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Research Vision


The size of my research group hovers around the 35 mark. Nowadays, it is composed, for the most part, of postdoctoral fellows and a few graduate students. Visitors at the undergraduate, graduate and faculty levels are made welcome. When it comes to the generation of new research projects, the dynamic is largely a bottom-up one. I encourage in-coming group members to introduce themselves into our midst in an incremental manner. Following short meetings with every present group member on arrival, the in-coming researcher is encouraged to join a team or two in the research laboratory. Once established, the group member is challenged to come up with his or her own ideas and assume the role of being a team-leader. Not only do I promote team-work within my group but I also look to members of my group to establish collaborations with other research groups at Northwestern University (NU). One of the major strengths of research in chemistry and materials science at NU is the fact that “we hunt in packs.”

The intellectual life of my group is sustained by weekly meetings held on Saturdays, starting at 11 am with a delivery of pizzas. Three members of the group present their most recent accomplishments in research. This meeting, which is held throughout the year, is called Group Therapy (GT) in order to differentiate it from the weekly Group Meeting (GM) which is held during term time at 5 pm on Wednesdays. GM is run like a tennis tournament, where three group members each select and speak about a recent article from the literature. After the presentations, votes are cast online to evaluate the speakers’ ability to discuss relevant background information, the paper’s contents, and a critical review. The presenter with the most votes goes forward to the next round; two semi-final rounds are followed by a final one, completing the competition.

The ambience that prevails in the research laboratory has earned the nickname of being called the Research Palace or RP for short.

When it comes to the writing up of research for publication, teams led by the first author produce drafts of a manuscript and supporting information to which I respond with written comments. Drafts can run anywhere between two or three up to more than a dozen. Before a manuscript is submitted all the authors meet in our Conference Room for a read-through. These events are highly interactive and enjoyable.

Beauty in a New Chemical Bond

Much has already been said and written about the presence of beauty in chemistry. For some chemists, beauty lies in the shape and clarity of a crystal or in the color or texture of a pigment. For others as chemists, beauty is expressed by wholly synthetic Platonic and Archimedean molecular structures, such as cubane, dodecahedrane and Buckminsterfullerene, for they can be prized for their symmetry, simplicity and uniformity. Put it another way, these structures, and many more into the bargain, are simply beautiful and beautifully simple. When, going back half a century ago, natural products, and the often referred to art of their synthesis, was all the rage, many in the chemical community were brainwashed by the great and good of the age into admiring this kind of technical wizardry for its complexity, elegance and sophistication. One can question whether it was art, or more likely, in my humble opinion, molecular engineering of exquisite beauty for those with an encyclopedic knowledge of chemical reactions.

For my own part, molecular nanotechnology has uncovered many other avenues to associate beauty with chemistry that include beautiful new ways of representing molecules using graphical representations which can be described more crudely as cartoons! My own abiding interest in molecular nanotechnology has revolved around the wonders of the mechanical bond which is ubiquitous in the macroscopic world, but has only seriously visited the molecular world during little more than the past quarter-of-a-century or so.

One of the really beautiful hallmarks of chemistry is its ability – because of its all-important making component – to keep reinventing itself over and over again. This endearing virtue places the chemist in the same arena as a painter of pictures or a sculptor of statues or a composer of music. I found myself acting out this privileged role, starting way back in the 1980s, as a maker of molecules with a brand new bond – the mechanical bond – which opened the door to crafting and producing mechanically interlocked molecules, or MIMs for short. These MIMs have arguably, not only played a central role in revolutionizing molecular nanotechnology, but they have also initiated a paradigm shift towards much more aesthetically pleasing and artistically attractive illustrations of molecules – call them graphic representations or cartoons, if you like – in the scientific literature. These eye-catching representations of MIMs are now part of the chemical lexicon, be they a molecule with two or more interlocked rings which we call a catenane, a name derived from the Latin word catena meaning chain – or a molecule, comprised of a dumbbell-shaped component, wherein a rod is threaded through one or more rings with ends (stoppers) that are too bulky for the rings to bypass – that we call a rotaxane, a name derived from the Latin words rota for a wheel and axis meaning axle.

Mechanical bonding has pervaded the natural world from time immemorial. Nature has been using mechanical bonds long before we humans came on the scene. DNA Catenanes (and knots) have constituted some of the front runners among the players in the field of biological MIMs. We are reminded constantly that Nature executes the chemistry of the mechanical bond with a level of elegance, complexity and beauty that will remain a source of inspiration to synthetic chemists for centuries to come.

Nowhere is the beauty of the mechanical bond more pervasive than in the art world. Artists have been drawing, painting and carving mechanical bonds for thousands of years. A class of MIMs that is worthy of special mention is that of the Borromean rings, a topology which consists of three rings mechanically interlocked in such a manner that the breaking of any one ring results in the whole caboodle falling apart. The mutual dependence, expressed by this topology, has rendered these rings a powerful symbol for threefold unification, originating in name from three wings of the Borromeo family in what is now known as northern Italy. It was the mechanical and physical beauty of this prevalent piece of topology present in so much art—not to mention logos—spanning many cultures for centuries, that inspired us to set out and finally make the molecular Borromean rings. After a decade of failed attempts, in 2004 we were able to synthesize the first-ever molecular Borromean rings using an approach known as dynamic covalent chemistry, which brings together no less than 18 components in one fell swoop. The dynamic nature of the synthesis also led, with a very small change in reaction conditions, to the formation of a Solomon knot (link), in which two of the three rings present in the Borromean rings form a doubly interlocked catenane. This particular topology is unconditionally handed (chiral), leading to pairs of MIMs that are related to each other as an object is to its mirror image, yet are non-superimposable and become, therefore, what chemists call a racemic mixture of enantiomers.

The mechanical bond is an integral part of our everyday lives. Rings, necklaces and belts, not to mention shirts and pants (trousers), all form mechanical bonds with our bodies and with themselves. Even before we learn how to walk and talk, we will most likely have become familiar with a vast range of mechanically interlocked toys, of which a rattle – reminiscent of a rotaxane – is one of the more common examples that undoubtedly played a part in my own design and synthesis in 1991, for the first time, of a molecular shuttle based on a degenerate rotaxane architecture. The introduction of bistability, by the breaking of symmetry, of a palindromic molecular shuttle led to molecular switches and ultimately molecular machines – all examples of MIMs based on the in-depth understanding and exploitation of the mechanical bond.

The journey from the playpen to being able to play life’s games, from understanding Nature to an appreciation of art, from learning about the microscopic world to mechanical and electrical engineering has been one of sheer joy for me. There is no denying that enjoyment is a beautiful experience, particularly when you realize that the physics which dictate the workings of micro- and nanomachines are not the physics that define and control the macroscopic world we know so well. Beauty is to be found in surprises that force us to think differently about the biological world in which we live and die. When it comes to making molecular machines, e.g., elevators, that remind us of ones we use every day then be prepared to accept that their mode of operation will be governed either by flashing energy ratchets or information ratchets. In many ways small is more beautiful than we might expect at first glance.

While there are probably many thousands of new chemical compounds that are made every week in chemical laboratories all around the world and, in any one year there may well be discovered several dozen genuinely new chemical reactions, it is only once in a blue moon that a new chemical bond, which rivals the strength of that old (covalent) chemical bond, breaks upon the scene. When something that is really new happens, it offers the opportunity to call into question the bigger picture. So it was with the advent of the mechanical bond. Not only did it open the door to the introduction of graphical representations and cartoons, it also called out loudly for the use of color to enhance the grey message that had been the use of black-and-white in chemistry for more than a century. Much to the chagrin of some in the chemical community, reds and blues, greens and purples, oranges and pinks started to invade chemistry journals starting in the late 1980s. To this day, the “little blue box” occupies a special place in chemistry, while the use of color has become commonplace throughout the chemical literature. Although, on occasions, it might come at a price, the beauty that we all associate with color has done much to brighten up chemistry, making it more accessible, more understandable and more pleasurable.



Research Key Words

Analytical Chemistry / Batteries / Biological Chemistry / Bistable Systems / Carbohydrate Chemistry / Catalysis / Catenanes / Chemical Topology / Chirality / Circular Dichroism / Coordination Chemistry / Crown Ethers / Crystallography / Cucurbiturils / Cyclodextrins / Dendrimers / Drug Delivery Systems / Dynamic Covalent Chemistry / Electrochemistry / Emergent Behavior / Flashing Energy Ratchets / Gold Chemistry / Hydrogen Bonding / Inorganic Chemistry / Information Ratchets / Isothermal Titration Calorimetry / Liquid Crystals / Macrocyclic Chemistry / Macromolecular Chemistry / Mass Spectrometry / Materials Chemistry / Mechanical Bonds / Mechanically Interlocked Molecules / Mechanostereochemistry / Mesoporous Silica Nanoparticles / Metal-Organic Frameworks / Molecular Belts / Molecular Borromean Rings / Molecular Boxes / Molecular Cages / Molecular Knots / Molecular Mechanics / Molecular Machines / Molecular Motors / Molecular Nanotechnology / Molecular Pumps / Molecular Recognition / Molecular Shuttles / Molecular Solomon Knots / Molecular Switches / Noncovalent Bonding Interactions / Nuclear Magnetic Resonance Spectroscopy / Out-of-Equilibrium Systems / Photochemistry / Physical Chemistry / Physical Organic Chemistry / Polymer Chemistry / Radical Chemistry / Rotaxanes / Second-Sphere Coordination / Self-Assembled Monolayers / Self-Assembly / Self-Replication / Stereoelectronic Effects / Stereochemistry / Structure-Directed Synthesis / Supramolecular Chemistry / Supramolecular Polymers / Template-Directed Synthesis / Synthetic Chemistry / Unnatural Product Synthesis.


Boxes and Cages

Cyclobis(paraquat-p-phenylene) – a bipyridinium-based cyclophane – plays a central role in the development of mechanically interlocked molecules and molecular machines. A synthetic protocol, using tetrabutylammonium iodide as a catalyst, facilitates the extension of this cyclophane, resulting in a series of extended cyclophanes using a wide range of building blocks. We are exploring the emergent properties of these pyridinium-based cyclophanes, whose roles cover ground that spans (i) synthetic methodology, (ii) extraction and sequestration, (iii) physical organic chemistry, (iv) supramolecular chemistry, (v) catalysis and (vi) molecular electronics.


CD-Containing Frameworks


Renewable, edible, and extended porous frameworks—namely cyclodextrin-based metal‒organic frameworks (CD-MOFs) derived from γ-cyclodextrin (γ-CD) and alkali metal salts—constitute a class of metal-organic frameworks (MOFs) that can be synthesized from nontoxic, naturally occurring starting materials on a bulk scale. On account of the chiral building units present (γ-CD) present in CD-MOFs, they have the ability to exhibit molecular recognition and enantiomeric differentiation. Our research focuses on the development of new porous materials by adding to the family of CD-MOFs and increasing their moisture stability, as well as probing their versatile applications potential in areas such as gas sensing, adsorption and separation, chiral differentiation, template syntheses of metal-based nanoparticles and gels, electronic memory, optical materials, drug delivery, and catalyst stabilization.


Drug Delivery

The development of new methods to administer drugs with low solubility or bioavailability, limited chemical stability, along with the need to deliver drugs selectively, and to targeted locations around the body, are amongst the most critical areas of research in drug development. Effective delivery of drugs into live-cells with spatiotemporal control is, however, challenging, on account of the fact that lots of these drug molecules cannot freely enter through the cell membrane, and they lack sustained release on reaching their target. Our research into drug delivery in the Stoddart group focuses on the exploitation of supramolecular architectures for developing smart drug formulations—employing mechanically interlocked molecules (MIMs) based porous nanoparticles, cyclodextrin metal-organic frameworks (CD-MOFs) and their composites, and cyclophanes—for targeted and programmed drug delivery into mammalian cells and in animal models.  We are also working on developing next-generation drug formulations by using artificial molecular machines (AMMs).


Energy Storage

The battery community is paying increasing attention to post-lithium (Li)-ion batteries, which can transcend current Li-ion batteries with respect to key electrochemical properties, cost, and safety. As a promising alternative, rechargeable aluminum batteries (ALBs) and aqueous rechargeable zinc batteries (ZBs) are gaining considerable attention since they are cost-effective, safe and environmentally benign. ALBs and ZBs, however, still linger at the research stage, awaiting the development of high-performance cathode materials. Research on Energy Storage in the Stoddart group focuses on developing emerging materials such as redox-active macrocycles and conductive metal-organic frameworks (MOFs) in order to supply cathode materials for ALBs or ZBs.

Molecular Belts


Hydrocarbon belts (HCBs) have fascinated scientists for over half a century because of their aesthetically appealing structures and potential applications in carbon nanotechnology. The foremost challenge in the synthesis of HCBs is how to build up the accumulation of energy in these highly strained structures. Successful constructions of HCBs offer, not only well-defined templates, but also practical principles that could be useful in the atomically precise and structurally predictable synthesis of uniform carbon nanotubes (CNTs) with singular chiralities—a long-standing goal in nanocarbon science.

Over three decades ago, we pioneered regio- and diastereoselective approaches to precursors of [12]cyclacene and accomplished the synthesis of [12]collarene in 1988 on the eve of the isolation of CNTs. We are currently making efforts to aromatize the partially saturated precursors into the fully fused and conjugated molecules with belt shapes—namely belt[12]arene and belt[14]arene.

Molecular Electronics

Understanding the movement of electrons to and through a single molecule is central to the field of molecular electronics which has been investigated for more than 40 years. When it comes to supermolecules or mechanically interlocked molecules (MIMs), the situation becomes more complicated. Not only is the focus on the charge transport within an individual supermolecule, but one must also pay special attention to the delicate and complex weak interactions between different components in complexes and in MIMs. Research in the Stoddart Group covers three different scales, starting with (i) investigation of the single-molecule transport properties of macrocycles and macrobicycles and their related host-guest supermolecules, (ii) followed by detecting and manipulating the weak interactions in supermolecules and MIMs, and (iii) finally applying the fundamental knowledge gained in the first two stages to construction of new single-molecule functional devices and even integrated circuits.


Molecular Machines

The design and synthesis of functional molecules with machine-like behavior enable chemists to pursue chemistry away-from-equilibrium. Mechanically interlocked molecules (MIMs) have been at the forefront of this research endeavor towards the production of molecular machines which can open doors to unprecedent research opportunities. We have designed and synthesized a so-called artificial molecular pump, a subset of artificial molecular machines, which is employed to produce enthalpically and entropically demanding rotaxanes and polyrotaxanes.


Molecular Photochemistry


The phenomenon of photoluminescence (PL) from exciplexes presents countless opportunities for applications. Although PL has been investigated extensively,  less is known about the precise control of the molecular aggregates and their persistence at very low concentrations. Our approach to obtaining permanent exciplex PL begins with the incorporation of anthracene moieties into pyridinium-containing mechanically interlocked molecules (MIMs). The difference in the optical properties of the anthracene-based cyclophanes and the precursor homo[2]catenane are consistent with the role of the mechanical bond in the emergence of the low energy exciplex emission in the catenane. Furthermore, this exciplex emission has been detected under high-dilution conditions and applied successfully in live-cell imaging. These results shed light on the importance of photoactive polyaromatic components like anthracene as self-templating systems for promoting the formation of homo[2]catenanes, while the mechanical bond can bring fluorophores into close proximity for generating permanent exciplex emissions.

Porous Materials

Hydrogen-bonded organic frameworks (HOFs), assembled from organic molecules by means of hydrogen bonding, are emerging as promising porous materials in conjunction with metal-organic and covalent-organic frameworks (MOFs and COFs) thanks to their ease of their synthesis under mild conditions and their solution processabilities that are generally not characteristic of robust polymeric networks. We have been exploring the use of triptycenes with peripheral aryl carboxyl groups as the building blocks to assemble 3D HOFs. These peripherally extended triptycenes (PETs), which exhibit a rigid trigonal prismatic geometry, can form porous HOFs with a variety of complex 3D supramolecular architectures. Our research in this area focuses on 1) the discovery and design of 3D HOFs with mechanically interlocked network topologies, and 2) the utilization of these porous frameworks for molecular recognition and separation.

Supramolecular Systems

Supramolecular systems explore the properties and functions beyond molecules. Molecular recognition, a central theme of supramolecular chemistry, is the key to unlocking and releasing the hidden potential of supramolecular materials. In the Stoddart group, we design and synthesize molecular receptors with tunable cavity sizes and shapes, which selectively and effectively recognize various functional substrates and realize emergent functions in separation, catalysis, stabilization, imaging, sensing, capture and release.


Current Research

A Precise Polyrotaxane Synthesizer / Yunyan Qiu

Publications – 1193

The assembly line-like emergence of polyrotaxanes with increasingly higher energies by harnessing artificial molecular pumps to deliver tetracationic rings in pairs by cyclical redox-driven processes has been reported in Science. This controlled strategy leads to the precise installation of two, four, six, eight, and 10 rings carrying 8+, 16+, 24+, 32+, and 40+ charges, respectively, onto hexacationic polymer dumbbells. This strategy allows for the production of away-from-equilibrium polyrotaxanes with control over the numbers, sequences, and functions of threaded rings. This research program is opening up new avenues that represent little more than the tip of the iceberg.

Molecular-Pump-Enabled Polymerization / Kang Cai

Publications – 1192

A kinetically stable daisy chain polymer has been synthesized out-of-equilibrium, using a self-complementary monomer by means of a redox-controlled molecular pumping process. The polymer can also be depolymerized and thus the monomer recycled under redox control.

Suit[4]ane / Wenqi (Vince) Liu

Publications – 1191

Suitanes are two-component mechanically interlocked molecules in which one (torso) of the components, with several protruding limbs, is encompassed by another (suit) all-in-one component. We have reported a suit[4]ane, wherein a porphyrin with its four protruding limbs, encompassed by a tricyclic cyclophane, rocks back and forth inside the cyclophane.

Cyclophane-Sustained Ultrastable Porphyrins / Wenqi (Vince) Liu

Publications – 1190

The encapsulation of free-base and zinc porphyrins by a tricyclic cyclophane receptor, XCage, is sustained by subnanomolar binding affinities in water. The resulting complexes demonstrate emergent photophysical enhancements and enjoy unprecedented chemical stabilities, where their D/H exchange, protonation, and solvolysis, under extremely acidic conditions, are completely blocked.

Non-Equilibrium Kinetics & Thermodynamics of Molecular Pumps / Yuanning Feng

Publications – 1189

Non-equilibrium kinetics and thermodynamics associated with transporters and pumps featuring different design principles — i.e., energy and information ratchet mechanisms have been summarized. The limitation of stochastic thermodynamics for catalytic processes has been discussed.

Mechanical-Bond-Induced Exciplex Fluorescence / Amine Garci

Publications – 1188

Our approach to obtaining permanent exciplex photoluminescence begins with the incorporation of anthracene moieties into pyridinium-containing mechanically interlocked molecules (MIMs). The difference in the optical properties of the anthracene-based cyclophanes and the precursor homo[2]catenane are consistent with the role of the mechanical bond in the emergence of the low energy exciplex emission in the catenane.

Ultraporous MOFs / Penghao Li

In Collaboration with – Farha Group / Zhijie Chen

Publications – 1184

The simulation-motivated synthesis of ultraporous metal–organicf rameworks (MOFs) based on metal trinuclear clusters, namely NU-1501-M (M=AlorFe), was realized. Relative to other ultraporous MOFs, NU-1501-Al exhibits a concurrently high gravimetric Brunauer−Emmett−Teller(BET) area of 7310 m2/g-1and av olumetric BET area of 2060 m2/cm-3. The high porosity and surface area of this MOF yielded impressive gravimetric and volumetric storage performances for hydrogen and methane.

Stabilizing Bisradicals with Mechanical Bond / Kang Cai

Publications – 1184

Two new highly charged [2]catenanes have been synthesized and isolated as air-stable singlet bisradicals displaying mixed-valency and multiple redox-states thanks to the unique nano-confinement induced by mechanical bonds in these catenanes.

Single-Crystal Polymers / Qinghui Guo

Publications – 1183

A new principle has been established for preparing single-crystal polycationic polymers utilizing an ultraviolet/sunlight-induced single-crystal-to-single-crystal photopolymerization on a gram-scale in quantitative yield from tricationic monomers possessing self-complementary building blocks.

Tetrazine Box / Qinghui Guo

Publications – 1182

We have made a TetrazineBox, which serves as a toolbox for probing the radical properties and generating efficiently a range of structurally diverse cyclophanes by box-to-box cascade transformations, taking advantage of either reductions or an inverse electron-demand Diels-Alder reaction.

Single-Molecule Conductance of Charged Cyclophanes / Hongliang Chen

Publications – 1181

Intramolecular circuits are built with two-channel charged cyclophanes. An interchannel gating effect and constructive quantum interference act synergistically, leading to a conductance that is 50-fold higher than that of a single-channel control, breaking the single-molecule superposition law.

XCage / Wenqi (Vince) Liu

Publications – 1180

A new tricyclic octacationic cyclophane, XCage, which has a stereoelectronic complementarity towards perylene diimide and shows a picomolar binding affinity in water, has been designed and synthesized.

Redox-Active Macrocycles for Zinc Batteries / Kwan Woo Nam

Publications – 1179

A two-dimensional (2D) conductive metal-organic framework (MOF) with large one-dimensional channels has been developed as a zinc battery cathode. Owing to its unique structure, hydrated Zn2+ ions which are inserted directly into the host structure, Cu3(HHTP)2, allow high-rate performance.

CD-Containing Hybrid Frameworks / Dengke Shen

Publications – 1178

A class of γ-cyclodextrin-containing hybrid frameworks (CD-HFs) has been synthesized, employing γ-cyclodextrin (γ-CD) as the primary building blocks, along with 4-methoxysalicylate (4-MS) anions as the secondary building blocks.

Semi-Artificial Photosynthetic System / Penghao Li

In Collaboration with – Farha Group / Zhijie Chen

Publications – 1177

A prototypical semi-artificial photosynthetic system for efficient carbon dioxide fixation was realized using a modified metal-organic framework NU-1006, which comprises a pre-installed Rh-based electron mediator and also encapsulates coenzyme NAD+/NADH.

Radical-Pairing Interactions in New Hosts / Kang Cai

Publications – 1176

The structure-property relationships between cavity sizes and binding affinities for radical-pairing interactions have been investigated using a series of bisradical dicationic cyclophanes (purple) with different linker units (Ar1 and Ar2 / light pink) to modulate their cavity sizes.

2D Tessellations by Charged Cyclophanes / Yassine Beldjoudi

Publications – 1175

Electron donor-acceptor cyclophanes are programmable building blocks which adopt different 2D tessellations using charge transfer (CT) interactions. The TTF–cyclophane 2D tessellations display dual intra- and intermolecular CT behavior, offering multi-responsive materials.

A molecular dual pump / Yunyan Qiu

Publications – 1172

A molecular dual pump, which consists of two individual pumps linked in a head-to-tail fashion, has been designed and synthesized for the controlled capture and release of a ring via a [2]rotaxane intermediate.

Conductive 2D MOFs for Zinc Batteries / Kwan Woo Nam

Publications – 1170

A redox-active triangular phenanthrenequinone-based macrocycle (PQ-Δ) with a rigid geometry has been developed as a zinc battery cathode. The macrocyclic nature of the PQ-Δ cathode provides a dramatically increased capacity and cyclability compared to that of traditional organic materials.

Cyclophane-Protected NDI Radical / Kang Cai

Publications – 1169

A new strategy has been presented which stabilizes the NDI•– radical anion and modulates its redox properties, by host-guest encapsulation and/or mechanical interlocking with a tetracationic cyclophane, namely, ExBox4+.

Artificial Allomelanin Nanoparticles / Yuanning Feng

In Collaboration with – Gianneschi Group / Xuhao Zhou

Publications – 1168

Artificial allomelanin nanoparticles (AMNPs), analogous to one type of melanin produced by radiation-resistant fungi, have been prepared with well-defined nanostructures. They can be taken up by human epidermal keratinocytes and act as radical scavengers.

A Supramolecular Diamond / Qinghui Guo

Publications – 1167

A unique approach has been established for constructing supramolecular diamond crystals with nanoporous diamondoid superstructures and octahedral shapes, resulting from the hierarchical self-assembly of preorganized hexa-charged molecules quantitatively within seconds under ambient conditions.

Cyclotris(paraquat-p-phenylenes) / Qinghui Guo

Publications – 1165

Redox-active and shape-persistent cyclophanes, namely CTPQT6+ and MCTPQT6+, which are the homologous tricyclic derivatives of the trademark Blue Box from our group, have been synthesized. These derivatives adopt triangular conformations and the 3D packing of MCTPQT6+ results in nanometer-sized channels in the solid state.

Supramolecular Polyknot / Penghao Li

Publications – 1166

A hydrogen-bonded three-dimensional porous supramolecular polyknot with unprecedented self-entangled topology is assembled from a rigid trigonal prismatic triptycene building block with six extended peripheral aryl-carboxyl groups.

Regulated Photodynamic Activity of a Photosensitizer / Indranil Roy

Publications – 1164

A multifunctional synthetic receptor ExBox4+ has been employed to achieve supramolecular photoprotection, lysosomal delivery, and pH-triggered release of a photosensitizer. The use of the ExBox4+ -bound photosensitizer in anticancer treatment using regulated photodynamic therapy is described.

Ligand-Directed Synthesis of Zr-MOFs / Penghao Li

In Collaboration with – Farha Group / Zhijie Chen

Publications – 1163

A series of zirconium-based metal-organic frameworks (Zr-MOFs), i.e. NU160X, with the edge-transitive alb net, was synthesized reticularly from 12-connected hexagonal Zr6 nodes and 6-connected trigonal-prismatic triptycene linkers. These Zr-MOFs exhibit remarkable activities toward the destruction of a nerve agent (Soman) and a nerve agent simulant.

In Situ Photoconversion of Multicolor Luminescence / Huang Wu

Publications – 1160

A photoluminescent supramolecular assembly, the fluorescence of which can be changed efficiently from yellow to blue in an in situ photo-controlled manner, has been prepared in two stages. Employing this assembly, white light emission can be realized expeditiously by a luminescence color-conversion process.

Cyclophane for Live-Cell Imaging / Indranil Roy

Publications – 1141

A glowing tetracationic cyclophane (ExTzBox•4Cl) with unity quantum yield has been synthesized and utilized for live-cell imaging. This work, which describes the significance of using box-like cyclophanes for bioimaging, holds promise for the development of multimodal imaging platforms.

Highly Porous acs-MOFs for Water Sorption / Penghao Li

In Collaboration with – Farha Group / Zhijie Chen

Publications – 1158

A series of non-catenated metal-organic frameworks based on the acs net (acs-MOFs), i.e. NU-1500, was synthesized from trivalent trinuclear metal (Fe3+, Cr3+ and Sc3+) clusters and 6-connected trigonal-prismatic linkers. The highly porous and hydrolytically stable NU-1500-Cr can be activated directly from water and displays an impressive water vapor uptake with a trace of hysteresis.

Interpenetration Isomerism in HOFs / Penghao Li

Publications – 1157

A trigonal prismatic triptycene building block assembles into either a two‐fold interpenetrated acs network (acs‐2 c) or a five‐fold interpenetrated acs network (acs‐5 c) depending upon the crystallization conditions.

Controllable Molecular Encapsulation with Dynamic Host / Huang Wu

Publications – 1156

When a photo-switchable oligo(p-phenylenevinylene) bipyridinium unit (light pink) is incorporated into a tetracationic cyclophane (light blue), it confers upon the cyclophane the ability to direct reversible guest (red and pink) capture and release using thermal and photo stimuli.




Ongoing Research


Nanocomposites for Heterogenous Photocatalysis / Yassine Beldjoudi

A supramolecular photosensitizer with efficient intersystem crossing was achieved by combining the spin-orbit coupling associated with heavy Br atoms in TBP and the photoinduced electron transfer in a TBPExbox4+ dyad. Incorporation of the TBPExbox4+ into PSS matrix forms a nanocomposite photosensitizer.

Self-Replicating Macrocycles / Baillie DeHaven

This project seeks to exploit the cooperativity between non-covalent interactions for the design of macrocycles capable of templating their own formation.

Systems Chemistry in Flow / Baillie DeHaven

This project seeks to utilize the synergy between experimental and computational science for the design and synthesis of wholly synthetic chemical systems that display complex behavior in out-of-equilibrium environments, in order to gain insight into processes important to the origin of life.

Probing Single-Molecule Reaction and Supramolecular Interaction Dynamics under Nanoconfinement / Hongliang Chen

Molecules with nanocavities—e.g., cages, CDs and CBs—provide an elegant platform to host two molecules which can undergo bimolecular reactions. The single-molecule technique will be used to monitor the reaction dynamics under nanoconfinement in order to provide more information compared with that hidden in ensemble experiments.

Single-Molecule Transistors / Hongliang Chen

Charged molecules—e.g., macrocycles, supermolecules and MIMs—have demonstrated excellent electrical performance in our previous projects. We will continue to explore the unique properties of these charged systems—including the Kondo effect and Coulomb blockade—and apply them in the construction of single-molecule transistors.

Photoswitchable Cyclophanes / Alan Enciso

We are currently developing cyclophanes capable of modifying their shapes upon light irradiation. Such stimulus-responsive molecular structures may lead to the fabrication of liquid crystal displays (LCDs) and advanced drug delivery systems.

Four-Stroke Molecular Rotary Motors / Yuanning Feng

Molecular motors in biological systems have inspired attempts to create artificial molecular machines that can produce controlled motion at the molecular level. A four-stroke molecular rotary motor has been designed and is being synthesized. This investigation features a revolutionary strategy to produce artificial molecular machines with the potential to perform work on their environment.

Dynamic Fluorescent Molecules / Yuanning Feng

Our group is working on new functional molecules that exhibit switchable fluorescent properties depending on their dynamic state. We are currently developing new molecular backbones with easy synthetic routes and tunable functional motifs.

Self-Replicating Supramolecular Polymers / Yuanning Feng

A new class of supramolecular polymers, in which cross-linking is mediated by noncovalent or dynamic covalent bonds, has expanded the potential applications of polymeric materials even further. We are making novel supramolecular polymers built up from a monomer that serves as an initiator for the autocatalytic, template-directed replication process to polymerization itself.

MIMs as New Probes for Live-Cell Imaging / Amine Garci

Recently, we reported an anthracene-based homo[2]catenane that emits long-lived and well-controlled exciplex fluorescence, even at the very dilute concentrations needed for imaging living cells. We are now working on expanding this new family of fluorescent homo[2]catenanes by incorporating other fluorophores, such as pyrene and perylene, into the pyridnium-containing mechanically interlocked structures.

Light-Triggered One-Step Downhill Movement / Qinghui Guo

While a molecular pump works repetitively and progressively to move molecules away-from-equilibrium uphill in energy, we are making a revised version of the molecular pump which is able to release the stored energy when triggered by light and do useful work in membranes.

Emergence of Chirality in HOFs / Penghao Li

We observed the emergence of chirality in hydrogen-bonded organicf rameworks (HOFs) in the form of a racemic mixture, from the chiral entanglement (Solomon link) of chiral networks which are assembled from chiral molecular building blocks. We are currently investigating the use of chiral solvents to induce the formation of homochiralHOFs.

3D Nanocarbons / Penghao Li

We are currently developing a divergent strategy to synthesize three-dimensional (3D) nanocarbons for the applications of porous materials and organic optoelectronics.

Single-Molecule Electronics in Confined Nanospaces / Wenqi Liu

The physical and chemical properties of a given molecule are dictated by the nanoenvironment surrounding the molecule. We are currently exploring the electronic properties of single molecules under the influence of molecular encapsulation.

Mechanically Interlocked Architectures Constructed by Dynamic Covalent Chemistry / Wenqi Liu

Dynamic covalent chemistry (DCC) features error-checking and proof-reading properties, which we are currently exploring to construct novel supramolecular and mechanically interlocked architectures such as linear and radial poly[n]catenanes.

The Utility of a Polyrotaxane Synthesizer / Yunyan Qiu

A precise polyrotaxane synthesizer, comprised of various ring-collecting polymer chains and artificial molecular pumps, will be utilized to produce sequence-controlled polyrotaxanes reflecting the co-constitutionally heterotopic nature of the rings.

Chiroptical and Switchable Mechanically Interlocked Systems / Masoud Rostami

A variety of stimuli-responsive molecular components are being developed in the Stoddart group, contributing to the design of mechanically interlocked systems towards the tuning of the chemistry and topology of the mechanical bond. Molecularmachines incorporating such structures may be capable of powering small gadgets like flexible digital screens.

Photon Upconversion in MOFs / Indranil Roy

The interaction of low-energy light with matter and the production of high-energy light is called photon upconversion. New strategies are being developed for harnessing upconversion in metal–organic frameworks.

Stitching Cyclophanes Together for Membrane Applications  / Indranil Roy

Two-dimensional polymers are being prepared by stitching together functionalized cyclophanes covalently. These polymers are being utilized as molecular-sieving membranes for water treatment applications.

Artificial Molecular Machines for Theranostics  / Indranil Roy

Artificial molecular machines are being used to achieve medical benefits—in particular, for theranostics applications—with molecular-level precision.

Porous Materials for Theranostics / Dengke Shen

γ-Cyclodextrin-containing frameworks (CD-MOFs) are a class of highly porous, biocompatible materials obtained from natural products. They have been widely used for drug encapsulation and drug delivery. We are designing and synthesizing a new type of crystalline nanocapsules based on CD-MOFs.

Radical-Induced Foldameric Oligorotaxanes / Long Zhang

Muscle fibers can switch conformations reversibly among different states under the influence of various stimuli and conditions. In order to emulate the behavior of biomolecules such as muscle fibers, we are interested in designing and synthesizing oligorotaxanes which, as a result of their redox properties, are capable of folding and unfolding in response to electrical stimuli.





Research Facilities

The main office suite is located in Ryan Hall and is divided into three offices of similar sizes, one for Dr Stoddart, one for Dr Margaret (Peggy) Schott, Dr Stoddart’s Personal Assistant, and one for use by visiting professors. Two new offices have been commissioned in the past year and house Stephanie Teterycz (Director of Operations) and Dr Mark Olson (Associate Research Professor).

The laboratory space devoted to wet chemistry is housed in Silverman Hall 2710 and comprises ca. 600 m2 of floor space equipped with 33 energy-efficient ultra-low flow fume hoods. Each fume hood is adjacent to personal work benches, while communal bench space accommodates laboratory equipment used routinely. Three interconnected rooms of about 50 m2 host a supplies delivery and check-in area, a flammable solvent storage cupboard, consumable supplies shelving, and a chemical waste collection area, in what is colloquially referred to as the “Boom Room”. Off of the main laboratory space, three instrumentation rooms (about 90 m2 of total space) house a selection of larger instruments and equipment, as well as providing additional storage space, and two extra fume hoods which are located in these rooms and are used for sample preparation. Across the hallway from the main laboratory space, a separate room (40 m2) houses the main chemical inventory (4000+ chemicals). Office space for postdoctoral fellows and graduate students is all along one side of the laboratory in the form of rooms that house 2–7 researchers. The laboratory also has an integral and dedicated conference room (18 seats) and a small cloakroom. Adjacent to the research laboratory is a shared meeting room. Both the conference room and meeting room are outfitted with A/V equipment. All this space has been designed and built to a remarkably high standard, so much so that it is referred to by the ca. 35 group members as the RP—which is short for the Research Palace!

Research Equipment

The research laboratory is well equipped with all the tackle one would wish for in a modern laboratory where making, measuring and modelling are carried out. Each fume hood is equipped with a minimum of two hot-plate stirrers, heating mantles, a vacuum pump, and a Schlenk-line for synthetic manipulations in inert atmosphere. In order to satisfy the workload of the laboratory, we run 11 rotary evaporators—each one with its dedicated vacuum pump and pressure controller—two centrifuges for sample separation, and 10 laboratory balances for weighing materials as low as 0.01 mg. Dry solvents for syntheses are produced in-house using a solvent purification/drying system (DMF/CH2Cl2/THF/MeCN/PhMe). We produce our own ultra-pure water (18 MOhm). In addition, we are equipped with three temperature-controlled ovens for sample preparation and drying, a spin-coater for thin-film deposition, an ozone-cleaner for surface activation, and three sonicators for cleaning, sample dispersion and dissolution.

The following pieces of equipment are available —

Argon Glove-Box

Equipment details: Pure Lab HE Two Glove-Box

How is this equipment helping our research?

  • Assemble lithium-ion batteries based on organic electrolytes
  • Perform reactions that are sensitive to moisture and oxygen
  • Grow single crystals of organic radicals that are very sensitive to oxygen and moisture.


Atomic Force / Scanning Tunneling Microscope

Equipment details: Asylum Research MFP-3D Origin / In-house built STM break junction

How is this equipment helping our research?

  • Surface imaging (x-y plane) on films, surfaces, and in liquid samples using AFM techniques
  • Superior force measurements (z-axis) on single molecules, complexes, and nanometer-scale structures
  • Acoustic isolation for vibration suppression
  • Glove-box enclosure for measurement in inert atmosphere (N2)
  • Electrochemical and liquid sample holders allow for the measurement of samples submerged in liquids and upon application of an electrochemical potential.
  • STM enables us to explore the electronic properties of individual molecules by ‘wiring’ them up into nanoscale junctions.


Battery Analyzer

Equipment details: MTI Corp. 8-channel battery analyzer

How is this equipment helping our research?

With this equipment we can evaluate the performance of batteries made in-house with a standard 2032 coin-cell, including charge-discharge cycles, capacity, and cycle life.



Equipment details: Gamry 600 Potentiostat

How is this equipment helping our research?

  • Measure oxidation and reduction potentials for electro-active molecules, including the number of electrons exchanged and the reversibility of the redox process, in aqueous and non-aqueous solvents
  • Determine binding constants for supramolecular systems, also in combination with spectrophotometric studies—spectroelectrochemistry
  • Determine electrochemical kinetic constants in supramolecular systems or mechanically interlocked molecules.
  • Perform bulk electrolysis using dedicated electrolytical cells with frit-, membrane- or a chamber-separated half-cell—preparative electrochemistry


Flash Chromatography

Equipment details: Teledyne ISCO Combiflash Rf 200 (normal phase) / Combiflash Nextgen 300+ (reverse phase)

How is this equipment helping our research?

  • Isocratic and gradient elution purification of reaction mixtures in medium-pressure flash chromatography conditions (0-120 bar)
  • Normal phase for low-medium polarity mixtures—Combiflash Rf 200
  • Reverse phase for polar and charged compounds (e.g., bipyridinium derivatives) on C18-functionalized silica—Combiflash Nextgen 300+
  • UV-Vis dual channel detection and automatic fraction collection
  • Screening of small-scale reactions (<50 mg) or purification of preparative scale reactions (1 g)



Equipment details: Horiba Fluoromax-4 Spectrofluorometer

How is this equipment helping our research?

  • Collect excitation and emission spectra on solutions, powders or films of emissive materials
  • Measure absolute quantum yields—using an integrating sphere
  • Determine excited state lifetimes—range 200 ps – 0.1 ms


Isothermal Titration Calorimeter

Equipment details: TA Instruments – Affinity ITC

How is this equipment helping our research?

Isothermal Titration Calorimetry is a physical technique used to determine the parameters of a binding event in solution. We can determine constants ranging from 102 M–1 and up to 1012 M–1.

  • Thermodynamic parameters, such as: free energy, enthalpy, and entropy of a chemical process
  • Association constant of a binding event
  • Stoichiometry of a complex


LC-MS (Analytical)

Equipment details: Agilent Infinity LC 1260 Quad-pump / Single Quadrupole MS 6120

How is this equipment helping our research?

  • Reverse phase isocratic/gradient elution of analytical samples of small polar molecules
  • UV-Vis and MS detection
  • Fully automated with autosampler or manual injection


Microwave Reactor

Equipment details: Biotage Microwave Initiator 2.5 – with automatic sample loader

How is this equipment helping our research?

  • Screen reactions faster and on smaller scale in a fully automated mode – up to 8 samples in queue
  • Achieve temperatures and pressures not attainable easily through conventional heating
  • Superior control of reaction temperature and time
  • Reactions are typically complete in one-tenth of the time it would take through conventional heating


Nitrogen Glove Box

Equipment details: Innovative Technology

How is this equipment helping our research?

This glove box assists us in performing long-term reactions in the absence of oxygen. For example: reductions and reactions of radicals of bipyridinium species. Additionally, it is used for the slow crystallization of radical species into single crystals suitable for XRD structure determination.


Optical Microscope

Equipment details: Olympus BX3 Polarized Light Microscope

How is this equipment helping our research?

  • Inspection of crystalline materials, single-crystals, films, and particles in solution
  • Polarized light for characterization of single-crystals, liquid-crystalline films
  • Trans- and epi-illumination, possibility of imaging of fluorescent species with UV-excitation
  • Image collection with a cooled CCD camera



Equipment details: Shimadzu UV-Vis-NIR 3600 / 3600Plus

How is this equipment helping our research?

  • Collect the absorption spectrum of molecules in solution or solid state in the UV, visible, and near infra-red regions of the electromagnetic spectrum (190 – 3300 nm)
  • Measure spectrophotometric association and kinetic constants

The 3600 Model is equipped with a variable temperature stage for measurements between 0 °C and 100 °C.


Safety in the Research Laboratory

Safety in the laboratory is at the top of the Stoddart group’s and Northwestern’s priorities. We strive to provide one of the cleanest and safest chemistry laboratory spaces on the campus by constantly keeping our day-to-day work practices up-to-date with the current safety standards and through the practice of having all of our students, postdoctoral researchers, and managers trained in safe practices and hazard mitigation.

The Office for Research Safety (ORS) (link: surveys all safety operations on campus and administers periodical training modules through the LUMEN online platform (link: Biannual safety inspections conduced by the campus safety officer are organized to identify all potential safety issues and correct them promptly. In addition, the group’s managers and safety designate perform regular inspections to highlight minor safety issues, while regular, quarterly clean-ups help us by keeping the laboratory and office spaces tidy and organized.

Researchers are equipped with state-of-the-art personal protective equipment (PPE); safety equipment, such as full showers, eye showers, first-aid kits, and spill kits are disseminated throughout the laboratory space. All our researchers receive hands-on training on the use of fire extinguishers and first intervention against small fires.

With the safety of our researchers our first priority, we have implemented a milestone-based transition plan to improve constantly the safety culture and reduce chemical hazards, not only internally, but with the intent of communicate our successful strategies to ORS and across campus.


Living in Evanston and Chicagoland

Nestled on the southwestern shore of Lake Michigan, almost 10 million residents call home the third metropolitan area by size in the US. “Chicagoland” offers a vibrant cultural environment all-year around.

Living nearby Northwestern’s campus in Evanston will grant you fast access to the university and many services. Affordable housing options—in the range of $1000-$1400 / month for a one-bedroom apartment—are available within walking distance to the building (Silverman Hall) housing the Stoddart laboratory. Rents drop as one goes further west or south of downtown Evanston. Another hot spot for living is in the northernmost neighborhood of Chicago, Rogers Park. More specifically, accommodation can be found along the tracks near Red Line stations at Loyola, Morse, and Jarvis, giving you access to a fast commute to and from Northwestern’s campus.

Evanston is well served by an efficient public transportation system. Our own “EL” train is the Purple Line, which connects the city of Evanston to the Chicago Loop with express trains during rush hours. Chicago Transit Authority Buses and Metra Commuter trains complete a capillary network of transportation that will allow you to reach virtually anywhere in the greater Chicago area.

By living in Evanston or Rogers Park you will have ready access to a variety of shopping and dining opportunities, in one of the most diverse and most well-educated communities in the country. Plenty of out-of-doors recreational activities are possible during the warmer months—May through September—and continue indoors during the harsher winter months. Sports and music events, art festivals, cultural fairs, and numerous green areas and beaches on the Lake are accessible year-long and will make your experience a unique one.

Living in a densely populated area can be stressful for some. Evanston and Rogers Park are safe communities; use common sense and avoid walking alone or in poorly frequented areas at night.




Northwestern Shuttle Bus



Airports – O’Hare / Midway

Train – Amtrak


Driver’s License / Car Registration:

IL Secretary of State



Evanston District 65 (K-8)

Evanston Township High-School

Chicago Public School System (K-12)






Things to do in the Chicago area