With this award from the Major Research Instrumentation (MRI) program, Professor Brent P. Krueger and colleagues William Polik of Hope College, Scott E. Feller of Wabash College, Keith T. Kuwata of Macalaster College and Daniela Kohen from Carleton College will acquire a computer cluster for computational research and education. It will support projects at Wabash College and Carleton College focused on molecular dynamics and Monte Carlo simulations to study aluminosilicates (zeolites) that act as gas absorbents and to investigate problems in membrane biophysics such as polyunsaturated fatty acids in lipid-protein interactions. Quantum mechanical methods will be used to support projects at Hope College, Ripon College, Temple University and the University of Wisconsin-River Falls including computation of highly accurate potential energy surfaces to interpret molecular spectra and predict reaction pathways, studies of silver-based catalysts, characterization of electronically excited states and solvation effects for a variety of systems, and the photochemical deoxygenation of aromatic sulfoxides and selenoxides. Combined quantum chemical and statistical/dynamical calculations will be employed at Hope College, Macalaster College, and Grand Valley State College to model fluorescent probe behavior, to study high-energy intermediates that impact atmospheric chemistry, and to investigate the formation, aging, and radiative properties of tropospheric aerosols, which impact air quality, visibility, and global climate change.
Computer systems and clusters of computers are used by chemists and biochemists to investigate reactions and the properties of chemicals and materials using theoretical models and programs. The computer calculations are used, often along with experimental data, to model and better understand many types of complex chemical and biological phenomena. They are also used to predict results and guide experiments. This resource will be used in research and in course work by undergraduate students and faculty at eight institutions training them in computational chemistry methodology with a modern computer system.
brings together faculty and undergraduate research students with a common interest in using computers to understand a broad range of chemical phenomena. NSF-MRI funding in 2005 and 2010 enabled MU3C to purchase two high-performance computer clusters which students at the ten consortium institutions use extensively in both research and in classes. Intellectual Merit During the current grant period, MU3C students and faculty published 39 peer-reviewed articles based on research done on the NSF-MRI supported clusters. We apply computational methods to answer questions in fields such as catalysis, materials, atmospheric chemistry, electron transfer, photochemistry, spectroscopy, and biochemistry. The methods we use likewise cover a wide range: quantum mechanics, molecular dynamics, Monte Carlo simulations, and statistical rate theory. An example of MU3C biochemical research comes from the lab of Hope College Professor Brent P. Krueger, who is using both fluorescence spectroscopy and computation to probe the internal motion of large biological molecules such as proteins. Figure 1 shows a quantum mechanical prediction of the charge distribution (more precisely, the electrostatic potential) of the light-absorbing section of EGFP, a fluorescent protein commonly used in biochemical experiments. The electrostatic potential serves as an input for molecular dynamics simulations of the constantly fluctuating internal structure of the protein, and those simulations are, in turn, used to extract important information from fluorescence experiments. MU3C laboratories have also used computational chemistry to reveal the precise mechanisms of chemical reactions. Such insight drives advances in fields such as catalysis and atmospheric chemistry. Ripon College Professor Joseph D. Scanlon and his students study how individual metal atoms catalyze chemically useful transformations that are exceedingly slow otherwise. Figure 2 shows the transition state in which a hydrocarbon is gaining an oxygen atom thanks to the action of a single rhodium atom. Figure 3 shows another transition state, this time from the internal transfer of a hydrogen atom with a molecule known as a Criegee intermediate. Macalester College Professor Keith T. Kuwata and his students have shown how such hydrogen transfer reactions can make an enormous contribution to free radical concentrations in the atmosphere. Finally, computational studies by MU3C laboratories have advanced both fundamental scientific knowledge and our ability to solve real-world problems. An example is the work of Professor Daniela Kohen and her students at Carleton College. They have performed Monte Carlo simulations on zeolites, minerals composed of the earth-abundant elements aluminum, silicon, and oxygen. Certain specific zeolite structures are known to selectively adsorb carbon dioxide (CO2) from gas streams. Simulations by the Kohen laboratory account for this selectivity by showing how CO2 outcompetes N2, the major component of air, for binding sites within the zeolite (Figure 4). These simulations have the potential to inform the creation of zeolites that are even better at removing CO2 from industrial gas flues, which could greatly mitigate the impact of fossil fuel combustion on climate. Broader Impacts During the current grant period, 80 undergraduate students have conducted research on the MRI-supported computer cluster, 38 of them women and 8 of them underrepresented minorities. Most of these students participated in at least one of the MU3C undergraduate research conferences. Our summer conferences, hosted at a leading Midwestern research university, feature talks by MU3C students, presentations by computational chemists at the host university, and informal interactions among faculty, postdoctoral fellows, graduate students, and undergraduates. These conferences build relationships among the geographically separated MU3C students and faculty, inspire MU3C students to pursue graduate studies, and give hosting institutions opportunities to recruit well-trained students to their graduate programs. Since the current MRI grant started, summer meetings have been hosted by the University of Chicago (2011), the University of Minnesota-Twin Cities (2012), the University of Michigan-Ann Arbor (2013), and Iowa State University (2014). Our winter conferences are online, and each features three days of posters presented by MU3C students, who respond to questions posed by fellow students and faculty. Here, the positive impact of our consortium's scientific breadth is fully felt. No one is an expert in all of the computational methods used or the research areas explored by the students in their presentations. Therefore, everyone is learning new chemistry during every winter conference. Typically, each meeting has some 200 posts (questions, answers, and comments). While primarily used in research, the MU3C cluster also supports the efforts of consortium faculty to incorporate computation throughout their departments' chemistry curricula. Several hundred students each year at MU3C schools experience computational chemistry in their general, organic, physical, inorganic, and biological chemistry classes.
