Julian Vogel

aza‐BODIPY comes alive! Living supramolecular polymerization was demonstrated by aza‐BODIPY 1 bearing hydrogen‐bond accepting triazole units that can be facilely constructed through click chemistry. The H‐bonding unit of amide‐linked triazole in dye 1 could be employed as a general motif for encoding conformational information and developing polymorphic supramolecular systems.

Abstract

An aza‐BODIPY dye 1 bearing two hydrophobic fan‐shaped tridodecyloxybenzamide pendants through 1,2,3‐triazole linkages was synthesized by a click reaction and characterized. ¹H NMR studies indicated that dye 1 exhibited variable conformations through intramolecular H‐bonding interaction, which is beneficial for the polymorphism of aggregation. The thermodynamic, structural, and kinetic aspect of the supramolecular polymerization of dye 1 was investigated by UV/Vis absorption spectroscopy, IR spectroscopy, AFM, TEM, and SEM. Biphasic aggregation pathways of dye 1, leads to the formation of off‐pathway, metastable Agg. I and thermodynamically stable Agg. II with distinct H‐aggregation spectra and nanoscale morphology. The living manner of the supramolecular polymerization of dye 1 was demonstrated in seeded polymerization experiments with temperature‐modulated successive cooling–heating cycles.

Ingenious design: Strategies to construct fuel‐driven self‐assembled systems are reviewed, including systems in which the construction is assisted by enzymes, as well as those employing entirely synthetic chemicals. Applications, challenges and future perspectives of fuel‐driven self‐assembly are discussed.

Abstract

Fuel‐driven self‐assembly widely exists in the biological world since functional micro‐ or nanostructures in living bodies are usually transiently formed by biomolecular self‐assembly far from thermodynamic equilibrium driven by active molecules (chemical fuel), for example, adenosine triphosphate (ATP). Therefore, research focusing on artificial fuel‐driven self‐assembly has drawn extensive attention in recent years. Compared with spontaneous molecular self‐assembly at thermodynamic equilibrium, constructing a fuel‐driven self‐assembly remains complicated because it requires a delicately designed chemical reaction network mainly involving an “activation” and a “deactivation”. In this Minireview, we will review recent developments in fuel‐driven self‐assembly and generalize several strategies for constructing such a self‐assembly. Besides that, the functional micro‐ or nanostructures and materials achieved by these fuel‐driven self‐assemblies will also be discussed.

To be or not to be (reversible): The interaction strength between building blocks determines whether self‐assembly occurs under kinetic or thermodynamic control. The self‐assembly process under thermodynamic control permits reversible transitions between the different assembly states.

Abstract

Non‐covalent synthesis aims at exploiting non‐covalent interactions for the controlled hierarchical assembly of nanostructures. Just as the covalent synthesis of molecules is affected by the conditions under which the chemical reaction is carried out, the outcome of a non‐covalent synthesis process can be likewise affected by the experimental pathway in case the assembled structures are kinetic, rather than thermodynamic, products. Here, we show that the ATP‐templated formation of metallo‐amphiphile assemblies results in different kinetically stable structures depending on the self‐assembly pathway. Interconversion between the different assembled states is not possible and neither is ATP subject to enzymatic hydrolysis which would convert the system back to the unassembled state. The high stability of the different assembly states is a result of the strong interaction between ATP and the metallo‐amphiphile. Indeed, the use of AMP as a weakly interacting template leads to thermodynamically stable assemblies which can be transitioned between different states. The results underline that control over the kinetic processes that regulate self‐assembly is a fundamental tool for the hierarchical self‐assembly of complex nanostructures and the development of energy‐driven synthetic systems.

Eight new macrocycles with reactive functional handles were synthesized through metalloid‐assisted self‐assembly. “Design of experiments” was utilized to optimize reaction conditions for multiple systems to significantly increase the yield of a single, targeted macrocycle.

Abstract

Cyclophanes are a venerable class of macrocyclic and cage compounds that often contain unusual conformations, high strain, and unusual properties. However, synthesis of complex, functional derivatives remains difficult due to low functional group tolerance, high dilution, extreme reaction conditions, and sometimes low yields using traditional stepwise synthetic methods. “Design of experiments” (DOE) is a method employed for the optimization of reaction conditions, and we showcase this approach to generate a dramatic increase in the yield of specific targets from two different self‐assembling systems. These examples demonstrate that DOE provides an additional tool in tuning self‐assembling, dynamic covalent systems.

A Type I porous liquid is synthesized by transforming porous organic cages into porous ionic liquids via a supramolecular complexation strategy. Simple physical mixing of 18‐crown‐6 with an anionic porous organic cage affords a porous ionic liquid with anionic porous organic cages as the anionic parts and 18‐crown‐6/potassium ion complexes as the cationic parts.

Abstract

Porous liquids are a type of porous materials that engineer permanent porosity into unique flowing liquids, exhibiting promising functionalities for a variety of applications. Here a Type I porous liquid is synthesized by transforming porous organic cages into porous ionic liquids via a supramolecular complexation strategy. Simple physical mixing of 18‐crown‐6 with task‐specific anionic porous organic cages affords a porous ionic liquid with anionic porous organic cages as the anionic parts and 18‐crown‐6/potassium ion complexes as the cationic parts. In contrast, mixing of 15‐crown‐5 and anionic porous organic cages in a 2:1 ratio gives only solids, while the addition of excess 15‐crown‐5 affords a Type II porous liquid. The permanent porosity in the cage‐based porous liquids has been also confirmed by molecular simulation, positron (e⁺) annihilation lifetime spectroscopy, and enhanced gas sorption capacity compared with pure crown ethers.

Iron and cyanide: A new role is proposed for cyanide as a geochemical agent in promoting prebiotic phosphorylation. Cyanide and its metal complexes can transform and mobilize phosphate from its insoluble iron and calcium minerals, suggesting that phosphate could have been more mobile and prebiotic phosphorylation not as challenging as previously believed on the early Earth.

Abstract

Organophosphates were likely an important class of prebiotic molecules. However, their presence on the early Earth is strongly debated because the low availability of phosphate, which is generally assumed to have been sequestered in insoluble calcium and iron minerals, is widely viewed as a major barrier to organophosphate generation. Herein, we demonstrate that cyanide (an essential prebiotic precursor) and urea‐based solvents could promote nucleoside phosphorylation by transforming insoluble phosphate minerals in a “warm little pond” scenario into more soluble and reactive species. Our results suggest that cyanide and its derivatives (metal cyanide complexes, urea, ammonium formate, and formamide) were key reagents for the participation of phosphorus in chemical evolution. These results allow us to propose a holistic scenario in which an evaporitic environment could concentrate abiotically formed organics and transform the underlying minerals, allowing significant organic phosphorylation under plausible prebiotic conditions.

Non-enzymatic RNA self-replication is integral to the emergence of the ‘RNA World’. Despite considerable progress in non-enzymatic template copying, demonstrating a full replication cycle remains challenging due to the difficulty of separating the strands of the product duplex. Here, we report a prebiotically plausible approach to strand displacement synthesis in which short ‘invader’ oligonucleotides unwind an RNA duplex through a toehold/branch migration mechanism, allowing non-enzymatic primer extension on a template that was previously occupied by its complementary strand. Kinetic studies of single-step reactions suggest that following invader binding, branch migration results in a 2:3 partition of the template between open and closed states. Finally, we demonstrate continued primer extension with strand displacement by employing activated 3′-aminonucleotides, a more reactive proxy for ribonucleotides. Our study suggests that complete cycles of non-enzymatic replication of the primordial genetic material may have been facilitated by short RNA oligonucleotides.

Make and break: A chemically fuelled self‐regulating dynamic system is designed that undergoes a pre‐programmed gel‐to‐gel transition through successive covalent bond formation and rupture. We show that the final properties of the gel differ significantly from those of the gel obtained directly from the gelator in the absence of the fuel.

Abstract

Artificial self‐regulating materials can be prepared by exploiting fuel‐driven pathways. Dynamic covalent bonds are formed and broken reversibly under mild reaction conditions. Herein, we utilise this concept to programme a system that can undergo a fuel‐driven self‐regulated gel‐to‐gel transition. The reaction between the gelator and the fuel resulted in a change in chemical structure of the gelator that initially causes a transition from a solution to gel state by co‐assembly. With time, the intermediate complex collapses, re‐forming the gelator structure. However, the gel does not collapse. This method allows us to prepare gels with improved mechanical strength. Unlike conventional gel‐to‐gel transitions, exploitation of dynamic covalent chemistry provides an opportunity to access materials that cannot be prepared directly under similar final conditions.

An old bond : A meteorite of the aubrite type catalyzed the phosphorylation of nucleosides to nucleotides in the presence of orthophosphate, formamide and proton beams, mimicking the effect of the solar wind on prebiotic phosphorylation processes. The reaction occurred also with hydroxyapatite as a well‐recognized phosphorus mineral source on the Primitive Earth. Polyphosphate condensation and radical pathways emerged from experimental data and theoretical calculations as effective reaction pathways.

Abstract

The abiotic phosphorylation of nucleosides is a major hurdle in origin‐of‐life studies. We suggest a plausible pathway for the synthesis of adenosine nucleotides from adenosine and NaH₂PO₄ under radiative conditions mimicking the solar wind in the presence of a meteorite of the aubrite‐type. Hydroxyapatite also performed as a mineral heterogeneous phosphorus source. Adenosine polyphosphate derivatives and inorganic polyphosphates were detected in the reaction mixture, highlighting the high reactivity of the system. Both the total yield of adenosine nucleotides and the conversion of adenosine increased upon performing the irradiation in the presence of formamide (NH₂CHO) and aubrite. These experiments simulate conditions in space or on an early Earth fluxed by protons from the solar wind, potentially mimicking a plausible prebiotic phosphorylation scenario.

Size matters: Coordination isomerism was exploited for the first time to control the morphology of a supramolecular polymer. These observations pave the way for novel stimuli‐responsive materials and offer a new approach for size control in self‐assembled systems.

Abstract

We exploited the inherent geometrical isomerism of a Pt^II complex as a new tool to control supramolecular assembly processes. UV irradiation and careful selection of solvent, temperature, and concentration leads to tunable coordination isomerism, which in turn allows fully reversible switching between two distinct aggregate species (1D fibers↔2D lamellae) with different photoresponsive behavior. Our findings not only broaden the scope of coordination isomerism, but also open up exciting possibilities for the development of novel stimuli‐responsive nanomaterials.

Coming full circle? We report the design and study of a new chemical reaction network for fuel‐driven transient formation of covalent bonds, based on redox‐controlled conjugate addition and elimination chemistry. Although parts of the cycle work, substantial side reactivity prevents achieving repeated operation of a full cycle in a single system.

Abstract

Fuel‐driven chemical reaction networks provide an opportunity to develop chemical systems that operate out‐of‐equilibrium. There remains a need to design and develop new fuel‐driven chemical reaction networks capable of repeated operation using simple and benign chemistry. Herein, we propose a new chemical reaction network for fuel‐driven transient formation of covalent bonds, based on redox‐controlled conjugate addition and elimination chemistry. By investigating the separate reactions making up the cycle, we find that the bond formation, breaking and regeneration processes can be realized. At present, substantial side reactivity prevents achieving repeated operation of a full cycle in a single system. If such obstacles would be overcome, this chemical reaction network could be a valuable addition to the toolbox for out‐of‐equilibrium systems chemistry.

Nature, Published online: 04 October 2019; doi:10.1038/d41586-019-02622-4

The chemical feat strengthens theory that the first life on Earth was based on RNA.

Let's make it simple: Pathway complexity, hierarchy, out‐of‐equilibrium, and metastable or kinetically trapped species are common terms in the field of supramolecular polymers. In this Minireview, the existing concepts used to describe the different species and self‐assembly pathways are classified, differentiated, and correlated to provide a general insight into thermodynamic and kinetic aspects of complex supramolecular polymerization.

Abstract

Pathway complexity, hierarchical organization, out of equilibrium, and metastable or kinetically trapped species are common terms widely used in recent, high‐quality publications in the field of supramolecular polymers. Often, the terminologies used to describe the different self‐assembly pathways, the species involved, as well as their relationship and relative stability are not trivial. Different terms and classifications are commonly found in the literature, however, in many cases, without clear definitions or guidelines on how to use them and how to determine them experimentally. The aim of this Minireview is to classify, differentiate, and correlate the existing concepts with the help of recent literature reports to provide the reader with a general insight into thermodynamic and kinetic aspects of complex supramolecular polymerization processes. A good comprehension of these terms and concepts should contribute to the development of new complex, functional materials.

The prebiotic starting molecules bis‐urea (biuret) and tris‐urea (triuret) directly react with ribose. The urea‐ribosides are remarkably stable because of a network of intramolecular, bifurcated hydrogen bonds, which even allowed the synthesis of phosphoramidite building blocks and incorporation of the units into RNA. Urea‐containing RNA bases are therefore good candidates for a proto‐RNA world.

Abstract

The RNA world hypothesis assumes that life on Earth began with nucleotides that formed information‐carrying RNA oligomers able to self‐replicate. Prebiotic reactions leading to the contemporary nucleosides are now known, but their execution often requires specific starting materials and lengthy reaction sequences. It was therefore proposed that the RNA world was likely proceeded by a proto‐RNA world constructed from molecules that were likely present on the early Earth in greater abundance. Herein, we show that the prebiotic starting molecules bis‐urea (biuret) and tris‐urea (triuret) are able to directly react with ribose. The urea‐ribosides are remarkably stable because they are held together by a network of intramolecular, bifurcated hydrogen bonds. This even allowed the synthesis of phosphoramidite building blocks and incorporation of the units into RNA. Investigations of the nucleotides’ base‐pairing potential showed that triuret:G RNA base pairs closely resemble U:G wobble base pairs. Based on the probable abundance of urea on the early Earth, we postulate that urea‐containing RNA bases are good candidates for a proto‐RNA world.

Switch it up: Chemically fuelled transient self‐assembly processes closely resemble living systems and are applicable for designing systems with pre‐programmable and re‐configurable properties. Herein, through kinetic simulation, we have demonstrated a multivalent fuel driven transient multi‐step self‐assembly process. The composition of transiently formed intermediate species changes in a non‐linear manner and is a function of the strength of dissipation.

Abstract

Multivalent chemical fuel driven transient assembly plays a critical role in biological processes. This inspires chemists to design synthetic systems having transient and dynamic functionalities. However, a detailed understanding about the temporal evolution of each of the intermediate species in a multi‐step assembly under dissipative conditions has not yet been explored. Herein, we have shown under dissipative conditions, how the strength of dissipation can modulate the compositional behavior of each of the intermediate species during their survival period by using kinetic modeling (with Python). We have observed that the appearance and disappearance of intermediates (formed either at the first or penultimate assembly step) are highly non‐linear in nature, and it is possible to trap any of the desired intermediates or a mixture of them of certain compositions at a definite time interval simply by tuning the strength of dissipation.

Timing prebiotic RNA formation: Models for Earth′s impact history explain the late delivery of platinum, gold, and other siderophiles via a ∼10²³ kg impactor (Moneta) circa 4.48 billion years ago. The iron core from this impactor would have reduced the atmosphere above a relatively oxidized mantle, opening a window of opportunity for RNA precursor synthesis. Surprisingly, this suggests that RNA formation was most probable ∼4.36±0.1 billion years ago.

Abstract

The widespread presence of ribonucleic acid (RNA) catalysts and cofactors in the Earth′s biosphere today suggests that RNA was the first biopolymer to support Darwinian evolution. However, most “path‐hypotheses” to generate building blocks for RNA require reduced nitrogen‐containing compounds not made in useful amounts in the CO₂−N₂−H₂O atmospheres of the Hadean. We review models for Earth′s impact history that invoke a single ∼10²³ kg impactor (Moneta) to account for measured amounts of platinum, gold, and other siderophilic (“iron‐loving”) elements on the Earth and Moon. If it were the last sterilizing impactor, by reducing the atmosphere but not the mantle Moneta, would have opened a “window of opportunity” for RNA synthesis, a period when RNA precursors rained from the atmosphere onto land holding oxidized minerals that stabilize advanced RNA precursors and RNA. Surprisingly, this combination of physics, geology, and chemistry suggests a time when RNA formation was most probable, ∼120±100 million years after Moneta′s impact, or ∼4.36±0.1 billion years ago. Uncertainties in this time are driven by uncertainties in rates of productive atmosphere loss and amounts of sub‐aerial land.

Lock on: A pair of radial [5]catenane isomers with different sequences of the peripheral macrocycles, β‐cyclodextrin and cucurbit[6]uril units, was obtained in high yield. Given the marked difference in binding strength and interlocking sequence of the peripheral macrocycles, interesting sequence‐dependent properties, characteristic of mechanically bonded macrocycles, were realized.

Abstract

A pair of radial [5]catenanes, with either an isomeric cyclic ‐AABB‐ or ‐ABAB‐ type sequence of the interlocked β‐cyclodextrin (β‐CD) and cucurbit[6]uril (CB[6]) units, has been efficiently synthesized. Because of a marked difference in the binding strength and interlocking sequence of the peripheral macrocycles, interesting sequence‐dependent properties, characteristic of mechanically bonded macrocycles, were realized. Variable‐temperature ¹H NMR studies showed that the ‐ABAB‐ isomer has a more independent β‐CD dynamic, whereas the β‐CD motions in the ‐AABB‐ isomer are coupled. Dynamics of the pH‐insensitive β‐CD can also be further modulated upon base‐triggered mobilization of the CB[6]. These unique properties of the mechanical bond expressed in a sequence‐specific fashion and the transmission of the control on the macrocycle dynamics from one interlocked component to another, highlight the potential of similar complex hetero[n]catenanes in the design of advanced, multicomponent molecular machines.

Nature, Published online: 19 September 2019; doi:10.1038/d41586-019-02791-2

From Bangkok to Brisbane, researchers were among those protesting to urge action on global warming.

Nature Chemistry, Published online: 16 September 2019; doi:10.1038/s41557-019-0322-x

The emergence of pristine RNA and DNA on the early Earth would have been hindered by a lack of specificity in their prebiotic syntheses. Now, it has been shown that chimeric sequences—with a mixture of RNA and DNA backbones—mediate the template-directed ligation of oligomers present in mixtures of nucleic acids, enabling the simultaneous appearance of RNA and DNA.