Computational Analysis of the Kinetic Requirements for Coupled Reaction Systems

Molecules, Год журнала: 2025, Номер 30(4), С. 911 - 911

Опубликована: Фев. 15, 2025

The art of designing coupling systems to drive reactions for endergonic synthesis is a subject great interest in the scientific community, but it still presents major challenges. aim this kinetic study was run simulations COPASI 4.39 test behavior hypothetical models system that couples two independent reactions, one exergonic and other endergonic. In our computational study, we unraveled qualitative quantitative conditions allow benefit coupling, considering all possible reaction pathways within network. Optimal were reached by assigning favorable directionalities low activation energies six steps network featured twenty steps. Moreover, different designed tested order investigate availability with

Язык: Английский

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Memory-induced current reversal of Brownian motors

Physical review. E, Год журнала: 2025, Номер 111(2)

Опубликована: Фев. 18, 2025

The kinetics of biological motors such as kinesin or dynein is notably influenced by a viscoelastic intracellular environment. characteristic relaxation time the cytosol not separable from colloidal timescale and therefore their dynamics inherently non-Markovian. In this paper, we consider variant Brownian motor model, namely, ratchet immersed in correlated thermal bath, analyze how memory influences its dynamics. particular, demonstrate memory-induced current reversal effect explain phenomenon applying effective mass approximation well uncovering dynamical localization trajectories phase space. Our results reveal new aspects role microscopic systems out equilibrium.

Язык: Английский

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Organic Reactivity Matters for the Emergence of Life: Kinetic Barriers and Molecular Diversity Are Suggested as Crucial Factors by Emerging Autonomous System Models

ChemSystemsChem, Год журнала: 2025, Номер unknown

Опубликована: Март 13, 2025

Abstract The idea that organic chemistry can gradually self‐organize towards the emergence of life has been challenged by views considering most important driver should be existence a crucial thermodynamic disequilibrium. In this work, past are critically addressed and mechanism through which disequilibrium promote development organized systems is suggested. This analysis based on propensity carbon to form covalent bonds with other elements, usually corresponds deep energy wells generating high kinetic barriers hindering reactions. Potential associated considered as storing prepaid entropy loss within potential surface therefore constitute giving room for subsequent self‐organization processes. notion Kinetically Stable Thermodynamically Activated (KSTA) compounds gives rise possibility alternative pathways non‐linear autocatalytic As working in far‐from‐equilibrium context, like molecular machines, parameters determining how they proceed change, suggests interactions between fields machines could mutually beneficial.

Язык: Английский

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A Catalysis-Driven Dual Molecular Motor

Journal of the American Chemical Society, Год журнала: 2025, Номер unknown

Опубликована: Март 17, 2025

We report on a head-to-tail dual molecular motor consisting of two (identical) units whose pyrrole-2-carboxylic rings are turned in contra-rotary (i.e., disrotatory) fashion about common phenyl-2,5-dicarboxylic acid stator. The motors directionally rotate via information ratchet mechanisms, which the hydration carbodiimide (fuel) to form urea (waste) is catalyzed through chemomechanical cycle unit, resulting directional rotation biaryl C–N bond. arrangement produces coaxial contra-rotation end groups while central phenyl ring axis remains dynamically unbiased. electron-rich nature stator contributes rotary catalysis by dual-motor (and therefore itself) being ∼7× faster than parent 1-phenylpyrrole-2,2-dicarboxylic single-motor when operated under identical conditions, and 90× using originally reported reaction conditions. Under batch-fueled operation all fuel present at start operation), rotates an initial rate 0.43 rotations per minute (rpm). Chemostating concentration syringe pump addition produced sustained repetitive 0.24 rpm for period 100 min. demonstration chemically fueled continuous time scale 2–4 min significantly advances chemistry mechanics artificial catalysis-driven machinery.

Язык: Английский

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Imine-Based Transient Supramolecular Polymers

Journal of the American Chemical Society, Год журнала: 2025, Номер unknown

Опубликована: Март 19, 2025

Systems that change properties upon exposure to chemical stimuli offer the interesting prospect of (partially) mimicking functions living systems. Over past decade, numerous supramolecular systems whose composition and are regulated by dissipation fuels have been reported. These typically based on transient transformation a "dormant" species into an active, self-assembling monomer. The process is powered fuel consumption terminates depletion, restoring initial dormant state. Previously reported out-of-equilibrium polymerizations relied activation adding or removing small structural units enable polymerization. Here, we present approach combines reversibility dynamic covalent chemistry trigger "recycling" components combinatorial library (DCL). Treatment equilibrated DCL aliphatic imines aromatic amines with activated carboxylic acid (ACA) generates dissipative protonated amines. acidic conditions creation polymer held together interactions between crown ether moieties embedded in scaffold imines. Thus, reshuffles connectivity enables temporary purely (polymeric) system polymer. We demonstrate strategy using two different feedstocks consisting diimine macrocycle involving calix[4]arene distribution imine (cyclo)oligomers derived from isophthalaldehyde skeleton.

Язык: Английский

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Acyclic cucurbit[n]uril bearing alkyl sulfate ionic groups

Beilstein Journal of Organic Chemistry, Год журнала: 2025, Номер 21, С. 717 - 726

Опубликована: Апрель 3, 2025

We report the synthesis and characterization of a new acyclic cucurbit[ n ]uril (CB[ ]) host C1 that features four alkyl sulfate ionic groups. The X-ray crystal structure C1·Me 6 CHDA complex is reported. Host significantly less soluble in water (4 mM) compared to analogous CB[ ] M1 which sulfonate groups (346 mM). does not undergo significant self-association according results 1 H NMR dilution experiments. molecular recognition behavior hosts toward panel seven ammonium ions was explored by spectroscopy isothermal titration calorimetry (ITC). find generally binds slightly more tightly than specific guest. quaternary guests corresponding primary ions.

Язык: Английский

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Catalytic resonance theory: the catalytic mechanics of programmable ratchets

Chemical Science, Год журнала: 2024, Номер 15(34), С. 13872 - 13888

Опубликована: Янв. 1, 2024

Catalytic reaction networks of multiple elementary steps operating under dynamic conditions

Язык: Английский

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Directionality Reversal and Shift of Rotational Axis in a Hemithioindigo Macrocyclic Molecular Motor

Journal of the American Chemical Society, Год журнала: 2024, Номер 146(33), С. 23387 - 23397

Опубликована: Авг. 7, 2024

Molecular motors are central driving units for nanomachinery, and control of their directional motions is fundamental importance functions. Light-driven variants use easy to provide, dose, waste-free fuel with high energy content, making them particularly interesting applications. Typically, light-driven molecular work via rotations around dedicated chemical bonds where the directionality rotation dictated by steric effects asymmetry in close vicinity axis. In this work, we show how unidirectional a virtual axis can be realized reprogramming motor. To end, classical motor restricted macrocyclization, its intrinsic transformed into macrocyclic chain opposite direction. Further, solvent polarity changes allow toggle function machine between nondirectional photoswitch. way, new concept design delivered together elaborate over functions simple changes. The possibility sensing environmental correspondingly adjusting opens up next level responsiveness nanoscopic motors.

Язык: Английский

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Supramolecular polymerization induced by the rotation of light-driven molecular motors

Опубликована: Авг. 16, 2024

Molecular motors are capable of producing mechanical work on their environment by using unique capacity to generate non-reciprocal autonomous motions at the nanoscale. Although operating principles now well understood, artificial molecular have yet demonstrate general confer novel properties (supra)molecular systems and materials. Here we show that amphiphilic light-driven can adsorb onto air-water interface form Langmuir monolayers upon compression. Under irradiation, surface pressure isotherms these films reveal a drastic shift toward smaller areas as consequence motors’ activation. We explain this counterintuitive phenomenon rotation-induced supramolecular polymerization motors, limited maximal torque they deliver, leading formation highly organized patterns. This serendipitous discovery highlights opportunities offered control processes active nanostructures for design innovative

Язык: Английский

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Abiotic Acyl Transfer Cascades Driven by Aminoacyl Phosphate Esters and Self-Assembly

Journal of the American Chemical Society, Год журнала: 2024, Номер 146(43), С. 29621 - 29629

Опубликована: Окт. 17, 2024

Biochemical acyl transfer cascades, such as those initiated by the adenylation of carboxylic acids, are central to various biological processes, including protein synthesis and fatty acid metabolism. Designing cascade reactions in aqueous media remains challenging due need control multiple, sequential a single pot manage stability reactive intermediates. Herein, we developed abiotic cascades using aminoacyl phosphate esters, synthetic counterparts adenylates, drive chemical self-assembly pot. We demonstrated that structural elements amino side chains (aromatic versus aliphatic) significantly influence reactivity half-lives ranging from hours days. This behavior, turn, affects number couplings can achieve network propensity activated intermediate structures. The constructed bifunctional peptide substrates featuring chain nucleophiles. Specifically, aromatic acids facilitate formation transient thioesters, which preorganized into spherical aggregates further couple chimeric assemblies composed esters thioesters. In contrast, aliphatic lack ability form structures, predominantly undergo hydrolysis, bypassing transformations after thioester formation. Additionally, mixtures containing multiple substrates, achieved selective product following distinct pathway favors subsequent through changes self-assembly. By coupling with molecules varying time scales, reaction clocks lifetimes dynamics, facilitating precise temporal regulation.

Язык: Английский

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