Kateri H. DuBayAssistant Professor of Chemistry
The design of self-assembling nanomaterials stands as one of the great challenges in modern molecular science. The DuBay group employs theoretical and computational tools to address this challenge through investigations that lie at the intersection of soft condensed matter physics, polymer chemistry, biophysics, and nanomaterials.
At these very small length scales, the effects of thermal fluctuations, entropy, energy, and kinetics are often comparable in magnitude, rendering materials highly sensitive to perturbations such as chemical doping and environmental changes. While a wide variety of useful structures can be made via self-assembly within a static environment by precisely tuning the interactions between assembling components, environmental controls give us the means to advance beyond the limitations of such endeavors. Biological systems provide a host of examples, demonstrating the remarkable complexity and high responsivity of materials formed via environmentally-directed assembly. Specifically our group looks at assembly within environments that vary either in space, such as in the presence of a chemical gradient, or in time, such as in response to biological signaling.
Given the physical length-scales of the systems we study and the time-scale over which they evolve, we design theoretical models to capture the essential physics of the studied phenomenon. Such schematic models leave out unnecessary details in order to isolate the factors of interest and enable us to probe more directly the fundamental questions surrounding the emergence of order and responsivity within the studied nanoassemblies.
An improved understanding of the rules governing assembly in these environments will yield novel insights into the formation of functional biomaterials as well as information useful for improving light harvesting, drug-delivery, environmental-sensing, and material fabrication; countless technological innovations await the ability to rationally design artificially-ordered and environmentally-responsive nanomaterials.
Construction of Donor-Acceptor Polymers via Cyclopentannulation of Poly (arylene ethynylene)s. X Zhu, S.R. Bheemireddy, S.V. Sambasivarao, P.W. Rose, R. Torres Guzman, A.G. Waltner, K.H. DuBay, and K.N. Plunkett. Macromolecules, 49 (1), 127-133 (2016).
Fluctuations within Folded Proteins: Implications for Thermodynamic and Allosteric Regulation. K.H. DuBay, G.R. Bowman, P.L. Geissler, Accounts of Chemical Research, 48 (4), pp 1098–1105 (2015).
A First-Principles Polarized Raman Method for Determining Whether a Uniform Region of a Sample is Crystalline or Isotropic. A.L. Weisman, K.H. DuBay, K.A. Willets, R.A. Friesner, The Journal of Chemical Physics 141(22), 224702 (2014).
Impact of Molecular Symmetry on Single-Molecule Conductance. E. J. Dell, B. Capozzi, K. H. DuBay, T. C. Berkelbach, J. R. Moreno, D. R. Reichman, L. Venkataraman, and L. M. Campos. J. Am. Chem. Soc. 135:32, 11724-27 (2013).
Chromophore-Controlled Self-Assembly of Highly Ordered Polymer Nanostructures. M. C. Traub, K. H. DuBay, S. E. Ingle, X. Zhu, K. N. Plunkett, D. R. Reichman, and D. A. Vanden Bout. J. Phys. Chem. Lett. 4:15, 2520-4 (2013).
Accurate Force Field Development for Modeling Conjugated Polymers. K. H. DuBay, M. L. Hall, T. F. Hughes, C. Wu, D. R. Reichman, and R. A. Friesner. J. Chem. Theory. Comput. 8, 4556-69 (2012).
Polarized Raman Spectroscopy of Oligothiophene Crystals to Determine Unit Cell Orientation. J. C. Heckel, A. L. Weisman, S. T. Schneebeli, M. L. Hall, L. J. Sherry, S. M. Stranahan, K. H. DuBay, R. A. Friesner, and K. A. Willets. J. Phys. Chem. A 116, 6804-16 (2012).
Long-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations Alone. K. H. DuBay, J. P. Bothma, and P. L. Geissler. PLoS Comput. Biol. 7:9, e1002168 (2011).
Andreas GahlmannAssistant Professor of Chemistry and Molecular Physiology and Biological Physics
One key area in understanding bacterial cell biology is spatiotemporal phenomena: Where, when, and how do individual biomolecules act and interact to govern the overall physiology of the cell? To answer this question, we develop new high-resolution imaging methods for 3D single-molecule localization in intact bacterial cells. In particular, we combine the resolving power of the electron microscope with the single-molecule sensitivity and specificity of fluorescence-based methods. With these tools, we can localize single biomolecules in 3D space with a precision of a few nanometers, track their motion over time, and then zoom in further to visualize how specific biomolecules combine with others to produce functioning assemblies in their native environment.
Bacteria are highly relevant to important challenges of our time. For example, the looming inability to effectively combat pathogenic bacteria with current antibiotics presents a major health concern. Finding new avenues to selectively target and alter key molecular pathways can provide us with further options for effective antibiotic drug development. Because bacteria are the smallest and arguably the simplest living organisms on the planet, they are also fundamentally interesting to study the molecular-level biology of the cell. Bacteria are able to precisely regulate protein activity throughout the intracellular space through finely tuned molecular interactions. Of particular importance are scaffolding proteins that partition the cytoplasm and provide specialized subcellular compartments for specific biochemical reactions to occur. On a smaller scale, scaffolding proteins are hypothesized to spatially organize multiple enzymes into biomolecular assemblies. Parts of these assemblies can be highly dynamic and therefore the precise architectures and the resulting functional consequences remain elusive.
Rapid progress of evolution has made the bacteria an extremely diverse and widely abundant group of single-celled organisms that affects almost every aspect of life on earth. The resulting bacterial physiological traits present a biological treasure trove that remains to be investigated with molecular resolution and, where possible, exploited to our benefit. With this in mind, we continue to push the limits of cellular imaging, as well as in situ structural characterization of biomolecular assemblies.
Single-molecule tracking in live Yersinia enterocolitica reveals distinct cytosolic complexes of injectisome subunits. J. Rocha, C. Richardson, M. Zhang, C. Darch, E. Cai, A. Diepold, A. Gahlmann, Integrative Biology, 2018, 10, 502 (Cover Article)
BACT-3D: A level set segmentation approach for dense multi-layered 3D bacterial biofilms. J. Wang, R. Sarkar, A. Aziz, A. Vaccari, A. Gahlmann, S. Acton, 2017 IEEE International Conference on Image Processing (ICIP)
Bacterial Scaffold Directs Pole-Specific Centromere Segregation. J.L. Ptacin, A. Gahlmann, G.R. Bowman , A.M. Perez, A.R.S. von Diezmann, M.R. Eckart, W.E. Moerner, and L. Shapiro. Proc. Natl. Acad. Sci. USA, 2014, 111, E2046
Exploring Bacterial Cell Biology with Single-Molecule Tracking and Super-Resolution Imaging. A. Gahlmann and W.E. Moerner. Nat. Rev. Microbiol., 2013, 12, 9 (Cover Article)
Quantitative Multicolor Subdiffraction Imaging of Bacterial Protein Ultrastructures in Three Dimensions. A. Gahlmann, J.L. Ptacin, G. Grover, S. Quirin, A.R.S. von Diezmann, M.K. Lee, M.P. Backlund, L. Shapiro, R. Piestun, and W.E. Moerner. Nano Lett., 2013, 13, 987
Direct Structural Determination of Conformations of Photoswitchable Molecules by Laser Desorption-Electron Diffraction. A. Gahlmann, I-R. Lee, and A.H. Zewail. Angew. Chem. Int. Ed., 2010, 49, 6524
Michael HilinskiAssistant Professor of Chemistry
The science of organic synthesis is central to both the discovery and manufacturing of pharmaceuticals and other fine chemicals and the emergence of subdisciplines of biology that are becoming increasingly focused on phenomena at the molecular level (e.g., synthetic biology and chemical biology). Over the last half-century revolutionary advances in synthetic organic chemistry have made it possible to synthesize virtually any molecule given enough time, money, and manpower. However, this is frequently not enough since a lack of practical and cost-effective synthetic access can and does prevent promising drug leads from ever helping patients. The grand challenge for synthetic organic chemistry is therefore to advance the field of synthesis to the point where any molecule can be not only synthesized, but also synthesized in a way that minimizes the cost, time, and manpower required as well as environmental impact. Our group’s research is focused on eliminating synthetic considerations as a barrier to the discovery of new therapeutics.
Organocatalytic, Dioxirane-Mediated C-H Hydroxylation under Mild Conditions Using Oxone. W. G. Shuler, S. L. Johnson, M. K. Hilinski, Org. Lett. 2017, 19, 4790–4793. An Iminium Salt Organocatalyst for Selective Aliphatic C–H Hydroxylation. D. Wang, W. G. Shuler, C. J. Pierce, M. K. Hilinski, Org. Lett. 2016, 18, 3826–3829. Intermolecular Electrophilic Addition of Epoxides to Alenes: [3+2] Cycloadditions Catalyzed by Lewis Acids. W. G. Shuler, L. A. Combee, I. D. Falk, M. K. Hilinski, Eur. J. Org. Chem. 2016, 3335–3338. Chemoselective Hydroxylation of Aliphatic sp3 C–H Bonds Using a Ketone Catalyst and Aqueous H2O2. C. J. Pierce, M. K. Hilinski, Org. Lett. 2014, 16, 6504–6507.
Brooks H. PateWilliam R. Kenan, Jr. Professor of Chemistry
Vibrational Dynamics and the Spectroscopy of Highly Excited Molecules
Our group studies the dynamics of molecules with significant amounts of vibrational energy. The flow of vibrational energy in a molecule, a process known as intramolecular vibrational energy redistribution (IVR), lies at the heart of chemical reactivity. We study the kinetics of energy flow in isolated molecules and molecules in solution. A major emphasis of our work is understanding the spectroscopy of molecules as the IVR process, and possibly reaction, occurs. In particular, we are interested in how coherent excitation of highly excited molecules can be used to influence reaction products.
We have developed a new type of molecular spectroscopy called dynamic rotational spectroscopy to study isomerization reactions of isolated molecules. The basis of rotational (or microwave) spectroscopy is that the geometry determines the measured rotational frequencies. When the molecule has more energy than the barrier to isomerization, reaction can occur and the geometry becomes time dependent. As a result, the rotational frequency is modulated by the reaction rate. When the reaction causes the frequency to switch between the characteristic values of the reactant and product, the spectrum undergoes the phenomenon known as coalescence. Therefore, the isomerization kinetics can be investigated through the changes in the line shape of the rotational spectrum. We have developed new high-resolution, molecular-beam spectroscopy techniques to obtain the rotational spectrum of single quantum states of a highly excited molecule. These measurements combine ultrasensitive infrared laser spectroscopy methods with strong-field microwave excitation. Application of this technique to conformational isomerization reactions has shown that this class of reactions violates the predictions of quantum transition state theory. We are presently developing new techniques to improve our sensitivity for single quantum state measurements and to extend our measurements to higher energy. A more complete description of the projects we are currently pursuing can be found on our research group web pages.
The second area of research in our group investigates the vibrational dynamics of molecules in dilute solution. Using our molecular-beam spectroscopy techniques we can quantitatively measure energy flow rates for the isolated molecule. Our goal for solution phase studies is to understand how solvent molecules modify the dynamics and reactivity of the isolated molecule. This work is performed in the Ultrafast Laser Facility that is part of the university's SELIM program. We have an impressive array of laser tools available for this work including a two-color femtosecond laser system, a two-color picosecond laser system, and a 32-element infrared array detector for multichannel detection. Our first studies have shown that the basic features of isolated molecule IVR dynamics are preserved in solution. In particular, we have found that a new relaxation channel opens for large molecules that correlates with the onset of fast IVR in the isolated system. From this work, we can identify a time window where the molecule in solution retains the energy deposited by the laser (i.e., before interaction with the solvent causes conversion of the internal energy to heat). Knowing this time scale gives us a window of opportunity to study the spectroscopy and kinetics of the vibrationally hot molecule. Examples of our recent work in this area, as well as descriptions of projects planned for the near future, can be found on our research web pages.
Broadband Fourier transform rotational spectroscopy for structure determination: The water heptamer. Perez C, Lobsiger S, Seifert NA, Zaleski DP, Temelso B, Shields GC, Kisiel Z, Pate BH. Chem. Phys Let. 571:1-15 (2013).
High-Resolution Electronic Spectroscopy of the Doorway States to Intramolecular Charge Transfer. Fleisher AJ, Bird RG, Zaleski DP, Pate BH, Pratt DW. J. Phys. Chem B. 117:4231-4240 (2013).
. Pate BH, Seifert NA, Guirgis GA, Deodhar BS, Klaassen JJ, Darkhalil ID, Crow JA, Wyatt JK, Dukes HW, Durig JR. Chemical Physics. 416: 33-42 (2013).
The detection of interstellar ethanimine (CH3CHNH) from observations taken during the GBT PRIMOS survey. Loomis RA, Zaleski DP, Steber AL, Neill JL, Muckle MT, Harris BJ, Hollis JM, Jewell PR, Lattanzi V, Lovas FJ, Martinez O, McCarthy MC, Remijan AJ, Pate BH, Corby JF. Astrophysical Journal Letters. 765:L9 (2013).
Detection of E-cyanomethanimine towards Sagittarius B2(N) in the Green Bank Telescope PRIMOS Survey. Zaleski DP, Seifert NA, Steber AL, Muckle MT, Loomis RA, Corby JF, Martinez O, Crabtree KN, Jewell PR, Hollis JM, Lovas FJ, Vasquez D, Nyiramahirwe J, Sciortino N, Johnson K, McCarthy MC, Remijan AJ, Pate BH. Astrophysical Journal Letters. 765:L10 (2013).
Lin PuProfessor of Chemistry
Organic, Polymer and Organometallic Chemistry; Asymmetric Catalysis; Chiral Sensors; Optically Active Materials
Multi-disciplinary research programs involving organic synthesis, molecular recognition, fluorescent sensing, asymmetric catalysis, and polymers are conducted in our laboratory. The 1,1′-bi-2-naphthol (BINOL) and its derivatives are chosen as the chiral building blocks to construct novel chiral molecules and macromolecules for diverse applications. We have developed a family of enantioselective fluorescent sensors for the recognition of organic molecules such as alpha-hydroxycarboxylic acids, amino acids, amino alcohols, and amines. These sensors are potentially useful for rapid assay of the enantiomeric composition of chiral compounds and for high throughput chiral catalyst screening. They are also potentially useful for biological analysis and imaging. New chiral conjugated polymers and dendrimers are prepared for applications in materials, catalysis, and sensing. We have discovered that the Lewis acid complexes of the optically active binaphthyl molecules and polymers can carry out highly enantioselective organic reactions such as organozinc additions to aldehydes, hetero-Diels-Alder reactions, 1,3-dipolar cycloadditions, reductions of ketones, Michael additions, epoxidations, and others. Interesting chiral organic molecules including those of biological functions are prepared by using these catalysts.
Enantioselective Fluorescent Sensors
Simultaneous Determination of Concentration and Enantiomeric Composition in Fluorescent Sensing. Lin Pu. Acc. Chem. Res. 2017, 50, 1032-1040.
Regiospecific Hydration of N-(Diphenylphosphinoyl)propargyl amines: Synthesis of b-Amino Ketones by Au(III) Catalysis. Ying, J.; Pu, L. J. Org. Chem. 2016, 81, 8135−8141. A Featured Article. Highlight on the cover.
Conjugated polymer-enhanced enantioselectivity in fluorescent sensing. Zhang, X. –P.; Wang, C.; Wang, P.; Du, J. –J.; Zhang, G. –Q.; Pu, L. Chem. Sci. 2016, 7, 3614–3620.
Rational Design of a Fluorescent Sensor to Simultaneously Determine Both the Enantiomeric Composition and Concentration of Chiral Functional Amines. Wen, K. –L.; Yu, S. –S.; Huang, Z.; Chen, L. –M.; Xiao, M.; Yu, X. –Q.; Pu, L. J. Am. Chem. Soc. 2015, 137, 4517-4524.
Asymmetric Functional Organozinc Additions to Aldehydes Catalyzed by BINOLs. Pu, L. Acc. Chem. Res. 2014, 47, 1523–1535.
Zn(II) Promoted Dramatic Enhancement in the Enantioselective Fluorescent Recognition of Chiral Amines by a Chiral Aldehyde. Huang, Z.; Yu, S. S.; Yu, X. Q.; Pu. L. Chem. Sci. 2014, 5, 3457-3462.
Enantioselective Fluorescent Sensors: A Tale of BINOL. Pu, L. Acc. Chem. Res. 2012, 45, 150–163.
Simultaneous Determination of Both the Enantiomeric Composition and Concentration of a Chiral Substrate with One Fluorescent Sensor. Yu, S.; Plunkett, W.; Kim, M.; Pu, L. J. Am. Chem. Soc. 2012, 134, 20282–20285. A spotlight article reported in J. Am. Chem. Soc., 2013, 135 (3), 949–950.