March Research Round-Up

Congratulations to our amazing research teams here in the Department of Chemistry for their publications this month!

Bowman Group

Nandi, A., Qu, C., & Bowman, J. M. (2019). Using Gradients in Permutationally Invariant Polynomial Potential fitting: A Demonstration for CH4 Using as Few as 100 ConfigurationsJournal of chemical theory and computation.

Davies Group

Davies, H.M.L., Chennamadhavuni, S., Martin, T.J., Childers, S.R. (2019). U.S. Patent Application No. 15 /145,323

Evangelista Group

Li, C., & Evangelista, F. A. (2019). Multireference Theories of Electron Correlation Based on the Driven Similarity Renormalization GroupAnnual review of physical chemistry70.

Hill Group

Kaledin, A. L., Hill, C. L., Lian, T., & Musaev, D. G. (2019). Modulating electronic coupling at the quantum dot/molecule interface by wavefunction engineeringThe Journal of Chemical Physics150(12), 124704.

Lian Group

Li, Q., Liu, Q., Schaller, R. D., & Lian, T. (2019). Reducing Optical Gain Threshold in Two-Dimensional CdSe Nanoplatelets by Giant Oscillator Strength Transition EffectThe journal of physical chemistry letters.

Kaledin, A. L., Hill, C. L., Lian, T., & Musaev, D. G. (2019). Modulating electronic coupling at the quantum dot/molecule interface by wavefunction engineeringThe Journal of Chemical Physics150(12), 124704.

Lynn Group

Taran, O., Patel, V., & Lynn, D. (2019). Small Molecules Reaction Network That Models ROS Dynamic of the RhizosphereChemical Communications.

Musaev Group

Kaledin, A. L., Hill, C. L., Lian, T., & Musaev, D. G. (2019). Modulating electronic coupling at the quantum dot/molecule interface by wavefunction engineeringThe Journal of Chemical Physics150(12), 124704.

Salaita Group

Sylber, C., Petree, J., Baker, N., Salaita, K., & Wongtrakool, C. (2019). 3582 Scavenger Receptor Expression is Differentially Affected by DNAzyme-Gold Nanoparticle ConjugatesJournal of Clinical and Translational Science3(s1), 20-21.

Wuest Group

Scharnow, A. M., Solinski, A. E., & Wuest, W. M. (2019). Targeting S. mutans biofilms: a perspective on preventing dental cariesMedChemComm.

Post, S., Shapiro, J., & Wuest, W. (2019). Connecting iron acquisition and biofilm formation in the ESKAPE pathogens as a strategy for combatting antibiotic resistanceMedChemComm.

December Research Round-Up

Congratulations to our amazing research teams here in the Department of Chemistry for their publications this month!

Bowman Group

Babikov, D., Benoit, D., Bowman, J., Burd, T., Clary, D., Donovan, R., … & Kirrander, A. (2018). Quantum dynamics of isolated molecules: general discussionFaraday discussions.

Ban, L., Bowman, J., Bradforth, S., Chambaud, G., Dracinsky, M., Fischer, I., … & McCoy, A. B. (2018). Molecules in confinement in liquid solvents: general discussionFaraday discussions.

Qu, C., & Bowman, J. M. (2018). Assessing the Importance of the H2 (H2O) 2 3-Body Interaction on the Vibrational Frequency Shift of H2 in the sII Clathrate Hydrate and Comparison with ExperimentThe Journal of Physical Chemistry A.

Davies Group

Fu, J., Ren, Z., Bacsa, J., Musaev, D. G., & Davies, H. M. (2018). Desymmetrization of cyclohexanes by site-and stereoselective C–H functionalizationNature564(7736), 395.

Dyer Group

Zhao, J., Su, H., Vansuch, G. E., Liu, Z., Salaita, K., & Dyer, R. B. (2018). Localized Nanoscale Heating Leads to Ultrafast Hydrogel Volume-Phase TransitionACS nano.

Heaven Group

Kaledin, L. A., Kaledin, A. L., & Heaven, M. C. (2019). The electronic structure of thorium monoxide: Ligand field assignment of states in the range 0–5 eVJournal of computational chemistry40(2), 430-446.

Kindt Group

Zhang, X., Arce, J. G., & Kindt, J. T. (2018). Derivation of micelle size-dependent free energies of aggregation for octyl phosphocholine from molecular dynamics simulationFluid Phase Equilibria.

Lynn Group

McGill, T. L., Williams, L. C., Mulford, D. R., Blakey, S. B., Harris, R. J., Kindt, J. T., … & Powell, N. L. (2018). Chemistry Unbound: Designing a New Four-Year Undergraduate CurriculumJournal of Chemical Education.

Musaev Group

Fu, J., Ren, Z., Bacsa, J., Musaev, D. G., & Davies, H. M. (2018). Desymmetrization of cyclohexanes by site-and stereoselective C–H functionalizationNature564(7736), 395.

Salaita Group

Zhao, J., Su, H., Vansuch, G. E., Liu, Z., Salaita, K., & Dyer, R. B. (2018). Localized Nanoscale Heating Leads to Ultrafast Hydrogel Volume-Phase TransitionACS nano.

October Research Round-Up

Congratulations to our amazing research teams here in the Department of Chemistry for their publications this month!

Bowman Group:

Nandi, A., Qu, C., & Bowman, J. M. (2018). Diffusion Monte Carlo Calculations of Zero‐Point Energies of Methanol and Deuterated Methanol. Journal of computational chemistry.

Davies Group:

Davies, H. M., Itami, K., & Stoltz, B. M. (2018). New directions in natural product synthesisChemical Society Reviews.

Evangelista Group:

Huang, Y., Xu, Z., Jin, S., Li, C., Warncke, K., Evangelista, F. A., … & Egap, E. (2018). Conjugated Oligomers with Stable Radical Substituents: Synthesis, Single Crystal Structures, Electronic Structure and Excited State DynamicsChemistry of Materials.

Heaven Group

Torbin, A., Pershin, A., Zagidullin, M., Heaven, M., Mebel, A., & Azyazov, V. (2018). Ozone recovery in the presence of CO and N2O. In MATEC Web of Conferences(Vol. 209, p. 00016). EDP Sciences.

Tolstov, G. I., Zagidullin, M. V., Khvatov, N. A., Medvedkov, I. A., Mebel, A. M., Heaven, M. C., & Azyazov, V. N. (2018). Measurements of rate constants of O2 (b) quenching by CH4, NO, N2O at temperatures 300-800 K. In MATEC Web of Conferences(Vol. 209, p. 00006). EDP Sciences.

Heaven, M. C. (2018, October). Optically pumped rare gas lasers (Conference Presentation). In High-Power Lasers: Technology and Systems, Platforms, and Effects II(Vol. 10798, p. 1079806). International Society for Optics and Photonics.

Heemstra Group

Wilson, C. J., Bommarius, A. S., Champion, J. A., Chernoff, Y. O., Lynn, D. G., Paravastu, A. K., … & Heemstra, J. M. (2018). Biomolecular Assemblies: Moving from Observation to Predictive DesignChemical reviews.

Morris, F. D., Peterson, E. M., Heemstra, J. M., & Harris, J. M. (2018). Single-Molecule Kinetic Investigation of Cocaine-Dependent Split-Aptamer AssemblyAnalytical chemistry.

Hill Group

Kaledin, A. L., Hill, C. L., Lian, T., & Musaev, D. G. (2018). A bulk adjusted linear combination of atomic orbitals (BA‐LCAO) approach for nanoparticlesJournal of computational chemistry.

Ke Group

Wang, P., & Ke, Y. (2018). Attack on the Cell Membrane: The Pointy Ends of DNA Nanostructures Lead the Way.

Wang, D., Song, J., Wang, P., Pan, V., Zhang, Y., Cui, D., & Ke, Y. (2018). Design and operation of reconfigurable two-dimensional DNA molecular arraysNature protocols, 1.

Kindt Group

Patel, L. A., & Kindt, J. T. (2018). Simulations of NaCl Aggregation from Solution: Solvent Determines Topography of Free Energy LandscapeJournal of computational chemistry.

Guo, Z., & Kindt, J. T. (2018). Partitioning of Size-mismatched Impurities to Grain Boundaries in 2-d Solid Hard Sphere MonolayersLangmuir.

Lian Group

Kaledin, A. L., Hill, C. L., Lian, T., & Musaev, D. G. (2018). A bulk adjusted linear combination of atomic orbitals (BA‐LCAO) approach for nanoparticlesJournal of computational chemistry.

Huang, Y., Xu, Z., Jin, S., Li, C., Warncke, K., Evangelista, F. A., … & Egap, E. (2018). Conjugated Oligomers with Stable Radical Substituents: Synthesis, Single Crystal Structures, Electronic Structure and Excited State DynamicsChemistry of Materials.

Lynn Group

Wilson, C. J., Bommarius, A. S., Champion, J. A., Chernoff, Y. O., Lynn, D. G., Paravastu, A. K., … & Heemstra, J. M. (2018). Biomolecular Assemblies: Moving from Observation to Predictive DesignChemical reviews.

Musaev Group

Kaledin, A. L., Hill, C. L., Lian, T., & Musaev, D. G. (2018). A bulk adjusted linear combination of atomic orbitals (BA‐LCAO) approach for nanoparticles. Journal of computational chemistry.

Haines, B. E., Nelson, B. M., Grandner, J. M., Kim, J., Houk, K. N., Movassaghi, M., & Musaev, D. G. (2018). Mechanism of Permanganate-Promoted Dihydroxylation of Complex Diketopiperazines: Critical Roles of Counter-cation and Ion-PairingJournal of the American Chemical Society.

Wuest Group

Ernouf, G., Wilt, I., Zahim, S., & Wuest, W. M. (2018). Epoxy isonitriles, a unique class of antibiotics–Synthesis of their metabolites and biological investigationsChemBioChem.

 

Congratulations, Dr. Noel Xiang’ An Li!

Photo credit: Dr. Shaoxiong Wu

On Wednesday, April 25th, Noel Xiang’ An Li successfully defended his thesis, “Amyloid-beta strain amplification and their connection to tau in Alzheimer’s Disease”. Noel’s thesis committee included his thesis advisor, Dr. David Lynn, and members Dr. Stefan Lutz, Dr. Vincent Conticello, Dr. Lary Walker (Emory Neurology), and Dr. Yury Chernoff (GA Tech Biological Sciences).

Noel is applying for jobs in the pharmaceutical/biotech industry while wrapping up some experiments in the Lynn Lab.

Congratulations, Dr. Li!

Atlanta Science Festival: Beatrice the Biologist and Science Communication

The Atlanta Science Festival brings STEM out of the lab and into the Atlanta community with two weeks of events culminating in the “Exploration Expo” regularly attended by over 18,000 people. ASF was founded in 2014 by a group of Emory staff and faculty, including former chemistry (now ASF!) staff Meisa Salaita and Sarah Peterson and chemistry faculty member David Lynn. Chemistry has sponsored at least one festival event every year. This blog series covers just some of chemistry’s involvement in the 2018 festival.

Beatrice the Biologist (a.k.a Katie McKissick) discusses a comic concept with postdoc Claire Jarvis (Wuest Group).

As part of the festivities, the Department of Chemistry at Emory welcomed Katie McKissick to learn about her career as author and illustrator of Beatrice the Biologist. Katie’s visit was initiated by chemistry graduate student Anthony Sementilli (Lynn Group) as an outgrowth of the Emory “Chemmy” seminars that seek to bring speakers to campus with student hosts. Anthony felt that Katie’s work would interest other students looking towards a career in outreach or seeking to share their day-to-day work via a social media presence. Anthony received support for Katie’s visit from Emory’s Hightower Fund, AWIS, the ILA, and Biology as well as the Atlanta Science Festival. “Anthony was able to help cover his costs through multiple funding sources, but more importantly, he was successful in engaging a wide community with what Katie has to teach,” says chemistry outreach coordinator Kira Walsh, who provided administrative support for the visit. “It was great to see students from across Emory benefiting from Katie’s perspective. And the Atlanta community also got into the act with the standing room only comics workshop at historic Manuel’s tavern.”

Before Beatrice the Biologist, Katie was a high school biology teacher. During her time as an educator, she found that she was incredibly passionate about the way in which the information was taught. Specifically, she appreciated the process of lesson planning and preparing scientific information in a format that would be more approachable and interesting to her students. “I enjoyed thinking about how people learned more than I liked actually teaching” says Katie. This prompted her to start her blog, Beatrice the Biologist.

As Beatrice the Biologist grew in popularity, Katie was recruited to blog for Scientific American, worked in the Communications Office for the School of Engineering at USC, and later for NASA’s jet-propulsion laboratory where she wrote about space for children and adult audiences. Katie now writes for the Natural History Museum of Los Angeles County and produces her own podcast called “Science Brunch”, co-hosted by Mae Prynce.

During her visit to Emory, Katie gave students the chance to get to know the face behind Beatrice the Biologist. She taught multiple workshops about how to draw science cartoons and how to use blogs to build an online presence. She also gave a career seminar about pursuing scientific outreach. Katie’s love of teaching was apparent in her approach—she gave students a list of action items that she found to be the most valuable during her journey into scientific communication and encouraged them to think in depth about possible audiences, content strategy, platforms, and branding. In the comics workshop, students generated a draft comic on the spot!

“My audience,” says Katie, “are people like my former students who think they don’t like science only to discover that they actually do.” She reaches this audience using short, digestible content in the form of fun comics that focus on commonly misunderstood concepts. She explains that her comics can capture the attention of people who either already know the information and, therefore, appreciate the humor or people who don’t already know the information and can then learn something new.

Of course, effective science communication depends on more than just the quality of the content. Katie also provided the audience at her blogging workshop with insight into how to grow a brand and develop a far-reaching online presence. “We live in an amazing time when people are actually so accessible,” says Katie, emphasizing the importance of social media for disseminating information.  She even provided attendees with advice on how to “navigate rough waters” when it comes to social media faux pas. “You never want to assume people have context,” says Katie, “Especially if you are trying to make jokes!” Katie helped students to define their approach by encouraging them to complete a mission statement that could guide the curation of their online presence.

Katie’s visit to Emory gave students and faculty the unique chance to get to know the person behind Beatrice the Biologist and to learn all the best tips and tricks of science communication. She showed us how passion and creativity evolved “nerdy” science comics into a dynamic and entertaining platform for “cultivating curiosity and appreciation for science and nature one giggle at a time.”

To check out more from Beatrice the Biologist, click [here].

Applying to Graduate School 101: Unpacking the Personal Statement

Graduate student Autumn Flynn (Jui Group) is pictured writing in a notebook.
Graduate student Autumn Flynn (Jui Group) is pictured writing in a notebook.

This Fall, we are publishing a special series of blog posts about applying to graduate school–at Emory and in general. Our goal is to demystify the application process and help applicants feel confident as they seek a home for their graduate studies. This post is the second in the series, advice on writing a personal statement from Kira Walsh, Outreach Coordinator in the Department of Chemistry.

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The personal statement is a challenging genre. You’re tasked with packing years of experience into just a few pages. You want to sound smart and unique–but there are only so many ways to explain that you won an award or researched in a lab. How many times can you say “It was a great experience” in one document? Do you sound too confident? Not confident enough?

I’m going to share a method that I think leads to great personal statements–and it’s deceptively simple.

First, though, it’s important to remember that the admissions committee wants you to succeed. They want to get to know you. They want to recruit awesome students and build the careers of future leaders in the field. Don’t let the personal statement be an obstacle. We are excited to hear what you have to say and we’re not setting out to be critical. At Emory, we are particularly interested in your experience of and interest in research. If you’ve been in a lab, we want to hear about that–particularly the things you really enjoyed or the challenges you overcame. If you don’t have a lot of research experience, tell us WHY you want to spend more time in the lab!

Now, about that method. There is no magic bullet–nothing will work perfectly for everyone. But a mistake students make in crafting a personal statement is to focus too much on making things sound good and not enough time on sharing their own voice.

Simply put, your statement should be honest. The secret is: tell the truth.

Don’t tell us that everything has always been bright and shiny and perfect. It’s helpful to know what you’ve experienced that didn’t go right. We’d rather hear that you were professional and capable in a difficult situation than be told that you “loved” your laboratory experience even though you spent all your time washing test tubes and waiting for an experiment that never. seemed. to. work.

There is, of course,  a caveat to this advice. Don’t tell us your deepest, darkest secrets (unless they are clearly chemistry related.) Relationships, family matters, roommate troubles–they probably don’t belong in your statement, except where addressing them is key to your personal academic journey. Use your judgement–if you wouldn’t tell a professor at your current school, probably don’t tell us. (There’s always Post Secret.)

Sometimes, seeing an example can really help. I’ve asked one of our current graduate students, Anthony Sementilli (Lynn Group), to share a short section of a personal statement before and after a “truthy” revision.

Example: The Truth About Tutoring

Personal Statement Draft One:

[The students I tutored in the academic retention program were] usually the most driven and enthusiastic students I’ve had, and as someone who also depended on financial aid, I was sympathetic to my tutees’ struggles. 

Personal Statement Revision:

Understandably, students sometimes became upset after having the academic dean insist they seek extra help on top of recovering from tragedy. However, as someone who also depended on scholarships, I was sympathetic to my tutees’ struggles. I’m grateful that I could help my tutees pick up the pieces because it taught me the greatest lesson I’ve learned as a teacher so far: the most important students aren’t always the ones that come to your office bearing an apple with your name it. Over three years, I’m proud to say that I helped almost 20 students keep their scholarships.

Anthony is a great writer. In both drafts, the information is clear and persuasive. However, in the second version, Anthony makes the story a little bit less cheerful. It was challenging to provide mandatory tutoring! He had to build empathy with the students he worked with and also learn the lesson that student interactions can  be rewarding and important even if they are not overwhelmingly positive. The specific facts–3 years and 20 scholarships saved–really makes Anthony’s point.

Good luck with your personal statement! Share your story and tell the truth!

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Ready to apply? Visit chemistry.emory.edu/apply. Applications are due by December 1st, 2018 for entry in Fall 2019.

Want to learn more about chemistry @ Emory? Fill out an inquiry form and join our mailing list!

 

New Research from the Lynn Group on How Protein Misfolding May Kickstart Chemical Evolution

Photo of Brain from eScience Commons
Photo of Brain from eScience Commons

Exciting new research from the Lynn Group is featured in this week’s eScience Commons blog:

Alzheimer’s disease, and other neurodegenerative conditions involving abnormal folding of proteins, may help explain the emergence of life – and how to create it.

Researchers at Emory University and Georgia Tech demonstrated this connection in two new papers published by Nature Chemistry: “Design of multi-phase dynamic chemical networks” and “Catalytic diversity in self-propagating peptide assemblies.”

“In the first paper we showed that you can create tension between a chemical and physical system to give rise to more complex systems. And in the second paper, we showed that these complex systems can have remarkable and unexpected functions,” says David Lynn, a systems chemist in Emory’s Department of Chemistry who led the research. “The work was inspired by our current understanding of Darwinian selection of protein misfolding in neurodegenerative diseases.”

The Lynn lab is exploring ways to potentially control and direct the processes of these proteins – known as prions – adding to knowledge that might one day help to prevent disease, as well as open new realms of synthetic biology.

Read the [Full Story] by Carol Clark on Emory’s eScience Commons blog!

Research Spotlight: Chen Liang Shines Light on Amyloid’s Shape-Shifting Properties

By: Chen Liang (Lynn Group)

The hallmark of Alzheimer’s disease is the presence of plaques in the brain formed by the aggregation of Aβ peptide with heavy β-sheet content–also known as amyloid. Amyloid is hypothesized to be causative in Alzheimer’s disease through multiple mechanisms such as oxidative stress, interaction with receptors and synaptic loss. Currently, over five million Americans are living with Alzheimer’s disease, costing the nation 236 billion a year. It’s expected that by 2050,healthcare spending on Alzheimer’s will reach one trillion. The NIH invests around 500 million annually for Alzheimer’s research. Despite the prevalence of Alzheimer’s and the intensive efforts of researchers, no effective therapeutics for the disease is yet available. This dilemma attracted me to the study of amyloid as my PhD research project.

Current drug design for Alzheimer’s disease focuses on finding molecules that bind and block the action of these deleterious proteins. Typically, a disease—like cancer, diabetes, and, as some have believed, Alzheimer’s—is caused by proteins with a fixed structure. However, my study in Dr. David Lynn’s lab at Emory University demonstrates that amyloid, unlike conventional drug targets, is highly dynamic and can change structure over time. My research could potentially explain why conventional drug discovery methods don’t succeed with Alzheimer’s –they generally ignore the structural diversity and the changing nature of amyloid.

The peptide I use in this research is the nucleating core of Aβ Dutch mutant, Aβ(16-22)E22Q or KLVFFAQ. People with this genetic mutation develop a more severe form of Alzheimer’s. I discovered that early on, after dissolving, this peptide forms ribbon shaped structures and later autocatalytically change into fibers (Figure 1). More detailed characterization using IE-IR (isotope edited infrared spectroscopy) and solid state NMR (Nuclear Magnetic Resonance) reveals that in the ribbon shape, two neighboring peptides within a β-sheet are pointing in the opposite direction—a state that is commonly referred to as an anti-parallel β-sheet arrangement. Yet the conformation is transient. After a week, the peptides autocatalytically switch into parallel β-sheet where all peptides are pointing in the same direction. Furthermore, by simply adding salt, I was able to control the speed of such shape shifting and even greatly expand the range of observed structures.

Figure 1. Amyloid could change shape during assembly. E22Q initially forms anti-parallel ribbons (left) and later automatically changes into parallel fibers(right). Scale bar 200nm
Figure 1. Amyloid could change shape during assembly. E22Q initially forms anti-parallel ribbons (left) and later automatically changes into parallel fibers (right). Scale bar 200nm. Reprinted (adapted) with permission from Chen Liang et al. “Kinetic Intermediates in Amyloid Assembly.” J. Am. Chem. Soc., 2014, 136 (43), pp 15146-15149. Copyright 2016 American Chemical Society.

This research is significant in the study of Alzheimer’s disease and drug development because it begins to explain why no effective therapeutics have been developed for Alzheimer’s disease. Due to the high thermo-stability of amyloid, researchers commonly assume amyloid structure remains static upon assembly. My study demonstrates the opposite: amyloid can change structure and such a change is sensitive to environmental conditions. Now people can imagine the change and diversity that could occur when amyloid is spreading through different cellular environments as it ravages the brain.

Such an “environmental dependent conformational change” is an important property of Aβ protein and these dynamics are beginning to gain more attention in the scientific community despite being counter-intuitive. Amyloid’s high thermostability has led researchers to reason that once formed amyloid should be stable and their structure should be faithfully replicated throughout the brain. The implication of my study on the treatment of Alzheimer is that instead of measuring the amount of amyloid and treating patients non-discriminately, the structure diversity of amyloids should be central to any consideration in developing diagnostics and therapeutics. New methods of drug discovery—taking into account amyloid’s unique properties—will certainly be necessary for treating Alzheimer’s and the increasing number of amyloid diseases.

Further Reading:

Chen Liang et al. “Kinetic Intermediates in Amyloid Assembly.” J. Am. Chem. Soc., 2014, 136 (43), pp 15146-15149. Copyright 2016 American Chemical Society.

Adams Invited to ACS Green Chemistry and Sustainable Energy Summer School

Congratulations to Savannah Adams (1st-year student in the Lynn Group) for being invited to the American Chemical Society summer school on Green Chemistry and Sustainable Energy at the School of Mines in Golden, CO. From ACS:

The Summer School is open to graduate students and postdoctoral scholars studying in the United States, Canada, and Latin America. Most applicants are studying for or have earned advanced degrees in chemistry or chemical engineering, but applicants from other fields will also be considered. The program is sponsored by the ACS, ACS Petroleum Research Fund, and ACS Green Chemistry Institute. Coach-class airfare, ground transportation, shared on-campus housing, meals, and all program costs are provided to students.