Materials Chemistry

Cherie Kagan

Photo: 
First Name: 
Cherie
Last Name: 
Kagan
Official Title: 
Stephen J. Angello Professor
Additional Titles: 
Professor of Electrical And Systems Engineering
Professor of Materials Science and Engineering
Contact Information
Office Location: 
Room 254 Levine Hall
Email: 
kagan@seas.upenn.edu
Phone: 
(215) 573-4384
Education: 
  • Ph.D. Materials Science and Engineering, MIT 1996
  • B.S.E. Materials Science and Engineering, University of Pennsylvania 1991
  • B.A. Mathematics, University of Pennsylvania 1991
Research Interests: 

Cherie earned both a B.S.E. in Materials Science and Engineering and a B.A. in Mathematics from the University of Pennsylvania in 1991. In 1996, she received her Ph.D. in Electronic Materials from MIT. Her thesis work focused on the self-assembly of close packed solids of semiconductor nanocrystals and the unique electronic and optical properties that arise from cooperative interactions between neighboring nanocrystals. In 1996, Cherie went to Bell Laboratories as a Postdoctoral Fellow where she built a scanning confocal Raman microscope to study the mechanistics of hologram formation in multicomponent photopolymers. In 1998 she joined IBM's T. J. Watson Research Center where she most recently managed the "Molecular Assemblies and Devices Group." In January, 2007 Cherie joined the faculty of the University of Pennsylvania's Departments of Electrical and Systems Engineering and Materials Science and Engineering as an associate professor. In addition she assumed the position as the Director of the University's Nanofabrication facility.

 

Cherie was selected by the American Chemical Society Women Chemist Committee in 2002 as one of 12 "Outstanding Young Woman Scientists who is expected to make a substantial impact in chemistry during this century." She was featured by the American Physical Society in "Physics in Your Future" and in 2000 chosen by the MIT Technology Review TR10. In 2005, she received IBM's Outstanding Technical Achievement award. She is on the editorial board of American Chemical Society's journal "Nano Letters" and serves on the Materials Research Society's Board of Directors and the NSF advisory board for the US Summer School in Condensed Matter and Materials Physics.

 

Chemical and physical properties of molecular, supramolecular, and nanoscale assemblies and devices; intramolecular, intermolecular, and interfacial charge and excitonic transport and interactions for the application of molecular and nanoscale materials in transistors and memory devices, photovoltaic devices, and chemical and biological sensors.

Zahra Fakhraai

Photo: 
First Name: 
Zahra
Last Name: 
Fakhraai
Official Title: 
Associate Professor of Chemistry

Physical Chemistry, Materials Chemistry, Nanoscale Science and Engineering

Contact Information
Email: 
fakhraai@sas.upenn.edu
Admin Support: 
Education: 
  • B.Sc. Physics, Sharif University of Technology, Iran 1999
  • M. Sc. Physics, Sharif University of Technology, Iran 2001
  • Ph.D. Physics, University of Waterloo, 2007
  • Post-Doctoral associate, Chemistry, University of Toronto, 2007-08.
  • NSERC Post-Doctoral Fellow, Chemistry, University of Wisconsin-Madison, 2009-11.
Research Interests: 

Our group is interested to study the effect of nano-confinement on structure, dynamics and other properties of materials. Materials behave differently on surfaces, interfaces or small length scales compared to their bulk properties.  Understanding such differences are crucial in many technological applications where materials are constrained in nanometer size spaces, such as organic electronics, polymer applications and drug delivery. One can take advantage of such difference to produce novel materials, such asexceptionally stable glasses or harvest light for various applications. In biological systems, most of the dynamics happens in nanometer size proximity of surfaces and interfaces, and understanding the properties in confinement is a key in predicting function. We focus our efforts on understanding the origins of such modified properties on a fundamental level as well as possible application of such phenomena in producing novel materials or experimental tools.


Enhanced Mobility at the Surface of Polymeric and Organic Glasses: 

 

We study the properties of glasses at the air/glass interface. Our studies show that below the glass transition temperature, where the bulk of the material is in an out of equilibrium state, the interfacial dynamics are many orders of magnitude faster that the bulk dynamics. As a result a layer close to the interface maintains equilibrium properties. We study the dynamics of this layer, its thickness, and its effect on the properties of the underlying glass. The interfacial layer can strongly modify properties of amorphous materials in nanometer length scales. They also allow one to produce near-equilibrium structures at temperatures well below bulk glass transition temperature, through physical vapor deposition.


Exceptionally Stable Glasses: 


 

The enhanced mobility of the interfacial layer allows us to produce near-equilibrium glasses at temperatures well below the bulk glass transition temperature, Tg, by means of physical vapor deposition (PVD). Exceptionally stable glasses are formed when the substrate temperature during PVD is maintained just below the glass transition temperature. We study the morphology and the kinetics of PVD films during formation and their relationship to the final properties of the stable glass. These studies provide information on mechanisms of rapid aging below Tg and stable glass formation. We also investigate exceptional material properties of these glasses and the role of the chemical structure in these properties such as the optical birefringence and electronic properties.


 

Novel Emergent Optical Properties in Disordered Nanoparticle Clusters: 


 

Using simple synthetic routs we can produce dielectric core-gold shell nanoparticles decorated with randomly packed nanoparticles of various shapes and sizes. Spiky nanoparticles are a good example of such nanoparticles. Broadband and tunable structure of spiky gold nanoshells makes them ideal for various applications such as enhanced Raman scattering, temperature and index sensing and sensors for biological and light harvesting applications. Exceptional properties, such as higher order quadrupoloar scattering and magnetic dipole plasmons in these nanoparticles are due to inherent disorder in their structure and random packing arrangements. We explore optical properties of these nanoshells, using various theoretical and experimental tools. We also develop new techniques that allow us to study properties of meta materials formed from these types of particles.

 


Surface Mediated Self-assembly of Amyloid Aggregrates: 


 

Surface self-assembly provides an alternative pathway for amyloid aggregation that is not available in bulk solutions. We us high-resolution atomic force microscopy and other imaging techniques to study the adhesion and diffusion of peptides on various surfaces and their role in facilitating amyloid fibril formation through self-assembly routs. We also use our exceptional capabilities in high-resolution imaging to study the conformation of amyloids formed under various conditions in aqueous conditions.

Selected Publications: 

1.     T. Liu, K. Cheng, E. Salami, F. Gao, C. Li, X. Tong, Y. Lin, Y. Zhang, W. Zhang, L. Klinge, P. Walsh and Z. Fakhraai, "The effect of chemical structure on the stability of physical vapor deposited glasses of 1,3,5-triarylbenzene"J. Chem. Phys. 143, 084506 (2015). 

2.     Z. Qian, S.P. Hastings, C. Li, B. Edward, C.K. McGinn, N. Engheta, Z. Fakhraai* and S.J. Park, "Raspberry-like Metamolecules Exhibiting Strong Magnetic Resonances",  ACS Nano9, 1263-1270 (2015). 

3.     E. Glor, and Z. Fakhraai, "Facilitation of Interfacial Dynamics in Entangled Polymer Films", J. Chem. Phys. 141, 194505 (2014).

4.     Y. Lin, E.J. Peterson, and Z. Fakhraai, "Surface Effects Mediate Self-Assembly of Amyloid-β Peptides"ACS Nano8, 10178-10186 (2014).

5.     S. P. Hastings, P. Swanglap, Z. Qian, Y. Fang, S.J. Park, S. Link, N. Engheta, and Z. Fakhraai, "Quadrupole-Enhanced Raman Scattering", ACS Nano,  8 , 9025-9034 (2014).

6.     B. Sanchez-Gaytan, Z. Qian, S. Hastings, M. Reca, Z. Fakhraai, and S. J. Park, “Controlling
the Topography and Surface Plasmon Resonance of Gold Nanoshells by a Templated Surfactant-Assisted Seed Growth Method
 ”, J. Phys. Chem. C. 117, 8916-8923 (2013).

7.     C. R. Daley, Z. Fakhraai, M. D. Ediger, and J. A. Forrest, “Comparing Surface and Bulk Flow of a Molecular Glass Former”, Soft Matter, 8, 2206-2212 (2012). 

8.     M. Paulite, Z. Fakhraai, N. Gunari, A. Tanur, and G. C. Walker, “Imaging Secondary Structure of Individual Amyloid Fibrils of a β(2)-Microglobulin Fragment Using Near-Field Infrared Spectroscopy”, J. Am. Chem. Soc. 133, 7376-7383 (2011).

9.     Z. Fakhraai and J. A. Forrest, “Measuring the Surface Dynamics of Glassy Polymers”, Science, 319, 600- 604 (2008).

10.  Z. Fakhraai, and J. A. Forrest, “Probing Slow Dynamics in Supported Thin Polymer Films”, Phys. Rev. Lett. 95, 025701(2005).

Ivan J. Dmochowski

Photo: 
First Name: 
Ivan J.
Last Name: 
Dmochowski
Official Title: 
Professor of Chemistry

Bioinorganic, Bioorganic, Biophysical Chemistry

Additional Titles: 
Undergraduate Chair
Contact Information
Office Location: 
348 N, Lab: 332, 334, 336, 338 N
Email: 
ivandmo@sas.upenn.edu
Phone: 
215-898-6459
Twitter: 
@DmochowskiUPenn
Admin Support: 
Education: 
  • B.A. Harvard College (1994)
  • Research Fellow, Johannes Gutenberg Universitaet, Mainz, DE (1994-1995)
  • Ph.D. California Institute of Technology (2000)
  • Caltech Herbert Newby McCoy Award (2000)
  • Helen Hay Whitney Postdoctoral Fellow, Biophysics, Caltech (2000-2002)
  • Camille and Henry Dreyfus New Faculty Award (2003)
  • National Science Foundation CAREER Award (2005)
  • Camille and Henry Dreyfus Teacher-Scholar Award (2007)
Research Interests: 

Our lab is developing chemical and biophysical tools to study and manipulate complex biological systems. Projects span many areas of synthetic organic, inorganic, and biophysical chemistry; molecular, cell, and developmental biology; and bioengineering. We are particularly interested in developing new technologies for biomolecular imaging and the fabrication of functional bio-nanomaterials.

Hyperpolarized 129Xe Biosensors for Early Cancer Detection

Molecular imaging technologies hold great promise for early cancer diagnosis and intervention. Our goal is to develop new reagents that extend the capabilities of magnetic resonance imaging (MRI) for monitoring multiple cancer markers simultaneously in vivo. 129Xe has found increasing use for biological imaging applications, due to its biological compatibility (xenon is an anesthetic at high concentrations), hyperpolarizability (this enhances signals 1,000-fold), and high affinity for organic cages such as cryptophanes. The chemical shift of 129Xe varies by a remarkable 200 ppm, depending on its molecular environment: Thus, a 129Xe atom encapsulated inside a cryptophane is a sensitive reporter of perturbations outside the cage. Based on this principle, our lab is generating new biosensors that will identify biomarkers associated with cancers of the breast, lungs, brain, and pancreas. The long-range goal of this project is to use MRI to detect aberrant proteins that cause cancer in humans, years before the formation of a tumor.

Ferritin Templates for Nanoparticle Synthesis and Assembly

The goal of this project is to use ferritin proteins as templates for synthesizing and assembling inorganic nanoparticles with nanometer precision. Ferritins contain 24 four-helix bundle subunits that self-assemble to create a large central cavity. We have made water-stable, 10-12-nm gold and silver nanoparticles inside ferritin (gray sphere). Particles are fully characterized using facilities at the UPenn Laboratory for Research on the Structure of Matter (LRSM). We are functionalizing the surface of these ferritin-metal nanoparticles for sensing and nano/biomaterials applications. We are also performing computational protein design, in collaboration with the Saven lab, to mutate residues inside the ferritin cavity to enhance their metal-binding properties. Methods for organizing ferritin metal nanoparticles in 2- and 3-dimensions are being developed, in order to build very small conducting circuits. 

Laser-Activated Chemical Biology: Controlling Genes with Light

The goal of this project is to develop methods for turning genes "on" and "off" with light inside neurons and developing zebrafish embryos with high spatial and temporal control. As a first step, we have developed methods for incorporating a photoactive blocking group in the middle of a DNA or RNA oligonucleotide. In one application, we modulated primer extension by DNA polymerase (KF) using UV light. Photoactivation was monitored using a fluorescent reporter. We are now developing methods to control protein translation by the ribosome using similarly caged RNA. Blocking groups mask the messenger RNA start codon, and are designed to prevent translation until photocleavage. We will control complex gradients of proteins involved in cell signaling during zebrafish development and wound healing, using a state-of-the-art UV confocal microscope in the lab.

Selected Publications: 

 

X. Tang, J. Swaminathin, A.M. Gewirtz, I.J. Dmochowski, Regulating gene expression in human leukemia cells using light-activated oligodeoxynucleotides, Nucl. Acids Res. (36) 559-569, 2008.

 

J.A. Aaron, J.M. Chambers, K.M. Jude, L. Di Costanzo, I.J. Dmochowski, D.W. Christianson, Structure of a 129Xe-cryptophane biosensor complexed with human carbonic anhydrase II, J. Am. Chem. Soc. (130) 6942-6943, 2008.

 

G.K. Seward, Q. Wei, I.J. Dmochowski, Peptide-mediated cellular uptake of cryptophane, Bioconjug. Chem. (19) 2129-2135, 2008.

 

J.L. Richards, X. Tang, A. Turetsky, I.J. Dmochowski, RNA bandages for photomodulating in vitro protein synthesis, Bioorg. Med. Chem. Lett. (18) 6255-6258, 2008.

 

C. Butts, J. Swift, S.-G. Kang, L. Di Costanzo, D.W. Christianson, J.G. Saven, I.J. Dmochowski, Directing noble metal ion chemistry within a designed ferritin protein, Biochemistry (47) 12729-12739, 2008.

 

J.L. Chambers, P.A. Hill, J.A. Aaron, Z. Han, D.W. Christianson, N.N. Kuzma, I.J. Dmochowski, Cryptophane xenon-129 nuclear magnetic resonance biosensors targeting human carbonic anhydrase, J. Am. Chem. Soc. (131) 563-569, 2009.

 

P.A. Hill, Q. Wei, T. Troxler, I.J. Dmochowski, Substituent effects on xenon binding affinity and solution behavior of water-soluble cryptophanes, J. Am. Chem. Soc. (131) 3069-3077, 2009.

 

G.P. Robbins, M. Jimbo, J. Swift, M.J. Therien, D.A. Hammer, I.J. Dmochowski, Photo-initiated destruction of composite porphyrin-protein polymersomes, J. Am. Chem. Soc., (131) 3872-3874, 2009. 

 

J. Swift, C. Butts, J. Cheung-Lau, V. Yerubandi, I.J. Dmochowski, Efficient self-assembly of Archaeoglobus fulgidus ferritin around metallic cores, Langmuir, (25) 5219-5225, 2009.

 

C.A. Butts, J. Xi, G. Brannigan, M.L. Klein, R.G. Eckenhoff, I.J. Dmochowski, Identification of a fluorescent general anesthetic, 1-aminoanthracene, Proc. Natl. Acad. Sci. U.S.A. (106) 6501-6506, 2009.

 

I.J. Dmochowski, Xenon out of its shell, Nature Chemistry, ‘In Your Element’ invited feature article, vol. 1, 250, June 2009.

 

O. Taratula, I.J. Dmochowski, Functionalized 129Xe contrast agents for magnetic resonance imaging, Curr. Opin. Chem. Biol. (14) 97-104, 2010.

 

J.L. Richards, G.K. Seward, Y. Huang, I.J. Dmochowski, Turning DNAzymes on and off with light, ChemBioChem (11) 320-324, 2010.

 

J. Lampe, Z. Liao, I.J. Dmochowski, P.S. Ayyaswamy, D.M. Eckmann, Imaging macromolecular interactions at an interface, Langmuir (26) 2452-2459, 2010.

Courses Taught: 
  • Chemistry 101, "General Chemistry"
  • Chemistry 559, "Biomolecular Imaging"
  • Chemistry 567, “Bioinorganic Chemistry”

David M. Chenoweth

Photo: 
First Name: 
David M.
Last Name: 
Chenoweth
Official Title: 
Associate Professor of Chemistry

Organic and Bioorganic Chemistry

Contact Information
Office Location: 
2002 IAST, lab: 2020,2080,2100 IAST
Email: 
dcheno@sas.upenn.edu
Phone: 
215-­573-­1953
Admin Support: 
Education: 
  • B.S. Indiana University-Purdue University Indianapolis (1999)
  • Organic Chemist, Eli Lilly & Co., Indianapolis, IN (2000 – 2004)
  • Ph.D. California Institute of Technology (2009)
  • Kanel Foundation Predoctoral Fellow (2007 – 2009)
  • Caltech Herbert Newby McCoy Award (2009)
  • NIH/NIGMS Postdoctoral Fellow, Massachusetts Institute of Technology (2009 – 2010)
Research Interests: 

Research in the Chenoweth laboratory is grounded in organic chemistry and molecular recognition with applications to biological and materials problems. We synthesize molecules and study their properties and interactions for a broad range of applications in bioorganic and materials chemistry. We are particularly interested in the design and synthesis of new molecules that can modulate nucleic acid and protein structure. Additionally, we are equally interested in the synthesis of new materials with sensing and self-assembly properties.

 

Undergraduate students, graduate students, and postdoctoral researchers are exposed to a diverse array of topics including organic chemistry, synthesis, bioorganic chemistry, macromolecular structure (nucleic acids and proteins), biochemistry, and polymer chemistry.

Selected Publications: 

Zhang, Yitao; Malamakal, Roy M.; Chenoweth, David M. “Aza-Glycine Induces Collagen Hyperstability” J. Am. Chem. Soc. 2015, ASAP. DOI: 10.1021/jacs.5b04590. See Chemical & Engineering News story by Stu Borman: “Chemical Modification Is Best Ever At Strengthening And Stabilizing Collagen” Chemical & Engineering News, Volume 93, Issue 38, p. 7, News of The Week.

 

Zhang, Yitao; Malamakal, Roy M.; Chenoweth, David M. “A Single Stereodynamic Center Modulates the Rate of Self-Assembly in a Biomolecular System” Angew. Chem. Int. Ed. 2015, 54, 10826-10832.

 

Suh, Sung-Eun; Barros, Stephanie A.; Chenoweth, David M. “Triple Aryne–Tetrazine Reaction Enabling Rapid Access to a New Class of Polyaromatic Heterocycles” Chemical Science 2015, 6, 5128-5132.

 

Tran, Mai N.; Chenoweth, David M. “Synthesis and Properties of Lysosome-Specific Photoactivatable Probes for Live-Cell Imaging” Chemical Science 2015, 6, 4508-4512.

 

Barros, Stephanie A.; Chenoweth, David M. “Triptycene-Based Small Molecules Modulate (CAG)·(CTG) Repeat Junctions" Chemical Science 2015, 6, 4752-4755.

 

Tran, Mai N.; Chenoweth, David M. “Photoelectrocyclization as an Activation Mechanism for Organelle Specific Live-Cell Imaging Probes” Angew. Chem. Int. Ed. 2015, 54, 6442-6446.

 

Ballister, Edward R.; Ayloo, Swathi; Chenoweth, David M.; Lampson, Michael A.; Holzbaur, Erika L.F. “Optogenetic Control of Organelle Transport Using a Photocaged Chemical Inducer of Dimerization” Current Biology 2015, 10, R407-R408.

 

Ballister, Edward R.; Aonbangkhen, Chanat; Mayo, Alyssa M.; Lampson, Michael A.; Chenoweth, David M. "Localized Light-Induced Protein Dimerization in Living Cells using a Photocaged Dimerizer” Nature Communications 2014, 5, 5475.

 

Barros, Stephanie A.; Chenoweth, David M. "Recognition of Nucleic Acid Junctions Using Triptycene-Based Molecules” Angew. Chem. Int. Ed. 2014, 53, 13746-13750.

 

Rarig, Robert-André F.; Tran, Mai N.; Chenoweth, David M. "Synthesis and Conformational Dynamics of the Reported Structure of Xylopyridine A” J. Am. Chem. Soc. 2013, 135, 9213–9219, ASAP.

 

Chenoweth, David M.; Meier, Jordan L.; Dervan, Peter B. "Pyrrole-Imidazole Polyamides Distinguish Between Double-Helical DNA and RNA” Angew. Chem. Int. Ed. 2013, 52, 415-418.

 

Weizmann, Yossi; Chenoweth, David M.; Swager, Timothy, M. "DNA−CNT Nanowire Networks for DNA Detection” J. Am. Chem. Soc. 2011, 133, 3238–3241.

 

Chenoweth, David M.; Dervan, Peter B. “Structural Basis for Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding” J. Am. Chem. Soc. 2010, 132, 14521. Selected for the cover of JACS Oct. 20, 2010, Vol 132, Issue 41. Covered by Chemical and Engineering News Sept. 27, 2010 issue, “Putting DNA in a Bind”.

 

Weizmann, Yossi; Chenoweth, David M.; Swager, Timothy, M. “Addressable Terminally-Linked DNA-CNT Nanowires” J. Am. Chem. Soc. 2010, 132, 14009.

 

Weizmann, Yossi; Lim, Jeewoo; Chenoweth, David M.; Swager, Timothy, M. “Regiospecific Synthesis of Au-Nanorod/SWCNT/Au-Nanorod Heterojunctions” Nano Lett. 2010, 10, 2466.

 

Chenoweth, Kimberly; Chenoweth, David M.; Goddard III, William A. “Cyclooctyne-based Reagents for Uncatalyzed Click Chemistry: A Computational Survey” Org. Biomol. Chem. 2009, 7, 5255.

 

Chenoweth, David M.; Harki, Daniel A.; Dervan, Peter B. “Oligomerization Route to DNA Binding Py-Im Polyamide Macrocycles” Org. Lett. 2009, 11, 3590.

 

Chenoweth, David M.; Dervan, Peter B. “Allosteric Modulation of DNA by Small Molecules” Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 13175. Covered by Nature News: "Get into the groove" Nature 2009, 460, 669. Also selected by the Stanford Synchrotron (SSRL) as a science highlight for November 2009.

 

Chenoweth, David M.; Harki, Daniel A.; Dervan, Peter B. “Solution-Phase Synthesis of Pyrrole-Imidazole Polyamides” J. Am. Chem. Soc. 2009, 131, 7175.

 

Chenoweth, David M.; Harki, Daniel A.; Phillips, John W.; Dose, Christian; Dervan, Peter B. “Cyclic Pyrrole-Imidazole Polyamides Targeted to the Androgen Response Element” J. Am. Chem. Soc. 2009, 131, 7182.

 

Chenoweth, David M.; Chenoweth, Kimberly; Goddard III, William A. “Lancifodilactone G: Insights about an Unusually Stable Enol” J. Org. Chem., 2008, 73, 6853.

 

Dose, Christian; Farkas, Michelle E.; Chenoweth, David M.; Dervan, Peter B. “Next Generation Hairpin Polyamides with (R)-3,4-Diaminobutyric Acid Turn Unit” J. Am. Chem. Soc., 2008, 130, 6859.

 

Chenoweth, David M.; Viger, Anne; Dervan, Peter B. “Fluorescent Sequence-Specific dsDNA Binding Oligomers” J. Am. Chem. Soc., 2007, 129, 2216. Covered by Chemical and Engineering News.

 

Chenoweth, David M.; Poposki, Julie A.; Marques, Michael A.; Dervan, Peter B. “Programmable oligomers targeting 5'-GGGG-3' in the minor groove of DNA and NF-k B binding inhibition” Bioorg. Med. Chem., 2007, 15, 759.

 

Doss, Raymond M.; Marques, Michael M.; Foister, Shane; Chenoweth, David M.; Dervan, Peter B. “Programmable Oligomers for Minor Groove DNA Recognition” J. Am. Chem. Soc., 2006, 128, 9074.

 

Nurok, D.; Frost, M. C.; Chenoweth, D. M. “Separation using planar chromatography with electroosmotic flow” J. Chromatogr., A, 2000, 903, 211. 

 

Nurok, David; Frost, Megan C.; Pritchard, Cary L.; Chenoweth, David M. “The performance of planar chromatography using electroosmotic flow” J. Planar Chromatogr.-Mod. TLC, 1998, 11, 244.

Department of Chemistry

231 S. 34 Street, Philadelphia, PA 19104-6323

215.898.8317 voice | 215.573.2112 fax | web@chem.upenn.edu

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