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The challenge of finding “green” energy resources to replace non-renewable fossil fuels is a topic of great interest for researchers. Chris Cramer (Distinguished McKnight Professor of Chemistry; MSI Fellow) and his research group and collaborators are among those who are using high-performance computational methods for their research in this area.
Plants have been using solar power to generate energy for millions of years. In photosynthesis, plants transform the sun’s rays into chemical energy that they can use. This process involves the oxidation of water in the plant. Researchers are interesting in creating artificial systems that can mimic this process. The method is known as water-oxidation catalysis, and, while it has been receiving a great deal of attention in recent years, a great deal of work still needs to be done to create a system that is economically practical for large-scale use.
Professor Cramer and a former student and MSI researcher, Dr. Mehmed Ertem, in collaboration with other investigators at Brookhaven National Laboratory, the Catalonian Institute for Chemical Research, Berlin Technical University, and Yale University, recently published a paper in Angewandte Chemie that discusses a new water-oxidation catalyst (Lopez, Isidoro, Mehmed Z. Ertem, Somnath Maji, Jordi Benet-Buchholz, Anke Keidel, Uwe Kuhlmann, Peter Hildebrandt, Christopher J. Cramer, Victor S. Batista, and Antoni Llobet. 2014. A self-improved water-oxidation catalyst: Is one site really enough? Angewandte Chemie-International Edition 53 (1) (JAN 3): 205-9). The authors have demonstrated a dinuclear ruthenium (Ru) water-oxidation catalyst that is created from a mononuclear catalyst during the catalytic process. The dinuclear catalyst is rugged and powerful and does not decompose over time. The researchers used kinetic analysis and density functional theory computational studies to characterize this reaction.
Green energy is just one of the many topics under investigation by the Cramer group. They are developing computer models to study many areas of chemical, biological, and environmental interest and have a large number of publications. A sample is shown below:
• Angeles-Boza, Alfredo M., Mehmed Z. Ertem, Rupam Sarma, Christian H. Ibanez, Somnath Maji, Antoni Llobet, Christopher J. Cramer, and Justine P. Roth. 2014. Competitive oxygen-18 kinetic isotope effects expose O-O bond formation in water oxidation catalysis by monomeric and dimeric ruthenium complexes.Chemical Science 5 (3) (MAR): 1141-52.
• Gao, Jiali, B.J. Jankiewicz, J. Reece, H. Sheng, Christopher J. Cramer, J.J. Nash, H.I. Kenttämaa. 2014. On the factors that control the reactivity of meta-benzynes. Chemical Science. In press.
• Isley, William C., III, S. Zarra, R.K. Carlso, R.A. Bilbeisi, T.K. Ronson, J.R. Nitschke, Laura Gagliardi, Christopher J. Cramer. 2014. Predicting paramagnetic 1H NMR chemical shifts and state-energy separations in spin-crossover host-guest systems. Physical Chemistry Chemical Physics. In press.
• Lee, Kyuho, William C. Isley, III, Allison L. Dzubak, Pragya Verma, Samuel J. Stoneburner, Li-Chiang Lin, Joshua D. Howe, et al. [Christopher Cramer; Donald Truhlar; Laura Gagliardi] 2014. Design of a metal-organic framework with enhanced back bonding for separation of N2 and CH4. Journal of the American Chemical Society 136 (2) (JAN 15): 698-704.
• Meng, W., A.B. League, T.K. Ronson, J.K. Clegg, William C. Isley, D. Semrouni, Laura Gagliardi, Christopher J. Cramer, J.R. Nitschke. 2014. Empirical and theoretical insights into the structural features and host-guest chemistry of M8L4 tube architectures. Journal of the American Chemical Society 136, 3972.
• Hirahara, Masanari, Mehmed Z. Ertem, Manabu Komi, Hirosato Yamazaki, Christopher J. Cramer, and Masayuki Yagi. 2013. Mechanisms of photoisomerization and water-oxidation catalysis of mononuclear ruthenium(II) monoaquo complexes. Inorganic Chemistry 52 (11) (JUN 3): 6354-64.
• Marenich, Aleksandr V., Christopher J. Cramer, and Donald G. Truhlar. 2013. Generalized born solvation model SM12. Journal of Chemical Theory and Computation 9 (1) (JAN): 609-20.
• Marenich, Aleksandr V., Christopher J. Cramer, and Donald G. Truhlar. 2013. Reduced and quenched polarizabilities of interior atoms in molecules. Chemical Science 4 (6): 2349-56.
• Marenich, Aleksandr V., Christopher J. Cramer, and Donald G. Truhlar. 2013. Uniform treatment of solute-solvent dispersion in the ground and excited electronic states of the solute based on a solvation model with state-specific polarizability. Journal of Chemical Theory and Computation 9 (8) (AUG): 3649-59.
• McGrath, Matthew J., I-F Will Kuo, Brice F. W. Ngouana, Julius N. Ghogomu, Christopher J. Mundy, Aleksandr V. Marenich, Christopher J. Cramer, Donald G. Truhlar, and J. Ilja Siepmann. 2013. Calculation of the Gibbs free energy of solvation and dissociation of HCl in water via Monte Carlo simulations and continuum solvation models. Physical Chemistry Chemical Physics 15 (32): 13578-85.
• Miro, Pere, and Christopher J. Cramer. 2013. Water clusters to nanodrops: A tight-binding density functional study. Physical Chemistry Chemical Physics 15 (6): 1837-43.
• Semrouni, David, Isley,William C.,,III, Carine Clavaguera, Jean-Pierre Dognon, Christopher J. Cramer, and Laura Gagliardi. 2013. Ab initio extension of the AMOEBA polarizable force field to Fe2+. Journal of Chemical Theory and Computation 9 (7) (JUL): 3062-71.
• Suess, Alison M., Mehmed Z. Ertem, Christopher J. Cramer, and Shannon S. Stahl. 2013. Divergence between organometallic and single-electron-transfer mechanisms in copper(II)-mediated aerobic C-H oxidation. Journal of the American Chemical Society 135 (26) (JUL 3): 9797-804.
Professor Cramer is a long-time MSI Principal Investigator and Fellow of the Institute. He is also a member of the Chemical Theory Center, whose other members include several MSI Principal Investigators: Regents Professor Donald Truhlar, Professor Laura Gagliardi, Professor J. Ilja Siepmann, and Professor Jiali Gao. MSI interviewed Professor Cramer about his research in September 2012.
Image Description: Ball-and-stick representation of the optimized transition-state structures for O–O bond-formation (left) and O2-evolution steps (right) for the Ru catalyst. H atoms are shown only for the aqua and hydroxy ligands. Figure and description © Angewandte Chemie; Lopez, I., et al., Angewandte Chemie-International Edition 53(1):205-9 (2014)
posted on May 7, 2014
Left: Jos Moore, University of Melbourne (Australia)/Monash University (Australia)
Right: T. Michael Anderson and T. Morrison
Human activities, such as farming and burning fossil fuels, have more than doubled the amount of nitrogen and phosphorus, entering the earth’s ecosystems. Eutrophication, the ecosystem’s response to the addition of artificial or natural nutrients can result in dramatic changes. In aquatic ecosystems, eutrophication can result in a “bloom” of algae as a result of nitrates or phosphates being washed into the system from a fertilized field. Our understanding of the impacts in terrestrial systems are much more limited.
An international collaborative of scientists have developed the Nutrient Network, or NutNet (http://nutnet.org), which includes researchers at more than 75 sites across North and South America, Europe, Australia, Asia, and Africa to understand the impacts of nutrient additions on global grassland ecosystems. In addition, they are studying whetehr herbivores can lessen the effects of eutrophication by consuming the fast growing plants. The NutNet project enables collaborative research that will advance knowledge about how ecosystems respond to global ecological changes.
Associate Professor Eric Seabloom, an MSI Principal Investigator in the Department of Ecology, Evolution, and Behavior (EEB), and his University of Minnesota colleagues, Associate Professor Elizabeth Borer and Dr. Eric Lind (both also in EEB) coordinate the NutNet collaboration. The researchers use MSI resources to run data-processing scripts and to host the mySQL database for the global experiment collaboration. They have also used MSI nodes for retrieving and processing data-intensive projects such as sub-daily weather data for all the NutNet sites over multiple years. They are planning to further automate data handling and quality control, develop advanced data metadata documentation, and develop web-based database capabilities.
Seabloom and his colleagues recently published two letters in the prestigious journal Nature that demonstrate that nutrient addition causes a loss of species diversity and that lower diversity grasslands become less stable. The news isn’t all-bad though; herbivores can reduce the negative effects of fertilization on diversity by consuming plants and increasing light availability.
• Borer, Elizabeth T., Eric W. Seabloom, Daniel S. Gruner, W. Stan Harpole, Helmut Hillebrand, Eric M. Lind, Peter B. Adler, et al. 2014. Herbivores and nutrients control grassland plant diversity via light limitation. Nature. 9 March 2014, published online ahead of print.
• Hautier, Yann, Eric W. Seabloom, Elizabeth T. Borer, Peter B. Adler, W. Stan Harpole, Helmut Hillebrand, Eric M. Lind, et al. 2014. Eutrophication weakens stabilizing effects of diversity in natural grasslands. Nature. 16 February 2014, published online ahead of print.
Image description: Left: Spring wildflowers with Nutrient Network fences, in the mountains of southeastern Australia. Right: Zebras and wildebeest graze near experimental enclosures in Tanzania, East Africa. (Photos and descriptions from National Science Foundation Discoveries website, “Herbivores + light = more plant biodiversity in fertilized grasslands,” March 10, 2014, downloaded April 4, 2014.)
posted on April 16, 2014
MSI researchers will present posters of their work at the 2014 MSI Research Exhibition on Thursday, April 24, 1:30-3:30 p.m., on the fourth floor of Walter Library. This is the fifth year that MSI has held this event.
Everyone is invited! This is an excellent opportunity to find out about the research being done among other groups and to make connections for future collaborations.
The posters will be judged by a panel of faculty members who are MSI Principal Investigators and prizes will be awarded. Posters compete in one of two categories, Physical Sciences and Engineering or Biological and Medical Sciences. Entrants are from a wide variety of disciplines.
Light refreshments will be served. More information can be found on the 2014 Research Exhibition webpage.
The pictures above were taken at the 2013 MSI Research Exhibition.
posted on April 2, 2014
The research group of Professor Steven Girshick (MSI Fellow; Mechanical Engineering) uses MSI to support their development of computational models of gas plasmas in which nanoparticles nucleate and grow. These plasmas have industrial applications, such as semiconductor processing and materials synthesis. As part of this research, the Girshick group, along with the research group of Regents Professor Donald Truhlar (MSI Fellow; Chemistry) and Professor Mark Kushner (University of Michigan), are developing a cyber platform that will integrate models of particle nucleation and aerosol dynamics together with a detailed plasma kinetics model. This model incorporates quantum mechanical calculations of properties and reactivities and will be optimized for parallel computation on high-performance computing (HPC) systems. It will include a user-friendly graphical user interface and will be useful for students, researchers, and industrial designers.
Dr. David Porter and Brent Swartz of the MSI staff are assisting with this project, helping develop the cyberinfrastructure components. These include: an integrated graphical user interface, a parallel and optimized version, and an automated post-processing pipeline which spans a heterogeneous mix of HPC platforms and high-end graphics generation and display systems. The project uses high-end HPC computational and visualization resources and specialized software.
This project is funded by the National Science Foundation.
Image description: Left: Particle size distribution and average particle charge in a plasma afterglow, from a simulation. Right: Plasma in experimental system designed for model validation.
posted on March 19, 2014
Cilia and flagella are small, hairlike protrusions that are found on the surface of a cell body. They can be sense organs, or they can move, beating in a coordinated motion to either move the cell or to move liquids or small solids across the cell surface. A disease known as primary ciliary dyskinesia (PCD) can cause a number of human disorders. One of these is chronic destructive airway disease, where the cilia of the respiratory system are unable to move mucus out of the airways, and male infertility caused by poor movement of sperm flagella.
Professor Mary Porter (Genetics, Cell Biology, and Development) and her research group and collaborators are studying the proteins that regulate the activity of dynein motors in cilia and flagella. They are using software available through MSI to analyze and compare wild-type and mutant strains in the Chlamydomonas, a type of algae that moves using flagella. Results from studying Chlamydomonas can be applied to research in humans.
In research published last year in the journal Nature Genetics, Professor Porter and her colleagues discovered genetic mutations that are involved in PCD pathogenesis (“The nexin-dynein regulatory complex subunit DRC1 is essential for motile cilia function in algae and humans,” M. Wirschell, H. Obrich, C. Werner, D. Trischler, R. Bower, W.S. Hale, N.T. Loges, P. Pennekamp, S. Lindberg, U. Stenram, B. Carlen, E. Horak, G. Kohler, P. Nurnberg, G. Nurnberg, M.E. Porter, and H. Omran, Nature Genetics 45, 262-268 (2013)). They have identified the DRC1 subunit of the nexin-dynein regulatory complex, and showed that mutations disrupting DRC1 result in defects that can cause cilia to be defective. This is the first direct evidence that mutations in DRC genes cause human disease.
Image description: Diagrams of the DRC1 subunit in Chlamydomonas (top) and its human counterpart CCDC164 (bottom). The coiled-coil motifs are shown in dark gray. The positions of the protein alterations identified in algae and human are indicated with arrows. (Image and description from M. Wirschell et al., Nature Genetics 45, 262-268 (2013). © Nature Genetics)
posted on March 5, 2014