Using Catalysis to Drive Chemistry Away from Equilibrium: Relating Kinetic Asymmetry, Power Strokes, and the Curtin-Hammett Principle in Brownian Ratchets.

Chemically fueled autonomous molecular machines are catalysis-driven systems governed by Brownian information ratchet mechanisms. One fundamental principle behind their operation is kinetic asymmetry, which quantifies the directionality of molecular motors. However, it is difficult for synthetic chemists to apply this concept to molecular design because kinetic asymmetry is usually introduced in abstract mathematical terms involving experimentally inaccessible parameters. Furthermore, two seemingly contradictory mechanisms have been proposed for chemically driven autonomous molecular machines: Brownian ratchet and power stroke mechanisms. This Perspective addresses both these issues, providing accessible and experimentally useful design principles for catalysis-driven molecular machinery. We relate kinetic asymmetry to the Curtin-Hammett principle using a synthetic rotary motor and a kinesin walker as illustrative examples. Our approach describes these molecular motors in terms of the Brownian ratchet mechanism but pinpoints both chemical gating and power strokes as tunable design elements that can affect kinetic asymmetry. We explain why this approach to kinetic asymmetry is consistent with previous ones and outline conditions where power strokes can be useful design elements. Finally, we discuss the role of information, a concept used with different meanings in the literature. We hope that this Perspective will be accessible to a broad range of chemists, clarifying the parameters that can be usefully controlled in the design and synthesis of molecular machines and related systems. It may also aid a more comprehensive and interdisciplinary understanding of biomolecular machinery.

Social Self-Sorting Synthesis of Molecular Knots.

We report the synthesis of molecular prime and composite knots by social self-sorting of 2,6-pyridinedicarboxamide (pdc) ligands of differing topicity and stereochemistry. Upon mixing achiral monotopic and ditopic pdc-ligand strands in a 1:1:1 ratio with Lu(III), a well-defined heteromeric complex featuring one of each ligand strand and the metal ion is selectively formed. Introducing point-chiral centers into the ligands leads to single-sense helical stereochemistry of the resulting coordination complex. Covalent capture of the entangled structure by ring-closing olefin metathesis then gives a socially self-sorted trefoil knot of single topological handedness. In a related manner, a heteromeric molecular granny knot (a six-crossing composite knot featuring two trefoil tangles of the same handedness) was assembled from social self-sorting of ditopic and tetratopic multi-pdc strands. A molecular square knot (a six-crossing composite knot of two trefoil tangles of opposite handedness) was assembled by social self-sorting of a ditopic pdc strand with four (S)-centers and a tetratopic strand with two (S)- and six (R)-centers. Each of the entangled structures was characterized by 1H and 13C NMR spectroscopy, mass spectrometry, and circular dichroism spectroscopy. The precise control of composition and topological chirality through social self-sorting enables the rapid assembly of well-defined sequences of entanglements for molecular knots.

Autonomous fuelled directional rotation about a covalent single bond.

Biology operates through autonomous chemically fuelled molecular machinery1, including rotary motors such as adenosine triphosphate synthase2 and the bacterial flagellar motor3. Chemists have long sought to create analogous molecular structures with chemically powered, directionally rotating, components4-17. However, synthetic motor molecules capable of autonomous 360° directional rotation about a single bond have proved elusive, with previous designs lacking either autonomous fuelling7,10,12 or directionality6. Here we show that 1-phenylpyrrole 2,2'-dicarboxylic acid18,19 (1a) is a catalysis-driven20,21 motor that can continuously transduce energy from a chemical fuel9,20-27 to induce repetitive 360° directional rotation of the two aromatic rings around the covalent N-C bond that connects them. On treatment of 1a with a carbodiimide21,25-27, intramolecular anhydride formation between the rings and the anhydride's hydrolysis both occur incessantly. Both reactions are kinetically gated28-30 causing directional bias. Accordingly, catalysis of carbodiimide hydration by the motor molecule continuously drives net directional rotation around the N-C bond. The directionality is determined by the handedness of both an additive that accelerates anhydride hydrolysis and that of the fuel, and is easily reversed additive31. More than 97% of fuel molecules are consumed through the chemical engine cycle24 with a directional bias of up to 71:29 with a chirality-matched fuel and additive. In other words, the motor makes a 'mistake' in direction every three to four turns. The 26-atom motor molecule's simplicity augurs well for its structural optimization and the development of derivatives that can be interfaced with other components for the performance of work and tasks32-36.

Insights from an information thermodynamics analysis of a synthetic molecular motor.

Information is physical, a realization that has transformed the physics of measurement and communication. However, the flow between information, energy and mechanics in chemical systems remains largely unexplored. Here we analyse a minimalist autonomous chemically driven molecular motor in terms of information thermodynamics, a framework that quantitatively relates information to other thermodynamic parameters. The treatment reveals how directional motion is generated by free energy transfer from chemical to mechanical (conformational and/or co-conformational) processes by 'energy flow' and 'information flow'. It provides a thermodynamic level of understanding of molecular motors that is general, complements previous analyses based on kinetics and has practical implications for machine design. In line with kinetic analysis, we find that power strokes do not affect the directionality of chemically driven machines. However, we find that power strokes can modulate motor velocity, the efficiency of free energy transfer and the number of fuel molecules consumed per cycle. This may help explain the role of such (co-)conformational changes in biomachines and illustrates the interplay between energy and information in chemical systems.

Vernier template synthesis of molecular knots.

Molecular knots are often prepared using metal helicates to cross the strands. We found that coordinatively mismatching oligodentate ligands and metal ions provides a more effective way to synthesize larger knots using Vernier templating. Strands composed of different numbers of tridentate 2,6-pyridinedicarboxamide groups fold around nine-coordinate lanthanide (III) ions to generate strand-entangled complexes with the lowest common multiple of coordination sites for the ligand strands and metal ions. Ring-closing olefin metathesis then completes the knots. A 3:2 (ditopic strand:metal) Vernier assembly produces +31#+31 and -31#-31 granny knots. Vernier complexes of 3:4 (tetratopic strand:metal) stoichiometry selectively form a 378-atom-long trefoil-of-trefoils triskelion knot with 12 alternating strand crossings or, by using opposing stereochemistry at the terminus of the strand, an inverted-core triskelion knot with six alternating and six nonalternating strand crossings.

Direct solid-phase synthesis of molecular heterooligonuclear lanthanoid-complexes.

Molecular lanthanoid complexes are highly valuable building blocks for a number of important technological applications, e.g. as contrast agents in magnetic resonance imaging (MRI) or as luminescent probes for bioassays. For the next generation of advanced applications based on molecular species, heterooligonuclear lanthanoid complexes with well-defined chemical and structural compositions are required. The great kinetic lability of trivalent lanthanoids so far prevents the realization of such molecular architectures with a universally applicable methodology. Here, we have developed functionalized molecular lanthanoid cryptates as monomeric building blocks which can be directly linked by standard solid-phase peptide synthesis to yield sequence-specific heterooligonuclear lanthanoid complexes. These molecular materials enable unique applications such as the generation of molecular codes with very convenient luminescence read-out.

Circularly Polarised Luminescence in Enantiopure Samarium and Europium Cryptates.

Circularly polarised luminescence (CPL) is a chiroptical phenomenon gaining more and more attention, as the availability of the necessary spectrometers is getting better and first applications in bioimaging or for the preparation of OLEDs (organic light emitting diodes) are coming within range. Until now most examples of distinctly CPL-active compounds were europium and terbium complexes though theoretically the electronic structure of samarium should be as suitable as the one of terbium. This discrepancy can be accounted for by the high susceptibility of samarium to non-radiative deactivation processes. The aim of this study was to strategically circumvent this difficulty by the use of a ligand scaffold which has already proven to efficiently suppress these processes, namely the cryptates. The prepared partly deuterated samarium and europium complexes exhibit distinct circularly polarised luminescence with dissymmetry factors up to glum =+0.13 (SmIII ) or glum =-0.19 (EuIII ).

Deuterated Molecular Ruby with Record Luminescence Quantum Yield.

The recently reported luminescent chromium(III) complex 13+ ([Cr(ddpd)2 ]3+ ; ddpd=N,N'-dimethyl-N,N'-dipyridine-2-yl-pyridine-2,6-diamine) shows exceptionally strong near-IR emission at 775 nm in water under ambient conditions (Φ=11 %) with a microsecond lifetime as the ligand design in 13+ effectively eliminates non-radiative decay pathways, such as photosubstitution, back-intersystem crossing, and trigonal twists. In the absence of energy acceptors, such as dioxygen, the remaining decay pathways are energy transfer to high energy solvent and ligand oscillators, namely OH and CH stretching vibrations. Selective deuteration of the solvents and the ddpd ligands probes the efficiency of these oscillators in the excited state deactivation. Addressing these energy-transfer pathways in the first and second coordination sphere furnishes a record 30 % quantum yield and a 2.3 millisecond lifetime for a metal complex with an earth-abundant metal ion in solution at room temperature.

Chiral Resolution of Lanthanoid Cryptates with Extreme Configurational Stability.

Chiral resolution is achieved for racemic tris(2,2'-bipyridine)-based lanthanoid cryptates by chiral HPLC. The resolved complexes exhibit very rare configurational stability under extreme conditions.

Magnetic Anisotropy in Functionalized Bipyridyl Cryptates.

The magnetic properties of molecular lanthanoid complexes are very important for a variety of scientific and technological applications, with the unique magnetic anisotropy being one of the most important features. In this context, a very rigid tris(bipyridine) cryptand was synthesized with a primary amine functionality for future bioconjugation. The magnetic anisotropy was investigated for the corresponding paramagnetic ytterbium cryptate. With the use of a combination of density functional theory calculations and lanthanoid-induced NMR shift analysis, the magnetic susceptibility tensor was determined and compared to the unfunctionalized cryptate analogue. The size and orientation of the axial and rhombic tensor components show remarkably great resilience toward the decrease of local symmetry around the metal and anion exchange in the inner coordination sphere. In addition, the functionalized ytterbium cryptate also exhibits efficient near-IR luminescence.

Breakdown of the energy gap law in molecular lanthanoid luminescence: the smallest energy gap is not universally relevant for nonradiative deactivation.

For several decades, the energy gap law has been the prevalent theoretical framework for the discussion of nonradiative deactivation of lanthanoid luminescence in molecular coordination chemistry. Here we show experimentally on samarium and dysprosium model complexes that the size of the energy gap ΔE between a lanthanoid emitting state and the next-lower electronic state cannot be considered a reliable and accurate predictor of the quantitative extent of nonradiative deactivation by aromatic C-H and C-D oscillator overtones. Because the energy gap is the central pillar for the entire conceptual framework of the energy gap law, this finding amounts to largely invalidating this theory for the quantitative description of molecular multiphonon relaxation.