Megan L. Matthews

First Name: 
Megan L.
Last Name: 
Official Title: 
Assistant Professor of Chemistry
Contact Information
Office Location: 
2003 Vagelos
Admin Support: 

B.S., Chemistry, Miami University (2005)


Ph.D., Chemistry, The Pennsylvania State University (2011)


Merck Helen Hay Whitney Postdoctoral Fellow (2012–2015) and postdoctoral associate (2015–2017), Department of Molecular Medicine, The Scripps Research Institute

Research Interests: 

Research in the Matthews group unites enzymology and chemical biology to develop novel chemical proteomics technologies for the discovery of enzyme cofactors and regulatory post-translational modifications that cannot readily be predicted by gene or protein sequence.


Intrinsic nucleophiles abound among the proteinogenic amino acids, but, interestingly, reactive electrophiles are essentially absent. Therefore, the majority of chemical probes target nucleophilic sites to discover enzymes, inhibitors and drug therapies. However, by acquiring them through post-translational modifications, enzymes do indeed exploit diverse classes of protein-bound electrophiles for catalysis and other essential functions. Owing to this mode of acquisition, functional electrophiles are not generally predictable from sequence; thus, their breadth and prevalence remain to be found. Our group is exploring this unknown to understand the functions of reactive modifications that we have found unexpectedly on drug targets implicated in cancer and Alzheimer’s disease. Such discoveries can be uncovered using the ‘reverse-polarity’ chemical probes that we develop. We expect that this largely un-profiled half of the reactive proteome – the covalent ‘electrophilome’ – will be found to rival its 'nucleophilome' counterpart in functional diversity and disease relevance.

Selected Publications: 

The Scripps Research Institute

17.    Matthews ML*, He L, Olson EJ, Horning BD, Correia BE, Yates JR, III, Dawson PE & Cravatt BF*. “Chemoproteomic profiling and discovery of protein electrophiles in human cells.” Nat. Chem. 9, 234–243 (2017).

16.    Horning BD, Suciu RM, Ghadiri D, Ulanovskaya O, Matthews ML, Lum KM, Backus KM, Brown SJ, Rosen H & Cravatt BF. “Chemical proteomic profiling of human methyltransferases.” J. Am. Chem. Soc. 138, 13335–13343 (2016).

15.    Rajagopalan S, Wang C, Yu K, Kuzin AP, Richter F, Lew S, Miklos AE, Matthews ML, Seetharaman J, Su M, Hunt JF, Cravatt BF & Baker D. “Design of activated serine-containing catalytic triads with atomic-level accuracy.” Nat. Chem. Biol. 10, 386-391 (2014).

14.    Chang JW, Niphakis MJ, Lum KM, Cognetta AB, Wang C, Matthews ML, Niessen S, Buczynski MW, Parsons LH & Cravatt BF. “Highly selective inhibitors of monoacylglycerol lipase bearing a reactive group that is bioisosteric with endocannabinoid substrates.” Chem. Biol. 19, 579-588 (2012).

The Pennsylvania State University

13.    Srnec M, Wong SD, Matthews ML, Krebs C, Bollinger JM, Jr. & Solomon EI. “Electronic structure of the ferryl intermediate in the a-ketoglutarate dependent non-heme iron halogenase SyrB2: Contributions to H-atom abstraction reactivity.” J. Am. Chem. Soc. 138, 5110-5122 (2016). 

12.    Matthews ML*, Chang WC, Layne AP, Miles LA, Krebs C & Bollinger JM, Jr.* “Direct nitration and azidation of aliphatic carbons by an iron-dependent halogenase.” Nat. Chem. Biol. 10, 209-215 (2014).  

11.    Wong SD, Srnec M, Matthews ML, Liu LV, Kwak Y, Park K, Bell CB, Alp EE, Zhao JY, Yoda Y, Kitao S, Seto M, Krebs C, Bollinger JM, Jr. & Solomon EI. “Elucidation of the Fe(IV)=O intermediate in the catalytic cycle of the halogenase SyrB2.” Nature 499, 320-323 (2013).

10.    Krebs C, Dassama LMK, Matthews ML, Jiang W, Price JC, Korboukh V, Li N & Bollinger JM, Jr. “Novel approaches for the accumulation of oxygenated intermediates to multi-millimolar concentrations.” Coord. Chem. Rev. 257, 234-243 (2013).

9.      Hollenhorst MA, Bumpus SB, Matthews ML, Bollinger JM, Jr. Kelleher NL & Walsh CT. “The nonribosomal peptide synthetase enzyme DdaD tethers N(b)-fumaramoyl-L-2,3-diaminopropionate for Fe(II)/a-ketoglutarate-dependent epoxidation by DdaC during dapdiamide antibiotic biosynthesis.” J. Am. Chem. Soc. 132, 15773-15781 (2010).

8.      Bollinger JM, Jr. & Matthews ML. “Remote enzyme microsurgery.” Science 327, 1337-1338 (2010).

7.      Matthews ML, Neumann CS, Miles LA, Grove TL, Booker SJ, Krebs C, Walsh CT & Bollinger JM, Jr. “Substrate positioning controls the partition between halogenation and hydroxylation in the aliphatic halogenase, SyrB2.” Proc. Natl. Acad. Sci. USA 106, 17723-17728 (2009).

6.      Matthews ML, Krest CM, Barr EW, Vaillancourt FH, Walsh CT, Green MT, Krebs C & Bollinger JM, Jr. “Substrate-triggered formation and remarkable stability of the C–H bond-cleaving chloroferryl intermediate in the aliphatic halogenase, SyrB2.” Biochemistry 48, 4331-4343 (2009).

5.      Bollinger JM, Jr., Diao Y, Matthews ML, Xing G & Krebs C. “Myo-inositol oxygenase: a radical new pathway for O2 and C-H activation at a nonheme diiron cluster.” Dalton Trans. 905-914 (2009).

4.      Krebs C, Matthews ML, Jiang W & Bollinger JM, Jr. “AurF from Streptomyces thioluteus and a possible new family of manganese/iron oxygenases.” Biochemistry 46, 10413-10418 (2007).

3.      Fujimori DG, Barr EW, Matthews ML, Koch GM, Yonce JR, Walsh CT, Bollinger JM, Jr., Krebs C & Riggs-Gelasco PJ. “Spectroscopic evidence for a high-spin Br-Fe(IV)-oxo intermediate in the a-ketoglutarate-dependent halogenase CytC3 from Streptomyces.”  J. Am. Chem. Soc. 129, 13408-13409 (2007).


Miami University, 2001–2005

2.      Matthews ML, Periyannan G, Hajdin C, Sidgel TK, Bennett B & Crowder MW. “Probing the reaction mechanism of the D-ala-D-ala dipeptidase, VanX, by using stopped-flow kinetic and rapid-freeze quench EPR studies on the Co(II)-substituted enzyme.” J. Am. Chem. Soc. 128, 13050-13051 (2006).

1.      Breece RM, Costello A, Bennett B, Sigdel TK, Matthews ML, Tierney DL & Crowder MW. “A five-coordinate metal center in Co(II)-substituted VanX.” J. Biol. Chem. 280, 11074-11081 (2005).

Karen I. Goldberg

First Name: 
Karen I.
Last Name: 
Official Title: 
Vagelos Professor of Energy Research

Starting September 1, 2017.




Activation of Strong Bonds - CENTC


CENTC (Center for Enabling New Technology through Catalysis) and is a collaboration with a number of departments from around the United States. A major focus of the center is in elucidating and applying the fundamental principles necessary for the catalytic transformations of strong chemical bonds including C-H, C-C, C-O, C-N, N-H. Our group's work and contributions to the center include:


A.B.: Barnard College of Columbia University Ph.D.: University of California at Berkeley Postdoctoral Fellow: The Ohio State University
Selected Publications: 

Hydrogen Addition to (pincer)IrI(CO) Complexes: The Importance of Steric and Electronic Factors

Goldberg, J. M.; Cherry, S. D. T.; Guard, L. M.; Kaminsky, W.; Goldberg, K. I.; Heinekey, D. M. Organometallics 2016, 35, 3546-3556


High Catalytic Efficiency Combined with High Selectivity for the Aldehyde-Water Shift Reaction using (para-cymene)Ruthenium Precatalysts

Brewster, T. P.; Goldberg, J. M.; Tran, J. C.; Heinekey, D. Michael; Goldberg, K. I. ACS Catalysis, 2016, 6, 6302-6305.


Base-Free Iridium-Catalyzed Hydrogenation of Esters and Lactones

Brewster, T. P.; Rezayee, N. M.; Culakova, Z.; Sanford, M. S.; Goldberg, K. I. ACS Catalysis 2016, 6, 3113-3117.


The Importance of Steric Factors in Iridium Pincer Complexes

Goldberg, J. M.; Wong, G. W.; Brastow, K. E.; Kaminsky, W.; Goldberg, K. I.; Heinekey, D. M. Organometallics 2015, 34, 753-762.


Pyrazole-Based PCN Pincer Complexes of Palladium(II): Mono- and Dinuclear Hydroxide Complexes and Ligand Rollover C–H Activation

Bailey, W. D.; Luconi, L.; Rossin, A.; Yakhvarov, D.; Flowers, S. E.; Kaminsky, W.; Kemp, R. A.; Giambastiani, G.; Goldberg, K. I. Organometallics 2015, 34, 3998-4010.

Jisun Lee

First Name: 
Last Name: 
Official Title: 
Lecturer A
Organic Chemistry
Contact Information
Office Location: 
448 N

A.B. Bryn Mawr College (2006)

Ph.D. University of Pennsylvania (2014)

Postdoctoral Research Fellow and Instructor, University of Pennsylvania (2014-2016)

Research Interests: 
Application of synthetic organic chemistry and catalysis in the generation of biologically relevant molecules
Courses Taught: 

CHEM 241: Organic Chemistry I

CHEM 242: Organic Chemistry II

CHEM 245: Organic Chemistry Lab

CHEM 246: Advanced Synthesis and Spectroscopy

Sergei Vinogradov

First Name: 
Last Name: 
Official Title: 
Associate Professor of Biochemistry and Biophysics

Biophysical Chemistry, Photochemistry/Photophysics

Contact Information

M.S. (Chemistry) Moscow State University, Russia, 1988.

Ph.D. (Organic Chemistry) Moscow State University, Russia, 1995.

Research Interests: 
Dr. Vinogradov's research is focused on the development of advanced probes for microscopy and imaging applications. On the fundamental level our interests encompass chemistry of porphyrins and other pyrrolic dyes, energy and electron transfer in multichromophoric systems, spectroscopy and imaging. Essentially, we are a group of synthetic and physical chemists developing new techniques for biomedical research. Over the past years the main focus of the lab has been optical imaging of oxygen in biological systems, including chemistry of imaging probes, phosphorescence lifetime imaging instrumentation, image reconstruction methods and a variety of applications of phosphorescence. Other bio-analytes of interests have been pH and metal ions. Currently the laboratory also pursues interests in optical energy upconversion and magnetic field effects on luminescence in view of their applications in imaging. Dr. Vinogradov collaborates broadly with laboratories across the world whose interests include basic studies of cellular metabolism and applications in neuroscience, stem cell biology, cancer therapy, tissue engineering and ophthalmology.
Selected Publications: 

Esipova, T. V., Ye, X. C., Collins, J. E., Sakadzic, S., Mandeville, E. T., Murray, C. B., Vinogradov, S. A.: Dendritic upconverting nanoparticles enable in vivo multiphoton microscopy with low-power continuous wave sources. PNAS 109(51): 20826-20831, 2012.


Mani, T., Tanabe, M., Yamauchi, S., Tkachenko, N. V., Vinogradov, S. A.: Modulation of Visible Room Temperature Phosphorescence by Weak Magnetic Fields. Journal of Physical Chemistry Letters 3(21): 3115-3119, 2012.


Mani, T., Niedzwiedzki, D.M., Vinogradov, S.A.: Generation of Phosphorescent Triplet States via Photoinduced Electron Transfer: Energy and Electron Transfer Dynamics in Pt Porphyrin-Rhodamine B Dyads. J. Phys. Chem. A. 116: 3598−3610, 2012.


Vinogradov, S.A., Wilson, D.F. : Porphyrin-dendrimers as biological oxygen sensors. Designing dendrimers. Wiley, 2012.


Esipova, T. V., Karagodov, A., Miller, J., Wilson, D. F., Busch, T. M., Vinogradov, S. A.: Two new "protected" oxyphors for biological oximetry: properties and application in tumor imaging. Analytical Chemistry 83(22): 8756-8765, 2011.


Lecoq, J., Parpaleix, A., Roussakis, E., Ducros, M., Houssen, Y. G., Vinogradov, S. A.*, Charpak, S.*: Simultaneous two-photon imaging of oxygen and blood flow in deep cerebral vessels. Nature Medicine 17(7): 893-U262, 2011 Notes: Note that postdoc E. Roussakis is a co-first author and I am one of the two senior corresponding authors. My lab is entirely responsible for the new oxygen microscopy technology and worked with the collaborator to implement it in the brain.


Finikova, O. S., Lebedev, A. Y., Aprelev, A., Troxler, T., Gao, F., Garnacho, C., Muro, S., Hochstrasser, R. M., Vinogradov, S. A.: Oxygen microscopy by two-photon-excited phosphorescence. ChemPhysChem 9(12): 1673-1679, 2008.


Apreleva, S. V., Wilson, D. F., Vinogradov, S. A.: Tomographic imaging of oxygen by phosphorescence lifetime. Applied Optics 45(33): 8547-8559, 2006.

Abraham Nitzan

First Name: 
Last Name: 
Official Title: 
Professor of Chemistry
Chemical Physics and Physical Chemistry, Theory Simulation and Modeling
Other Information: 
Abraham Nitzan was born in Israel in 1944, received B.Sc. and M.Sc. degrees from the Hebrew University, and Ph.D degree from Tel Aviv University (TAU) in 1972. Following post doctoral studies at MIT and the University of Chicago he has returned to Tel Aviv University in 1975 where he has served as a professor of Chemistry since 1982 (Emeritus since 2014), chairman of the School of Chemistry in 1984-7, dean of the Faculty of Sciences in 1995-8 and director of the Institute of Advanced Studies 2003-15. Since 2015 he is a professor of Chemistry at the University of Pennsylvania, USA. His research focuses on the interaction of light with molecular systems, chemical reactions in condensed phases and interfaces and charge transfer processes in such environments. During 1992-2015 Nitzan was the incumbent of the Kodesh Chair of Chemical Dynamics at Tel Aviv University. Among his main recognitions are the Humboldt Award, the Israel Chemical Society Prize (2004) and Medal (2015), the Emet Prize and the Israel Prize in Chemistry. He is a Fellow of the American Physical Society and of the American Association for the Advancement of Science, a Foreign Honorary member of the American Academy of Arts and Sciences, a Foreign Associate of the US National Academy of Sciences and a member of the Israel Academy of Arts and Sciences. In 2010 he has received an honorary doctorate (Dr. Honoris Causa) from the University of Konstanz.
Contact Information
Office Location: 
260A Cret
Admin Support: 
CV (file): 
  • 1961-1964 Hebrew University, Jerusalem Chemistry B.Sc.
  • 1964-1965 Hebrew University, Jerusalem Chemistry M.Sc.
  • 1970-1972 Tel-Aviv University Chemistry Ph.D. 
Research Interests: 
Research in my group focuses on theoretical aspects of chemical dynamics, the branch of chemistry that describes the nature of physical and chemical processes that underline the progress of chemical reactions with the aim to achieve understanding of such processes and the ability to predict their course of evolution. In particular, our studies deal with chemical processes involving interactions between light and matter, chemical reactions in condensed phases and at interfaces and transport phenomena in complex systems, focusing mainly on the following directions:
  • Energy transfer processes in molecular systems. 
  • Molecular dynamics in condensed phases. 
  • Ionic transport in complex environments.
  • Optical properties and photochemistry of adsorbed molecules. 
  • Electron transport through molecular layers and wires. 
  • Classical and quantum thermodynamics of energy conversion processes. 



Selected Publications: 


A. Nitzan

Chemical Dynamics in Condensed Phases

Oxford University Press, 2006 (744 pages)


PAPERS (Last 15 years)


K. Kaasbjerg and A. Nitzan

Theory of light emission from quantum noise in plasmonic contacts: above-threshold

emission from higher-order electron-plasmon scattering

Phys. Rev. Letters, 114, 126803(1-5) (2015)


A. Migliore and A. Nitzan

Irreversibility and hysteresis in redox molecular conduction junctions

J.Am.Chem.Soc, 135, 9420-32 (2013)


K. Kaasbjerg, T. Novotny and A. Nitzan

Carrier-induced renormalization of vibrational frequencies in nanoscale junctions: Signatures of vibrational damping and heating

Phys. Rev. B (Rapid Communication), 88, 201405(R) (2013) (Editor Choice)


J. Gersten, K. Kaasbjerg and A. Nitzan

Induced spin filtering in electron transmission through chiral molecular layers adsorbed on metals with strong spin-orbit coupling

J. Chem. Phys. 139, 114111(1-20) (2013)


H. Nakanishi, K. J. M. Bishop, B. Kowalczyk, A. Nitzan, E. A. Weiss, K. V. Tretiakov, M. M. Apodaca, R. Klajn, J. F. Stoddart and B. A. Grzybowski

Photoconductance and inverse photoconductance in films of functionalized metal nanoparticles

Nature, 460, 371-375 (2009)


S. S. Skourtis, D. N. Beratan, R. Naaman, A. Nitzan and D. H. Waldeck

Chiral control of electron transmission through molecules

Phys. Rev. Letters, 101, 238103(1-4) (2008)


M. Galperin, M.A. Ratner, A. Nitzan and A. Troisi

Nuclear Coupling and Polarization in Molecular Transport Junctions: Beyond Tunneling to Function

Science, 319, 1056-1060 (2008)


M. Galperin, M.A. Ratner and A. Nitzan

Heat conduction in molecular transport junctions

Phys. Rev. B 75, 155312(1-14) (2007)


M. Galperin, A. Nitzan, and M. A. Ratner

Resonant inelastic tunneling in molecular junctions

Phys. Rev. B 73, 045314 (1-13) (2006)


M. Galperin, M. A. Ratner and A. Nitzan

Hysteresis, switching, and negative differential resistance in molecular junctions: A polaron Model

Nano Letters, 5, 125-130 (2005)


D. Segal and A. Nitzan

A spin boson thermal rectifier

Phys. Rev Letters. 94, 034301 (1-4) (2005)


M. Galperin, M. Ratner and A. Nitzan

Inelastic electron tunneling spectroscopy in molecular junctions: Peaks and dips

J. Chem. Phys. 121, 11965-11979 (2004)


D. Segal, A. Nitzan and P. Hänggi

Thermal conductance through molecular wires

J. Chem. Phys. 119, 6840-6855 (2003)


A. Nitzan and Mark Ratner

Electron transport in molecular wire junctions: Models and Mechanisms

Science, 300, 1384-1389 (2003)


J. Lehmann, S. Kohler, P. Hänggi and A. Nitzan

Molecular Wires Acting as Coherent Quantum Ratchets

Phys. Rev. Letters, 88, 228305 (2002)


A. Nitzan

A relationship between electron transfer rates and molecular conduction.

J. Phys. Chem. A 105, 2677-2679(2001)


A. Nitzan

Electron transmission through molecules and molecular interfaces

Annu. Rev. Phys. Chem. 52, 681– 750 (2001)

Other Affiliations: 
School of Chemistry, Tel Aviv University, Israel

Jessica M. Anna

First Name: 
Jessica M.
Last Name: 
Official Title: 
Assistant Professor of Chemistry

Physical Chemistry, Laser Spectroscopy, Ultrafast Dynamics, Chemical Reaction Dynamics, and Energy Science

Additional Titles: 
Elliman Faculty Fellow
Contact Information
Office Location: 
251 Chem
Admin Support: 

B.S. University of Pittsburgh (2006)


Ph.D. University of Michigan (2011)


Postdoctoral Research Fellow, University of Michigan (2011)


Postdoctoral Research Fellow, University of Toronto (2011-2014)

Research Interests: 

Solar energy conversion, in both natural and artificial systems, involves the absorption of a photon that can then lead to a series of energy and electron transfer events. Research in the Anna group focuses on understanding these photoinitiated processes. More specifically we are interested in exploring (1) the interplay of vibrational motion with both electronic energy transfer and electron transfer reactions, and (2) the role the environment plays in these processes. To begin to answer these questions we employ both well-established and novel multidimensional spectroscopic techniques to explore photoinitiated processes in a range of systems, spanning interests in biology, chemistry, and physics.

Selected Publications: 

J. M. Anna, M. R. Ross, K. J. Kubarych, “Dissecting Enthalpic and Entropic Barriers to Ultrafast Equilibrium Isomerization of a Flexible Molecule Using 2DIR Chemical Exchange Spectroscopy”, J. Phys. Chem. A 113 (2009) 6544-6547.


J. M. Anna and K. J. Kubarych, “Watching Solvent Friction Impede Ultrafast Barrier Crossings: A Direct Test of Kramers Theory”, J. Chem. Phys. 133 (2010) 174596.


J. M. Anna, M. J. Nee, C. R. Baiz, R. McCanne, K. J. Kubarych, “Measuring Absorptive Two-Dimensional Infrared Spectra Using Chirped-Pulse Upconversion Detection”, J. Opt. Soc. Am. B. 27 (2010) 382-393.


J. M. Anna, E. E. Ostroumov, K. Maghlaoui, J. Barber, and G. D. Scholes “Two-Dimensional Electronic Spectroscopy Reveals Ultrafast Downhill Energy Transfer in Photosystem I Trimers of the Cyanobacterium Thermosynechococcus elongatus”, J. Phys. Chem. Lett. (2012), 3, 3677-3684.


J. M. Anna, Y. Song, R. Dinshaw and G. D. Scholes “Two-dimensional electronic spectroscopy for mapping photophysics”, Pure. Appl. Chem. (2013), 85, 1307-1319.


J. M. Anna, G. D. Scholes, and R. van Grondelle, “A Little Coherence in Photosynthetic Light Harvesting”, BioScience (2014), 64, 14-25

Neil C. Tomson

First Name: 
Neil C.
Last Name: 
Official Title: 
Assistant Professor of Chemistry

Inorganic and Organometallic Synthesis, Energy Storage Chemistry, Materials Chemistry

Contact Information
Office Location: 
3002 IAST
(215) 898-6208
(215) 573-2112
Admin Support: 
  • B.A. in Chemistry, with honors, Grinnell College (2004)
  • Ph.D. in Chemistry, University of California, Berkeley (2009)
  • Post-doctoral Associate, Max Planck Institute for Bioinorganic Chemistry (2009-2011)
  • Adjunct Assistant Professor of Chemistry, College of St. Benedict | St. John’s University (2011-2012)
  • Post-doctoral Associate, Los Alamos National Laboratory (2012-2013)
  • Glenn T. Seaborg Institute Post-doctoral Fellow, Los Alamos National Laboratory (2013)
  • Director’s Post-doctoral Fellow, Los Alamos National Laboratory (2013-2015)
Research Interests: 

Our group performs synthetic inorganic and organometallic chemistry as a way of investigating new concepts in structure, bonding, catalysis, and materials chemistry.  The research involves the use of rigorous air-sensitive synthetic techniques and draws on a wide range of physical methods for characterizing novel compounds. 


With a particular interest in energy problems, our work takes advantage of modern concepts in bonding theory to generate materials that can influence how energy from renewable sources is collected, stored, and released.  To do this, we develop both new catalysts for reactions that store energy in chemical bonds and battery materials that can reversibly deliver multiple electrons with minimal energy loss.  Our current areas of focus include:


• Understanding the effects of molecular-scale electrostatic fields on electronic structure and reactivity, particularly as they relate to both bioinorganic chemistry and homogeneous catalysis.


• Developing molecular cluster compounds that incorporate redox-active ligands as a way of modeling the chemistry occurring on the surfaces of heterogeneous, metallic catalysts.


• Generating molecules for use as multi-electron, redox-flow battery materials, especially those that can undergo potential inversion.

Elizabeth Rhoades

First Name: 
Last Name: 
Official Title: 
Associate Professor of Chemistry
Contact Information
Office Location: 
258 Chemistry Building
Admin Support: 
  • postdoctoral associate with Professor Watt Webb at Cornell University (2003-2006)
  • postdoctoral associate with Professor Gilad Haran at the Weizmann Institute of Science (2001-2003)
  • PhD in Biophysics from the University of Michigan, Ann Arbor (2001)
  • B.S. in Physics from Duke University (1994)
Research Interests: 

Research in the Rhoades lab aims to elucidate the principles that link protein conformational change with structure-function relationships, focusing on understanding structural plasticity in intrinsically disordered proteins (IDPs). IDPs do not form stable structures under physiological conditions; for many, function is dependent upon disorder. This is in striking contrast to the structure-function paradigm that dominates our understanding of globular proteins. Given the large fraction of the eukaryotic proteome predicted to be disordered, the scope of the problem and the need for new insights are enormous.


Much of our effort is directed towards IDPs whose aggregation is central to the pathology of several degenerative diseases: α-synuclein (Parkinson’s disease), tau (Alzheimer’s disease), and IAPP (Type II Diabetes). These three proteins have diverse native functions and binding partners, but share intriguing commonalities of toxic mechanism and the importance of templated selfassembly. Studying systems in parallel allows us to generate protein and disease-specific insights as well as determine principles relevant to general functional and dysfunctional mechanisms of IDPs.


Our primary approaches center on single molecule optical techniques. These approaches enable quantitative and structural assessments of our systems in isolation and in the context of biologically relevant interactions. Single molecule approaches are unique in their ability to characterize systems which exist and function as a dynamic ensemble of states.

Selected Publications: 

1.      X.-H. Li, J. A. Culver, and E. Rhoades (2015) “Tau binds to multiple tubulin dimers with helical structure” Journal of the American Chemical Society, 137: 9218-921

2.     A. Nath, D. E. Schlamadinger, E. Rhoades, and A.D. Miranker (2015) “Structure-based small molecule modulation of a pre-amyloid state: pharmacological enhancement of IAPP membrane-binding and toxicity” Biochemistry, 349: 54-58

3.     D. Jülich, G. Cobb,  A.M. Melo, P. McMillen, A. Lawton,  S.G.J. Mochrie, E. Rhoades, and S.A. Holley (2015) “Cross-scale Integrin regulation organizes ECM and tissue topology” Developmental Cell, 34: 33-44

4.     J. LaRochelle, G. Cobb, A. Steinauer, E. Rhoades, and A. Schepartz (2015) “Fluorescence correlation spectroscopy revealsy highly efficient endosomal escape by certain penta-arg proteins and stapled peptides” Journal of the American Chemical Society. 127: 2536-2541 January 2015

5.     S.Kumar, D.E. Schlamadinger, M.A. Brown, J.M. Dunn, B. Mercado, J.A. Hebda, I Saraogi, E. Rhoades, A.D. Hamilton, and A.D. Miranker (2014) “IAPP and the shared molecular origins of leakage and toxicity” Chemistry and Biology, 19: 369-378

6.     A.R. Braun, M.M. Lacy, V.C. Ducas, E. Rhoades, and J.N. Sachs (2014) “α-Synuclein-induced membrane remodeling is driven by binding affinity, partition depth, and interleaflet order asymmetry” Journal of the American Chemical Society, 136: 9962-9972

7.  S. Elbaum-Garfinkle, G. Cobb, J. T. Compton, X. Li and E. Rhoades (2014)“Tau mutants bind tubulin heterodimers with enhanced affinity” Proceedings of the National Academy of Sciences U.S.A., 111: 6311-6316

8.  D. C. DeWitt and E. Rhoades (2013) “α-Synuclein Inhibits SNARE-mediated Vesicle Fusion Through Direct Interactions with Lipid Bilayer” Biochemistry, 52: 2385-2387

9.  B. R. Capraro, Z. Shi, J.M. Dunn, T. Wu, E. Rhoades, and T. Baumgart (2013) “Kinetics of endophilin N-BAR domain dimerization and membrane interactions” Journal of Biological Chemistry, 288: 12533-12543

10.  S. Elbaum-Garfinkle and E. Rhoades (2012) “Long-Range Interactions Modulate Aggregation of Tau by Altering the Conformational Ensemble” Journal of the American Chemical Society, 134: 16607-16613

11.     A. Nath, M. Sammalkorpi, D. DeWitt, A.J. Trexler, S. Elbaum-Garfinkle, C.S. O’Hern and  E. Rhoades (2012) “The Conformational Ensembles of  α-Synuclein and Tau:  Combining Single-Molecule FRET and Simulations”  Biophysical Journal, 103: 1940-1949

12.     V. Ducas and E. Rhoades (2012) “Quantifying β-Synuclein and g-Synuclein Membrane Interactions”  Journal of Molecular Biology, 423:528-539

13.     A.J. Trexler and E. Rhoades  (2012) “N-terminal acetylation is critical for forming α-helical oligomer of α-Synuclein” Protein Science, 21:601-605  

14.     A.R. Braun, E. Sevcsik, P. Chin, E. Rhoades, S. Tristram-Nagle, and J.N. Sachs (2012) “α-Synuclein Induces Both Positive Mean Curvature and Negative Gaussian Curvature in Membranes” Journal of the American Chemical Society,  134: 2613-2620  

15.     A. Nath, A. D. Miranker, and E. Rhoades (2011) “A Membrane-bound Dimer of Islet Amyloid  Polypeptide Studied by Single-Particle FRET”  Angewandte Chemie, 50: 10859-10862   
16.     N.B. Last, E. Rhoades, and A.D. Miranker (2011) “Islet Amyloid Polypeptide Demonstrates A Persistent Capacity to Disrupt Membrane Integrity” Proceedings of the National Academy of Sciences, U.S.A., 108: 9460-9465   

17.     E. Sevcsik, A.J. Trexler, J.M. Dunn, and E. Rhoades (2011) “Allostery in a disordered protein: Oxidative modifications to α-Synuclein act distally to regulate membrane binding” Journal of the American Chemical Society, 133: 7152-7158  

18.  A.J. Trexler and E. Rhoades (2010) “Single molecule characterization of α-Synuclein in aggregation-prone states” Biophysical Journal, 99: 3048-3055    

19.  E. R. Middleton and E. Rhoades (2010) “Effects of vesicle curvature and composition on α-Synuclein binding to lipid vesicles” Biophysical Journal, 99: 2279-2288  

20.  A . J. Trexler and E. Rhoades (2009) “α-Synuclein binds large unilamellar vesicles as an extended helix”Biochemistry, 48: 2304-2306  

Daniel J. Mindiola

First Name: 
Daniel J.
Last Name: 
Official Title: 
Presidential Professor

Inorganic and Organometallic Synthesis, Catalysis, and Mechanistic Chemistry

Contact Information
Office Location: 
550 Chemistry
(215) 898-5247
Admin Support: 

• B.S. in Chemistry with honors, Michigan State University (1996)

• Ph.D., Massachusetts Institute of Technology (2000)

• NIH and FORD Postdoctoral Fellow, University of Chicago (2000-02)

• Assistant Professor, Indiana University-Bloomington (2002)

• Associate Professor, Indiana University-Bloomington (2007)

• Full Professor, Indiana University-Bloomington (2010)

Research Interests: 

The Mindiola research program entails the synthesis of transition metal complexes that possess interesting coordination environments, reactive ligand scaffolds, and unusual electronic and magnetic features. Most of our efforts are devoted to the synthesis of early- and mid-transition metal complexes, especially systems that are unsaturated and reactive.  We enjoy preparing and studying transition metal radicals, in particular those of the 3d series. In addition to synthesis, we explore new reaction chemistry with small molecules and novel mechanisms in order to understand how these transformations can improve or be of importance to industrial processes. One of our themes has been the assembly of metal-complexes having metal-ligand multiple bonds and their reactivity with small saturated and unsaturated molecules. To date, the Mindiola group has produced more than 120 peer reviewed scientific contributions.

Donald A. Tomalia

First Name: 
Donald A.
Last Name: 
Official Title: 
Adjunct Professor of Chemistry

Dr. Tomalia received his B.A. in chemistry from the University of Michigan and while at The Dow Chemical Company completed his Ph.D.

  • B.A. University of Michigan
  • Ph.D. Michigan State University
Other Affiliations: 

National Dendrimer Center at Central Michigan University

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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