Indiana University Department of Chemistry Indiana University Department of Chemistry - Amar Flood Research Group Indiana University Department of Chemistry - Amar Flood Research Group Indiana university Bloomington


Relevant Disciplines

Physical Organic / Inorganic / Materials

Related Areas

Supramolecular Chemistry / Spectroscopy and Electrochemistry / Interfacial Science / Nanoscience


1. Anion RecognitionAmar Flood

We have three main motifs: triazolophane macrocycles, aryl-triazole foldamers, and cyanostar macrocycles

We have developed a novel shape-persistent macrocycle (see image below) that is easily constructed using click chemistry and displays a high affinity for anions. This is one of the first three examples of the weak CH•••anion hydrogen bond (the weakest among Nature's cohort) to be reported and therefore represents an iconoclastic breakthrough in the design of anion receptors. Consequently, the extreme modularity provided by the click chemistry as well as the high affinity (some approaching Ka values of 1,000,000 M–1) open up a new and uncharted realm of opportunities. One of our goals are to sequester toxic anions from aqueous environment, deliver them to safe locations and, by using our knowledge of molecular machines, to release them into captivity using a photo-driven light switch – which is where we were able to highlight our use of aryl-triazole foldamers.

New goals include the chelation, sensing, regulation, and transport of chloride in biological mileu.

We have leveraged our understanding of receptor design and CH based hydrogen bonding to create a wholly new class of macrocyclic receptors, called cyanostars. We made a couple of exciting discoveries during our initial studies, as outlined in the Nature Chemistry article. First, the macrocycles can be made in one pot with high yields (>80%) and on 10-g scales. Second, we were able to bind anions like PF6 that were originally thought to be non-coordinating and then, after re-evaluation in the 1970's to be "weakly coordinating" – perhaps that idea needs to be completely reformulated because of the extremely high affinities observed with cyanostars showing logK ~ 12. Third, we created a new class of anion-templated rotaxanes using dialkylphosphates. All of these discoveries represent areas for deeper understanding and further exploration.


NSF-CAREER Award (CHE-0844441, 2009–2014)

DOE-BES (2009–2012, 2012–2015)

Indiana University (FRSP and Collaborative Research Award)

References for the Triazolophanes and Aryl-triazole Series

97. Ramabhadran, R. O.; Liu, Y.; Hua, Y.; Ciardi, M.; Flood, A. H.; Raghavachari, K., An Overlooked yet Ubiquitous Fluoride Congenitor: Binding Bifluoride in Triazolophanes using Computer-Aided Design, J. Am. Chem. Soc. 2014, ASAP DOI

96. Ramabhadran, R. O.; Hua, Y.; Flood, A. H.; Raghavachari, K., C vs N: Which End of the Cyanide Anion is a Better Hydrogen Bond Acceptor?, J. Phys. Chem. 2014, accepted

93. Hua, Y; Liu, Y; Chen, C.-H.; Flood, A. H., Hydrophobic Collapse of Foldamer Capsules Drives Picomolar-Level Chloride Binding in Aqueous Acetonitrile Solutions, J. Am. Chem. Soc. 2013, 135, 14401–14412. DOI

90. Lee, S.; Flood, A. H., Photoresponsive receptors for binding and releasing anions (Mini Review), J. Phys. Org. Chem. 2013 26, 79-86. Cover Art DOI

83 Lee, S.; Flood, A. H., Binding anions in rigid and reconfigurable triazole receptors, Topics Het. Chem. 2012, 28, 85-107. DOI

82 McDonald, K. P.; Hua, Y.; Lee, S.; Flood, A. H., Shape Persistence Delivers Lock-and-Key Chloride Binding in Triazolophanes, Chem. Commun. 2012, 48, 5065-5075. Cover Art DOI

81 Flood, A. H., Profile: Early Excellence in Physical Organic Chemistry J. Phys. Org. Chem. 2011 DOI

80 McDonald, K. P.; Ramabhadran, R. O.; Lee, S.; Raghavachari, K., Flood, A. H., Polarized Naphthalimide CH Donors Enhance Cl Binding Within an Aryl-Triazole Receptor, Org. Lett. 2011, 13, 6260-6263. DOI

78 Ramabhadran, R. O.; Hua, Y.; Flood, A. H.; Raghavachari, K., From Atomic to Molecular Anions: A Neutral Receptor Captures Cyanide using Strong C–H Hydrogen Bonds, Chem. Eur. J. 2011, 17, 9123-9129. DOI

75 Hua, Y.; Ramabhadran, R. O.; Karty, J. A.; Raghavachari, K.; Flood, A. H., Two levels of conformational pre-organization consolidate strong CH hydrogen bonds in chloride-triazolophane complexes, Chem. Commun. 2011, 47, 5979-5981. DOI

74 Zahran, E. M.; Hua, Y.; Lee, S.; Flood, A. H.; Bachas, L. G., Ion-selective electrodes based on a pyridyl-containing triazolophane: Manipulating halide selectivity by mixing dipole-promoted cooperativity with hydrogen bonding, Anal. Chem. 2011, 83, 3455-3461. DOI

73 Hua, Y.; Ramabhadran, R. O.; Uduehi, E. O.; Karty, J. A.; Raghavachari, K.; Flood, A. H., Aromatic and aliphatic CH hydrogen bonds fight for chloride while competing alongside ion pairing within triazolophanes, Chem. Eur. J. 2011, 17, 312-321. DOI.

72 Hua, Y.; Flood, A. H., Flipping the switch on chloride concentrations with a light-active foldamer, J. Am. Chem. Soc. 2010, 132, 12838-12840. DOI.

70 Lee, S.; Hua, Y. Park, H.; Flood, A. H., Intramolecular hydrogen bonds preorganize aryl-triazole receptor into a crescent for chloride binding, Org. Lett. 2010, 12, 2100-2101. DOI

66 Hua, Y.; Flood, A. H., Click chemistry generates priviliged CH hydrogen-bonding triazoles: the latest addition to anion supramolecular chemistry, Chem. Soc. Rev. 2010, 39, 1262-1271. DOI

65 McDonald, K. P.; Hua, Y.; Flood, A. H., 1,2,3-Triazoles and the Expanding Utility of Charge Neutral CH•••Anion Interactions, Anion Receptors Special Issue in Topic in Heterocyclic Chemistry, Springer, 2010. DOI

63 Zahran, E.; Hua, Y.; Li, Y.; Flood, A. H.; Bachas , L. G., Triazolophanes: A new class of halide-selective ionophores for potentiometric sensors, Anal. Chem. 2010,  82, 368-375. DOI

60 Bandyopadhyay, I.; Raghavachari, K.; Flood, A. H., Strong CH•••halide hydrogen bonds from 1,2,3-triazoles quantified using pre-organized and shape-persistent triazolophanes, ChemPhysChem. 2009, 10, 2535-2540. DOI

59 Li, Y.; Vander Griend, D. A.; Flood, A. H., Modelling triazolophane-halide binding equilibria using Sivvu analysis of UV-vis titration data recorded under medium binding conditions, Supramolec. Chem. 2009, 21, 111-117. (Special Issue for the III International Symposium on Macrocyclic and Supramolecular Chemistry, Las Vegas 2008), DOI

55 Li, Y.; Pink, M.; Karty, J. A.; Flood, A. H., Dipole-Promoted and Size-Dependent Cooperativity between Pyridyl-Containing Triazolophanes and Halides Leads to Persistent Sandwich Complexes with Iodide, J. Am. Chem. Soc., 2008, 130, 17293-17295. DOI

53 Li, Y.; Flood, A. H., “Strong, size-selective, and electronically-tunable C–H•••halide binding with steric control over aggregation from synthetically modular, shape-persistent [34]triazolophanes, J. Am. Chem. Soc. 2008, 130, 12111-12122. DOI

52   Li, Y.; Flood, A. H., "Pure CH hydrogen bonding to chloride ions: A pre-organized and rigid macrocyclic receptor," Angew. Chem. Int. Ed. 2008, 47, 2649-2652. DOI

See also the news coverage by: Chem. & Eng. News,NatureChemistry World




CS Dimer

References for the Cyanostar Series

91. Lee, S.; Chen, C.-H.; Flood, A. H., A pentagonal cyanostar macrocycle with cyanostilbene CH donors binds anions and forms dialkylphosphate [3]rotaxanes, Nature Chem. 2013, 5, 704-710. DOI

See also the news coverage by: Chem. & Eng. News,NSFAnalytical Scientist



2. Molecular Machines and Assemblies

Molecular robots are electromechanical machines that are integrated with feedback control systems to achieve autonomous operation at the nanoscale. This goal is increasingly becoming a reality. While many molecular actuators, in the form of molecular machines, are being realized, the true revolution in control will come once we begin to understand the mechanisms of motion. To this end, we are focused on quantifying the thermodynamics and kinetics of movement. We also contend that the integration with control systems will be facilitated with voltage-gated molecular systems. With that goal in mind, we have developed redox-active ligands that can serve as switches to the investigation of mechanical motion at the molecular level. Attention is focused on the Cu(I) as a labile transition metal coupled with non-innocent bridging ligands. . We intend to broaden the diversity of ligand-based switching to other metals and extend the complexity of what can be achieved using catenates and rotaxanes that can perform a range of functions -- such as molecular muscles. See also our work on light-driven foldamers for binding and releasing anions.


94. Benson, C. R.; Hui, A. K.; Parimal, K.; Cook, B. J.; Chen, C.-H.; Lord, R. L.; Flood, A. H.; Caulton, K. C., Amplifying the Redox Activity of a bis-Tetrazine Pincer Ligand, Dalton. 2014, 43, online. DOI

93. Manck, L. E.; Benson, C. R.; Share, A. I.; Park, H.; Vander Griend, D. A.; Flood, A. H., Self-Assembly Snapshots of a 2×2 Copper(I) Grid, Supramol. Chem. 2014, 26, accepted (Special Issue for the ISMSC-8, Arlington, VA, July 7-11, 2013)

88. Book Chapter: Benson, C. R.; Share, A. I., Flood, A. H., Bioinspired Molecular Machines, in Bioinspiration and Biomimicry in Chemistry: Reverse Engineering Nature, Ed. Swiegers, G. F., Wiley, Hoboken, 2012. ebook

85. Book Chapter: Flood, A. H.; Kaifer, A. E., Supramolecular Electrochemistry, (Volume 2: Techniques), in Supramolecular Chemistry: From Molecules to Nanomaterial, Eds. Gale, P. A.; Steed, J. W., John Wiley and Sons, 2012. DOI

78 Parimal, K.; Vyas, S.; Chen, C.-H.; Hadad, C. M.; Flood, A. H., Bond Elongation in the Anion Radical of Coordinated Tetrazine Ligands: A Crystallographic, Spectroscopic and Computational Study of a Reduced {Re(CO)3Cl} Complex, Inorg. Chim. Acta. 2011, 374, 620-626. Special Issue Dedicated to Wolfgang Kaim. DOI

68 Parimal, K.; Witlicki, E. H.; Flood, A. H., Two different classes of architectures can be interconverted by reduction of a self-sorting mixture, Angew. Chem. Int. Ed. 2010, 49, 4628-4632. DOI

67 Share, A. I.; Flood, A. H., Thinking inside and outside the box (News and Views Article), Nature Chem. 2010, 2, 349-350. DOI

66 Share, A. I.; Parimal, K.; Flood, A. H., Bi-lability is defined when one electron is used to switch between concerted and step-wise pathways in Cu(I)-based bi-stable [2/3]pseudorotaxanes, J. Am. Chem. Soc. 2010, 132, 1665-1675. DOI

62 Li, G.; Parimal, K.; Vyas, S.; Hadad, C. M.; Flood, A. H.; Glusac, K. D., Pinpointing the extent of electronic delocalization in the Re(I)-to-tetrazine charge-separated excited state using time-resolved infrared spectroscopy, J. Am. Chem. Soc. 2009, 131, 11656-11657. DOI

57 McNitt, K. A.; Parimal, K.; Share, A. I.; Fahrenbach, A. C.; Witlicki, E. H.; Pink, M.; Bediako, D. K.; Plaisier, C. L.; Le, N.; Heeringa, L. P.; Vander Griend, D. A.; Flood, A. H., Reduction of a redox-active ligand drives switching in a Cu(I) pseudorotaxane by a bimolecular mechanism, J. Am. Chem. Soc. 2009, 131, 1305-1313. DOI

47     Li, Y.; Huffman, J. C.; Flood, A. H. “Can Terdentate 2,6-Bis(1,2,3-Triazol-4-yl)Pyridines form Stable Coordination Compounds?” Chem. Commun. 2007, 2692-2694. DOI

Book Chapter

* Flood, A. H.; Kaifer, A. E., Supramolecular Electrochemistry, for Supramolecular Chemistry: From Molecules to Nanomaterials, Eds. Steed, J. W.; Gale, P. A. John Wiley and Sons, in press

Collaborations on Molecular Switches

We are extending the capabilities learnt on Cu(I)-based supramolecular switches to redox-active systems of collaborators


Yi Liu

54 Koshkakaryan, G.; Parimal, K.; He, J.; Zhang, X.; Abliz, Z.; Flood, A. H.; Liu, Y., pi-Stacking enhanced dynamic and redox-switchable self-assembly of donor-acceptor metallo-[2]catenanes from diimide derivatives and crown ethers, Chem. Eur. J. 2008, 14, 10211-10218. DOI


Jan O Jeppesen

90. Sorensen, A.; Andersen S. S.; Flood, A. H.; Jeppesen, J. O., Pressure effects in the synthesis of isomeric rotaxanes, Chem. Commun. 2013, 49, 5936–5938. DOI

87. Andersen, S. S.; Jensen, M.; Sorensen, A.; Miyazaki, E.; Takimiya, K.; Laursen, B. W.; Flood, A. H.; Jeppesen, J. O., Anion effects on the cyclobis(paraquat-p-phenyelen) host, Chem. Commun. 2012, 48, 5157-5159. DOI

82 Hansen, S. W.; Stein, P. C.; Sorensen, A.; Share, A. I.; Witlicki, E. H.; Kongsted, J.; Flood, A. H.; Jeppesen, J. O., Quantification of the pi-pi Interactions that Govern Tertiary Structure in Donor-Acceptor [2]Pseudorotaxanes, J. Am. Chem. Soc. 2012, asap. DOI

49   Nygaard, S.; Laursen, B. W.; Hansen, T. S.; Bond, A. D.; Flood, A. H.; Jeppesen, J. O., “Preparation of cyclobis(paraquat-p-phenylene)-based [2]rotaxanes without flexible glycol chains”, Angew. Chem. Int. Ed. 2007, 46, 6093-6097. DOI

48    Nygaard, S.; Hansen, S. W.; Huffman, J. C.; Jensen, F.; Flood, A. H.; Jeppesen, J. O. “Two Classes of Alongside Charge-Transfer Interactions Defined in One [2]Catenane,” J. Am. Chem. Soc. 2007, 129, 7354-7363. DOI

46    Nygaard, S.; Liu, Y.; Stein, P. C.; Flood, A. H.; Jeppesen, J. O. “Using Molecular Force to Overcome Steric Barriers in a Spring-Like Molecular Ouroborous,” Adv. Funct. Mat. 2007, 17, 751-762.

42    Nygaard, S.; Flood, A. H.; Jeppesen, J. O.; Bond, A. D. “Cis- and Trans-Bis(2-cyanoethylsulfanyl)(decane-1,10-diyldithio)Tetrathiafulvalene,” Acta. Cryst. C 2006, 62, 677-680.



3. Active Plasmonics

Active molecular plasmonics involves the manipulation of light at the nanoscale using functional chromophores. Presently, large progress has been made in generating reproducible nanopatterns with tunable plasmons. The opportunity now emerges to interface functional molecules to these surfaces that have the potential information processing and sensing. However, fundamental questions remain such as how to tune molecular chromophores to couple the plasmons of patterned surfaces. This research program harnesses synthesis, spectroscopy and theory to address this question using colored host-guest complexes as the functional units. Here at IU, we make use of surface-enhanced resonance Raman scattering (SERRS) spectroscopy to quantify the coupling between plasmon and chromophore. Insight gained from these studies will also allow for quantitative studies of the numbers and identities of molecules on surfaces – laying the foundation for sensing.


75 Witlicki, E. H.; Johnsen, C.; Hansen, S. W.; Silverstein, D. W.; Bottomley, V. J.; Jeppesen, J. O.; Wong, E. W.; Jensen, L.; Flood, A. H.* Molecular Logic Gates Using Surface-Enhanced Raman-Scattered Light, J. Am. Chem. Soc.. 2011, 133, 7288–7291. DOI

70 Witlicki, E. H.; Andersen, S. S.; Hansen, S. W.; Jeppesen, J. O.; Wong, E. W.; Jensen, L. Flood, A. H., Turning on resonant SERRS using the chromophore-plasmon coupling created by host-guest complexation at a plasmonic nanoarray, J. Am. Chem. Soc. 2010, 132, 6099-6107. DOI

61 Witlicki, E. H.; Hansen, S.; Christensen, M.; Hansen, T.; Nygaard, S.; Jeppesen, J. O.; Wong, E. W.; Jensen, L.; Flood, A. H., Determination of binding strengths of a host-guest complex using resonance Raman scattering, J. Phys. Chem. A 2009, 113, 9450-9457. DOI



4. Dynamic 2D Crystals

In collaboration with Steve Tait, we are investigating the design rules that control the organization of molecules under conditions of dynamic self-assembly when they order on graphite surfaces. We take advantage of molecular design to test how the information encoded into the molecules dictate their packing on the surface. We employ scanning tunneling microscopy (STM) to generate images, e.g., 50 x 50 nm, that often afford sub-molecular resolution to generate 2D crystal structures. Ongoing projects are focussing on the ordering and anion-binding chemistry of aryl-triazole oligomers.


Co-advised student: Brandon E. Hirsch

Image courtesy of Kenji Matsuda, University of Kyoto



Past Projects