour during the poster session, speaking with other students, faculty at undergraduate colleges, and the six invited speakers.    Justin and Alex have posted trip reports.    Here are the vital pictures  — they both did a great job!


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MERCURY: Guest Speakers and Poster Presentations

This past weekend, our research group attended talks by guest speakers, presented our abstracts, and fielded questions by our posters at the 2016 MERCURY Conference at Bucknell University.

There were six guest speakers: Chris Cramer, Steven Wheeler, Jeffrey Evanseck, Chris Wilmer, Richard Pastor, and Kate Holloway.

Cramer gave a crash course in quantum mechanics and computational chemistry. He referred to the psi operator in the Schrödinger equation as an oracle, and he said it is important to ask the oracle something you know before you ask it something you don’t know, i.e. to validate a computational method before using it to predict new information. He stated that the total energy of a molecule can be determined exclusively from its electron density. However, he pointed out self-interaction error as the biggest error in DFT, in which the calculation averages the position of one electron, so that in the calculation, the election repels itself (impossible). This error needs to be corrected for in the calculation. After the crash course, he discussed his research with MOFs (Metal Organic Frameworks), porous materials on the nano scale that can store and separate liquids or gases.

Wheeler delineated important goals and advice for computational chemists. He proposed that you only really learn how quantum chemistry methods work by programming them yourself, that you should learn a programming language (especially Python), and that you should take a course in linear algebra, if possible. Wheeler described three main types of functionals: semi-empirical (approximate/Hartree-Fock theory for 1000s of atoms), ab initio (MO-based methods for 10s to 100s of atoms, depending on the level of theory), and DFT (for 20 to 200 atoms). He asserted that choosing the appropriate level of theory for calculations is a primary focus of computational chemists. He mentioned his trials to find an appropriate functional with DFT for his research. Because traditional DFT functionals completely fail to capture dispersion interactions, he decided on B97-D, as a fast, accurate functional, though it had problems with long-range interactions. His research group studies the pi-pi* stacking of substituted benzene rings.

Evanseck introduced molecular dynamics. He stated three reasons for computation: to interpret experimental data, to extend (fill gaps) in experimental data, and to make predictions to guide the experiment. He made an analogy to the Pople Diagram (see below), with force field sophistication instead of level of theory. He then broke down the pros and cons on molecular dynamics methods vs. quantum methods. In addition, he pointed out that it is much easier to tweak the existing potential energy functions than to write new ones.


Wilmer has become successful with a start-up called NuMat Technologies Inc., which develops new MOFs with programs that general hypothetical MOFs and calculates their ability to store and separate natural gases for motor vehicles and CO2 capture. He advanced with the help of some business majors by participating in business plan competitions.

Pastor informed us of the tremendous difficulty and computing time of membrane simulations, specifically looking at natural antibiotics in epithelial layers. He said it was appropriate for early grad students to be inexperienced and lazy (to learn but not disrupt the work of the professors or pursue fruitless projects), post-docs to be smart and hard-working (to effectively collaborate with professors), and PIs to be smart and lazy (to delegate tasks properly and be able to respond to post-docs and students). He encouraged students to seek truth, work within a community, and to be a good and generous friend by keeping friends out of the wrong quadrants (smart/inexperienced, hardworking/lazy), where inexperienced and hardworking was the most dangerous for everyone.

Holloway has worked on finding cures for AIDS and hepatitis C at Merck. She described her career trajectory, having decided on computational chemistry because she was good at it and didn’t like lab work. She became a computational chemist at Merck straight from her Ph.D. She emphasized the cost (>$2.5 billion) and waiting time (>10 years) for new drugs to get on the market. However, potentially saving people’s lives motivated her and her fellow researchers.

Presenting abstracts seemed like it would be easy enough, but I got some of the ordering of my spiel wrong and flubbed some of the wording. This experience has taught me that memorizing and practicing a short speech might be a good idea in the future.

Poster presentations went much better for me. Because we had rehearsed, I was comfortable with the flow of my presentation, and I adjusted the length and detail of it based on the knowledge of the person listening (anyone from Steven Wheeler to students with no knowledge of Gaussian). One student named Clorice was particularly interested in my poster, because she was also starting some excited state optimizations with TD-DFT. However, she did not experience the same difficulty optimizing first and second excited energy states, because her project involved pi-pi* stacking and enzyme activity, not a molecule with fluorescent properties similar to indole.

A highlight of the stay was hearing Chris Cramer expertly sing some folk songs at karaoke night (not to mention the our own group’s hoe-down of “Sweet Home Alabama”). That night, along with conversations with students and faculty in chemistry who are also involved in music, gave me hope that music and art will stay relevant to me if I pursue a career in chemistry.

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MERCURY Conference

I really enjoyed going to this year’s MERCURY conference. In fact, a few of the speakers were very inspirational, as were some posters. The speakers that I most enjoyed were Kate Holloway and Chris Wilmer. Kate Holloway talked about drug design to combat HIV and HCV and I was really intrigued by the details and difficulties in this process. Chris Wilmer discussed MOF’s and how they can be used to model methane consumption. I think I liked these presentations the most, both because the speakers were very good and also because I could clearly see the applications of their research in our lives. I also really enjoyed the poster session. My presentation went well, except I was asked a few questions I was uncertain about and Chris Cramer didn’t come to talk to me 🙁 . However, I enjoyed looking at other posters more than presenting my own. There were three posters that I enjoyed the most. First, a student researched nano-aggregates and measured their speed of aggregation to be able to find a solution to clogging when these nano-aggregates interact with waxes in pipes. Her research seemed very simple on the poster, but the work was quite fascinating. Second, a student experimented with different halogens and leaving groups to see if he could make a bi-molecular reaction become a concerted reaction. I don’t think I realized how many different directions molecular dynamics could go; including organic chemistry. Lastly, two girls presented their poster about enzyme inhibitors. I can’t quite remember the entire purpose but I know that they were working with inhibitors, derivatives of some molecule (which included tryptophan), and dopamine. They measured interaction energies between the derivatives and dopamine to find the best one, with two different conformations.

I was disappointed that I wasn’t able to get any suggestions about Gaussian’s confusion problem from any of the quantum professors or speakers there who are familiar with the program. I would have liked to been able to discuss more with them the problems that we have been  having. Overall, I enjoyed seeing the subjects that other students were researching with computational chemistry. Also, the conference made me sad that I am not taking a science class next semester. . .

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