Competing Hydrogen-Bond Polarities in a Dynamic Oligourea Foldamer: A Molecular Spring Torsion Balance

Markov State Models Reveal How Folding Kinetics Influence Absorption Spectra of Foldamers

Self-assembly of platinum(II) complex foldamers is an essential approach to fabricate advanced luminescent materials. However, a comprehensive understanding of folding kinetics and their absorption spectra remains elusive. By constructing Markov state models (MSMs) from large-scale molecular dynamics simulations, we reveal that two largely similar dinuclear alknylplatinum(II) terpyridine foldamers, Pt-PEG and Pt-PE with slightly different bridges, exhibit distinctive folding kinetics. Particularly, Pt-PEG bears bridge-dominant, plane-dominant, and cooperative pathways, while Pt-PE only prefers the plane-dominant pathway. Such preference originates from their difference in intrabridge electrostatic interactions, leading to contrastive distributions of metastable states. We also found that the bridge-dominant pathway for Pt-PEG becomes more favorable when lowering the temperature. Interestingly, based on the comprehensive conformation ensembles from our MSMs, we reveal the conformation-dependent absorption spectra of Pt-PEG and Pt-PE. Our theoretical spectra not only align with experimental results but also reveal the contributions of diverse conformations to the overall absorption bands explicitly, facilitating the rational design of stimuli-responsive smart luminescent molecules.

Pronounced Self-Induced Diastereomeric Anisochronism in Anisidine Amino Acid Diamides

The emergent properties resulting from selective supramolecular interactions are of significant importance for materials and chemical systems. For the directed use of such properties, a fundamental understanding of the interaction mechanism and the resulting mode of function is necessary for a tailored design. The self-induced diastereomeric anisochronism effect (SIDA), which occurs in the intermolecular interaction of chiral molecules, generates unique properties such as chiral self-recognition and nonlinear effects. Here we show that anisidine amino acid diamides lead to extraordinary signal splitting in NMR spectra through supramolecular interaction and homochiral self-recognition. By systematic experiments we have investigated the underlying SIDA effect, explored its limits and finally successfully utilized it in the determination of enantiomeric ratios by NMR spectroscopy of chiral 'SIDA-inactive' compounds such as thalidomide.

Multiple hydrogen bonding driven supramolecular architectures and their biomedical applications

Supramolecular chemistry combines the strength of molecular assembly via various molecular interactions. Hydrogen bonding facilitated self-assembly with the advantages of directionality, specificity, reversibility, and strength is a promising approach for constructing advanced supramolecules. There are still some challenges in hydrogen bonding based supramolecular polymers, such as complexity originating from tautomerism of the molecular building modules, the assembly process, and structure versatility of building blocks. In this review, examples are selected to give insights into multiple hydrogen bonding driven emerging supramolecular architectures. We focus on chiral supramolecular assemblies, multiple hydrogen bonding modules as stimuli responsive sources, interpenetrating polymer networks, multiple hydrogen bonding assisted organic frameworks, supramolecular adhesives, energy dissipators, and quantitative analysis of nano-adhesion. The applications in biomedical materials are focused with detailed examples including drug design evolution for myotonic dystrophy, molecular assembly for advanced drug delivery, an indicator displacement strategy for DNA detection, tissue engineering, and self-assembly complexes as gene delivery vectors for gene transfection. In addition, insights into the current challenges and future perspectives of this field to propel the development of multiple hydrogen bonding facilitated supramolecular materials are proposed.

Stimuli-responsive synthetic helical polymers

Synthetic dynamic helical polymers (supramolecular and covalent) and foldamers share the helix as a structural motif. Although the materials are different, these systems also share many structural properties, such as helix induction or conformational communication mechanisms. The introduction of stimuli responsive building blocks or monomer repeating units in these materials triggers conformational or structural changes, due to the presence/absence of the external stimulus, which are transmitted to the helix resulting in different effects, such as assymetry amplification, helix inversion or even changes in the helical scaffold (elongation, J/H helical aggregates). In this review, we show through selected examples how different stimuli (e.g., temperature, solvents, cations, anions, redox, chiral additives, pH or light) can alter the helical structures of dynamic helical polymers (covalent and supramolecular) and foldamers acting on the conformational composition or molecular structure of their components, which is also transmitted to the macromolecular helical structure.

Herringbone Helical Foldamers from Aromatic Ether Derived ϵ-Amino Acid Peptides

Oligomers based on an aromatic ether derived ϵ-amino acid peptides folded into herringbone helical structures, induced by successive NH-O-NH & O-NH-O bifurcated hydrogen bonding interactions and reinforced by π-π stacking between aryls from adjacent layers. The diaryl ether bonds -O- worked both as structural units to provide turn motifs for changing the amplitude of the slope along the axis of helix for herringbone formation, and also as acceptors for hydrogen bonding. Attachment of a single chiral carbon to the C-termini of the peptides induced excess of single-handed screw sense and amplification through the chain propagation as exemplified by chain length dependent circular dichroism (CD) investigations.

Anion-Dependent Hydrogen-Bond Polarity Switching in Ethylene-bridged Urea Oligomers

The reversible coordination of anions to an N,N'-disubstituted 3,5-bis(trifluoromethyl)phenylurea located at a terminus of a linear chain of ethylene-bridged hydrogen-bonded ureas triggers a cascade of conformational changes. A series of hydrogen-bond polarity reversals propagates along the oligomer, leading to a global switch of its hydrogen-bond directionality. The induced polarity switch, transmitted through four reversible urea groups, results in a change in emission and excitation wavelengths of a fluorophore located at the opposite terminus of the oligomer. The molecule thus behaves as a chemical sensor with a relayed remote spectroscopic response to variations in anion concentration. The polarity switch induced by anion concentration constitutes an artificial communication mechanism for conveying information through oligomeric structures.

Chemically Fueled Communication Along a Scaffolded Nanoscale Array of Squaramides

Relaying conformational change over several nanometers is central to the function of allosterically regulated proteins. Replicating this mechanism artificially would provide important communication tools, but requires nanometer-sized molecules that reversibly switch between defined shapes in response to signaling molecules. In this work, 1.8 nm long rigid rod oligo(phenylene-ethynylene)s are scaffolds for switchable multi-squaramide hydrogen-bond relays. Each relay can adopt either a parallel or an antiparallel orientation relative to the scaffold; the preferred orientation is dictated by a director group at one end. An amine director responded to proton signals, with acid-base cycles producing multiple reversible changes in relay orientation that were reported by a terminal NH, which is 1.8 nm distant. Moreover, a chemical fuel acted as a dissipative signal. As the fuel was consumed, the relay reverted to its original orientation, illustrating how information from out-of-equilibrium molecular signals can be communicated to a distant site.

Screw sense and screw sensibility: communicating information by conformational switching in helical oligomers

Biological systems have evolved a number of different strategies to communicate information on the molecular scale. Among these, the propagation of conformational change is among the most important, being the means by which G-protein coupled receptors (GPCRs) use extracellular signals to modulate intracellular processes, and the way that opsin proteins translate light signals into nerve impulses. The developing field of foldamer chemistry has allowed chemists to employ conformationally well-defined synthetic structures likewise to mediate information transfer, making use of mechanisms that are not found in biological contexts. In this review, we discuss the use of switchable screw-sense preference as a communication mechanism. We discuss the requirements for functional communication devices, and show how dynamic helical foldamers derived from the achiral monomers such as α-aminoisobutyric acid (Aib) and meso-cyclohexane-1,2-diamine fulfil them by communicating information in the form of switchable screw-sense preference. We describe the various stimuli that can be used to switch screw sense, and explore the way that propagation of the resulting conformational preference in a well-defined helical molecule allows screw sense to control chemical events remote from a source of information. We describe the operation of these conformational switches in the membrane phase, and outline the progress that has been made towards using conformational switching to communicate between the exterior and interior of a phospholipid vesicle.

A Chiral 19F NMR Reporter of Foldamer Conformation in Bilayers

Understanding and controlling peptide foldamer conformation in phospholipid bilayers is a key step toward their use as molecular information relays in membranes. To this end, a new 19F "reporter" tag has been developed and attached to dynamic peptide foldamers. The (R)-1-(trifluoromethyl)ethylamido ((R)-TFEA) reporter was attached to the C-terminus of α-amino-iso-butyric acid (Aib) foldamers. Crystallography confirmed that the foldamers adopted 310 helical conformations. Variable temperature (VT) NMR spectroscopy in organic solvents showed that the (R)-TFEA reporter had an intrinsic preference for P helicity, but the overall screw-sense was dominated by a chiral "controller" at the N-terminus. The 19F NMR chemical shift of the CF3 resonance was correlated with the ability of different N-terminal groups to induce either an M or a P helix in solution. In bilayers, a similar correlation was found. Solution 19F NMR spectroscopy on small unilamellar vesicle (SUV) suspensions containing the same family of (R)-TFEA-labeled foldamers showed broadened but resolvable 19F resonances, with each chemical shift mirroring their relative positions in organic solvents. These studies showed that foldamer conformational preferences are the same in phospholipid bilayers as in organic solvents and also revealed that phospholipid chirality has little influence on conformation.

Supramolecular interactions between ethylene-bridged oligoureas: nanorings and chains formed by cooperative positive allostery

Ethylene-bridged oligoureas are dynamic foldamers in which the polarity of a coherent chain of intramolecular hydrogen bonds may be controlled by intra- or intermolecular interactions with hydrogen-bond donors or acceptors. In this paper, we describe the way that supramolecular interactions between ethylene-bridged oligoureas bearing a 3,5-bis(trifluoromethyl)phenylurea (BTMP) terminus leads to higher-order structures both in the crystalline state and in solution. The oligoureas self-assemble by head-to-tail hydrogen bonding interactions to form either supramolecular 'nanorings' with cyclic hydrogen bond chain directionality, or supramolecular helical chains of hydrogen bonds. The self-assembly process features a cascade of cooperative positive allostery, in which each intermolecular hydrogen bond formation at the BTMP terminus switches the native hydrogen bond chain directionality of monomers, favouring further assembly. Monomers with a benzyl urea terminus self-assemble into nanorings, whereas monomers with a N-ethyl urea terminus form helical chains. In the crystal state, parallel helices have identical handedness and polarity, whereas antiparallel helices have opposite handedness. The overall dipole moment of crystals is zero due to the antiparallel arrangements of local dipoles in the crystal packing. Supramolecular interactions in solution were also examined by VT and DOSY NMR spectroscopy, up to the point of crystal formation. The size of higher aggregates in dichloromethane was estimated by their hydrodynamic radius. The relative orientation of the monomers within the aggregates, determined by 2D ROESY NMR, was the same as in the crystals, where syn-orientations lead to the formation of rings and anti-orientations result in chains. Overall, the switch of hydrogen bond polarity propagates intermolecularly in crystal and solution states, constituting an example of intermolecular communication within supramolecular polymers.

Folded Propeller Chiral Structures Exclusively Adaptive to Chloroform

Intramolecular folding is a strategy to construct aryl chiral compounds with applications in chiroptical materials and asymmetrical catalysts. However, beyond polarity the role of solvent in controlling the folded chirality is ambiguous. Here, we report a simple folding protocol to build chiral benzimidazole skeleton with propeller chirality, which could be adaptive to chloroform (CHCl₃) with high selectivity. Benzimidazole conjugated with diamino acid arms underwent folding driven by hydrogen bonds, exhibiting propeller chirality of which handedness could be tuned by the absolute chirality of amino acids. Reversible unfolding/folding behavior was realized by heating/cooling process, giving rise to the thermomediated chiroptical switch. Among up to 32 common solvents, chloroform exclusively inverted the propeller chirality. The geometry and hydrogen bonding sites of chloroform allow rearrangement of diamino acid arms into an opposite packing propensity. The chloroform behaves as an invasive linker between diamino acid arms to replace the pristine hydrogen bonds. This work reports the fabrication of chiral aryl compounds by simple folding, which shows the adaptiveness to the chloroform. It demonstrates that not only polarity but also the active participation of solvent could change the chirality and optical activities of small folded molecules.

A molecular communication channel consisting of a single reversible chain of hydrogen bonds in a conformationally flexible oligomer

Communication of information through the global switching of conformation in synthetic molecules has hitherto entailed the inversion of chirality. Here, we report a class of oligomer through which information may be communicated through a global reversal of polarity. Ethylene-bridged oligoureas are constitutionally symmetrical, conformationally flexible molecules organized by a single chain of hydrogen bonds running the full length of the oligomer. NMR reveals that this hydrogen-bonded chain may undergo a coherent reversal of directionality. The directional uniformity of the hydrogen-bond chain allows it to act as a channel for the spatial communication of information on a molecular scale. A binding site at the terminus of an oligomer detects local information about changes in pH or anion concentration and transmits that information—in the form of a directionality switch in the hydrogen-bond chain—to a remote polarity-sensitive fluorophore. This propagation of polarity-encoded information provides a new mechanism for molecular communication.

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Simple urea oligomers organize themselves with a single coherent hydrogen-bond chain

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Reversing the polarity of the hydrogen bonding sends a message through the molecule

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Conformational messages can be transmitted by changes in pH or by anion binding

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Receipt of the conformational message is indicated by a remote fluorescent response

Despite the progress made by synthetic chemistry in building the molecular structures of nature, there are still domains of molecular science where biology is immensely more sophisticated than even the most advanced artificial chemical systems. One of these is the ability to use molecular structures to encode and communicate information. Nature stores information in the hydrogen-bond polarity of the base pairs and translates it into molecular function using the polarity matching of these bonds. Here, we outline an early step toward replicating this ability in the design, synthesis, and operation of a series of synthetic molecular devices that employ a structurally simple family of oligomeric molecules that can communicate information in the form of hydrogen-bond polarity. This study marks a significant step in the design of molecular systems that manipulate information, which will form the basis of the many compartmentalization-based nanotechnologies of the future.

Urea based foldamers

N,N'-linked oligoureas are a class of enantiopure, sequence-defined peptidomimetic oligomers without amino acids that form well-defined and predictable helical structures akin to the peptide α-helix. Oligourea-based foldamers combine a number of features-such as synthetic accessibility, sequence modularity, and folding fidelity-that bode well for their use in a range of applications from medicinal chemistry to catalysis. Moreover, it was recently recognized that this synthetic helical backbone can be combined with regular peptides to generate helically folded peptide-oligourea hybrids that display additional features in terms of helix mimicry and protein-surface recognition properties. Here we provide detailed protocols for the preparation of requested monomers and for the synthesis and purification of homo-oligoureas and peptide-oligourea hybrids.

Self-Assembly of Size-Controlled m-Pyridine-Urea Oligomers and Their Biomimetic Chloride Ion Channels

The m-pyridine urea (mPU) oligomer was constructed by using the intramolecular hydrogen bond formed by the pyridine nitrogen atom and the NH of urea and the intermolecular hydrogen bond of the terminal carbonyl group and the NH of urea. Due to the synergistic effect of hydrogen bonds, mPU oligomer folds and exhibits strong self-assembly behaviour. Affected by folding, mPU oligomer generates a twisted plane, and one of its important features is that the carbonyl group of the urea group orientates outwards from the twisted plane, while the NHs tend to direct inward. This feature is beneficial to NH attraction for electron-rich species. Among them, the trimer self-assembles into helical nanotubes, and can efficiently transport chloride ions. This study provides a novel and efficient strategy for constructing self-assembled biomimetic materials for electron-rich species transmission.

Quantifying Through-Space Substituent Effects

The description of substituents as electron donating or withdrawing leads to a perceived dominance of through-bond influences. The situation is compounded by the challenge of separating through-bond and through-space contributions. Here, we probe the experimental significance of through-space substituent effects in molecular interactions and reaction kinetics. Conformational equilibrium constants were transposed onto the Hammett substituent constant scale revealing dominant through-space substituent effects that cannot be described in classic terms. For example, NO2 groups positioned over a biaryl bond exhibited similar influences as resonant electron donors. Meanwhile, the electro-enhancing influence of OMe/OH groups could be switched off or inverted by conformational twisting. 267 conformational equilibrium constants measured across eleven solvents were found to be better predictors of reaction kinetics than calculated electrostatic potentials, suggesting utility in other contexts and for benchmarking theoretical solvation models.

Local versus Global Control of Helical Folding in β-Peptide Segments Using Hydrazino Turns

Rational control of the self-organization of β-peptides sequences to adopt regular secondary structures is an important challenge in peptidomimetic foldamer science. By replacing the N- and C-terminal residues of homooligomers of trans-2-aminocyclobutanecarboxylic acid (tACBC)_n with N-aminoazetidine-2-carboxylic acid, an 8-helical topology is shown to dominate for sequences up to n = 7. This constitutes an atomic-level tool to override locally the preferred global 12-helix secondary structure of the corresponding tACBC homooligomers of the same length.

Gold-catalyzed domino cyclization enabling construction of diverse fused azaspiro tetracyclic scaffolds: a cascade catalysis mechanism due to a substrate and counterion

The detailed mechanism and origins of gold-catalyzed domino cyclization to diverse fused azaspiro tetracyclic scaffolds by cooperative dual catalysis and cascade catalysis are systematically studied.

Structures, Phase Behavior, and Fluorescent Properties of 3-Phenyl-1-(pyridin-2-yl)-1H-pyrazol-5-amine and Its ZnCl2 Complex

The synthesis of the asymmetric ligand 3-phenyl-1-(pyridin-2-yl)-1H-pyrazol-5-amine (L1) and its single-crystal X-ray structure are reported. L1 displays crystallographic symmetry (orthorhombic, Pccn) higher than its molecular symmetry (point group C₁) and also displays supercooling, with a difference in the melting and solidification points of over 100 °C. Upon complexation with ZnCl₂, L1 engages in both primary cation and secondary anion coordination via hydrogen bonding, and the complex exhibits a room-to-low-temperature single crystal-to-crystal phase transition. The ZnCl₂ complex becomes a birefringent fluid mixed with crystalline domains at high temperatures, as detected by polarized optical microscopy. Examination of the photoluminescence properties showed that the emission intensity increased and a pronounced bathochromic shift was observed in the emission maximum upon going from solution to the solid state, for both the ligand and complex, consistent with aggregation-induced emission behavior.

Organic molecular tessellations and intertwined double helices assembled by halogen bonding

Crystalline polymorphs featuring halogen-bonded single-component supramolecular polygonal tessellations, a network of 4₁- and 4₃-double helices, and intertwined 3₁ and 3₂meso-helices.

Biomimetic folding of small organic molecules driven by multiple non-covalent interactions

The supramolecular self-folding of UPy-based monomers with low molecular weight driven by multiple non-covalent interactions has been developed.

The effects of different heterocycles and solvents on the ESIPT mechanisms of three novel photoactive mono-formylated benzoxazole derivatives

The detailed effects of different heterocycles and solvents on the dynamical ESIPT mechanisms of three novel mono-formylated benzoxazole derivatives A–C in two different surroundings have been expounded by the TDDFT method at the B3LYP/TZVP level.