Stoddart Mechanostereochemistry Group





Stoddart Mechanostereochemistry Group



Jonathan Barnes

Graduate Student

Hometown: Louisville, KY

Joined group: 2010


PhD - Northwestern University (2014)

MS - University of Kentucky (2006)

BS - University of Kentucky (2004)



20) Juríček, M.‡; Barnes, J. C.‡; Strutt, N. L.‡; Vermeulen, N. A.; Ghooray, K. C.; Dale, E. J.; McGonigal, P. R.; Blackburn, A. K.; Avestro, A.-J.; Stoddart, J. F. An ExBox [2]Catenane. Chem. Sci. 2014, DOI:10.1039/C4SC00488D. ‡Authors contributed equally

19) Dyar, S. M.; Barnes, J. C.; Juríček, M.; Stoddart, J. F.; Co, D. T.; Young, R. M.; Wasielewski, M. R. Electron Transfer and Multi-Electron Accumulation in ExBox4+. Angew. Chem. Int. Ed. 2014, DOI: 10.1002/anie.201402444.

18) Fathalla, M.; Strutt, N. L. Barnes, J. C.; Stern, C. L.; Ke, C.; Stoddart, J. F. Fluorescence Enhancement of a Porphyrin-Viologen Dyad via Pseudorotaxane Formation with Cucurbit[7]uril. Eur. J. Org. Chem. 2014, DOI: 10.1002/ejoc.201402018.

17) Tarn, D.; Ferris, D. P.; Barnes, J. C.; Ambrogio, M. W.; Stoddart, J. F.; Zink, J. I. A Reversible Light-Operated Nanovalve on Mesoporous Silica Nanoparticles. Nanoscale 2014, 6, 3335—3343.

16) Juríček, M.; Strutt, N. L.; Barnes, J. C.; Butterfield, A. M.; Dale, E. J.; Baldridge, K. K.; Stoddart, J. F.; Siegel, J. S. Induced-Fit Catalysis of Corannulene Bowl-to-Bowl Inversion. Nature Chem. 2014, 6, 222—228.

15) Kung, C.-W.; Wang, T. C.; Mondloch, J. E.; Fairen-Jimenez, D.; Gardner, D. M.; Bury, W.; Klingsporn, J. M.; Barnes, J. C.; Van Duyne, R.; Stoddart, J. F.; Wasielewski, M. R.; Farha, O. K.; Hupp, J. T. Metal-Organic Framework Thin Films Composed of Free-Standing Acicular Nanorods Exhibiting Reversible Electrochromism. Chem. Mater. 2013, 25, 5012—5017.

14) Young, R. M.; Dyar, S. M.; Barnes, J. C.; Juríček, M.; Stoddart, J. F.; Co, D. T.; Wasielewski, M. R. Ulftrafast Conformational Dynamics of Electron Transfer in ExBox4+—Perylene. J. Phys. Chem. A 2013, 117, 12438—12448.

13) Barnes, J. C.; Juríček, M.; Vermeulen, N. A.; Dale, E. J.; Stoddart, J. F. Synthesis of ExnBox Cyclophanes. J. Org. Chem. 2013, 78, 11962—11969.

12) Juríček, M.‡; Barnes, J. C.‡; Dale, E. J.; Liu, W.-G.; Strutt, N. L.; Bruns, C. J.; Vermeulen, N. A.; Ghooray, K. C.; Sarjeant, A. A.; Stern, C. L.; Botros, Y. Y.; Goddard, W. A., III; Stoddart, J. F. Ex2Box: Interdependent Modes of Binding in a Two-Nanometer-Long Synthetic Receptor. J. Am. Chem. Soc. 2013, 135, 12736—12746. ‡Authors contributed equally

11) Barnes, J.C.; Fahrenbach, A.C.; Cao, D.; Dyar, S.M.; Frasconi, M.; Giesener, M.A.; Benitez,D.; Tkatchouk, E.; Chernyashevskyy, O.; Shin, W.H.; Li, H.; Sampath, S.; Stern, C.L.; Sarjeant, A.A.; Hartlieb, K.J.; Liu, Z.; Carmieli, R.; Botros, Y.Y.; Choi, J.W.; Slawin, A.M.Z.; Ketterson, J.B.; Wasielewski, M.R.; Goddard, W.A., III; Stoddart, J.F. A Radically Configurable Six-State Compound. Science, 2013, 339, 429—433.

10) Li, H.; Zhu, Z.; Fahrenbach, A.C.; Savoie, B.M.; Ke, C.; Barnes, J.C.; Lei, J.; Zhao, Y.-L.; Lilley, L.M; Marks, T.J.; Ratner, M.A.; Stoddart, J.F. Mechanical Bond-Induced Radical Stabilization. J. Am. Chem. Soc. 2013, 135, 456—467.

9) Barnes, J.C.‡; Juricek, M‡; Strutt, N.L.; Frasconi, M.; Sampath, S.; Giesener, M.A.; McGrier, P.L.; Bruns, C.J.; Stern, C.L.; Sarjeant, A.A.; Stoddart, J.F. ExBox: A Polycyclic Aromatic Hydrocarbon Scavenger. J. Am. Chem. Soc., 2013, 135, 183–192. Published as the Cover Article ‡Authors contributed equally

8) Fahrenbach, A.C.; Warren, S.C.; Incorvati, J.T.; Avestro, A.-J.; Barnes, J.C.; Stoddart, J.F.; Grzybowski, B.A. Organic Switches for Surfaces and Devices. Adv. Mater., 2013, 3, 331–348.

7) Fahrenbach, A.C.; Sampath, S.; Late, D.J.; Barnes, J.C.; Kleinman, S.L.; Valley, N.; Hartlieb, K.J.; Liu, Z.; Dravid, V.P.; Schatz, G.C.; Van Duyne, R.P.; Stoddart, J.F. A Semiconducting Organic Radical Cationic Host-Guest Complex. ACS Nano, 2012, 6, 9964–9971.

6) Zhu, Z.; Fahrenbach, A.C.; Li, H.; Barnes, J.C.; Liu, Z.; Dyar, S.M.; Zhang, H.; Lei, J.; Carmieli, R.; Sarjeant, A.; Stern, C.; Wasielewski, M.R.; Stoddart, J.F.; Controlling Switching in Bistable [2]Catenanes by Combining Donor-Acceptor and Radical-Radical Interactions. J. Am. Chem. Soc. 2012, 134, 11709–11720.

5) Barnes, J.C., Fahrenbach, A.C.; Dyar, S.M.; Frasconi, M.; Giesener, M.A.; Zhu, Z.; Liu, Z.; Hartlieb, K.J.; Carmieli, R.; Wasielewski, M.R.; Stoddart, J.F. Mechanically-Induced Intramolecular Electron Transfer in a Mixed-Valence Molecular Shuttle. Proc. Natl. Acad. Sci. USA 2012, 109, 11546–11551. Published as the Cover Article

4) Li, Z.; Barnes, J.C., Bosoy, A.; Stoddart, J.F.; Zink, J.I. Mesoporous Silica Nanoparticles in Biomedical Applications. Chem. Soc. Rev. 2012, 41, 2590–2605.

3) Fahrenbach, A.C.; Barnes, J.C.; Lanfranchi, D. A.; Li, H.; Coskun, A.; Gassensmith, J. J.; Liu, Z.; Benítez, D.; Trabolsi, A.; Goddard, W. A., III; Elhabiri, M.; Stoddart, J. F. Solution–Phase Mechanistic Study and Solid–State Structure of a Tris(Bipyridinium Radical Cation) Inclusion Complex. J. Am. Chem. Soc. 2012, 134, 3061–3072.

2) Fahrenbach, A.C.; Barnes, J.C.; Li, H.; Benítez, D.; Basuray, A. N.; Fang, L.; Sue, C.-H.; Barin, G.; Dey, S. K.; Goddard, W. A., III; Stoddart, J. F. Measurement of the Ground-State Distributions in Bistable Mechanically Interlocked Molecules Using Slow Scan Rate Cyclic Voltammetry. Proc. Natl. Acad. Sci. USA 2011, 108, 20416–20421.

1) Dirk, L.M.A.; Schmidt, J.J.; Cai, Y.; Barnes, J.C., et al. Insights into the Substrate Specificity of Plant Peptide Deformylase, an Essential Enzyme with Potential for the Development of Novel Biotechnology Applications in Agriculture. Biochem. J. 2008, 413, 417–427.


I was born and raised in Louisville, KY. I obtained BS/MS degrees from the University of Kentucky where my research entailed the modeling, design, synthesis, and biological analysis of inhibitors of the enzyme peptide deformylase.

After graduation, I worked for a biotech company in Los Angeles - Synedgen,Inc. - developing novel antimicrobial derivatives of chitosan and I also designed biocompatible, hemostatic foams for the US military.

I'm currently back in graduate school at Northwestern University pursuing that all-enabling degree. I officially joined the renowned Stoddart group in the fall of 2010 and I will focus on developing new synthetic methodologies for the preparation of robust mechanically interlocked molecules (MIMs), which are based on the rich redox chemistry of 4,4'-bipyridine and tetrathiafulvalene as well as synthesizing functionalized silica nanoparticles with the aim of combating nasty bugs, such as methicillin-resistant S. aureus (MRSA).

In April of 2012, I was awarded a National Defense Science and Engineering Graduate (NDSEG) Fellowship by the Department of Defense. Additionally, I was awarded a Ryan Fellowship in July 2012 through the International Institute for Nanotechnology (IIN) at Northwestern University.

Chemistry aside, I love watching movies, reading, and playing basketball. I am an avid Lakers and UK basketball fan, and I am so proud of Calipari's first, and the school's eighth championship!


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