Kateri H. DuBayAssociate 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 GahlmannAssociate 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
Ian HarrisonProfessor of Chemistry
Surface Chemistry: Catalysis, Photochemistry, Reaction Kinetics & Dynamics
Catalysis is an essential technology supporting our way of life and contributes towards roughly 1/3 of the material GDP of the US economy. At the beginning of the 20th Century, the catalytic transformation of nitrogen on nanoscale, potassium promoted, iron catalysts to ammonia, and ultimately fertilizer, profoundly changed the human condition and currently supports an additional 2.4 billion people beyond what the Earth could otherwise sustain. In the 21st Century, the catalytic challenge will be to facilitate a rapid transition from a petroleum-based energy and chemical economy to a more generalized one based on natural gas, hydrogen, coal, biomass, and solar energy (photochemistry). Energy efficient chemical transformations, environmental protection, and green chemistry will continue to rely heavily on catalysis. Most industrially viable catalysis takes place on the surfaces of transition metal nanocrystallites dispersed on oxide supports. Our research focuses on understanding gas-surface reactions on simplified scientific model surfaces, namely, on single crystal surfaces. Recent progress includes the development of quantitative models for (i) the C-H bond activation of CH4 on metal surfaces that relates to the industrial production of H2 via natural gas reforming on metal nanocatalysts, and (ii) the chemical vapor deposition of Si on Si (100) by SiH4 that is central to Si homoepitaxy in microelectronics manufacturing. Current activities focus on exploring the thermal and photochemical reaction dynamics of catalytically important and energy-related small molecules, such as H2, CO2, CH4, alkanes, and alcohols, on transition metal surfaces. Our research typically employs ultrahigh vacuum surface analytical techniques (e.g., TPD, AES, XPS, RAIRS, STM, LEED) as well as some more specialized laser techniques (SFG, TOF) and/or microcanonical unimolecular rate theory. Our goal is to characterize the transition states of important catalytic reactions and to develop an improved understanding of how to design efficient & selective thermal and photochemically driven catalysts.
Rice−Ramsperger−Kassel−Marcus Simulation of Hydrogen Dissociation on Cu(111): Addressing Dynamical Biases, Surface Temperature, and Tunneling. Donald SB and. Harrison I. J. Phys. Chem. C, 118, 320-337 (2014).
Methane dissociative chemisorption and detailed balance on Pt(111): Dynamical constraints and the modest influence of tunneling. Donald SB, Navin JK and Harrison I. J. Chem. Phys. 139, 214707 (2013).
Communication: angle-resolved thermal dissociative sticking of CH4 on Pt(111): further indication that rotation is a spectator to the gas-surface reaction dynamics. Navin JK, Donald SB, Tinney DG, Cushing GW, Harrison I. J Chem Phys. 136:061101 (2012).
Dynamically biased RRKM model of activated gas-surface reactivity: vibrational efficacy and rotation as a spectator in the dissociative chemisorption of CH4 on Pt(111). Donald SB, Harrison I. Phys Chem Chem Phys. 214:1784-95 (2012).
An effusive molecular beam technique for studies of polyatomic gas-surface reactivity and energy transfer. Cushing GW, Navin JK, Valadez L, Johánek V, Harrison I. Rev Sci Instrum. 82(4):044102 (2011).
James P. LandersCommonwealth Professor in the Departments of Chemistry, Mechanical Engineering and Pathology
Polyethylene Terephthalate Microdevices
Our research group has developed a technique for fabricating microfluidic devices with complex multilayer architectures using a laser printer, a CO2 laser cutter, an office laminator, and common overhead transparencies as a printable substrate via a laser print/cut and laminate (PCL) methodology. The printer toner serves three functions; (1) it defines the microfluidic architecture, (2) acts as the bonding agent, and (3) provides printable, hydrophobic "valves" for fluidic flow control. Using common graphics software, the protocol produces microfluidic devices with a design-to-device time of ~40 min. Devices of any shape can be generated for an array of multistep assays with colorimetric detection of molecular species ranging from small molecules to proteins. The simplicity of the protocol, availability of the equipment and substrate and cost-effective nature of the process make microfluidic devices available to those who might benefit most from expedited, microscale chemistry.
Figure 1. A microfluidic chip designed to dispense sample and mix reagents by rotating at varying speeds. This specific device is used to measure albumin concentration, white blood cell count, and hematocrit in whole blood.
Biological, Bioanalytical and Clinical Chemistry
Almost every aspect of the biochemical, biomedical and clinical sciences involves separation of species in complex matrices. Electrophoresis has been a benchmark technique for separation and characterization of biologically-active species. Instead of using conventional slab gel electrophoretic approaches, electrophoresis in micron-scale capillaries using applied fields as high as 30,000 volts, results in unprecedented resolution with unique selectivities and short analysis times. As a result of the microscalar nature of the capillary, only microliters of reagent are consumed by analysis with only a few nanoliters of samples injected for analysis. These characteristics, as well as the ability for on-line detection with laser-induced fluorescence sensitivities in the attomole (10-18 moles) range, made capillary electrophoresis (CE) appealing as a replacement for electrophoretic gels in the biomedical and clinical arenas. We have demonstrated the potential impact of CE on clinical diagnostics through the development of new CE-based assays for measuring kidney function, detecting multiple sclerosis and viral infections, screening for lymphoma, as well as for diagnosing drug abuse and alcoholism.
While the diagnostic impact of standard CE technology is clear, an alternative platform for electrophoresis in microscalar structures has evolved in the form of microchip electrophoresis. The use of microfabricated glass devices containing etched capillary-like channels provides an electrophoretic platform akin to CE but with more flexibility. “Microchip electrophoresis” allows for analysis times to be decreased by an order of magnitude over times achievable by CE (as fast as 10-200 seconds) and two orders of magnitude faster than gel electrophoresis. This provides obvious value to clinical diagnostic laboratories in terms of more rapid turn around time and capability for high throughput screening. We have demonstrated this with the detection T-cell and B-cell lymphoma in a separation remarkably faster than with conventional means.
Figure 2. Demonstration of microchip electrophoresis as a technique for rapid diagnosis of T-Cell lymphoma. Sample T1 shows a negative sample, which is represented by the smear after 100 seconds of separation. T4 is a positive sample with a sharp peak.
With a program focused on the application of miniaturized electrophoretic technology to the clinical and forensic sciences, our current efforts involve broadening the scope of applications for microchip technology. This involves addressing issues associated with integrating functions other than "separation" onto microchips. For example, we are focused on defining approaches for integrating DNA sample preparation into microchips. PCR amplification of DNA carried out using infrared-mediated thermocycling for rapid on-chip amplification and rapid DNA extraction using microchamber-bound solid phases are two examples of our integration efforts.
The successful integration of DNA extraction and amplification will lead to the development of an “Integrated Diagnostic” or ID-chip, which we ultimately hope will improve laboratory medicine. Efforts are also underway to 1) define better detection systems using acoustic-optic technology, 2) develop multichannel devices for high-throughput analysis using this optical technology, 3) explore proteomic aspects of disease using multi-dimensional microchips for protein separations, and 4) apply the relevant methods to forensic applications.
Simultaneous metering and dispensing of multiple reagents on passivelycontrolled microdevice solely by finger pressing. Xu K, Begley M, Landers JP. Lab on a Chip. 15: 867-876 (2015).
Integrated sample-in-answer-out microfluidic chip for Rapid HumanIdentification by STR analysis. Le Roux D, Root B, Reedy C, Hickey J, Scott O, Bienvenue J, Landers JP, Chassagne L, Mazancourt P. Lab on a Chip. 14:4415-4425 (2014).
DNA Analysis Using an Integrated Microchip for Multiplex PCRAmplification and Electrophoresis for Reference Samples. Le Roux D, Root B, Reedy C, Hickey J, Scott O, Bienvenue J, Landers JP, Chassagne L, Mazancourt P. Analytical Chemistry. 86:8192-8199 (2014).
Rapid, cost-effective DNA quantification via a visually-detectableaggregation of superparamagnetic silica-magnetite nanoparticles. Liu Q, Li J, Liu H, Tora I, Ide M, Lu J, Davis R, Green D, Landers JP. Nano Research. 7:755-764 (2014).
Dual-force aggregation of magnetic particles enhances label-freequantification of DNA at the sub-single cell level. Nelson D, Strachan B, Sloane H, Li J, Landers JP. Analytica Chimica Acta. 819:34-41 (2014).
Enhanced recovery of spermatozoa and comprehensive lysis of epithelialcells from sexual assault samples having a low cell counts or aged up to one year. Loundsbury J, Nambia S, Karlsson A, Cunniffe H, Norris J, Ferrance J, Landers JP. Forensic Science International: Genetics. 8:84-89 (2014).
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
Enantioselective Fluorescent Recognition of Free Amino Acids: Challenges and Opportunities. Pu, L. Angew. Chem. Int. Ed. 2020, 59, 21814-21828.
Free Amino Acid Recognition: A Bisbinaphthyl-Based Fluorescent Probe with High Enantioselectivity. Zhu, Y.-Y.; Wu, X.-D.; Gu, S.-X.; Pu, L. J. Am. Chem. Soc. 2019, 141, 175−181.
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.
Jelena SamoninaAssistant Professor of Chemistry, General Faculty
Dr. Jelena Samonina joined the faculty of the UVA Chemistry Department in 2019, where her teaching interests include Organic Chemistry and Chemistry for the Health Sciences. She earned her M.S. and her Ph.D. in Organic Chemistry at Warsaw University. After two postdoctoral trainings at the University of Virginia and at Stanford University she joined the faculty of Washington and Lee University.
Dr. Samonina is passionate about teaching and she designs her courses to motivate and excite students through proactive learning. Her teaching style effectively engages the students and encourage them to develop into future thinkers, inventors, and researchers, whether it be in industry, academia, or public service.
Dr. Samonina’s research interests lie at the interface of Organic and Polymer Chemistry, Nanomaterials and Medicine, and include the development of new concepts in drug delivery, imaging and diagnostics.
Sawyer C. W., Suffield B. H., Finnefrock A. C., Billings H. M., Uffelman E. S., Zoeller J. R., Dombrowski M. S., Delaney J.K., Dooley K. A., Mass J. L., Samonina J., Whitesell M. M., A John White Alexander Painting at the Virginia Museum of Fine Arts: A Comparison of Imaging Technologies for Resolving a Painting under Another Painting, Journal of American Institute for Concervation. 2019, 58, 37–53.
De Crisci A. G., Samonina-Kosicka J., Gieleciak R., Fleischauer M., Morris R. H., Waymouth R. M., Electrocatalytic Transfer Hydrogenation for Carbon Dioxide (CO2) Activation and Utilization” – 2018. Poster won first prize at the Connaught Global Challenge Symposium on CO2 Solution to Climate Change.
Butler, T.; Morris, W.; Samonina-Kosicka, J.; Fraser, C., Mechanochromic Luminescence and Aggregation Induced Emission of Dinaphthoylmethane β-Diketones and their Boronated Counterparts – ACS Applied Materials & Interfaces. 2016, 8, 1242–1251
Samonina-Kosicka, J.; Weitzel, D. H.; Hofmann, C. L.; Hendargo, H.; Hanna, G.; Dewhirst, M. W.; Palmer, G. M.; Fraser, C. L., Luminescent Difluoroboron β-Diketonate PEG-PLA Oxygen Nanosensors for Tumor Imaging. Macromolecular Rapid Communications 2015, 36, 694-699.
Butler, T.; Morris, W. A.; Samonina-Kosicka, J.; Fraser, C. L., Mechanochromic Luminescence and Aggregation Induced Emission for a Metal-Free Beta-Diketone. Chemical Communications 2015, 51, 3359-3362. - highlighted as "Noteworthy Chemistry" by ACS
DeRosa, C. A.; Samonina-Kosicka, J.; Fan, Z.; Hendargo, H. C.; Weitzel, D. H.; Palmer, G. M.; Fraser, C. L., Oxygen Sensing Difluoroboron Dinaphthoylmethane Polylactide. Macromolecules 2015, 48, 2967-2977.
Samonina-Kosicka, J.; Kańska, M., Synthesis of Selectively Labeled Histidine and its Methylderivatives with Deuterium, Tritium, and Carbon-14. Journal of Labelled Compounds and Radiopharmaceuticals 2013, 56, 317-320.
Kevin WelchAssociate Professor, General Faculty
Professor Kevin Welch is interested in developing curricula for undergraduate instruction in general chemistry and organic chemistry. In particular, his focus is on updating these courses to accommodate the diverse educational background in chemistry of the students enrolling in chemistry at the University of Virginia, as well as providing a strong chemical foundation for the students as they continue on in their educational and post-educational careers in a variety of fields. In the past, he has taught undergraduate courses in general chemistry, organic chemistry, inorganic chemistry, environmental chemistry, and scientific writing.
In addition to a focus on undergraduate education, Kevin’s interests in chemistry involve research investigating metal-ligand bonding interactions and the use of transition metal complexes to address challenges in fuel generation and energy storage.
A native of northern Virginia, Kevin received his B.S. in chemistry from Gettysburg College in 2002, and his Ph.D. in chemistry from the University of Virginia in 2007, where he focused on synthetic organometallic chemistry. He spent three years in central Washington as a Department of Energy Postdoctoral Researcher at the Pacific Northwest National Laboratory, working on the development of transition metal catalysts for energy storage and fuel cell technology. From 2010 to 2016, Kevin was a visiting assistant professor at Swarthmore College outside of Philadelphia, Pennsylvania, where he taught and conducted research with undergraduate students. He returned to the University of Virginia in the fall of 2016 and currently teaches courses in general chemistry and laboratories for organic chemistry.