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Fluorescent chromophores are compounds that can emit light under certain circumstances. They are useful to chemists as dyes or markers, and can be used for such applications as medical and biological imaging.
In a recent paper that appeared in the Journal of the American Chemical Society, Professor Victor Nemykin (Chemistry and Biochemistry, University of Minnesota Duluth) and his collaborators at the University of Akron (Akron, Ohio) discuss a new fluorescent chromophore, or fluorophore, called BOPHY. (BOPHY stands for bis(difluoroboron)1,2-bis(1H-pyrrol-2-yl)methylene)hydrazine.) This compound is related to a very successful class of fluorophores already in use, the boron dipyrromethene family of compounds. BOPHY is important because it can be produced with a simple two-step procedure, and it is highly fluorescent.
The researchers studied two compounds, the BOPHY chromophore and a tetrameythyl-substituted BOPHY analogue called Me4BOPHY. They investigated the absorption and emissions spectra of these compounds using density functional theory (DFT) and time-dependent DFT (TDDFT) calculations. The graphs on the right side of the figure above show the (top) experimental and (middle, bottom) TDDFT-predicted absorption spectra of (left) 2 and (right) 4 in dichloromethane, showing the excellent agreement between theory and experiment. The left of the figure shows a schematic of BOPHY (2) and Me4BOPHY (4) (top) and their fluorescence property.
This paper first appeared on the JACS website in April 2014. It was published in the April 16, 2014 print edition of the journal (Tamgho, Ingrid-Suzy, Abed Hasheminasab, James T. Engle, Victor N. Nemykin, and Christopher J. Ziegler. 2014. A new highly fluorescent and symmetric pyrrole-BF2 chromophore: BOPHY. Journal of the American Chemical Society 136 (15) (APR 16): 5623-6).
posted on August 6, 2014
Nanostructures are devices built on an extremely tiny scale - a nanometer is one-billionth of a meter. Materials at this scale show unique properties that affect how they behave. These properties mean than nanomaterials may be useful for novel and interesting applications, but we need to understand how to work with them and how they will react.
One feature of nanomaterials is that they seem to have a random (stochastic) response when subjected to external loading. In a recent paper that appeared in the Proceedings of the National Academy of Science of the USA, two MSI Principal Investigators, Associate Professor Ryan Elliott and Professor Ellad Tadmor, worked with Subrahmanyam Pattamatta to investigate this behavior. The authors are in the Department of Aerospace Engineering and Mechanics in the College of Science and Engineering. Because standard simulation methods are insufficient to deal with the complex behavior of nanomaterials, the authors developed a new method to simulate this behavior. They created an equilibrium map (EM) that characterizes the material's responses. This EM-based approach allows for simulation of nanostructure experiments. The paper shows how the method works in the case of a nanoslab of nickel. The paper can be found on the PNAS website: Pattamatta, Subrahmanyam, Ryan Elliott, and Ellad Tadmor. 2014. Mapping the stochastic response of nanostructures. Proceedings of the National Academy of Science of the USA 111(17):E1678-E1686. Published online before print.
Professor Elliott and his research group use MSI for research into objective structures using a parallel code. The group is investigating the scalability and performance of the code. Professor Tadmor and his group are developing an optimal and parallel version of the quasicontinuum method, which is a multiscale technique based on the idea of representative atoms and finite element interpolation.
Image description: A schematic of the possible behaviors of a compressed nickel nanoslab. As the compression increases with time, the initially perfect structure (bottom) develops defects associated with minima on its evolving potential energy surface. The sequence of states observed in repeated experiments on nominally identical nanostructures is highly stochastic and rate dependent. Each colored line in the figure represents one such realization obtained using a new computational method described in the paper by S. Pattamatta et al.. Image courtesy of Subrahmanyam Pattamatta, Ryan Elliott, and Ellad Tadmor.
posted on July 23, 2014
In the ongoing study of viruses, researchers are using powerful computer resources to create visualizations of virus structures. MSI Principal Investigator Wei Zhang, a research assistant professor in the Department of Diagnostic and Biological Sciences (School of Dentistry), is investigating several viruses by using cryoelectron microscopy and creating three-dimensional reconstructions of their structures using advanced software.
In a recent paper that appeared in the Proceedings of the National Academy of Sciences of the USA, Professor Zhang and Research Associate Dr. Sheng Cao described how they were able to create visualizations of an intermediate step in membrane fusion, using the Sindbis virus, a prototypical alphavirus. (Sheng Cao and Wei Zhang. 2013. Characterization of an early-stage fusion intermediate of Sindbis virus using cryoelectron microscopy. Proceedings of the National Academy of Sciences of the United States of America 110 (33) (AUG 13): 13362-7.) The authors created an environment where the virus could bind with liposomes, took electron micrographs of the virus-liposome complex, and generated three-dimensional reconstructions. These 3D images show the structure of an early-stage fusion intermediate of an enveloped virus and may be beneficial in determining target locations for antiviral drugs. The authors have placed the reconstructions in the EMDataBank (www.emdatabank.org), an online resource for storing and sharing electron microscopy images.
Professor Zhang also uses MSI resources to study the human T-lymphotropic virus type 1 (HTLV-1), which is responsible for a number of disorders including adult T cell leukemia/lymphoma and HTLV-1 associated myelopathy/tropical paraperesis. As they did with the Sindbis virus, the Zhang group uses cryoelectron microscopy and three-dimensional reconstruction to study the structure of HTLV-1. This work may provide insights that will help in drug design.
Image description: Cryo-EM image and reconstruction of Sindbis viruses (SINV). (A-B) 3D reconstruction and cross-section of SINV (Zhang, W., S. Mukhopadhyay, S. V. Pletnev, T. S. Baker, R. J. Kuhn, M. G. Rossmann. 2002. Placement of the structural proteins in Sindbis virus. J. Virol. 76:11645-11658). (C) Image of the SINV viral particles (arrows) attached to a liposome (L) at acidic pH (Sheng Cao and Wei Zhang. 2013. Characterization of an Early-Stage Fusion Intermediate of Sindbis Virus using Cryo-electron Microscopy. PNAS 110: 13362-13367).
posted July 9, 2014
People have always talked about the weather, but these days weather and climate have become a major topic for discussion. Extreme weather events throughout the country and the world lead news stories and many people are concerned with what is causing these events and how the climate may be changing.
Assistant Professor Peter Snyder (Soil, Water, and Climate) is using MSI to support his work examining how climate change will affect extreme precipitation and severe weather in the central U.S. over the next century. The group uses the Weather Research and Forecasting (WRF) model, which is ideal for examining future changes in drought both because simulations with extremely high spatial and temporal resolution can effectively resolve the physical processes that drive precipitation processes and the model can efficiently represent synoptic-scale dynamical motion (e.g., blocking highs) that contribute to initiation and persistence of drought. This model is especially valuable for simulating events in the central region of the U.S., where severe weather and extremes in precipitation happen often. This region is the home of major agricultural production, so changes in climate and increases in drought may have significant effects on food security.
In a recent paper, Professor Snyder and members of his research group investigated whether dynamical downscaling could improve the WRF’s simulation capabilities for precipitation extremes. Their results showed a positive affect on the model’s results, which could mean that it would be easier to make predictions about rainfall. The researchers were able to use models that performed well to predict how rainfall might change over the Midwest in different climate-change scenarios. This work also provided some indications about the mechanisms that contribute to the intensification of heavy precipitation events. The paper appeared in November 2013 in the Journal of Geophysical Research - Atmospheres (Harding, Keith J., Peter K. Snyder, and Stefan Liess. 2013. Use of dynamical downscaling to improve the simulation of central US warm season precipitation in CMIP5 models. Journal of Geophysical Research: Atmospheres 118 (22) (NOV 27): 12522-36). Professor Snyder and his research group are continuing their research at MSI, performing additional simulations using different datasets. These simulations will provide insights into how droughts in the Midwest might change in the future and how they might impact water resources and food security.
The Snyder group is also participating in a study of the phenomenon of “urban heat islands,” which is a situation where cities have higher temperatures that the surrounding areas. The study, called Islands in the Sun, is a four-year project funded by the University of Minnesota Institute on the Environment and the College of Food, Agricultural, and Natural Resource Sciences. An article about this study recently appeared in the Minnesota Daily (Kristopher Teague, “Can’t take the heat? Get out of the city,” Minnesota Daily, May 6, 2014, online, downloaded May 7, 2014.)
Image description: The 1979–2005 June-July-August (a and b) precipitation (mm), (c and d) 850 hPa wind speed (m s−1). Figures a and c show the average of all observational (or reanalysis) datasets for each variable. Figure b shows the multimodel ensemble (MME) mean minus observations, while Figure d shows the MME mean. Image and description adapted from Harding, KJ, et al., Journal of Geophysical Research: Atmospheres, 118(22):12522-12636 (2013). © American Geophysical Union.
posted on June 18, 2014
Associate Professor Jeff Schwinefus, who is a faculty member at St. Olaf College in Northfield, Minnesota, is a physical chemist investigating the role of naturally occurring organic molecules in the hydration and stability of nucleic acids. He and his students perform experiments in the lab and also use molecule dynamics (MD) simulation techniques. This is interdisciplinary research that involves chemistry, biology, and physics.
The Schwinefus group’s research at MSI studies the cosolutes glycine betaine, proline, and urea, which all destabilize DNA and RNA secondary structures. The cosolutes interact with the nucleic acid surface area exposed during unfolding. The group is using lab work and MD simulations to understand this process.
Professor Schwinefus, members of his research group, and colleagues at the University of Wisconsin-Madison, published a recent paper about their work in the Journal of the American Chemical Society (Guinn, Emily J., Jeffrey J. Schwinefus, Hyo Keun Cha, Joseph L. McDevitt, Wolf E. Merker, Ryan Ritzer, Gregory W. Muth, Samuel W. Engelsgjerd, Kathryn E. Mangold, Perry J. Thompson, Michael J. Kerins, and M. Thomas Record. 2013. Quantifying functional group interactions that determine urea effects on nucleic acid helix formation. Journal of the American Chemical Society 135 (15) (APR 17): 5828-38). This paper investigated urea as a destabilizing agent of the helical and folded conformations of nucleic acids and proteins as well as protein-nucleic acid complexes. Their results demonstrated that urea can be used as a quantitative probe of conformational changes in nucleic acid processes.
Image description: Interaction potentials quantifying interactions of urea with unit surface areas of nucleic acid functional groups (heterocyclic aromatic ring, ring methyl, carbonyl and phosphate O, amino N, sugar (C and O)); urea interacts favorably with all these groups. Image and description taken from Guinn, EJ, et al., 2013. JACS 135(15): 5828-38. © American Chemical Society
Posted on June 4, 2014.